text: The biochemical basis for the toxicity of oxygen is the partial reduction of oxygen by one or two electrons to form reactive oxygen species, which are natural by-products of the normal metabolism of oxygen and have important roles in cell signalling. One species produced by the body, the superoxide anion (), is possibly involved in iron acquisition. Higher than normal concentrations of oxygen lead to increased levels of reactive oxygen species. Oxygen is necessary for cell metabolism, and the blood supplies it to all parts of the body. When oxygen is breathed at high partial pressures, a hyperoxic condition will rapidly spread, with the most vascularised tissues being most vulnerable. During times of environmental stress, levels of reactive oxygen species can increase dramatically, which can damage cell structures and produce oxidative stress.

text: The biochemical basis for the toxicity of oxygen is the partial reduction of oxygen by one or two electrons to form reactive oxygen species, which are natural by-products of the normal

entity_name: Metabolism

text: metabolism

text: of oxygen and have important roles in

entity_name: Cell signaling

text: cell signalling

text: . One species produced by the body, the

entity_name: Superoxide

text: superoxide

text: anion (), is possibly involved in iron acquisition. Higher than normal concentrations of oxygen lead to increased levels of reactive oxygen species. Oxygen is necessary for cell metabolism, and the blood supplies it to all parts of the body. When oxygen is breathed at high partial pressures, a hyperoxic condition will rapidly spread, with the most vascularised tissues being most vulnerable. During times of environmental stress, levels of reactive oxygen species can increase dramatically, which can damage cell structures and produce

entity_name: Oxidative stress

text: oxidative stress

method: ICT-DRMMTKS

text: Alberty is also known for his textbooks on physical chemistry, which have gone through many editions. The first one, Physical Chemistry, co-authored with Farrington Daniels, was published in 1957. More recent books of the same title have been co-authored with Robert J. Silbey and Moungi G. Bawendi (2004). Other works include Thermodynamics of Biochemical Reactions   (2003) and Biochemical Thermodynamics: Applications of Mathematica (Methods of Biochemical Analysis) (2006).

text: Alberty is also known for his textbooks on

entity_name: Physical chemistry

text: physical chemistry

text: , which have gone through many editions. The first one, Physical Chemistry, co-authored with

entity_name: Farrington Daniels

text: Farrington Daniels

text: , was published in 1957. More recent books of the same title have been co-authored with

text: Robert J. Silbey

text: and

text: Moungi G. Bawendi

text: (2004). Other works include Thermodynamics of Biochemical Reactions   (2003) and Biochemical Thermodynamics: Applications of Mathematica (Methods of Biochemical Analysis) (2006).

method: UvABottomUpChangeOrder

method: UNH-tfidf-stem

method: UNH-tfidf-ptsim

method: UNH-tfidf-lem

text: Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

text: Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as

entity_name: Amino acid

text: amino acid

text: s,

entity_name: Monosaccharide

text: monosaccharide

text: s,

entity_name: Terpenoid

text: isoprenoids

text: and

entity_name: Nucleotide

text: nucleotide

text: s, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as

entity_name: Protein

text: protein

text: s,

entity_name: Polysaccharide

text: polysaccharide

text: s,

entity_name: Lipid

text: lipid

text: s and

entity_name: Nucleic acid

text: nucleic acid

text: s.

text: The improvements of metabolic engineering by synthetic biology is an example of a biotechnological technique utilized in industry to discover pharmaceuticals and fermentative chemicals. Synthetic biology may investigate modular pathway systems in biochemical production and increase yields of metabolic production. Artificial enzymatic activity and subsequent effects on metabolic reaction rates and yields may develop “efficient new strategies for improving cellular properties . . . for industrially important biochemical production."

method: UNH-qee

text: Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism.

text: Like other biological macromolecules such as

text: polysaccharide

text: s and

text: nucleic acid

text: s, proteins are essential parts of organisms and participate in virtually every process within

entity_name: Cell (biology)

text: cell

text: s. Many proteins are

entity_name: Enzyme

text: enzyme

text: s that

entity_name: Catalysis

text: catalyse

text: biochemical reactions and are vital to

text: metabolism

text: . Proteins also have structural or mechanical functions, such as

entity_name: Actin

text: actin

text: and

entity_name: Myosin

text: myosin

text: in muscle and the proteins in the

entity_name: Cytoskeleton

text: cytoskeleton

text: , which form a system of

entity_name: Scaffolding

text: scaffolding

text: that maintains cell shape. Other proteins are important in

text: cell signaling

entity_name: Antibody

text: immune response

text: s,

entity_name: Cell adhesion

text: cell adhesion

text: , and the

entity_name: Cell cycle

text: cell cycle

text: . In animals, proteins are needed in the

entity_name: Diet (nutrition)

text: diet

text: to provide the

entity_name: Essential amino acid

text: essential amino acids

text: that cannot be

entity_name: Amino acid synthesis

text: synthesized

entity_name: Digestion

text: Digestion

text: breaks the proteins down for use in the metabolism.

text: A cyclase is an enzyme, almost always a lyase, that catalyzes a chemical reaction to form a cyclic compound. Important cyclase enzymes include:

text: A cyclase is an

text: enzyme

text: , almost always a

entity_name: Lyase

text: lyase

text: , that

text: catalyzes

text: a

entity_name: Chemical reaction

text: chemical reaction

text: to form a

entity_name: Cyclic compound

text: cyclic compound

text: . Important cyclase enzymes include:

text: In 1897 Eduard Buchner began to study the ability of yeast extracts to ferment sugar despite the absence of living yeast cells. In a series of experiments at the University of Berlin, he found that the sugar was fermented even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose "zymase". In 1907 he received the Nobel Prize in Chemistry "for his biochemical research and his discovery of cell-free fermentation". Following Buchner's example; enzymes are usually named according to the reaction they carry out. Typically the suffix -ase is added to the name of the substrate (e.g., lactase is the enzyme that cleaves lactose) or the type of reaction (e.g., DNA polymerase forms DNA polymers).

text: In 1897

entity_name: Eduard Buchner

text: Eduard Buchner

text: began to study the ability of yeast extracts to ferment sugar despite the absence of living yeast cells. In a series of experiments at the

entity_name: Humboldt University of Berlin

text: University of Berlin

text: , he found that the sugar was fermented even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose "

entity_name: Zymase

text: zymase

text: ". In 1907 he received the

entity_name: Nobel Prize in Chemistry

text: Nobel Prize in Chemistry

text: "for his biochemical research and his discovery of cell-free fermentation". Following Buchner's example; enzymes are usually named according to the reaction they carry out. Typically the suffix -ase is added to the name of the

entity_name: Substrate (chemistry)

text: substrate

text: (e.g.,

entity_name: Lactase

text: lactase

text: is the enzyme that cleaves

entity_name: Lactose

text: lactose

text: ) or the type of reaction (e.g.,

entity_name: DNA polymerase

text: DNA polymerase

text: forms DNA polymers).

text: Fru-2,6-P plays an important role in the regulation of triose phosphates, the end products of the Calvin Cycle.  In the Calvin Cycle, 5/6th of triose phosphates are recycled to make ribulose 1,5-bisphosphate.  The remaining 1/6 of triose phosphate can be converted into sucrose or stored as starch.  Fru-2,6-P inhibits production of fructose 6-phosphate, a necessary element for sucrose synthesis.  When the rate of photosynthesis in the light reactions is high, triose phosphates are constantly produced and the production of Fru-2,6-P is inhibited, thus producing sucrose.  Fru-2,6-P production is activated when plants are in the dark and photosynthesis and triose phosphates are not produced.

text: Fru-2,6-P plays an important role in the regulation of triose phosphates, the end products of the

entity_name: Light-independent reactions

entity_section: Calvin Cycle

text: Calvin Cycle

text: .  In the Calvin Cycle, 5/6th of triose phosphates are recycled to make

text: ribulose 1,5-bisphosphate

text: .  The remaining 1/6 of triose phosphate can be converted into

entity_name: Sucrose

text: sucrose

text: or stored as starch.  Fru-2,6-P inhibits production of fructose 6-phosphate, a necessary element for sucrose synthesis.  When the rate of

entity_name: Photosynthesis

text: photosynthesis

text: in the light reactions is high, triose phosphates are constantly produced and the production of Fru-2,6-P is inhibited, thus producing sucrose.  Fru-2,6-P production is activated when plants are in the dark and photosynthesis and triose phosphates are not produced.

method: Bert-DRMMTKS

text: Photosynthesis is a fundamental biochemical process in which plants, algae, and some bacteria convert sunlight to chemical energy. The process was discovered by Jan Ingenhousz in 1779. The chemical energy is used to drive reactions such as the formation of sugars or the fixation of nitrogen into amino acids, the building blocks for protein synthesis. Ultimately, nearly all living things depend on energy produced from photosynthesis. It is also responsible for producing the oxygen that makes animal life possible. Organisms that produce energy through photosynthesis are called photoautotrophs. Plants are the most visible representatives of photoautotrophs, but bacteria and algae also employ the process.

text: Photosynthesis

text: is a fundamental

entity_name: Biochemistry

text: biochemical

text: process in which plants,

entity_name: Algae

text: alga

text: e, and some

entity_name: Bacteria

text: bacteria

text: convert sunlight to chemical energy. The process was discovered by

entity_name: Jan Ingenhousz

text: Jan Ingenhousz

text: in 1779. The chemical energy is used to drive reactions such as the formation of sugars or the fixation of nitrogen into

text: amino acid

text: s, the building blocks for

entity_section: Synthesis

text: protein synthesis

text: . Ultimately, nearly all living things depend on energy produced from photosynthesis. It is also responsible for producing the

entity_name: Oxygen

text: oxygen

text: that makes animal life possible. Organisms that produce energy through photosynthesis are called

entity_name: Phototroph

entity_section: Photoautotroph

text: photoautotroph

text: s. Plants are the most visible representatives of photoautotrophs, but bacteria and algae also employ the process.

text: Technetium-99m ("m" indicates that this is a metastable nuclear isomer) is used in radioactive isotope medical tests.  For example Technetium-99m is a radioactive tracer that medical imaging equipment tracks in the human body. It is well suited to the role because it emits readily detectable 140 keV gamma rays, and its half-life is 6.01 hours (meaning that about 94% of it decays to technetium-99 in 24 hours). The chemistry of technetium allows it to be bound to a variety of biochemical compounds, each of which determines how it is metabolized and deposited in the body, and this single isotope can be used for a multitude of diagnostic tests. More than 50 common radiopharmaceuticals are based on technetium-99m for imaging and functional studies of the brain, heart muscle, thyroid, lungs, liver, gall bladder, kidneys, skeleton, blood, and tumors.

text: ("m" indicates that this is a

entity_name: Nuclear isomer

entity_section: Metastable isomers

text: metastable

text: nuclear isomer) is used in radioactive isotope

entity_name: Nuclear medicine

text: medical tests

text: .  For example Technetium-99m is a

entity_name: Radioactive tracer

text: radioactive tracer

text: that medical imaging equipment tracks in the human body. It is well suited to the role because it emits readily detectable 140

entity_name: Electronvolt

text: keV

entity_name: Gamma ray

text: gamma ray

text: s, and its half-life is 6.01 hours (meaning that about 94% of it decays to technetium-99 in 24 hours). The chemistry of technetium allows it to be bound to a variety of biochemical compounds, each of which determines how it is metabolized and deposited in the body, and this single isotope can be used for a multitude of diagnostic tests. More than 50 common

entity_name: Radiopharmaceutical

text: radiopharmaceuticals

text: are based on technetium-99m for imaging and functional studies of the

entity_name: Human brain

text: brain

text: , heart muscle,

entity_name: Thyroid

text: thyroid

entity_name: Lung

text: lungs

entity_name: Liver

text: liver

entity_name: Gallbladder

text: gall bladder

entity_name: Kidney

text: kidney

text: s,

entity_name: Human skeleton

text: skeleton

entity_name: Blood

text: blood

text: , and

entity_name: Neoplasm

text: tumor

text: s.

text: Acetyl coenzyme A or acetyl-CoA is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for energy production. Coenzyme A (CoASH or CoA) consists of a β-mercaptoethylamine group linked to the vitamin pantothenic acid through an amide linkage. The acetyl group (indicated in blue in the structural diagram on the right) of acetyl-CoA is linked  to the sulfhydryl substituent of the β-mercaptoethylamine group. This thioester linkage is a "high energy" bond, which is particularly reactive. Hydrolysis of the thioester bond is exergonic (-31.5 kJ/mol).

text: Acetyl coenzyme A or acetyl-CoA is a molecule that participates in many

text: biochemical reaction

text: s in protein, carbohydrate and lipid

text: metabolism

text: . Its main function is to deliver the

entity_name: Acetyl group

text: acetyl

text: group to the

entity_name: Citric acid cycle

text: citric acid cycle

text: (Krebs cycle) to be

entity_name: Redox

text: oxidized

text: for energy production.

text: Coenzyme A

text: (CoASH or CoA) consists of a

text: β-mercaptoethylamine group

text: linked to the vitamin

text: pantothenic acid

text: through an amide linkage. The acetyl group (indicated in blue in the structural diagram on the right) of acetyl-CoA is linked  to the sulfhydryl substituent of the β-mercaptoethylamine group. This

text: thioester

text: linkage is a "high energy" bond, which is particularly reactive. Hydrolysis of the thioester bond is exergonic (-31.5 kJ/mol).

text: The model is used in a variety of biochemical situations other than enzyme-substrate interaction, including antigen-antibody binding, DNA-DNA hybridization, and protein-protein interaction. It can be used to characterise a generic biochemical reaction, in the same way that the Langmuir equation can be used to model generic adsorption of biomolecular species. When an empirical equation of this form is applied to microbial growth, it is sometimes called a Monod equation.

text: The model is used in a variety of biochemical situations other than enzyme-substrate interaction, including

text: antigen-antibody binding

text: DNA-DNA hybridization

text: , and

text: protein-protein interaction

text: . It can be used to characterise a generic biochemical reaction, in the same way that the

text: Langmuir equation

text: can be used to model generic

text: adsorption

text: of biomolecular species. When an empirical equation of this form is applied to microbial growth, it is sometimes called a

text: Monod equation

text: Cellular waste products are formed as a by-product of cellular respiration, a series of processes and reactions that generate energy for the cell, in the form of ATP. Two examples of cellular respiration creating cellular waste products are aerobic respiration and anaerobic respiration.

text: Cellular waste products are formed as a by-product of

text: cellular respiration

text: , a series of processes and reactions that generate energy for the cell, in the form of

text: ATP

text: . Two examples of cellular respiration creating cellular waste products are

text: aerobic respiration

text: and

text: anaerobic respiration

text: Spectrophotometry is an important technique used in many biochemical experiments that involve DNA, RNA, and protein isolation, enzyme kinetics and biochemical analyses. A brief explanation of the procedure of spectrophotometry includes comparing the absorbency of a blank sample that does not contain a colored compound to a sample that contains a colored compound. The spectrophotometer is used to measure colored compounds in the visible region of light (between 350 nm and 800 nm), thus it can be used to find more information about the substance being studied. In biochemical experiments, a chemical and/or physical property is chosen and the procedure that is used is specific to that property in order to derive more information about the sample, such as the quantity, purity, enzyme activity, etc. Spectrophotometry is also a helpful procedure for protein purification  and can also be used as a method to create optical assays of a compound. Because a spectrophotometer measures the wavelength of a compound through its color, a dye binding substance can be added so that it can undergo a color change and be measured. Spectrophotometers have been developed and improved over decades and have been widely used among chemists. It is considered to be a highly accurate instrument that is also very sensitive and therefore extremely precise, especially in determining color change. This method is also convenient for use in laboratory experiments because it is an inexpensive and relatively simple process.

text: Serendipity followed de Duve for another major discovery. After confirmation of lysosome, de Duve's team was troubled by the existence of another enzyme urate oxidase in rat liver cell fraction. He was convinced that it did not belong to lysosome because it is not an acid hydrolase, typical of lysosomal enzymes, but still had similar distribution as acid phosphatase. In 1960 he further found that other enzymes such as catalase and D-amino acid oxidase were similarly distributed in cell fraction, and they were believed to be mitochondrial enzymes. (W. Bernhard and C. Rouillier had described such extra-mitochodrial organelles as microbodies, and believed that they were precursors to mitochondria.) de Duve discovered that these three enzymes exhibited similar chemical properties and were similar to those of other peroxide-producing oxidases. He was sceptical of referring to them as microbodies because, as he noted, "too little is known of their enzyme complement and of their role in the physiology of the liver cells to substantiate a proposal at the present time". He suggested that these enzymes belonged to the same cell organelle, but different from previously known organelles. But it would take some years before he publicised his hypothesis, as strong evidences were still lacking. In 1955 his team demonstrated similar cell fractions with same biochemical properties from the ciliated protozoan Tetrahymena pyriformis, from which it was indicated that these particles were new cell organelles unrelated to mitochondria. He presented his discovery at a meeting of the American Society for Cell Biology in 1955, and formally published in 1966 in which he created the name peroxisomes for the organelles as they are involved in peroxidase reactions. In 1968 he achieved  the first large-scale preparation of peroxisomes, confirming that l-α hydroxyacid oxidase, d-amino acid oxidase, and catalase were all the unique enzymes of peroxisomes. de Duve and his team went on to show that peroxisomes play important metabolic roles, including the β-oxidation of very long-chain fatty acids by a pathway different from that in mitochondria, and that they are members of a large family of evolutionarily related organelles present in diverse cells including plants, and protozoa, where they carry out distinct functions and have been given specific names, such as glyoxysomes and glycosomes.

text: Serendipity followed de Duve for another major discovery. After confirmation of lysosome, de Duve's team was troubled by the existence of another enzyme

text: urate oxidase

text: in rat liver cell fraction. He was convinced that it did not belong to lysosome because it is not an acid hydrolase, typical of lysosomal enzymes, but still had similar distribution as acid phosphatase. In 1960 he further found that other enzymes such as

text: catalase

text: and

text: D-amino acid oxidase

text: were similarly distributed in cell fraction, and they were believed to be mitochondrial enzymes. (W. Bernhard and C. Rouillier had described such extra-mitochodrial organelles as

text: microbodies

text: , and believed that they were precursors to mitochondria.) de Duve discovered that these three enzymes exhibited similar chemical properties and were similar to those of other peroxide-producing oxidases. He was sceptical of referring to them as microbodies because, as he noted, "too little is known of their enzyme complement and of their role in the physiology of the liver cells to substantiate a proposal at the present time". He suggested that these enzymes belonged to the same cell organelle, but different from previously known organelles. But it would take some years before he publicised his hypothesis, as strong evidences were still lacking. In 1955 his team demonstrated similar cell fractions with same biochemical properties from the ciliated protozoan

text: Tetrahymena pyriformis

text: , from which it was indicated that these particles were new cell organelles unrelated to mitochondria. He presented his discovery at a meeting of the

text: American Society for Cell Biology

text: in 1955, and formally published in 1966 in which he created the name peroxisomes for the organelles as they are involved in peroxidase reactions. In 1968 he achieved  the first large-scale preparation of peroxisomes, confirming that

entity_name: Hydroxyacid oxidase (glycolate oxidase) 1

text: l-α hydroxyacid oxidase

text: , d-amino acid oxidase, and catalase were all the unique enzymes of peroxisomes. de Duve and his team went on to show that peroxisomes play important metabolic roles, including the

text: β-oxidation

text: of very long-chain fatty acids by a pathway different from that in mitochondria, and that they are members of a large family of evolutionarily related organelles present in diverse cells including plants, and protozoa, where they carry out distinct functions and have been given specific names, such as

text: glyoxysomes

text: and

text: glycosome

text: s.

text: The teaching of food chemistry and technology has a long-standing tradition in the Czech lands, and is closely connected with the teaching of chemistry and chemical technology. The Faculty of Food and Biochemical Technology was established in 1952.

text: In the midreaches of a river, river structures such as rocks and trees play an important role as a supplier of organic material such as periphyton and other autochthonous (see limnology section of link) organic materials.  The photosynthesis to respiration ratio is larger in this section and amounts to P: R> 1.  The percentage of shredders in this area is less than that of the headwaters, due to lack of coarse plant particulate.  Collectors and grazers make up a majority of the macro invertebrate structure in this area, with the predator's share remaining unchanged.

text: In the midreaches of a river, river structures such as rocks and trees play an important role as a supplier of organic material such as

text: periphyton

text: and other

text: autochthonous

text: (see limnology section of link) organic materials.  The photosynthesis to respiration ratio is larger in this section and amounts to P: R> 1.  The percentage of shredders in this area is less than that of the headwaters, due to lack of coarse plant particulate.  Collectors and grazers make up a majority of the macro invertebrate structure in this area, with the predator's share remaining unchanged.

text: Heterozygous carriers (individuals who inherit one mutant allele) show abnormal enzyme activity but manifest no disease symptoms. This phenomenon is called dominance; the biochemical reason for wild-type alleles' dominance over nonfunctional mutant alleles in inborn errors of metabolism comes from how enzymes function. Enzymes are protein catalysts for chemical reactions; as catalysts, they speed up reactions without being used up in the process, so only small enzyme quantities are required to carry out a reaction. Someone homozygous for a nonfunctional mutation in the enzyme-encoding gene has little or no enzyme activity, so will manifest the abnormal phenotype. A heterozygote (heterozygous individual) has at least half of the normal enzyme activity level, due to expression of the wild-type allele. This level is normally enough to enable normal function and thus prevent phenotypic expression.

text: Heterozygous carriers (individuals who inherit one mutant allele) show abnormal enzyme activity but manifest no disease symptoms. This phenomenon is called dominance; the biochemical reason for

text: wild-type

text: alleles' dominance over nonfunctional mutant alleles in

text: inborn errors of metabolism

text: comes from how

text: enzymes

text: function. Enzymes are

text: protein

text: catalysts

text: for chemical reactions; as catalysts, they speed up reactions without being used up in the process, so only small enzyme quantities are required to carry out a reaction. Someone homozygous for a nonfunctional mutation in the enzyme-encoding gene has little or no enzyme activity, so will manifest the abnormal

text: phenotype

text: . A heterozygote (heterozygous individual) has at least half of the normal enzyme activity level, due to expression of the wild-type allele. This level is normally enough to enable normal function and thus prevent phenotypic expression.

text: Catabolism (from Greek κάτω kato, "downward" and βάλλειν ballein, "to throw") is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks down large molecules (such as polysaccharides, lipids, nucleic acids and proteins) into smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively).

text: Catabolism (from

text: Greek

text: κάτω kato, "downward" and βάλλειν ballein, "to throw") is the set of

text: metabolic

text: pathways that breaks down

text: molecule

text: s into smaller units that are either oxidized to release

text: energy

text: , or used in other

text: anabolic

text: reactions. Catabolism breaks down large molecules (such as

text: polysaccharide

text: s,

text: lipid

text: s,

text: nucleic acid

text: s and

text: protein

text: s) into smaller units (such as

text: monosaccharide

text: s,

text: fatty acid

text: s,

text: nucleotide

text: s, and

text: amino acid

text: s, respectively).

text: Traube's main work, the Theorie der Fermentwirkungen (1858) is the first comprehensive theory of fermentation to be based on experiments and elaborated consequently from the chemical point of view. The discovery in 1837 that yeast was a living organism suggested that fermentation itself was a living process. Only a few scientists rejected this vitalistic protoplasm theory, notably Traube. He was the first to define enzymes as specific protein-like compounds and to formulate the necessity of direct molecular contact between enzyme and substrate for fermentation to occur. He classified enzymes by reaction type, much as is done today. Long before Eduard Buchner discovered non-cellular fermentation in 1897, Traube isolated an enzyme from potatoes which could turn guaiacum blue, thus demonstrating the continued efficacy of plant enzymes after they had been extracted from the cell. Until recently, biochemical history has not noted that Traube began to investigate the kinetics of reactions and also demonstrated a reciprocal relationship between reaction time and quantity of enzyme. To defend his theory, Traube had to argue vigorously against Louis Pasteur and Felix Hoppe-Seyler. He contradicted Pasteur's assertion that fermentation could not occur without vital activity. In the context of these experiments Traube became the first to describe a process for making pure yeast. His differences with Hoppe-Seyler had to do with the mechanism by which oxygen was activated in fermentation reactions.  Traube's experiments were designed to demonstrate activation via enzymes as catalysts and refute Hoppe-Seyler's hypothesis of oxygen activation by nascent hydrogen produced by enzymes.

text: Traube's main work, the Theorie der Fermentwirkungen (1858) is the first comprehensive theory of

text: fermentation

text: to be based on experiments and elaborated consequently from the chemical point of view. The discovery in 1837 that

text: yeast

text: was a living organism suggested that fermentation itself was a living process. Only a few scientists rejected this

text: vitalistic

text: protoplasm

text: theory, notably Traube. He was the first to define

text: enzymes

text: as specific protein-like compounds and to formulate the necessity of direct molecular contact between enzyme and

text: substrate

text: for fermentation to occur. He classified enzymes by reaction type, much as is done today. Long before

text: Eduard Buchner

text: discovered

text: non-cellular fermentation

text: in 1897, Traube isolated an enzyme from potatoes which could turn

text: guaiacum

text: blue, thus demonstrating the continued efficacy of plant enzymes after they had been extracted from the cell. Until recently, biochemical history has not noted that Traube began to investigate the

text: kinetics

text: of reactions and also demonstrated a reciprocal relationship between reaction time and quantity of enzyme. To defend his theory, Traube had to argue vigorously against

text: Louis Pasteur

text: and

text: Felix Hoppe-Seyler

text: . He contradicted Pasteur's assertion that fermentation could not occur without vital activity. In the context of these experiments Traube became the first to describe a process for making pure yeast. His differences with Hoppe-Seyler had to do with the mechanism by which oxygen was activated in fermentation reactions.  Traube's experiments were designed to demonstrate activation via enzymes as catalysts and refute Hoppe-Seyler's hypothesis of

text: oxygen

text: activation by nascent hydrogen produced by enzymes.

text: Luminescence is the result of a chemical or biochemical reaction. Luminescence detection is simpler optically than fluorescence detection because luminescence does not require a light source for excitation or optics for selecting discrete excitation wavelengths. A typical luminescence optical system consists of a light-tight reading chamber and a PMT detector. Some plate readers use an Analog PMT detector while others have a photon counting PMT detector. Photon Counting is widely accepted as the most sensitive means of detecting luminescence. Some plate readers offer filter wheel or tunable wavelength monochromator optical systems for selecting specific luminescent wavelengths.  The ability to select multiple wavelengths, or even wavelength ranges, allows for detection of assays that contain multiple luminescent reporter enzymes, the development of new luminescence assays, as well as a means to optimize signal to noise.

text: Luminescence is the result of a chemical or biochemical reaction. Luminescence detection is simpler optically than fluorescence detection because luminescence does not require a light source for excitation or optics for selecting discrete excitation wavelengths. A typical luminescence optical system consists of a light-tight reading chamber and a

text: PMT

text: detector. Some plate readers use an Analog PMT detector while others have a

text: photon counting

text: PMT detector. Photon Counting is widely accepted as the most sensitive means of detecting luminescence. Some plate readers offer filter wheel or tunable wavelength monochromator optical systems for selecting specific luminescent wavelengths.  The ability to select multiple wavelengths, or even wavelength ranges, allows for detection of assays that contain multiple luminescent reporter enzymes, the development of new luminescence assays, as well as a means to optimize signal to noise.

text: Demethylases are enzymes that remove methyl (CH-) groups from nucleic acids, proteins (in particular histones),  and other molecules. Demethylase enzymes are important in epigenetic modification mechanisms. The demethylase proteins alter transcriptional regulation of the genome by controlling the methylation levels that occur on DNA and histones and, in turn, regulate the chromatin state at specific gene loci within organisms.

text: Demethylases are

text: enzymes

text: that remove

text: methyl

text: (CH-) groups from

text: nucleic acid

text: s, proteins (in particular

text: histone

text: s),  and other molecules. Demethylase enzymes are important in

text: epigenetic

text: modification mechanisms. The demethylase proteins alter

text: transcriptional regulation

text: of the

text: genome

text: by controlling the

text: methylation

text: levels that occur on DNA and histones and, in turn, regulate the

text: chromatin

text: state at specific

text: gene

text: loci within organisms.

text: Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to signal transduction, and a single protein may play a role in multiple processes or cellular pathways.

text: Protein function prediction methods are techniques that

text: bioinformatics

text: researchers use to assign biological or biochemical roles to

text: proteins

text: . These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid

text: sequence homology

text: gene expression

text: profiles,

text: protein domain

text: structures,

text: text mining

text: of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to

text: signal transduction

text: , and a single protein may play a role in multiple processes or cellular pathways.

text: Nutrients that are commonly used by animal and plant cells in respiration include sugar, amino acids and fatty acids, and the most common oxidizing agent (electron acceptor) is molecular oxygen (O). The chemical energy stored in ATP (its third phosphate group is weakly bonded to the rest of the molecule and is cheaply broken allowing stronger bonds to form, thereby transferring energy for use by the cell) can then be used to drive processes requiring energy, including biosynthesis, locomotion or transportation of molecules across cell membranes.

text: Nutrients that are commonly used by animal and plant cells in respiration include

text: sugar

text: amino acids

text: and

text: fatty acids

text: , and the most common

text: oxidizing agent

text: electron acceptor

text: ) is molecular

text: oxygen

text: (O). The chemical energy stored in ATP (its third phosphate group is weakly bonded to the rest of the molecule and is cheaply broken allowing stronger bonds to form, thereby transferring energy for use by the cell) can then be used to drive processes requiring energy, including

text: biosynthesis

text: locomotion

text: or transportation of molecules across

text: cell membrane

text: s.

text: Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide and water using energy from light. However, not all organisms that use light as a source of energy carry out photosynthesis; photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae, and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are some differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also many varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria, which consume carbon dioxide but do not release oxygen.

text: Photosynthetic organisms are

text: photoautotroph

text: s, which means that they are able to

text: synthesize

text: food directly from carbon dioxide and water using energy from light. However, not all organisms that use light as a source of energy carry out photosynthesis;

text: photoheterotroph

text: s use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae, and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are some differences between oxygenic photosynthesis in

text: plants

text: algae

text: , and

text: cyanobacteria

text: , the overall process is quite similar in these organisms. There are also many varieties of

text: anoxygenic photosynthesis

text: , used mostly by certain types of bacteria, which consume carbon dioxide but do not release oxygen.

text: An initial metabolic reconstruction of a genome is typically far from perfect due to the high variability and diversity of microorganisms.  Often, metabolic pathway databases such as KEGG and MetaCyc will have "holes", meaning that there is a conversion from a substrate to a product (i.e., an enzymatic activity) for which there is no known protein in the genome that encodes the enzyme that facilitates the catalysis.  What can also happen in semi-automatically drafted reconstructions is that some pathways are falsely predicted and don't actually occur in the predicted manner.  Because of this, a systematic verification is made in order to make sure no inconsistencies are present and that all the entries listed are correct and accurate.  Furthermore, previous literature can be researched in order to support any information obtained from one of the many metabolic reaction and genome databases. This provides an added level of assurance for the reconstruction that the enzyme and the reaction it catalyzes do actually occur in the organism.

text: The physiological definition of respiration should not be confused with the biochemical definition, which refers to cellular respiration, a metabolic process by which an organism obtains energy (in the form of ATP) by oxidizing nutrients and releasing waste products. Although physiologic respiration is necessary to sustain cellular respiration and thus life in animals, the processes are distinct: cellular respiration takes place in individual cells of the organism, while physiologic respiration concerns the bulk flow and transport of metabolites between the organism and the external environment.

text: The physiological definition of respiration should not be confused with the

text: biochemical

text: definition, which refers to

text: cellular respiration

text: , a

text: metabolic

text: process by which an

text: organism

text: obtains energy (in the form of

text: ATP

text: ) by

text: oxidizing

text: nutrients and releasing waste products. Although physiologic respiration is necessary to sustain cellular respiration and thus life in animals, the processes are distinct: cellular respiration takes place in individual cells of the organism, while physiologic respiration concerns the

text: bulk flow

text: and transport of metabolites between the organism and the external environment.

text: The test was originally developed by Ludwig Wilhelm Winkler, in later literature referred to as Lajos Winkler, while working at Budapest University on his doctoral dissertation in 1888. The amount of dissolved oxygen is a measure of the biological activity of the water masses. Phytoplankton and macroalgae present in the water mass-produce oxygen by way of photosynthesis.  Bacteria and eukaryotic organisms (zooplankton,fish) consume this oxygen through cellular respiration. The result of these two mechanisms determines the concentration of dissolved oxygen, which in turn indicates the production of biomass. The difference between the physical concentration of oxygen in the water (or the theoretical concentration if there were no living organisms) and the actual concentration of oxygen is called the biochemical demand in oxygen. The Winkler test is often controversial as it is not 100% accurate and the oxygen levels may fluctuate from test to test despite using the same constant sample.

text: The test was originally developed by Ludwig Wilhelm Winkler, in later literature referred to as

text: Lajos Winkler

text: , while working at Budapest University on his doctoral dissertation in 1888. The amount of

text: dissolved oxygen

text: is a measure of the biological activity of the water masses.

text: Phytoplankton

text: and macroalgae present in the water mass-produce oxygen by way of

text: photosynthesis

text: Bacteria

text: and eukaryotic organisms (zooplankton,fish) consume this oxygen through

text: cellular respiration

text: . The result of these two mechanisms determines the concentration of dissolved oxygen, which in turn indicates the production of biomass. The difference between the physical concentration of oxygen in the water (or the theoretical concentration if there were no living organisms) and the actual concentration of oxygen is called the biochemical demand in oxygen. The Winkler test is often controversial as it is not 100% accurate and the oxygen levels may fluctuate from test to test despite using the same constant sample.

text: Glycosylation reactions are very important reactions in carbohydrate chemistry leading to the synthesis of oligosaccharides, preferably in a stereoselective manner. The stereoselectivity of these reactions has been shown to be affected by both the nature and the configuration of the protecting group at C-2 on the glycosyl donor ring. While 1,2-trans-glycosides (e.g. alpha-mannosides and β-glucosides) can be synthesised easily in the presence of a participating group (such as OAc, or NHAc) at the C-2 position in the glycosyl donor ring, 1,2-cis-glycosides are more difficult to prepare. 1,2-cis-glycosides with the alpha configuration (e.g. glucosides or galactosides) can often be prepared using a non-participating protecting group (such as Bn, or All) at C-2 (OH). However, 1,2-cis-glycosides with the β configuration are the most difficult to achieve, and present the greatest challenge in glycosylation reactions.

text: Glycosylation

text: reactions are very important reactions in

text: carbohydrate chemistry

text: leading to the synthesis of

text: oligosaccharides

text: , preferably in a stereoselective manner. The stereoselectivity of these reactions has been shown to be affected by both the nature and the configuration of the protecting group at C-2 on the

text: glycosyl donor

text: ring. While 1,2-trans-glycosides (e.g. alpha-mannosides and β-glucosides) can be synthesised easily in the presence of a participating group (such as OAc, or NHAc) at the C-2 position in the glycosyl donor ring, 1,2-cis-glycosides are more difficult to prepare. 1,2-cis-glycosides with the alpha configuration (e.g. glucosides or galactosides) can often be prepared using a non-participating protecting group (such as Bn, or All) at C-2 (OH). However, 1,2-cis-glycosides with the β configuration are the most difficult to achieve, and present the greatest challenge in glycosylation reactions.

text: The Woodward–Hoffmann rules, devised by Robert Burns Woodward and Roald Hoffmann, are a set of rules in organic chemistry predicting the barrier heights of pericyclic reactions based upon conservation of orbital symmetry. The Woodward–Hoffmann rules can be applied to understand electrocyclic reactions, cycloadditions (including cheletropic reactions), sigmatropic reactions, and group transfer reactions. Reactions are classified as allowed if the electronic barrier is low, and forbidden if the barrier is high.  Forbidden reactions can still take place but require significantly more energy.

text: The Woodward–Hoffmann rules, devised by

text: Robert Burns Woodward

text: and

text: Roald Hoffmann

text: , are a set of rules in

text: organic chemistry

text: predicting the barrier heights of

text: pericyclic reaction

text: s based upon conservation of

text: orbital symmetry

text: . The Woodward–Hoffmann rules can be applied to understand

text: electrocyclic reaction

text: s,

text: cycloaddition

text: s (including

text: cheletropic reaction

text: s),

text: sigmatropic reaction

text: s, and

text: group transfer reaction

text: s. Reactions are classified as allowed if the electronic barrier is low, and forbidden if the barrier is high.  Forbidden reactions can still take place but require significantly more energy.

text: The first step in photosynthesis is the light-driven reduction (splitting) of water to provide the electrons for the photosynthetic electron transport chains as well as protons for the establishment of a proton gradient. The water-splitting reaction occurs on the lumenal side of the thylakoid membrane and is driven by the light energy captured by the photosystems. It is interesting to note that this oxidation of water conveniently produces the waste product O that is vital for cellular respiration. The molecular oxygen formed by the reaction is released into the atmosphere.

text: The first step in photosynthesis is the light-driven reduction (splitting) of water to provide the electrons for the photosynthetic electron transport chains as well as protons for the establishment of a proton gradient. The water-splitting reaction occurs on the lumenal side of the thylakoid membrane and is driven by the light energy captured by the photosystems. It is interesting to note that this oxidation of water conveniently produces the waste product O that is vital for

text: cellular respiration

text: . The molecular oxygen formed by the reaction is released into the atmosphere.

text: In addition, in living systems, most biochemical reactions (including ATP hydrolysis) take place during the catalysis of enzymes. The catalytic action of enzymes allows the hydrolysis of proteins, fats, oils, and carbohydrates. As an example, one may consider proteases (enzymes that aid digestion by causing hydrolysis of peptide bonds in proteins). They catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases (another class of enzymes, that catalyse the hydrolysis of terminal peptide bonds, liberating one free amino acid at a time).

text: In addition, in living systems, most biochemical reactions (including ATP hydrolysis) take place during the catalysis of

text: enzyme

text: s. The catalytic action of enzymes allows the hydrolysis of

text: protein

text: s, fats, oils, and

text: carbohydrate

text: s. As an example, one may consider

text: protease

text: s (enzymes that aid

text: digestion

text: by causing hydrolysis of

text: peptide bond

text: s in

text: protein

text: s). They catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to

text: exopeptidase

text: s (another class of enzymes, that catalyse the hydrolysis of terminal peptide bonds, liberating one free amino acid at a time).

text: Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by proteins called reaction centres that contain green chlorophyll pigments. In plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances, such as water, producing oxygen gas. The hydrogen freed by the splitting of water is used in the creation of two further compounds that act as an immediate energy storage means: reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the "energy currency" of cells.

text: Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by

text: protein

text: s called

text: reaction centres

text: that contain green

text: chlorophyll

text: pigments. In plants, these proteins are held inside

text: organelle

text: s called

text: chloroplast

text: s, which are most abundant in leaf cells, while in bacteria they are embedded in the

text: plasma membrane

text: . In these light-dependent reactions, some energy is used to strip

text: electron

text: s from suitable substances, such as water, producing oxygen gas. The hydrogen freed by the splitting of water is used in the creation of two further compounds that act as an immediate energy storage means: reduced

entity_name: Nicotinamide adenine dinucleotide phosphate

text: nicotinamide adenine dinucleotide phosphate

text: (NADPH) and

text: adenosine triphosphate

text: (ATP), the "energy currency" of cells.

text: Exergonic reactions are energy-releasing reactions and are generally catabolic. Endergonic reactions require energy and include anabolic reactions and the contraction of muscle. Metabolism is the total of all catabolic, exergonic, anabolic, endergonic reactions.

text: Exergonic reaction

text: s are energy-releasing reactions and are generally catabolic. Endergonic reactions require energy and include anabolic reactions and the contraction of muscle. Metabolism is the total of all catabolic, exergonic, anabolic, endergonic reactions.

text: The chance to discover a form of life with a different biochemistry than Earth has led some researchers to consider Titan the most important world on which to search for extraterrestrial life. A few scientists hypothesize that if the hydrocarbon chemistry on Titan crossed the threshold from inanimate matter to some form of life, it would be difficult to detect. Moreover, because Titan is so cold, the amount of energy available for building complex biochemical structures is limited, and any water-based life would freeze without a heat source. However, some scientists have suggested that hypothetical life forms may be able to exist in a methane-based solvent.Ellen Stofan, TiME's Principal Investigator, thinks that life as we know it is not viable in Titan's seas, but stated that "there will be chemistry in the seas that may give us insight into how organic systems progress toward life."

text: The chance to discover

text: a form of life

text: with a

text: different biochemistry

text: than Earth has led some researchers to consider Titan the most important world on which to search for

text: extraterrestrial life

text: . A few scientists hypothesize that if the hydrocarbon chemistry on Titan crossed the threshold from inanimate matter to some form of life, it would be difficult to detect. Moreover, because Titan is so cold, the amount of energy available for building complex biochemical structures is limited, and any water-based life would freeze without a heat source. However, some scientists have suggested that hypothetical life forms may be able to exist in a

text: methane-based solvent

text: .Ellen Stofan, TiME's Principal Investigator, thinks that life as we know it is not viable in Titan's seas, but stated that "there will be chemistry in the seas that may give us insight into how organic systems progress toward life."

text: In his early career, he was mainly working on enzyme structure and function. He had invented the now standard stopped-flow device to measure the existence of the enzyme-substrate complex in enzyme reaction. He was a pioneer in the numerical simulations of biochemical reactions and metabolic pathways.

text: In his early career, he was mainly working on enzyme structure and function. He had invented the now standard

text: stopped-flow

text: device to measure the existence of the enzyme-substrate complex in enzyme reaction. He was a pioneer in the numerical simulations of

text: biochemical reaction

text: s and

text: metabolic pathways

text: It is important that these two electron carriers are easily distinguished, because they participate in very different reactions.  NADP mainly functions with enzymes that catalyze anabolic, or biosynthetic, pathways. Specifically, NADPH will act as a reducing agent in these reactions, resulting in NADP. These are pathways that convert substrates to more complicated products, using ATP. The reasoning behind having two separate electron carriers for anabolic and catabolic pathways relates to regulation of metabolism.

text: Professor Robert Jensen of the School of Journalism at the University of Texas has commented on the Anabolic production A Cum Sucking Whore Named Kimberly. He alleges the film portrays Kimberly as merely "three holes and two hands", and that it is an example of "pornography that is rooted in the pain and humiliation of women". Anabolic's President and Founder Christopher Alexander states "At Anabolic we have the utmost respect for all of our talent, we allow them the artistic freedom to deliver scenes that are as wild as they wish them to be  (with a few limits). We encourage the talent to be passionate, exciting, and to deliver the best scenes that they have ever done."

text: Professor Robert Jensen of the School of Journalism at the

text: University of Texas

text: has commented on the Anabolic production A Cum Sucking Whore Named Kimberly. He alleges the film portrays Kimberly as merely "three holes and two hands", and that it is an example of "pornography that is rooted in the pain and humiliation of women". Anabolic's President and Founder Christopher Alexander states "At Anabolic we have the utmost respect for all of our talent, we allow them the artistic freedom to deliver scenes that are as wild as they wish them to be  (with a few limits). We encourage the talent to be passionate, exciting, and to deliver the best scenes that they have ever done."

text: Many reactions classified as reductions also appear in other classes. For instance conversion of the ketone to an alcohol by lithium aluminium hydride can be considered a reduction but the hydride is also a good nucleophile in nucleophilic substitution. Many redox reactions in organic chemistry have coupling reaction reaction mechanism involving free radical intermediates. True organic redox chemistry can be found in electrochemical organic synthesis or electrosynthesis. Examples of organic reactions that can take place in an electrochemical cell are the Kolbe electrolysis.

text: Many reactions classified as reductions also appear in other classes. For instance conversion of the ketone to an alcohol by lithium aluminium hydride can be considered a reduction but the hydride is also a good

text: nucleophile

text: in

text: nucleophilic substitution

text: . Many redox reactions in organic chemistry have

text: coupling reaction

text: reaction mechanism

text: involving

text: free radical

text: intermediates. True organic redox chemistry can be found in electrochemical organic synthesis or

text: electrosynthesis

text: . Examples of organic reactions that can take place in an

text: electrochemical cell

text: are the

text: Kolbe electrolysis

text: Although roughly cellular in appearance, microspheres in and of themselves are not alive.  Although they do reproduce asexually by budding, they do not pass on any type of genetic material.  However they may have been important in the development of life, providing a membrane-enclosed volume which is similar to that of a cell. Microspheres, like cells, can grow and contain a double membrane which undergoes diffusion of materials and osmosis. Sidney Fox postulated that as these microspheres became more complex, they would carry on more lifelike functions. They would become heterotrophs, organisms with the ability to absorb nutrients from the environment for energy and growth. As the amount of nutrients in the environment decreased at that period, competition for those precious resources increased. Heterotrophs with more complex biochemical reactions would have an advantage in this competition. Over time, organisms would evolve that used photosynthesis to produce energy.

text: Although roughly

text: cellular

text: in appearance, microspheres in and of themselves are not alive.  Although they do reproduce asexually by budding, they do not pass on any type of

text: genetic

text: material.  However they may have been important in the development of life, providing a

text: membrane

text: -enclosed volume which is similar to that of a cell. Microspheres, like cells, can grow and contain a double membrane which undergoes diffusion of materials and

text: osmosis

text: . Sidney Fox postulated that as these microspheres became more complex, they would carry on more lifelike functions. They would become heterotrophs, organisms with the ability to absorb nutrients from the environment for energy and growth. As the amount of nutrients in the environment decreased at that period, competition for those precious resources increased. Heterotrophs with more complex biochemical reactions would have an advantage in this competition. Over time, organisms would evolve that used

text: photosynthesis

text: to produce energy.

text: catabolic intermediates:

text: catabolic intermediates:

text: The two photosystems absorb light energy through pigments - primarily the chlorophylls, which are responsible for the green color of leaves.  The light-dependent reactions begin in photosystem II. When a chlorophyll a molecule within the reaction center of PSII absorbs a photon, an electron in this molecule attains a higher energy level. Because this state of an electron is very unstable, the electron is transferred from one to another molecule creating a chain of redox reactions, called an electron transport chain (ETC). The electron flow goes from PSII to cytochrome b6f to PSI. In PSI, the electron gets the energy from another photon. The final electron acceptor is NADP. In oxygenic photosynthesis, the first electron donor is water, creating oxygen as a waste product. In anoxygenic photosynthesis various electron donors are used.

text: The two photosystems absorb light energy through

text: pigment

text: s - primarily the

text: chlorophylls

text: , which are responsible for the green color of leaves.  The light-dependent reactions begin in photosystem II. When a

text: chlorophyll a

text: molecule within the

text: reaction center

text: of PSII absorbs a

text: photon

text: , an

text: electron

text: in this molecule attains a higher

text: energy level

text: . Because this state of an electron is very unstable, the electron is transferred from one to another molecule creating a chain of

text: redox reactions

text: , called an

text: electron transport chain

text: (ETC). The electron flow goes from PSII to cytochrome b6f to PSI. In PSI, the electron gets the energy from another photon. The final electron acceptor is NADP. In

text: oxygenic photosynthesis

text: , the first electron donor is

text: water

text: , creating

text: oxygen

text: as a waste product. In

text: anoxygenic photosynthesis

text: various electron donors are used.

text: There is an interesting and critical difference in the coenzymes used in catabolic and anabolic pathways; in catabolism NAD+ serves as an oxidizing agent when it is reduced to NADH. Whereas in anabolism the coenzyme NADPH serves as the reducing agent and is converted to its oxidized form NADP+.

text: There is an interesting and critical difference in the coenzymes used in catabolic and anabolic pathways; in catabolism

text: NAD+

text: serves as an oxidizing agent when it is reduced to NADH. Whereas in anabolism the coenzyme NADPH serves as the reducing agent and is converted to its oxidized form NADP+.

text: In 1904, the German chemist Franz Knoop elucidated the steps in beta-oxidation by feeding dogs odd- and even-chain ω-phenyl fatty acids, such as ω-phenylvaleric acid and ω-phenylbutyric acid, respectively. The mechanism of beta-oxidation, i.e. successive removal of two carbons, was realized when it was discovered that the odd-chain ω-phenylvaleric acid was metabolized to hippuric acid, and that the even-chain ω-phenylbutyric acid was metabolized to phenaceturic acid. At this time, any reaction mechanism involving oxidation at the beta carbon was as yet unknown in organic chemistry.

text: In 1904, the German chemist Franz Knoop elucidated the steps in beta-oxidation by feeding dogs odd- and even-chain ω-phenyl fatty acids, such as ω-phenylvaleric acid and ω-phenylbutyric acid, respectively. The mechanism of beta-oxidation, i.e. successive removal of two carbons, was realized when it was discovered that the odd-chain ω-phenylvaleric acid was metabolized to

text: hippuric acid

text: , and that the even-chain ω-phenylbutyric acid was metabolized to

text: phenaceturic acid

text: . At this time, any reaction mechanism involving oxidation at the

text: beta carbon

text: was as yet unknown in

text: organic chemistry

text: After being ingested, ethanol is first converted to acetaldehyde by the enzyme alcohol dehydrogenase and then to acetic acid by oxidation process. These reactions also convert nicotinamide adenine dinucleotide (NAD) to its reduced form NADH in a redox reaction. By causing an imbalance of the NAD/NADH redox system, alcoholic beverages make normal bodily functions more difficult. Consequences of the alcohol induced redox changes in the human body include increased triglyceride production, increased amino acid catabolism, inhibition of the citric acid cycle, lactic acidosis, ketoacidosis, hyperuricemia, disturbance in cortisol and androgen metabolism and increased fibrogenesis.The metabolism of glucose and insulin are also influenced. However, recent studies showed no significant correlation between hangover severity and the concentrations of various hormones, electrolytes, free fatty acids, triglycerides, lactate, ketone bodies, cortisol, and glucose in blood and urine samples.

text: After being ingested, ethanol is first converted to

text: acetaldehyde

text: by the enzyme

text: alcohol dehydrogenase

text: and then to

text: acetic acid

text: by oxidation process. These reactions also convert

text: nicotinamide adenine dinucleotide

text: (NAD) to its reduced form NADH in a

text: redox reaction

text: . By causing an imbalance of the NAD/NADH redox system, alcoholic beverages make normal bodily functions more difficult. Consequences of the alcohol induced redox changes in the human body include increased

text: triglyceride

text: production, increased

text: amino acid catabolism

text: , inhibition of the

text: citric acid cycle

text: lactic acidosis

text: ketoacidosis

text: hyperuricemia

text: , disturbance in

text: cortisol

text: and

text: androgen

text: metabolism and increased

text: fibrogenesis

text: .The metabolism of

text: glucose

text: and

text: insulin

text: are also influenced. However, recent studies showed no

text: significant

text: correlation between hangover severity and the concentrations of various

text: hormones

text: electrolytes

text: free fatty acids

text: triglycerides

text: , lactate,

text: ketone bodies

text: , cortisol, and glucose in blood and urine samples.

text: Purine metabolism refers to the metabolic pathways to synthesize and break down purines that are present in many organisms.

text: Purine metabolism refers to the

text: metabolic pathway

text: s to synthesize and break down

text: purine

text: s that are present in many organisms.

text: Pyruvate kinase also serves as a regulatory enzyme for gluconeogenesis, a biochemical pathway in which the liver generates glucose from pyruvate and other substrates. Gluconeogenesis utilizes noncarbohydrate sources to provide glucose to the brain and red blood cells in times of starvation when direct glucose reserves are exhausted. During a fasting state, pyruvate carboxylase phosphorylates pyruvate kinase, inactivating the enzyme and therefore, preventing phosphoenolpyruvate from being converted into pyruvate. Instead, phosphoenolpyruvate is converted into glucose via a cascade of gluconeogenesis reactions. Although it utilizes similar enzymes, gluconeogenesis is not the reverse of glycolysis. It is instead a pathway that circumvents the irreversible steps of glycolysis. Furthermore, gluconeogenesis and glycolysis do not occur concurrently in the cell at any given moment as they are reciprocally regulated by cell signaling. Once the gluconeogenesis pathway is complete, the glucose produced is expelled from the liver, proving energy for the vital tissues in the fasting state.

text: Pyruvate kinase also serves as a regulatory enzyme for

text: gluconeogenesis

text: , a biochemical pathway in which the liver generates

text: glucose

text: from pyruvate and other substrates. Gluconeogenesis utilizes noncarbohydrate sources to provide glucose to the brain and red blood cells in times of starvation when direct glucose reserves are exhausted. During a

text: fasting state

text: pyruvate carboxylase

text: phosphorylates pyruvate kinase, inactivating the enzyme and therefore, preventing

text: phosphoenolpyruvate

text: from being converted into pyruvate. Instead, phosphoenolpyruvate is converted into glucose via a cascade of gluconeogenesis reactions. Although it utilizes similar enzymes, gluconeogenesis is not the reverse of glycolysis. It is instead a pathway that circumvents the irreversible steps of glycolysis. Furthermore, gluconeogenesis and glycolysis do not occur concurrently in the cell at any given moment as they are reciprocally regulated by cell signaling. Once the gluconeogenesis pathway is complete, the glucose produced is expelled from the liver, proving energy for the vital tissues in the fasting state.

text: The term bioorthogonal chemistry refers to any chemical reaction that can occur inside of living systems without interfering with native biochemical processes. The term was coined by Carolyn R. Bertozzi in 2003. Since its introduction, the concept of the bioorthogonal reaction has enabled the study of biomolecules such as glycans, proteins, and lipids in real time in living systems without cellular toxicity. A number of chemical ligation strategies have been developed that fulfill the requirements of bioorthogonality, including the 1,3-dipolar cycloaddition between azides and cyclooctynes (also termed copper-free click chemistry), between nitrones and cyclooctynes, oxime/hydrazone formation from aldehydes and ketones, the tetrazine ligation, the isocyanide-based click reaction, and most recently, the quadricyclane ligation.

text: The term bioorthogonal chemistry refers to any

text: chemical reaction

text: that can occur inside of

text: living systems

text: without interfering with native biochemical processes. The term was coined by

text: Carolyn R. Bertozzi

text: in 2003. Since its introduction, the concept of the bioorthogonal reaction has enabled the study of biomolecules such as

text: glycan

text: s,

text: protein

text: s, and

text: lipid

text: s in real time in living systems without cellular toxicity. A number of chemical ligation strategies have been developed that fulfill the requirements of bioorthogonality, including the

text: 1,3-dipolar cycloaddition

text: between

text: azide

text: s and

text: cyclooctyne

text: s (also termed

text: copper-free click chemistry

text: ), between

text: nitrone

text: s and cyclooctynes,

text: oxime

text: hydrazone

text: formation from

text: aldehyde

text: s and

text: ketone

text: s, the

text: tetrazine

text: ligation, the

text: isocyanide

text: -based click reaction, and most recently, the quadricyclane ligation.

text: Alkylimino-de-oxo-bisubstitution in organic chemistry is the organic reaction of carbonyl compounds with amines to imines. The reaction name is based on the IUPAC Nomenclature for Transformations. The reaction is acid catalyzed and the reaction type is nucleophilic addition of the amine to the carbonyl compound followed by transfer of a proton from nitrogen to oxygen to a stable hemiaminal or carbinolamine. With primary amines water is lost in an elimination reaction to an imine. With aryl amines especially stable Schiff bases are formed.

text: Alkylimino-de-oxo-bisubstitution in

text: organic chemistry

text: is the

text: organic reaction

text: of

text: carbonyl

text: compounds with

text: amine

text: s to

text: imine

text: s. The reaction name is based on the

entity_name: IUPAC nomenclature for organic transformations

text: IUPAC Nomenclature for Transformations

text: . The reaction is

text: acid catalyzed

text: and the reaction type is

text: nucleophilic addition

text: of the amine to the carbonyl compound followed by transfer of a

text: proton

text: from nitrogen to oxygen to a stable

text: hemiaminal

text: or carbinolamine. With primary amines water is lost in an

text: elimination reaction

text: to an

text: imine

text: . With

text: aryl

text: amines especially stable

text: Schiff base

text: s are formed.

text: C3 carbon fixation - C4 photosynthesis - Calvin cycle - CAM photosynthesis - CAM plants - cancer - capacitation - capillary - carbohydrate - carbon cycle - carbon fixation - carnivore - Carl Linnaeus - carotene - carrying capacity - cartilage - Casparian strip - CASY cell counting technology - catabolism - cell - cell biology - cell division - cell growth - cell nucleus - cell wall - cellular differentiation - cellular respiration - cellulose - centriole - centromere - centrosome - chaperone protein - Charles Robert Darwin - chemiosmosis - chemautotrophic - chiasma (genetics) - chimera (genetics) - Chi square test - chlorophyll - chloroplast - chloroplast membrane - cholesterine - chromatid - chromatin - chromatography - chromosomal crossover - chromosome - chromosome walking - chronotype - cilium - circadian rhythm - circulatory system - cis face - cisterna - citric acid cycle - cladistics - classical genetics - clearance (medicine) - cloning - codon - codon usage bias - coenzyme - colchicine - collagen - colony - commensalism - common descent - communicable disease - community - community ecology - competition - competitive exclusion principle - competitive inhibition - computational biology - concentration gradient - conservation biology - continental drift -  convergent evolution - cooperativity - cooperativity cellular respiration - cork cambium - cotransport metabolism - cotyledon - Coulter counter - Craig Venter - cristae - cryptobiology - cryptobiosis - CT - C-terminus - culture - cuticula - cyclic electron flow - cytokinesis - cytoplasm - cytoskeleton - cytosol - cytotoxic T cell -

text: C3 carbon fixation

text: C4 photosynthesis

text: Calvin cycle

text: CAM photosynthesis

text: CAM plants

text: cancer

text: capacitation

text: capillary

text: carbohydrate

text: carbon cycle

text: carbon fixation

text: carnivore

text: Carl Linnaeus

text: carotene

text: carrying capacity

text: cartilage

text: Casparian strip

text: CASY cell counting technology

text: catabolism

text: cell

text: cell biology

text: cell division

text: cell growth

text: cell nucleus

text: cell wall

text: cellular differentiation

text: cellular respiration

text: cellulose

text: centriole

text: centromere

text: centrosome

text: chaperone protein

text: Charles Robert Darwin

text: chemiosmosis

text: chemautotrophic

text: chiasma (genetics)

text: chimera (genetics)

text: Chi square test

text: chlorophyll

text: chloroplast

text: chloroplast membrane

text: cholesterine

text: chromatid

text: chromatin

text: chromatography

text: chromosomal crossover

text: chromosome

text: chromosome walking

text: chronotype

text: cilium

text: circadian rhythm

text: circulatory system

text: cis face

text: cisterna

text: citric acid cycle

text: cladistics

text: classical genetics

text: clearance (medicine)

text: cloning

text: codon

text: codon usage bias

text: coenzyme

text: colchicine

text: collagen

text: colony

text: commensalism

text: common descent

text: communicable disease

text: community

text: community ecology

text: competition

text: competitive exclusion principle

text: competitive inhibition

text: computational biology

text: concentration gradient

text: conservation biology

text: continental drift

text: convergent evolution

text: cooperativity

text: - cooperativity cellular respiration -

text: cork cambium

text: cotransport metabolism

text: cotyledon

text: Coulter counter

text: Craig Venter

text: cristae

text: cryptobiology

text: cryptobiosis

text: CT

text: C-terminus

text: culture

text: cuticula

text: cyclic electron flow

text: cytokinesis

text: cytoplasm

text: cytoskeleton

text: cytosol

text: cytotoxic T cell

text: The development of the first correct double helix molecular model of DNA by Crick and Watson may not have been possible without the biochemical evidence for the nucleotide base-pairing ([A---T]; [C---G]), or Chargaff's rules. Although such initial studies of DNA structures with the help of molecular models were essentially static, their consequences for explaining the in vivo functions of DNA were significant in the areas of protein biosynthesis and the quasi-universality of the genetic code. Epigenetic transformation studies of DNA in vivo were however much slower to develop despite their importance for embryology, morphogenesis and cancer research. Such chemical dynamics and biochemical reactions of DNA are much more complex than the molecular dynamics of DNA physical interactions with water, ions and proteins/enzymes in living cells.

text: The development of the first correct double helix molecular model of DNA by Crick and Watson may not have been possible without the biochemical evidence for the nucleotide base-pairing ([A---T]; [C---G]), or

text: Chargaff's rules

text: . Although such initial studies of DNA structures with the help of molecular models were essentially static, their consequences for explaining the in vivo functions of DNA were significant in the areas of protein biosynthesis and the quasi-universality of the genetic code. Epigenetic transformation studies of DNA in vivo were however much slower to develop despite their importance for embryology, morphogenesis and cancer research. Such chemical dynamics and biochemical reactions of DNA are much more complex than the molecular dynamics of DNA physical interactions with water, ions and proteins/enzymes in living cells.

text: The hydrolysis of inorganic pyrophosphate (PPi) to two phosphate ions is utilized in many biochemical pathways to render reactions effectively irreversible. This process is highly exergonic (accounting for approximately a −19kJ change in free energy), and therefore greatly increases the energetic favorability of reaction system when coupled with a typically less-favorable reaction.

text: The hydrolysis of inorganic

text: pyrophosphate

text: (PPi) to two

text: phosphate

text: ions is utilized in many biochemical pathways to render reactions effectively irreversible. This process is highly

text: exergonic

text: (accounting for approximately a −19kJ change in

text: free energy

text: ), and therefore greatly increases the energetic favorability of reaction system when coupled with a typically less-favorable reaction.

text: Brueckner and Weigand extended the use of this allylation chemistry to beta-substituted stannanes, including those that contain heterocycles, in 1996, exploring a variety of titanium alkoxides, premixing times, and reaction temperatures. The optimal discovered conditions were 10 mol% Ti(OiPr)4 or Ti(OEt)4, 20mol% enantiopure BINOL, with a premixing period of 2 hours, giving enantiomeric excesses of up to 99%. The general reaction scheme is shown below.

text: Sverdrup defines the critical depth at which integrated photosynthesis equals integrated respiration. This can also be described as the depth at which the integral of net growth rate over the water column becomes zero.  The net growth rate equals the gross photosynthetic rate minus loss terms.  Gross photosynthesis exponentially decays from a maximum near the surface to approach zero with depth.  It is affected by the amount and angle of solar radiation and the clarity of the water.  The loss rate is the sum of cellular respiration, grazing, sinking, advection, viral lysis, and mortality.  In his hypothesis, Sverdrup made the approximation that the loss rate for a phytoplankton community is constant at all depths and times.

text: Sverdrup defines the critical depth at which integrated photosynthesis equals integrated respiration. This can also be described as the depth at which the integral of net growth rate over the

text: water column

text: becomes zero.  The net growth rate equals the gross photosynthetic rate minus loss terms.  Gross

text: photosynthesis

text: exponentially decays from a maximum near the surface to approach zero with depth.  It is affected by the amount and angle of

text: solar radiation

text: and the clarity of the water.  The loss rate is the sum of

text: cellular respiration

text: grazing

text: , sinking,

text: advection

text: viral lysis

text: , and mortality.  In his hypothesis, Sverdrup made the approximation that the loss rate for a phytoplankton community is constant at all depths and times.

text: Ivar Karl Ugi (9 September 1930 in Saaremaa, Estonia – 29 September 2005 in Munich) was an Estonian-born German chemist who made major contributions to organic chemistry. He is known for the research on multicomponent reactions, yielding the Ugi reaction.

text: Ivar Karl Ugi (9 September 1930 in

text: Saaremaa

text: Estonia

text: – 29 September 2005 in

text: Munich

text: ) was an

text: Estonia

text: n-born German

text: chemist

text: who made major contributions to

text: organic chemistry

text: . He is known for the research on

text: multicomponent reaction

text: s, yielding the

text: Ugi reaction

text: In a healthy body, blood cortisone and cortisol levels are roughly equimolar. Cortisone reductase deficiency leads to an elevated level of inert cortisone to active cortisol in adipose tissue. Cortisone reductase deficiency is caused by dysregulation of the 11β-hydroxysteroid dehydrogenase type 1 enzyme, otherwise known as cortisone reductase. The 11β-HSD1 enzyme is responsible for catalyzing the interconversion of circulating cortisone to cortisol, using NADH as a co-factor. The oxidative or reductive capacity of the enzyme is regulated by NADH produced by hexose-6-phosphate dehydrogenase (H6PD). H6PD is distinct from its isozyme, glucose-6-phosphate dehydrogenase (G6PDH) in that G6PDH is a cytolytic enzyme and draws from a separate pool of NAD+. H6PD is also capable of catalyzing the oxidation of several phosphorylated hexoses, while G6PDH shows affinity for glucose, specifically. The enzyme cortisone reductase exists in a tightly controlled reaction space, facing the lumen of the endoplasmic reticulum of cells in the liver and lungs. NADH produced by hexose-6-phosphate is delivered directly to the catalytic site of cortisone reductase. If NADH production is limited, then cortisone reductase is also capable of catalysing the reverse reaction taking circulating cortisol and reducing it to cortisone. Dysregulation of hexose-6-phosphate dehydrogenase occurs as a result of gene mutation. Cortisol is important in signalling inhibition of adrenocorticotropic hormone release from the pituitary. Reduced cortisol in circulation activates the H-P-A Axis to produce and release more cortisol, and therefore androgen.

text: In a healthy body, blood cortisone and cortisol levels are roughly equimolar. Cortisone reductase deficiency leads to an elevated level of inert cortisone to active cortisol in adipose tissue. Cortisone reductase deficiency is caused by dysregulation of the 11β-hydroxysteroid dehydrogenase type 1 enzyme, otherwise known as

text: cortisone reductase

text: . The 11β-HSD1 enzyme is responsible for catalyzing the interconversion of circulating

text: cortisone

text: to

text: cortisol

text: , using NADH as a co-factor. The oxidative or reductive capacity of the enzyme is regulated by NADH produced by

text: hexose-6-phosphate dehydrogenase

text: (H6PD). H6PD is distinct from its isozyme, glucose-6-phosphate dehydrogenase (G6PDH) in that G6PDH is a cytolytic enzyme and draws from a separate pool of NAD+. H6PD is also capable of catalyzing the oxidation of several phosphorylated hexoses, while G6PDH shows affinity for glucose, specifically. The enzyme cortisone reductase exists in a tightly controlled reaction space, facing the lumen of the endoplasmic reticulum of cells in the liver and lungs. NADH produced by hexose-6-phosphate is delivered directly to the catalytic site of cortisone reductase. If NADH production is limited, then cortisone reductase is also capable of catalysing the reverse reaction taking circulating cortisol and reducing it to cortisone. Dysregulation of hexose-6-phosphate dehydrogenase occurs as a result of gene mutation. Cortisol is important in signalling inhibition of

text: adrenocorticotropic hormone

text: release from the pituitary. Reduced cortisol in circulation activates the H-P-A Axis to produce and release more cortisol, and therefore androgen.

text: Plants synthesise a number of unique polymers like the polysaccharide molecules cellulose, pectin and xyloglucan from which the land plant cell wall is constructed.Vascular land plants make lignin, a polymer used to strengthen the secondary cell walls of xylem tracheids and vessels to keep them from collapsing when a plant sucks water through them under water stress. Lignin is also used in other cell types like sclerenchyma fibres that provide structural support for a plant and is a major constituent of wood. Sporopollenin is a chemically resistant polymer found in the outer cell walls of spores and pollen of land plants responsible for the survival of early land plant spores and the pollen of seed plants in the fossil record. It is widely regarded as a marker for the start of land plant evolution during the Ordovician period.The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the Ordovician and Silurian periods. Many monocots like maize and the pineapple and some dicots like the Asteraceae have since independently evolved pathways like Crassulacean acid metabolism and the  carbon fixation pathway for photosynthesis which avoid the losses resulting from photorespiration in the more common  carbon fixation pathway. These biochemical strategies are unique to land plants.

text: Plants synthesise a number of unique

text: polymer

text: s like the

text: polysaccharide

text: molecules

text: cellulose

text: pectin

text: and

text: xyloglucan

text: from which the land plant cell wall is constructed.Vascular land plants make

text: lignin

text: , a polymer used to strengthen the

text: secondary cell walls

text: of xylem

text: tracheids

text: and

text: vessels

text: to keep them from collapsing when a plant sucks water through them under water stress. Lignin is also used in other cell types like

text: sclerenchyma fibres

text: that provide structural support for a plant and is a major constituent of wood.

text: Sporopollenin

text: is a chemically resistant polymer found in the outer cell walls of spores and pollen of land plants responsible for the survival of early land plant spores and the pollen of seed plants in the fossil record. It is widely regarded as a marker for the start of land plant evolution during the

text: Ordovician

text: period.The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the

text: Ordovician

text: and

text: Silurian

text: periods. Many

text: monocots

text: like

text: maize

text: and the

text: pineapple

text: and some

text: dicots

text: like the

text: Asteraceae

text: have since independently evolved pathways like

text: Crassulacean acid metabolism

text: and the

text: carbon fixation

text: pathway for photosynthesis which avoid the losses resulting from

text: photorespiration

text: in the more common

text: carbon fixation

text: pathway. These biochemical strategies are unique to land plants.

text: The goals of agricultural chemistry are to expand understanding of the causes and effects of biochemical reactions related to plant and animal growth, to reveal opportunities for controlling those reactions, and to develop chemical products that will provide the desired assistance or control. Every scientific discipline that contributes to agricultural progress depends in some way on chemistry. Hence agricultural chemistry is not a distinct discipline, but a common thread that ties together genetics, physiology, microbiology, entomology, and numerous other sciences that impinge on agriculture.

text: The goals of agricultural chemistry are to expand understanding of the causes and effects of biochemical reactions related to plant and animal growth, to reveal opportunities for controlling those reactions, and to develop chemical products that will provide the desired assistance or control. Every scientific discipline that contributes to agricultural progress depends in some way on chemistry. Hence agricultural chemistry is not a distinct discipline, but a common thread that ties together

text: genetics

text: physiology

text: microbiology

text: entomology

text: , and numerous other sciences that impinge on agriculture.

text: Enzyme inhibitors are also important in metabolic control. Many metabolic pathways in the cell are inhibited by metabolites that control enzyme activity through allosteric regulation or substrate inhibition. A good example is the allosteric regulation of the glycolytic pathway. This catabolic pathway consumes glucose and produces ATP, NADH and pyruvate. A key step for the regulation of glycolysis is an early reaction in the pathway catalysed by phosphofructokinase-1 (PFK1). When ATP levels rise, ATP binds an allosteric site in PFK1 to decrease the rate of the enzyme reaction; glycolysis is inhibited and ATP production falls. This negative feedback control helps maintain a steady concentration of ATP in the cell. However, metabolic pathways are not just regulated through inhibition since enzyme activation is equally important. With respect to PFK1, fructose 2,6-bisphosphate and ADP are examples of metabolites that are allosteric activators.

text: Enzyme inhibitors are also important in metabolic control. Many

text: metabolic pathway

text: s in the cell are inhibited by

text: metabolite

text: s that control enzyme activity through

text: allosteric regulation

text: or substrate inhibition. A good example is the allosteric regulation of the

text: glycolytic pathway

text: . This

text: catabolic

text: pathway consumes

text: glucose

text: and produces

text: ATP

text: NADH

text: and

text: pyruvate

text: . A key step for the regulation of glycolysis is an early reaction in the pathway catalysed by

text: (PFK1). When ATP levels rise, ATP binds an allosteric site in PFK1 to decrease the rate of the enzyme reaction; glycolysis is inhibited and ATP production falls. This

text: negative feedback

text: control helps maintain a steady concentration of ATP in the cell. However, metabolic pathways are not just regulated through inhibition since enzyme activation is equally important. With respect to PFK1,

text: fructose 2,6-bisphosphate

text: and

text: ADP

text: are examples of metabolites that are allosteric activators.

text: Adenain () is an enzyme. This enzyme catalyses the following chemical reaction

text: Adenain () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: The most commonly synthesized ring sizes are between 5-7 atoms; however, reported syntheses include 45- up to 90- membered macroheterocycles. These reactions are metal-catalyzed and proceed through a metallacyclobutane intermediate. It was first published by Dider Villemin in 1980 describing the synthesis of an Exaltolide precursor, and later become popularized by Robert H. Grubbs and Richard R. Schrock, who shared the Nobel Prize in Chemistry, along with Yves Chauvin, in 2005 for their combined work in olefin metathesis. RCM is a favorite among organic chemists due to its synthetic utility in the formation of rings, which were previously difficult to access efficiently, and broad substrate scope. Since the only major by-product is ethylene, these reactions may also be considered atom economic, an increasingly important concern in the development of green chemistry.

text: The most commonly synthesized ring sizes are between 5-7 atoms; however, reported syntheses include 45- up to 90- membered macroheterocycles. These reactions are metal-catalyzed and proceed through a

text: metallacyclobutane

text: intermediate. It was first published by Dider Villemin in 1980 describing the synthesis of an Exaltolide precursor, and later become popularized by

text: Robert H. Grubbs

text: and

text: Richard R. Schrock

text: , who shared the

text: Nobel Prize in Chemistry

text: , along with

text: Yves Chauvin

text: , in 2005 for their combined work in

text: olefin metathesis

text: . RCM is a favorite among organic chemists due to its synthetic utility in the formation of rings, which were previously difficult to access efficiently, and broad substrate scope. Since the only major

text: by-product

text: is

text: ethylene

text: , these reactions may also be considered

text: atom economic

text: , an increasingly important concern in the development of

text: green chemistry

text: In biochemical reactions, the redox reactions are sometimes more difficult to see, such as this reaction from glycolysis:

text: In biochemical reactions, the

text: redox

text: reactions are sometimes more difficult to see, such as this reaction from

text: glycolysis

text: All aerobic organisms produce  when they oxidize carbohydrates, fatty acids, and proteins. The large number of reactions involved are exceedingly complex and not described easily. Refer to (cellular respiration, anaerobic respiration and photosynthesis). The equation for the respiration of glucose and other monosaccharides is:

text: All

text: aerobic

text: organisms produce  when they oxidize

text: carbohydrate

text: s,

text: fatty acid

text: s, and proteins. The large number of reactions involved are exceedingly complex and not described easily. Refer to (

text: cellular respiration

text: anaerobic respiration

text: and

text: photosynthesis

text: ). The equation for the respiration of glucose and other

text: monosaccharide

text: s is:

text: In enzymology, a [formate-C-acetyltransferase]-activating enzyme () is an enzyme that catalyzes the chemical reaction

text: In

text: enzymology

text: , a [formate-C-acetyltransferase]-activating enzyme () is an

text: enzyme

text: that

text: catalyzes

text: the

text: chemical reaction

text: reflects the fact that there is only one expectation value that must be held constant: the free energy (due to conservation of energy). For chemistry problems involving chemical reactions, the grand canonical ensemble provides the appropriate foundation, and there are two Lagrange multipliers.  One is to hold the energy constant, and another, the fugacity, is to hold the particle count constant (as chemical reactions involve the recombination of a fixed number of atoms).

text: reflects the fact that there is only one expectation value that must be held constant: the

text: free energy

text: (due to

text: conservation of energy

text: ). For chemistry problems involving chemical reactions, the

text: grand canonical ensemble

text: provides the appropriate foundation, and there are two Lagrange multipliers.  One is to hold the energy constant, and another, the

text: fugacity

text: , is to hold the particle count constant (as chemical reactions involve the recombination of a fixed number of atoms).

text: Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled.

text: Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of

text: functional group

text: s of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called

text: coenzyme

text: s. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the

text: substrate

text: for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled.

text: Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cells' production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enzymes that allow cells to convert raw materials into molecules necessary for the cell’s survival. Metabolic engineering specifically seeks to mathematically model these networks, calculate a yield of useful products, and pin point parts of the network that constrain the production of these products.  Genetic engineering techniques can then be used to modify the network in order to relieve these constraints.   Once again this modified network can be modeled to calculate the new product yield.

text: Metabolic engineering is the practice of optimizing

text: genetic

text: and regulatory processes within

text: cells

text: to increase the cells' production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and

text: enzymes

text: that allow cells to convert raw materials into molecules necessary for the cell’s survival. Metabolic engineering specifically seeks to mathematically model these networks, calculate a yield of useful products, and pin point parts of the network that constrain the production of these products.

text: Genetic engineering

text: techniques can then be used to modify the network in order to relieve these constraints.   Once again this modified network can be modeled to calculate the new product yield.

text: Methylmalonyl-CoA mutase is a member of the isomerase subfamily of adensylcobalamin-dependent enzymes. Furthermore, it is classified as class I, as it is a ‘DMB-off’/’His-on’ enzyme. This refers to the nature of the AdoCbl cofactor in the active site of methylmalonyl CoA. AdoCbl is composed of a central cobalt-containing Corrin ring, an upper axial ligand (β-axial ligand), and a lower axial ligand (α-axial ligand). Both axial ligands are initially bonded to the central cobalt atom. In methylmalonyl-CoA mutase the β-axial ligand is 5’-deoxy-5’-adenosine and is involved in the free radical chemistry of the reaction. The α-axial ligand is 5,6-dimethylbenzimidazole (DMB) and is involved in organizing the active site to enable Histidine-610 to bond with Co, instead of DMB (the reason for the ‘DMB-off’/’His-on’ notation). The Histidine-610 residue is critical to enzyme functionality. Its binding increases the rate of homolytic β-axial ligand – Co bond breakage by a factor of 10.

text: Methylmalonyl-CoA mutase is a member of the

text: isomerase

text: subfamily of adensylcobalamin-dependent enzymes. Furthermore, it is classified as class I, as it is a ‘DMB-off’/’His-on’ enzyme. This refers to the nature of the AdoCbl cofactor in the active site of methylmalonyl CoA. AdoCbl is composed of a central

text: cobalt

text: -containing

text: Corrin ring

text: , an upper axial ligand (β-axial ligand), and a lower axial ligand (α-axial ligand). Both axial ligands are initially bonded to the central cobalt atom. In methylmalonyl-CoA mutase the β-axial ligand is 5’-deoxy-5’-adenosine and is involved in the

text: free radical

text: chemistry of the reaction. The α-axial ligand is 5,6-dimethylbenzimidazole (DMB) and is involved in organizing the active site to enable

text: Histidine

text: -610 to bond with Co, instead of DMB (the reason for the ‘DMB-off’/’His-on’ notation). The Histidine-610 residue is critical to enzyme functionality. Its binding increases the rate of homolytic β-axial ligand – Co bond breakage by a factor of 10.

text: Fructokinase (/fruc•to•ki•nase/ [-ki´nas]) (), also known as D-fructokinase or D-fructose (D-mannose) kinase, is an enzyme of the liver, intestine, and kidney cortex.  Fructokinase is in a family of enzymes called transferases, meaning that this enzyme transfers functional groups; it is also considered a phosphotransferase (or, frequently, a kinase) since it specifically transfers a phosphate group. Fructokinase specifically catalyzes the transfer of a phosphate group from ATP (the substrate) to fructose as the initial step in its utilization. The main role of fructokinase is in carbohydrate metabolism, more specifically, sucrose and fructose metabolism.  The reaction equation is as follows: ATP + D-fructose = ADP + D-fructose 1-phosphate. This is notable because in most tissues this reaction is catalyzed by hexokinase, forming instead fructose 6-phosphate.

text: Fructokinase (/fruc•to•ki•nase/ [-ki´nas]) (), also known as D-fructokinase or D-fructose (D-mannose) kinase, is an enzyme of the

text: liver

text: intestine

text: , and

text: kidney cortex

text: .  Fructokinase is in a family of enzymes called

text: transferase

text: s, meaning that this enzyme transfers functional groups; it is also considered a

text: phosphotransferase

text: (or, frequently, a

text: kinase

text: ) since it specifically transfers a phosphate group. Fructokinase specifically catalyzes the transfer of a phosphate group from ATP (the substrate) to fructose as the initial step in its utilization. The main role of fructokinase is in carbohydrate metabolism, more specifically, sucrose and fructose metabolism.  The reaction equation is as follows: ATP + D-fructose = ADP + D-fructose 1-phosphate. This is notable because in most tissues this reaction is catalyzed by hexokinase, forming instead fructose 6-phosphate.

text: In enzymology, an enzyme-thiol transhydrogenase (glutathione-disulfide) () is an enzyme that catalyzes the chemical reaction

text: In

text: enzymology

text: , an enzyme-thiol transhydrogenase (glutathione-disulfide) () is an

text: enzyme

text: that

text: catalyzes

text: the

text: chemical reaction

text: Roger John Williams was born in Ootacamund, India, of American parents on 14 August 1893. At age 2, his family returned to the U.S., where he grew up in Kansas and California. His formal education culminated in a Ph.D. degree (magna cum laude) from the University of Chicago in 1919. He taught at the University of Oregon, Oregon State University, and beginning in 1940, at the University of Texas at Austin. He authored several widely used textbooks of organic chemistry and biochemistry. Much of his work emphasized the role of heritable (genetic) differences among humans in response to foods and other environmental factors. His book "Biochemical Individuality" is a core text in nutrigenomics and what is now called precision medicine. He became Emeritus Professor of Chemistry in 1971, and retired from that position in 1986 at age 92. He is one of the founders of the field of personalized medicine.

text: Roger John Williams was born in

text: Ootacamund

text: India

text: , of American parents on 14 August 1893. At age 2, his family returned to the U.S., where he grew up in

text: Kansas

text: and

text: California

text: . His formal education culminated in a

text: Ph.D.

text: degree (

text: magna cum laude

text: ) from the

text: University of Chicago

text: in 1919. He taught at the

text: University of Oregon

text: Oregon State University

text: , and beginning in 1940, at the

text: University of Texas at Austin

text: . He authored several widely used textbooks of

text: organic chemistry

text: and

text: biochemistry

text: . Much of his work emphasized the role of heritable (genetic) differences among humans in response to foods and other environmental factors. His book "Biochemical Individuality" is a core text in

text: nutrigenomics

text: and what is now called

text: precision medicine

text: . He became

text: Emeritus Professor

text: of

text: Chemistry

text: in 1971, and retired from that position in 1986 at age 92. He is one of the founders of the field of

text: personalized medicine

text: Through the process of photosynthesis, plants capture energy from light and use it to combine carbon dioxide and water to produce carbohydrates and oxygen. The photosynthesis carried out by all the plants in an ecosystem is called the gross primary production (GPP). About 48–60% of the GPP is consumed in plant respiration. The remainder, that portion of GPP that is not used up by respiration, is known as the net primary production (NPP). Total photosynthesis is limited by a range of environmental factors. These include the amount of light available, the amount of leaf area a plant has to capture light (shading by other plants is a major limitation of photosynthesis), rate at which carbon dioxide can be supplied to the chloroplasts to support photosynthesis, the availability of water, and the availability of suitable temperatures for carrying out photosynthesis.

text: Through the process of photosynthesis, plants capture energy from light and use it to combine

text: carbon dioxide

text: and water to produce

text: carbohydrate

text: s and

text: oxygen

text: . The photosynthesis carried out by all the plants in an ecosystem is called the gross primary production (GPP). About 48–60% of the GPP is consumed in plant respiration. The remainder, that portion of GPP that is not used up by respiration, is known as the net primary production (NPP). Total photosynthesis is limited by a range of environmental factors. These include the amount of light available, the amount of

text: leaf

text: area a plant has to capture light (shading by other plants is a major limitation of photosynthesis), rate at which carbon dioxide can be supplied to the

text: chloroplast

text: s to support photosynthesis, the availability of water, and the availability of suitable temperatures for carrying out

text: photosynthesis

text: This crowding effect can make molecules in cells behave in radically different ways than in test-tube assays. Consequently, measurements of the properties of enzymes or processes in metabolism that are made in the laboratory (in vitro) in dilute solutions may be different by many orders of magnitude from the true values seen in living cells (in vivo). The study of biochemical processes under realistically crowded conditions is very important, since these conditions are a ubiquitous property of all cells and crowding may be essential for the efficient operation of metabolism.

text: This crowding effect can make molecules in cells behave in radically different ways than in test-tube assays. Consequently, measurements of the properties of

text: enzyme

text: s or processes in

text: metabolism

text: that are made in the laboratory (

text: in vitro

text: ) in dilute solutions may be different by many orders of magnitude from the true values seen in living cells (

text: in vivo

text: ). The study of biochemical processes under realistically crowded conditions is very important, since these conditions are a ubiquitous property of all cells and crowding may be essential for the efficient operation of metabolism.

text: The biochemical reactions catalyzed by NDP kinase in plants are analogous to activities described in humans as autophosphorylation activity takes place from ATP and GTP. In addition to this, plants have four types of NDPK isoforms. Cytosolic type I NDPK is involved in metabolism, growth, and stress responses in plants. Type II NDPK is concentrated in the chloroplast and it’s believed to be involved in the photosynthesis process and the oxidative stress management, but its function is not yet known clearly. Type III NDPK targets both mitochondria and chloroplast, and it’s mainly involved in energy metabolism. The localization and exact function of the type IV NDPK is not yet well known and needs further investigations. In addition, NDPK is associated with H2O2-mediated mitogen-activated protein kinase signaling in plants.

text: In most of his research his original training physical chemistry is quite evident as he focused mainly on the physical/chemical aspects of biology. Much of his early work includes work on practical chemistry, kinetics of enzyme reactions and very little on genetics. His work falls into four distinct categories: 1. building a foundation in physical chemistry; 2. development of metabolic control analysis; 3. consolidation and 4. expansion. Only in the third phase of his career his expertise in genetics came to light when he set out to find experimental models to demonstrate the correctness of his paper on metabolic control analysis.

text: In most of his research his original training physical chemistry is quite evident as he focused mainly on the physical/chemical aspects of biology. Much of his early work includes work on practical chemistry,

text: kinetics of enzyme reactions

text: and very little on

text: genetics

text: . His work falls into four distinct categories: 1. building a foundation in physical chemistry; 2. development of metabolic control analysis; 3. consolidation and 4. expansion. Only in the third phase of his career his expertise in genetics came to light when he set out to find experimental models to demonstrate the correctness of his paper on

text: metabolic control analysis

text: In nucleotide sugar metabolism a group of biochemicals known as nucleotide sugars act as donors for sugar residues in the glycosylation reactions that produce polysaccharides. They are substrates for glycosyltransferases. The nucleotide sugars are also intermediates in nucleotide sugar interconversions that produce some of the activated sugars needed for glycosylation reactions. Since most glycosylation takes place in the endoplasmic reticulum and golgi apparatus, there are a large family of nucleotide sugar transporters that allow nucleotide sugars to move from the cytoplasm, where they are produced, into the organelles where they are consumed.

text: In nucleotide sugar metabolism a group of

text: biochemical

text: s known as

text: nucleotide sugars

text: act as donors for sugar residues in the

text: glycosylation

text: reactions that produce

text: polysaccharide

text: s. They are substrates for

text: glycosyltransferase

text: s. The nucleotide sugars are also intermediates in nucleotide sugar interconversions that produce some of the activated sugars needed for glycosylation reactions. Since most glycosylation takes place in the

text: endoplasmic reticulum

text: and

text: golgi apparatus

text: , there are a large family of

text: nucleotide sugar transporter

text: s that allow nucleotide sugars to move from the

text: cytoplasm

text: , where they are produced, into the organelles where they are consumed.

text: Most Europeans have two major isozymes, while approximately 50% of  Northeast Asians have one normal copy of the ALDH2 gene and one variant copy that encodes an inactive mitochondrial isoenzyme. In native Japanese, this variant ALDH2 gene encodes lysine instead of glutamic acid at amino acid 487 and therefore encodes a product protein that is completely inactive in metabolizing acetaldehyde to acetic acid. In the overall Japanese population, about 57% of individuals are homozygous for the normal gene, 40% are heterozygous for the variant gene, and 3% are homozygous for the variant gene.  Since ALDH2 assembles and functions as a tetramer and requires all four of its components to be active in order to metabolize acetaldehyde, heterozygotes have very little ALDH2 activity.  Accordingly, Japanese individuals heterozygous or homozygous for the abnormal gene metabolize ethanol to acetaldehyde normally but metabolize acetaldehyde poorly and are thereby susceptible to certain adverse effects of alcoholic (i.e. ethanol-containing) beverages; these effects include the transient accumulation of acetaldehyde in blood and tissues; facial flushing (i.e. the "oriental flushing syndrome"), urticaria, systemic dermatitis, and alcohol-induced respiratory reactions such as rhinitis and the exacerbation of asthma bronchoconstriction.  The cited allergic reaction-like symptoms: a) do not appear due to classical IgE or T cell-related allergen-induced reactions but rather to the actions of acetaldehyde in stimulating the release of histamine, a probable mediating cause of these symptoms; b) typically occur within 30–60 minutes of ingesting alcoholic beverages; and c) occur in other Asian as well as non-Asian individuals that are either seriously defective in metabolizing ingested ethanol past acetaldehyde to acetic acid or, alternatively, that metabolize ethanol too rapidly for ALDH2 processing.

text: Most Europeans have two major isozymes, while approximately 50% of  Northeast Asians have one normal copy of the ALDH2 gene and one variant copy that encodes an inactive mitochondrial isoenzyme. In native Japanese, this variant ALDH2 gene encodes

text: lysine

text: instead of

text: glutamic acid

text: at

text: amino acid

text: 487 and therefore encodes a product protein that is completely inactive in metabolizing acetaldehyde to acetic acid. In the overall Japanese population, about 57% of individuals are

text: homozygous

text: for the normal gene, 40% are

text: heterozygous

text: for the variant gene, and 3% are homozygous for the variant gene.  Since ALDH2 assembles and functions as a

text: tetramer

text: and requires all four of its components to be active in order to metabolize acetaldehyde, heterozygotes have very little ALDH2 activity.  Accordingly, Japanese individuals heterozygous or homozygous for the abnormal gene metabolize ethanol to acetaldehyde normally but metabolize acetaldehyde poorly and are thereby susceptible to certain adverse effects of alcoholic (i.e. ethanol-containing) beverages; these effects include the transient accumulation of acetaldehyde in blood and tissues; facial

text: flushing

text: (i.e. the "oriental flushing syndrome"),

text: urticaria

text: , systemic

text: dermatitis

text: , and

text: alcohol-induced respiratory reactions

text: such as

text: rhinitis

text: and the exacerbation of

text: asthma

text: bronchoconstriction

text: .  The cited allergic reaction-like symptoms: a) do not appear due to classical

text: IgE

text: or

text: T cell

text: -related

text: allergen

text: -induced reactions but rather to the actions of acetaldehyde in stimulating the release of

text: histamine

text: , a probable mediating cause of these symptoms; b) typically occur within 30–60 minutes of ingesting alcoholic beverages; and c) occur in other Asian as well as non-Asian individuals that are either seriously defective in metabolizing ingested ethanol past acetaldehyde to acetic acid or, alternatively, that metabolize ethanol too rapidly for ALDH2 processing.

text: With regard to the last argument, proponents note that nobody has studied the effects of increased efficiency in plants in such a way to make this determination possible. Some plants have more and less efficient photosynthesis reactions, such as the C3, C4, and CAM photosynthesis reactions. No such "damaging chemical reactions" occur in the more effective processes.

text: With regard to the last argument, proponents note that nobody has studied the effects of increased efficiency in plants in such a way to make this determination possible. Some plants have more and less

text: efficient photosynthesis

text: reactions, such as the

text: , and

text: CAM

text: photosynthesis reactions. No such "damaging chemical reactions" occur in the more effective processes.

text: Metabolism-like reactions could have occurred naturally in early oceans, before the first organisms evolved. Metabolism may predate the origin of life and life may have evolved from the chemical conditions that prevailed in the world's earliest oceans. Reconstructions in laboratories show that some of these reactions can produce RNA, and some others resemble two essential reaction cascades of metabolism: glycolysis and the pentose phosphate pathway, that provide essential precursors for nucleic acids, amino acids and lipids. A study at the University of Dusseldorf created phylogenic trees based upon 6 million genes from bacteria and archaea, and identified 355 protein families that were probably present in LUCA.  They were based upon an anaeobic metabolism fixing carbon dioxide and nitrogen.  It suggests that LUCA evolved in an environment rich in hydrogen, carbon dioxide and iron.  Following are some observed discoveries and related hypotheses.

text: Metabolism-like reactions could have occurred naturally in early oceans, before the first organisms evolved. Metabolism may predate the origin of life and life may have evolved from the chemical conditions that prevailed in the world's earliest oceans. Reconstructions in laboratories show that some of these reactions can produce RNA, and some others resemble two essential reaction cascades of metabolism:

text: glycolysis

text: and the

text: pentose phosphate pathway

text: , that provide essential precursors for nucleic acids, amino acids and lipids. A study at the University of Dusseldorf created

text: phylogenic trees

text: based upon 6 million genes from

text: bacteria

text: and

text: archaea

text: , and identified 355 protein families that were probably present in

text: LUCA

text: .  They were based upon an anaeobic metabolism fixing

text: carbon dioxide

text: and

text: nitrogen

text: .  It suggests that LUCA evolved in an environment rich in

text: hydrogen

text: , carbon dioxide and

text: iron

text: .  Following are some observed discoveries and related hypotheses.

text: Bioenergetics is a field in biochemistry and cell biology that concerns energy flow through living systems. This is an active area of biological research that includes the study of the transformation of energy in living organisms and the study of thousands of different cellular processes such as cellular respiration and the many other metabolic processes that can lead to production and utilization of energy in forms such as ATP molecules.

text: Bioenergetics is a field in

text: biochemistry

text: and

text: cell biology

text: that concerns

text: energy

text: flow through living systems. This is an active area of

text: biological

text: research that includes the study of the transformation of energy in living organisms and the study of thousands of different

text: cellular

text: processes such as

text: cellular respiration

text: and the many other

text: metabolic

text: processes that can lead to production and utilization of energy in forms such as

text: ATP

text: molecules.

text: Fatty acids are preferentially oxidized because of the inactivation of PDH by fatty acid oxidation inhibiting glucose oxidation. This suggests that mitochondrial metabolism may control fuel selection. Cellular respiration is stimulated by fatty acids and this relates to an increase in the mitochondrial NADH to NAD+ ratio, suggesting that energy provision overtakes energy consumption. Switching from glucose to fatty acid oxidation leads to a bigger proportion of electrons being transported to complex 2 rather than complex 1 of the respiratory chain. This difference leads to a less efficient oxidative phosphorylation. By oxidizing fatty acids, mitochondria increase their respiration while increasing the production of ROS.

text: Natural sources of atmospheric carbon dioxide include volcanic outgassing, the combustion of organic matter, wildfires and the respiration processes of living aerobic organisms. Man-made sources of carbon dioxide include the burning of fossil fuels for heating, power generation and transport, as well as some industrial processes such as cement making. It is also produced by various microorganisms from fermentation and cellular respiration. Plants, algae and cyanobacteria convert carbon dioxide to carbohydrates by a process called photosynthesis. They gain the energy needed for this reaction from absorption of sunlight by chlorophyll and other pigments. Oxygen, produced as a by-product of photosynthesis, is released into the atmosphere and subsequently used for respiration by heterotrophic organisms and other plants, forming a cycle.

text: Natural sources of atmospheric carbon dioxide include

text: volcanic

text: outgassing

text: , the

text: combustion

text: of

text: organic matter

text: wildfires

text: and the

text: respiration

text: processes of living

text: aerobic organism

text: s. Man-made sources of carbon dioxide include the burning of

text: fossil fuels

text: for heating,

text: power generation

text: and

text: transport

text: , as well as some industrial processes such as cement making. It is also produced by various

text: microorganism

text: s from

text: fermentation

text: and

text: cellular respiration

text: Plant

text: s,

text: algae

text: and

text: cyanobacteria

text: convert carbon dioxide to

text: carbohydrate

text: s by a process called

text: photosynthesis

text: . They gain the energy needed for this reaction from absorption of sunlight by

text: chlorophyll

text: and other pigments. Oxygen, produced as a by-product of photosynthesis, is released into the atmosphere and subsequently used for respiration by

text: heterotrophic

text: organisms and other plants, forming a

text: cycle

text: Further examples of modern drugs, where enzymes are used in the synthesis, are Pfizer’s Lipitor (atorvastatin), where the pivotal intermediate R-3-Hydroxy-4-cyanobutyrate is now made with a nitrilase, and Merck & Co.’s Singulair (montelukast), where the reduction of a ketone to S-alcohol, which had required stoichiometric amounts of expensive and moisture sensitive “(-)-DIP chloride” is now replaced by a ketoreductase enzyme catalyst step. Similar rewarding switches from chemical steps to enzymatic ones have also been achieved in steroid synthesis. Thus, it has been possible to reduce the number of steps required for the synthesis of Dexamethasone from bile from 28 to 15.  Enzymes differ from chemical catalysts particularly with regard to stereoselectivity, regioselectivity, and chemoselectivity. They can also be modified (“reshuffled”) for specific reactions, for use in chemical synthesis. “Immobilized enzymes” are those fixed on solid supports. They can be recovered by filtration after completion of the reaction. Conventional plant equipment can be used with no, or only modest, adaptations. The International Union of Biochemistry and Molecular Biology (IUBMB)  has developed a classification for enzymes. The main categories are Oxidoreductases, Transferases, Hydrolases, Lipases (subcategory), Lyases, Isomerases and Ligases, Companies specializing in making enzymes are Novozymes, Danisco (Genencor). Codexis is the leader in modifying enzymes to specific chemical reactions. The highest-volume chemicals made by biocatalysis are bio-ethanol (70 million metric tons), high-fructose corn syrup (2 million metric tons); acrylamide, 6-aminopenicillanic acid (APA), L-lysine and other amino acids, citric acid and niacinamide (all more than 10’000 metric tons).

text: Further examples of modern drugs, where enzymes are used in the synthesis, are

text: Pfizer

text: ’s

text: Lipitor

text: (atorvastatin), where the pivotal intermediate R-3-Hydroxy-4-cyanobutyrate is now made with a

text: nitrilase

text: , and Merck & Co.’s

text: Singulair

text: (montelukast), where the reduction of a ketone to S-alcohol, which had required stoichiometric amounts of expensive and moisture sensitive “

text: (-)-DIP chloride

text: ” is now replaced by a

text: ketoreductase

text: enzyme catalyst step. Similar rewarding switches from chemical steps to enzymatic ones have also been achieved in steroid synthesis. Thus, it has been possible to reduce the number of steps required for the synthesis of

text: Dexamethasone

text: from bile from 28 to 15.  Enzymes differ from chemical catalysts particularly with regard to

text: stereoselectivity

text: regioselectivity

text: , and

text: chemoselectivity

text: . They can also be modified (“reshuffled”) for specific reactions, for use in chemical synthesis. “

text: Immobilized enzymes

text: ” are those fixed on solid supports. They can be recovered by filtration after completion of the reaction. Conventional plant equipment can be used with no, or only modest, adaptations. The International Union of Biochemistry and Molecular Biology (IUBMB)  has developed a classification for enzymes. The main categories are

text: Oxidoreductases

text: Transferases

text: Hydrolases

text: Lipases

text: (subcategory),

text: Lyases

text: , Isomerases and

text: Ligases

text: , Companies specializing in making enzymes are

text: Novozymes

text: Danisco

text: (Genencor).

text: Codexis

text: is the leader in modifying enzymes to specific chemical reactions. The highest-volume chemicals made by biocatalysis are

text: bio-ethanol

text: (70 million metric tons),

text: high-fructose corn syrup

text: (2 million metric tons);

text: acrylamide

text: 6-aminopenicillanic acid

text: (APA),

text: L-lysine

text: and other amino acids,

text: citric acid

text: and

text: niacinamide

text: (all more than 10’000 metric tons).

text: Van 't Hoff studied chemical dynamics and published in 1884 his famous "Etudes de dynamique chimique". In 1901 he was awarded by the first Nobel Prize in Chemistry "in recognition of the extraordinary services he has rendered by the discovery of the laws of chemical dynamics and osmotic pressure in solutions". After van 't Hoff, chemical kinetics deals with the experimental determination of reaction rates from which rate laws and rate constants are derived. Relatively simple rate laws exist for zero order reactions (for which reaction rates are independent of concentration), first order reactions, and second order reactions, and can be derived for others. Elementary reactions follow the law of mass action, but the rate law of stepwise reactions has to be derived by combining the rate laws of the various elementary steps, and can become rather complex. In consecutive reactions, the rate-determining step often determines the kinetics. In consecutive first order reactions, a steady state approximation can simplify the rate law. The activation energy for a reaction is experimentally determined through the Arrhenius equation and the Eyring equation. The main factors that influence the reaction rate include: the physical state of the reactants, the concentrations of the reactants, the temperature at which the reaction occurs, and whether or not any catalysts are present in the reaction.

text: Van 't Hoff

text: studied chemical dynamics and published in 1884 his famous "Etudes de dynamique chimique". In 1901 he was awarded by the first Nobel Prize in Chemistry "in recognition of the extraordinary services he has rendered by the discovery of the laws of chemical dynamics and osmotic pressure in solutions". After van 't Hoff, chemical kinetics deals with the experimental determination of

text: reaction rate

text: s from which

text: rate law

text: s and

text: rate constants

text: are derived. Relatively simple

text: rate law

text: s exist for

text: zero order reactions

text: (for which reaction rates are independent of concentration),

text: first order reaction

text: s, and

text: second order reaction

text: s, and can be derived for others.

text: Elementary reaction

text: s follow the

text: law of mass action

text: , but the rate law of

text: stepwise reaction

text: s has to be derived by combining the rate laws of the various elementary steps, and can become rather complex. In consecutive reactions, the

text: rate-determining step

text: often determines the kinetics. In consecutive first order reactions, a

text: steady state

text: approximation can simplify the

text: rate law

text: . The

text: activation energy

text: for a reaction is experimentally determined through the

text: Arrhenius equation

text: and the

text: Eyring equation

text: . The main factors that influence the

text: reaction rate

text: include: the

text: physical state

text: of the reactants, the

text: concentrations

text: of the reactants, the

text: temperature

text: at which the reaction occurs, and whether or not any

text: catalysts

text: are present in the reaction.

text: Low-density lipoprotein (LDL) particles in blood plasma invade the endothelium and become oxidized, creating risk of cardiovascular disease. A complex set of biochemical reactions regulates the oxidation of LDL, involving enzymes (such as Lp-LpA2) and free radicals in the endothelium.

text: Low-density lipoprotein

text: (LDL) particles in blood plasma invade the

text: endothelium

text: and become oxidized, creating risk of

text: cardiovascular disease

text: . A complex set of biochemical reactions regulates the oxidation of LDL, involving enzymes (such as

text: ) and

text: free radical

text: s in the endothelium.

text: Despite the observations of hammerhead ribozyme catalysis in a crystal of the minimal hammerhead sequence in which the crystal lattice packing contacts by necessity confined the global positions of the distal termini of all three flanking helical stems, many biochemical experiments designed to probe transition-state interactions and the chemistry of catalysis appeared to be irreconcilable with the crystal structures.

text: In synthetic organic chemistry orthogonal protection is a strategy allowing the deprotection of functional groups independently of each other. In chemistry and biochemistry, an orthogonal interaction occurs when there are two pairs of substances and each substance can interact with their respective partner, but does not interact with either substance of the other pair. For example, DNA has two orthogonal pairs: cytosine and guanine form a base-pair, and adenine and thymine form another base-pair, but other base-pair combinations are strongly disfavored. As a chemical example, tetrazine reacts with transcyclooctene and azide reacts with cyclooctyne without any cross-reaction, so these are mutually orthogonal reactions, and so, can be performed simultaneously and selectively. Bioorthogonal chemistry refers to chemical reactions occurring inside living systems without reacting with naturally present cellular components. In supramolecular chemistry the notion of orthogonality refers to the possibility of two or more supramolecular, often non-covalent, interactions being compatible; reversibly forming without interference from the other.

text: In

text: synthetic organic chemistry

text: orthogonal

text: protection

text: is a strategy allowing the deprotection of

text: functional group

text: s independently of each other. In chemistry and biochemistry, an orthogonal interaction occurs when there are two pairs of substances and each substance can interact with their respective partner, but does not interact with either substance of the other pair. For example,

text: DNA

text: has two orthogonal pairs: cytosine and guanine form a base-pair, and adenine and thymine form another base-pair, but other base-pair combinations are strongly disfavored. As a chemical example, tetrazine reacts with transcyclooctene and azide reacts with cyclooctyne without any cross-reaction, so these are mutually orthogonal reactions, and so, can be performed simultaneously and selectively.

text: Bioorthogonal chemistry

text: refers to chemical reactions occurring inside living systems without reacting with naturally present cellular components. In

text: supramolecular chemistry

text: the notion of orthogonality refers to the possibility of two or more supramolecular, often

text: non-covalent

text: , interactions being compatible; reversibly forming without interference from the other.

text: Note that during fatty synthesis the reducing agent is NADPH, whereas  NAD is the oxidizing agent in beta-oxidation (the breakdown of fatty acids to acetyl-CoA). This difference exemplifies a general principle that NADPH is consumed during biosynthetic reactions, whereas NADH is generated in energy-yielding reactions. (Thus NADPH is also required for the synthesis of cholesterol from acetyl-CoA; while NADH is generated during glycolysis.) The source of the NADPH is two-fold. When malate is oxidatively decarboxylated by “NADP-linked malic enzyme" pyruvate, CO and NADPH are formed. NADPH is also formed by the pentose phosphate pathway which converts glucose into ribose, which can be used in synthesis of nucleotides and nucleic acids, or it can be catabolized to pyruvate.

text: Note that during fatty synthesis the reducing agent is

text: NADPH

text: , whereas

text: NAD

text: is the oxidizing agent in

text: beta-oxidation

text: (the breakdown of fatty acids to acetyl-CoA). This difference exemplifies a general principle that NADPH is consumed during biosynthetic reactions, whereas NADH is generated in energy-yielding reactions. (Thus NADPH is also required for the synthesis of

text: cholesterol

text: from acetyl-CoA; while NADH is generated during

text: glycolysis

text: .) The source of the NADPH is two-fold. When

text: malate

text: is oxidatively decarboxylated by “NADP-linked malic enzyme"

text: pyruvate

text: , CO and NADPH are formed. NADPH is also formed by the

text: pentose phosphate pathway

text: which converts glucose into ribose, which can be used in synthesis of

text: nucleotides

text: and

text: nucleic acids

text: , or it can be catabolized to pyruvate.

text: Cellular respiration, for instance, is the oxidation of glucose (CHO) to CO and the reduction of oxygen to water. The summary equation for cell respiration is:

text: Cellular respiration

text: , for instance, is the oxidation of

text: glucose

text: (CHO) to

text: CO

text: and the reduction of

text: oxygen

text: to

text: water

text: . The summary equation for cell respiration is:

text: Metabolic (or biochemical) genetics involves the diagnosis and management of inborn errors of metabolism in which patients have enzymatic deficiencies that perturb biochemical pathways involved in metabolism of carbohydrates, amino acids, and lipids.  Examples of metabolic disorders include galactosemia, glycogen storage disease, lysosomal storage disorders, metabolic acidosis, peroxisomal disorders, phenylketonuria, and urea cycle disorders.

text: Metabolic (or biochemical) genetics involves the diagnosis and management of

text: inborn errors of metabolism

text: in which patients have enzymatic deficiencies that perturb

text: biochemical

text: pathways involved in metabolism of

text: carbohydrates

text: amino acids

text: , and

text: lipids

text: .  Examples of metabolic disorders include

text: galactosemia

text: glycogen storage disease

text: lysosomal storage disorder

text: s,

text: metabolic acidosis

text: peroxisomal disorders

text: phenylketonuria

text: , and

text: urea cycle disorder

text: s.

text: Plants use CAM to different degrees. Some are "obligate CAM plants", i.e. they use only CAM in photosynthesis, although they vary in the amount of  they are able to store as organic acids; they are sometimes divided into "strong CAM" and "weak CAM" plants on this basis. Other plants show "inducible CAM", in which they are able to switch between using either the  or  mechanism and CAM depending on environmental conditions. Another group of plants employ "CAM-cycling", in which their stomata do not open at night; the plants instead recycle  produced by respiration as well as storing some  during the day.

text: Plants use CAM to different degrees. Some are "obligate CAM plants", i.e. they use only CAM in photosynthesis, although they vary in the amount of  they are able to store as organic acids; they are sometimes divided into "strong CAM" and "weak CAM" plants on this basis. Other plants show "inducible CAM", in which they are able to switch between using either the  or  mechanism and CAM depending on environmental conditions. Another group of plants employ "CAM-cycling", in which their stomata do not open at night; the plants instead recycle  produced by

text: respiration

text: as well as storing some  during the day.

text: The technique developed by Gaarder and Gran uses variations in the concentration of oxygen under different experimental conditions to infer gross primary production.  Typically, three identical transparent vessels are filled with sample water and stoppered.  The first is analysed immediately and used to determine the initial oxygen concentration; usually this is done by performing a Winkler titration.  The other two vessels are incubated, one each in under light and darkened.  After a fixed period of time, the experiment ends, and the oxygen concentration in both vessels is measured.  As photosynthesis has not taken place in the dark vessel, it provides a measure of ecosystem respiration.  The light vessel permits both photosynthesis and respiration, so provides a measure of net photosynthesis (i.e. oxygen production via photosynthesis subtract oxygen consumption by respiration).  Gross primary production is then obtained by adding oxygen consumption in the dark vessel to net oxygen production in the light vessel.

text: The technique developed by Gaarder and Gran uses variations in the concentration of oxygen under different experimental conditions to infer gross primary production.  Typically, three identical transparent vessels are filled with sample water and

text: stoppered

text: .  The first is analysed immediately and used to determine the initial oxygen concentration; usually this is done by performing a

text: Winkler titration

text: .  The other two vessels are incubated, one each in under light and darkened.  After a fixed period of time, the experiment ends, and the oxygen concentration in both vessels is measured.  As photosynthesis has not taken place in the dark vessel, it provides a measure of

text: ecosystem respiration

text: .  The light vessel permits both photosynthesis and respiration, so provides a measure of net photosynthesis (i.e. oxygen production via photosynthesis subtract oxygen consumption by respiration).  Gross primary production is then obtained by adding oxygen consumption in the dark vessel to net oxygen production in the light vessel.

text: Methylmalonyl CoA epimerase plays an important role in the catabolism of fatty acids with odd-length carbon chains.  In the catabolism of even-chain saturated fatty acids, the β-oxidation pathway breaks down fatty acyl-CoA molecules in repeated sequences of four reactions to yield one acetyl CoA per repeated sequence.  This means that, for each round of β-oxidation, the fatty acyl-Co-A is shortened by two carbons.  If the fatty acid began with an even number of carbons, this process could break down an entire saturated fatty acid into acetyl-CoA units.  If the fatty acid began with an odd number of carbons, however, β-oxidation would break the fatty acyl-CoA down until the three carbon propionyl-CoA is formed.  In order to convert this to the metabolically useful succinyl-CoA, three reactions are needed.  The propionyl-CoA is first carboxylated to (S)-methylmalonyl-CoA by the enzyme Propionyl-CoA carboxylase.  Methylmalonyl CoA epimerase then catalyzes the rearrangement of (S)-methylmalonyl-CoA to the (R) form in a reaction that uses a vitamin B12 cofactor and a resonance-stabilized carbanion intermediate.  The (R)-methylmalonyl-CoA is then converted to succinyl-CoA in a reaction catalyzed by methylmalonyl-CoA mutase.

text: Methylmalonyl CoA epimerase plays an important role in the catabolism of

text: fatty acids

text: with odd-length carbon chains.  In the catabolism of even-chain

text: saturated

text: fatty acids, the

text: β-oxidation pathway

text: breaks down fatty acyl-CoA molecules in repeated sequences of four reactions to yield one

text: acetyl CoA

text: per repeated sequence.  This means that, for each round of β-oxidation, the fatty acyl-Co-A is shortened by two carbons.  If the fatty acid began with an even number of carbons, this process could break down an entire saturated fatty acid into acetyl-CoA units.  If the fatty acid began with an odd number of carbons, however, β-oxidation would break the fatty acyl-CoA down until the three carbon propionyl-CoA is formed.  In order to convert this to the metabolically useful

text: succinyl-CoA

text: , three reactions are needed.  The propionyl-CoA is first carboxylated to (S)-methylmalonyl-CoA by the enzyme

text: Propionyl-CoA carboxylase

text: .  Methylmalonyl CoA epimerase then catalyzes the rearrangement of (S)-methylmalonyl-CoA to the (R) form in a reaction that uses a

text: vitamin B12

text: cofactor

text: and a resonance-stabilized

text: carbanion

text: intermediate

text: .  The (R)-methylmalonyl-CoA is then converted to succinyl-CoA in a reaction catalyzed by

text: methylmalonyl-CoA mutase

text: It is thought that through a combination of biochemical and biophysical stimuli, the uncommitted stem cells of the embryo will undergo differentiation into certain cell lineages. However the exact mechanism and signalling pathways are still unclear. Studies have shown that embryonic stem cells are more mechanosensitive than their differentiated counterparts.During embryonic development mesenchymal cells will form cellular structures known as ‘condensations.’ These cellular units will then develop into skeletal and other tissues, such as cartilage, tendon, ligament and muscle tissue.

text: Chemiluminescent reactions are widely used in analytical chemistry [14, 15]

text: Chemiluminescent reactions

text: are widely used in

text: analytical chemistry

text: The majority of the genes in the mitochondria and plastids are related to the expression (transcription, translation and replication) of genes encoding proteins involved in either photosynthesis (in plastids) or cellular respiration (in mitochondria). One might predict, that the loss of photosynthesis or cellular respiration would allow for the complete loss of the plastid genome or the mitochondrial genome respectively. While there are numerous examples of mitochondrial descendants (mitosomes and hydrogenosomes) that have lost their entire organellar genome, non-photosynthetic plastids tend to retain a small genome. There are two main hypotheses to explain this occurrence:

text: The majority of the genes in the mitochondria and plastids are related to the expression (transcription, translation and replication) of genes encoding proteins involved in either photosynthesis (in plastids) or cellular respiration (in mitochondria). One might predict, that the loss of photosynthesis or cellular respiration would allow for the complete loss of the plastid genome or the mitochondrial genome respectively. While there are numerous examples of mitochondrial descendants (

text: mitosome

text: s and

text: hydrogenosome

text: s) that have lost their entire organellar genome, non-photosynthetic plastids tend to retain a small genome. There are two main hypotheses to explain this occurrence:

text: It is one of the end products of photophosphorylation, aerobic respiration, and fermentation, and is used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division. One molecule of ATP contains adenine, ribose, and three phosphate groups, and it is produced by a wide variety of enzymes, including ATP synthase, from adenosine diphosphate (ADP) or adenosine monophosphate (AMP) and various phosphate group donors. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three major mechanisms of ATP biosynthesis.

text: It is one of the end products of

text: photophosphorylation

text: aerobic respiration

text: , and

text: fermentation

text: , and is used by

text: enzyme

text: s and

text: structural proteins

text: in many cellular processes, including

text: biosynthetic reactions

text: motility

text: , and

text: cell division

text: . One molecule of ATP contains

text: adenine

text: ribose

text: , and three

text: phosphate

text: groups, and it is produced by a wide variety of enzymes, including

text: ATP synthase

text: , from

text: adenosine diphosphate

text: (ADP) or

text: adenosine monophosphate

text: (AMP) and various phosphate group donors.

text: Substrate-level phosphorylation

text: oxidative phosphorylation

text: in

text: cellular respiration

text: , and

text: photophosphorylation

text: in

text: photosynthesis

text: are three major mechanisms of ATP biosynthesis.

text: Metabolism (from  metabolē, "change") is the set of life-sustaining chemical transformations within the cells of living organisms. The three main purposes of metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

text: Metabolism (from  metabolē, "change") is the set of

text: life

text: -sustaining

text: chemical transformations

text: within the

text: cells

text: of living

text: organisms

text: . The three main purposes of metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for

text: protein

text: s,

text: lipid

text: s,

text: nucleic acid

text: s, and some

text: carbohydrate

text: s, and the elimination of

text: nitrogenous waste

text: s. These

text: enzyme

text: -catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including

text: digestion

text: and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

text: The compensation depth between photosynthesis and respiration of phytoplankton in the ocean must be dependent on some factors: the illumination at the surface, the transparency of the water, the biological character of the plankton present, and the temperature. The compensation point was found nearer to the surface as you move closer to the coast  It is also lower in the winter seasons in the Baltic Sea according to a study that examined the compensation point of multiple photosynthetic species. The blue portion of the visible spectrum, between 455-495 nanometers, dominates light at the compensation depth.

text: Over the past twenty-five years the Gray group has been measuring the kinetics of long-range ET reactions in metalloproteins labeled with inorganic redox reagents. Early research by his lab members showed that details of the internal structures of the proteins dominate the ET rates.  Current research is aimed at understanding how intermediate protein radicals accelerate long-range ET. In collaboration with Jay R. Winkler of the Beckman Institute at Caltech they have developed new techniques for measuring ET rates in crystals of Ru-, Os-, and Re-modified azurins, as well as crystals of Fe(III)-cytochrome c doped with Zn(II)-cytochrome c. This method of integrating photosensitizers into protein crystals has provided a powerful new tool for studying biochemical reaction dynamics. The Gray/Winkler group is also using ET chemistry to probe the dynamics of protein folding in cytochrome c.

text: Over the past twenty-five years the Gray group has been measuring the kinetics of long-range ET reactions in metalloproteins labeled with inorganic

text: redox

text: reagents. Early research by his lab members showed that details of the internal structures of the proteins dominate the ET rates.  Current research is aimed at understanding how intermediate protein radicals accelerate long-range ET. In collaboration with

text: Jay R. Winkler

text: of the

text: Beckman Institute at Caltech

text: they have developed new techniques for measuring ET rates in crystals of Ru-, Os-, and Re-modified

text: azurin

text: s, as well as crystals of Fe(III)-

text: cytochrome c

text: doped with Zn(II)-cytochrome c. This method of integrating

text: photosensitizers

text: into protein crystals has provided a powerful new tool for studying biochemical reaction dynamics. The Gray/Winkler group is also using ET chemistry to probe the dynamics of

text: protein folding

text: in

text: cytochrome c

text: The apparent shortcoming for enolate alkylation reactions is over-alkylation, even if the amount of base added for enolization as well as the reaction temperature are carefully controlled. The ketene formation during the deprotonation process for substrates possessing Evans' oxazolidinone is also a main side reaction for the related alkylation reactions. Development in the field of enamine chemistry and the utilization of imine derivatives of enolates managed to provide an alternative for enolate alkylation reactions.

text: The apparent shortcoming for enolate alkylation reactions is over-alkylation, even if the amount of base added for enolization as well as the reaction temperature are carefully controlled. The ketene formation during the deprotonation process for substrates possessing Evans' oxazolidinone is also a main side reaction for the related alkylation reactions. Development in the field of

text: enamine

text: chemistry and the utilization of

text: imine

text: derivatives of enolates managed to provide an alternative for enolate alkylation reactions.

text: Since photosynthesis is the single most effective natural regulator of carbon dioxide in the Earth's atmosphere, a biochemical model of RuBisCO reaction is used as the core module of climate change models. Thus, a correct model of this reaction is essential to the basic understanding of the relations and interactions of environmental models. A new theory and model of the biochemical reaction of photosynthesis and the drawbacks of today's most widely used model of photosynthesis is discussed in volume 29 of Advances in Photosynthesis and Respiration.

text: Since photosynthesis is the single most effective natural regulator of

text: carbon dioxide in the Earth's atmosphere

text: , a biochemical model of RuBisCO reaction is used as the core module of climate change models. Thus, a correct model of this reaction is essential to the basic understanding of the relations and interactions of environmental models. A new theory and model of the biochemical reaction of photosynthesis and the drawbacks of today's most widely used model of photosynthesis is discussed in volume 29 of Advances in Photosynthesis and Respiration.

text: The simple Streeter-Phelps model is based on the assumptions that a single BOD input is distributed evenly at the cross section of a stream or river and that it moves as plug flow with no mixing in the river. Furthermore only one DO sink (carbonaceous BOD) and one DO source (reaeration) is considered in the classical Streeter-Phelps model. These simplifications will give rise to errors in the model. For example the model does not include BOD removal by sedimentation, that suspended BOD is converted to a dissolved state, that sediment has an oxygen demand and that photosynthesis and respiration will impact the oxygen balance.

text: The simple Streeter-Phelps model is based on the assumptions that a single BOD input is distributed evenly at the cross section of a stream or river and that it moves as

text: plug flow

text: with no mixing in the river. Furthermore only one DO sink (carbonaceous BOD) and one DO source (reaeration) is considered in the classical Streeter-Phelps model. These simplifications will give rise to errors in the model. For example the model does not include BOD removal by sedimentation, that suspended BOD is converted to a dissolved state, that sediment has an oxygen demand and that photosynthesis and respiration will impact the oxygen balance.

text: Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide (CO). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin – Benson cycle. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO directly, while C4 and CAM photosynthesis incorporate the CO into other compounds first, as adaptations to deal with intense sunlight and dry conditions.

text: Photosynthesis is the synthesis of carbohydrates from sunlight and

text: carbon dioxide

text: (CO). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the

text: photosynthetic reaction centre

text: s, as described above, to convert CO into

text: glycerate 3-phosphate

text: , which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme

text: RuBisCO

text: as part of the

text: Calvin – Benson cycle

text: . Three types of photosynthesis occur in plants,

text: C3 carbon fixation

text: C4 carbon fixation

text: and

text: CAM photosynthesis

text: . These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO directly, while C4 and CAM photosynthesis incorporate the CO into other compounds first, as adaptations to deal with intense sunlight and dry conditions.

text: Enzymes are biological catalysts: biopolymers that catalyze a reaction. Although a small number natural enzymes are build from RNA–termed Ribozymes–most enzymes are proteins.  Like any other protein an enzyme is an amino acid polymer with added cofactors and other post-translational modifications.   Often most of the amino acid polymer is indirectly involved with the enzymes function, perhaps providing ancillary structure or connectivity, indirect activity regulation, or molecular identification of the enzyme.  As a result, most enzymes are large molecules weighing many kilodaltons.  This bulk can obscure various investigative techniques such as NMR, EPR, electrochemistry, crystallography, among others.   It is standard practice to compare spectroscopic data from enzymes to similar spectroscopic data derived from better characterized small molecules.  In this way the understanding of metalloenzymes and other metalloproteins have developed.  In many cases the small molecule analogs were created for other reasons; however, it has been increasingly common for groups to intentionally make small molecule analogs also known as enzyme mimics.  These enzyme mimics are prime examples of bioinorganic chemistry.

text: Enzymes

text: are biological catalysts: biopolymers that

text: catalyze

text: a

text: reaction

text: . Although a small number natural enzymes are build from

text: RNA

text: –termed

text: Ribozymes

text: –most enzymes are

text: proteins

text: .  Like any other protein an enzyme is an

text: amino acid

text: polymer

text: with added

text: cofactors

text: and other

text: post-translational modifications

text: .   Often most of the amino acid polymer is indirectly involved with the enzymes function, perhaps providing ancillary structure or connectivity, indirect activity regulation, or molecular identification of the enzyme.  As a result, most enzymes are large molecules weighing many

text: kilodalton

text: s.  This bulk can obscure various investigative techniques such as

text: NMR

text: EPR

text: electrochemistry

text: crystallography

text: , among others.   It is standard practice to compare spectroscopic data from enzymes to similar spectroscopic data derived from better characterized small molecules.  In this way the understanding of metalloenzymes and other

text: metalloprotein

text: s have developed.  In many cases the small molecule analogs were created for other reasons; however, it has been increasingly common for groups to intentionally make small molecule analogs also known as enzyme mimics.  These enzyme mimics are prime examples of

text: bioinorganic chemistry

text: A zymogen (), also called a proenzyme (), is an inactive precursor of an enzyme.  A zymogen requires a biochemical change (such as a hydrolysis reaction revealing the active site, or changing the configuration to reveal the active site) for it to become an active enzyme. The biochemical change usually occurs in Golgi bodies, where a specific part of the precursor enzyme is cleaved in order to activate it. The inactivating piece which is cleaved off can be a peptide unit, or can be independently folding domains comprising more than 100 residues. Although they limit the enzyme's ability, these n-terminal extensions of the enzyme or a “prosegment” often aid in the stabilizing and folding of the enzyme they inhibit.

text: A zymogen (), also called a proenzyme (), is an inactive

text: precursor

text: of an

text: enzyme

text: .  A zymogen requires a

text: biochemical

text: change (such as a

text: hydrolysis

text: reaction revealing the active site, or changing the configuration to reveal the active site) for it to become an active enzyme. The biochemical change usually occurs in

text: Golgi bodies

text: , where a specific part of the precursor enzyme is cleaved in order to activate it. The inactivating piece which is cleaved off can be a

text: peptide

text: unit, or can be independently folding domains comprising more than 100

text: residues

text: . Although they limit the enzyme's ability, these n-terminal extensions of the enzyme or a “prosegment” often aid in the stabilizing and

text: folding

text: of the enzyme they inhibit.

text: Both UV endonuclease V from bacteriophage T4 (UV endonuclease V) and UV endonuclease III from E. coli catalyze N- glycosylase and the 3‘-abasic endonuclease reactions. Bacteriophage T4 and Micrococcus luteus UV endonucleases were actually shown not to be under the class of "endonuclease," but rather were β-elimination catalysts for reactions at AP sites at the C-O-P bond—thus, classifying them as AP lyases. Phage-T4 UV endonucleases  also catalyze the reaction of the δ-reaction, nicking C-O-P bond at AP sites, although this reaction is slow and the enzyme should still be classified as AP lyase. This open ring allows the substitution of the correct base by other enzymes.

text: Both UV endonuclease V from

text: bacteriophage T4

text: (UV endonuclease V) and UV endonuclease III from E. coli catalyze N- glycosylase and the 3‘-abasic endonuclease reactions. Bacteriophage T4 and Micrococcus luteus UV endonucleases were actually shown not to be under the class of "endonuclease," but rather were β-elimination catalysts for reactions at AP sites at the C-O-P bond—thus, classifying them as AP lyases. Phage-T4 UV endonucleases  also catalyze the reaction of the δ-reaction, nicking C-O-P bond at AP sites, although this reaction is slow and the enzyme should still be classified as AP lyase. This open ring allows the substitution of the correct base by other enzymes.

text: Since the forest is considered an ecosystem, it is dependent on all of the living and non-living factors within itself. This is a major part of why the forest needs to be sustainable before it is harvested. For example, a tree would convert sunlight to sugars for respiration to keep the tree alive. The remains of the converted sugars is left in roots for consumption by the organisms surrounding the tree in the habitat. This shows the productivity of an ecosystem with its inhabitants. Productivity within the ecosystem cannot come to fruition unless the forest is sustainable enough to be harvested. If all of the organisms of the ecosystem are non existent, the ecosystem itself will soon come to be non existent. Once that happens, there is no longer any forest to harvest from. The overall productivity of a system can be found in an equation where the Net Primary Production, or NPP, is equal to the Gross Primary Production, or GPP, minus the Respiration, or R. The formula is the NPP = GPP - R. The NPP is the overall efficiency of the plants in the ecosystem. Through having a constant efficiency in NPP, the ecosystem is then more sustainable. The GPP refers to the rate of energy stored by photosynthesis in plants. The R refers to the maintenance and reproduction of plants from the energy expended.

text: Since the forest is considered an

text: ecosystem

text: , it is dependent on all of the living and non-living factors within itself. This is a major part of why the forest needs to be sustainable before it is harvested. For example, a tree would convert sunlight to sugars for respiration to keep the tree alive. The remains of the converted sugars is left in roots for consumption by the organisms surrounding the tree in the habitat. This shows the productivity of an ecosystem with its inhabitants. Productivity within the ecosystem cannot come to fruition unless the forest is sustainable enough to be harvested. If all of the organisms of the ecosystem are non existent, the ecosystem itself will soon come to be non existent. Once that happens, there is no longer any forest to harvest from. The overall productivity of a system can be found in an equation where the Net Primary Production, or NPP, is equal to the Gross Primary Production, or GPP, minus the

text: Respiration

text: , or R. The formula is the NPP = GPP - R. The NPP is the overall efficiency of the plants in the ecosystem. Through having a constant efficiency in NPP, the ecosystem is then more sustainable. The GPP refers to the rate of energy stored by

text: photosynthesis

text: in plants. The R refers to the maintenance and reproduction of plants from the energy expended.

text: At its broadest definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life, and the history of biochemistry may therefore go back as far as the ancient Greeks. However, biochemistry as a specific scientific discipline has its beginning sometime in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on. Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen, while others considered Eduard Buchner's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry.  Some might also point as its beginning to the influential 1842 work by Justus von Liebig, Animal chemistry, or, Organic chemistry in its applications to physiology and pathology, which presented a chemical theory of metabolism, or even earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier. Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry, for example Emil Fischer for his work on the chemistry of proteins, and F. Gowland Hopkins on enzymes and the dynamic nature of biochemistry.

text: At its broadest definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life, and the history of biochemistry may therefore go back as far as the

text: ancient Greeks

text: . However, biochemistry as a specific

text: scientific discipline

text: has its beginning sometime in the

text: 19th century

text: , or a little earlier, depending on which aspect of biochemistry is being focused on. Some argued that the beginning of biochemistry may have been the discovery of the first

text: enzyme

text: diastase

text: (today called

text: amylase

text: ), in 1833 by

text: Anselme Payen

text: , while others considered

text: Eduard Buchner

text: 's first demonstration of a complex biochemical process

text: alcoholic fermentation

text: in cell-free extracts in 1897 to be the birth of biochemistry.  Some might also point as its beginning to the influential 1842 work by

text: Justus von Liebig

text: , Animal chemistry, or, Organic chemistry in its applications to physiology and pathology, which presented a chemical theory of metabolism, or even earlier to the 18th century studies on

text: fermentation

text: and

text: respiration

text: by

text: Antoine Lavoisier

text: . Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry, for example

text: Emil Fischer

text: for his work on the chemistry of proteins, and

text: F. Gowland Hopkins

text: on enzymes and the dynamic nature of biochemistry.

text: Now limitations emerge from the chemistry of the probe to its target. In order for this technique to be useful in biological systems, click chemistry must run at or near biological conditions, produce little and (ideally) non-toxic byproducts, have (preferably) single and stable products at the same conditions, and proceed quickly to high yield in one pot. Existing reactions, such as Staudinger ligation and the Huisgen 1,3–dipolar cycloaddition, have been modified and optimized for such reaction conditions. Today, research in the field concerns not only understanding and developing new reactions and repurposing and re-understanding known reactions, but also expanding methods used to incorporate reaction partners into living systems, engineering novel reaction partners, and developing applications for bioconjugation.

text: Now limitations emerge from the chemistry of the probe to its target. In order for this technique to be useful in biological systems, click chemistry must run at or near biological conditions, produce little and (ideally) non-toxic byproducts, have (preferably) single and stable products at the same conditions, and proceed quickly to high yield in

text: one pot

text: . Existing reactions, such as

text: Staudinger ligation

text: and the

text: Huisgen

text: 1,3–dipolar cycloaddition

text: , have been modified and optimized for such reaction conditions. Today, research in the field concerns not only understanding and developing new reactions and repurposing and re-understanding known reactions, but also expanding methods used to incorporate reaction partners into living systems, engineering novel reaction partners, and developing applications for bioconjugation.

text: The primary biochemical reaction catalyzed by the adenosylcobalamin-5'-phosphate phosphatase(formerly: alpha-ribazole phosphatase) () enzyme is

text: The primary biochemical reaction catalyzed by the adenosylcobalamin-5'-phosphate phosphatase(formerly: alpha-ribazole phosphatase) ()

text: enzyme

text: is

text: Scrutton was awarded the Colworth Medal in 1999 from the Biochemical Society and the Enzyme Chemistry Award (The Charmian Medal) from the Royal Society of Chemistry in 2002.

text: Scrutton was awarded the

text: Colworth Medal

text: in 1999 from the

text: Biochemical Society

text: and the Enzyme Chemistry Award (The Charmian Medal) from the

text: Royal Society of Chemistry

text: in 2002.

text: As mentioned above, sucrose phosphorylase is a very important enzyme in metabolism.  The reaction catalyzed by sucrose phosphorylase produces the valuable byproducts α-D-glucose-1-phosphate and fructose.  α-D-glucose-1-phosphate can be reversibly converted by phosphoglucomutase to glucose-6-phosphate (Tedokon et al. 1992), which is an important intermediate used in glycolysis.  In addition, fructose can be reversibly converted into fructose 6-phosphate (Reid and Abratt 2005), also found in the glycolytic pathway.  In fact, fructose-6-phosphate and glucose-6-phosphate can be interconverted in the glycolytic pathway by phosphohexose isomerase (Nelson and Cox 2005).  The final product of glycolysis, pyruvate, has multiple implications in metabolism.  During anaerobic conditions, pyruvate con be converted into either lactate or ethanol, depending on the organism, providing a quick source of energy.  In aerobic conditions,pyruvate can be converted into Acetyl-CoA, which has many possible fates including catabolism in the Citric Acid Cycle for energy use and anabolism in the formation of fatty acids for energy storage.  Through these reactions, sucrose phosphorylase becomes important in the regulation of metabolic functions.

text: As mentioned above, sucrose phosphorylase is a very important enzyme in metabolism.  The reaction catalyzed by sucrose phosphorylase produces the valuable byproducts α-D-glucose-1-phosphate and fructose.  α-D-glucose-1-phosphate can be reversibly converted by

text: phosphoglucomutase

text: to glucose-6-phosphate (Tedokon et al. 1992), which is an important intermediate used in glycolysis.  In addition, fructose can be reversibly converted into

text: fructose 6-phosphate

text: (Reid and Abratt 2005), also found in the glycolytic pathway.  In fact, fructose-6-phosphate and glucose-6-phosphate can be interconverted in the glycolytic pathway by

text: phosphohexose isomerase

text: (Nelson and Cox 2005).  The final product of glycolysis,

text: pyruvate

text: , has multiple implications in metabolism.  During

text: anaerobic

text: conditions, pyruvate con be converted into either

text: lactate

text: or

text: ethanol

text: , depending on the organism, providing a quick source of energy.  In

text: aerobic

text: conditions,pyruvate can be converted into

text: Acetyl-CoA

text: , which has many possible fates including

text: catabolism

text: in the

text: Citric Acid Cycle

text: for energy use and

text: anabolism

text: in the formation of

text: fatty acids

text: for energy storage.  Through these reactions, sucrose phosphorylase becomes important in the regulation of metabolic functions.

text: Glucose-6-Phosphate Translocase is an enzyme that in humans is encoded by the SLC37A4 gene. It consists of three subunits, each of which are vital components of the multi-enzyme Glucose-6-Phosphatase Complex (G6Pase). This important enzyme complex is located within the membrane of the endoplasmic reticulum, and catalyzes the terminal reactions in both glycogenolysis and gluconeogenesis. The G6Pase complex is most abundant in liver tissue, but also present in kidney cells, small intestine, pancreatic islets and at a lower concentration in the gallbladder. The G6Pase complex is highly involved in the regulation of homeostasis and blood glucose levels. Within this framework of glucose regulation, the translocase components are responsible for transporting the substrates and products across the endoplasmic reticulum membrane, resulting in the release of free glucose into the bloodstream.

text: Glucose-6-Phosphate Translocase is an

text: enzyme

text: that in humans is encoded by the

text: gene. It consists of three

text: subunits

text: , each of which are vital components of the multi-enzyme

text: Complex (G6Pase). This important enzyme complex is located within the

text: membrane

text: of the

text: endoplasmic reticulum

text: , and catalyzes the terminal reactions in both

text: glycogenolysis

text: and

text: gluconeogenesis

text: . The G6Pase complex is most abundant in liver tissue, but also present in

text: kidney cells

text: small intestine

text: pancreatic islets

text: and at a lower concentration in the

text: gallbladder

text: . The G6Pase complex is highly involved in the regulation of

text: homeostasis

text: and

text: blood glucose

text: levels. Within this framework of glucose regulation, the translocase components are responsible for transporting the substrates and products across the endoplasmic reticulum membrane, resulting in the release of free glucose into the bloodstream.

text: Nucleic acid metabolism is the process by which nucleic acids (DNA and RNA) are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base.  Destruction of nucleic acid is a catabolic reaction. Additionally, parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

text: Nucleic acid metabolism is the process by which

text: nucleic acids

text: DNA

text: and

text: RNA

text: ) are synthesized and degraded. Nucleic acids are polymers of

text: nucleotides

text: . Nucleotide synthesis is an

text: anabolic

text: mechanism generally involving the chemical reaction of

text: phosphate

text: , pentose

text: sugar

text: , and a

text: nitrogenous base

text: .  Destruction of nucleic acid is a

text: catabolic

text: reaction. Additionally, parts of the

text: nucleotide

text: s or

text: nucleobase

text: s can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require

text: enzymes

text: to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

text: The creek area in the upper reaches or headwaters of a water system is usually very narrow and lined by thick shore vegetation.  This prevents the penetration of sunlight, in turn decreasing the production of organic material through photosynthesis in the water.  The majority of the organic matter that does make its way into the system is in the form allochthonous plant material that falls into the river, such as leaves and sticks.  In this section, respiration (consumption) out paces production (P/R<1).  Here shredders play a major role in breaking down coarse plant material.  In this area, the largest diversity of organic material can be expected.

text: The creek area in the upper reaches or headwaters of a water system is usually very narrow and lined by thick shore vegetation.  This prevents the penetration of sunlight, in turn decreasing the production of organic material through

text: photosynthesis

text: in the water.  The majority of the organic matter that does make its way into the system is in the form

text: allochthon

text: ous plant material that falls into the river, such as leaves and sticks.  In this section, respiration (consumption) out paces production (P/R<1).  Here shredders play a major role in breaking down coarse plant material.  In this area, the largest diversity of organic material can be expected.

text: The isolation of enzymes from infected tissue can also provide the basis of a biochemical diagnosis of an infectious disease. For example, humans can make neither RNA replicases nor reverse transcriptase, and the presence of these enzymes are characteristic of specific types of viral infections. The ability of the viral protein hemagglutinin to bind red blood cells together into a detectable matrix may also be characterized as a biochemical test for viral infection, although strictly speaking hemagglutinin is not an enzyme and has no metabolic function.

text: The isolation of

text: enzymes

text: from infected tissue can also provide the basis of a biochemical diagnosis of an infectious disease. For example, humans can make neither

text: RNA replicase

text: s nor

text: reverse transcriptase

text: , and the presence of these enzymes are characteristic of specific types of viral infections. The ability of the viral protein

text: hemagglutinin

text: to bind

text: red blood cells

text: together into a detectable matrix may also be characterized as a biochemical test for viral infection, although strictly speaking hemagglutinin is not an enzyme and has no metabolic function.

text: Organic reactions are chemical reactions involving organic compounds.   The basic organic chemistry reaction types are addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions, photochemical reactions and redox reactions. In organic synthesis, organic reactions are used in the construction of new organic molecules. The production of many man-made chemicals such as drugs, plastics, food additives, fabrics depend on organic reactions.

text: Organic reactions are

text: chemical reaction

text: s involving

text: organic compound

text: s.   The basic

text: organic chemistry

text: reaction types are

text: addition reaction

text: s,

text: elimination reaction

text: s,

text: substitution reaction

text: s,

text: pericyclic reaction

text: s,

text: rearrangement reaction

text: s,

text: photochemical reactions

text: and

text: redox reactions

text: . In

text: organic synthesis

text: , organic reactions are used in the construction of new organic molecules. The production of many man-made chemicals such as drugs, plastics, food additives, fabrics depend on organic reactions.

text: The Barbier reaction is an organic reaction between an alkyl halide and a carbonyl group as an electrophilic substrate in the presence of magnesium, aluminium, zinc, indium, tin or its salts. The reaction product is a primary, secondary or tertiary alcohol. The reaction is similar to the Grignard reaction but the crucial difference is that the Barbier reaction is a one-pot synthesis whereas a Grignard reagent is prepared separately before addition of the carbonyl compound. Barbier reactions are nucleophilic addition reactions that usually take place with relatively inexpensive and water insensitive metals or metal compounds in contrast to Grignard reagents or organolithium reagents. For this reason it is possible in many cases to run the reaction in water which makes the procedure part of green chemistry. The Barbier reaction is named after Victor Grignard's teacher Philippe Barbier.

text: The Barbier reaction is an

text: organic reaction

text: between an

text: alkyl halide

text: and a

text: carbonyl

text: group as an

text: electrophilic

text: substrate in the presence of

text: magnesium

text: aluminium

text: zinc

text: indium

text: tin

text: or its salts. The reaction product is a primary, secondary or tertiary

text: alcohol

text: . The reaction is similar to the

text: Grignard reaction

text: but the crucial difference is that the Barbier reaction is a

text: one-pot synthesis

text: whereas a Grignard reagent is prepared separately before addition of the carbonyl compound. Barbier reactions are

text: nucleophilic addition

text: reactions that usually take place with relatively inexpensive and water insensitive metals or metal compounds in contrast to Grignard reagents or

text: organolithium reagent

text: s. For this reason it is possible in many cases to run the reaction in water which makes the procedure part of

text: green chemistry

text: . The Barbier reaction is named after

text: Victor Grignard

text: 's teacher

text: Philippe Barbier

text: Biological energy is frequently stored and released by means of redox reactions. Photosynthesis involves the reduction of carbon dioxide into sugars and the oxidation of water into molecular oxygen. The reverse reaction, respiration, oxidizes sugars to produce carbon dioxide and water. As intermediate steps, the reduced carbon compounds are used to reduce nicotinamide adenine dinucleotide (NAD), which then contributes to the creation of a proton gradient, which drives the synthesis of adenosine triphosphate (ATP) and is maintained by the reduction of oxygen.In animal cells, mitochondria perform similar functions. See the Membrane potential article.

text: Biological energy is frequently stored and released by means of redox reactions. Photosynthesis involves the reduction of

text: carbon dioxide

text: into

text: sugar

text: s and the oxidation of

text: water

text: into molecular oxygen. The reverse reaction, respiration, oxidizes sugars to produce carbon dioxide and water. As intermediate steps, the reduced carbon compounds are used to reduce

text: nicotinamide adenine dinucleotide

text: (NAD), which then contributes to the creation of a

text: proton gradient

text: , which drives the synthesis of

text: adenosine triphosphate

text: (ATP) and is maintained by the reduction of oxygen.In animal cells,

text: mitochondria

text: perform similar functions. See the

text: Membrane potential

text: article.

text: Physical organic chemists use both experimental and theoretical disciplines such as spectroscopy, spectrometry, crystallography, computational chemistry, and quantum theory to study both the rates of organic reactions and the relative chemical stability of the starting materials, transition states, and products. Chemists in this field work to understand the physical underpinnings of modern organic chemistry, and therefore physical organic chemistry has applications in specialized areas including polymer chemistry, supramolecular chemistry, electrochemistry, and photochemistry.

text: Physical organic chemists use both experimental and theoretical disciplines such as

text: spectroscopy

text: spectrometry

text: crystallography

text: computational chemistry

text: , and

text: quantum theory

text: to study both the

text: rates

text: of

text: organic reactions

text: and the relative

text: chemical stability

text: of the starting materials,

text: transition state

text: s, and products. Chemists in this field work to understand the physical underpinnings of modern

text: organic chemistry

text: , and therefore physical organic chemistry has applications in specialized areas including

text: polymer chemistry

text: supramolecular chemistry

text: electrochemistry

text: , and

text: photochemistry

text: In amino acid production, one encounters an important problem in biosynthesis, namely stereochemical control. Because all amino acids except glycine are chiral, biosynthetic pathways must generate the correct isomer with high fidelity. In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon atom is established by a transamination reaction that involves pyridoxal phosphate. Almost all the transaminases that catalyze these reactions descend from a common ancestor, illustrating once again that effective solutions to biochemical problems are retained throughout evolution.

text: In amino acid production, one encounters an important problem in

text: biosynthesis

text: , namely

text: stereochemical

text: control. Because all amino acids except

text: glycine

text: are

text: chiral

text: , biosynthetic pathways must generate the correct

text: isomer

text: with high fidelity. In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon atom is established by a

text: transamination

text: reaction that involves

text: pyridoxal phosphate

text: . Almost all the transaminases that

text: catalyze

text: these reactions descend from a common ancestor, illustrating once again that effective solutions to biochemical problems are retained throughout

text: evolution

text: A compact graphical description of major biochemical reactions involved can be found at KEGG  This provides information on the relevant enzymes and details the relationship with several other metabolic processes: glycine, serine, and threonine metabolism which provides hydroxypyruvate and glyoxylate, purine metabolism which provides glyoxylate, pyruvate metabolism which provides (S)-malate and formate, carbon fixation which consumes 3-phospho-D-glycerate and provides D-ribulose 1,5-P2, ascorbate and aldarate metabolism which shares tartronate-semialdehyde, nitrogen metabolism which shares formate, pyruvate metabolism and the citrate cycle which share oxaloacetate, and vitamin B metabolism which consumes glycolaldehyde.

text: A compact graphical description of major biochemical reactions involved can be found at

text: KEGG

text: This provides information on the relevant

text: enzyme

text: s and details the relationship with several other metabolic processes:

text: glycine, serine, and threonine metabolism

text: which provides

text: hydroxypyruvate

text: and

text: glyoxylate

text: purine metabolism

text: which provides glyoxylate,

text: pyruvate metabolism

text: which provides (S)-

text: malate

text: and

text: formate

text: carbon fixation

text: which consumes

text: and provides D-

text: ribulose

text: ascorbate and aldarate metabolism

text: which shares

text: tartronate-semialdehyde

text: nitrogen metabolism

text: which shares

text: formate

text: pyruvate metabolism

text: and the

text: citrate cycle

text: which share

text: oxaloacetate

text: , and

text: vitamin B metabolism

text: which consumes

text: glycolaldehyde

text: Together with F. J. M. Horn and Roy Jackson, Feinberg created chemical reaction network theory, a field of mathematics that connects the graphical and algebraic structure of chemical reaction networks with their dynamic behavior. He is best known for stating and proving the deficiency zero theorem (together with Horn and Jackson) and the deficiency one theorem. He has also articulated complete necessary and sufficient conditions for detailed balancing in mass-action systems.More recently, Feinberg has turned his attention to problems arising from biology. Together with Gheorghe Craciun, he developed the theory of injective reaction networks and explored its implications for biochemistry. A current research focus (together with Guy Shinar) is the application of chemical reaction network theory to questions of robustness in biochemical reaction networks.He has also worked with Richard Lavine on foundations of classical thermodynamics.

text: Together with F. J. M. Horn and Roy Jackson, Feinberg created

text: chemical reaction network theory

text: , a field of

text: mathematics

text: that connects the graphical and algebraic structure of chemical reaction networks with their

text: dynamic behavior

text: . He is best known for stating and proving the deficiency zero theorem (together with Horn and Jackson) and the deficiency one theorem. He has also articulated complete necessary and sufficient conditions for detailed balancing in

text: mass-action systems

text: .More recently, Feinberg has turned his attention to problems arising from biology. Together with Gheorghe Craciun, he developed the theory of injective reaction networks and explored its implications for

text: biochemistry

text: . A current research focus (together with Guy Shinar) is the application of chemical reaction network theory to questions of robustness in biochemical reaction networks.He has also worked with Richard Lavine on foundations of classical

text: thermodynamics

text: Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy in the process, as weak so-called "high-energy" bonds are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. Cellular respiration is considered an exothermic redox reaction which releases heat. The overall reaction occurs in a series of biochemical steps, most of which are redox reactions themselves. Although technically, cellular respiration is a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow release of energy from the series of reactions.

text: Cellular respiration is a set of

text: metabolic

text: reactions and processes that take place in the

text: cell

text: s of

text: organism

text: s to convert

text: biochemical energy

text: from

text: nutrients

text: into

text: adenosine triphosphate

text: (ATP), and then release waste products. The reactions involved in respiration are

text: catabolic reactions

text: , which break large molecules into smaller ones, releasing energy in the process, as weak so-called "high-energy" bonds are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. Cellular respiration is considered an

text: exothermic

text: redox reaction

text: which releases heat. The overall reaction occurs in a series of biochemical steps, most of which are redox reactions themselves. Although technically, cellular respiration is a

text: combustion reaction

text: , it clearly does not resemble one when it occurs in a living cell because of the slow release of energy from the series of reactions.

text: The series of biochemical redox reactions which take place in the stroma are collectively called the Calvin cycle or light-independent reactions. There are three phases: carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.

text: The series of

text: biochemical

text: redox

text: reactions which take place in the stroma are collectively called the

text: Calvin cycle

text: or

text: light-independent reactions

text: . There are three phases:

text: carbon fixation

text: , reduction reactions, and

text: ribulose 1,5-bisphosphate

text: (RuBP) regeneration.

text: Environmental chemistry is the scientific study of the chemical and biochemical phenomena that occur in natural places. It should not be confused with green chemistry, which seeks to reduce potential pollution at its source. It can be defined as the study of the sources, reactions, transport, effects, and fates of chemical species in the air, soil, and water environments; and the effect of human activity and biological activity on these. Environmental chemistry is an interdisciplinary science that includes atmospheric, aquatic and soil chemistry, as well as heavily relying on analytical chemistry and being related to environmental and other areas of science.

text: Environmental chemistry is the

text: scientific study

text: of the chemical and biochemical phenomena that occur in natural places. It should not be confused with

text: green chemistry

text: , which seeks to reduce potential pollution at its source. It can be defined as the study of the sources, reactions, transport, effects, and fates of chemical species in the

text: air

text: soil

text: , and

text: water

text: environments; and the effect of human activity and biological activity on these. Environmental chemistry is an

text: interdisciplinary

text: science that includes

text: atmospheric

text: aquatic

text: and

text: soil chemistry

text: , as well as heavily relying on

text: analytical chemistry

text: and being related to

text: environmental

text: and other areas of science.

text: Carbon dioxide is converted into sugars in a process called carbon fixation. Carbon fixation is an endothermic redox reaction, so photosynthesis needs to supply both a source of energy to drive this process, and the electrons needed to convert carbon dioxide into a carbohydrate via a reduction reaction. The addition of electrons to a chemical species is called reduction. In general outline and in effect, photosynthesis is the opposite of cellular respiration, in which glucose and other compounds are oxidized to produce carbon dioxide and water, and to release chemical energy (an exothermic reaction) to drive the organism's metabolism. The two processes, reduction of carbon dioxide to carbohydrate and then later oxidation of the carbohydrate, are distinct: photosynthesis and cellular respiration take place through a different sequence of chemical reactions and in different cellular compartments.

text: Carbon dioxide is converted into sugars in a process called

text: carbon fixation

text: . Carbon fixation is an

text: endothermic

text: redox

text: reaction, so photosynthesis needs to supply both a source of energy to drive this process, and the electrons needed to convert carbon dioxide into a

text: carbohydrate

text: via a

text: reduction reaction

text: . The addition of electrons to a chemical species is called reduction. In general outline and in effect, photosynthesis is the opposite of

text: cellular respiration

text: , in which glucose and other compounds are oxidized to produce carbon dioxide and water, and to release chemical energy (an

text: exothermic

text: reaction) to drive the organism's

text: metabolism

text: . The two processes, reduction of carbon dioxide to carbohydrate and then later oxidation of the carbohydrate, are distinct: photosynthesis and cellular respiration take place through a different sequence of chemical reactions and in different cellular compartments.

text: Enzymes are generally globular proteins, acting alone or in larger complexes. Like all proteins, enzymes are linear chains of amino acids that fold to produce a three-dimensional structure. The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzyme's activity cannot yet be predicted from its structure alone. Enzyme structures unfold (denature) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above a species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate.

text: Enzymes are generally

text: globular protein

text: s, acting alone or in larger

text: complexes

text: . Like all proteins, enzymes are linear chains of

text: amino acids

text: that

text: fold

text: to produce a

text: three-dimensional structure

text: . The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzyme's activity cannot yet be predicted from its structure alone. Enzyme structures unfold (

text: denature

text: ) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above a species' normal level; as a result, enzymes from bacteria living in volcanic environments such as

text: hot spring

text: s are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate.

text: The two most important kinetic properties of an enzyme are how quickly the enzyme becomes saturated with a particular substrate, and the maximum rate it can achieve. Knowing these properties suggests what an enzyme might do in the cell and can show how the enzyme will respond to changes in these conditions.

text: Amino acid synthesis is the set of biochemical processes (metabolic pathways) by which the various amino acids are produced from other compounds. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesise all amino acids. Humans are excellent example of this, since humans can only synthesise 11 of the 20 standard amino acids (aka non-essential amino acid), and in time of accelerated growth, histidine, can be considered an essential amino acid.

text: Amino acid synthesis is the set of

text: biochemical

text: processes (

text: metabolic pathways

text: ) by which the various

text: amino acid

text: s are produced from other

text: compounds

text: . The substrates for these processes are various compounds in the

text: organism

text: 's diet or growth media. Not all organisms are able to synthesise all amino acids. Humans are excellent example of this, since humans can only synthesise 11 of the 20 standard amino acids (aka

text: non-essential amino acid

text: ), and in time of accelerated growth,

text: histidine

text: , can be considered an

text: essential amino acid

text: Asclepain () is an enzyme. This enzyme catalyses the following chemical reaction

text: Asclepain () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Temperature has a multiplicity of effects on plants depending on a variety of factors, including the size and condition of the plant and the temperature and duration of exposure. The smaller and more succulent the plant, the greater the susceptibility to damage or death from temperatures that are too high or too low. Temperature affects the rate of biochemical and physiological processes, rates generally (within limits) increasing with temperature. However, the Van’t Hoff relationship for monomolecular reactions (which states that the velocity of a reaction is doubled or trebled by a temperature increase of 10 °C) does not strictly hold for biological processes, especially at low and high temperatures.

text: Temperature has a multiplicity of effects on plants depending on a variety of factors, including the size and condition of the plant and the temperature and duration of exposure. The smaller and more

text: succulent the plant

text: , the greater the susceptibility to damage or death from temperatures that are too high or too low. Temperature affects the rate of biochemical and physiological processes, rates generally (within limits) increasing with temperature. However, the Van’t Hoff relationship for monomolecular reactions (which states that the velocity of a reaction is doubled or trebled by a temperature increase of 10 °C) does not strictly hold for biological processes, especially at low and high temperatures.

text: Dissolved organic material is most commonly measured using either the Biochemical oxygen demand (BOD) test or the Chemical oxygen demand (COD) test. Organic constituents are significant in river chemistry for the effect that they have on dissolved oxygen concentration and for the impact that individual organic species may have directly on aquatic biota.

text: Dissolved organic material is most commonly measured using either the

text: Biochemical oxygen demand

text: (BOD) test or the

text: Chemical oxygen demand

text: (COD) test. Organic constituents are significant in river chemistry for the effect that they have on dissolved oxygen concentration and for the impact that individual organic species may have directly on aquatic biota.

text: In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell.  The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. In a metabolic pathway, the product of one enzyme acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function.

text: In

text: biochemistry

text: , a metabolic pathway is a linked series of

text: chemical reaction

text: s occurring within a

text: cell

text: .  The reactants, products, and intermediates of an enzymatic reaction are known as

text: metabolites

text: , which are modified by a sequence of chemical reactions

text: catalyze

text: d by

text: enzyme

text: s. In a metabolic pathway, the

text: product

text: of one enzyme acts as the

text: substrate

text: for the next. These enzymes often require dietary minerals, vitamins, and other

text: cofactors

text: to function.

text: Microbes are ideally suited for biochemical and genetics studies and have made huge contributions to these fields of science such as the demonstration that DNA is the genetic material, that the gene has a simple linear structure, that the genetic code is a triplet code, and that gene expression is regulated by specific genetic processes. Jacques Monod and François Jacob used Escherichia coli, a type of bacteria, in order to develop the operon model of gene expression, which lay down the basis of gene expression and regulation.  Furthermore the hereditary processes of single-celled eukaryotic microorganisms are similar to those in multi-cellular organisms allowing researchers to gather information on this process as well. Another bacterium which has greatly contributed to the field of genetics is Thermus aquaticus, which  is a bacterium that tolerates high temperatures. From this microbe scientists isolated the enzyme Taq polymerase, which is now used in the powerful experimental technique, Polymerase chain reaction(PCR). Additionally the development of recombinant DNA technology through the use of bacteria has led to the birth of modern genetic engineering and biotechnology.

text: Microbes are ideally suited for

text: biochemical

text: and

text: genetics

text: studies and have made huge contributions to these fields of science such as the demonstration that DNA is the genetic material, that the gene has a simple linear structure, that the genetic code is a triplet code, and that gene expression is regulated by specific genetic processes.

text: Jacques Monod

text: and

text: François Jacob

text: used

text: Escherichia coli

text: , a type of bacteria, in order to develop the

text: operon

text: model of

text: gene expression

text: , which lay down the basis of gene expression and regulation.  Furthermore the

text: hereditary

text: processes of single-celled eukaryotic microorganisms are similar to those in multi-cellular organisms allowing researchers to gather information on this process as well. Another bacterium which has greatly contributed to the field of

text: genetics

text: is

text: Thermus aquaticus

text: , which  is a bacterium that tolerates high temperatures. From this microbe scientists isolated the enzyme

text: Taq polymerase

text: , which is now used in the powerful experimental technique,

text: Polymerase chain reaction

text: (PCR). Additionally the development of

text: recombinant DNA technology

text: through the use of bacteria has led to the birth of modern

text: genetic engineering

text: and

text: biotechnology

text: General chemistry courses typically introduce concepts such as stoichiometry, prediction of reaction products, thermodynamics, nuclear chemistry, electrochemistry, chemical kinetics, and many of the rudiments of physical chemistry. Though the list of subjects covered is typically broad, leading some to criticize both the class and the discipline as encouraging memorization, most general chemistry courses are firmly grounded in several fundamental physical rules for which the primary challenge is understanding when the rules are applicable.

text: General chemistry courses typically introduce concepts such as

text: stoichiometry

text: , prediction of reaction products,

text: thermodynamics

text: nuclear chemistry

text: electrochemistry

text: chemical kinetics

text: , and many of the rudiments of

text: physical chemistry

text: . Though the list of subjects covered is typically broad, leading some to criticize both the class and the discipline as encouraging memorization, most general chemistry courses are firmly grounded in several fundamental physical rules for which the primary challenge is understanding when the rules are applicable.

text: Metabolic myopathies are myopathies that result from defects in biochemical metabolism that primarily affect muscle. They include:

text: Metabolic myopathies are

text: myopathies

text: that result from defects in biochemical metabolism that primarily affect muscle. They include:

text: Thermopsin () is an enzyme. This enzyme catalyses the following chemical reaction

text: Thermopsin () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: The enzymes transketolase, pyruvate dehydrogenase (PDH), and 2-oxoglutarate dehydrogenase (OGDH) are all important in carbohydrate metabolism. The cytosolic enzyme transketolase is a key player in the pentose phosphate pathway, a major route for the biosynthesis of the pentose sugars deoxyribose and ribose. The mitochondrial PDH and OGDH are part of biochemical pathways that result in the generation of adenosine triphosphate (ATP), which is a major form of energy for the cell. PDH links glycolysis to the citric acid cycle, while the reaction catalyzed by OGDH is a rate-limiting step in the citric acid cycle. In the nervous system, PDH is also involved in the production of acetylcholine, a neurotransmitter, and for myelin synthesis.

text: The enzymes

text: transketolase

text: pyruvate dehydrogenase

text: (PDH), and 2-

text: oxoglutarate dehydrogenase

text: (OGDH) are all important in

text: carbohydrate metabolism

text: . The cytosolic enzyme transketolase is a key player in the

text: pentose phosphate pathway

text: , a major route for the biosynthesis of the pentose

text: sugar

text: s

text: deoxyribose

text: and

text: ribose

text: . The mitochondrial PDH and OGDH are part of biochemical pathways that result in the generation of

text: adenosine triphosphate

text: (ATP), which is a major form of energy for the cell. PDH links glycolysis to the citric acid cycle, while the reaction catalyzed by OGDH is a rate-limiting step in the

text: citric acid cycle

text: . In the nervous system, PDH is also involved in the production of acetylcholine, a neurotransmitter, and for myelin synthesis.

text: For example, frogs in cold climates can survive for extended periods of time with most of their body water in a frozen state, whereas desert frogs in Australia can become inactive and dehydrate in dry periods, losing up to 75% of their fluids, yet return to life by rapidly rehydrating in wet periods. Either type of frog would appear biochemically inactive (i.e. not living) during dormant periods to anyone lacking a sensitive means of detecting low levels of metabolism.

text: The discovery of catalytic RNA (ribozymes) showed that RNA could both encode genetic information (like DNA) and catalyze specific biochemical reactions (like protein enzymes). This realization led to the RNA World Hypothesis, a proposal that RNA may have played a critical role in prebiotic evolution at a time before the molecules with more specialized functions (DNA and proteins) came to dominate biological information coding and catalysis. Although it is not possible for us to know the course of prebiotic evolution with any certainty, the presence of functional RNA molecules with common ancestry in all modern-day life forms is a strong argument that RNA was widely present at the time of the last common ancestor.

text: The discovery of catalytic RNA (

text: ribozymes

text: ) showed that RNA could both encode genetic information (like DNA) and catalyze specific biochemical reactions (like protein

text: enzymes

text: ). This realization led to the

text: RNA World Hypothesis

text: , a proposal that RNA may have played a critical role in

text: prebiotic evolution

text: at a time before the molecules with more specialized functions (DNA and proteins) came to dominate biological information coding and catalysis. Although it is not possible for us to know the course of prebiotic evolution with any certainty, the presence of functional RNA molecules with common ancestry in all modern-day life forms is a strong argument that RNA was widely present at the time of the

text: last common ancestor

text: This subunit, known as E1o, catalyzes a rate-limiting step in the citric acid cycle and lies far from equilibrium; the total change in Gibbs free energy is ΔG = −33 kJ/mol. The significant energy change makes it a crucial point of regulation not only for the citric acid cycle, but also for the entire cellular respiration pathway. As such, E1o is inhibited by both NADH and Succinyl-CoA via non competitive feedback inhibition.

text: This subunit, known as E1o, catalyzes a rate-limiting step in the

text: citric acid cycle

text: and lies far from equilibrium; the total change in

text: Gibbs free energy

text: is ΔG = −33 kJ/mol. The significant energy change makes it a crucial point of regulation not only for the citric acid cycle, but also for the entire

text: cellular respiration

text: pathway. As such, E1o is inhibited by both NADH and Succinyl-CoA via non competitive feedback inhibition.

text: A light-harvesting complex is a complex of subunit proteins that may be part of a larger supercomplex of a photosystem, the functional unit in photosynthesis. It is used by plants and photosynthetic bacteria to collect more of the incoming light than would be captured by the photosynthetic reaction center alone. Light-harvesting complexes are found in a wide variety among the different photosynthetic species. The complexes consist of proteins and photosynthetic pigments and surround a photosynthetic reaction center to focus energy, attained from photons absorbed by the pigment, toward the reaction center using Förster resonance energy transfer.

text: A light-harvesting complex is a complex of

text: subunit protein

text: s that may be part of a larger supercomplex of a

text: photosystem

text: , the functional unit in

text: photosynthesis

text: . It is used by

text: plant

text: s and

text: photosynthetic bacteria

text: to collect more of the incoming light than would be captured by the

text: photosynthetic reaction center

text: alone. Light-harvesting complexes are found in a wide variety among the different photosynthetic species. The complexes consist of proteins and

text: photosynthetic pigment

text: s and surround a

text: photosynthetic reaction center

text: to focus energy, attained from photons absorbed by the

text: pigment

text: , toward the reaction center using

text: Förster resonance energy transfer

text: Mitochondria are organelles which function to transform energy as a result of cellular respiration. Chloroplasts are organelles which function to produce sugars via photosynthesis in plants and algae. The genes located in mitochondria and chloroplasts are very important for proper cellular function, yet the genomes replicate independently of the DNA located in the nucleus, which is typically arranged in chromosomes that only replicate one time preceding cellular division. The extranuclear genomes of mitochondria and chloroplasts however replicate independently of cell division. They replicate in response to a cell's increasing energy needs which adjust during that cell's lifespan. Since they replicate independently, genomic recombination of these genomes is rarely found in offspring contrary to nuclear genomes, in which recombination is common.Mitochondrial disease are received from the mother, fathers don't as sperm do not contribute (but a sperm contains a mitochondrion for its energy production).

text: Mitochondria are organelles which function to transform energy as a result of

text: cellular respiration

text: . Chloroplasts are organelles which function to produce sugars via

text: photosynthesis

text: in plants and algae. The

text: genes

text: located in

text: mitochondria

text: and chloroplasts are very important for proper cellular function, yet the genomes replicate independently of the DNA located in the nucleus, which is typically arranged in chromosomes that only replicate one time preceding cellular division. The extranuclear genomes of mitochondria and chloroplasts however replicate independently of cell division. They replicate in response to a cell's increasing energy needs which adjust during that cell's lifespan. Since they replicate independently, genomic recombination of these genomes is rarely found in offspring contrary to nuclear genomes, in which recombination is common.Mitochondrial disease are received from the mother, fathers don't as sperm do not contribute (but a sperm contains a mitochondrion for its energy production).

text: 1,3-Difluoro-2-propanol is a metabolic poison which disrupts the citric acid cycle and is used as a rodenticide, similar to sodium fluoroacetate. It is the main ingredient (along with 1-chloro-3-fluoro-2-propanol) in the rodenticide product Gliftor which was widely used in the former USSR.<ref>{{cite journal |vauthors=Feldwick MG, Noakes PS, Prause U, Mead RJ, Kostyniak PJ |title=The biochemical toxicology of 1,3-difluoro-2-propanol, the major ingredient of the pesticide gliftor: the potential of 4-methylpyrazole as an antidote |journal=J. Biochem. Mol. Toxicol. |volume=12 |issue=1 |pages=41–52 |year=1998 |pmid=9414486 |doi= 10.1002/(SICI)1099-0461(1998)12:1

text: 1,3-Difluoro-2-propanol is a

text: metabolic poison

text: which disrupts the

text: citric acid cycle

text: and is used as a

text: rodenticide

text: , similar to

text: sodium fluoroacetate

text: . It is the main ingredient (along with 1-chloro-3-fluoro-2-propanol) in the rodenticide product Gliftor which was widely used in the former USSR.<ref>{{cite journal |vauthors=Feldwick MG, Noakes PS, Prause U, Mead RJ, Kostyniak PJ |title=The biochemical toxicology of 1,3-difluoro-2-propanol, the major ingredient of the pesticide gliftor: the potential of 4-methylpyrazole as an antidote |journal=J. Biochem. Mol. Toxicol. |volume=12 |issue=1 |pages=41–52 |year=1998 |pmid=9414486 |doi= 10.1002/(SICI)1099-0461(1998)12:1

text: According to this relationship, metabolic rate is a function of an organism’s body mass and body temperature.  By this equation, large organisms have higher metabolic rates (in Watts) than small organisms, and organisms at high body temperatures have higher metabolic rates than those that exist at low body temperatures. However, specific metabolic rate (SMR, in Watts/kg)  is given by

text: HDDA-derived benzynes have also been shown to dehydrogenate saturated alkanes to form alkenes. In the absence of external trapping reagents, the benzyne intermediate can abstract vicinal (chemistry) hydrogen atoms from a suitable donor, often the reaction solvent (such as tetrahydrofuran or cyclooctane). This desaturates the donor alkane, forming an alkene, and traps the benzyne to a dihydrobenzenoid product. Isotopic labelling and computational studies suggest that the double hydrogen transfer mechanism occurs by a concerted pathway and that the rate of reaction is highly dependent on the conformation of the alkane donor. This reaction can be used to access 1,2,3,4-tetrasubstituted aromatic rings, a substitution pattern that can be difficult to access through other synthetic methodology.

text: HDDA-derived benzynes have also been shown to

text: dehydrogenate

text: saturated

text: alkanes

text: to form

text: alkenes

text: . In the absence of external trapping reagents, the benzyne intermediate can abstract

text: vicinal (chemistry)

text: hydrogen atoms from a suitable donor, often the reaction

text: solvent

text: (such as

text: tetrahydrofuran

text: or

text: cyclooctane

text: ). This desaturates the donor alkane, forming an

text: alkene

text: , and traps the benzyne to a dihydrobenzenoid product. Isotopic labelling and computational studies suggest that the double hydrogen transfer mechanism occurs by a concerted pathway and that the rate of reaction is highly dependent on the

text: conformation

text: of the alkane donor. This reaction can be used to access 1,2,3,4-tetrasubstituted aromatic rings, a substitution pattern that can be difficult to access through other synthetic methodology.

text: The GEBIK and GEBIF equations are the most generalized approach to describe isotopic effects in any chemical, catalytic reaction and biochemical reactions because they can describe isotopic effects in equilibrium reactions, kinetic chemical reactions and kinetic biochemical reactions. In the latter two cases, they can describe both stationary and non-stationary fractionation (i.e., variable and inverse fractionation). In general, isotopic effects depend on the number of reactants and on the number of combinations resulting from the number of substitutions in all reactants and products. Describing with accuracy isotopic effects, however, depends also on the specific rate law used to describe the chemical or biochemical reaction that produces isotopic effects. Normally, regardless of whether a reaction is purely chemical or whether it involves some enzyme of biological nature, the equations used to describe isotopic effects base on first-order kinetics. This approach systematically leads to isotopic effects that can be described by means of the Rayleigh equation. In this case, isotopic effects will always be expressed as a constant, hence will not be able to describe isotopic effects in reactions where fractionation and enrichment are variable or inverse during the course of a reaction. Most chemical reactions do not follow first-order kinetics; neither biochemical reactions can normally be described with first-order kinetics. To properly describe isotopic effects in chemical or biochemical reactions, different approaches must be employed such as the use of Michaelis–Menten reaction order (for chemical reactions) or coupled Michaelis–Menten and Monod reaction orders (for biochemical reactions). However, conversely to Michaelis–Menten kinetics, GEBIK and GEBIF equations are solved under the hypothesis of non-steady state. This characteristic allows GEBIK and GEBIF to capture transient isotopic effects.

text: The GEBIK and GEBIF equations are the most generalized approach to describe isotopic effects in any

text: chemical

text: catalytic reaction

text: and

text: biochemical

text: reactions because they can describe isotopic effects in equilibrium reactions, kinetic chemical reactions and kinetic biochemical reactions. In the latter two cases, they can describe both stationary and non-stationary fractionation (i.e., variable and inverse fractionation). In general, isotopic effects depend on the number of reactants and on the number of combinations resulting from the number of substitutions in all reactants and products. Describing with accuracy isotopic effects, however, depends also on the specific

text: rate law

text: used to describe the chemical or biochemical reaction that produces isotopic effects. Normally, regardless of whether a reaction is purely chemical or whether it involves some

text: enzyme

text: of biological nature, the equations used to describe isotopic effects base on first-order kinetics. This approach systematically leads to isotopic effects that can be described by means of the Rayleigh equation. In this case, isotopic effects will always be expressed as a constant, hence will not be able to describe isotopic effects in reactions where fractionation and enrichment are variable or inverse during the course of a reaction. Most chemical reactions do not follow first-order kinetics; neither biochemical reactions can normally be described with first-order kinetics. To properly describe isotopic effects in chemical or biochemical reactions, different approaches must be employed such as the use of

text: Michaelis–Menten

text: reaction order (for chemical reactions) or coupled Michaelis–Menten and Monod reaction orders (for biochemical reactions). However, conversely to Michaelis–Menten kinetics, GEBIK and GEBIF equations are solved under the hypothesis of non-steady state. This characteristic allows GEBIK and GEBIF to capture transient isotopic effects.

text: Harris says the idea of free will is incoherent and "cannot be mapped on to any conceivable reality." Humans have no free will and no sense can be given to the concept that we might have. According to Harris, science "reveals you to be a biochemical puppet." People's thoughts and intentions, Harris says, "emerge from background causes of which we are unaware and over which we exert no conscious control." Every choice we make is made as a result of preceding causes. These choices we make are determined by those causes, and are therefore not really choices at all. Harris also draws a distinction between conscious and unconscious reactions to the world. Even without free will, consciousness has an important role to play in the choices we make. Harris argues that this realization about the human mind does not undermine morality or diminish the importance of social and political freedom, but it can and should change the way we think about some of the most important questions in life.

text: Phytepsin () is an enzyme. This enzyme catalyses the following chemical reaction

text: Phytepsin () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Mercury coulometer is an electroanalytical chemistry device using mercury to determine the amount of matter transformed (in coulombs) during the following reaction:<br>

text: Mercury coulometer is an

text: electroanalytical chemistry device

text: using

text: mercury

text: to determine the amount of matter transformed (in

text: coulomb

text: s) during the following reaction:<br>

text: If a reaction rate depends on a single reactant and the value of the exponent is one, then the reaction is said to be first order. In organic chemistry, the class of S1 (nucleophilic substitution unimolecular) reactions consists of first-order reactions. For example, in the reaction of aryldiazonium ions with nucleophiles in aqueous solution ArN + X → ArX + N, the rate equation is r = k[ArN], where Ar indicates an aryl group.

text: If a reaction rate depends on a single reactant and the value of the exponent is one, then the reaction is said to be first order. In organic chemistry, the class of

text: (nucleophilic substitution unimolecular) reactions consists of first-order reactions. For example, in the reaction of

text: aryldiazonium

text: ions with

text: nucleophiles

text: in aqueous solution ArN + X → ArX + N, the rate equation is r = k[ArN], where Ar indicates an

text: aryl

text: group.

text: In organometallic chemistry the nucleophilic abstraction reaction occurs with a nucleophilic substitution mechanism.

text: In

text: organometallic chemistry

text: the

text: nucleophilic abstraction

text: reaction occurs with a nucleophilic substitution mechanism.

text: Novel proline racemases of medical and veterinary importance were described respectively in Clostridium difficile () and Trypanosoma vivax (). These studies showed that a peptide motif used as a minimal pattern signature to identify putative proline racemases (motif III*) is insufficient stringent per se to discriminate proline racemases from 4-hydroxyproline epimerases (HyPRE). Also, additional, non-dissociated elements that account for the discrimination of these enzymes were identified, based for instance on polarity constraints imposed by specific residues of the catalytic pockets. Based on those elements, enzymes incorrectly described as proline racemases were biochemically proved to be hydroxyproline epimerases (i.e. HyPREs from Pseudomonas aeruginosa (Q9I476), Burkholderia pseudomallei (), Brucella abortus (), Brucella suis () and Brucella melitensis ().

text: Novel proline racemases of medical and veterinary importance were described respectively in

text: Clostridium difficile

text: () and

text: Trypanosoma vivax

text: (). These studies showed that a peptide motif used as a minimal pattern signature to identify putative proline racemases (motif III*) is insufficient stringent per se to discriminate proline racemases from

text: 4-hydroxyproline epimerase

text: s (HyPRE). Also, additional, non-dissociated elements that account for the discrimination of these enzymes were identified, based for instance on polarity constraints imposed by specific residues of the catalytic pockets. Based on those elements, enzymes incorrectly described as proline racemases were biochemically proved to be hydroxyproline epimerases (i.e. HyPREs from

text: Pseudomonas aeruginosa

text: Burkholderia pseudomallei

text: Brucella abortus

text: Brucella suis

text: () and

text: Brucella melitensis

text: Myron Lee Bender (1924–1988) was born in St. Louis, Missouri. He obtained his B.S. (1944) and his Ph.D. (1948) from Purdue University.  The latter was under the direction of Henry B. Hass.  After postdoctoral research under Paul D. Barlett (Harvard University), and Frank H. Westheimer (University of Chicago), he spent one year as a faculty member at the University of Connecticut. Thereafter, he was a professor of Chemistry at Illinois Institute of Technology in 1951, and then at Northwestern University in 1960. He worked primarily in the study of reaction mechanisms and the biochemistry of enzyme action. Myron L. Bender demonstrated the two-step mechanism of catalysis for serine proteases, nucleophilic catalysis in ester hydrolysis and intramolecular catalysis in water.  He also showed that cyclodextrin can be used to investigate catalysis of organic reactions within the scope of host-guest chemistry. Finally, he and others reported on the synthesis of an organic compound as a model of an acylchymotrypsin intermediate.

text: Myron Lee Bender (1924–1988) was born in

text: St. Louis

text: Missouri

text: . He obtained his B.S. (1944) and his Ph.D. (1948) from

text: Purdue University

text: .  The latter was under the direction of

text: Henry B. Hass

text: .  After

text: postdoctoral research

text: under

text: Paul D. Barlett

text: Harvard University

text: ), and

text: Frank H. Westheimer

text: University of Chicago

text: ), he spent one year as a faculty member at the

text: University of Connecticut

text: . Thereafter, he was a professor of

text: Chemistry

text: at

text: Illinois Institute of Technology

text: in 1951, and then at

text: Northwestern University

text: in 1960. He worked primarily in the study of

text: reaction mechanism

text: s and the biochemistry of

text: enzyme

text: action. Myron L. Bender demonstrated the two-step mechanism of catalysis for serine proteases, nucleophilic catalysis in ester hydrolysis and intramolecular catalysis in water.  He also showed that

text: cyclodextrin

text: can be used to investigate catalysis of organic reactions within the scope of host-guest chemistry. Finally, he and others reported on the synthesis of an organic compound as a model of an acylchymotrypsin intermediate.

text: Catabolism is the metabolic reaction which cells undergo to extract energy. There are two major metabolic pathways of monosaccharide catabolism: glycolysis and the citric acid cycle.

text: Catabolism is the metabolic reaction which cells undergo to extract energy. There are two major

text: metabolic pathway

text: s of monosaccharide

text: catabolism

text: glycolysis

text: and the

text: citric acid cycle

text: The process of cell respiration also depends heavily on the reduction of NAD to NADH and the reverse reaction (the oxidation of NADH to NAD). Photosynthesis and cellular respiration are complementary, but photosynthesis is not the reverse of the redox reaction in cell respiration:

text: The process of cell respiration also depends heavily on the reduction of

text: NAD

text: to NADH and the reverse reaction (the oxidation of NADH to NAD).

text: Photosynthesis

text: and cellular respiration are complementary, but photosynthesis is not the reverse of the redox reaction in cell respiration:

text: The 2-oxoglutarate (2OG) dependent oxygenases are a superfamily of non-haem iron dependent oxygenases, most of which use the Krebs cycle intermediate, 2-oxoglutarate (2OG), as a cosubstrate. The group are interested in understanding these enzymes for their ability to catalyse synthetically difficult or ‘impossible’ reactions (e.g. the stereoselective hydroxylation of unactivated carbon-hydrogen bonds), for their diverse physiological roles, and for their links to disease. The research focuses on members of the family that are linked to disease, or can be targeted for the treatment of disease. Techniques involved in this interdisciplinary research include proteomics, X-ray crystallography, biological mass spectrometry, molecular biology, enzyme kinetics and organic synthesis/medicinal chemistry.

text: The

text: (2OG) dependent

text: oxygenase

text: s are a superfamily of non-haem

text: iron

text: dependent

text: oxygenase

text: s, most of which use the

text: Krebs cycle

text: intermediate,

text: (2OG), as a

text: cosubstrate

text: . The group are interested in understanding these enzymes for their ability to catalyse synthetically difficult or ‘impossible’ reactions (e.g. the

text: stereoselective

text: hydroxylation

text: of unactivated

text: carbon-hydrogen

text: bonds), for their diverse physiological roles, and for their links to disease. The research focuses on members of the family that are linked to disease, or can be targeted for the treatment of disease. Techniques involved in this interdisciplinary research include

text: proteomics

text: X-ray crystallography

text: , biological

text: mass spectrometry

text: molecular biology

text: enzyme kinetics

text: and

text: organic synthesis

text: medicinal chemistry

text: The Journal of Polymer Science Part A: Polymer Chemistry is a peer-reviewed scientific journal covering  polymer science. The journal is dedicated to studies in fundamental organic polymer chemistry and physical organic chemistry. This includes all related topics (such as organic, bio-organic, bio-inorganic, and biological chemistry of monomers, polymers, oligomers and model compounds, inorganic and organometallic chemistry for catalysts, mechanistic studies, supramolecular chemistry aspects relevant to polymers and reactions on polymers). It is published by Wiley. According to the Journal Citation Reports, the journal has a 2012 impact factor of 3.245.

text: The Journal of Polymer Science Part A: Polymer Chemistry is a

text: peer-reviewed

text: scientific journal

text: covering

text: polymer science

text: . The journal is dedicated to studies in fundamental organic polymer chemistry and physical organic chemistry. This includes all related topics (such as organic, bio-organic, bio-inorganic, and biological chemistry of monomers, polymers, oligomers and model compounds, inorganic and organometallic chemistry for catalysts, mechanistic studies, supramolecular chemistry aspects relevant to polymers and reactions on polymers). It is published by

text: Wiley

text: . According to the

text: Journal Citation Reports

text: , the journal has a 2012

text: impact factor

text: of 3.245.

text: The S1 reaction is a substitution reaction in organic chemistry. "S" stands for nucleophilic substitution and the "1" represents the fact that the rate-determining step is unimolecular. Thus, the rate equation is often shown as having first-order dependence on electrophile and zero-order dependence on nucleophile. This relationship holds for situations where the amount of nucleophile is much greater than that of the carbocation intermediate. Instead, the rate equation may be more accurately described using steady-state kinetics.  The reaction involves a carbocation intermediate and is commonly seen in reactions of secondary or tertiary alkyl halides under strongly basic conditions or, under strongly acidic conditions, with secondary or tertiary alcohols.  With primary alkyl halides, the alternative S2 reaction occurs.  In inorganic chemistry, the S1 reaction is often known as the dissociative mechanism. This dissociation pathway is well-described by the cis effect. A reaction mechanism was first proposed by Christopher Ingold et al. in 1940. This reaction does not depend much on the strength of the nucleophile unlike the S2 mechanism.

text: The S1 reaction is a

text: substitution reaction

text: in

text: organic chemistry

text: . "S" stands for

text: nucleophilic substitution

text: and the "1" represents the fact that the

text: rate-determining step

text: is

text: unimolecular

text: . Thus, the rate equation is often shown as having first-order dependence on

text: electrophile

text: and zero-order dependence on

text: nucleophile

text: . This relationship holds for situations where the amount of nucleophile is much greater than that of the carbocation intermediate. Instead, the rate equation may be more accurately described using

text: steady-state kinetics

text: .  The reaction involves a

text: carbocation

text: intermediate and is commonly seen in reactions of secondary or tertiary

text: alkyl halide

text: s under strongly basic conditions or, under strongly acidic conditions, with

entity_section: Primary.2C secondary.2C and tertiary alcohols

text: secondary or tertiary alcohols

text: .  With primary alkyl halides, the alternative

text: S2 reaction

text: occurs.  In

text: inorganic chemistry

text: , the S1 reaction is often known as the dissociative mechanism. This dissociation pathway is well-described by the

text: cis effect

text: . A

text: reaction mechanism

text: was first proposed by

text: Christopher Ingold

text: et al. in 1940. This reaction does not depend much on the strength of the nucleophile unlike the S2 mechanism.

text: Sir Hans Adolf Krebs ( or ) (25 August 1900 – 22 November 1981) was a German-born British physician and biochemist. He was the pioneer scientist in study of cellular respiration, a biochemical pathway in cells for production of energy. He is best known for his discoveries of two important chemical reactions in the body, namely the urea cycle and the citric acid cycle. The latter, the key sequence of metabolic reactions that produces energy in cells, often eponymously known as the "Krebs cycle", earned him a Nobel Prize in Physiology or Medicine in 1953. With Hans Kornberg, he also discovered the glyoxylate cycle, which is a slight variation of the citric acid cycle found in plants, bacteria, protists, and fungi.

text: Sir Hans Adolf Krebs ( or ) (25 August 1900 – 22 November 1981) was a German-born British

text: physician

text: and

text: biochemist

text: . He was the pioneer scientist in study of

text: cellular respiration

text: , a

text: biochemical pathway

text: in cells for

text: production of energy

text: . He is best known for his discoveries of two important chemical reactions in the body, namely the

text: urea cycle

text: and the

text: citric acid cycle

text: . The latter, the key sequence of metabolic reactions that produces energy in cells, often eponymously known as the "Krebs cycle", earned him a

text: Nobel Prize in Physiology or Medicine

text: in 1953. With

text: Hans Kornberg

text: , he also discovered the

text: glyoxylate cycle

text: , which is a slight variation of the citric acid cycle found in plants, bacteria,

text: protists

text: , and

text: fungi

text: A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants. These striking similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy.

text: A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species. For example, the set of

text: carboxylic acid

text: s that are best known as the intermediates in the

text: citric acid cycle

text: are present in all known organisms, being found in species as diverse as the

text: unicellular

text: bacterium

text: Escherichia coli

text: and huge

text: multicellular

text: organisms like

text: elephant

text: s. These striking similarities in metabolic pathways are likely due to their early appearance in

text: evolutionary history

text: , and their retention because of their

text: efficacy

text: Many important biochemical reactions, such as energy generation, use concentration gradients across membranes. The general lack of internal membranes in bacteria means reactions such as electron transport occur across the cell membrane between the cytoplasm and the periplasmic space. However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane. These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria. Other proteins import nutrients across the cell membrane, or expel undesired molecules from the cytoplasm.

text: Many important

text: biochemical

text: reactions, such as

text: energy

text: generation, use

text: concentration gradient

text: s across membranes. The general lack of internal membranes in bacteria means reactions such as

text: electron transport

text: occur across the cell membrane between the cytoplasm and the

text: periplasmic space

text: . However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane. These light-gathering complexes may even form lipid-enclosed structures called

text: chlorosome

text: s in

text: green sulfur bacteria

text: . Other proteins import nutrients across the cell membrane, or expel undesired molecules from the cytoplasm.

text: Kharasch, in his seminal 1933 paper entitled "The Addition of Hydrogen Bromide to Allyl Bromide", proposed that the anti-Markovnikov addition of HBr to allyl bromide to yield 1,3-dibromopropane was due to the presence of peroxides. He termed this the "peroxide effect", which he proposed proceeds through a free radical chain reaction addition. Elsewhere in the literature, other examples of anti-Markovnikov additions were observed by Whitmore and Homeyer as well as Sherril, Mayer and Walter, all of whom rejected Kharasch's conclusions.  They instead argued that the direction in which the reaction proceeds is determined not by the presence or absence of peroxides, but by the nature of the solvent in which the reaction is taking place.  In this paper, Kharasch analyzed one at a time the effects of temperature, solvent, and light on the direction in which the reaction proceeded.  He concluded that the presence of peroxides was the driving force for anti-Markovnikov addition and that any changes in temperature, solvent, or light affected the orientation of addition only through the chemistry of the peroxides.

text: Kharasch, in his seminal 1933 paper entitled "The Addition of Hydrogen Bromide to Allyl Bromide", proposed that the anti-Markovnikov addition of HBr to allyl bromide to yield 1,3-dibromopropane was due to the presence of

text: peroxide

text: s. He termed this the "peroxide effect", which he proposed proceeds through a free radical

text: chain reaction

text: addition. Elsewhere in the

text: literature

text: , other examples of anti-Markovnikov additions were observed by Whitmore and Homeyer as well as Sherril, Mayer and Walter, all of whom rejected Kharasch's conclusions.  They instead argued that the direction in which the reaction proceeds is determined not by the presence or absence of peroxides, but by the nature of the

text: solvent

text: in which the reaction is taking place.  In this paper, Kharasch analyzed one at a time the effects of temperature, solvent, and light on the direction in which the reaction proceeded.  He concluded that the presence of peroxides was the driving force for anti-Markovnikov addition and that any changes in

text: temperature

text: , solvent, or

text: light

text: affected the orientation of addition only through the chemistry of the peroxides.

text: The predictive aspect of a metabolic reconstruction hinges on the ability to predict the biochemical reaction catalyzed by a protein using that protein's amino acid sequence as an input, and to infer the structure of a metabolic network based on the predicted set of reactions. A network of enzymes and metabolites is drafted to relate sequences and function.  When an uncharacterized protein is found in the genome, its amino acid sequence is first compared to those of previously characterized proteins to search for homology.  When a homologous protein is found, the proteins are considered to have a common ancestor and their functions are inferred as being similar.  However, the quality of a reconstruction model is dependent on its ability to accurately infer phenotype directly from sequence, so this rough estimation of protein function will not be sufficient.  A number of algorithms and bioinformatics resources have been developed for refinement of sequence homology-based assignments of protein functions:

text: Dixon's research investigated the purification of enzymes and the enzyme kinetics of enzyme-catalyzed reactions. He studied the oxidation of glutathione and other thiols by molecular oxygen and measured the redox potential of the thiol-disulfide system, also establishing that the oxidation of glutathione was catalyzed by trace metals. He investigated xanthine oxidase, and thereby elucidated many aspects of the chemistry of dehydrogenases. He showed that the hydrogen peroxide formed in the reaction of xanthine oxidase with molecular oxygen inactivated the enzyme and that the inhibition could be relieved by the addition of catalase, thus helping to establish a biochemical role for the latter enzyme. Dixon published a series of papers on D-amino acid oxidase, detailing the kinetics and thermodynamics of association of the coenzyme with the apoprotein, the substrate and inhibitor specificity, and the effect of pH on the kinetic constants.

text: Dixon's research investigated the purification of

text: enzymes

text: and the

text: enzyme kinetics

text: of enzyme-catalyzed reactions. He studied the oxidation of

text: glutathione

text: and other

text: thiols

text: by molecular oxygen and measured the

text: redox

text: potential of the thiol-

text: disulfide

text: system, also establishing that the oxidation of glutathione was catalyzed by trace metals. He investigated

text: xanthine oxidase

text: , and thereby elucidated many aspects of the chemistry of

text: dehydrogenase

text: s. He showed that the

text: hydrogen peroxide

text: formed in the reaction of xanthine oxidase with molecular oxygen inactivated the enzyme and that the inhibition could be relieved by the addition of

text: catalase

text: , thus helping to establish a biochemical role for the latter enzyme. Dixon published a series of papers on D-amino acid

text: oxidase

text: , detailing the kinetics and thermodynamics of association of the

text: coenzyme

text: with the

text: apoprotein

text: , the substrate and inhibitor specificity, and the effect of

text: pH

text: on the kinetic constants.

text: Glucose is a simple sugar with the molecular formula CHO. Glucose circulates in the blood of animals as blood sugar. It is made during photosynthesis from water and carbon dioxide, using energy from sunlight. The reverse of the photosynthesis reaction, which releases this energy, is an important source of power for cellular respiration. Glucose is stored as a polymer, in plants as starch and in animals as glycogen, for times when the organism will need it.

text: Glucose is a simple

text: sugar

text: with the

text: molecular formula

text: C

text: H

text: O

text: . Glucose circulates in the blood of animals as

text: blood sugar

text: . It is made during

text: photosynthesis

text: from water and carbon dioxide, using energy from sunlight. The reverse of the photosynthesis reaction, which releases this energy, is an important source of power for

text: cellular respiration

text: . Glucose is stored as a

text: polymer

text: , in plants as

text: starch

text: and in animals as

text: glycogen

text: , for times when the organism will need it.

text: Glyceroneogenesis is a metabolic pathway which synthesizes glycerol 3-phosphate or triglyceride from precursors other than glucose. Usually glycerol 3-phosphate is generated from glucose by glycolysis, but when glucose concentration drops in the cytosol, it is generated by another pathway called glyceroneogenesis. Glyceroneogenesis uses pyruvate, alanine, glutamine or any substances from the TCA cycle as precursors for glycerol 3-phosphate. Phosphoenolpyruvate carboxykinase (PEPC-K), which is an enzyme that catalyzes the decarboxylation of oxaloacetate to phosphoenolpyruvate is the main regulator for this pathway. Glyceroneogenesis can be observed in adipose tissue and also liver. It is a significant biochemical pathway which regulates cytosolic lipid levels. Intense suppression of glyceroneogenesis may lead to metabolic disorder such as type 2 diabetes.

text: Glyceroneogenesis is a

text: metabolic pathway

text: which synthesizes

text: glycerol 3-phosphate

text: or

text: triglyceride

text: from precursors other than

text: glucose

text: . Usually glycerol 3-phosphate is generated from glucose by

text: glycolysis

text: , but when glucose concentration drops in the

text: cytosol

text: , it is generated by another pathway called glyceroneogenesis. Glyceroneogenesis uses

text: pyruvate

text: alanine

text: glutamine

text: or any substances from the

text: TCA cycle

text: as precursors for glycerol 3-phosphate.

text: Phosphoenolpyruvate carboxykinase

text: (PEPC-K), which is an

text: enzyme

text: that catalyzes the

text: decarboxylation

text: of

text: oxaloacetate

text: to

text: phosphoenolpyruvate

text: is the main regulator for this pathway. Glyceroneogenesis can be observed in

text: adipose tissue

text: and also

text: liver

text: . It is a significant biochemical pathway which regulates cytosolic

text: lipid

text: levels. Intense suppression of glyceroneogenesis may lead to

text: metabolic disorder

text: such as

text: type 2 diabetes

text: Though simple in idea and technical design - and low in traffic volume (about 1 to 10 postings a day) - it has become quite a unique phenomenon in the area of Inborn Errors of Metabolism: By December 2015 (in its 21st year) Metab-L had a subscription base of almost 1600 subscribers worldwide, which is still growing on an almost daily basis. Although of initially  European-German origin, Metab-L members today come mainly from the USA and the UK with growing participation by scientists from all parts of the world. Inborn error of metabolism specialists taking part in Metab-L are mostly clinicians/ pediatricians or coming from a biochemical and laboratory professional or geneticist background. A great portion of members of the most important metabolic scientific societies, SSIEM and SIMD, regularly participate in Metab-L discussions. The renowned Journal of Inherited Metabolic Disease now explicitly publishes "summaries of contributions e.g. to the metabolic Email list metab-l" and in other places, as well, Metab-L is regularly cited in scientific literature: Example articles with Metab-L citation.

text: By bombarding matter with particles in the cyclotron, radioactive isotopes such as carbon-14, were generated. Using carbon-14, the order of events in biochemical reactions could be elucidated, showing the precursors of a particular biochemical product, revealing the network of reactions that constitute life.  Kamen is credited with confirming that all of the oxygen released in photosynthesis comes from water, not carbon dioxide. He also studied the role of molybdenum in biological nitrogen fixation, the biochemistry of cytochromes and their in photosynthesis and metabolism, the role of iron in the activity of porphyrin compounds in plants and animals, and calcium exchange in cancerous tumors.

text: By bombarding matter with particles in the

text: cyclotron

text: , radioactive isotopes such as carbon-14, were generated. Using carbon-14, the order of events in biochemical reactions could be elucidated, showing the precursors of a particular biochemical product, revealing the network of reactions that constitute life.  Kamen is credited with confirming that all of the

text: oxygen

text: released in

text: photosynthesis

text: comes from water, not

text: carbon dioxide

text: . He also studied the role of

text: molybdenum

text: in biological

text: nitrogen fixation

text: , the biochemistry of cytochromes and their in photosynthesis and

text: metabolism

text: , the role of iron in the activity of

text: porphyrin

text: compounds in plants and animals, and

text: calcium

text: exchange in cancerous

text: tumor

text: s.

text: Kalckar was fortunate to be working at an important period in biochemistry's evolution. The biochemical community was in the process of demonstrating the chemical reactions involved in breakdown of foodstuffs essential for growth. At the same time, physiologists were demonstrating the involvement of some of these reactions various physiological processes, e.g. muscle contraction. Kalckar's breakthrough work was the demonstration that organic compounds, which were phosphorylated during metabolic processes, involved oxygen consumption; oxygen consumption was linked to organic compound phosphorylation. His key experiment demonstrated that in frog muscles where glycolysis had been inhibited with iodoacetate, muscular contraction continued for a short period using phosphocreatine as a source of energy. Kalckar referred to this process as “aerobic phosphorylation” (now called oxidative phosphorylation, a biochemical process fundamental to all living organisms). The work was the first demonstration that carbohydrate oxidation and carbohydrate phosphorylation were linked, i.e. the two pathways were directly “coupled.”  Furthermore, the study helped establish the basic phenomenon of oxidative phosphorylation, opened the way for its systematic exploration, and suggested for the first time that phosphate compounds acted as a link between catabolism and anabolism.

text: Kalckar was fortunate to be working at an important period in biochemistry's evolution. The biochemical community was in the process of demonstrating the chemical reactions involved in breakdown of foodstuffs essential for growth. At the same time, physiologists were demonstrating the involvement of some of these reactions various physiological processes, e.g. muscle contraction. Kalckar's breakthrough work was the demonstration that organic compounds, which were phosphorylated during metabolic processes, involved oxygen consumption; oxygen consumption was linked to organic compound phosphorylation. His key experiment demonstrated that in frog muscles where

text: glycolysis

text: had been

text: inhibited

text: with

text: iodoacetate

text: , muscular contraction continued for a short period using

text: phosphocreatine

text: as a source of energy. Kalckar referred to this process as “aerobic phosphorylation” (now called oxidative phosphorylation, a biochemical process fundamental to all living organisms). The work was the first demonstration that carbohydrate oxidation and carbohydrate phosphorylation were linked, i.e. the two pathways were directly “coupled.”  Furthermore, the study helped establish the basic phenomenon of oxidative phosphorylation, opened the way for its systematic exploration, and suggested for the first time that phosphate compounds acted as a link between

text: catabolism

text: and

text: anabolism

text: The reaction is involved in the aerobic catabolism of nicotinic acid.

text: The reaction is involved in the aerobic

text: catabolism

text: of

text: nicotinic acid

text: The overall catabolic reaction catalyzed by the BCKDC is shown in Figure 1.

text: For many years it had been known that bacterial and other cells could respond to external conditions by regulating levels of their key metabolic enzymes, and/or the activity of these enzymes. For instance, if a bacterium finds itself in a broth containing lactose, rather than the simpler sugar glucose, it must adapt itself to the need to 1(import lactose, 2) cleave lactose to its constituents glucose and galactose, and 3) convert the galactose to glucose. It was known that cells ramp up their production of the enzymes that do these steps when exposed to lactose, rather than wastefully producing these enzymes all the time. Studies of enzyme activity control were progressing through theories of the (allosteric) action of small molecules on the enzyme molecule itself (switching it on or off), but the method of controlling the enzyme production was not well understood at the time.

text: For many years it had been known that

text: bacteria

text: l and other cells could respond to external conditions by regulating levels of their key

text: metabolic

text: enzyme

text: s, and/or the activity of these

text: enzyme

text: s. For instance, if a bacterium finds itself in a

text: broth

text: containing

text: lactose

text: , rather than the simpler sugar

text: glucose

text: , it must adapt itself to the need to 1(import lactose, 2) cleave lactose to its constituents glucose and

text: galactose

text: , and 3) convert the galactose to glucose. It was known that cells ramp up their production of the enzymes that do these steps when exposed to lactose, rather than wastefully producing these enzymes all the time. Studies of enzyme activity control were progressing through theories of the (allosteric) action of small

text: molecule

text: s on the enzyme molecule itself (switching it on or off), but the method of controlling the enzyme production was not well understood at the time.

text: The chemistry involved in the formation of these isopeptide bonds also tend to fall into these two categories. In the case of ubiquitin and ubiquitin-like proteins, tend to have a structured pathway of continuously passing along the peptide with a series of reactions, using multiple intermediate enzymes to reach the target protein for the conjugation reaction. The structural enzymes while varying from bacterial and eukaryotic domains, tend to be single enzymes that generally in a single step, fuse the two substrates together for a larger repetitive process of linking and inter-linking the said substrates to form and influence large macromolecular structures.

text: In general, bioluminescence is caused by the action of luciferases, enzymes that produce light by the oxidation of a luciferin (a pigment). Several studies have evaluated the biochemical basis of light production in Panellus stipticus, and concluded that there is no specific fungal luciferase. The fungus was shown in 1988 to contain the sesquiterpene panal, which has a cadinene keto-aldehyde chemical structure. Later, two additional precursors were isolated, PS-A (1-O-decanoylpanal) and PS-B (1-O-dodecanoylpanal). If these compounds are treated with salt of ammonia or primary amines in the presence of iron(II), hydrogen peroxide, and a cationic surfactant, light is emitted by a chemiluminescence reaction, suggesting that panal and its derivatives are fungal luciferins, and that the chemiluminescence reaction is the cause of in vivo bioluminescence. In the fungus, the level of activity of the enzyme superoxide dismutase (SOD) appears to play a critical role in the amount of light emission. SOD quenches the effect of the superoxide (O) anion required in the reaction, and thus SOD activity has to be inhibited for the reaction to occur.

text: In general, bioluminescence is caused by the action of

text: luciferase

text: s, enzymes that produce light by the

text: oxidation

text: of a

text: luciferin

text: (a

text: pigment

text: ). Several studies have evaluated the biochemical basis of light production in Panellus stipticus, and concluded that there is no specific fungal luciferase. The fungus was shown in 1988 to contain the

text: sesquiterpene

text: panal, which has a

text: cadinene

text: keto-aldehyde chemical structure. Later, two additional precursors were isolated, PS-A (1-O-decanoylpanal) and PS-B (1-O-dodecanoylpanal). If these compounds are treated with salt of

text: ammonia

text: or

text: primary amine

text: s in the presence of

text: iron(II)

text: hydrogen peroxide

text: , and a cationic

text: surfactant

text: , light is emitted by a

text: chemiluminescence

text: reaction, suggesting that panal and its derivatives are fungal luciferins, and that the chemiluminescence reaction is the cause of

text: in vivo

text: bioluminescence. In the fungus, the level of activity of the enzyme

text: superoxide dismutase

text: (SOD) appears to play a critical role in the amount of light emission. SOD quenches the effect of the

text: superoxide

text: (O) anion required in the reaction, and thus SOD activity has to be inhibited for the reaction to occur.

text: Biotic metabolism is directly tied to the global cycling of elements and compounds on Earth. The geochemical environment fuels life, which then produces different molecules that go into the external environment. (This is directly relevant to biogeochemistry.) In addition, biochemical reactions are catalyzed by enzymes which sometimes prefer one isotope over others. For example, oxygenic photosynthesis is catalyzed by RuBisCO, which prefers carbon-12 over carbon-13, resulting in carbon isotope fractionation in the rock record.

text: Biotic metabolism is directly tied to the global cycling of elements and compounds on Earth. The geochemical environment fuels life, which then produces different molecules that go into the external environment. (This is directly relevant to

text: biogeochemistry

text: .) In addition, biochemical reactions are catalyzed by enzymes which sometimes prefer one isotope over others. For example, oxygenic photosynthesis is catalyzed by

text: RuBisCO

text: , which prefers carbon-12 over carbon-13, resulting in carbon isotope fractionation in the rock record.

text: Vitamin K, the precursor of most vitamin K in nature, is a stereoisomer of phylloquinone, an important chemical in green plants, where it functions as an electron acceptor in photosystem I during photosynthesis. For this reason, vitamin K is found in large quantities in the photosynthetic tissues of plants (green leaves, and dark green leafy vegetables such as romaine lettuce, kale and spinach), but it occurs in far smaller quantities in other plant tissues (roots, fruits, etc.). Iceberg lettuce contains relatively little. The function of phylloquinone in plants appears to have no resemblance to its later metabolic and biochemical function (as "vitamin K") in animals, where it performs a completely different biochemical reaction.

text: Vitamin K, the precursor of most vitamin K in nature, is a

text: stereoisomer

text: of

text: phylloquinone

text: , an important chemical in green plants, where it functions as an electron acceptor in

text: photosystem I

text: during

text: photosynthesis

text: . For this reason, vitamin K is found in large quantities in the photosynthetic tissues of plants (green leaves, and dark green leafy vegetables such as

text: romaine lettuce

text: , kale and spinach), but it occurs in far smaller quantities in other plant tissues (roots, fruits, etc.).

text: Iceberg lettuce

text: contains relatively little. The function of phylloquinone in plants appears to have no resemblance to its later metabolic and biochemical function (as "vitamin K") in animals, where it performs a completely different biochemical reaction.

text: Although initial reports suggested meldonium is a non-competitive and non-hydroxylatable analogue of gamma-butyrobetaine; further studies have identified that meldonium is a substrate for gamma-butyrobetaine dioxygenase. X-ray crystallographic and in vitro biochemical studies suggest that meldonium binds to the substrate pocket of γ-butyrobetaine hydroxylase and acts as an alternative substrate, and therefore a competitive inhibitor. Normally, this enzyme's action on its substrates γ-butyrobetaine and 2-oxoglutarate gives, in the presence of the further substrate oxygen, the products L-carnitine, succinate, and carbon dioxide; in the presence of this alternate substrate, the reaction yields malonic acid semialdehyde, formaldehyde (akin to the action of histone demethylases), dimethylamine, and (1-methylimidazolidin-4-yl)acetic acid, "an unexpected product with an additional carbon-carbon bond resulting from N-demethylation coupled to oxidative rearrangement, likely via an unusual radical mechanism." The unusual mechanism is thought likely to involve a Steven's type rearrangement.

text: Although initial reports suggested meldonium is a

text: non-competitive

text: and non-hydroxylatable analogue of gamma-butyrobetaine; further studies have identified that meldonium is a substrate for

text: gamma-butyrobetaine dioxygenase

text: . X-ray crystallographic and in vitro biochemical studies suggest that meldonium binds to the substrate pocket of γ-butyrobetaine hydroxylase and acts as an alternative

text: substrate

text: , and therefore a

text: competitive inhibitor

text: . Normally, this enzyme's action on its substrates γ-butyrobetaine and 2-oxoglutarate gives, in the presence of the further substrate oxygen, the products L-carnitine, succinate, and carbon dioxide; in the presence of this alternate substrate, the reaction yields malonic acid semialdehyde,

text: formaldehyde

text: (akin to the action of histone

text: demethylase

text: s),

text: dimethylamine

text: , and (1-methylimidazolidin-4-yl)acetic acid, "an unexpected product with an additional carbon-carbon bond resulting from N-demethylation coupled to oxidative rearrangement, likely via an unusual radical mechanism." The unusual mechanism is thought likely to involve a

text: Steven's type rearrangement

text: In physiology, respiration is defined as the movement of oxygen from the outside air to the cells within tissues, and the transport of carbon dioxide in the opposite direction.

text: In

text: physiology

text: , respiration is defined as the movement of oxygen from the outside air to the cells within

text: tissue

text: s, and the

text: transport

text: of

text: carbon dioxide

text: in the opposite direction.

text: Hydrogen ions drive ATP synthase in photosynthesis. This happens when hydrogen ions get pushed across the membrane creating a high concentration inside the thylakoid membrane and a low concentration in the cytoplasm. However, because of osmosis the H+ will force itself out of the membrane through ATP synthase. Utilizing their kinetic energy to escape, the protons will spin the ATP synthase which in turn will create ATP. This happens in cellular respiration as well though the concentrated membrane will instead be the inner membrane of the mitochondria.

text: Hydrogen ions drive

text: ATP synthase

text: in

text: photosynthesis

text: . This happens when hydrogen ions get pushed across the membrane creating a high concentration inside the

text: thylakoid membrane

text: and a low concentration in the cytoplasm. However, because of osmosis the H+ will force itself out of the membrane through ATP synthase. Utilizing their

text: kinetic energy

text: to escape, the protons will spin the ATP synthase which in turn will create

text: ATP

text: . This happens in

text: cellular respiration

text: as well though the concentrated membrane will instead be the inner membrane of the

text: mitochondria

text: Recently, large pharmaceutical process chemists have relied heavily on the development of enzymatic reactions to produce important chiral building blocks for API synthesis. Many varied classes of naturally occurring enzymes have been co-opted and engineered for process pharmaceutical chemistry applications. The widest range of applications come from ketoreductases and transaminases, but there are isolated examples from hydrolases, aldolases, oxidative enzymes, esterases and dehalogenases, among others.

text: Recently, large pharmaceutical process chemists have relied heavily on the development of enzymatic reactions to produce important chiral building blocks for API synthesis. Many varied classes of naturally occurring enzymes have been co-opted and engineered for process pharmaceutical chemistry applications. The widest range of applications come from

text: ketoreductases

text: and

text: transaminase

text: s, but there are isolated examples from

text: hydrolases

text: aldolase

text: s, oxidative enzymes,

text: esterase

text: s and

text: dehalogenase

text: s, among others.

text: Water is fundamental to photosynthesis and respiration. Photosynthetic cells use the sun's energy to split off water's hydrogen from oxygen. Hydrogen is combined with CO (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the sun's energy and reform water and CO in the process (cellular respiration).

text: The Petersen matrix is a comprehensive description of systems of biochemical reactions used to model reactors for pollution control (engineered decomposition) as well as in environmental systems. It has got as many columns as the number of relevant involved components (chemicals, pollutants, biomasses, gases) and as many rows as the number of involved processes (biochemical reactions and physical degradation). One further column is added to host the description of the kinetics of each transformation (rate equation).

text: The Petersen matrix is a comprehensive description of systems of

text: biochemical reactions

text: used to model

text: reactors

text: for

text: pollution control

text: (engineered

text: decomposition

text: ) as well as in

text: environmental systems

text: . It has got as many columns as the number of relevant involved components (

text: chemicals

text: pollutants

text: biomass

text: es,

text: gases

text: ) and as many rows as the number of involved

text: processes

text: (biochemical reactions and physical degradation). One further column is added to host the description of the

text: kinetics

text: of each transformation (

text: rate equation

text: The tertiary structure of proteins deal with their folding process and how the overall molecule is arranged.  Finally, a quaternary structure is a group of tertiary proteins coming together and binding.With all of these levels, proteins have a wide variety of places in which they can be manipulated and adjusted.  Techniques are used to affect the amino acid sequence of the protein (site-directed mutagenesis), the folding and conformation of the protein, or the folding of a single tertiary protein within a quaternary protein matrix.  Proteins that are the main focus of manipulation are typically enzymes.  These are proteins that act as catalysts for biochemical reactions.  By manipulating these catalysts, the reaction rates, products, and effects can be controlled. Enzymes and proteins are important to the biological field and research that there are specific subsets of engineering focusing only on proteins and enzymes.

text: The tertiary structure of proteins deal with their folding process and how the overall molecule is arranged.  Finally, a quaternary structure is a group of tertiary proteins coming together and binding.With all of these levels, proteins have a wide variety of places in which they can be manipulated and adjusted.  Techniques are used to affect the amino acid sequence of the protein (site-directed mutagenesis), the folding and conformation of the protein, or the folding of a single tertiary protein within a quaternary protein matrix.  Proteins that are the main focus of manipulation are typically

text: enzymes

text: .  These are proteins that act as

text: catalysts

text: for

text: biochemical reaction

text: s.  By manipulating these catalysts, the reaction rates, products, and effects can be controlled. Enzymes and proteins are important to the biological field and research that there are specific subsets of engineering focusing only on proteins and enzymes.

text: Otto Heinrich Warburg and Dean Burk discovered the I-quantum photosynthesis reaction that splits the CO, activated by the respiration.

text: Otto Heinrich Warburg

text: and

text: Dean Burk

text: discovered the I-quantum photosynthesis reaction that splits the CO, activated by the respiration.

text: German-British medical doctor and biochemist Hans Krebs' 1957 book Energy Transformations in Living Matter (written with Hans Kornberg) was the first major publication on the thermodynamics of biochemical reactions. In addition, the appendix contained the first-ever published thermodynamic tables, written by Kenneth Burton, to contain equilibrium constants and Gibbs free energy of formations for chemical species, able to calculate biochemical reactions that had not yet occurred.

text: German-British medical doctor and biochemist

text: Hans Krebs

text: ' 1957 book Energy Transformations in Living Matter (written with

text: Hans Kornberg

text: ) was the first major publication on the thermodynamics of biochemical reactions. In addition, the appendix contained the first-ever published thermodynamic tables, written by

text: Kenneth Burton

text: , to contain equilibrium constants and

text: Gibbs free energy

text: of formations for

text: chemical specie

text: s, able to calculate

text: biochemical reaction

text: s that had not yet occurred.

text: Cells vary in the metabolites they contain, which are the intermediary compounds and end products of complex biochemical reactions that sustain the cell. Genetically identical cells in different conditions and environments can use different metabolic pathways to sustain themselves. By measuring the metabolites present, scientists can infer the metabolic pathways used, and infer useful information about the state of the cell. An example of this is found in the immune system, where CD4+ cells can differentiate into Th17 or TReg cells (among other possibilities), both of which direct the immune system’s response in different ways. Th17 cells stimulate a strong inflammatory response, whereas TReg cells stimulate the opposite effect. The former tend to rely much more on glycolysis, due to their increased energy demands.

text: Cells vary in the

text: metabolites

text: they contain, which are the intermediary compounds and end products of complex biochemical reactions that sustain the cell. Genetically identical cells in different conditions and environments can use different metabolic pathways to sustain themselves. By measuring the metabolites present, scientists can infer the metabolic pathways used, and infer useful information about the state of the cell. An example of this is found in the immune system, where

text: CD4+ cells

text: can differentiate into Th17 or TReg cells (among other possibilities), both of which direct the immune system’s response in different ways. Th17 cells stimulate a strong inflammatory response, whereas TReg cells stimulate the opposite effect. The former tend to rely much more on

text: glycolysis

text: , due to their increased energy demands.

text: He received his Ph.D in organic chemistry from Basel University, Switzerland in 1940. Being Jewish, Basel provided a safe haven for him during the Second World War and he stayed there until 1947 as Assistant to Professor Hans Friedrich Albrecht Erlenmeyer (1900 - 1967), the son of Friedrich Gustav Carl Emil Erlenmeyer (Emil Jr.) and grandson of Richard August Carl Emil Erlenmeyer (Emil Sr.). During his time there he compiled the data for the first two volumes of "Synthetische Methoden der Organische Chemie" published by S. Karger Verlag in Basel in 1946 and 1948. These built on the system of Conrad Weygand (Organic Preparations, Interscience Publishers, Inc., New York, 1945) for grouping similar reactions together, but used "Theilheimer reaction symbols" that summarised the most significant bond formed, the reaction type (addition reaction, rearrangement reaction, exchange reaction/substitution reaction or elimination reaction), and the bond broken or fragment lost, as well as a specific reagent order based on the periodic table.

text: He received his Ph.D in organic chemistry from

text: Basel University

text: , Switzerland in 1940. Being Jewish, Basel provided a safe haven for him during the

text: Second World War

text: and he stayed there until 1947 as Assistant to Professor

text: Hans Friedrich Albrecht Erlenmeyer

text: (1900 - 1967), the son of

text: Friedrich Gustav Carl Emil Erlenmeyer

text: (Emil Jr.) and grandson of

text: Richard August Carl Emil Erlenmeyer

text: (Emil Sr.). During his time there he compiled the data for the first two volumes of "Synthetische Methoden der Organische Chemie" published by S. Karger Verlag in Basel in 1946 and 1948. These built on the system of

text: Conrad Weygand

text: (Organic Preparations, Interscience Publishers, Inc., New York, 1945) for grouping similar reactions together, but used "Theilheimer reaction symbols" that summarised the most significant bond formed, the reaction type (

text: addition reaction

text: rearrangement reaction

text: exchange reaction

text: substitution reaction

text: or

text: elimination reaction

text: ), and the bond broken or fragment lost, as well as a specific reagent order based on the

text: periodic table

text: Matthaei was born in Kensington in a family of German, Swiss and French ancestry. She was the daughter of the commission merchant Carl Hermann Ernst Matthaei and the musician Louise Henriette Elizabeth Sueur, and had a brother and three younger sisters, including Louise Howard. Matthaei attended North London Collegiate School for Girls and Newnham College, Cambridge, and later worked as assistant to Frederick Blackman, producing significant work on cellular respiration. Between 1902 and 1905, Blackman and Matthaei set out to discover the role of temperature in photosynthesis and performed the first such experiments, finding that carbon fixation is based on biochemical reactions which depend on temperature. Although the experiment is inaccurately known as the Blackman Reaction, a significant part of the work was carried out by Matthaei and the 1904 paper communicated to the Royal Society by Francis Darwin bears only her name.

text: Matthaei was born in

text: Kensington

text: in a family of German, Swiss and French ancestry. She was the daughter of the commission merchant Carl Hermann Ernst Matthaei and the musician Louise Henriette Elizabeth Sueur, and had a brother and three younger sisters, including

text: Louise Howard

text: . Matthaei attended

text: North London Collegiate School for Girls

text: and

text: Newnham College, Cambridge

text: , and later worked as assistant to

text: Frederick Blackman

text: , producing significant work on

text: cellular respiration

text: . Between 1902 and 1905, Blackman and Matthaei set out to discover the role of temperature in

text: photosynthesis

text: and performed the first such experiments, finding that

text: carbon fixation

text: is based on biochemical reactions which depend on temperature. Although the experiment is inaccurately known as the Blackman Reaction, a significant part of the work was carried out by Matthaei and the 1904 paper communicated to the

text: Royal Society

text: by

text: Francis Darwin

text: bears only her name.

text: Aposhian's first academic appointment was to Vanderbilt University School of Medicine, and he was an instructor there from 1954 to 1956. Some of his research has been published in the Journal of Virology, and in the autism omnibus trial he testified that he was "the first one to show that a virus could transfer genetic information that was not in it originally." He also testified that he acted as a biochemical geneticist from 1959 until he went to teach at Tufts University in 1967, during which time he was affiliated with Stanford University. He would leave Tufts in 1970 to become department chair at the University of Maryland School of Medicine. He has published more than 100 peer-reviewed studies on heavy metal poisoning. In 1964, Aposhian, along with, notably Arthur Kornberg, both of whom were affiliated with Stanford University at the time, published "Enzymatic Synthesis of Deoxyribonucleic Acid" in the Journal of Biological Chemistry. Kornberg would go on to win the Nobel Prize for discovering the biological mechanism by which DNA is synthesized. His more recent research has focused on the metabolism of arsenic compounds, in particular, deciphering polymorphisms in the gene that codes for glutathione S-transferase, which is involved in arsenic detoxification. Some of this research he has authored along with his wife, Mary M. Aposhian, who died in 2009. He has extensive research experience and publications dealing with the toxicology of heavy metals, in particular arsenic and mercury. This has included enzymology of arsenic biotransformation; the study of human populations in Chile, Inner Mongolia, Romania, Mexico and rural Southwest China as to their body burden of arsenic or mercury; the human metabolism of chelating agents; and biochemical genetics in particular gene transfer in mammalian cells.

text: Aposhian's first academic appointment was to

entity_name: Vanderbilt University School of Medicine

text: Vanderbilt University School of Medicine

text: , and he was an instructor there from 1954 to 1956. Some of his research has been published in the

text: Journal of Virology

text: , and in the

entity_name: Cedillo v. Secretary of Health and Human Services

text: autism omnibus trial

text: he testified that he was "the first one to show that a virus could transfer genetic information that was not in it originally." He also testified that he acted as a

text: biochemical geneticist

text: from 1959 until he went to teach at

text: Tufts University

text: in 1967, during which time he was affiliated with Stanford University. He would leave Tufts in 1970 to become department chair at the

entity_section: University of Maryland School of Medicine

text: University of Maryland School of Medicine

text: . He has published more than 100 peer-reviewed studies on heavy metal poisoning. In 1964, Aposhian, along with, notably

text: Arthur Kornberg

text: , both of whom were affiliated with

text: Stanford University

text: at the time, published "Enzymatic Synthesis of Deoxyribonucleic Acid" in the

text: Journal of Biological Chemistry

text: . Kornberg would go on to win the

text: Nobel Prize

text: for discovering the biological mechanism by which DNA is synthesized. His more recent research has focused on the metabolism of

text: arsenic

text: compounds, in particular, deciphering polymorphisms in the gene that codes for

text: glutathione S-transferase

text: , which is involved in arsenic detoxification. Some of this research he has authored along with his wife, Mary M. Aposhian, who died in 2009. He has extensive research experience and publications dealing with the toxicology of heavy metals, in particular arsenic and mercury. This has included enzymology of arsenic biotransformation; the study of human populations in Chile, Inner Mongolia, Romania, Mexico and rural Southwest China as to their body burden of arsenic or mercury; the human metabolism of chelating agents; and biochemical genetics in particular gene transfer in mammalian cells.

text: Physical organic chemistry, a term coined by Louis Hammett in 1940, refers to a discipline of organic chemistry that focuses on the relationship between chemical structures and reactivity, in particular, applying experimental tools of physical chemistry to the study of organic molecules. Specific focal points of study include the rates of organic reactions, the relative chemical stabilities of the starting materials, reactive intermediates, transition states, and products of chemical reactions, and non-covalent aspects of solvation and molecular interactions that influence chemical reactivity. Such studies provide theoretical and practical frameworks to understand how changes in structure in solution or solid-state contexts impact reaction mechanism and rate for each organic reaction of interest. Physical organic chemists use theoretical and experimental approaches work to understand these foundational problems in organic chemistry, including classical and statistical thermodynamic calculations, quantum mechanical theory and computational chemistry, as well as experimental spectroscopy (e.g., NMR), spectrometry (e.g., MS), and crystallography approaches. The field therefore has applications to a wide variety of more specialized fields, including electro- and photochemistry, polymer and supramolecular chemistry, and bioorganic chemistry, enzymology, and chemical biology, as well as to commercial enterprises involving process chemistry, chemical engineering, materials science and nanotechnology, and drug discovery.

text: Physical organic chemistry, a term coined by

text: Louis Hammett

text: in 1940, refers to a discipline of

text: organic chemistry

text: that focuses on the relationship between

text: chemical structure

text: s and

text: reactivity

text: , in particular, applying experimental tools of

text: physical chemistry

text: to the study of

text: organic molecules

text: . Specific focal points of study include the

text: rates

text: of

text: organic reactions

text: , the relative

text: chemical stabilities

text: of the starting materials,

text: reactive intermediate

text: s,

text: transition state

text: s, and products of

text: chemical reaction

text: s, and non-covalent aspects of

text: solvation

text: and

text: molecular interaction

text: s that influence chemical reactivity. Such studies provide theoretical and practical frameworks to understand how changes in structure in solution or solid-state contexts impact

text: reaction mechanism

text: and

text: rate

text: for each

text: organic reaction

text: of interest. Physical organic chemists use theoretical and experimental approaches work to understand these foundational problems in

text: organic chemistry

text: , including classical and statistical

text: thermodynamic

text: calculations,

text: quantum mechanical theory

text: and

text: computational chemistry

text: , as well as experimental

text: spectroscopy

text: (e.g.,

text: NMR

text: spectrometry

text: (e.g.,

text: MS

text: ), and

text: crystallography

text: approaches. The field therefore has applications to a wide variety of more specialized fields, including

text: electro-

text: and

text: photochemistry

text: polymer

text: and

text: supramolecular chemistry

text: , and

text: bioorganic chemistry

text: enzymology

text: , and

text: chemical biology

text: , as well as to commercial enterprises involving

text: process chemistry

text: chemical engineering

text: materials science

text: and

text: nanotechnology

text: , and

text: drug discovery

text: Histochemistry uses knowledge about biochemical reaction properties of the chemical constituents of the brain (including notably enzymes) to apply selective methods of reaction to visualize where they occur in the brain and any functional or pathological changes. This applies importantly to molecules related to neurotransmitter production and metabolism, but applies likewise in many other directions chemoarchitecture, or chemical neuroanatomy.

text: Histochemistry

text: uses knowledge about biochemical reaction properties of the chemical constituents of the brain (including notably enzymes) to apply selective methods of reaction to visualize where they occur in the brain and any functional or pathological changes. This applies importantly to molecules related to neurotransmitter production and metabolism, but applies likewise in many other directions chemoarchitecture, or chemical neuroanatomy.

text: From a biological standpoint, water has many distinct properties that are critical for the proliferation of life. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the body's solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Without water, these particular metabolic processes could not exist.

text: From a

text: biological

text: standpoint, water has many distinct properties that are critical for the proliferation of

text: life

text: . It carries out this role by allowing

text: organic compound

text: s to react in ways that ultimately allow

text: replication

text: . All known forms of life depend on water. Water is vital both as a

text: solvent

text: in which many of the body's solutes dissolve and as an essential part of many

text: metabolic

text: processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Without water, these particular metabolic processes could not exist.

text: The first cacti are thought to have been only slightly succulent shrubs or small trees whose leaves carried out photosynthesis. They lived in tropical areas that experienced periodic drought. If Pereskia clade A is a good model of these early cacti, then, although they would have appeared superficially similar to other trees growing nearby, they had already evolved strategies to conserve water (some of which are present in members of other families in the order Caryophyllales). These strategies included being able to respond rapidly to periods of rain, and keeping transpiration low by using water very efficiently during photosynthesis. The latter was achieved by tightly controlling the opening of stomata. Like Pereskia species today, early ancestors may have been able to switch from the normal C mechanism, where carbon dioxide is used continuously in photosynthesis, to CAM cycling, in which when the stomata are closed, carbon dioxide produced by respiration is stored for later use in photosynthesis.

text: The first cacti are thought to have been only slightly succulent shrubs or small trees whose leaves carried out photosynthesis. They lived in tropical areas that experienced periodic drought. If Pereskia clade A is a good model of these early cacti, then, although they would have appeared superficially similar to other trees growing nearby, they had already evolved strategies to conserve water (some of which are present in members of other families in the order

text: Caryophyllales

text: ). These strategies included being able to respond rapidly to periods of rain, and keeping transpiration low by using water very efficiently during photosynthesis. The latter was achieved by tightly controlling the opening of stomata. Like Pereskia species today, early ancestors may have been able to switch from the normal C mechanism, where carbon dioxide is used continuously in photosynthesis, to CAM cycling, in which when the stomata are closed, carbon dioxide produced by respiration is stored for later use in photosynthesis.

text: Several catabolic pathways converge on the TCA cycle. Most of these reactions add intermediates to the TCA cycle, and are therefore known as anaplerotic reactions, from the Greek meaning to "fill up".  These increase the amount of acetyl CoA that the cycle is able to carry, increasing the mitochondrion's capability to carry out respiration if this is otherwise a limiting factor. Processes that remove intermediates from the cycle are termed "cataplerotic" reactions.

text: Several

text: catabolic

text: pathways converge on the TCA cycle. Most of these reactions add intermediates to the TCA cycle, and are therefore known as

text: anaplerotic reactions

text: , from the Greek meaning to "fill up".  These increase the amount of acetyl CoA that the cycle is able to carry, increasing the mitochondrion's capability to carry out respiration if this is otherwise a limiting factor. Processes that remove intermediates from the cycle are termed "cataplerotic" reactions.

text: Endothelin-converting enzyme 1 (, endothelin-converting enzyme, ECE-1) is an enzyme. This enzyme catalyses the following chemical reaction

text: Endothelin-converting enzyme 1 (, endothelin-converting enzyme, ECE-1) is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: The clinical data includes information on >10,000 metabolite-biofluid concentrations and metabolite concentration information on more than 600 different human diseases. The biochemical data includes 5,688 protein (and DNA) sequences and more than 5000 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the HMDB contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, MetaCyc, PubChem, Protein Data Bank, ChEBI, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches. It has been widely used in metabolomics, clinical chemistry, biomarker discovery and general biochemistry education.

text: The clinical data includes information on >10,000 metabolite-

text: biofluid

text: concentrations and metabolite concentration information on more than 600 different human

text: diseases

text: . The biochemical data includes 5,688

text: protein

text: (and

text: DNA

text: ) sequences and more than 5000

text: biochemical reaction

text: s that are linked to these metabolite entries. Each metabolite entry in the HMDB contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (

text: KEGG

text: MetaCyc

text: PubChem

text: Protein Data Bank

text: ChEBI

text: Swiss-Prot

text: , and

text: GenBank

text: ) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, spectral,

text: chemical structure

text: and

text: relational query

text: searches. It has been widely used in metabolomics,

text: clinical chemistry

text: biomarker

text: discovery and general biochemistry education.

text: In nuclear physics and nuclear chemistry, a nuclear reaction is semantically considered to be the process in which two nuclei, or else a nucleus of an atom and a subatomic particle (such as a proton, neutron, or high energy electron) from outside the atom, collide to produce one or more nuclides that are different from the nuclide(s) that began the process. Thus, a nuclear reaction must cause a transformation of at least one nuclide to another. If a nucleus interacts with another nucleus or particle and they then separate without changing the nature of any nuclide, the process is simply referred to as a type of nuclear scattering, rather than a nuclear reaction.

text: In

text: nuclear physics

text: and

text: nuclear chemistry

text: , a nuclear reaction is semantically considered to be the process in which two

text: nuclei

text: , or else a nucleus of an atom and a

text: subatomic particle

text: (such as a proton,

text: neutron

text: , or high

text: energy

text: electron

text: ) from outside the atom, collide to produce one or more

text: nuclide

text: s that are different from the nuclide(s) that began the process. Thus, a nuclear reaction must cause a transformation of at least one

text: nuclide

text: to another. If a nucleus interacts with another nucleus or particle and they then separate without changing the nature of any nuclide, the process is simply referred to as a type of nuclear

text: scattering

text: , rather than a nuclear reaction.

text: There are many receptors on the surface membrane capable of binding IL-8; the most frequently studied types are the G protein-coupled serpentine receptors CXCR1 and CXCR2. Expression and affinity for IL-8 differs between the two receptors (CXCR1 > CXCR2). Through a chain of biochemical reactions, IL-8 is secreted and is an important mediator of the immune reaction in the innate immune system response.

text: There are many receptors on the surface membrane capable of binding IL-8; the most frequently studied types are the

text: G protein-coupled

text: serpentine receptors

text: and

text: . Expression and affinity for IL-8 differs between the two receptors (CXCR1 > CXCR2). Through a chain of biochemical reactions, IL-8 is secreted and is an important mediator of the immune reaction in the innate immune system response.

text: Numerous biological processes involve ET reactions. These processes include oxygen binding, photosynthesis, respiration, and detoxification.  Additionally, the process of energy transfer can be formalized as a two-electron exchange (two concurrent ET events in opposite directions) in case of small distances between the transferring molecules.  ET reactions commonly involve transition metal complexes, but there are now many examples of ET in organic chemistry.

text: Numerous

text: biological process

text: es involve ET reactions. These processes include oxygen binding,

text: photosynthesis

text: respiration

text: , and detoxification.  Additionally, the process of

text: energy transfer

text: can be formalized as a two-electron exchange (two concurrent ET events in opposite directions) in case of small distances between the transferring molecules.  ET reactions commonly involve

text: transition metal complex

text: es, but there are now many examples of ET in

text: organic chemistry

text: For example, consider an enzyme with multiple alleles in the population. Each allele catalyzes the same reaction, but with a different level of activity. However, even after millions of years of evolution, exploring many sequences with similar function, no mutation might exist that gives this enzyme the ability to catalyze a different reaction. Thus, although the enzyme’s activity is evolvable in the first sense, that does not mean that the enzyme's function is evolvable in the second sense. However, every system evolvable in the second sense must also be evolvable in the first.

text: For example, consider an

text: enzyme

text: with multiple

text: alleles

text: in the population. Each allele catalyzes the same reaction, but with a different level of activity. However, even after millions of years of evolution, exploring many sequences with similar function, no mutation might exist that gives this enzyme the ability to catalyze a different reaction. Thus, although the enzyme’s activity is evolvable in the first sense, that does not mean that the enzyme's function is evolvable in the second sense. However, every system evolvable in the second sense must also be evolvable in the first.

text: Charles Cagniard-Latour, Theodor Schwann and Friedrich Traugott Kützing  identified independently yeast as a living organism that nourishes itself by the sugar it ferments, a process which referred to the ethanol fermentation (alcoholic fermentation). Liebig, Berzelius, and Wohler rejected the ideas of Schwann, Latour and Kutzing. In 1839, Liebig and Wohler published a paper on the role of yeast in alcoholic fermentation. In 1858, Liebig’s student Moritz Traube enunciated the theorem, which was used for alcoholic fermentation, that all fermentations produced by living organisms are based on chemical reactions rather than a vital force itself.	The dispute between Liebig and Pasteur had, in a way, slowed down the advances of science and medicine in the area of fermentation, alcohol fermentation, and the enzymes. On the other hand, the conflicting ideas sped up the research in the area of fermentation and enzymes through other scientists and chemists. Through Büchner and his experiment in fermentation, the world of science and medicine went further as to pave ways in enzyme and fermentation studies and marked one of the critical points of the history of modern chemistry.

text: Charles Cagniard-Latour

text: Theodor Schwann

text: and

text: Friedrich Traugott Kützing

text: identified independently yeast as a living organism that nourishes itself by the sugar it ferments, a process which referred to the

text: ethanol fermentation

text: (alcoholic fermentation). Liebig, Berzelius, and Wohler rejected the ideas of Schwann, Latour and Kutzing. In 1839, Liebig and Wohler published a paper on the role of yeast in alcoholic fermentation. In 1858, Liebig’s student

text: Moritz Traube

text: enunciated the theorem, which was used for alcoholic fermentation, that all fermentations produced by living organisms are based on chemical reactions rather than a vital force itself.	The dispute between Liebig and Pasteur had, in a way, slowed down the advances of science and medicine in the area of fermentation, alcohol fermentation, and the enzymes. On the other hand, the conflicting ideas sped up the research in the area of fermentation and enzymes through other scientists and chemists. Through Büchner and his experiment in fermentation, the world of science and medicine went further as to pave ways in enzyme and fermentation studies and marked one of the critical points of the history of modern chemistry.

text: Group specificity occurs when an enzyme will only reacts with molecules that have specific functional groups, such as aromatic structures, phosphate groups, and methyls. One example is Pepsin, an enzyme that is crucial in digestion of foods ingested in our diet, that hydrolyzes peptide bonds in between hydrophobic amino acids, with recognition for aromatic side chains such as phenylalanine, tryptophan, and tyrosine. Another example is hexokinase, in enzyme involved in glycolysis that phosphorylate glucose to produce glucose-6-phosphate. This enzyme exhibits group specificity by allowing multiple hexoses (6 carbon sugars) as its substrate. Glucose is one of the most important substrates in metabolic pathways involving hexokinase due to its role in glycolysis, but is not the only substrate that hexokinase can catalyze a reaction with.

text: The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or to signals from other cells.

text: The chemical reactions of metabolism are organized into

text: metabolic pathway

text: s, in which one chemical is transformed through a series of steps into another chemical, by a sequence of

text: enzyme

text: s. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require

text: energy

text: that will not occur by themselves, by

text: coupling

text: them to

text: spontaneous reactions

text: that release energy. Enzymes act as

text: catalysts

text: that allow the reactions to proceed more rapidly. Enzymes also allow the

text: regulation

text: of metabolic pathways in response to changes in the

text: cell's

text: environment or to

text: signals

text: from other cells.

text: Excessive formation of the biological film may lead to certain problems such as sloughing, it is an important factor to maintain optimum biological film. Maintaining the biological film is accomplished by proper moisture content. For this purpose the humidity of the air is adjusted within the reaction chamber before the vapor flows over the packing media. The biological packing media may be natural or made of synthetic plastic. Recirculation of the water is always completed in the biological oxidation system to make the system more cost-effective. Biochemical oxygen demand (BOD) indirectly measures the amount of easily biodegradable organic matters thus very low values indicate direct waste water disposal.

text: Excessive formation of the biological film may lead to certain problems such as sloughing, it is an important factor to maintain optimum biological film. Maintaining the biological film is accomplished by proper moisture content. For this purpose the humidity of the air is adjusted within the reaction chamber before the vapor flows over the packing media. The biological packing media may be natural or made of synthetic

text: plastic

text: . Recirculation of the water is always completed in the biological oxidation system to make the system more cost-effective.

text: Biochemical oxygen demand

text: (BOD) indirectly measures the amount of easily biodegradable organic matters thus very low values indicate direct waste water disposal.

text: The study of enzyme kinetics is important for two basic reasons. Firstly, it helps explain how enzymes work, and secondly, it helps predict how enzymes behave in living organisms. The kinetic constants defined above, K and V, are critical to attempts to understand how enzymes work together to control metabolism.

text: The study of enzyme kinetics is important for two basic reasons. Firstly, it helps explain how enzymes work, and secondly, it helps predict how enzymes behave in living organisms. The kinetic constants defined above, K and V, are critical to attempts to understand how enzymes work together to control

text: metabolism

text: Soon after completing the work on alcohol dehydrogenase, Westheimer moved to Harvard where the chemistry department was seeking to broaden the scope of research interests to include biological aspects of organic chemistry. He continued his interest in reaction mechanisms, isotopes and oxidation with a landmark study of chromic acid oxidations. He then reawakened his interests in phosphate reactions related to biochemical processes, an area related to his original doctoral work with Conant on fragmentation reactions. He proposed that ATP transfers phosphate through a reactive monomeric metaphosphate species. While this did not turn out to be the literal case, many enzymic reactions do proceed through transition states that have this as a significant component. He also approached the reactions of phosphate transfer through mechanisms that involve five-coordinate intermediates. He showed the significance of this route and the importance of stereochemical rearrangements of the intermediates. His work in this area set up the modern field and contributed to the understanding of reactions of RNA, DNA, and ribozymes. At the same time, he developed the idea of photoaffinity labeling of the active site of proteins. The identification of an "active site" is difficult in cases where proteins have hydrocarbon-rich sites. The photolabel generates a reactive carbenoid species that inserts into hydrocarbon C-H bonds.

text: Soon after completing the work on alcohol dehydrogenase, Westheimer moved to Harvard where the chemistry department was seeking to broaden the scope of research interests to include biological aspects of organic chemistry. He continued his interest in reaction mechanisms, isotopes and oxidation with a landmark study of

text: chromic acid

text: oxidations. He then reawakened his interests in phosphate reactions related to biochemical processes, an area related to his original doctoral work with Conant on fragmentation reactions. He proposed that ATP transfers phosphate through a reactive monomeric metaphosphate species. While this did not turn out to be the literal case, many enzymic reactions do proceed through transition states that have this as a significant component. He also approached the reactions of phosphate transfer through mechanisms that involve five-coordinate intermediates. He showed the significance of this route and the importance of stereochemical rearrangements of the intermediates. His work in this area set up the modern field and contributed to the understanding of reactions of RNA, DNA, and ribozymes. At the same time, he developed the idea of photoaffinity labeling of the active site of proteins. The identification of an "active site" is difficult in cases where proteins have hydrocarbon-rich sites. The photolabel generates a reactive carbenoid species that inserts into hydrocarbon C-H bonds.

text: In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis of urea, and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry.

text: In these early studies, the mechanisms of these metabolic processes had not been identified and a

text: vital force

text: was thought to animate living tissue. In the 19th century, when studying the

text: fermentation

text: of sugar to

text: alcohol

text: by

text: yeast

text: Louis Pasteur

text: concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." This discovery, along with the publication by

text: Friedrich Wöhler

text: in 1828 of a paper on the chemical synthesis of

text: urea

text: , and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry.

text: Only if the light intensity is above a plant specific value, called the compensation point the plant assimilates more carbon and releases more oxygen by photosynthesis than it consumes by cellular respiration for its own current energy demand.<br>Photosynthesis measurement systems are not designed to directly measure the amount of light absorbed by the leaf. Nevertheless, the light response curves that the class produces do allow comparisons in photosynthetic efficiency between plants.

text: Only if the light intensity is above a plant specific value, called the

text: compensation point

text: the plant assimilates more carbon and releases more oxygen by photosynthesis than it consumes by

text: cellular respiration

text: for its own current energy demand.<br>Photosynthesis measurement systems are not designed to directly measure the amount of light absorbed by the leaf. Nevertheless, the light response curves that the class produces do allow comparisons in photosynthetic efficiency between plants.

text: In 2009, Larhlimi and Bockmayr presented a new approach called "minimal metabolic behaviors" for the analysis of metabolic networks. Like elementary modes or extreme pathways, these are uniquely determined by the network, and yield a complete description of the flux cone. However, the new description is much more compact. In contrast with elementary modes and extreme pathways, which use an inner description based on generating vectors of the flux cone, MMBs are using an outer description of the flux cone. This approach is based on sets of non-negativity constraints. These can be identified with irreversible reactions, and thus have a direct biochemical interpretation. One can characterize a metabolic network by MMBs and the reversible metabolic space.

text: Lineweaver received his Bachelor of Arts degree in Chemistry from George Washington University in 1930, and continued on to receive his Masters of Arts degree there in 1933. He obtained his PhD in Physical Chemistry from Johns Hopkins University in 1936. In 1929, a year before graduating, he was appointed a Junior Scientific Aid to the U.S. Department of Agriculture, and worked as a chemist in the fertilizer section of the Bureau of Chemistry and Soils. In 1930, Lineweaver was transferred to the Food Research Division of the USDA as an Associate Chemist pursuing enzyme research. In 1939, he was transferred to the newly built Western Regional Research Laboratory of the USDA in Albany, California as Senior Biochemist and head of the enzyme section in the biochemical division. During and after World War II, Dr. Lineweaver collaborated with the Quartermasters Corps of the Armed Services in enzyme work related to poultry and powdered egg flavor and processing. In 1948, he was appointed Chief of the WRRL Poultry Laboratory in 1949, a position he held until his retirement in 1973, after 44 years of continuous service for the U.S. Department of Agriculture.

text: Lineweaver received his Bachelor of Arts degree in Chemistry from

text: George Washington University

text: in 1930, and continued on to receive his Masters of Arts degree there in 1933. He obtained his PhD in Physical Chemistry from

text: Johns Hopkins University

text: in 1936. In 1929, a year before graduating, he was appointed a Junior Scientific Aid to the U.S. Department of Agriculture, and worked as a chemist in the fertilizer section of the

text: Bureau of Chemistry and Soils

text: . In 1930, Lineweaver was transferred to the Food Research Division of the USDA as an Associate Chemist pursuing enzyme research. In 1939, he was transferred to the newly built

text: Western Regional Research Laboratory

text: of the USDA in

text: Albany, California

text: as Senior Biochemist and head of the enzyme section in the biochemical division. During and after

text: World War II

text: , Dr. Lineweaver collaborated with the Quartermasters Corps of the Armed Services in enzyme work related to poultry and powdered egg flavor and processing. In 1948, he was appointed Chief of the WRRL Poultry Laboratory in 1949, a position he held until his retirement in 1973, after 44 years of continuous service for the U.S. Department of Agriculture.

text: ATP citrate lyase is an enzyme that in animals represents an important step in fatty acid biosynthesis.  ATP citrate lyase is important in that, by converting citrate to acetyl CoA, it links the metabolism of carbohydrates, which yields citrate as an intermediate, and the production of fatty acids, which requires acetyl CoA.In plants, ATP citrate lyase generates cytosolic acetyl-CoA precursor of thousands of specialized metabolites including waxes, sterols, and polyketides.

text: ATP citrate lyase is an

text: enzyme

text: that in animals represents an important step in

text: fatty acid biosynthesis

text: .  ATP citrate lyase is important in that, by converting citrate to acetyl CoA, it links the metabolism of carbohydrates, which yields citrate as an intermediate, and the production of fatty acids, which requires acetyl CoA.In plants, ATP citrate lyase generates cytosolic acetyl-CoA precursor of thousands of specialized metabolites including waxes, sterols, and polyketides.

text: There are at least 14 different isoforms in mammals. Plants contain a different form called β-carbonic anhydrase, which, from an evolutionary standpoint, is a distinct enzyme, but participates in the same reaction and also uses a zinc ion in its active site.  In plants, carbonic anhydrase helps raise the concentration of CO within the chloroplast in order to increase the carboxylation rate of the enzyme RuBisCO. This is the reaction that integrates CO into organic carbon sugars during photosynthesis, and can use only the CO form of carbon, not carbonic acid or bicarbonate.

text: There are at least 14 different isoforms in mammals.

text: Plant

text: s contain a different form called β-carbonic anhydrase, which, from an evolutionary standpoint, is a distinct enzyme, but participates in the same reaction and also uses a zinc ion in its active site.  In plants, carbonic anhydrase helps raise the concentration of CO within the

text: chloroplast

text: in order to increase the carboxylation rate of the enzyme

text: RuBisCO

text: . This is the reaction that integrates CO into

text: organic carbon

text: sugars during

text: photosynthesis

text: , and can use only the CO form of carbon, not carbonic acid or bicarbonate.

text: Cellular metabolism is represented by a large number of metabolic reactions involving the conversion of the carbon source (usually glucose) into the building blocks needed for macromolecular biosynthesis. These reactions form metabolic networks within cells. These networks can then themselves be used to study metabolism within cells.

text: Cellular metabolism is represented by a large number of metabolic reactions involving the conversion of the carbon source (usually

text: glucose

text: ) into the building blocks needed for macromolecular

text: biosynthesis

text: . These reactions form metabolic networks within cells. These networks can then themselves be used to study metabolism within cells.

text: Alterations in the expression and function of OAT1 play important roles in intra- and inter-individual variability of the therapeutic efficacy and the toxicity of many drugs. As a result, the activity of OAT1 must be under tight regulation so as to carry out their normal functions. The regulation of OAT transport activity in response to various stimuli can occur at several levels such as transcription, translation, and posttranslational modification. Posttranslational regulation is of particular interest, because it usually happens within a very short period of time (minutes to hours) when the body has to deal with rapidly changing amounts of substances as a consequence of variable intake of drugs, fluids, or meals as well as metabolic activity. Post-translational modification is a process where new functional group(s) are conjugated to the amino acid side chains in a target protein through reversible or irreversible biochemical reactions. The common modifications include glycosylation, phosphorylation, ubiquitination, sulfation, methylation, acetylation, and hydroxylation.

text: An artificial chemistryis a chemical-like system that usually consists of objects, called molecules, that interact according to rules resembling chemical reaction rules. Artificial chemistries are created and studied in order to understand fundamental properties of chemical systems, including prebiotic evolution, as well as for developing chemical computing systems. Artificial chemistry is a field within computer science wherein chemical reactions—often biochemical ones—are computer-simulated, yielding insights on evolution, self-assembly, and other biochemical phenomena. The field does not use actual chemicals, and should not be confused with either synthetic chemistry or computational chemistry. Rather, bits of information are used to represent the starting molecules, and the end products are examined along with the processes that led to them. The field originated in artificial life but has shown to be a versatile method with applications in many fields such as chemistry, economics, sociology and linguistics.

text: An artificial chemistryis a chemical-like system that usually consists of objects, called molecules, that interact according to rules resembling chemical reaction rules. Artificial chemistries are created and studied in order to understand fundamental properties of chemical systems, including prebiotic evolution, as well as for developing chemical computing systems. Artificial chemistry is a field within computer science wherein chemical reactions—often biochemical ones—are computer-simulated, yielding insights on evolution, self-assembly, and other biochemical phenomena. The field does not use actual chemicals, and should not be confused with either synthetic chemistry or computational chemistry. Rather, bits of information are used to represent the starting molecules, and the end products are examined along with the processes that led to them. The field originated in

text: artificial life

text: but has shown to be a versatile method with applications in many fields such as

text: chemistry

text: economics

text: sociology

text: and

text: linguistics

text: The database contains more than 40 data fields with enzyme-specific information on more than 4800 EC numbers that are classified according to the IUBMB.The different data fields cover information on the enzyme's nomenclature, reaction and specificity, enzyme structure, isolation and preparation, enzyme stability, kinetic parameters such as Km value and turnover number, occurrence and localization, mutants and engineered enzymes, application of enzymes and ligand-related data. Currently, BRENDA contains manually annotated data from over 130,000 different scientific articles. Each enzyme entry is clearly linked to at least one literature reference, to its source organism, and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the more than 107,000 enzyme ligands, which are available on their names, synonyms or via the chemical structure. The term "ligand" is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors but also enzyme inhibitors or metal ions. The origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides.Furthermore, cross-references to external information resources such as sequence and 3D-structure databases, as well as biomedical ontologies, are provided.

text: The database contains more than 40 data fields with enzyme-specific information on more than 4800

text: EC numbers

text: that are classified according to the

entity_name: International Union of Biochemistry and Molecular Biology

text: IUBMB

text: .The different data fields cover information on the enzyme's nomenclature, reaction and specificity,

text: enzyme structure

text: , isolation and preparation, enzyme stability, kinetic parameters such as

text: Km value

text: and

text: turnover number

text: , occurrence and localization, mutants and engineered enzymes, application of enzymes and ligand-related data. Currently, BRENDA contains manually annotated data from over 130,000 different

text: scientific articles

text: . Each enzyme entry is clearly linked to at least one literature reference, to its source

text: organism

text: , and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the more than 107,000 enzyme ligands, which are available on their names, synonyms or via the chemical structure. The term "ligand" is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors but also enzyme inhibitors or metal ions. The origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides.Furthermore, cross-references to external information resources such as

text: sequence

text: and

text: databases, as well as

text: biomedical ontologies

text: , are provided.

text: Different chemical reactions are used in combinations during chemical synthesis in order to obtain a desired product. In biochemistry, a consecutive series of chemical reactions (where the product of one reaction is the reactant of the next reaction) form metabolic pathways. These reactions are often catalyzed by protein enzymes. Enzymes increase the rates of biochemical reactions, so that metabolic syntheses and decompositions impossible under ordinary conditions can occur at the temperatures and concentrations present within a cell.

text: Different chemical reactions are used in combinations during

text: chemical synthesis

text: in order to obtain a desired product. In

text: biochemistry

text: , a consecutive series of chemical reactions (where the product of one reaction is the reactant of the next reaction) form

text: metabolic pathway

text: s. These reactions are often

text: catalyzed

text: by protein

text: enzyme

text: s. Enzymes increase the rates of biochemical reactions, so that

text: metabolic

text: syntheses and decompositions impossible under ordinary conditions can occur at the temperatures and concentrations present within a

text: cell

text: In enzymology, an acetylacetone-cleaving enzyme () is an enzyme that catalyzes the chemical reaction

text: In

text: enzymology

text: , an acetylacetone-cleaving enzyme () is an

text: enzyme

text: that

text: catalyzes

text: the

text: chemical reaction

text: In chemistry, reaction progress kinetic analysis (RPKA) is a subset of a broad range of kinetic techniques utilized to determine the rate laws of chemical reactions and to aid in elucidation of reaction mechanisms. While the concepts guiding reaction progress kinetic analysis are not new, the process was formalized by Professor Donna Blackmond (currently at Scripps Research Institute) in the late 1990s and has since seen increasingly widespread use. Unlike more common pseudo-first-order analysis, in which an overwhelming excess of one or more reagents is used relative to a species of interest, RPKA probes reactions at synthetically relevant conditions (i.e. with concentrations and reagent ratios resembling those used in the reaction when not exploring the rate law.) Generally, this analysis involves a system in which the concentrations of multiple reactants are changing measurably over the course of the reaction. As the mechanism can vary depending on the relative and absolute concentrations of the species involved, this approach obtains results that are much more representative of reaction behavior under commonly utilized conditions than do traditional tactics. Furthermore, information obtained by observation of the reaction over time may provide insight regarding unexpected behavior such as induction periods, catalyst deactivation, or changes in mechanism.

text: In

text: chemistry

text: , reaction progress kinetic analysis (RPKA) is a subset of a broad range of

text: kinetic

text: techniques utilized to determine the

text: rate law

text: s of chemical reactions and to aid in elucidation of

text: reaction mechanism

text: s. While the concepts guiding reaction progress kinetic analysis are not new, the process was formalized by Professor

text: Donna Blackmond

text: (currently at

text: Scripps Research Institute

text: ) in the late 1990s and has since seen increasingly widespread use. Unlike more common

text: pseudo-first-order

text: analysis, in which an overwhelming excess of one or more reagents is used relative to a species of interest, RPKA probes reactions at synthetically relevant conditions (i.e. with concentrations and reagent ratios resembling those used in the reaction when not exploring the rate law.) Generally, this analysis involves a system in which the concentrations of multiple reactants are changing measurably over the course of the reaction. As the

text: mechanism

text: can vary depending on the relative and absolute

text: concentration

text: s of the species involved, this approach obtains results that are much more representative of reaction behavior under commonly utilized conditions than do traditional tactics. Furthermore, information obtained by observation of the reaction over time may provide insight regarding unexpected behavior such as induction periods, catalyst deactivation, or changes in mechanism.

text: The chemistry of the Mg ion, as applied to enzymes, uses the full range of this ion’s unusual reaction chemistry to fulfill a range of functions. Mg interacts with substrates, enzymes, and occasionally both (Mg may form part of the active site). In general, Mg interacts with substrates through inner sphere coordination, stabilising anions or reactive intermediates, also including binding to ATP and activating the molecule to nucleophilic attack. When interacting with enzymes and other proteins, Mg may bind using inner or outer sphere coordination, to either alter the conformation of the enzyme or take part in the chemistry of the catalytic reaction. In either case, because Mg is only rarely fully dehydrated during ligand binding, it may be a water molecule associated with the Mg that is important rather than the ion itself. The Lewis acidity of Mg (pK 11.4) is used to allow both hydrolysis and condensation reactions (most common ones being phosphate ester hydrolysis and phosphoryl transfer) that would otherwise require pH values greatly removed from physiological values.

text: The chemistry of the Mg ion, as applied to enzymes, uses the full range of this ion’s unusual reaction chemistry to fulfill a range of functions. Mg interacts with substrates, enzymes, and occasionally both (Mg may form part of the active site). In general, Mg interacts with substrates through inner sphere coordination, stabilising anions or reactive intermediates, also including binding to ATP and activating the molecule to nucleophilic attack. When interacting with enzymes and other proteins, Mg may bind using inner or outer sphere coordination, to either alter the conformation of the enzyme or take part in the chemistry of the catalytic reaction. In either case, because Mg is only rarely fully dehydrated during ligand binding, it may be a water molecule associated with the Mg that is important rather than the ion itself. The Lewis acidity of Mg (

text: pK

text: 11.4) is used to allow both hydrolysis and condensation reactions (most common ones being phosphate ester hydrolysis and phosphoryl transfer) that would otherwise require pH values greatly removed from physiological values.

text: A catabolic pathway is a series of reactions that bring about a net release of energy in the form of a high energy phosphate bond formed with the energy carriers Adenosine Diphosphate (ADP) and Guanosine Diphosphate (GDP) to produce Adenosine Triphosphate (ATP) and Guanosine Triphosphate (GTP), respectively. The net reaction is, therefore, thermodynamically favorable, for it results in a lower free energy for the final products. A catabolic pathway is an exergonic system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc. from energy containing sources such as carbohydrates, fats, and proteins. The end products are often carbon dioxide, water, and ammonia. Coupled with an endergonic reaction of anabolism, the cell can synthesize new macromolecules using the original precursors of the anabolic pathway. An example of a coupled reaction is the phosphorylation of fructose-6-phosphate to form the intermediate fructose-1,6-bisphosphate by the enzyme phsophofructokinase accompanied by the hydrolysis of ATP in the pathway of glycolysis. The resulting chemical reaction within the metabolic pathway is highly thermodynamically favorable and, as a result, irreversible in the cell.

text: A

text: catabolic pathway

text: is a series of reactions that bring about a net release of energy in the form of a high energy phosphate bond formed with the energy carriers Adenosine Diphosphate (ADP) and Guanosine Diphosphate (GDP) to produce Adenosine Triphosphate (ATP) and Guanosine Triphosphate (GTP), respectively. The net reaction is, therefore, thermodynamically favorable, for it results in a lower free energy for the final products. A catabolic pathway is an exergonic system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc. from energy containing sources such as carbohydrates, fats, and proteins. The end products are often carbon dioxide, water, and ammonia. Coupled with an endergonic reaction of anabolism, the cell can synthesize new macromolecules using the original precursors of the anabolic pathway. An example of a coupled reaction is the phosphorylation of

text: to form the intermediate

text: by the enzyme

text: phsophofructokinase

text: accompanied by the hydrolysis of ATP in the pathway of

text: glycolysis

text: . The resulting chemical reaction within the metabolic pathway is highly thermodynamically favorable and, as a result, irreversible in the cell.

text: Another procedure consists in the thermally induced solid-state polycondensation of halogenoacetates with general formulaX-—CHCOOM (where M is a monovalent metal like sodium and X is a halogen like chlorine), resulting in the production of polyglycolide and small crystals of a salt. Polycondensation is carried out by heating an halogenoacetate, like sodium chloroacetate, at a temperature between 160-180 °C, continuously passing nitrogen through the reaction vessel. During the reaction polyglycolide is formed along with sodium chloride which precipitates within the polymeric matrix; the salt can be conveniently removed by washing the product of the reaction with water.<ref name="apple">{{cite journal | last = Epple | first = Matthias | title = A detailed characterization of polyglycolide prepared by solid-state polycondensation reaction | journal = Macromolecular Chemistry and Physics | volume = 200 | issue = 10 | pages = 2221–2229 | publisher = Wiley | year = 1999 | doi = 10.1002/(SICI)1521-3935(19991001)200:10

text: Another procedure consists in the thermally induced solid-state polycondensation of halogenoacetates with general formulaX-—CHCOOM (where M is a monovalent metal like

text: sodium

text: and X is a

text: halogen

text: like

text: chlorine

text: ), resulting in the production of polyglycolide and small

text: crystal

text: s of a

text: salt

text: . Polycondensation is carried out by heating an halogenoacetate, like

text: sodium chloroacetate

text: , at a temperature between 160-180 °C, continuously passing nitrogen through the reaction vessel. During the reaction polyglycolide is formed along with

text: sodium chloride

text: which precipitates within the polymeric matrix; the salt can be conveniently removed by washing the product of the reaction with water.<ref name="apple">{{cite journal | last = Epple | first = Matthias | title = A detailed characterization of polyglycolide prepared by solid-state polycondensation reaction | journal = Macromolecular Chemistry and Physics | volume = 200 | issue = 10 | pages = 2221–2229 | publisher = Wiley | year = 1999 | doi = 10.1002/(SICI)1521-3935(19991001)200:10

text: The reaction for biochemical oxidation may be written as:

text: Exhaled CO(g) depletes CO(aq) which in turn consumes HCO causing the aforementioned shift left in the first reaction by Le Châtelier's principle.  By the same principle when the pH is too high, the kidneys excrete bicarbonate () into urine as urea via the urea cycle (a.k.a. the Krebs–Henseleit ornithine cycle).  By removing the bicarbonate more H is generated from carbonic acid (HCO) which come from CO(g) produced by cellular respiration.

text: Exhaled CO(g) depletes CO(aq) which in turn consumes HCO causing the aforementioned shift left in the first reaction by

text: Le Châtelier's principle

text: .  By the same principle when the pH is too high, the kidneys excrete bicarbonate () into urine as urea via the

text: urea cycle

text: (a.k.a. the Krebs–Henseleit ornithine cycle).  By removing the bicarbonate more H is generated from carbonic acid (HCO) which come from CO(g) produced by

text: cellular respiration

text: The increase in body temperature that results from a breakdown in thermoregulation affects the body biochemically. Enzymes involved in metabolic pathways within the body such as cellular respiration fail to work effectively at higher temperatures, and further increases can lead them to denature, reducing their ability to catalyse essential chemical reactions. This loss of enzymatic control affects the functioning of major organs with high energy demands such as the heart and brain.

text: The increase in body temperature that results from a breakdown in thermoregulation affects the body biochemically.

text: Enzyme

text: s involved in metabolic pathways within the body such as cellular respiration fail to work effectively at higher temperatures, and further increases can lead them to

text: denature

text: , reducing their ability to catalyse essential chemical reactions. This loss of enzymatic control affects the functioning of major organs with high energy demands such as the heart and brain.

text: An important function of enzymes is in the digestive systems of animals. Enzymes such as amylases and proteases break down large molecules (starch or proteins, respectively) into smaller ones, so they can be absorbed by the intestines. Starch molecules, for example, are too large to be absorbed from the intestine, but enzymes hydrolyze the starch chains into smaller molecules such as maltose and eventually glucose, which can then be absorbed. Different enzymes digest different food substances. In ruminants, which have herbivorous diets, microorganisms in the gut produce another enzyme, cellulase, to break down the cellulose cell walls of plant fiber.

text: An important function of enzymes is in the

text: digestive systems

text: of animals. Enzymes such as

text: amylases

text: and

text: proteases

text: break down large molecules (

text: starch

text: or

text: protein

text: s, respectively) into smaller ones, so they can be absorbed by the intestines. Starch molecules, for example, are too large to be absorbed from the intestine, but enzymes hydrolyze the starch chains into smaller molecules such as

text: maltose

text: and eventually

text: glucose

text: , which can then be absorbed. Different enzymes digest different food substances. In

text: ruminants

text: , which have

text: herbivorous

text: diets, microorganisms in the gut produce another enzyme,

text: cellulase

text: , to break down the cellulose cell walls of plant fiber.

text: Vitamins have diverse biochemical functions. Some, such as vitamin D, have hormone-like functions as regulators of mineral metabolism, or regulators of cell and tissue growth and differentiation (such as some forms of vitamin A). Others function as antioxidants (e.g., vitamin E and sometimes vitamin C). The largest number of vitamins, the B complex vitamins, function as enzyme cofactors (coenzymes) or the precursors for them; coenzymes help enzymes in their work as catalysts in metabolism. In this role, vitamins may be tightly bound to enzymes as part of prosthetic groups: For example, biotin is part of enzymes involved in making fatty acids. They may also be less tightly bound to enzyme catalysts as coenzymes, detachable molecules that function to carry chemical groups or electrons between molecules. For example, folic acid may carry methyl, formyl, and methylene groups in the cell. Although these roles in assisting enzyme-substrate reactions are vitamins' best-known function, the other vitamin functions are equally important.

text: Vitamins have diverse biochemical functions. Some, such as

text: vitamin D

text: , have hormone-like functions as regulators of mineral metabolism, or regulators of cell and tissue growth and differentiation (such as some forms of vitamin A). Others function as

text: antioxidants

text: (e.g.,

text: vitamin E

text: and sometimes

text: vitamin C

text: ). The largest number of vitamins, the

text: B complex

text: vitamins, function as enzyme

text: cofactor

text: s (

text: coenzymes

text: ) or the

text: precursors

text: for them; coenzymes help

text: enzyme

text: s in their work as

text: catalyst

text: s in

text: metabolism

text: . In this role, vitamins may be tightly bound to enzymes as part of

text: prosthetic group

text: s: For example,

text: biotin

text: is part of enzymes involved in making

text: fatty acid

text: s. They may also be less tightly bound to enzyme catalysts as coenzymes, detachable molecules that function to carry

text: chemical groups

text: or electrons between molecules. For example,

text: folic acid

text: may carry

text: methyl

text: formyl

text: , and

text: methylene

text: groups in the cell. Although these roles in assisting enzyme-substrate reactions are vitamins' best-known function, the other vitamin functions are equally important.

text: Robert Hill FRS (2 April 1899 – 15 March 1991), known as Robin Hill, was a British plant biochemist who, in 1939, demonstrated the 'Hill reaction' of photosynthesis, proving that oxygen is evolved during the light requiring steps of photosynthesis. He also made significant contributions to the development of the Z-scheme of oxygenic photosynthesis.

text: Robert Hill

text: FRS

text: (2 April 1899 – 15 March 1991), known as Robin Hill, was a

text: British

text: plant biochemist

text: who, in 1939, demonstrated the '

text: Hill reaction

text: ' of

text: photosynthesis

text: , proving that

text: oxygen

text: is

text: evolved

text: during the

text: light requiring steps

text: of photosynthesis. He also made significant contributions to the development of the

text: Z-scheme

text: of oxygenic photosynthesis.

text: Biochemical kinetic reactions of type () are often catalytic reactions in which one or more substrates, <math chem>\ce{S}_j

text: Biochemical reactions are mainly controlled by enzymes. These proteins can specifically catalyze a single reaction, so that reactions can be controlled very precisely. The reaction takes place in the active site, a small part of the enzyme which is usually found in a cleft or pocket lined by amino acid residues, and the rest of the enzyme is used mainly for stabilization. The catalytic action of enzymes relies on several mechanisms including the molecular shape ("induced fit"), bond strain, proximity and orientation of molecules relative to the enzyme, proton donation or withdrawal (acid/base catalysis), electrostatic interactions and many others.

text: Biochemical reactions

text: are mainly controlled by

text: enzymes

text: . These

text: protein

text: s can specifically

text: catalyze

text: a single reaction, so that reactions can be controlled very precisely. The reaction takes place in the

text: active site

text: , a small part of the enzyme which is usually found in a cleft or pocket lined by

text: amino acid

text: residues, and the rest of the enzyme is used mainly for stabilization. The catalytic action of enzymes relies on several mechanisms including the molecular shape ("induced fit"), bond strain, proximity and orientation of molecules relative to the enzyme, proton donation or withdrawal (acid/base catalysis), electrostatic interactions and many others.

text: For larger neighborhoods, similar spiraling behavior occurs for low thresholds, but for sufficiently high thresholds the automaton stabilizes in the block of color stage without forming spirals. At intermediate values of the threshold, a complex mix of color blocks and partial spirals, called turbulence, can form. For appropriate choices of the number of states and the size of the neighborhood, the spiral patterns formed by this automaton can be made to resemble those of the Belousov-Zhabotinsky reaction in chemistry, or other systems of autowaves, although other cellular automata more accurately model the excitable medium that leads to this reaction.

text: For larger neighborhoods, similar spiraling behavior occurs for low thresholds, but for sufficiently high thresholds the automaton stabilizes in the block of color stage without forming spirals. At intermediate values of the threshold, a complex mix of color blocks and partial spirals, called turbulence, can form. For appropriate choices of the number of states and the size of the neighborhood, the spiral patterns formed by this automaton can be made to resemble those of the

text: Belousov-Zhabotinsky reaction

text: in chemistry, or other systems of

text: autowave

text: s, although other cellular automata more accurately model the

text: excitable medium

text: that leads to this reaction.

text: suggest that service vehicles and emergency vehicles should use minimax paths when returning from a service call to their base. In this application, the time to return is less important than the response time if another service call occurs while the vehicle is in the process of returning. By using a minimax path, where the weight of an edge is the maximum travel time from a point on the edge to the farthest possible service call, one can plan a route that minimizes the maximum possible delay between receipt of a service call and arrival of a responding vehicle.  use maximin paths to model the dominant reaction chains in metabolic networks; in their model, the weight of an edge is the free energy of the metabolic reaction represented by the edge.

text: suggest that service vehicles and emergency vehicles should use minimax paths when returning from a service call to their base. In this application, the time to return is less important than the response time if another service call occurs while the vehicle is in the process of returning. By using a minimax path, where the weight of an edge is the maximum travel time from a point on the edge to the farthest possible service call, one can plan a route that minimizes the maximum possible delay between receipt of a service call and arrival of a responding vehicle.  use maximin paths to model the dominant reaction chains in

text: metabolic network

text: s; in their model, the weight of an edge is the free energy of the metabolic reaction represented by the edge.

text: The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.

text: The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate

text: Richard Willstätter

text: ) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926,

text: James B. Sumner

text: showed that the enzyme

text: urease

text: was a pure protein and crystallized it; he did likewise for the enzyme

text: catalase

text: in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by

text: John Howard Northrop

text: and

text: Wendell Meredith Stanley

text: , who worked on the digestive enzymes

text: pepsin

text: trypsin

text: and

text: chymotrypsin

text: . These three scientists were awarded the 1946 Nobel Prize in Chemistry.

text: Developments in genomics, transcriptomics, proteomics, and metabolomics are now yielding large volumes of biochemical data. "Metabolic profiling" allows for comparison between biologically active and inactive samples and identification of compounds present at low concentrations using mass spectrometry. These samples may then be compared by principal component analysis. Characterization of the compounds present in the active sample (but not in the inactive sample) may then be identified and characterized using standard methods in mass spectroscopy. Isotope labeling may also be used to identify the pathways used in phycotoxin biosynthesis.

text: Developments in

text: genomics

text: transcriptomics

text: proteomics

text: , and

text: metabolomics

text: are now yielding large volumes of biochemical data. "

text: Metabolic profiling

text: " allows for comparison between biologically active and inactive samples and identification of compounds present at low concentrations using

text: mass spectrometry

text: . These samples may then be compared by

text: principal component analysis

text: . Characterization of the compounds present in the active sample (but not in the inactive sample) may then be identified and characterized using standard methods in mass spectroscopy.

text: Isotope labeling

text: may also be used to identify the pathways used in phycotoxin

text: biosynthesis

text: Spin Chemistry is a sub-field of chemistry and physics, positioned at the intersection of chemical kinetics, photochemistry, magnetic resonance and free radical chemistry, and dealing with magnetic and spin effects in chemical reactions. The examples of phenomena that Spin Chemistry deals with are Chemically Induced Dynamic Nuclear and Electron Polarization (CIDNP and CIDEP), magnetic isotope effects in chemical reactions, as well as the environmental,  health effects of static and oscillating electromagnetic fields, and avian magnetoreception, particularly as radical-pair reaction kinetics are dependent on the direction of magnetic fields.

text: Spin Chemistry is a sub-field of

text: chemistry

text: and

text: physics

text: , positioned at the intersection of

text: chemical kinetics

text: photochemistry

text: magnetic resonance

text: and

text: free radical

text: chemistry, and dealing with magnetic and

text: spin

text: effects in chemical reactions. The examples of phenomena that Spin Chemistry deals with are Chemically Induced Dynamic Nuclear and Electron Polarization (

text: CIDNP

text: and

text: CIDEP

text: ), magnetic

text: isotope

text: effects in chemical reactions, as well as the environmental,  health effects of static and oscillating electromagnetic

text: fields

text: , and avian

text: magnetoreception

text: , particularly as radical-pair reaction kinetics are dependent on the direction of magnetic fields.

text:
related_synonym: "Enzyme activity"
"Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic."
Note: see the Wikipedia enzymes category.

text: related_synonym: "

text: Enzyme

text: activity"<BR>"Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as

text: substrates

text: , and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess

text: specific binding sites for substrates

text: , and are usually composed wholly or largely of protein, but RNA that has catalytic activity (

text: ribozyme

text: ) is often also regarded as enzymatic."<BR>Note: see the Wikipedia

text: enzymes category

text: Myricetin also impacts the biochemical efficacy and binding ability of large intracelluar biomolecules. Myricetin has been shown to inhibit viral reverse transcriptase, cellular DNA polymerase, and cellular RNA polymerase. Inhibition of cellular DNA polymerases could have dangerous effects on the cell’s ability to replicate its genome and its progression through the cell cycle. Inhibition of cellular RNA polymerase could have deleterious effects on the cell’s capacity to transcribe and translate DNA and RNA to produce vital proteins for the cell. Researchers have found that myricetin has the ability to interfere in the RNA polymerase pathway in two different ways. In E. coli myricetin competitively inhibited GTP substrate binding to RNA polymerase. In T7 bacteriophages myricetin competitively inhibited DNA template binding to RNA polymerase.

text: Myricetin also impacts the biochemical efficacy and binding ability of large intracelluar biomolecules. Myricetin has been shown to inhibit viral

text: reverse transcriptase

text: , cellular

text: DNA polymerase

text: , and cellular

text: RNA polymerase

text: . Inhibition of cellular DNA polymerases could have dangerous effects on the cell’s ability to replicate its genome and its progression through the

text: cell cycle

text: . Inhibition of cellular RNA polymerase could have deleterious effects on the cell’s capacity to transcribe and translate DNA and RNA to produce vital proteins for the cell. Researchers have found that myricetin has the ability to interfere in the RNA polymerase pathway in two different ways. In

text: E. coli

text: myricetin competitively inhibited

text: GTP

text: substrate binding to RNA polymerase. In T7

text: bacteriophages

text: myricetin competitively inhibited DNA template binding to RNA polymerase.

text: According to some opinions, living eukaryotic cells perform isoelectric focusing of proteins in their interior to overcome a limitation of the rate of metabolic reaction by diffusion of enzymes and their reactants, and to regulate the rate of particular biochemical processes. By concentrating the enzymes of particular metabolic pathways into distinct and small regions of its interior, the cell can increase the rate of particular biochemical pathways by several orders of magnitude. By modification of the isoelectric point (pI) of molecules of an enzyme by, e.g., phosphorylation or dephosphorylation, the cell can transfer molecules of the enzyme between different parts of its interior, to switch on or switch off particular biochemical processes.

text: According to some opinions, living

text: eukaryotic

text: cells perform isoelectric focusing of proteins in their interior to overcome a limitation of the rate of metabolic reaction by diffusion of enzymes and their reactants, and to regulate the rate of particular biochemical processes. By concentrating the enzymes of particular metabolic pathways into distinct and small regions of its interior, the cell can increase the rate of particular biochemical pathways by several orders of magnitude. By modification of the isoelectric point (pI) of molecules of an enzyme by, e.g.,

text: phosphorylation

text: or dephosphorylation, the cell can transfer molecules of the enzyme between different parts of its interior, to switch on or switch off particular biochemical processes.

text: This is the first enzyme of its kind ever reported and was discovered in streptococcal and staphylococcal lysates due to its high cleavage activity for the LPXTG sequence  (200x more active than sortase).  While there are only three publications describing this enzyme, all from the same source, they are in high quality peer reviewed journals.  One reason for this limitation is that there is no single gene that codes for LPXTGase (it does not fit the "one gene one enzyme" theory) making its manipulation purely biochemical. Thus, reproducibility from other sources is a slow limiting process.

text: This is the first enzyme of its kind ever reported and was discovered in

text: streptococcal

text: and

text: staphylococcal

text: lysates due to its high cleavage activity for the LPXTG sequence  (200x more active than

text: sortase

text: ).  While there are only three publications describing this enzyme, all from the same source, they are in high quality peer reviewed journals.  One reason for this limitation is that there is no single gene that codes for LPXTGase (it does not fit the "one gene one enzyme" theory) making its manipulation purely biochemical. Thus, reproducibility from other sources is a slow limiting process.

text: The degradation of organic matter through respiration in the modern ocean is facilitated by different electron acceptors, their favorability based on Gibbs free energy law, and the laws of thermodynamics.  This redox chemistry is the basis for life in deep sea sediments and determines the obtainability of energy to organisms that live there.  From the water interface moving toward deeper sediments, the order of these acceptors is oxygen, nitrate, manganese, iron, and sulfate.  The zonation of these favored acceptors can be seen in Figure 1.  Moving downwards from the surface through the zonation of these deep ocean sediments, acceptors are used and depleted.  Once depleted the next acceptor of lower favorability takes its place.  Thermodynamically, oxygen represents the most favorable electron accepted but is quickly used up in the water sediment interface and O concentrations extends only millimeters to centimeters down into the sediment in most locations of the deep sea.  This favorability indicates an organism's ability to obtain higher energy from the reaction which helps them complete with other organisms.  In the absence of these acceptors, organic matter can also be degraded through methanogenesis, but the net oxidation of this organic matter is not fully represented by this process. Each pathway and the stoichiometry of its reaction are listed in table 1.

text: The degradation of organic matter through respiration in the modern ocean is facilitated by different electron acceptors, their favorability based on

text: Gibbs free energy law

text: , and the

text: laws of thermodynamics

text: .  This

text: redox

text: chemistry is the basis for life in

text: deep sea

text: sediment

text: s and determines the obtainability of energy to organisms that live there.  From the water interface moving toward deeper sediments, the order of these acceptors is

text: oxygen

text: nitrate

text: manganese

text: iron

text: , and

text: sulfate

text: .  The zonation of these favored acceptors can be seen in Figure 1.  Moving downwards from the surface through the zonation of these deep ocean sediments, acceptors are used and depleted.  Once depleted the next acceptor of lower favorability takes its place.  Thermodynamically, oxygen represents the most favorable electron accepted but is quickly used up in the water sediment interface and O concentrations extends only millimeters to centimeters down into the sediment in most locations of the deep sea.  This favorability indicates an organism's ability to obtain higher energy from the reaction which helps them complete with other organisms.  In the absence of these acceptors, organic matter can also be degraded through methanogenesis, but the net oxidation of this organic matter is not fully represented by this process. Each pathway and the stoichiometry of its reaction are listed in table 1.

text: This framework, which became known as Biochemical Systems Theory, has been developed since the 1960s by Michael Savageau and others for the systems analysis of biochemical processes. According to Cornish-Bowden (2007) they "regarded this as a general theory of metabolic control, which includes both metabolic control analysis and flux-oriented theory as special cases".

text: This framework, which became known as Biochemical Systems Theory, has been developed since the 1960s by

text: Michael Savageau

text: and others for the

text: systems analysis

text: of

text: biochemical

text: processes. According to Cornish-Bowden (2007) they "regarded this as a general theory of

text: metabolic

text: control, which includes both metabolic control analysis and flux-oriented theory as special cases".

text: Anabolic processes tend toward "building up" organs and tissues. These processes produce growth and differentiation of cells and increase in body size, a process that involves synthesis of complex molecules. Examples of anabolic processes include the growth and mineralization of bone and increases in muscle mass. Endocrinologists have traditionally classified hormones as anabolic or catabolic, depending on which part of metabolism they stimulate. The classic anabolic hormones are the anabolic steroids, which stimulate protein synthesis, muscle growth, and insulin. The balance between anabolism and catabolism is also regulated by circadian rhythms, with processes such as glucose metabolism fluctuating to match an animal's normal periods of activity throughout the day.

text: Anabolic processes tend toward "building up"

text: organ

text: s and

text: tissue

text: s. These processes produce growth and differentiation of cells and increase in body size, a process that involves

text: synthesis

text: of complex

text: molecule

text: s. Examples of anabolic processes include the growth and mineralization of

text: bone

text: and increases in

text: muscle

text: mass.

text: Endocrinologist

text: s have traditionally classified

text: hormone

text: s as anabolic or catabolic, depending on which part of metabolism they stimulate. The classic anabolic hormones are the

text: anabolic steroid

text: s, which stimulate protein synthesis, muscle growth, and

text: insulin

text: . The balance between anabolism and catabolism is also regulated by

text: circadian rhythm

text: s, with processes such as glucose metabolism fluctuating to match an animal's normal periods of activity throughout the day.

text: The equilibrium of the reaction favors the formation of barbituric acid.  Barbiturase is very specific to barbituric acid and will not react with derivatives.  Urea, malonate, and cyanuric acid inhibit the hydrolysis of barbituric acid.  Dihydro-L-orotate is an intermediate in the pyrimidine biosynthesis pathway and competitively inhibits barbiturase.  In addition, barbituric acid inhibits multiple enzymes that are involved in de novo pyrimidine synthesis.  These last two points suggest a connection between pyrimidine anabolism and oxidative catabolism.

text: The equilibrium of the reaction favors the formation of barbituric acid.  Barbiturase is very specific to barbituric acid and will not react with derivatives.

text: Urea

text: malonate

text: , and cyanuric acid inhibit the hydrolysis of barbituric acid.  Dihydro-L-orotate is an intermediate in the pyrimidine biosynthesis pathway and competitively inhibits barbiturase.  In addition, barbituric acid inhibits multiple

text: enzyme

text: s that are involved in de novo pyrimidine synthesis.  These last two points suggest a connection between pyrimidine anabolism and oxidative catabolism.

text: This term was proposed by B.Davis in 1961 to emphasise the dual metabolic role of such pathway. The citric acid cycle (The Krebs Cycle) is a good example of amphibolic pathway. The first reaction of the cycle, in which oxaloacetate (a four carbon compound) condenses with acetate (a two carbon compound) to form citrate (a six carbon compound) is typically anabolic. The next few reactions, which are intramolecular rearrangements, produce isocitrate. The following two reactions are typically catabolic. COO is lost in each step and succinate (a four carbon compound) is produced.

text: This term was proposed by

text: B.Davis

text: in 1961 to emphasise the dual metabolic role of such pathway. The

text: citric acid cycle

text: (The Krebs Cycle) is a good example of amphibolic pathway. The first reaction of the cycle, in which oxaloacetate (a four carbon compound) condenses with acetate (a two carbon compound) to form citrate (a six carbon compound) is typically anabolic. The next few reactions, which are intramolecular rearrangements, produce isocitrate. The following two reactions are typically catabolic. COO is lost in each step and succinate (a four carbon compound) is produced.

text: The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD) into NADH.

text: The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as

text: protein

text: s,

text: polysaccharide

text: s or

text: lipid

text: s are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually

text: acetyl coenzyme A

text: (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the

text: citric acid cycle

text: and

text: electron transport chain

text: , releasing the energy that is stored by reducing the coenzyme

text: nicotinamide adenine dinucleotide

text: (NAD) into NADH.

text: PPIs have been studied from different perspectives: biochemistry, quantum chemistry, molecular dynamics, signal transduction, among others. All this information enables the creation of large protein interaction networks – similar to metabolic or genetic/epigenetic networks – that empower the current knowledge on biochemical cascades and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest.

text: PPIs have been studied from different perspectives:

text: biochemistry

text: quantum chemistry

text: molecular dynamics

text: signal transduction

text: , among others. All this information enables the creation of large protein interaction networks – similar to

text: metabolic

text: or

text: genetic/epigenetic networks

text: – that empower the current knowledge on

text: biochemical cascade

text: s and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest.

text: Cytocidal infections are often associated with changes in cell morphology, physiology and are thus important for the complete viral replication and transformation.  Cytopathic Effects, often include a change in cell's morphology such as fusion with adjacent cells to form polykaryocytes as well as the synthesis of nuclear and cytoplasmic inclusion bodies.  Physiological changes include the insufficient movement of ions, formation of secondary messengers, and activation of cellular cascades to continue cellular activity.  Biochemically, many viruses inhibit the synthesis of host DNA, RNA, proteins directly or even interfere with protein-protein, DNA-protein, RNA-protein interactions at the subcellular level.  Genotoxicity involves breaking, fragmenting, or rearranging chromosomes of the host.  Lastly, biologic effects include the viruses' ability to affect the activity of antigens and immunologlobulins in the host cell.

text: Cytocidal infections are often associated with changes in cell morphology, physiology and are thus important for the complete viral replication and transformation.  Cytopathic Effects, often include a change in cell's morphology such as fusion with adjacent cells to form polykaryocytes as well as the synthesis of nuclear and cytoplasmic

text: inclusion bodies

text: .  Physiological changes include the insufficient movement of ions, formation of secondary messengers, and activation of cellular cascades to continue cellular activity.  Biochemically, many viruses inhibit the synthesis of host DNA, RNA, proteins directly or even interfere with protein-protein, DNA-protein, RNA-protein interactions at the subcellular level.  Genotoxicity involves breaking, fragmenting, or rearranging chromosomes of the host.  Lastly, biologic effects include the viruses' ability to affect the activity of

text: antigens

text: and

text: immunologlobulins

text: in the host cell.

text: The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions occurring in many animals that produce urea ((NH)CO) from ammonia (NH). This cycle was the first metabolic cycle discovered (Hans Krebs and Kurt Henseleit, 1932), five years before the discovery of the TCA cycle. In mammals, the urea cycle takes place primarily in the liver, and to a lesser extent in the kidney.

text: The urea cycle (also known as the ornithine cycle) is a cycle of

text: biochemical

text: reactions occurring in many animals that produce

text: urea

text: N

text: H

text: C

text: O

text: ) from

text: ammonia

text: (NH). This cycle was the first metabolic cycle discovered (

text: Hans Krebs

text: and Kurt Henseleit, 1932), five years before the discovery of the

text: TCA cycle

text: . In

text: mammal

text: s, the urea cycle takes place primarily in the

text: liver

text: , and to a lesser extent in the

text: kidney

text: Transmetalation is often used as a step in the catalytic cycles of cross-coupling reactions. Some of the cross-coupling reactions that include a transmetalation step are Stille cross-coupling, Suzuki cross-coupling, Sonogashira cross-coupling, and Negishi cross-coupling. The most useful cross-coupling catalysts tend to be ones that contain palladium. Cross-coupling reactions have the general form of R′–X + M–R → R′–R + M–X and are used to form C–C bonds. R and R′ can be any carbon fragment. The identity of the metal, M, depends on which cross-coupling reaction is being used. Stille reactions use tin, Suzuki reactions use boron, Sonogashira reactions use copper, and Negishi reactions use zinc. The transmetalation step in palladium catalyzed reactions involve the addition of an R–M compound to produce an R′–Pd–R compound. Cross-coupling reactions have a wide range of applications in synthetic chemistry including the area of medicinal chemistry. The Stille reaction has been used to make an antitumor agent, (±)-epi-jatrophone; the Suzuki reaction has been used to make an antitumor agent, oximidine II; the Sonogashira reaction has been used to make an anticancer drug, eniluracil; and the Negishi reaction has been used to make the carotenoid β-carotene via a transmetalation cascade.

text: Transmetalation is often used as a step in the

text: catalytic cycle

text: s of

text: cross-coupling

text: reactions. Some of the cross-coupling reactions that include a transmetalation step are

text: Stille cross-coupling

text: Suzuki cross-coupling

text: Sonogashira cross-coupling

text: , and

text: Negishi cross-coupling

text: . The most useful cross-coupling catalysts tend to be ones that contain palladium. Cross-coupling reactions have the general form of R′–X + M–R → R′–R + M–X and are used to form C–C bonds. R and R′ can be any carbon fragment. The identity of the metal, M, depends on which cross-coupling reaction is being used. Stille reactions use tin, Suzuki reactions use boron, Sonogashira reactions use copper, and Negishi reactions use zinc. The transmetalation step in palladium catalyzed reactions involve the addition of an R–M compound to produce an R′–Pd–R compound. Cross-coupling reactions have a wide range of applications in synthetic chemistry including the area of

text: medicinal chemistry

text: . The Stille reaction has been used to make an antitumor agent, (±)-epi-jatrophone; the Suzuki reaction has been used to make an

text: antitumor

text: agent,

text: oximidine II

text: ; the Sonogashira reaction has been used to make an anticancer drug, eniluracil; and the Negishi reaction has been used to make the carotenoid β-carotene via a transmetalation cascade.

text: Cancer occurs when a single progenitor cell accumulates mutations and other changes in the DNA, histones, and other biochemical compounds that make up the cell's genome. The cell genome controls the structure of the cell's biochemical components, the biochemical reactions that occur within the cell, and the biological interactions of that cell with other cells. Certain combinations of mutations in the given progenitor cell ultimately result in that cell (also called a cancer stem cell) displaying a number of abnormal, malignant cellular properties that, when taken together, are considered characteristic of cancer, including:

text: Cancer occurs when a single progenitor cell accumulates

text: mutations

text: and other changes in the

text: DNA

text: histones

text: , and other biochemical compounds that make up the cell's

text: genome

text: . The cell genome controls the structure of the cell's biochemical components, the biochemical reactions that occur within the cell, and the biological interactions of that cell with other cells. Certain combinations of mutations in the given progenitor cell ultimately result in that cell (also called a cancer stem cell) displaying a number of abnormal,

text: malignant

text: cellular properties that, when taken together, are considered characteristic of cancer, including:

text: Metabolism involves two biochemical processes that occur in living organisms. The first is anabolism, which refers to the build up of molecules. The second is catabolism, the breakdown of molecules. These two processes work to regulate the amount of energy the body uses to maintain itself. During non-REM sleep, metabolic rate and brain temperature are lowered to deal with damages that may have occurred during time of wakefulness.

text: Metabolism

text: involves two

text: biochemical

text: processes that occur in living organisms. The first is

text: anabolism

text: , which refers to the build up of molecules. The second is

text: catabolism

text: , the breakdown of molecules. These two processes work to regulate the amount of energy the body uses to maintain itself. During non-REM sleep,

text: metabolic rate

text: and brain temperature are lowered to deal with damages that may have occurred during time of wakefulness.

text: The primary cause of squelching is believed to be the interaction of activator molecules disrupting the biochemical pathways associated with related processes due to structural similarity between the activators and important substrates along that pathway. In particular, the activator binds to transcription factors along alternative biochemical pathways, inhibiting the ability of these transcription factors to bind to their true targets. As in the example above, sequestration of an intermediate in a metabolic pathway is a confounding variable in genetic studies because knowledge of the expected binding targets of the primary molecules involved does not help predict why unexpected behavior results.

text: The primary cause of squelching is believed to be the interaction of activator molecules disrupting the

text: biochemical pathways

text: associated with related processes due to structural similarity between the activators and important substrates along that pathway. In particular, the activator binds to

text: transcription factors

text: along alternative biochemical pathways, inhibiting the ability of these transcription factors to bind to their true targets. As in the example above, sequestration of an intermediate in a metabolic pathway is a confounding variable in genetic studies because knowledge of the expected binding targets of the primary molecules involved does not help predict why unexpected behavior results.

text: It is thought that the two residues Glu270 and His288 are important for the enzyme's catalytic function, while the residue Arg241 is thought to be important for substrate specificity.

text: It is thought that the two

text: residues

text: Glu270 and His288 are important for the enzyme's catalytic function, while the residue Arg241 is thought to be important for substrate specificity.

text: Subsequent biochemical analysis supports the conclusion of a ribozyme function, and determined further characteristics of the chemical reaction catalyzed by the ribozyme.

text: A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions.

text: A metabolic network is the complete set of metabolic and physical processes that determine the

text: physiological

text: and

text: biochemical

text: properties of a

text: cell

text: . As such, these networks comprise the chemical reactions of

text: metabolism

text: , the

text: metabolic pathway

text: s, as well as the regulatory interactions that guide these reactions.

text: Although the individual members of the two recombinase families can perform reactions with same practical outcomes, the two families are unrelated to each other, having different protein structures and reaction mechanisms.  Unlike tyrosine recombinases, serine recombinases are highly modular as was first hinted by biochemical studies, and later shown by crystallographic structures. Knowledge of these protein structures could prove useful when attempting to reengineer recombinase proteins as tools for genetic manipulation.

text: All electronic states of methylidyne yield one unpaired electron, giving rise to varying degrees of radical chemistry. The ground state is a doublet radical with one unpaired electron (XΠ), and the first two excited states are a quartet radical with three unpaired electrons  (aΣ) and a doublet radical with one unpaired electron (AΔ). With the quartet radical only 71 kJ above the ground state, a sample of methylidyne exists as a mixture of electronic states even at room temperature, giving rise to complex reactions. For example, reactions of the doublet radical with non-radical species involves insertion or addition, whereas reactions of the quartet radical generally involves only abstraction.

text: 5α-Reductase is an enzyme that converts testosterone to 5α-dihydrotestosterone (DHT) in peripheral tissues. These enzymes also participate in the creation of such neurosteroids as allopregnanolone and THDOC, convert progesterone into dihydroprogesterone (DHP), and convert deoxycorticosterone (DOC) into dihydrodeoxycorticosterone (DHDOC). 5-ARD is biochemically characterized by low to low-normal levels of testosterone and decreased levels of DHT, creating a higher testosterone/DHT ratio.

text: is an

text: enzyme

text: that converts

text: testosterone

text: to

text: (DHT) in peripheral tissues. These enzymes also participate in the creation of such

text: neurosteroid

text: s as

text: allopregnanolone

text: and

text: THDOC

text: , convert progesterone into dihydroprogesterone (DHP), and convert deoxycorticosterone (DOC) into dihydrodeoxycorticosterone (DHDOC). 5-ARD is biochemically characterized by low to low-normal levels of testosterone and decreased levels of DHT, creating a higher testosterone/DHT ratio.

text: Allelopathy is a biological phenomenon by which an organism produces one or more biochemicals that influence the germination, growth, survival, and reproduction of other organisms. These biochemicals are known as allelochemicals and can have beneficial (positive allelopathy) or detrimental (negative allelopathy) effects on the target organisms and the community. Allelochemicals are a subset of secondary metabolites, which are not required for metabolism (i.e. growth, development and reproduction) of the allelopathic organism. Allelochemicals with negative allelopathic effects are an important part of plant defense against herbivory.

text: Allelopathy is a biological phenomenon by which an organism produces one or more

text: biochemical

text: s that influence the germination, growth, survival, and reproduction of other organisms. These biochemicals are known as allelochemicals and can have beneficial (positive allelopathy) or detrimental (negative allelopathy) effects on the target organisms and the community. Allelochemicals are a subset of

text: secondary metabolites

text: , which are not required for metabolism (i.e. growth, development and reproduction) of the allelopathic organism. Allelochemicals with negative allelopathic effects are an important part of

text: plant defense against herbivory

text: Other examples of this class of compound have been made; many inorganic chemists are now using FcPS (Fc = ferrocene) as a starting material in reactions investigating the general chemistry of the 1,3,2,4-dithiadiphosphetane 2,4-disulfides, one reaction for this is that the FcPS compound and all its derivatives are red which make column chromatography of the products more easy. Also the ferrocenyl groups provide an electrochemical handle which provide another means of investigating the properties of the products.

text: Other examples of this class of compound have been made; many inorganic chemists are now using FcPS (Fc =

text: ferrocene

text: ) as a starting material in reactions investigating the general chemistry of the 1,3,2,4-dithiadiphosphetane 2,4-disulfides, one reaction for this is that the FcPS compound and all its derivatives are red which make column chromatography of the products more easy. Also the ferrocenyl groups provide an electrochemical handle which provide another means of investigating the properties of the products.

text: Among the vast number of different biomolecules, many are complex and large molecules (called polymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types. For example, a protein is a polymer whose subunits are selected from a set of twenty or more amino acids, carbohydrates are formed from sugars known as monosaccharides, oligosaccharides, and polysaccharides, lipids are formed from fatty acids and glycerols, and nucleic acids are formed from nucleotides. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions. The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the genetic code (DNA, RNA), protein synthesis, cell membrane transport, and signal transduction.

text: Among the vast number of different biomolecules, many are complex and large molecules (called polymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types. For example, a protein is a polymer whose subunits are selected from a set of twenty or more amino acids, carbohydrates are formed from sugars known as monosaccharides, oligosaccharides, and polysaccharides, lipids are formed from fatty acids and glycerols, and nucleic acids are formed from nucleotides. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions. The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the

text: genetic code

text: (DNA, RNA),

text: protein synthesis

text: cell membrane transport

text: , and

text: signal transduction

text: People have different metabolic rates that can fluctuate due to activity level and environmental conditions. The ASHRAE 55-2010 Standard defines metabolic rate as the level of transformation of chemical energy into heat and mechanical work by metabolic activities within an organism, usually expressed in terms of unit area of the total body surface. Metabolic rate is expressed in met units, which are defined as follows:

text: Limulus clotting enzyme (, clotting enzyme) is an enzyme. This enzyme catalyses the following chemical reaction

text: Limulus clotting enzyme (, clotting enzyme) is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Chemical changes occur when a substance combines with another to form a new substance, called chemical synthesis or, alternatively, chemical decomposition into two or more different substances. These processes are called chemical reactions and, in general, are not reversible except by further chemical reactions. Some reactions produce heat and are called exothermic reactions and others may require heat to enable the reaction to occur, which are called endothermic reactions. Understanding chemical changes is a major part of the science of chemistry.

text: Chemical changes occur when a substance combines with another to form a new substance, called

text: chemical synthesis

text: or, alternatively,

text: chemical decomposition

text: into two or more different substances. These processes are called

text: chemical reaction

text: s and, in general, are not reversible except by further chemical reactions. Some reactions produce

text: heat

text: and are called

text: exothermic reaction

text: s and others may require heat to enable the reaction to occur, which are called

text: endothermic reactions

text: . Understanding chemical changes is a major part of the science of

text: chemistry

text: With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human. Several of these networks are available online:Kyoto Encyclopedia of Genes and Genomes (KEGG), EcoCyc , BioCyc  and metaTIGER .Metabolic networks are powerful tools for studying and modelling metabolism.

text: With the sequencing of complete

text: genomes

text: , it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human. Several of these networks are available online:Kyoto Encyclopedia of Genes and Genomes (KEGG), EcoCyc , BioCyc  and metaTIGER .Metabolic networks are powerful tools for studying and modelling metabolism.

text: There is a fairly large variation in the types of inorganic substrates that these microorganisms can use to produce energy. The chemolithotrophs that are best documented are aerobic respirers, meaning that they use oxygen in their metabolic process. The list of these microorganisms that employ anaerobic respiration though is growing. At the heart of this metabolic process is an electron transport system that is similar to that of chemoorganotrophs. The major difference between these two microorganisms is that chemolithotrophs directly provide electrons to the electron transport chain, while chemoorganotrophs must generate their own cellular reducing power by oxidizing reduced organic compounds. Chemolithotrophs bypass this by obtaining their reducing power directly from the inorganic substrate or by the reverse electron transport reaction.

text: There is a fairly large variation in the types of inorganic substrates that these

text: microorganisms

text: can use to produce energy. The chemolithotrophs that are best documented are aerobic respirers, meaning that they use oxygen in their metabolic process. The list of these

text: microorganisms

text: that employ anaerobic respiration though is growing. At the heart of this metabolic process is an electron transport system that is similar to that of chemoorganotrophs. The major difference between these two

text: microorganism

text: s is that chemolithotrophs directly provide electrons to the electron transport chain, while chemoorganotrophs must generate their own cellular reducing power by oxidizing reduced organic compounds. Chemolithotrophs bypass this by obtaining their reducing power directly from the inorganic substrate or by the reverse electron transport reaction.

text: SABIO-RK comprises a reaction-oriented representation of quantitative information on reaction dynamics based on a given selected publication.This comprises all available kinetic parameters together with their corresponding rate equations,as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined.Additionally, SABIO-RK contains information about the underlying biochemical reactions and pathways including their reaction participants,cellular location and detailed information about the enzymes catalysing the reactions.

text: SABIO-RK comprises a reaction-oriented representation of quantitative information on reaction dynamics based on a given selected publication.This comprises all available kinetic parameters together with their corresponding

text: rate equation

text: s,as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined.Additionally, SABIO-RK contains information about the underlying biochemical reactions and

text: pathways

text: including their

text: reaction participants

text: cellular

text: location and detailed information about the

text: enzymes

text: catalysing the reactions.

text: Plant respiration is limited by the process of diffusion. Plants take in carbon dioxide through holes on the undersides of their leaves known as stoma or pores. However, most plants require little air. Most plants have relatively few living cells outside of their surface because air (which is required for metabolic content) can penetrate only skin deep. However, most plants are not involved in highly aerobic activities, and thus have no need of these living cells.

text: Plant respiration is limited by the process of

text: diffusion

text: . Plants take in carbon dioxide through holes on the undersides of their

text: leaves

text: known as

text: stoma

text: or pores. However, most plants require little air. Most plants have relatively few living cells outside of their surface because air (which is required for metabolic content) can penetrate only skin deep. However, most plants are not involved in highly

text: aerobic

text: activities, and thus have no need of these living cells.

text: Gamma-renin () is an enzyme. This enzyme catalyses the following chemical reaction

text: Gamma-renin () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: In highly concentrated solutions, simple approximations such as the Henderson–Hasselbalch equation are no longer valid due to the variations of the activity coefficients. The Hammett acidity function is used in fields such as physical organic chemistry for the study of acid-catalyzed reactions, because some of these reactions use acids in very high concentrations, or even neat (pure).

text: In highly concentrated solutions, simple approximations such as the

text: Henderson–Hasselbalch equation

text: are no longer valid due to the variations of the

text: activity coefficient

text: s. The Hammett acidity function is used in fields such as

text: physical organic chemistry

text: for the study of

text: acid-catalyzed

text: reactions, because some of these reactions use acids in very high concentrations, or even neat (pure).

text: Macromonas bipunctata has been cultured in many studies that show HO   is formed in different biochemical reactions: not only in the process of respiration with the participation of enzymes of the electron transport chain, but also in the course of utilization of intracellular oxalate inclusions in the cytoplasm.  Oxidation of oxalate inclusions by oxalate oxidase leads to HO accumulation. Furthermore, in the end process of becoming a toxic metabolite, it would decompose upon chemical interaction with the reduced sulfur compounds, whose presence is characteristic for the habitat of these bacteria. When grown on the media containing organic acids of the TCA cycle, the unicellular sulfur bacterium M. bipunctata is able to synthesize and store calcium oxalates inside the cell. This process is possible due to the presence of the high oxaloacetate hydrolase activity in M. bipunctata.

text: Macromonas

text: bipunctata has been cultured in many studies that show

text: HO

text: is formed in different

text: biochemical reactions

text: : not only in the process of

text: respiration

text: with the participation of

text: enzyme

text: s of the

text: electron transport chain

text: , but also in the course of utilization of intracellular

text: oxalate

text: inclusions

text: in the

text: cytoplasm

text: Oxidation

text: of

text: oxalate

text: inclusions by

text: oxalate

text: oxidase

text: leads to HO accumulation. Furthermore, in the end process of becoming a toxic

text: metabolite

text: , it would decompose upon chemical interaction with the reduced sulfur compounds, whose presence is characteristic for the habitat of these bacteria. When grown on the media containing

text: organic acid

text: s of the

text: TCA cycle

text: , the unicellular sulfur bacterium M. bipunctata is able to synthesize and store

text: calcium oxalate

text: s inside the cell. This process is possible due to the presence of the high oxaloacetate hydrolase activity in M. bipunctata.

text: Flavastacin () is an enzyme. This enzyme catalyses the following chemical reaction

text: Flavastacin () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Guanosine is a purine nucleoside comprising guanine attached to a ribose (ribofuranose) ring via a β-N-glycosidic bond. Guanosine can be phosphorylated to become guanosine monophosphate (GMP), cyclic guanosine monophosphate (cGMP), guanosine diphosphate (GDP), and guanosine triphosphate (GTP). These forms play important roles in various biochemical processes such as synthesis of nucleic acids and proteins, photosynthesis, muscle contraction, and intracellular signal transduction (cGMP). When guanine is attached by its N9 nitrogen to the C1 carbon of a deoxyribose ring it is known as deoxyguanosine.

text: Guanosine is a

text: purine

text: nucleoside

text: comprising

text: guanine

text: attached to a

text: ribose

text: ribofuranose

text: ) ring via a β-N-

text: glycosidic bond

text: . Guanosine can be

text: phosphorylated

text: to become

text: guanosine monophosphate

text: (GMP),

text: cyclic guanosine monophosphate

text: (cGMP),

text: guanosine diphosphate

text: (GDP), and

text: guanosine triphosphate

text: (GTP). These forms play important roles in various biochemical processes such as synthesis of

text: nucleic acid

text: s and proteins,

text: photosynthesis

text: , muscle contraction, and intracellular signal transduction (cGMP). When guanine is attached by its N9 nitrogen to the C1 carbon of a

text: deoxyribose

text: ring it is known as

text: deoxyguanosine

text: He published several works analysing and summarising different physiological subfields, and on the chemical composition of body tissues such as muscles (creatine), brain tissue, breast milk, respiration, food chemistry, pathobiochemical investigations, and also purely chemical analyses. He also published a textbook on organic chemistry in 1850, titled Lehrbuch der organischen Chemie.

text: He published several works analysing and summarising different physiological subfields, and on the

text: chemical composition

text: of

text: body tissue

text: s such as

text: muscles

text: creatine

text: brain tissue

text: breast milk

text: respiration

text: food chemistry

text: pathobiochemical

text: investigations, and also purely chemical analyses. He also published a textbook on

text: organic chemistry

text: in 1850, titled Lehrbuch der organischen Chemie.

text: Pentosuria is a condition where the sugar xylitol, a pentose, presents in the urine in unusually high concentrations. It was characterized as an inborn error of carbohydrate metabolism in 1908. It is associated with a deficiency of L-xylulose reductase, necessary for xylitol metabolism.  L-Xylulose is a reducing sugar, so it may give false diagnosis of diabetes, as it is found in high concentrations in urine. However, people with pentosuria do not have nonstandard metabolism of glucose, like diabetics. Patients of pentosuria have a low concentration of the sugar d-xyloketose.  Using, Phenyl pentosazone crystals, phloroglucin reaction, and absorption spectrum, pentose can be traced back as the reducing substance in urine, with those that have pentosuria.

text: Pentosuria is a condition where the sugar

text: xylitol

text: , a

text: pentose

text: , presents in the

text: urine

text: in unusually high concentrations. It was characterized as an inborn error of

text: carbohydrate metabolism

text: in 1908. It is associated with a deficiency of

text: L-xylulose reductase

text: , necessary for xylitol metabolism.  L-

text: Xylulose

text: is a

text: reducing sugar

text: , so it may give false diagnosis of diabetes, as it is found in high concentrations in urine. However, people with pentosuria do not have nonstandard metabolism of glucose, like

text: diabetics

text: . Patients of pentosuria have a low concentration of the sugar d-xyloketose.  Using, Phenyl pentosazone crystals, phloroglucin reaction, and absorption spectrum, pentose can be traced back as the reducing substance in urine, with those that have pentosuria.

text: Isotopes of carbon are atomic nuclei that contain six protons plus a number of neutrons (varying from 2 to 16). Carbon has two stable, naturally occurring isotopes. The isotope carbon-12 (C) forms 98.93% of the carbon on Earth, while carbon-13 (C) forms the remaining 1.07%. The concentration of C is further increased in biological materials because biochemical reactions discriminate against C. In 1961, the International Union of Pure and Applied Chemistry (IUPAC) adopted the isotope carbon-12 as the basis for atomic weights. Identification of carbon in nuclear magnetic resonance (NMR) experiments is done with the isotope C.

text: Isotope

text: s of carbon are

text: atomic nuclei

text: that contain six

text: proton

text: s plus a number of

text: neutron

text: s (varying from 2 to 16). Carbon has two stable, naturally occurring

text: isotope

text: s. The isotope

text: (C) forms 98.93% of the carbon on Earth, while

text: (C) forms the remaining 1.07%. The concentration of C is further increased in biological materials because biochemical reactions discriminate against C. In 1961, the

entity_name: International Union of Pure and Applied Chemistry

text: International Union of Pure and Applied Chemistry

text: (IUPAC) adopted the isotope

text: as the basis for

text: atomic weight

text: s. Identification of carbon in

text: nuclear magnetic resonance

text: (NMR) experiments is done with the isotope C.

text: Born Paul George Gassman on June 22, 1935 in Alden, New York, Gassman is the son of Joseph Martin Gassman and Florence Marie Rautenstrauch Gassman, of German Swiss parentage. In 1957, he graduated with a B.S. degree in Chemistry from Canisius College in Buffalo, New York and received his Ph.D. in three years from Cornell University in 1960, where he studied under Jerrold Meinwald. He continued at Cornell as a postdoctoral fellow before his appointment as an Assistant Professor of Chemistry at the Ohio State University. After becoming a full professor at Ohio State in 1969, Gassman brought his research to the University of Minnesota in 1974. Leading organic chemistry research at the University of Minnesota until 1993, Gassman's work centered in the areas of organic reaction mechanisms (including the Gassman indole synthesis), mechanisms of catalysis (including hydrocarbon metathesis), X-ray photoelectron spectroscopy, cyclo-addition reactions, enzyme mechanisms, organoelectro-chemistry, carbanion chemistry, synthesis of heterocyclic molecules, oxidation of hydrocarbons, nitrenium ion chemistry, and electron-transfer reactions. This work helped him achieve status as an internationally recognized chemist  serving the American Chemical Society as Chairman of the Division of Organic Chemistry (1981) and eventually as President of the American Chemical Society in 1990.

text: Born Paul George Gassman on June 22, 1935 in Alden, New York, Gassman is the son of Joseph Martin Gassman and Florence Marie Rautenstrauch Gassman, of German Swiss parentage. In 1957, he graduated with a B.S. degree in Chemistry from

text: Canisius College

text: in Buffalo, New York and received his Ph.D. in three years from Cornell University in 1960, where he studied under

text: Jerrold Meinwald

text: . He continued at Cornell as a postdoctoral fellow before his appointment as an Assistant Professor of Chemistry at the

text: Ohio State University

text: . After becoming a full professor at Ohio State in 1969, Gassman brought his research to the

text: University of Minnesota

text: in 1974. Leading organic chemistry research at the University of Minnesota until 1993, Gassman's work centered in the areas of organic reaction mechanisms (including the

text: Gassman indole synthesis

text: ), mechanisms of catalysis (including hydrocarbon metathesis), X-ray photoelectron spectroscopy, cyclo-addition reactions, enzyme mechanisms, organoelectro-chemistry, carbanion chemistry, synthesis of heterocyclic molecules, oxidation of hydrocarbons, nitrenium ion chemistry, and electron-transfer reactions. This work helped him achieve status as an internationally recognized chemist  serving the American Chemical Society as Chairman of the Division of Organic Chemistry (1981) and eventually as

entity_name: Presidents of the American Chemical Society

text: President of the American Chemical Society

text: in 1990.

text: Although it is important in catabolism, NADH is also used in anabolic reactions, such as gluconeogenesis. This need for NADH in anabolism poses a problem for prokaryotes growing on nutrients that release only a small amount of energy. For example, nitrifying bacteria such as Nitrobacter oxidize nitrite to nitrate, which releases sufficient energy to pump protons and generate ATP, but not enough to produce NADH directly. As NADH is still needed for anabolic reactions, these bacteria use a nitrite oxidoreductase to produce enough proton-motive force to run part of the electron transport chain in reverse, generating NADH.

text: Although it is important in catabolism, NADH is also used in anabolic reactions, such as

text: gluconeogenesis

text: . This need for NADH in anabolism poses a problem for prokaryotes growing on nutrients that release only a small amount of energy. For example,

text: nitrifying

text: bacteria such as

text: Nitrobacter

text: oxidize nitrite to nitrate, which releases sufficient energy to pump protons and generate ATP, but not enough to produce NADH directly. As NADH is still needed for anabolic reactions, these bacteria use a

text: nitrite oxidoreductase

text: to produce enough

text: proton-motive force

text: to run part of the electron transport chain in reverse, generating NADH.

text: Some organisms employ even more radical variants of photosynthesis. Some archea use a simpler method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump. This produces a proton gradient more directly, which is then converted to chemical energy. The process does not involve carbon dioxide fixation and does not release oxygen, and seems to have evolved separately from the more common types of photosynthesis.

text: Some organisms employ even more radical variants of photosynthesis. Some

text: archea

text: use a simpler method that employs a pigment similar to those used for vision in animals. The

text: bacteriorhodopsin

text: changes its configuration in response to sunlight, acting as a proton pump. This produces a proton gradient more directly, which is then converted to chemical energy. The process does not involve carbon dioxide fixation and does not release oxygen, and seems to have evolved separately from the more common types of photosynthesis.

text: James Lake presented a 2 primary kingdom arrangement (Parkaryotae + eukaryotes and eocytes + Karyotae) and suggested a 5 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, Halobacteria, and Eubacteria) based on ribosomal structure and a 4 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, and Photocyta), bacteria being classified according to 3 major biochemical innovations: photosynthesis (Photocyta), methanogenesis (Methanobacteria), and sulfur respiration (Eocyta). He has also discovered evidence that Gram-negative bacteria arose from a symbiosis between 2 Gram-positive bacteria.

text: James Lake

text: presented a 2 primary kingdom arrangement (Parkaryotae + eukaryotes and eocytes + Karyotae) and suggested a 5 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, Halobacteria, and Eubacteria) based on ribosomal structure and a 4 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, and Photocyta), bacteria being classified according to 3 major biochemical innovations: photosynthesis (Photocyta), methanogenesis (Methanobacteria), and sulfur respiration (Eocyta). He has also discovered evidence that Gram-negative bacteria arose from a symbiosis between 2 Gram-positive bacteria.

text: Loss of nitrogen (urea) was observed already in the 1930s in fracture patients by the Scottish physician David Cuthbertson. The reason for the patients' catabolic response was not understood at the time, but later attention was turned to the stress reaction caused by the surgery.  The evolutionary background is believed to be that a wounded animal increases its chance of survival by using stored energy reserves. The stress reaction thus initiates a catabolic state by an increased release of catabolic hormones. Additionally immunosuppressive hormones are also released. In a surgery patient, the stress reaction is considered detrimental for wound healing. However, surgical stress reduced mortality from endotoxin shock. Today, development of new surgical techniques and anaesthetic protocols aim to minimise the surgical stress reaction.

text: Loss of nitrogen (urea) was observed already in the 1930s in fracture patients by the Scottish physician

text: David Cuthbertson

text: . The reason for the patients' catabolic response was not understood at the time, but later attention was turned to the stress reaction caused by the surgery.  The evolutionary background is believed to be that a wounded animal increases its chance of survival by using stored energy reserves. The stress reaction thus initiates a catabolic state by an increased release of catabolic hormones. Additionally immunosuppressive hormones are also released. In a surgery patient, the stress reaction is considered detrimental for wound healing. However, surgical stress reduced mortality from endotoxin shock. Today, development of new surgical techniques and anaesthetic protocols aim to minimise the surgical stress reaction.

text: The E. Coli Metabolome Database (ECMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Escherichia coli (E. coli strain K12, MG1655). Escherichia coli is perhaps the best studied bacterium on earth and has served as the "model microbe" in microbiology research for more than 60 years. The ECMDB is essentially an E. coli "omics" encyclopedia containing detailed data on E. coli's genome, proteome and its metabolome. ECMDB is part of a suite of organism-specific metabolomics databases that includes DrugBank, HMDB, YMDBand SMPDB. As a metabolomics resource, the ECMDB is designed to facilitate research in the area gut/microbiome metabolomics and environmental metabolomics. The ECMDB contains two kinds of data: 1) chemical data and 2) molecular biology and/or biochemical data. The chemical data includes more than 2700 metabolite structures with detailed metabolite descriptions along with nearly 5000 NMR, GC-MS and LC-MS spectra corresponding to these metabolites. The biochemical data includes nearly 1600 protein (and DNA) sequences and more than 3100 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the ECMDB contains more than 80 data fields with approximately 65% of the information being devoted to chemical data and the other 35% of the information devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank).  The ECMDB also has a variety of structure and pathway viewing applets. The ECMDB database offers a number of text, sequence, spectral, chemical structure and relational query searches.  These are described in more detail below.

text: The E. Coli Metabolome Database (ECMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Escherichia coli (E. coli strain K12, MG1655).

text: Escherichia coli

text: is perhaps the best studied

text: bacterium

text: on earth and has served as the "model microbe" in

text: microbiology

text: research for more than 60 years. The ECMDB is essentially an E. coli "omics" encyclopedia containing detailed data on E. coli's

text: genome

text: proteome

text: and its

text: metabolome

text: . ECMDB is part of a suite of organism-specific metabolomics databases that includes

text: DrugBank

text: HMDB

text: YMDB

text: and

text: SMPDB

text: . As a metabolomics resource, the ECMDB is designed to facilitate research in the area gut/microbiome metabolomics and

text: environmental metabolomics

text: . The ECMDB contains two kinds of data: 1) chemical data and 2) molecular biology and/or biochemical data. The chemical data includes more than 2700 metabolite structures with detailed metabolite descriptions along with nearly 5000 NMR,

text: GC-MS

text: and

text: LC-MS

text: spectra corresponding to these metabolites. The biochemical data includes nearly 1600 protein (and DNA) sequences and more than 3100 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the ECMDB contains more than 80 data fields with approximately 65% of the information being devoted to chemical data and the other 35% of the information devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (

text: KEGG

text: PubChem

text: MetaCyc

text: ChEBI

text: PDB

text: UniProt

text: , and

text: GenBank

text: ).  The ECMDB also has a variety of structure and pathway viewing applets. The ECMDB database offers a number of text, sequence, spectral, chemical structure and relational query searches.  These are described in more detail below.

text: Fructose-bisphosphate aldolase (), often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). Aldolase can also produce DHAP from other (3S,4R)-ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1,7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways,  use the reverse reaction. Glycolysis, a catabolic pathway, uses the forward reaction.  Aldolase is divided into two classes by mechanism.

text: Fructose-bisphosphate aldolase (), often just aldolase, is an

text: enzyme

text: catalyzing a

text: reversible reaction

text: that splits the

text: aldol

text: fructose 1,6-bisphosphate

text: , into the

text: triose

text: phosphates

text: dihydroxyacetone phosphate

text: (DHAP) and

text: glyceraldehyde 3-phosphate

text: (G3P). Aldolase can also produce DHAP from other (3S,4R)-

text: ketose

text: 1-phosphates such as

text: fructose 1-phosphate

text: and

text: sedoheptulose 1,7-bisphosphate

text: Gluconeogenesis

text: and the

text: Calvin cycle

text: , which are

text: anabolic pathway

text: s,  use the reverse reaction.

text: Glycolysis

text: , a

text: catabolic pathway

text: , uses the forward reaction.  Aldolase is divided into two classes by mechanism.

text: Some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. Virtually every reaction in a living cell requires an enzyme to lower the activation energy of the reaction. These molecules recognize specific reactant molecules called substrates; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 10 or more; a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

text: Some proteins perform largely structural roles. For instance, movements of the proteins

text: actin

text: and

text: myosin

text: ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind.

text: Antibodies

text: are an example of proteins that attach to one specific type of molecule. In fact, the

text: enzyme-linked immunosorbent assay

text: (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the

text: enzyme

text: s. Virtually every reaction in a living cell requires an enzyme to lower the activation energy of the reaction. These molecules recognize specific reactant molecules called

text: substrate

text: s; they then

text: catalyze

text: the reaction between them. By lowering the

text: activation energy

text: , the enzyme speeds up that reaction by a rate of 10 or more; a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

text: Atroxase () is an enzyme. This enzyme catalyses the following chemical reaction

text: Atroxase () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Glutamate synthase catalyzes the conversion of 2-oxoglutarate into L-glutamate with L-glutamine serving as the nitrogen source for the reaction. All glutamate synthases are iron-sulfur flavoproteins containing an iron-sulfur cluster and FMN. The three classes of glutamate synthases are categorized based on their sequences and biochemical properties. Even though there are three classes of this enzyme, it is believed that they all operate through the same mechanism, only differing by what first reduces the FMN. The enzyme produces two glutamate molecules: one by the hydrolysis of glutamine (forming glutamate and ammonia), and the second by the ammonia produced from the first reaction attacking 2-oxoglutarate, which is reduced by FMN to glutamate.

text: Enzymes catalyze chemical reactions at rates that are astounding relative to uncatalyzed chemistry at the same reaction conditions.  Each catalytic event requires a minimum of three or often more steps, all of which occur within the few milliseconds that characterize typical enzymatic reactions.  According to transition state theory, the smallest fraction of the catalytic cycle is spent in the most important step, that of the transition state.  The original proposals of absolute reaction rate theory for chemical reactions defined the transition state as a distinct species in the reaction coordinate that determined the absolute reaction rate.  Soon thereafter, Linus Pauling proposed that the powerful catalytic action of enzymes could be explained by specific tight binding to the transition state species   Because reaction rate is proportional to the fraction of the reactant in the transition state complex, the enzyme was proposed to increase the concentration of the reactive species.

text: Enzymes catalyze

text: chemical reactions at rates that are astounding relative to uncatalyzed chemistry at the same reaction conditions.  Each catalytic event requires a minimum of three or often more steps, all of which occur within the few milliseconds that characterize typical enzymatic reactions.  According to transition state theory, the smallest fraction of the catalytic cycle is spent in the most important step, that of the transition state.  The original proposals of absolute reaction rate theory for chemical reactions defined the transition state as a distinct species in the reaction coordinate that determined the absolute reaction rate.  Soon thereafter,

text: Linus Pauling

text: proposed that the powerful catalytic action of enzymes could be explained by specific tight binding to the transition state species   Because reaction rate is proportional to the fraction of the reactant in the transition state complex, the enzyme was proposed to increase the concentration of the reactive species.

text: The citric acid cycle – also known as the tricarboxylic acid (TCA) cycle or the Krebs cycle – is a series of chemical reactions used by all aerobic organisms to release stored  energy through the oxidation of acetyl-CoA derived from carbohydrates, fats and proteins into carbon dioxide and chemical energy in the form of adenosine triphosphate, (ATP.)  In addition, the cycle provides precursors of certain amino acids as well as the reducing agent NADH that is used in numerous other biochemical reactions.  Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically.

text: The citric acid cycle – also known as the tricarboxylic acid (TCA) cycle or the Krebs cycle – is a series of

text: chemical reaction

text: s used by all

text: aerobic organism

text: s to release stored  energy through the

text: oxidation

text: of

text: acetyl-CoA

text: derived from

text: carbohydrate

text: s,

text: fat

text: s and

text: protein

text: s into

text: carbon dioxide

text: and chemical energy in the form of

text: adenosine triphosphate

text: , (ATP.)  In addition, the cycle provides

text: precursors

text: of certain amino acids as well as the

text: reducing agent

text: NADH

text: that is used in numerous other biochemical reactions.  Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular

text: metabolism

text: and may have originated

text: abiogenically

text: The mechanism of FAS I and FAS II elongation and reduction is the same, as the domains of the FAS II enzymes are largely homologous to their domain counterparts in FAS I multienzyme polypeptides. However, the differences in the organization of the enzymes - integrated in FAS I, discrete in FAS II - gives rise to many important biochemical differences.

text: Nearly all other biochemical ester hydrolysis reactions occur through S2 reaction at the acyl carbon. However, isotope labeling studies have demonstrated that the oxygen on the final 11-cis-retinol product of RPE65 originates from the solvent rather than the reacting ester, supporting the O-alkyl cleavage mechanism. Additionally, an S2 ester hydrolysis reaction mechanism would rely on a separate, unfavorable S2 attack at electron rich C11 by some nucleophile - most likely a cystine residue - to complete the isomerization portion of the reaction. Not only is nucleophilic attack of an alkene energetically unfavorable, but the active site region is lacking cystine residues to act as the nucleophile.

text: Nearly all other biochemical ester hydrolysis reactions occur through

text: S2 reaction

text: at the

text: acyl carbon

text: . However, isotope labeling studies have demonstrated that the oxygen on the final 11-cis-retinol product of RPE65 originates from the solvent rather than the reacting ester, supporting the O-alkyl cleavage mechanism. Additionally, an S2 ester hydrolysis reaction mechanism would rely on a separate, unfavorable S2 attack at electron rich C11 by some

text: nucleophile

text: - most likely a

text: cystine

text: residue - to complete the isomerization portion of the reaction. Not only is nucleophilic attack of an

text: alkene

text: energetically unfavorable, but the active site region is lacking cystine residues to act as the nucleophile.

text: The fact that a reaction is thermodynamically possible does not mean that it will actually occur.  A mixture of hydrogen gas and oxygen gas does not spontaneously ignite. It is necessary either to supply an activation energy or to lower the intrinsic activation energy of the system, in order to make most biochemical reactions proceed at a useful rate.  Living systems use complex macromolecular structures to lower the activation energies of biochemical reactions.

text: The fact that a reaction is thermodynamically possible does not mean that it will actually occur.  A mixture of hydrogen gas and oxygen gas does not spontaneously ignite. It is necessary either to supply an

text: activation energy

text: or to lower the intrinsic activation energy of the system, in order to make most biochemical reactions proceed at a useful rate.  Living systems use complex macromolecular structures to lower the activation energies of biochemical reactions.

text: is produced in chemistry and biology laboratories, often as a by-product of other reactions; in industry for the hydrogenation of unsaturated substrates; and in nature as a means of expelling reducing equivalents in biochemical reactions.

text: is produced in chemistry and biology laboratories, often as a by-product of other reactions; in industry for the

text: hydrogenation

text: of

text: unsaturated

text: substrates; and in nature as a means of expelling

text: reducing

text: equivalents in biochemical reactions.

text: Within the kinetic paradigm, kinetic modelling of metabolic networks can be purely theoretical, exploring the potential space of dynamic metabolic fluxes under perturbations away from steady state using formalisms such as biochemical systems theory. Such explorations are most informative when accompanied by empirical measurements of the system under study following actual perturbations, as is the case in metabolic control analysis.

text: Within the kinetic paradigm, kinetic modelling of metabolic networks can be purely theoretical, exploring the potential space of dynamic metabolic fluxes under perturbations away from steady state using formalisms such as

text: biochemical systems theory

text: . Such explorations are most informative when accompanied by empirical measurements of the system under study following actual perturbations, as is the case in

text: metabolic control analysis

text: In addition to the anabolic carboxysomes, several catabolic BMCs have been characterized that participate in the heterotrophic metabolism via short-chain aldehydes; they are collectively termed metabolosomes.

text: In free radical halogenation reactions radical substitution takes place with halogen reagents and alkane substrates. Another important class of radical substitutions involve aryl radicals. One example is the hydroxylation of benzene by Fenton's reagent. Many oxidation and reduction reactions in organic chemistry have free radical intermediates, for example the oxidation of aldehydes to carboxylic acids with chromic acid. Coupling reactions can also be considered radical substitutions. Certain aromatic substitutions takes place by radical-nucleophilic aromatic substitution. Auto-oxidation is a process responsible for deterioration of paints and food and lab hazards such as diethyl ether peroxide.

text: In

text: free radical halogenation

text: reactions radical substitution takes place with

text: halogen

text: reagents and

text: alkane

text: substrates. Another important class of radical substitutions involve

text: aryl radical

text: s. One example is the hydroxylation of

text: benzene

text: by

text: Fenton's reagent

text: . Many oxidation and reduction reactions in organic chemistry have free radical

text: intermediate

text: s, for example the oxidation of

text: aldehyde

text: s to

text: carboxylic acid

text: s with

text: chromic acid

text: Coupling reaction

text: s can also be considered radical substitutions. Certain aromatic substitutions takes place by

text: radical-nucleophilic aromatic substitution

text: Auto-oxidation

text: is a process responsible for deterioration of paints and food and lab hazards such as

text: diethyl ether peroxide

text: Microbial biodegradation of recalcitrant organic pollutants is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbons and halogenated compounds have long been doubted to be anaerobically degradable, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria documented these processes in nature. Novel biochemical reactions were discovered, enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was slowed by the absence of genetic systems for most of them. However, several complete genome sequences later became available for such bacteria. The genome of the hydrocarbon degrading and iron-reducing species G. metallireducens (accession nr. NC_007517) was determined in 2008. The genome revealed the presence of genes for reductive dehalogenases, suggesting a wide dehalogenating spectrum. Moreover, genome sequences provided insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.

text: Microbial biodegradation

text: of recalcitrant organic

text: pollutant

text: s is of great environmental significance and involves intriguing novel biochemical reactions. In particular,

text: hydrocarbon

text: s and

text: halogenated

text: compounds have long been doubted to be anaerobically degradable, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating

text: bacteria

text: documented these processes in nature. Novel biochemical reactions were discovered, enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was slowed by the absence of genetic systems for most of them. However, several complete genome sequences later became available for such bacteria. The genome of the hydrocarbon degrading and iron-reducing species G. metallireducens (accession nr. NC_007517) was determined in 2008. The genome revealed the presence of genes for reductive

text: dehalogenase

text: s, suggesting a wide dehalogenating spectrum. Moreover, genome sequences provided insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.

text: Anaerobic microbial mineralization of recalcitrant organic pollutants is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbons and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria during the last decades provided ultimate proof for these processes in nature. While such research involved mostly chlorinated compounds initially, recent studies have revealed reductive dehalogenation of bromine and iodine moieties in aromatic pesticides.  Other reactions, such as biologically induced abiotic reduction by soil minerals, has been shown to deactivate relatively persistent aniline-based herbicides far more rapidly than observed in aerobic environments.  Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, with the increasing application of genomics in the field of environmental microbiology, a new and promising perspective is now at hand to obtain molecular insights into these new metabolic properties. Several complete genome sequences were determined during the last few years from bacteria capable of anaerobic organic pollutant degradation. The ~4.7 Mb genome of the facultative denitrifying Aromatoleum aromaticum strain EbN1 was the first to be determined for an anaerobic hydrocarbon degrader (using toluene or ethylbenzene as substrates). The genome sequence revealed about two dozen gene clusters (including several paralogs) coding for a complex catabolic network for anaerobic and aerobic degradation of aromatic compounds. The genome sequence forms the basis for current detailed studies on regulation of pathways and enzyme structures. Further genomes of anaerobic hydrocarbon degrading bacteria were recently completed for the iron-reducing species Geobacter metallireducens (accession nr. NC_007517) and the perchlorate-reducing Dechloromonas aromatica (accession nr. NC_007298), but these are not yet evaluated in formal publications. Complete genomes were also determined for bacteria capable of anaerobic degradation of halogenated hydrocarbons by halorespiration: the ~1.4 Mb genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1 and the ~5.7 Mb genome of Desulfitobacterium hafniense strain Y51. Characteristic for all these bacteria is the presence of multiple paralogous genes for reductive dehalogenases, implicating a wider dehalogenating spectrum of the organisms than previously known. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.

text: Anaerobic

text: microbial

text: mineralization of recalcitrant organic

text: pollutant

text: hydrocarbon

text: s and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating

text: bacteria

text: during the last decades provided ultimate proof for these processes in nature. While such research involved mostly

text: chlorinated

text: compounds initially, recent studies have revealed reductive dehalogenation of

text: bromine

text: and

text: iodine

text: moieties in aromatic pesticides.  Other reactions, such as biologically induced

text: abiotic

text: reduction by soil minerals, has been shown to deactivate relatively persistent aniline-based herbicides far more rapidly than observed in aerobic environments.  Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, with the increasing application of

text: genomics

text: in the field of

text: environmental microbiology

text: , a new and promising perspective is now at hand to obtain molecular insights into these new metabolic properties. Several complete genome sequences were determined during the last few years from bacteria capable of anaerobic organic pollutant degradation. The ~4.7 Mb

text: genome

text: of the facultative denitrifying

text: Aromatoleum aromaticum

text: strain EbN1 was the first to be determined for an anaerobic hydrocarbon degrader (using

text: toluene

text: or

text: ethylbenzene

text: as

text: substrate

text: s). The

text: genome sequence

text: revealed about two dozen

text: gene cluster

text: s (including several

text: paralog

text: s) coding for a complex catabolic network for anaerobic and aerobic degradation of aromatic compounds. The genome sequence forms the basis for current detailed studies on regulation of pathways and

text: enzyme

text: structures. Further genomes of anaerobic hydrocarbon degrading bacteria were recently completed for the iron-reducing species

text: Geobacter metallireducens

text: (accession nr. NC_007517) and the perchlorate-reducing

text: Dechloromonas aromatica

text: (accession nr. NC_007298), but these are not yet evaluated in formal publications. Complete genomes were also determined for bacteria capable of anaerobic degradation of halogenated hydrocarbons by

text: halorespiration

text: : the ~1.4 Mb genomes of

text: Dehalococcoides ethenogenes

text: strain 195 and

text: Dehalococcoides

text: sp. strain CBDB1 and the ~5.7 Mb genome of

text: Desulfitobacterium hafniense

text: strain Y51. Characteristic for all these bacteria is the presence of multiple paralogous genes for reductive dehalogenases, implicating a wider dehalogenating spectrum of the organisms than previously known. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.

text: About 60 GtC/yr is added to soil. This 60 GtC/yr is the balance of 120 GtC/yr taken out of the atmosphere by terrestrial plant photosynthesis reduced by 60 GtC/yr plant respiration. An equivalent 60 GtC/yr is respired from soil, joining the 60G tC/yr plant respiration to return to the atmosphere.

text: About 60 GtC/yr is added to soil. This 60 GtC/yr is the balance of 120 GtC/yr

text: taken out of the atmosphere

text: by terrestrial plant

text: photosynthesis

text: reduced by 60 GtC/yr plant

text: respiration

text: . An equivalent 60 GtC/yr is respired from soil, joining the 60G tC/yr plant respiration to return to the atmosphere.

text: The enzyme is also involved in a chiral inversion pathway which converts ibuprofen, a member of the 2-arylpropionic acid (2-APA)  non-steroidal anti-inflammatory drug family (NSAIDs), from the R-enantiomer to the S-enantiomer. The pathway is uni-directional because only R-ibuprofen can be converted into ibuprofenoyl-CoA, which is then epimerized by AMACR. Conversion of S-ibuprofenoyl-CoA to S-ibuprofen is assumed to be performed by one of the many human acyl-CoA thioesterase enzymes (ACOTs). The reaction is of pharmacological importance because ibuprofen is typically used as a racemic mixture, and the drug is converted to the S-isomer upon uptake, which inhibits the activity of the cyclo-oxygenase enzymes and induces an anti-inflammatory effect. Human AMACR 1A has been demonstrated to epimerise other 2-APA-CoA esters, suggesting a common chiral inversion pathway for this class of drugs.

text: The enzyme is also involved in a chiral inversion pathway which converts

text: ibuprofen

text: , a member of the 2-arylpropionic acid (2-APA)

text: non-steroidal anti-inflammatory drug

text: family (NSAIDs), from the R-enantiomer to the S-enantiomer. The pathway is uni-directional because only R-ibuprofen can be converted into ibuprofenoyl-CoA, which is then epimerized by AMACR. Conversion of S-ibuprofenoyl-CoA to S-ibuprofen is assumed to be performed by one of the many human acyl-CoA thioesterase enzymes (ACOTs). The reaction is of pharmacological importance because

text: ibuprofen

text: is typically used as a racemic mixture, and the drug is converted to the S-isomer upon uptake, which inhibits the activity of the

text: cyclo-oxygenase

text: enzymes and induces an anti-inflammatory effect. Human AMACR 1A has been demonstrated to epimerise other 2-APA-CoA esters, suggesting a common chiral inversion pathway for this class of drugs.

text: Lincoln can generate a biochemical explosion with just a touch. If he increases the kinetic force by hitting the object harder, the explosive force is also increased. Lincoln is also a fine hand-to-hand combatant and a talented chemist. The changes to his body chemistry seemed to have prolonged his life. Lincoln wears from head to toe, a containment suit made of "Fibro wax", which inhibits his biochemical explosive reaction. When he wants to use his powers, he simply removes his gloves.

text: The NADPH is the main reducing agent produced by chloroplasts, which then goes on to provide a source of energetic electrons in other cellular reactions. Its production leaves chlorophyll in photosystem I with a deficit of electrons (chlorophyll has been oxidized), which must be balanced by some other reducing agent that will supply the missing electron. The excited electrons lost from chlorophyll from photosystem I are supplied from the electron transport chain by plastocyanin. However, since photosystem II is the first step of the Z-scheme, an external source of electrons is required to reduce its oxidized chlorophyll a molecules. The source of electrons in green-plant and cyanobacterial photosynthesis is water. Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic oxygen and four hydrogen ions; the electrons yielded are transferred to a redox-active tyrosine residue that then reduces the oxidized chlorophyll a (called P680) that serves as the primary light-driven electron donor in the photosystem II reaction center. That photo receptor is in effect reset and is then able to repeat the absorption of another photon and the release of another photo-dissociated electron. The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions and a calcium ion; this oxygen-evolving complex binds two water molecules and contains the four oxidizing equivalents that are used to drive the water-oxidizing reaction. Photosystem II is the only known biological enzyme that carries out this oxidation of water. The hydrogen ions released contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-dependent reactions, but the majority of organisms on Earth use oxygen for cellular respiration, including photosynthetic organisms.

text: The NADPH is the main

text: reducing agent

text: produced by chloroplasts, which then goes on to provide a source of energetic electrons in other cellular reactions. Its production leaves chlorophyll in photosystem I with a deficit of electrons (chlorophyll has been oxidized), which must be balanced by some other reducing agent that will supply the missing electron. The excited electrons lost from chlorophyll from

text: photosystem I

text: are supplied from the electron transport chain by

text: plastocyanin

text: . However, since

text: photosystem II

text: is the first step of the Z-scheme, an external source of electrons is required to reduce its oxidized chlorophyll a molecules. The source of electrons in green-plant and cyanobacterial photosynthesis is water. Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic

text: oxygen

text: and four

text: hydrogen

text: ions; the electrons yielded are transferred to a redox-active

text: tyrosine

text: residue that then reduces the oxidized chlorophyll a (called P680) that serves as the primary light-driven electron donor in the photosystem II reaction center. That photo receptor is in effect reset and is then able to repeat the absorption of another photon and the release of another photo-dissociated electron. The oxidation of water is

text: catalyzed

text: in photosystem II by a redox-active structure that contains four

text: manganese

text: ions and a calcium ion; this

text: oxygen-evolving complex

text: binds two water molecules and contains the four oxidizing equivalents that are used to drive the water-oxidizing reaction. Photosystem II is the only known biological

text: enzyme

text: that carries out this oxidation of water. The hydrogen ions released contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-dependent reactions, but the majority of organisms on Earth use oxygen for

text: cellular respiration

text: , including photosynthetic organisms.

text: Several researchers, including Nobel Prize winner Dr. Richard Smalley (1943–2005), attacked the notion of universal assemblers, leading to a rebuttal from Drexler and colleagues, and eventually to an exchange of letters. Smalley argued that chemistry is extremely complicated, reactions are hard to control, and that a universal assembler is science fiction. Drexler and colleagues, however, noted that Drexler never proposed universal assemblers able to make absolutely anything, but instead proposed more limited assemblers able to make a very wide variety of things. They challenged the relevance of Smalley's arguments to the more specific proposals advanced in Nanosystems.  Also, Smalley argued that nearly all of modern chemistry involves reactions that take place in a solvent (usually water), because the small molecules of a solvent contribute many things, such as lowering binding energies for transition states.  Since nearly all known chemistry requires a solvent, Smalley felt that Drexler's proposal to use a high vacuum environment was not feasible.  However, Drexler addresses this in Nanosystems by showing mathematically that well designed catalysts can provide the effects of a solvent and can fundamentally be made even more efficient than a solvent/enzyme reaction could ever be. It is noteworthy that, contrary to Smalley's opinion that enzymes require water, "Not only do enzymes work vigorously in anhydrous organic media, but in this unnatural milieu they acquire remarkable properties such as greatly enhanced stability, radically altered substrate and enantiomeric specificities, molecular memory, and the ability to catalyse unusual reactions.""

text: Several researchers, including Nobel Prize winner

text: Dr. Richard Smalley

text: (1943–2005), attacked the notion of universal assemblers, leading to a rebuttal from Drexler and colleagues, and eventually to an exchange of letters. Smalley argued that chemistry is extremely complicated, reactions are hard to control, and that a universal assembler is science fiction. Drexler and colleagues, however, noted that Drexler never proposed universal assemblers able to make absolutely anything, but instead proposed more limited assemblers able to make a very wide variety of things. They challenged the relevance of Smalley's arguments to the more specific proposals advanced in Nanosystems.  Also, Smalley argued that nearly all of modern chemistry involves reactions that take place in a

text: solvent

text: (usually

text: water

text: ), because the

text: small molecules

text: of a solvent contribute many things, such as lowering

text: binding energies

text: for transition states.  Since nearly all known chemistry requires a solvent, Smalley felt that Drexler's proposal to use a high vacuum environment was not feasible.  However, Drexler addresses this in Nanosystems by showing mathematically that well designed

text: catalysts

text: can provide the effects of a solvent and can fundamentally be made even more efficient than a solvent/

text: enzyme

text: reaction could ever be. It is noteworthy that, contrary to Smalley's opinion that enzymes require water, "Not only do enzymes work vigorously in anhydrous organic media, but in this unnatural milieu they acquire remarkable properties such as greatly enhanced stability, radically altered substrate and

text: enantiomeric

text: specificities, molecular memory, and the ability to catalyse unusual reactions.""

text: The Calvin cycle, Calvin–Benson–Bassham (CBB) cycle, reductive pentose phosphate cycle or C3 cycle is a series of biochemical redox reactions that take place in the stroma of chloroplast in photosynthetic organisms. It is also known as the light-independent reactions.

text: The Calvin cycle, Calvin–Benson–Bassham (CBB) cycle, reductive pentose phosphate cycle or C3 cycle is a series of

text: biochemical

text: redox

text: reactions that take place in the

text: stroma

text: of

text: chloroplast

text: in

text: photosynthetic

text: organism

text: s. It is also known as the light-independent reactions.

text: For marine organisms, the details of the photosynthesis reactions are less well understood, and the  values for marine photosynthetic organisms are dependent on temperature. At higher temperatures,  has poor solubility in water, which means there is less  available for the photosynthetic reactions. Under these conditions, fractionation is reduced, and at temperatures above 14 °C the  values are correspondingly higher, while at lower temperatures,  becomes more soluble and hence more available to marine organisms. The  value for animals depends on their diet. An animal that eats food with high  values will have a higher  than one that eats food with lower  values. The animal's own biochemical processes can also impact the results: for example, both bone minerals and bone collagen typically have a higher concentration of  than is found in the animal's diet, though for different biochemical reasons. The enrichment of bone  also implies that excreted material is depleted in  relative to the diet.

text: On this track, students are introduced to the fundamental reaction mechanisms in the field of chemical and biochemical engineering.

text: Enzymes may use quantum tunneling to transfer electrons long distances. Tunneling refers to the ability of a small mass particle to travel through energy barriers. Studies show that long distance electron transfers between redox centers through quantum tunneling plays important roles in enzymatic activity of photosynthesis and cellular respiration. For example, studies show that long range electron tunneling on the order of 15–30 Å plays a role in redox reactions in enzymes of cellular respiration. Even though there are such large separations between redox sites within enzymes, electrons successfully transfer in a temperature independent and distance dependent manner. This suggests the ability of electrons to tunnel in physiological conditions. Further research is needed to determine whether this specific tunneling is also coherent.

text: Enzymes may use

text: quantum tunneling

text: to transfer electrons long distances. Tunneling refers to the ability of a small mass particle to travel through energy barriers. Studies show that long distance electron transfers between

text: redox

text: centers through quantum tunneling plays important roles in

text: enzymatic

text: activity of

text: photosynthesis

text: and

text: cellular respiration

text: . For example, studies show that long range electron tunneling on the order of 15–30 Å plays a role in redox reactions in enzymes of cellular respiration. Even though there are such large separations between redox sites within enzymes, electrons successfully transfer in a temperature independent and distance dependent manner. This suggests the ability of electrons to tunnel in physiological conditions. Further research is needed to determine whether this specific tunneling is also coherent.

text: The coupling of an optical probe to a molecule of interest must occur within a reasonably short time frame; therefore, the kinetics of the coupling reaction should be highly favorable.  Click chemistry is well suited to fill this niche, since click reactions are, by definition, rapid, spontaneous, selective, and high-yielding.<ref name="pmid11433435">{{cite journal | vauthors = Kolb HC, Finn MG, Sharpless KB | title = Click Chemistry: Diverse Chemical Function from a Few Good Reactions | journal = Angew. Chem. Int. Ed. Engl. | volume = 40 | issue = 11 | pages = 2004–2021 |date=June 2001 | pmid = 11433435 | doi = 10.1002/1521-3773(20010601)40:11

text: The coupling of an optical probe to a molecule of interest must occur within a reasonably short time frame; therefore, the kinetics of the coupling reaction should be highly favorable.

text: Click chemistry

text: is well suited to fill this niche, since click reactions are, by definition, rapid, spontaneous, selective, and high-yielding.<ref name="pmid11433435">{{cite journal | vauthors = Kolb HC, Finn MG, Sharpless KB | title = Click Chemistry: Diverse Chemical Function from a Few Good Reactions | journal = Angew. Chem. Int. Ed. Engl. | volume = 40 | issue = 11 | pages = 2004–2021 |date=June 2001 | pmid = 11433435 | doi = 10.1002/1521-3773(20010601)40:11

text: Primary metabolism in a plant comprises all metabolic pathways that are essential to the plant's survival. Primary metabolites are compounds that are directly involved in the growth and development of a plant whereas secondary metabolites are compounds produced in other metabolic pathways that, although important, are not essential to the functioning of the plant. However, secondary plant metabolites are useful in the long term, often for defense purposes, and give plants characteristics such as color. Secondary plant metabolites are also used in signalling and regulation of primary metabolic pathways. Plant hormones, which are secondary metabolites, are often used to regulate the metabolic activity within cells and oversee the overall development of the plant. As mentioned above in the History tab, secondary plant metabolites help the plant maintain an intricate balance with the environment, often adapting to match the environmental needs. Plant metabolites that color the plant are a good example of this, as the coloring of a plant can attract pollinators and also defend against attack by animals.

text: Pathways are required for the maintenance of homeostasis within an organism and the flux of metabolites through a pathway is regulated depending on the needs of the cell and the availability of the substrate. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The metabolism of a cell consists of an elaborate network of interconnected pathways that enable the synthesis and breakdown of molecules (anabolism and catabolism)

text: Pathways are required for the maintenance of

text: homeostasis

text: within an

text: organism

text: and the

text: flux

text: of metabolites through a pathway is

text: regulated

text: depending on the needs of the cell and the availability of the substrate. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The

text: metabolism

text: of a cell consists of an elaborate

text: network

text: of interconnected pathways that enable the synthesis and breakdown of molecules (anabolism and catabolism)

text: Potassium regulates the opening and closing of the stomata by a potassium ion pump. Since stomata are important in water regulation, potassium regulates water loss from the leaves and increases drought tolerance. Potassium deficiency may cause necrosis or interveinal chlorosis. The potassium ion (K) is highly mobile and can aid in balancing the anion (negative) charges within the plant. Potassium helps in fruit coloration, shape and also increases its brix. Hence, quality fruits are produced in potassium-rich soils. Potassium serves as an activator of enzymes used in photosynthesis and respiration. Potassium is used to build cellulose and aids in photosynthesis by the formation of a chlorophyll precursor. Potassium deficiency may result in higher risk of pathogens, wilting, chlorosis, brown spotting, and higher chances of damage from frost and heat.

text: Potassium

text: regulates the opening and closing of the

text: stomata

text: by a potassium ion pump. Since stomata are important in water regulation, potassium regulates water loss from the leaves and increases

text: drought

text: tolerance.

text: Potassium deficiency

text: may cause necrosis or interveinal chlorosis. The potassium ion (K) is highly mobile and can aid in balancing the anion (negative) charges within the plant. Potassium helps in fruit coloration, shape and also increases its

text: brix

text: . Hence, quality fruits are produced in potassium-rich soils. Potassium serves as an activator of enzymes used in photosynthesis and respiration. Potassium is used to build cellulose and aids in photosynthesis by the formation of a chlorophyll precursor.

text: Potassium deficiency

text: may result in higher risk of pathogens, wilting, chlorosis, brown spotting, and higher chances of damage from frost and heat.

text: An experimental system was developed in which an intron-containing rRNA precursor from the nucleus of the ciliated protozoan Tetrahymena could be spliced in vitro. Subsequent biochemical analysis shows that this group I intron was self-splicing; that is, the precursor RNA is capable of carrying out the complete splicing reaction in the absence of proteins. In separate work, the RNA component of the bacterial enzyme ribonuclease P (a ribonucleoprotein complex) was shown to catalyze its tRNA-processing reaction in the absence of proteins. These experiments represented landmarks in RNA biology, since they revealed that RNA could play an active role in cellular processes, by catalyzing specific biochemical reactions. Before these discoveries, it was believed that biological catalysis was solely the realm of protein enzymes.

text: An experimental system was developed in which an intron-containing rRNA precursor from the nucleus of the ciliated protozoan

text: Tetrahymena

text: could be spliced

text: in vitro

text: . Subsequent biochemical analysis shows that this

text: group I intron

text: was self-splicing; that is, the precursor RNA is capable of carrying out the complete splicing reaction in the absence of proteins. In separate work, the RNA component of the bacterial enzyme

text: ribonuclease P

text: (a

text: ribonucleoprotein

text: complex) was shown to catalyze its tRNA-processing reaction in the absence of proteins. These experiments represented landmarks in RNA biology, since they revealed that RNA could play an active role in cellular processes, by catalyzing specific biochemical reactions. Before these discoveries, it was believed that biological catalysis was solely the realm of

text: protein

text: enzymes

text: SCS is the only enzyme in the citric acid cycle that catalyzes a reaction in which a nucleoside triphosphate (GTP or ATP) is formed by substrate-level phosphorylation.  Research studies have shown that E. coli SCSs can catalyze either GTP or ATP formation.  However, mammals possess different types of SCSs that are specific for either GTP (G-SCS) or ATP (A-SCS) and are native to different types of tissue within the organism.  An interesting study using pigeon cells showed that GTP specific SCSs were located in pigeon liver cells, and ATP specific SCSs were located in the pigeon breast muscle cells.  Further research revealed a similar phenomenon of GTP and ATP specific SCSs in rat, mouse, and human tissue.  It appears that tissue typically involved in anabolic metabolism (like the liver and kidneys) express G-SCS, whereas tissue involved in catabolic metabolism (like the brain, the heart, and muscular tissue) express A-SCS.

text: SCS is the only enzyme in the citric acid cycle that catalyzes a reaction in which a nucleoside triphosphate (GTP or ATP) is formed by

text: substrate-level phosphorylation

text: .  Research studies have shown that E. coli SCSs can catalyze either GTP or ATP formation.  However, mammals possess different types of SCSs that are specific for either GTP (G-SCS) or ATP (A-SCS) and are native to different types of tissue within the organism.  An interesting study using

text: pigeon

text: cells showed that GTP specific SCSs were located in pigeon liver cells, and ATP specific SCSs were located in the pigeon breast muscle cells.  Further research revealed a similar phenomenon of GTP and ATP specific SCSs in rat, mouse, and human tissue.  It appears that tissue typically involved in

text: anabolic metabolism

text: (like the liver and kidneys) express G-SCS, whereas tissue involved in

text: catabolic metabolism

text: (like the brain, the heart, and muscular tissue) express A-SCS.

text: In organic chemistry, the Baudisch reaction is a process for the synthesis of nitrosophenols using metal ions. Although the products are of limited value, the reaction is of historical interest as an example of metal-promoted functionalization of aromatic substrates.

text: In

text: organic chemistry

text: , the Baudisch reaction is a process for the synthesis of nitrosophenols using metal ions. Although the products are of limited value, the reaction is of historical interest as an example of metal-promoted functionalization of aromatic substrates.

text: Cellular respiration (both aerobic and anaerobic) utilizes highly reduced chemical compounds such as NADH and FADH2 (for example produced during glycolysis and the citric acid cycle) to establish an electrochemical gradient (often a proton gradient) across a membrane, resulting in an electrical potential or ion concentration difference across the membrane. The reduced chemical compounds are oxidized by a series of respiratory integral membrane proteins with sequentially increasing reduction potentials with the final electron acceptor being oxygen (in aerobic respiration) or another chemical substance (in anaerobic respiration). A proton motive force or pmf drives protons down the gradient (across the membrane) through the proton channel of ATP synthase. The resulting current drives ATP synthesis from ADP and inorganic phosphate.

text: Cellular respiration (both

text: aerobic

text: and anaerobic) utilizes highly reduced chemical compounds such as

text: NADH

text: and

text: (for example produced during

text: glycolysis

text: and the

text: citric acid cycle

text: ) to establish an

text: electrochemical gradient

text: (often a proton gradient) across a membrane, resulting in an

text: electrical potential

text: or ion

text: concentration

text: difference across the membrane. The reduced chemical compounds are oxidized by a series of respiratory

text: integral membrane proteins

text: with sequentially increasing reduction potentials with the final electron acceptor being

text: oxygen

text: (in

text: aerobic respiration

text: ) or another chemical substance (in anaerobic respiration). A

text: proton motive force

text: or pmf drives

text: protons

text: down the gradient (across the membrane) through the proton channel of

text: ATP synthase

text: . The resulting current drives ATP synthesis from

text: ADP

text: and inorganic phosphate.

text: Some enzymes are inhibited by the product of their reaction binds to the enzyme and reduces its activity. This can be important in the regulation of metabolism as a form of negative feedback controlling metabolic pathways. Product inhibition is also an important topic in biotechnology, as overcoming this effect can increase the yield of a product.

text: Some enzymes are

text: inhibited

text: by the product of their

text: reaction

text: binds to the enzyme and reduces its activity. This can be important in the regulation of

text: metabolism

text: as a form of

text: negative feedback

text: controlling

text: metabolic pathway

text: s. Product inhibition is also an important topic in

text: biotechnology

text: , as overcoming this effect can increase the yield of a product.

text: There are many signals that control catabolism. Most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, depending on which part of metabolism they stimulate. The so-called classic catabolic hormones known since the early 20th century are cortisol, glucagon, and adrenaline (and other catecholamines). In recent decades, many more hormones with at least some catabolic effects have been discovered, including cytokines, orexin (also known as hypocretin), and melatonin.

text: There are many signals that control catabolism. Most of the known signals are

text: hormone

text: s and the molecules involved in metabolism itself.

text: Endocrinologist

text: s have traditionally classified many of the hormones as

text: anabolic

text: or catabolic, depending on which part of metabolism they stimulate. The so-called classic catabolic hormones known since the early 20th century are

text: cortisol

text: glucagon

text: , and

text: adrenaline

text: (and other

text: catecholamine

text: s). In recent decades, many more hormones with at least some catabolic effects have been discovered, including

text: cytokine

text: s,

text: orexin

text: (also known as

text: hypocretin

text: ), and

text: melatonin

text: 48.  Bradbury, A.F. and Smyth, D.G. (1987) Enzyme catalysed peptide amidation: isolation of a stable intermediate formed by reaction of the amidating enzyme with an imino acid. Eur. J. Biochem. 169, 579-584.

text: A bicarbonate indicator (hydrogencarbonate indicator) is a type of pH indicator that is sensitive enough to show a color change as the concentration of carbon dioxide gas in an aqueous solution increases. The indicator is used in photosynthesis and respiration experiments to find out whether carbon dioxide is being liberated. It is also used to test the carbon dioxide content during gaseous exchange of organisms. When the carbon dioxide content is higher than 0.04%, the initial red color changes to yellow as the pH becomes more acidic. If the carbon dioxide content is lower than 0.04%, it changes from red to magenta and, in relatively very low carbon dioxide concentrations, to purple. Carbon dioxide, even in the concentrations found in exhaled air, will dissolve in the indicator to form carbonic acid, a weak acid, which will lower the pH and give the characteristic colour change. A colour change to purple during photosynthesis shows a reduction in the percentage of carbon dioxide and is sometimes inferred as production of oxygen, but is not actually direct evidence for it.

text: A bicarbonate indicator (hydrogencarbonate indicator) is a type of

text: pH indicator

text: that is sensitive enough to show a color change as the concentration of

text: carbon dioxide

text: gas in an aqueous solution increases. The indicator is used in

text: photosynthesis

text: and

text: respiration

text: experiments to find out whether carbon dioxide is being liberated. It is also used to test the

text: carbon dioxide

text: content during gaseous exchange of organisms. When the carbon dioxide content is higher than 0.04%, the initial red color changes to yellow as the pH becomes more acidic. If the carbon dioxide content is lower than 0.04%, it changes from red to magenta and, in relatively very low carbon dioxide concentrations, to purple. Carbon dioxide, even in the concentrations found in exhaled air, will dissolve in the indicator to form

text: carbonic acid

text: , a weak acid, which will lower the pH and give the characteristic colour change. A colour change to purple during photosynthesis shows a reduction in the percentage of carbon dioxide and is sometimes inferred as production of oxygen, but is not actually direct evidence for it.

text: Pyrophosphatase (or inorganic pyrophosphatase) is an enzyme () that catalyzes the conversion of one molecule of pyrophosphate to two phosphate ions. This is a highly exergonic reaction, and therefore can be coupled to unfavorable biochemical transformations in order to drive these transformations to completion. The functionality of this enzyme plays a critical role in lipid metabolism (including lipid synthesis and degradation), calcium absorption and bone formation, and DNA synthesis, as well as other biochemical transformations.

text: Pyrophosphatase (or inorganic pyrophosphatase) is an

text: enzyme

text: () that catalyzes the conversion of one molecule of

text: pyrophosphate

text: to two

text: phosphate

text: ions. This is a highly

text: exergonic

text: reaction, and therefore can be coupled to unfavorable biochemical transformations in order to drive these transformations to completion. The functionality of this

text: enzyme

text: plays a critical role in

text: lipid metabolism

text: (including lipid synthesis and degradation), calcium absorption and bone formation, and DNA synthesis, as well as other

text: biochemical

text: transformations.

text: Water is treated by combined natural processes such as soil and root filtration, sedimentation and biochemical reactions including photosynthesis, anaerobic and aerobic digestion.

text: Water is treated by combined natural processes such as soil and root filtration, sedimentation and biochemical reactions including

text: photosynthesis

text: anaerobic

text: and

text: aerobic

text: digestion.

text: The reactions that transform ethanol into an aldehyde and then into a carboxylic acid are examples of oxidation reactions, which in organic chemistry, are typically characterized by the addition of oxygen onto a functional group.  The third reaction, the enzyme mediated formation of acetyl-CoA from acetic acid is an example of an enzymatic synthetase reaction where, through a complex intramolecular interaction a product molecule is formed from reactants.

text: Individually, the metabolic pathways of A. pisum and Buchnera are incomplete. Jointly, the genomes of these two organisms complement each other to produce complete metabolic pathways for the biosynthesis of nutrients such as amino acids and other essential molecules. The ancestral partners of this symbiosis are likely to have had complete metabolic pathways, however pressure to maintain these pathway genes was reduced due to redundancy as a result of the presence of the other partner’s genome. Unlike other related insects, the A. pisum genome is missing genes necessary for the urea cycle. the purine salvage pathway, and other genes that code enzymes necessary for the biosynthesis of molecules. These missing reaction intermediates are likely provided by genes within the Buchnera genome. For example, A. pisum is the only species with a sequenced genome known to be missing key components of the purine salvage pathway, essential for the production of DNA, RNA, signaling molecules, and ATP. The Buchnera genome contains the necessary genes to encode the reaction intermediates missing from the A. pisum genome. Through this complementation, the nucleotide requirements of both organisms are fulfilled: the purine salvage pathway is completed for A. pisum and Buchnera receives necessary guanosine.

text: These three pairs produce combinations of colors for us through the opponent process. Furthermore, according to this theory, for each of these three pairs, three types of chemicals in the retina occur, in which two types of chemical reactions exist. These reactions would yield one member of the pair in their building up phase, or anabolic process, whereas they would yield the other member while in a destructive phase, or a catabolic process.

text: These three pairs produce combinations of colors for us through the opponent process. Furthermore, according to this theory, for each of these three pairs, three types of chemicals in the retina occur, in which two types of chemical reactions exist. These reactions would yield one member of the pair in their building up phase, or

text: anabolic process

text: , whereas they would yield the other member while in a destructive phase, or a

text: catabolic process

text: At the compensation point, the rate of photosynthesis is balanced to the rate of respiration. Products of photosynthesis are used up in respiration so that the plant is neither consuming nor building biomass.

text: At the compensation point, the rate of photosynthesis is balanced to the rate of respiration. Products of photosynthesis are used up in respiration so that the

text: plant

text: is neither consuming nor building

text: biomass

text: In summary, and extrapolating from animal studies, the pathology of a concussion seems to start with the disruption of the cell membrane of nerve cells.  This results in a migration of potassium from within the cell into the extracellular space with subsequent release of glutamate which potentiates further potassium shift, in turn resulting in depolarization and suppression of nerve activity.  In an effort to restore ion balance, the sodium-potassium ion pumps increase activity, which results in excessive ATP (adenosine triphosphate) consumption and glucose utilization. Lactate accumulates but, paradoxically, cerebral blood flow decreases, which leads to a proposed "energy crisis." After this increase in glucose metabolism, there is a subsequent lower metabolic state which may persist for up to 4 weeks after injury.  A completely separate pathway involves a large amount of calcium accumulating in cells, which may impair oxidative metabolism and begin further biochemical pathways that result in cell death.  Again, both of these main pathways have been established from animal studies and the extent to which they apply to humans is still somewhat unclear.

text: Glycolysis, which means “sugar splitting,” is the initial process in the cellular respiration pathway. Glycolysis can be either an aerobic or anaerobic process. When oxygen is present then glycolysis will continue along the aerobic respiration pathway. If oxygen is not present, then ATP production will be restricted to anaerobic respiration. The location where glycolysis, aerobic or anaerobic, occurs is in the cytosol of the cell. In glycolysis, a six-carbon glucose molecule is split into two three-carbon molecules called pyruvate. These carbon molecules are oxidized into NADH and ATP.  In order for the glucose molecule to be oxidized into pyruvate, an input of ATP molecules is required. This is known as the investment phase, in which a total of two ATP molecules are consumed. At the end of glycolysis, the total yield of ATP is four molecules, but the net gain is two ATP molecules. Even though ATP is synthesized, the two ATP molecules produced are few compared to the second and third pathways, Krebs cycle and oxidative phosphorylation.

text: Glycolysis

text: , which means “sugar splitting,” is the initial process in the

text: cellular respiration

text: pathway. Glycolysis can be either an

text: aerobic

text: or

text: anaerobic

text: process. When

text: oxygen

text: is present then glycolysis will continue along the aerobic respiration pathway. If oxygen is not present, then

text: ATP

text: production will be restricted to

text: anaerobic respiration

text: . The location where glycolysis, aerobic or anaerobic, occurs is in the

text: cytosol

text: of the

text: cell

text: . In glycolysis, a six-carbon

text: glucose

text: molecule is split into two three-carbon molecules called

text: pyruvate

text: . These carbon molecules are

text: oxidized

text: into

text: NADH

text: and ATP.  In order for the glucose molecule to be oxidized into pyruvate, an input of ATP molecules is required. This is known as the investment phase, in which a total of two ATP molecules are consumed. At the end of glycolysis, the total yield of ATP is four molecules, but the net gain is two ATP molecules. Even though ATP is synthesized, the two ATP molecules produced are few compared to the second and third pathways,

text: Krebs cycle

text: and

text: oxidative phosphorylation

text: Formaldehyde is relatively inactive in gas phase chemistry in the interstellar medium.  Its action is predominantly focused in grain-surface chemistry on dust grains in interstellar clouds.  Reactions involving formaldehyde have been observed to produce molecules containing C-H, C-O, O-H, and C-N bonds.  While these products are not necessarily well known, Schutte et al. believe these to be typical products of formaldehyde reactions at higher temperatures, polyoxymethylene, methanolamine, methanediol, and methoxyethanol for example (see Table 2).  Formaldehyde is believed to be the primary precursor for most of the complex organic material in the interstellar medium, including amino acids.  Formaldehyde most often reacts with NH, HO, CHOH, CO, and itself, HCO.  The three dominating reactions are shown below.

text: Formaldehyde is relatively inactive in gas phase chemistry in the interstellar medium.  Its action is predominantly focused in grain-surface chemistry on dust grains in interstellar clouds.  Reactions involving formaldehyde have been observed to produce molecules containing C-H, C-O, O-H, and C-N bonds.  While these products are not necessarily well known, Schutte et al. believe these to be typical products of formaldehyde reactions at higher temperatures,

text: polyoxymethylene

text: methanolamine

text: methanediol

text: , and

text: methoxyethanol

text: for example (see Table 2).  Formaldehyde is believed to be the primary precursor for most of the complex organic material in the interstellar medium, including

text: amino acids

text: .  Formaldehyde most often reacts with NH, HO, CHOH, CO, and itself, HCO.  The three dominating reactions are shown below.

text: Michaelis–Menten kinetics have also been applied to a variety of spheres outside of biochemical reactions, including alveolar clearance of dusts, the richness of species pools, clearance of blood alcohol, the photosynthesis-irradiance relationship, and bacterial phage infection.

text: Michaelis–Menten kinetics have also been applied to a variety of spheres outside of biochemical reactions, including

text: alveolar

text: clearance of dusts, the

text: richness of species

text: pools, clearance of

text: blood alcohol

text: , the

text: photosynthesis-irradiance

text: relationship, and bacterial

text: phage

text: infection.

text: Metabolism involves two biochemical processes that occur in living organisms. The first is anabolism, which refers to the buildup of molecules. The second is catabolism, the breakdown of molecules. These two processes work to regulate the amount of energy the body uses to maintain itself. During non-REM sleep, metabolic rate and brain temperature are lowered to deal with damages that may have occurred during time of wakefulness.

text: Metabolism

text: involves two

text: biochemical

text: anabolism

text: , which refers to the buildup of molecules. The second is

text: catabolism

text: metabolic rate

text: The balance that is struck between anabolic and catabolic processes is strongly influenced by the type of loading that cartilage experiences.  High strain rates (such as which occurs during impact loading) cause tissue damage, degradation, decreased matrix production and apoptosis. Decreased mechanical loading over long periods, such as during extended bed-rest, causes a loss of matrix production. Static loads have been shown to be detrimental to biosynthesis while oscillatory loads at low frequencies (similar that of a normal walking gait) have been shown to be beneficial in maintaining health and increasing matrix synthesis. Due to the complexity of in-vivo loading conditions and the interplay of other mechanical and biochemical factors, the question of what an optimal loading regimen may be or whether one exists remain unanswered.

text: The balance that is struck between anabolic and catabolic processes is strongly influenced by the type of loading that cartilage experiences.  High strain rates (such as which occurs during impact loading) cause tissue damage, degradation, decreased matrix production and

text: apoptosis

text: . Decreased mechanical loading over long periods, such as during extended bed-rest, causes a loss of matrix production. Static loads have been shown to be detrimental to biosynthesis while oscillatory loads at low frequencies (similar that of a normal walking gait) have been shown to be beneficial in maintaining health and increasing matrix synthesis. Due to the complexity of in-vivo loading conditions and the interplay of other mechanical and biochemical factors, the question of what an optimal loading regimen may be or whether one exists remain unanswered.

text: As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis. Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway). For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.

text: As the environments of most organisms are constantly changing, the reactions of metabolism must be finely

text: regulated

text: to maintain a constant set of conditions within cells, a condition called

text: homeostasis

text: . Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the

text: flux

text: through the pathway). For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.

text: The metabolic theory of ecology’s main implication is that metabolic rate, and the influence of body size and temperature on metabolic rate, provide the fundamental constraints by which ecological processes are governed.  If this holds true from the level of the individual up to ecosystem level processes, then life history attributes, population dynamics, and ecosystem processes could be explained by the relationship between metabolic rate, body size, and body temperature. While different underlying mechanisms make somewhat different predictions, the following provides an example of some of the implications of the metabolism of individuals.

text: The inequality is balanced by photosynthesis. Photosynthesis emits oxygen with the same isotopic composition (i.e. the ratio between O and O) as the water (HO) used in the reaction, which is independent of the atmospheric ratio. Thus when atmospheric O levels are high enough, photosynthesis will act as a reducing factor. However, as a complicating factor, the degree of fractionation (i.e. change in isotope ratio) occurring due to photosynthesis is not entirely dependent on the water drawn up by the plant, as fractionation can occur as a result of preferential evaporation of  and other small but significant processes.

text: The inequality is balanced by

text: photosynthesis

text: . Photosynthesis emits oxygen with the same isotopic composition (i.e.

text: the ratio between O and O

text: ) as the water (HO) used in the reaction, which is independent of the atmospheric ratio. Thus when atmospheric O levels are high enough, photosynthesis will act as a reducing factor. However, as a complicating factor, the degree of fractionation (i.e. change in isotope ratio) occurring due to photosynthesis is not entirely dependent on the water drawn up by the plant, as fractionation can occur as a result of preferential evaporation of  and other small but significant processes.

text: There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with the utilization of energy (anabolic pathway) or break down of complex molecules by releasing energy in the process (catabolic pathway). The two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the energy required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the amphibolic pathway, which can be either catabolic or anabolic based on the need for or the availability of energy.

text: There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with the utilization of energy (

text: anabolic pathway

text: ) or break down of complex molecules by releasing energy in the process (

text: catabolic pathway

text: ). The two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the energy required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the amphibolic pathway, which can be either catabolic or anabolic based on the need for or the availability of energy.

text: Any oxidizable material present in an aerobic natural waterway or in an industrial wastewater will be oxidized both by biochemical (bacterial) or chemical processes. The result is that the oxygen content of the water will be decreased. Basically, the reaction for biochemical oxidation may be written as:

text: Any

text: oxidizable

text: material present in an aerobic natural waterway or in an industrial wastewater will be oxidized both by

text: biochemical

text: (bacterial) or chemical processes. The result is that the oxygen content of the water will be decreased. Basically, the reaction for biochemical oxidation may be written as:

text: Dehydrogenases oxidize a substrate by transferring a hydrogen to an electron acceptor, common electron acceptors being NAD or FAD. This would be considered an oxidation of the substrate, in which the substrate is losing electrons. When considered, the name "dehydrogenase" is a logical moniker for this enzyme, as it facilitates the removal (de-) of a hydrogen (-hydrogen-), by an enzyme (-ase). In contrast, reductases are a subclass of oxidoreductases that catalyze reduction reactions, or a reaction in which a compound is gaining electrons. Dehydrogenase reactions come most commonly in two forms: the transfer of a hydride and release of a proton, and the transfer of two hydrogens.

text: Dehydrogenases oxidize a substrate by transferring a hydrogen to an electron acceptor, common electron acceptors being

text: NAD

text: or

text: FAD.

text: This would be considered an oxidation of the substrate, in which the substrate is losing electrons. When considered, the name "dehydrogenase" is a logical moniker for this enzyme, as it facilitates the removal (de-) of a hydrogen (-hydrogen-), by an enzyme (-ase). In contrast, reductases are a subclass of oxidoreductases that catalyze reduction reactions, or a reaction in which a compound is gaining electrons. Dehydrogenase reactions come most commonly in two forms: the transfer of a hydride and release of a proton, and the transfer of two hydrogens.

text: Aspartyl aminopeptidase () is an enzyme. This enzyme catalyses the following chemical reaction

text: Aspartyl aminopeptidase () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Some examples of the anabolic effects of these hormones are increased protein synthesis from amino acids, increased appetite, increased bone remodeling and growth, and stimulation of bone marrow, which increases the production of red blood cells. Through a number of mechanisms AAS stimulate the formation of muscle cells and hence cause an increase in the size of skeletal muscles, leading to increased strength.

text: Some examples of the anabolic effects of these hormones are increased

text: protein synthesis

text: from

text: amino acid

text: s, increased appetite, increased bone remodeling and growth, and stimulation of

text: bone marrow

text: , which increases the production of

text: red blood cell

text: s. Through a number of

text: mechanisms

text: AAS stimulate the formation of muscle cells and hence cause an increase in the size of

text: skeletal muscles

text: , leading to increased strength.

text: Bioluminescence is light resulting from biochemical reaction by a living organism.

text: Carbon dioxide is converted into sugars in a process called carbon fixation. Carbon fixation is an endothermic redox reaction, so photosynthesis needs to supply both a source of energy to drive this process, and the electrons needed to convert  into a carbohydrate. This addition of the electrons is a reduction reaction. In general outline and in effect, photosynthesis is the opposite of cellular respiration, in which glucose and other compounds are oxidized to produce  and water, and to release exothermic chemical energy to drive the organism's metabolism. However, the two processes take place through a different sequence of chemical reactions and in different cellular compartments.

text: carbon fixation

text: . Carbon fixation is an

text: endothermic

text: redox

text: reaction, so photosynthesis needs to supply both a source of energy to drive this process, and the electrons needed to convert  into a

text: carbohydrate

text: . This addition of the electrons is a

text: reduction reaction

text: . In general outline and in effect, photosynthesis is the opposite of

text: cellular respiration

text: , in which glucose and other compounds are oxidized to produce  and water, and to release

text: exothermic

text: chemical energy to drive the organism's

text: metabolism

text: . However, the two processes take place through a different sequence of chemical reactions and in different cellular compartments.

text: Hepoxilin-epoxide hydrolase coverts the epoxide residue in hepoxilins A3 and B3 to Vicinal (chemistry) diols as exemplified in the following enzyme reaction for the metabolism of hepoxilin A3 to trioxilin A3:

text: Hepoxilin-epoxide hydrolase coverts the

text: epoxide

text: residue in hepoxilins A3 and B3 to

text: Vicinal (chemistry)

text: diol

text: s as exemplified in the following

text: enzyme reaction

text: for the metabolism of hepoxilin A3 to trioxilin A3:

text: Molybdenum (Mo) is the most abundant transition element in solution in the sea (mostly as dianionic molybdate ion) and in living organisms, its abundance in the Earth’s crust is quite low. Therefore, the use of Mo by living organisms seems surprising at first glance. Archaea, bacteria, fungi, plants, and animals, including humans, require molybdenum. It is also found in over 50 different enzymes. Its hydrolysis to water-soluble oxo-anionic species makes Mo readily accessible. Mo is found in the active sites of metalloenzymes that perform key transformations in the metabolism of carbon, nitrogen, arsenic, selenium, sulfur,  and chlorine compounds.The mononuclear Mo enzymes are widely distributed in the biosphere; they catalyze many significant reactions in the metabolism of nitrogen and sulfur-containing compounds as well as various carbonyl compounds (e.g., aldehydes, CO, and CO). Nitrate reductases enzymes are important for the nitrogen cycle. They belong to a class of enzymes with a mononuclear Mo center and they catalyze the metabolism reaction of C,  N, S, etc., in bacteria, plants, animals, and humans. Due to the oxidation of sulfides, The first considerable development was that of aerobic bacteria which could now utilize Mo. As oxygen began to accumulate in the atmosphere and oceans, the reaction of MoS to MoO also increased. This reaction made the highly soluble molybdate ion available for incorporation into critical metalloenzymes, and may have thus allowed life to thrive. It allowed organisms to occupy new ecological niches. Mo plays an important role in the reduction of dinitrogen to ammonia, which occurs in one type of nitrogenases. These enzymes are used by bacteria that usually live in a symbiotic relationship with plants; their role is nitrogen fixation, which is vital for sustaining life on earth. Mo enzymes also play important roles in sulfur metabolism of organisms ranging from bacteria to humans.

text: Molybdenum

text: (Mo) is the most abundant

text: transition element

text: in solution in the sea (mostly as dianionic molybdate ion) and in living organisms, its abundance in the Earth’s crust is quite low. Therefore, the use of Mo by living organisms seems surprising at first glance.

text: Archaea

text: , bacteria, fungi, plants, and animals, including humans, require molybdenum. It is also found in over 50 different

text: enzymes

text: . Its hydrolysis to water-soluble oxo-anionic species makes Mo readily accessible. Mo is found in the

text: active site

text: s of

text: metalloenzymes

text: that perform key transformations in the

text: metabolism

text: of carbon, nitrogen, arsenic, selenium, sulfur,  and chlorine compounds.The mononuclear Mo enzymes are widely distributed in the biosphere; they catalyze many significant reactions in the metabolism of nitrogen and sulfur-containing compounds as well as various

text: carbonyl compounds

text: (e.g., aldehydes, CO, and CO).

text: Nitrate reductases

text: enzymes are important for the nitrogen cycle. They belong to a class of enzymes with a mononuclear Mo center and they catalyze the metabolism reaction of C,  N, S, etc., in bacteria, plants, animals, and humans. Due to the oxidation of

text: sulfides

text: , The first considerable development was that of

text: aerobic bacteria

text: which could now utilize Mo. As oxygen began to accumulate in the atmosphere and oceans, the reaction of MoS to MoO also increased. This reaction made the highly soluble molybdate ion available for incorporation into critical metalloenzymes, and may have thus allowed life to thrive. It allowed organisms to occupy new ecological niches. Mo plays an important role in the reduction of

text: dinitrogen

text: to

text: ammonia

text: , which occurs in one type of

text: nitrogenase

text: s. These enzymes are used by bacteria that usually live in a

text: symbiotic

text: relationship with plants; their role is

text: nitrogen fixation

text: , which is vital for sustaining life on earth. Mo enzymes also play important roles in

text: sulfur metabolism

text: of organisms ranging from bacteria to humans.

text: ACSS3 is part of a family known as Acyl-coenzyme A synthetases (ACSs), which catalyze the initial reaction in fatty acid metabolism. This reaction activates fatty acids via thioesterification to CoA, thereby allowing their participation in both anabolic and catabolic pathways. The existence of many ACSs suggests that each plays a unique role, directing the acyl-CoA product to a specific metabolic fate. Knowing the full complement of ACS genes in the human genome will facilitate future studies to characterize their specific biological functions.

text: ACSS3 is part of a family known as Acyl-coenzyme A synthetases (ACSs), which catalyze the initial reaction in

text: fatty acid metabolism

text: . This reaction activates fatty acids via thioesterification to CoA, thereby allowing their participation in both anabolic and catabolic pathways. The existence of many ACSs suggests that each plays a unique role, directing the acyl-CoA product to a specific metabolic fate. Knowing the full complement of ACS genes in the human genome will facilitate future studies to characterize their specific biological functions.

text: Two styles have evolved in the use of gloveboxes for synthetic chemistry.  In a more conservative mode, they are used solely to store, weigh, and transfer air-sensitive reagents.  Reactions are thereafter carried out using Schlenk techniques. The gloveboxes are thus only used for the most air-sensitive stages in an experiment.  In their more liberal use, gloveboxes are used for the entire synthetic operations including reactions in solvents, work-up, and preparation of samples for spectroscopy.

text: Two styles have evolved in the use of gloveboxes for

text: synthetic chemistry

text: .  In a more conservative mode, they are used solely to store, weigh, and transfer air-sensitive

text: reagents

text: .  Reactions are thereafter carried out using Schlenk techniques. The gloveboxes are thus only used for the most air-sensitive stages in an experiment.  In their more liberal use, gloveboxes are used for the entire synthetic operations including reactions in solvents, work-up, and preparation of samples for spectroscopy.

text: Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through biochemical signaling and the flow of chemical energy through metabolism, biochemical processes give rise to the complexity of life. Over the last decades of the 20th century, biochemistry has become so successful at explaining living processes that now almost all areas of the life sciences from botany to medicine to genetics are engaged in biochemical research. Today, the main focus of pure biochemistry is on understanding how biological molecules give rise to the processes that occur within living cells, which in turn relates greatly to the study and understanding of tissues, organs, and whole organisms—that is, all of biology.

text: Biochemistry, sometimes called biological chemistry, is the study of

text: chemical process

text: es within and relating to living

text: organism

text: s. By controlling information flow through biochemical signaling and the flow of chemical energy through

text: metabolism

text: , biochemical processes give rise to the complexity of

text: life

text: . Over the last decades of the 20th century, biochemistry has become so successful at explaining living processes that now almost all

text: areas of the life sciences

text: from

text: botany

text: to

text: medicine

text: to

text: genetics

text: are engaged in biochemical research. Today, the main focus of

text: pure

text: biochemistry is on understanding how

text: biological molecules

text: give rise to the processes that occur within living

text: cells

text: , which in turn relates greatly to the study and understanding of

text: tissues

text: organs

text: , and whole organisms—that is, all of

text: biology

text: Some transformations, particularly substitutions, can proceed both biotically and abiotically, although enzyme-catalyzed reactions typically reach higher rates. For example, the hydrolytic dechlorination of atrazine to hydroxyatrazine in soil by atrazine-dechlorinating bacterial enzymes reached a second-order rate constant of 105/mole/second, likely dominating in the environment. In other cases, enzymes facilitate reactions with no abiotic counterpart, as with the herbicide glyphosate, which contains a C-P bond that is stable with respect to light, reflux in strong acid or base, and other abiotic conditions. Microbes that cleave the C-P bond are widespread in the environment, and some can metabolize glyphosate. The C-P lyase enzyme system is encoded by a complicated 14-gene operon.

text: Some transformations, particularly substitutions, can proceed both biotically and abiotically, although enzyme-catalyzed reactions typically reach higher rates. For example, the hydrolytic dechlorination of

text: atrazine

text: to hydroxyatrazine in soil by atrazine-dechlorinating bacterial enzymes reached a second-order rate constant of 105/

text: mole

text: /second, likely dominating in the environment. In other cases, enzymes facilitate reactions with no abiotic counterpart, as with the

text: herbicide

text: glyphosate

text: , which contains a C-P bond that is stable with respect to light, reflux in strong

text: acid

text: or

text: base

text: , and other abiotic conditions. Microbes that cleave the C-P bond are widespread in the environment, and some can metabolize glyphosate. The C-P lyase enzyme system is encoded by a complicated 14-gene

text: operon

text: The specific activity of an enzyme is another common unit. This is the activity of an enzyme per milligram of total protein (expressed in μmol minmg). Specific activity gives a measurement of enzyme purity in the mixture. It is the moles of product formed by an enzyme in a given amount of time (minutes) under given conditions per milligram of total proteins. Specific activity is equal to the rate of reaction multiplied by the volume of reaction divided by the mass of total protein. The SI unit is katal kg, but a more practical unit is μmol mg min. Specific activity is a measure of enzyme processivity, at a specific (usually saturating) substrate concentration, and is usually constant for a pure enzyme. For elimination of errors arising from differences in cultivation batches and/or misfolded enzyme etc. an active site titration needs to be done. This is a measure of the amount of active enzyme, calculated by e.g. titrating the amount of active sites present by employing an irreversible inhibitor. The specific activity should then be expressed as μmol min mg active enzyme. If the molecular weight of the enzyme is known, the turnover number, or μmol product per second per μmol of active enzyme, can be calculated from the specific activity. The turnover number can be visualized as the number of times each enzyme molecule carries out its catalytic cycle per second.

text: The specific activity of an enzyme is another common unit. This is the activity of an enzyme per milligram of total protein (expressed in μmol minmg). Specific activity gives a measurement of enzyme purity in the mixture. It is the moles of product formed by an

text: enzyme

text: in a given amount of time (minutes) under given conditions per milligram of total proteins. Specific activity is equal to the rate of reaction multiplied by the volume of reaction divided by the mass of total protein. The SI unit is katal kg, but a more practical unit is μmol mg min. Specific activity is a measure of enzyme processivity, at a specific (usually saturating)

text: substrate

text: concentration, and is usually constant for a pure enzyme. For elimination of errors arising from differences in cultivation batches and/or misfolded enzyme etc. an active site titration needs to be done. This is a measure of the amount of active enzyme, calculated by e.g. titrating the amount of active sites present by employing an irreversible inhibitor. The specific activity should then be expressed as μmol min mg active enzyme. If the molecular weight of the enzyme is known, the

text: turnover number

text: , or μmol product per second per μmol of active enzyme, can be calculated from the specific activity. The turnover number can be visualized as the number of times each enzyme molecule carries out its catalytic cycle per second.

text: Irwin Fridovich is an American biochemist who, together with his graduate student Joe M. McCord, discovered the enzymatic activity of copper,zinc superoxide dismutase (SOD),—to protect organisms from the toxic effects of superoxide free radicals formed as a byproduct of normal oxygen metabolism. Subsequently, Fridovich's research group also discovered the manganese-containing and the iron-containing SODs from E coli and the mitochondrial MnSOD (SOD2), now known to be an essential mammalian protein. He spent the rest of his career studying the biochemical mechanisms of SOD and of biological superoxide toxicity, using bacteria as model systems. Fridovich is currently Professor Emeritus of Biochemistry at Duke University.

text: Irwin Fridovich is an American

text: biochemist

text: who, together with his graduate student

text: Joe M. McCord

text: , discovered the enzymatic activity of copper,zinc

text: superoxide dismutase

text: (SOD),—to protect organisms from the toxic effects of superoxide free

text: radicals

text: formed as a byproduct of normal

text: oxygen metabolism

text: . Subsequently, Fridovich's research group also discovered the manganese-containing and the iron-containing SODs from E coli and the mitochondrial MnSOD (

text: ), now known to be an essential mammalian protein. He spent the rest of his career studying the biochemical mechanisms of SOD and of biological superoxide toxicity, using bacteria as model systems. Fridovich is currently Professor Emeritus of Biochemistry at

text: Duke University

text: Molecular oxygen, O, is essential for cellular respiration in all aerobic organisms. Oxygen is used as an electron acceptor in mitochondria to generate chemical energy in the form of adenosine triphosphate (ATP) during oxidative phosphorylation. The reaction for the aerobic respiration is essentially the reverse of photosynthesis, except that now there is a large release of chemical energy that is stored in ATP molecules (up to 38 ATP molecules are formed from one molecule of glucose). The simplified version of this reaction is:

text: Molecular oxygen, O, is essential for

text: cellular respiration

text: in all

text: aerobic organism

text: s. Oxygen is used as an electron acceptor in

text: mitochondria

text: to generate chemical energy in the form of

text: adenosine triphosphate

text: (ATP) during

text: oxidative phosphorylation

text: . The reaction for the aerobic respiration is essentially the reverse of photosynthesis, except that now there is a large release of chemical energy that is stored in

text: ATP

text: molecules (up to 38 ATP molecules are formed from one molecule of

text: glucose

text: ). The simplified version of this reaction is:

text: In biological systems, oxocarbenium ions are mostly seen during reactions of carbohydrates. Since sugars are present in the structure of nucleic acids, with a ribose sugar present in RNA and a deoxyribose present in the structure of DNA, their chemistry plays an important role in wide range of cellular functions of nucleic acids. In addition to their functions in nucleotides, sugars are also used for structural components of organisms, as energy storage molecules, cell signaling molecules, protein modification and play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development. The abundance of sugar chemistry in biological processes leads many reaction mechanisms to proceed through oxocarbenium ions. Several important biological reactions that utilize oxocarbenium ions are outlined in this section.

text: In biological systems, oxocarbenium ions are mostly seen during reactions of

text: carbohydrate

text: s. Since sugars are present in the structure of

text: nucleic acids

text: , with a

text: ribose

text: sugar

text: present in

text: RNA

text: and a

text: deoxyribose

text: present in the structure of

text: DNA

text: , their chemistry plays an important role in wide range of cellular functions of nucleic acids. In addition to their functions in nucleotides, sugars are also used for structural components of organisms, as energy storage molecules, cell signaling molecules, protein modification and play key roles in the

text: immune system

text: fertilization

text: , preventing

text: pathogenesis

text: blood clotting

text: , and

text: development

text: . The abundance of sugar chemistry in biological processes leads many reaction mechanisms to proceed through oxocarbenium ions. Several important biological reactions that utilize oxocarbenium ions are outlined in this section.

text: Catalysts: There are two types of catalysts, positive and negative. Positive catalysts increase the reaction rate and negative catalysts (or inhibitors) slow down a reaction and possibly cause the reaction not occur at all. The purpose of a catalyst is to alter the activation energy. Figure 12 illustrates the purpose of a catalyst in that only the activation energy is changed and not the relative thermodynamic stabilities, shown in the figure as ΔH, of the products and reactants. This means that a catalyst will not alter the equilibrium concentrations of the products and reactants but will only allow the reaction to reach equilibrium faster. Figure 13 shows the catalyzed pathway occurring in multiple steps which is a more realistic depiction of a catalyzed process. The new catalyzed pathway can occur through the same mechanism as the uncatalyzed reaction or through an alternate mechanism. An enzyme is a biological catalyst that increases the rate for many vital biochemical reactions. Figure 13 shows a common way to illustrate the effect of an enzyme on a given biochemical reaction.

text: Catalysts: There are two types of

text: catalysts

text: , positive and negative. Positive catalysts increase the reaction rate and negative catalysts (or inhibitors) slow down a reaction and possibly cause the reaction not occur at all. The purpose of a catalyst is to alter the activation energy. Figure 12 illustrates the purpose of a catalyst in that only the

text: activation energy

text: is changed and not the relative thermodynamic stabilities, shown in the figure as ΔH, of the products and reactants. This means that a catalyst will not alter the equilibrium concentrations of the products and reactants but will only allow the reaction to reach equilibrium faster. Figure 13 shows the catalyzed pathway occurring in multiple steps which is a more realistic depiction of a catalyzed process. The new catalyzed pathway can occur through the same mechanism as the uncatalyzed reaction or through an alternate mechanism. An

text: enzyme

text: is a biological catalyst that increases the rate for many vital biochemical reactions. Figure 13 shows a common way to illustrate the effect of an enzyme on a given biochemical reaction.

text: The reaction kinetics involved in biochemical operations is comparatively difficult to obtain than the chemical reaction kinetics. In biochemical operations, the cell kinetics is used for the unstructured models where balanced growth condition is assumed.

text: catabolic - of or relatig to the breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy; destructive metabolism (contrast anabolic)

text: A person's metabolism varies with their physical condition and activity. Weight training can have a longer impact on metabolism than aerobic training, but there are no known mathematical formulas that can exactly predict the length and duration of a raised metabolism from trophic changes with anabolic neuromuscular training.

text: A person's metabolism varies with their physical condition and activity.

text: Weight training

text: can have a longer impact on metabolism than

text: aerobic training

text: , but there are no known mathematical formulas that can exactly predict the length and duration of a raised metabolism from trophic changes with anabolic neuromuscular training.

text: Chemiosmosis is the movement of ions across a semipermeable membrane, down their electrochemical gradient. More specifically, it relates to the generation of adenosine triphosphate (ATP) by the movement of hydrogen ions across a membrane during cellular respiration or photosynthesis.

text: Chemiosmosis is the movement of

text: ion

text: s across a

text: semipermeable membrane

text: , down their

text: electrochemical gradient

text: . More specifically, it relates to the generation of

text: adenosine triphosphate

text: (ATP) by the movement of

text: hydrogen

text: ions across a

text: membrane

text: during

text: cellular respiration

text: or

text: photosynthesis

text: Although enzymes are typically highly specific, some are able to perform catalysis on more than one substrate, a property termed enzyme promiscuity. An enzyme may have many native substrates and broad specificity (e.g. oxidation by cytochrome p450s) or it may have a single native substrate with a set of similar non-native substrates that it can catalyse at some lower rate. The substrates that a given enzyme may react with in vitro, in a laboratory setting, may not necessarily reflect the physiological, endogenous substrates of the enzyme's reactions in vivo. That is to say that enzymes do not necessarily perform all the reactions in the body that may be possible in the laboratory. For example, while fatty acid amide hydrolase (FAAH) can hydrolyze the endocannabinoids 2-arachidonoylglycerol (2-AG) and anandamide at comparable rates in vitro, genetic or pharmacological disruption of FAAH elevates anandamide but not 2-AG, suggesting that 2-AG is not an endogenous, in vivo substrate for FAAH. In another example, the N-acyl taurines (NATs) are observed to increase dramatically in FAAH-disrupted animals, but are actually poor in vitro FAAH substrates.

text: Although enzymes are typically highly specific, some are able to perform catalysis on more than one substrate, a property termed

text: enzyme promiscuity

text: . An enzyme may have many native substrates and broad

text: specificity

text: (e.g. oxidation by

text: cytochrome p450

text: s) or it may have a single native substrate with a set of similar non-native substrates that it can catalyse at some lower rate. The substrates that a given enzyme may react with

text: in vitro

text: , in a laboratory setting, may not necessarily reflect the physiological, endogenous substrates of the enzyme's reactions

text: in vivo

text: . That is to say that enzymes do not necessarily perform all the reactions in the body that may be possible in the laboratory. For example, while

text: fatty acid amide hydrolase

text: (FAAH) can hydrolyze the endocannabinoids

text: (2-AG) and

text: anandamide

text: at comparable rates in vitro, genetic or pharmacological disruption of FAAH elevates anandamide but not 2-AG, suggesting that 2-AG is not an endogenous, in vivo substrate for FAAH. In another example, the N-acyl taurines (NATs) are observed to increase dramatically in FAAH-disrupted animals, but are actually poor in vitro FAAH substrates.

text: In the biorefining operations, biomass can be fractionated in its various parts. These operations involve a.o. milling and pulping, dispersion, homogenizing, physical separation such as centrifugation and decantation, filtration including dead end particulate filtration and cross flow membrane filtration,… Biomass can also be pretreated prior to enzymatic hydrolysis, involving pulping and homogenisation reactions, jet cooking, acid or alcaline treatment, steam explosion, etc. White or industrial biotechnology processes involves the use of microorganisms and their enzymes in so-called fermentation processes or biocatalytic reactions. Fermentations can be performed from 1 to 15.000 litre scale and involve both batch, fed batch or continuous operations. Reactors for enzymatic reactions are present that can be used with either water of organic solvents.Green chemistry is performed in explosion proof installations such as glass-lined chemical reactors (1 - 6.000 l scale) that are suited to perform under vacuum or under pressure. The Bio Base Europe Pilot Plant is also equipped with filter dryers for solvent extraction of liquids and solids.Downstream processing for the recovery of pure products after biochemical or chemical conversion involves various equipment for extraction, evaporation, demineralization, ion exchange, carbon treatment, crystallization, spray drying, lyophilisation, etc.

text: In the biorefining operations, biomass can be fractionated in its various parts. These operations involve a.o. milling and pulping, dispersion, homogenizing, physical separation such as centrifugation and decantation, filtration including dead end particulate filtration and cross flow membrane filtration,…

text: Biomass

text: can also be pretreated prior to enzymatic hydrolysis, involving pulping and homogenisation reactions, jet cooking, acid or alcaline treatment, steam explosion, etc. White or industrial biotechnology processes involves the use of microorganisms and their enzymes in so-called

text: fermentation

text: processes or biocatalytic reactions. Fermentations can be performed from 1 to 15.000 litre scale and involve both batch, fed batch or continuous operations. Reactors for enzymatic reactions are present that can be used with either water of organic solvents.Green chemistry is performed in explosion proof installations such as glass-lined chemical reactors (1 - 6.000 l scale) that are suited to perform under vacuum or under pressure. The Bio Base Europe Pilot Plant is also equipped with filter dryers for solvent extraction of liquids and solids.Downstream processing for the recovery of pure products after biochemical or chemical conversion involves various equipment for extraction, evaporation, demineralization, ion exchange, carbon treatment, crystallization, spray drying, lyophilisation, etc.

text: Sarcosine dehydrogenase is one of the enzymes in sarcosine metabolism, which catalyzes the demethylation of sarcosine to make glycine. It is preceded by dimethylglycine dehydrogenase which turns dimethylglycine into sarcosine. Glycine can also be turned into sarcosine by glycine N-methyltransferase. Since glycine is the production of sarcosine dehydrogenase catalyzed reaction, aside from sarcosine metabolism, the enzyme is also indirectly connected to the creatine cycle and the respiratory chain in the mitochondria  (See figure 4 for pathway). Even so, the biological significance of sarcosine dehydrogenase beyond sarcosine metabolism is not entirely known. In a study of hereditary hemochromatosis using both wild type and HFE (gene) deficient mice fed with 2 percent carbonyl iron supplemented diet, sarcosine dehydrogenase was shown to be down-regulated in HFE deficient mice, but role sarcosine dehydrogenase in iron metabolism is unknown from the experiment conducted.

text: Sarcosine dehydrogenase is one of the enzymes in sarcosine metabolism, which catalyzes the demethylation of sarcosine to make

text: glycine

text: . It is preceded by

text: dimethylglycine dehydrogenase

text: which turns

text: dimethylglycine

text: into sarcosine. Glycine can also be turned into sarcosine by

text: glycine N-methyltransferase

text: . Since glycine is the production of sarcosine dehydrogenase catalyzed reaction, aside from sarcosine metabolism, the enzyme is also indirectly connected to the

text: creatine

text: cycle and the respiratory chain in the mitochondria  (See figure 4 for pathway). Even so, the biological significance of sarcosine dehydrogenase beyond sarcosine metabolism is not entirely known. In a study of

text: hereditary hemochromatosis

text: using both wild type and

text: HFE (gene)

text: deficient mice fed with 2 percent carbonyl iron supplemented diet, sarcosine dehydrogenase was shown to be down-regulated in HFE deficient mice, but role sarcosine dehydrogenase in iron metabolism is unknown from the experiment conducted.

text: For non-equilibrium reactions, isotopic effects are better described by the GEBIK and GEBIF equations for transient kinetic isotope fractionation, which generalize non-steady isotopic effects in any chemical and biochemical reactions.

text: For non-equilibrium reactions, isotopic effects are better described by the GEBIK and GEBIF equations for

text: transient kinetic isotope fractionation

text: , which generalize non-steady isotopic effects in any chemical and biochemical reactions.

text: Having shown that enzymes could function outside a living cell, the next step was to determine their biochemical nature. Many early workers noted that enzymatic activity was associated with proteins, but several scientists (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis.  However, in 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; Sumner did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively proved by Northrop and Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.

text: Having shown that enzymes could function outside a living cell, the next step was to determine their biochemical nature. Many early workers noted that enzymatic activity was associated with proteins, but several scientists (such as Nobel laureate

text: Richard Willstätter

text: ) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis.  However, in 1926,

text: James B. Sumner

text: showed that the enzyme

text: urease

text: was a pure protein and crystallized it; Sumner did likewise for the enzyme

text: catalase

text: in 1937. The conclusion that pure proteins can be enzymes was definitively proved by

text: Northrop

text: and

text: Stanley

text: , who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.

text: Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and lipids (often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life.

text: Most of the structures that make up animals, plants and microbes are made from three basic classes of

text: molecule

text: amino acid

text: s,

text: carbohydrate

text: s and

text: lipid

text: s (often called

text: fat

text: s). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make

text: polymer

text: s such as

text: DNA

text: and

text: protein

text: s, essential

text: macromolecules

text: of life.

text: The effect of chondroitin sulfate in patients with osteoarthritis is likely the result of a number of reactions including its anti-inflammatory activity, the stimulation of the synthesis of proteoglycans and hyaluronic acid, and the decrease in catabolic activity of chondrocytes inhibiting the synthesis of proteolytic enzymes, nitric oxide, and other substances that contribute to damage cartilage matrix and cause death of articular chondrocytes. A recent review summarizes data from relevant reports describing the biochemical basis of the effect of chondroitin sulfate on osteoarthritis articular tissues. The rationale behind the use of chondroitin sulfate is based on the belief that osteoarthritis is associated with a local deficiency or degradation of natural substances, including internal chondroitin sulfate.

text: A core set of energy-producing catabolic pathways occur within all living organisms in some form. These pathways transfer the energy released by breakdown of nutrients into ATP and other small molecules used for energy (e.g. GTP, NADPH, FADH). All cells can perform anaerobic respiration by glycolysis. Additionally, most organisms can perform more efficient aerobic respiration through the citric acid cycle and oxidative phosphorylation. Additionally plants, algae and cyanobacteria are able to use sunlight to anabolically synthesize compounds from non-living matter by photosynthesis.

text: A core set of energy-producing

text: catabolic

text: pathways occur within all living organisms in some form. These pathways transfer the energy released by breakdown of

text: nutrient

text: s into

text: ATP

text: and other small molecules used for energy (e.g.

text: GTP

text: NADPH

text: FADH

text: ). All cells can perform

text: anaerobic respiration

text: by

text: glycolysis

text: . Additionally, most organisms can perform more efficient

text: aerobic respiration

text: through the

text: citric acid cycle

text: and

text: oxidative phosphorylation

text: . Additionally

text: plant

text: s,

text: algae

text: and

text: cyanobacteria

text: are able to use sunlight to

text: anabolic

text: ally synthesize compounds from non-living matter by

text: photosynthesis

text: Her first two publications in scientific journals showed the mechanisms for reactions that involved the enzymes enolase that metabolizes carbohydrates, and pyruvate kinase. Her first groundbreaking experiments were carried out in the late 1970s and early 1980s, while she was at Yale, then the University of Wisconsin. She was trying to understand how the hydroxyl group at the 2’ position of the ribonucleotide’s sugar was replaced by the hydrogen found in deoxyribonucleotides. To perform these experiments, she had to synthesize nucleotides that carried a heavy isotope at specific positions. Stubbe reportedly kept a bed in her office since she worked around the clock on her experiments. Stubbe pioneered the use of spectroscopic investigations of enzyme interactions and has devoted most of her career to elucidating the biochemical mechanisms behind free radicals. In her early work at Yale and then at the University of Wisconsin, Stubbe discovered how enzymes called ribonucleotide reductases use free-radical chemistry to convert nucleotides into deoxynucleotides, an essential process in DNA repair and replication. These enzymes catalyze the rate-determining step in DNA biosynthesis. Her analysis of the nucleotide reduction process led to a number of applications, including the anti-cancer drug gemcitabine, which is used to treat various carcinomas, such as pancreatic cancer, breast cancer, and non-small cell lung cancer.

text: Her first two publications in scientific journals showed the mechanisms for reactions that involved the enzymes enolase that

text: metabolizes

text: carbohydrate

text: s, and pyruvate kinase. Her first groundbreaking experiments were carried out in the late 1970s and early 1980s, while she was at Yale, then the University of Wisconsin. She was trying to understand how the

text: hydroxyl group

text: at the 2’ position of the

text: ribonucleotide’s

text: sugar was replaced by the

text: hydrogen

text: found in

text: deoxyribonucleotide

text: s. To perform these experiments, she had to synthesize nucleotides that carried a heavy

text: isotope

text: at specific positions. Stubbe reportedly kept a bed in her office since she worked around the clock on her experiments. Stubbe pioneered the use of

text: spectroscopic

text: investigations of

text: enzyme

text: interactions and has devoted most of her career to elucidating the biochemical mechanisms behind

text: free radicals

text: . In her early work at Yale and then at the University of Wisconsin, Stubbe discovered how enzymes called ribonucleotide reductases use free-radical chemistry to convert

text: nucleotide

text: s into deoxynucleotides, an essential process in

text: DNA repair

text: and

text: replication

text: . These enzymes catalyze the

text: rate-determining step

text: in DNA biosynthesis. Her analysis of the nucleotide reduction process led to a number of applications, including the anti-cancer drug

text: gemcitabine

text: , which is used to treat various

text: carcinoma

text: s, such as

text: pancreatic cancer

text: breast cancer

text: , and non-small cell

text: lung cancer

text: Gas exchange is a biological process through which different gases are transferred in opposite directions across a specialized respiratory surface. Gases are constantly required by, and produced as a by-product of, cellular and metabolic reactions, so an efficient system for their exchange is extremely important. It is linked with respiration in animals, and both respiration and photosynthesis in plants.

text: Gas exchange is a biological process through which different gases are transferred in opposite directions across a specialized respiratory surface. Gases are constantly required by, and produced as a by-product of,

text: cellular and metabolic reactions

text: , so an efficient system for their exchange is extremely important. It is linked with

text: respiration

text: in animals, and both respiration and

text: photosynthesis

text: in plants.

text: Fersht has received many prizes and medals including: the FEBS Anniversary Prize; Novo Biotechnology Award; Charmian Medal of the Royal Society of Chemistry; Max Tishler Lecture and Prize Harvard University; The Datta Lectureship and Medal of the Federation of European Biochemical Societies; Jubilee Lecture and the Harden Medal of the Biochemical Society; Feldberg Foundation Prize, Distinguished Service Award, Miami Nature Biotechnology Winter Symposium; Christian B. Anfinsen Award of the Protein Society; Natural Products Award of the Royal Society of Chemistry, Stein and Moore Award of the Protein Society; Bader Award of the American Chemical Society; Kaj Ulrik Linderstrøm-Lang  Prize and Medal; Johannes Martin Bijvoet Medal Utrecht University; and the Gilbert N. Lewis Medal University of California, Berkeley, and the Wilhelm Exner Medal in 2009.

text: Fersht has received many prizes and medals including: the

entity_name: Federation of European Biochemical Societies

text: FEBS

text: Anniversary Prize; Novo Biotechnology Award; Charmian Medal of the

text: Royal Society of Chemistry

text: Max Tishler

text: Lecture and Prize

text: Harvard University

text: The Datta Lectureship and Medal

text: of the

text: Federation of European Biochemical Societies

text: ; Jubilee Lecture and the Harden Medal of the

text: Biochemical Society

text: ; Feldberg Foundation Prize, Distinguished Service Award, Miami

text: Nature

text: Biotechnology Winter Symposium;

text: Christian B. Anfinsen Award

text: of the Protein Society; Natural Products Award of the

text: Royal Society of Chemistry

text: , Stein and Moore Award of the Protein Society; Bader Award of the

text: American Chemical Society

text: Kaj Ulrik Linderstrøm-Lang

text: Prize and Medal;

text: Johannes Martin Bijvoet

text: Medal

text: Utrecht University

text: ; and the

text: Gilbert N. Lewis

text: Medal

text: University of California, Berkeley

text: , and the

text: Wilhelm Exner Medal

text: in 2009.

text: Quantum biology refers to applications of quantum mechanics and theoretical chemistry to biological objects and problems. Many biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve chemical reactions, light absorption, formation of excited electronic states, transfer of excitation energy, and the transfer of electrons and protons (hydrogen ions) in chemical processes such as photosynthesis and cellular respiration. Quantum biology may use computations to model biological interactions in light of quantum mechanical effects. Quantum biology is concerned with the influence of non-trivial quantum phenomena, as opposed to the so-called trivial quantum phenomena present in all biology by reduction to fundamental physics.

text: Quantum biology refers to applications of

text: quantum mechanics

text: and

text: theoretical chemistry

text: to biological objects and problems. Many biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve

text: chemical reactions

text: light absorption

text: , formation of

text: excited electronic states

text: transfer of excitation energy

text: , and the transfer of electrons and protons (

text: hydrogen ion

text: s) in chemical processes such as

text: photosynthesis

text: and

text: cellular respiration

text: . Quantum biology may use computations to model biological interactions in light of quantum mechanical effects. Quantum biology is concerned with the influence of non-trivial quantum phenomena, as opposed to the so-called trivial quantum phenomena present in all biology by reduction to fundamental physics.

text: How did photosynthesis arise in bacteria? The answer to this question is complicated by the fact that there are several types of light-harvesting energy capture systems. Chloroflexus aurantiacus has been of interest in the search for origins of the so-called type II photosynthetic reaction center. One idea is that bacteria with respiratory electron transport evolved photosynthesis by coupling a light-harvesting energy capture system to the pre-existing respiratory electron transport chain. Thus, rare organisms like Chloroflexus aurantiacus that can survive using either respiration or photosynthesis are of interest in on-going attempts to trace the evolution of photosynthesis.

text: How did photosynthesis arise in bacteria? The answer to this question is complicated by the fact that there are several types of light-harvesting energy capture systems. Chloroflexus aurantiacus has been of interest in the search for origins of the so-called

text: type II

text: photosynthetic reaction center

text: . One idea is that bacteria with

text: respiratory

text: electron transport

text: evolved photosynthesis by coupling a light-harvesting energy capture system to the pre-existing respiratory electron transport chain. Thus, rare organisms like Chloroflexus aurantiacus that can survive using either respiration or photosynthesis are of interest in on-going attempts to trace the

text: evolution

text: of photosynthesis.

text: The Williamson ether synthesis is an organic reaction,  forming an ether from an organohalide and a deprotonated alcohol (alkoxide). This reaction was developed by Alexander Williamson in 1850. Typically it involves the reaction of an alkoxide ion with a primary alkyl halide via an S2 reaction. This reaction is important in the history of organic chemistry because it helped prove the structure of ethers.

text: The Williamson ether synthesis is an

text: organic reaction

text: ,  forming an

text: ether

text: from an

text: organohalide

text: and a deprotonated alcohol (

text: alkoxide

text: ). This reaction was developed by

text: Alexander Williamson

text: in 1850. Typically it involves the reaction of an

text: alkoxide ion

text: with a primary alkyl

text: halide

text: via an

text: S2 reaction

text: . This reaction is important in the history of organic chemistry because it helped prove the structure of

text: ether

text: s.

text: The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by enzymes. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called metabolic network. It is possible to use network analyses to infer how selection acts on metabolic pathways.

text: The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by

text: enzymes

text: . Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called

text: metabolic network

text: . It is possible to use network analyses to infer how selection acts on metabolic pathways.

text: Many of methylene's electronic states lie relatively close to each other, giving rise to varying degrees of radical chemistry. The ground state is a triplet radical with two unpaired electrons (X̃B), and the first excited state is a singlet non-radical (ãA). With the singlet non-radical only 38 kJ above the ground state, a sample of methylene exists as a mixture of electronic states even at room temperature, giving rise to complex reactions. For example, reactions of the triplet radical with non-radical species generally involves abstraction, whereas reactions of the singlet non-radical not only involves abstraction, but also insertion or addition.

text: Since all natural waterways contain bacteria and nutrients, almost any waste compounds introduced into such waterways will initiate biochemical reactions (such as shown above). Those biochemical reactions create what is measured in the laboratory as the biochemical oxygen demand (BOD). Such chemicals are also liable to be broken down using strong oxidizing agents and these chemical reactions create what is measured in the laboratory as the chemical oxygen demand (COD). Both the BOD and COD tests are a measure of the relative oxygen-depletion effect of a waste contaminant. Both have been widely adopted as a measure of pollution effect. The BOD test measures the oxygen demand of biodegradable pollutants whereas the COD test measures the oxygen demand of oxidizable pollutants.

text: Since all natural waterways contain bacteria and nutrients, almost any waste compounds introduced into such waterways will initiate biochemical reactions (such as shown above). Those biochemical reactions create what is measured in the laboratory as the

text: biochemical oxygen demand

text: (BOD). Such chemicals are also liable to be broken down using strong oxidizing agents and these chemical reactions create what is measured in the laboratory as the

text: chemical oxygen demand

text: (COD). Both the BOD and COD tests are a measure of the relative oxygen-depletion effect of a waste contaminant. Both have been widely adopted as a measure of

text: pollution

text: effect. The BOD test measures the oxygen demand of

text: biodegradable

text: pollutants whereas the COD test measures the oxygen demand of oxidizable pollutants.

text: Carbon dioxide is an end product of cellular respiration in organisms that obtain energy by breaking down sugars, fats and amino acids with oxygen as part of their metabolism. This includes all plants, algae and animals and aerobic fungi and bacteria. In vertebrates, the carbon dioxide travels in the blood from the body's tissues to the skin (e.g., amphibians) or the gills (e.g., fish), from where it dissolves in the water, or to the lungs from where it is exhaled. During active photosynthesis, plants can absorb more carbon dioxide from the atmosphere than they release in respiration.

text: Carbon dioxide is an end product of

text: cellular respiration

text: in organisms that obtain energy by breaking down sugars, fats and

text: amino acid

text: s with

text: oxygen

text: as part of their

text: metabolism

text: . This includes all plants, algae and animals and

text: aerobic

text: fungi and bacteria. In

text: vertebrate

text: s, the carbon dioxide travels in the blood from the body's tissues to the skin (e.g.,

text: amphibian

text: s) or the gills (e.g.,

text: fish

text: ), from where it dissolves in the water, or to the lungs from where it is exhaled. During active photosynthesis,

text: plants can absorb more carbon dioxide from the atmosphere than they release

text: in respiration.

text: In enzymology, a Mg-importing ATPase () is an enzyme that catalyzes the chemical reaction

text: In

text: enzymology

text: , a Mg-importing ATPase () is an

text: enzyme

text: that

text: catalyzes

text: the

text: chemical reaction

text: There are also biochemical reactions where enzymes such as Acetohydroxyacid Synthase I  from E. coli condense pyruvate and benzaldehyde into R-PAC. Such methods have much higher conversion rates in comparison to the conventional yeast fermentation.

text: Its importance in fatty acid metabolism makes CPT1 a potentially useful enzyme to focus on in the development of treatments of many other metabolic disorders as well.

text: In terms of measurement, four basic parameters are of key importance: Total inorganic carbon (TIC, T or C), Total alkalinity (T or A), pH, and pCO.  Measuring any two of these parameters allows for the determination of a wide range of pH-dependent species (including the above-mentioned species).  This balance can be changed by a number of processes.  For example, the air-sea flux of CO, the dissolution/precipitation of CaCO, or biological activity such as photosynthesis/respiration.  Each of these has different effects on each of the four basic parameters, and together they exert strong influences on global cycles.  The net and local charge of the oceans remains neutral during any chemical process.

text: In terms of measurement, four basic parameters are of key importance:

text: Total inorganic carbon

text: (TIC, T or C), Total

text: alkalinity

text: (T or A), pH, and

text: pCO

text: .  Measuring any two of these parameters allows for the determination of a wide range of pH-dependent species (including the above-mentioned species).  This balance can be changed by a number of processes.  For example, the

text: air-sea flux

text: of CO, the

text: dissolution

text: precipitation

text: of

text: CaCO

text: , or biological activity such as

text: photosynthesis

text: respiration

text: .  Each of these has different effects on each of the four basic parameters, and together they exert strong influences on global cycles.  The net and local charge of the oceans remains neutral during any chemical process.

text: The structure of oxytocin is very similar to that of vasopressin.  Both are nonapeptides with a single disulfide bridge, differing only by two substitutions in the amino acid sequence (differences from oxytocin bolded for clarity): Cys – Tyr – Phe – Gln – Asn – Cys – Pro – Arg – Gly – NH. A table showing the sequences of members of the vasopressin/oxytocin superfamily and the species expressing them is present in the vasopressin article. Oxytocin and vasopressin were isolated and their total synthesis reported in 1954, work for which Vincent du Vigneaud was awarded the 1955 Nobel Prize in Chemistry with the citation: "for his work on biochemically important sulphur compounds, especially for the first synthesis of a polypeptide hormone."

text: The structure of oxytocin is very similar to that of

text: vasopressin

text: .  Both are nonapeptides with a single disulfide bridge, differing only by two substitutions in the amino acid sequence (differences from oxytocin bolded for clarity): Cys – Tyr –

text: Phe

text: – Gln – Asn – Cys – Pro –

text: Arg

text: – Gly – NH. A table showing the sequences of members of the vasopressin/oxytocin superfamily and the species expressing them is present in the

text: vasopressin

text: article. Oxytocin and vasopressin were isolated and their

text: total synthesis

text: reported in 1954, work for which

text: Vincent du Vigneaud

text: was awarded the 1955

text: Nobel Prize in Chemistry

text: with the citation: "for his work on biochemically important sulphur compounds, especially for the first synthesis of a polypeptide hormone."

text: Because cordycepin is similar to adenosine, some enzymes cannot discriminate between the two. Therefore, it can participate in certain biochemical reactions (for example, be incorporated into an RNA molecule, thus causing the premature termination of its synthesis).

text: Because cordycepin is similar to

text: adenosine

text: , some

text: enzyme

text: s cannot discriminate between the two. Therefore, it can participate in certain biochemical reactions (for example, be incorporated into an

text: RNA

text: molecule, thus causing the premature termination of its synthesis).

text: PGK is present in all living organisms as one of the two ATP-generating enzymes in glycolysis. In the gluconeogenic pathway, PGK catalyzes the reverse reaction. Under biochemical standard conditions, the glycolytic direction is favored.

text: PGK is present in all living organisms as one of the two ATP-generating enzymes in glycolysis. In the gluconeogenic pathway, PGK catalyzes the reverse reaction. Under biochemical

entity_name: Standard conditions for temperature and pressure

text: standard conditions

text: , the glycolytic direction is favored.

text: A basic metabolic panel (BMP)  is a blood test consisting of a set of seven or eight biochemical tests and is one of the most common lab tests ordered by health care providers. Outside the United States, blood tests made up of the majority of the same biochemical tests are called urea and electrolytes (U&E or "Us and Es"), or urea, electrolytes, creatinine (UEC or EUC or CUE), and are often referred to as 'kidney function tests' as they also include a calculated estimated glomerular filtration rate. The BMP provides key information regarding fluid and electrolyte status, kidney function, blood sugar levels, and response to various medications and other medical therapies. It is frequently employed as a screening tool during a physical exam.

text: A basic metabolic panel (BMP)  is a blood test consisting of a set of seven or eight biochemical tests and is one of the most common lab tests ordered by health care providers. Outside the

text: United States

text: , blood tests made up of the majority of the same biochemical tests are called urea and electrolytes (U&E or "Us and Es"), or urea, electrolytes, creatinine (UEC or EUC or CUE), and are often referred to as 'kidney function tests' as they also include a calculated estimated

text: glomerular filtration rate

text: . The BMP provides key information regarding fluid and electrolyte status, kidney function, blood sugar levels, and response to various medications and other medical therapies. It is frequently employed as a screening tool during a

text: physical exam

text: Acidosis is a condition in which excess hydrogen ions are present, and the patient’s blood expresses a low pH value. Alkalosis is a condition in which there are too few hydrogen ions, and the patient’s blood has an elevated pH. Normal blood pH falls in the range of 7.35–7.45, so a number lower than this range represents acidosis and a higher number represents alkalosis. Enzymes, being the regulators or catalysts of virtually all biochemical reactions - are sensitive to pH and will change shape slightly with values outside their normal range. These variations in pH and accompanying slight physical changes to the active site on the enzyme decrease the rate of formation of the enzyme-substrate complex, subsequently decreasing the rate of many enzymatic reactions, which can have complex effects on HR. Severe changes in pH will lead to denaturation of the enzyme.

text: Apnea or apnoea is suspension of breathing. During apnea, there is no movement of the muscles of inhalation, and the volume of the lungs initially remains unchanged. Depending on how blocked the airways are (patency), there may or may not be a flow of gas between the lungs and the environment; gas exchange within the lungs and cellular respiration is not affected.

text: Apnea

entity_name: American and British English spelling differences

text: or

text: apnoea is suspension of

text: breathing

text: . During apnea, there is no movement of the

text: muscle

text: s of

text: inhalation

text: , and the volume of the

text: lung

text: s initially remains unchanged. Depending on how blocked the

text: airway

text: s are (

text: patency

text: ), there may or may not be a flow of

text: gas

text: between the lungs and the environment;

text: gas exchange

text: within the lungs and

text: cellular respiration

text: is not affected.

text: To further elucidate a biochemical explanation between mating arrest and cell cycle commitment, Doncic et al. conducted the same commitment assay described above on various mutant strains. The mutant, FAR1-S87A, lacks CDK phosphorylation sites, and thus Cln1/2 inhibition of Far1 is compromised.  The result is an increase in the amount of Whi5 export required to commit to cellular division, suggesting that Far 1 phosphorylation is key to cellular commitment.  Conversely, the mutant, STE5-8A, lacking CDK phosphorylation sites as well (and thus Cln1/2 inhibition of Ste5 is compromised), does not shift the commitment point, suggesting that such inhibition of the mating pathway is not critical for Start.  A further time-lapse analysis of STE5-8A cells reveals that these mutant cells cannot fully commit to cellular division, as cells exposed to alpha-factor will bud and then revert to mating without completing the cell cycle.  Doncic et al. proposed that the incomplete division was due to expression of genes in both the mating pathway and in the G1 cyclin-driven cellular progression.  Indeed, tracking the expression of FUS1pr-GFP, a mating pathway gene, and of CLN2pr-mCherry, a cell cycle gene, showed great coexpression in STE5-8A cells relative to wild type cells.

text: All respirators function by forming a seal on the users face with the respirator itself.  This is essential, as respirators are designed to come in contact with all air flowing through them, which is then delivered to the user.  Fit testing uses simple equipment that places the users face and head into a hood, into which flavored mist is sprayed.  Usually either bitter or sweet in flavor, with bitter flavors being favored for the almost involuntary reaction of users.  Following a standard procedure, the user then breathes through the chosen respirator, and indicates whether they can detect the mist.  If they cannot, the filter has passed the basic requirement of a face seal and the user also understands how to fit the mask.

text: Deficiency of GALT causes classic galactosemia.  Galactosemia is a childhood disease of hereditary nature.  The autosomal recessive trait affects approximately 1 in every 40,000-60,000 live-born infants.  Classical galactosemia (G/G) is caused by a deficiency in GALT activity, whereas the more common clinical affliction, Duarte/Classica (D/G) arises from attenuation of GALT activity.  Symptoms include ovarian failure, developmental coordination disorder (difficulty speaking correctly and consistently), and neurologic deficits.  A single mutation in any of several amino acids can lead to attenuation or deficiency in GALT activity.  For example, a single mutation from A to G in exon 6 of the GALT gene changes Glu188 to an arginine, and a mutation from A to G in exon 10 converts Asn314 to an aspartic acid.  These two mutations also add new restriction enzyme cut sites, which enable detection by and large-scale population screening with PCR (polymerase chain reaction).  Screening has mostly eliminated neonatal death by G/G galactosemia, but the disease, due to GALT’s role in the biochemical metabolism of ingested galactose (which is toxic when accumulated) to the energetically useful glucose, can certainly be fatal.  However, those afflicted with galactosemia can live relatively normal lives by avoiding milk products and anything else containing galactose (since it cannot be metabolized), although there is the potential for problems in neurological development, or other complications, even in those who avoid galactose.

text: Deficiency of GALT causes

text: classic galactosemia

text: Galactosemia

text: is a childhood disease of hereditary nature.  The autosomal recessive trait affects approximately 1 in every 40,000-60,000 live-born infants.

text: Classical galactosemia

text: (G/G) is caused by a deficiency in GALT activity, whereas the more common clinical affliction,

text: Duarte/Classica

text: (D/G) arises from attenuation of GALT activity.  Symptoms include ovarian failure,

text: developmental coordination disorder

text: (difficulty speaking correctly and consistently), and neurologic deficits.  A single mutation in any of several amino acids can lead to attenuation or deficiency in GALT activity.  For example, a single mutation from A to G in exon 6 of the GALT gene changes Glu188 to an

text: arginine

text: , and a mutation from A to G in exon 10 converts Asn314 to an

text: aspartic acid

text: .  These two mutations also add new

text: restriction enzyme

text: cut sites, which enable detection by and large-scale population screening with PCR (

text: polymerase chain reaction

text: ).  Screening has mostly eliminated neonatal death by G/G galactosemia, but the disease, due to GALT’s role in the biochemical

text: metabolism

text: of ingested

text: galactose

text: (which is toxic when accumulated) to the energetically useful

text: glucose

text: , can certainly be fatal.  However, those afflicted with galactosemia can live relatively normal lives by avoiding milk products and anything else containing galactose (since it cannot be metabolized), although there is the potential for problems in neurological development, or other complications, even in those who avoid galactose.

text: Organic biomolecules are generally depleted relative to the δD of leaf water. However, differences between organisms, biosynthetic pathways, and biological roles of different molecules can lead to huge variability in fractionation; the diversity of lipid biomarkers spans a 600‰ range of δD values. Lipid biosynthesis is biochemically complex, involving multiple enzyme-dependent steps that can lead to isotope fractionations. There are three major pathways of lipid biosynthesis, known as the mevalonate pathway, the acetogenic pathway, and the 1-deoxyD-xylulose-5-phosphate/2-methylerythroyl-4-phosphate pathway. The acetogenic pathway is responsible for the production of n-alkyl lipids like leaf waxes, and is associated with a smaller δD depletion relative to source water than the other two lipid biosynthesis pathways. While leaf water is the main source of hydrogen in leaf biomolecules, relatively depleted hydrogen from acetate or NADPH is often added during biosynthesis, and contributes to the hydrogen composition of the final molecule. Secondary hydrogen exchange reactions, meaning hydrogenation and dehydrogenation reactions outside of the primary biosynthetic pathway, also contribute substantially to the variability of lipid hydrogen isotope composition

text: Organic biomolecules are generally depleted relative to the δD of leaf water. However, differences between organisms, biosynthetic pathways, and biological roles of different molecules can lead to huge variability in fractionation; the diversity of lipid biomarkers spans a 600‰ range of δD values. Lipid

text: biosynthesis

text: is biochemically complex, involving multiple enzyme-dependent steps that can lead to isotope fractionations. There are three major pathways of lipid biosynthesis, known as

text: the mevalonate pathway

text: the acetogenic pathway

text: , and

text: the 1-deoxyD-xylulose-5-phosphate/2-methylerythroyl-4-phosphate pathway

text: . The acetogenic pathway is responsible for the production of n-alkyl lipids like leaf waxes, and is associated with a smaller δD depletion relative to source water than the other two lipid biosynthesis pathways. While leaf water is the main source of hydrogen in leaf biomolecules, relatively depleted hydrogen from acetate or NADPH is often added during biosynthesis, and contributes to the hydrogen composition of the final molecule. Secondary hydrogen exchange reactions, meaning hydrogenation and dehydrogenation reactions outside of the primary biosynthetic pathway, also contribute substantially to the variability of lipid hydrogen isotope composition

text: The Staudinger ligation is a reaction developed by the Bertozzi group in 2000 that is based on the classic Staudinger reaction of azides with triarylphosphines. It launched the field of bioorthogonal chemistry as the first reaction with completely abiotic functional groups although it is no longer as widely used. The Staudinger ligation has been used in both live cells and live mice.

text: The

text: Staudinger ligation

text: is a reaction developed by the Bertozzi group in 2000 that is based on the classic

text: Staudinger reaction

text: of azides with triarylphosphines. It launched the field of bioorthogonal chemistry as the first reaction with completely abiotic functional groups although it is no longer as widely used. The Staudinger ligation has been used in both live cells and live mice.

text: In biochemistry, several important enzymatic cascades and signal transduction cascades participate in metabolic pathways or signaling networks, in which enzymes are usually involved to catalyze the reactions. For example, the tissue factor pathway in the coagulation cascade of secondary hemostasis is the primary pathway leading to fibrin formation, therefore, the initiation of blood coagulation. The pathways are a series of reactions, in which a zymogen (inactive enzyme precursor) of a serine protease and its glycoprotein co-factors are activated to become active components that then catalyze the next reaction in the cascade, ultimately resulting in cross-linked fibrin.

text: In

text: biochemistry

text: , several important

text: enzymatic

text: cascades and

text: signal transduction

text: cascades participate in

text: metabolic

text: pathway

text: s or signaling networks, in which enzymes are usually involved to

text: catalyze

text: the reactions. For example, the tissue factor pathway in the

text: coagulation cascade

text: of secondary

text: hemostasis

text: is the primary pathway leading to

text: fibrin

text: formation, therefore, the initiation of blood coagulation. The pathways are a series of reactions, in which a

text: zymogen

text: (inactive enzyme precursor) of a

text: serine

text: protease

text: and its

text: glycoprotein

text: co-factors are activated to become active components that then catalyze the next reaction in the cascade, ultimately resulting in cross-linked

text: fibrin

text: The journal is abstracted and indexed in:According to the Journal Citation Reports, the journal has a 2014 impact factor of 3.028, ranking it 14th out of 74 journals in the category "Chemistry, Analytical" and 24th out of 79 in the category "Biochemical Research Methods".

text: The journal is abstracted and indexed in:According to the

text: Journal Citation Reports

text: , the journal has a 2014

text: impact factor

text: of 3.028, ranking it 14th out of 74 journals in the category "Chemistry, Analytical" and 24th out of 79 in the category "Biochemical Research Methods".

text: In organic chemistry, the Kumada coupling is a type of cross coupling reaction, useful for generating carbon–carbon bonds by the reaction of a Grignard reagent and an organic halide. The procedure uses transition metal catalysts, typically nickel or palladium, to couple a combination of two alkyl, aryl or vinyl groups. The groups of Robert Corriu and Makoto Kumada reported the reaction independently in 1972.

text: In

text: organic chemistry

text: , the Kumada coupling is a type of

text: cross coupling reaction

text: , useful for generating

text: carbon–carbon bond

text: s by the reaction of a

text: Grignard reagent

text: and an organic halide. The procedure uses

text: transition metal

text: catalysts

text: , typically nickel or palladium, to couple a combination of two

text: alkyl

text: aryl

text: or

text: vinyl

text: groups. The groups of

text: Robert Corriu

text: and

text: Makoto Kumada

text: reported the reaction independently in 1972.

text: Proteins can associate to form protein complexes, these often contain a set of proteins with similar functions, such as enzymes that carry out several steps in the same metabolic pathway. This organization can allow substrate channeling, which is when the product of one enzyme is passed directly to the next enzyme in a pathway without being released into solution. Channeling can make a pathway more rapid and efficient than it would be if the enzymes were randomly distributed in the cytosol, and can also prevent the release of unstable reaction intermediates. Although a wide variety of metabolic pathways involve enzymes that are tightly bound to each other, others may involve more loosely associated complexes that are very difficult to study outside the cell. Consequently, the importance of these complexes for metabolism in general remains unclear.

text: Proteins can associate to form

text: protein complex

text: es, these often contain a set of proteins with similar functions, such as enzymes that carry out several steps in the same metabolic pathway. This organization can allow

text: substrate channeling

text: , which is when the product of one enzyme is passed directly to the next enzyme in a pathway without being released into solution. Channeling can make a pathway more rapid and efficient than it would be if the enzymes were randomly distributed in the cytosol, and can also prevent the release of unstable reaction intermediates. Although a wide variety of metabolic pathways involve enzymes that are tightly bound to each other, others may involve more loosely associated complexes that are very difficult to study outside the cell. Consequently, the importance of these complexes for metabolism in general remains unclear.

text: In biochemical research, it has been investigated as an agent for limiting reactive oxygen species.  It catalyzes the disproportionation of superoxide, facilitates hydrogen peroxide metabolism, and inhibits Fenton chemistry.

text: In biochemical research, it has been investigated as an agent for limiting

text: reactive oxygen species

text: .  It catalyzes the

text: disproportionation

text: of

text: superoxide

text: , facilitates

text: hydrogen peroxide

text: metabolism, and inhibits

text: Fenton

text: chemistry.

text: An important limitation of the reaction is that only a single enantiomer of product is available when the wild type enzyme is used. Enzymes that generate "unnatural" enantiomers must be engineered via site-directed mutagenesis or other biochemical techniques. The development of organisms and enzymes that exhibit "unnatural" stereoselectivity is an ongoing research activity.

text: In chemistry, redistribution usually refers to the exchange of anionic ligands bonded to metal and metalloid centers. The conversion does not involve redox, in contrast to disproportionation reactions.  Redistribution reactions are usefully conducted at higher temperatures; upon cooling the mixture, the product mixture is kinetically frozen and the individual products can be separated.  In cases where redistribution is rapid at mild temperatures, the reaction is less useful synthetically but still important mechanistically.

text: In chemistry, redistribution usually refers to the exchange of anionic ligands bonded to metal and metalloid centers. The conversion does not involve redox, in contrast to

text: disproportionation

text: reactions.  Redistribution reactions are usefully conducted at higher temperatures; upon cooling the mixture, the product mixture is kinetically frozen and the individual products can be separated.  In cases where redistribution is rapid at mild temperatures, the reaction is less useful synthetically but still important mechanistically.

text: A ligand exchange (also ligand substitution) is a type of chemical reaction in which a ligand in a compound is replaced by another. One type of pathway for substitution is the ligand dependent pathway. In organometallic chemistry this can take place via associative substitution or by dissociative substitution. Another form of ligand exchange is seen in the nucleophilic abstraction reaction.

text: A ligand exchange (also ligand substitution) is a type of

text: chemical reaction

text: in which a ligand in a compound is replaced by another. One type of pathway for substitution is the

text: ligand dependent pathway

text: . In organometallic chemistry this can take place via

text: associative substitution

text: or by

text: dissociative substitution

text: . Another form of ligand exchange is seen in the

text: nucleophilic abstraction

text: reaction.

text: Some terrestrial water may have had a biochemical origin, during the Great Oxygenation Event, via redox reactions and photosynthesis.

text: Some terrestrial water may have had a biochemical origin, during the

text: Great Oxygenation Event

text: , via

text: redox reactions

text: and

text: photosynthesis

text: In humans, vitamin C is essential to a healthy diet as well as being a highly effective antioxidant, acting to lessen oxidative stress; a substrate for ascorbate peroxidase in plants (APX is plant specific enzyme); and an enzyme cofactor for the biosynthesis of many important biochemicals. Vitamin C acts as an electron donor for important enzymes:

text: In humans, vitamin C is essential to a healthy diet as well as being a highly effective

text: antioxidant

text: , acting to lessen

text: oxidative stress

text: ; a substrate for

text: ascorbate peroxidase

text: in plants (APX is plant specific enzyme); and an enzyme

text: cofactor

text: for the

text: biosynthesis

text: of many important biochemicals. Vitamin C acts as an

text: electron donor

text: for important

text: enzyme

text: s:

text: It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

text: It was the discovery of

text: enzyme

text: s at the beginning of the 20th century by

text: Eduard Buchner

text: that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of

text: biochemistry

text: . The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was

text: Hans Krebs

text: who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with

text: Hans Kornberg

text: , the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as

text: chromatography

text: X-ray diffraction

text: NMR spectroscopy

text: radioisotopic labelling

text: electron microscopy

text: and

text: molecular dynamics

text: simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

text: Hepsin () is an enzyme. This enzyme catalyses the following chemical reaction

text: Hepsin () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Two cycles of biochemical reactions constitute the basis of plant production, the light reaction and the dark reaction.

text: All P-type ATPases use the energy derived from ATP to drive transport. They generally form a high-energy aspartyl-phosphoanhydride intermediate in the reaction cycle, and they interconvert between at least two different conformations, denoted by E and E. The E-E notation stems from the initial studies on this family of enzymes made on the Na/K-ATPase, where the sodium form and the potassium form are referred to as E and E, respectively, in the "Post-Albers scheme". The E-E schema has been proven to work, but there exist more than two major conformational states. The E-E notation highlights the selectivity of the enzyme. In E, the pump has high affinity for the exported substrate and low affinity for the imported substrate. In E, it has low affinity of the exported substrate and high affinity for the imported substrate. Four major enzyme states form the cornerstones in the reaction cycle. Several additional reaction intermediates occur interposed. These are termed E~P, EP, E-P*, and E/E.

text: All P-type ATPases use the energy derived from

text: ATP

text: to drive transport. They generally form a high-energy aspartyl-phosphoanhydride intermediate in the reaction cycle, and they interconvert between at least two different conformations, denoted by E and E. The E-E notation stems from the initial studies on this family of enzymes made on the Na/K-ATPase, where the sodium form and the potassium form are referred to as E and E, respectively, in the "Post-Albers scheme". The E-E schema has been proven to work, but there exist more than two major conformational states. The E-E notation highlights the selectivity of the

text: enzyme

text: . In E, the pump has high affinity for the exported substrate and low affinity for the imported substrate. In E, it has low affinity of the exported substrate and high affinity for the imported substrate. Four major enzyme states form the cornerstones in the reaction cycle. Several additional reaction intermediates occur interposed. These are termed E~P, EP, E-P*, and E/E.

text: Certain cells such as the human neutrophil may further metabolize 5-(S)-HETE. First, cells use a acyltransferase-dependent acylation reaction to esterify 5(S)-HETE into the phospholipids of cell membranes; this reaction could serve as means for storing 5(S)-HETE for release during subsequent cell stimulation or, alternatively, alter the properties of cell membranes in functionally important ways. Second, cells use a C-20 hydroxylase, cytochrome P450 (probably CYP4F3), to metabolize 5(S)-HETE to 5-(S),20-dihydroxy-eicosatetraenoate (5,20-diHETE); since 5,20-diHETE is ~50- to 100-fold weaker than 5(S)-HETE in stimulating cells, this metabolism is proposed to represent a pathway for 5(S)-HETE inactivation.  Third, cells, particularly human eosinophils, use ALOX15 to metabolize 5(S)-HETE to 5-(S),15-(S)-dihydroxy-eicosatetraenoate (5,15-diHETE); 5,15-diHETE is ~3- to 10-fold weaker than 5(S)-HETE in stimulating cells. And, forth, cells use 12-lipoxygenase (i.e. ALOX12 to metabolize 5(S)-HETE to 5(S),12(S)-diHETE, cyclooxygenase-2 to metabolize 5(S)-HETE to 5-(S),15(R)-diHETE and 5-(S),11(R)-diHETE, and aspirin-treated cyclooxygenase-2 to metabolize 5(S)-HETE to 5-(S),15(R)-diHETE; these metabolites have yet to be evaluated for activity.

text: Certain cells such as the human neutrophil may further metabolize 5-(S)-HETE. First, cells use a

text: acyltransferase

text: -dependent

text: acylation

text: reaction to

text: ester

text: ify 5(S)-HETE into the

text: phospholipids

text: of cell membranes; this reaction could serve as means for storing 5(S)-HETE for release during subsequent cell stimulation or, alternatively, alter the properties of cell membranes in functionally important ways. Second, cells use a C-20 hydroxylase,

text: cytochrome P450

text: (probably

text: ), to metabolize 5(S)-HETE to 5-(S),20-dihydroxy-eicosatetraenoate (5,20-diHETE); since 5,20-diHETE is ~50- to 100-fold weaker than 5(S)-HETE in stimulating cells, this metabolism is proposed to represent a pathway for 5(S)-HETE inactivation.  Third, cells, particularly human

text: eosinophil

text: s, use

text: to metabolize 5(S)-HETE to 5-(S),15-(S)-dihydroxy-eicosatetraenoate (5,15-diHETE); 5,15-diHETE is ~3- to 10-fold weaker than 5(S)-HETE in stimulating cells. And, forth, cells use 12-lipoxygenase (i.e.

text: to metabolize 5(S)-HETE to 5(S),12(S)-diHETE,

text: to metabolize 5(S)-HETE to 5-(S),15(R)-diHETE and 5-(S),11(R)-diHETE, and

text: aspirin

text: -treated

text: to metabolize 5(S)-HETE to 5-(S),15(R)-diHETE; these metabolites have yet to be evaluated for activity.

text: Fatty acids may act directly upon the pancreatic β-cell to regulate glucose-stimulated insulin secretion. This effect is biphasic. Initially fatty acids potentiate the effects of glucose.  After prolonged exposure to high fatty acid concentrations this changes to an inhibition. Randle suggested that the term fatty acid syndrome would be appropriate to apply to the biochemical syndrome resulting from the high concentration of fatty acids and the relationship to abnormalities of carbohydrate metabolism, including starvation, diabetes and Cushing’s syndrome.

text: Fatty acids may act directly upon the pancreatic β-cell to regulate glucose-stimulated insulin secretion. This effect is biphasic. Initially fatty acids potentiate the effects of glucose.  After prolonged exposure to high fatty acid concentrations this changes to an inhibition. Randle suggested that the term fatty acid syndrome would be appropriate to apply to the biochemical syndrome resulting from the high concentration of fatty acids and the relationship to abnormalities of carbohydrate metabolism, including starvation,

text: diabetes

text: and

text: Cushing’s syndrome

text: The metabolic rate can be affected by some drugs, such as antithyroid agents, drugs used to treat hyperthyroidism, such as propylthiouracil and methimazole, bring the metabolic rate down to normal and restore euthyroidism. Some research has focused on developing antiobesity drugs to raise the metabolic rate, such as drugs to stimulate thermogenesis in skeletal muscle.

text: The metabolic rate can be affected by some drugs, such as

text: antithyroid agent

text: s, drugs used to treat

text: hyperthyroidism

text: , such as

text: propylthiouracil

text: and

text: methimazole

text: , bring the metabolic rate down to normal and restore

text: euthyroid

text: ism. Some research has focused on developing antiobesity drugs to raise the metabolic rate, such as drugs to stimulate

text: thermogenesis

text: in

text: skeletal muscle

text: The best-known role of proteins in the cell is as enzymes, which catalyse chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism, as well as manipulating DNA in processes such as DNA replication, DNA repair, and transcription. Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes. The rate acceleration conferred by enzymatic catalysis is often enormous—as much as 10-fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme).

text: The best-known role of proteins in the cell is as

text: enzyme

text: s, which

text: catalyse

text: chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in

text: metabolism

text: , as well as manipulating DNA in processes such as

text: DNA replication

text: DNA repair

text: , and

text: transcription

text: . Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes. The rate acceleration conferred by enzymatic catalysis is often enormous—as much as 10-fold increase in rate over the uncatalysed reaction in the case of

text: orotate decarboxylase

text: (78 million years without the enzyme, 18 milliseconds with the enzyme).

text: Carbon fixation produces the intermediate three-carbon sugar product, which is then converted to the final carbohydrate products. The simple carbon sugars produced by photosynthesis are then used in the forming of other organic compounds, such as the building material cellulose, the precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in plants but also in animals when the energy from plants is passed through a food chain.

text: Carbon fixation produces the intermediate three-carbon sugar product, which is then converted to the final carbohydrate products. The simple carbon sugars produced by photosynthesis are then used in the forming of other organic compounds, such as the building material

text: cellulose

text: , the precursors for

text: lipid

text: and

text: amino acid

text: biosynthesis, or as a fuel in

text: cellular respiration

text: . The latter occurs not only in plants but also in

text: animal

text: s when the energy from plants is passed through a

text: food chain

text: Hydrostatic pressure increases by 1 atmosphere for every 10m in depth. Deep-sea organisms have the same pressure within their bodies as is exerted on them from the outside, so they are not crushed by the extreme pressure. Their high internal pressure, however, results in the reduced fluidity of their membranes because molecules are squeezed together. Fluidity in cell membranes increases efficiency of biological functions, most importantly the production of proteins, so organisms have adapted to this circumstance by increasing the proportion of unsaturated fatty acids in the lipids of the cell membranes. In addition to differences in internal pressure, these organisms have developed a different balance between their metabolic reactions from those organisms that live in the epipelagic zone. David Wharton, author of Life at the Limits: Organisms in Extreme Environments, notes "Biochemical reactions are accompanied by changes in volume. If a reaction results in an increase in volume, it will be inhibited by pressure, whereas, if it is associated with a decrease in volume, it will be enhanced". This means that their metabolic processes must ultimately decrease the volume of the organism to some degree.

text: Niacin cannot be directly converted to nicotinamide, but both compounds are precursors of the coenzymes nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) in vivo. NAD converts to NADP by phosphorylation in the presence of the enzyme NAD+ kinase. NADP and NAD are coenzymes for many dehydrogenases, participating in many hydrogen transfer processes. NAD is important in catabolism of fat, carbohydrate, protein, and alcohol, as well as cell signaling and DNA repair, and NADP mostly in anabolism reactions such as fatty acid and cholesterol synthesis. High energy requirements (brain) or high turnover rate (gut, skin) organs are usually the most susceptible to their deficiency. Although the two are identical in their vitamin activity, nicotinamide does not have the same pharmacological effects (lipid modifying effects) as niacin. Nicotinamide does not reduce cholesterol or cause flushing. As the precursor for NAD and NADP, niacin is also involved in DNA repair.

text: Niacin cannot be directly converted to nicotinamide, but both compounds are precursors of the

text: coenzyme

text: s

text: nicotinamide adenine dinucleotide

text: (NAD) and

text: (NADP)

text: in vivo

text: . NAD converts to NADP by phosphorylation in the presence of the enzyme

text: NAD+ kinase

text: . NADP and NAD are coenzymes for many

text: dehydrogenase

text: s, participating in many hydrogen transfer processes. NAD is important in catabolism of fat, carbohydrate, protein, and alcohol, as well as cell signaling and DNA repair, and NADP mostly in anabolism reactions such as fatty acid and cholesterol synthesis. High energy requirements (brain) or high turnover rate (gut, skin) organs are usually the most susceptible to their deficiency. Although the two are identical in their vitamin activity, nicotinamide does not have the same pharmacological effects (lipid modifying effects) as niacin. Nicotinamide does not reduce cholesterol or cause

text: flushing

text: . As the precursor for NAD and NADP, niacin is also involved in DNA repair.

text: Breathing is the process that moves air in and out of the lungs, to allow the diffusion of oxygen and carbon dioxide to and from the external environment into and out of the blood. "Breathing" sometimes also refers to the equivalent process using other respiratory organs such as gills in fish and spiracles in certain arthropods. For organisms with lungs, breathing is also called pulmonary ventilation, which consists of inhalation (breathing in) and exhalation (breathing out). Breathing is one part of physiological respiration required to sustain life. Aerobic organisms (all animals, most plants and many micro-organisms) require oxygen at cellular level to release energy by metabolizing energy-rich molecules such as fatty acids and glucose. This is often referred to as cellular respiration. Breathing is only one of the processes that delivers oxygen to where it is needed in the body and removes excess carbon dioxide. After breathing, the next process in this chain of events is the transport of these gases throughout the body by the circulatory system, and then their uptake or release from the respiring cells. Breathing fulfills another vital function: that of regulating the pH of the extracellular fluids of the body. It is, in fact, this homeostatic function which determines the rate and depth of breathing. The medical term for normal relaxed breathing is eupnea.

text: Breathing is the process that moves air in and out of the

text: lung

text: s, to allow the diffusion of

text: oxygen

text: and

text: carbon dioxide

text: to and from the external environment into and out of the blood. "Breathing" sometimes also refers to the equivalent process using other

text: respiratory organ

text: s such as

text: gill

text: s in fish and

text: spiracles

text: in certain

text: arthropods

text: . For organisms with lungs, breathing is also called

text: pulmonary ventilation

text: , which consists of

text: inhalation

text: (breathing in) and

text: exhalation

text: (breathing out). Breathing is one part of

text: physiological respiration

text: required to sustain

text: life

text: Aerobic

text: organism

text: s (all animals, most plants and many micro-organisms) require oxygen at cellular level to release energy by

text: metabolizing

text: energy-rich

text: molecule

text: s such as

text: fatty acids

text: and

text: glucose

text: . This is often referred to as

text: cellular respiration

text: . Breathing is only one of the processes that delivers

text: oxygen

text: to where it is needed in the body and removes excess

text: carbon dioxide

text: . After breathing, the next process in this chain of events is the transport of these gases throughout the body by the circulatory system, and then their uptake or release from the respiring cells. Breathing fulfills another vital function: that of

text: regulating the pH

text: of the

text: extracellular fluids

text: of the body. It is, in fact, this

text: homeostatic

text: function which determines the rate and depth of breathing. The medical term for normal relaxed breathing is

text: eupnea

text: The mechanism of enzymatic catalysis by the BCKDC draws largely upon the elaborate structure of this large enzyme complex. This enzyme complex is composed of three catalytic components: alpha-ketoacid dehydrogenase (also referred to as the E component), dihydrolipoyl transacylase (E component), and dihydrolipoamide dehydrogenase (E component). In humans, 24 copies of E arranged in octahedral symmetry form the core of the BCKDC. Non-covalently linked to this polymer of 24 E subunits are 12 E α2β2 tetramers and 6 E homodimers.  In addition to the E/E-binding domain, there are 2 other important structural domains in the E subunit: (i) a lipoyl-bearing domain in the amino-terminal portion of the protein and (ii) an inner-core domain in the carboxy-terminal portion. The inner-core domain is linked to the other two domains of the E subunit by two interdomain segments (linkers). The inner-core domain is necessary to form the oligomeric core of the enzyme complex and catalyzes the acyltransferase reaction (shown in the "Mechanism" section below). The lipoyl domain of E is free to swing between the active sites of the E, E, and E subunits on the assembled BCKDC by virtue of the conformational flexibility of the aforementioned linkers (see Figure 2). Thus, in terms of function as well as structure, the E component plays a central role in the overall reaction catalyzed by the BCKDC.

text: The mechanism of enzymatic catalysis by the BCKDC draws largely upon the elaborate structure of this large enzyme complex. This enzyme complex is composed of three catalytic components: alpha-ketoacid dehydrogenase (also referred to as the E component), dihydrolipoyl transacylase (E component), and

text: dihydrolipoamide dehydrogenase

text: (E component). In humans, 24 copies of E arranged in octahedral symmetry form the core of the BCKDC. Non-covalently linked to this

text: polymer

text: of 24 E subunits are 12 E α2β2

text: tetramers

text: and 6 E

text: homodimers

text: .  In addition to the E/E-binding domain, there are 2 other important structural domains in the E subunit: (i) a lipoyl-bearing domain in the

text: amino-terminal

text: portion of the protein and (ii) an inner-core domain in the

text: carboxy-terminal

text: portion. The inner-core domain is linked to the other two domains of the E subunit by two interdomain segments (linkers). The inner-core domain is necessary to form the oligomeric core of the enzyme complex and catalyzes the

text: acyltransferase

text: reaction (shown in the "Mechanism" section below). The lipoyl domain of E is free to swing between the

text: active site

text: s of the E, E, and E subunits on the assembled BCKDC by virtue of the conformational flexibility of the aforementioned linkers (see Figure 2). Thus, in terms of function as well as structure, the E component plays a central role in the overall reaction catalyzed by the BCKDC.

text: One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between catabolism and anabolism. Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylation reactions.

text: One central coenzyme is

text: adenosine triphosphate

text: (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between

text: catabolism

text: and

text: anabolism

text: . Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in

text: phosphorylation

text: reactions.

text: CYP2D6, a member of the cytochrome P450 mixed-function oxidase system, is one of the most important enzymes involved in the metabolism of xenobiotics in the body. In particular, CYP2D6 is responsible for the metabolism and elimination of approximately 25% of clinically used drugs, via the addition or removal of certain functional groups – specifically, hydroxylation, demethylation, and dealkylation – at various points along a substrate's core structure.  This enzyme also metabolizes several endogenous substances, such as hydroxytryptamines, neurosteroids, and both m-tyramine and p-tyramine which CYP2D6 metabolizes into dopamine in the brain and liver.

text: CYP2D6, a member of the

text: cytochrome P450

text: mixed-function oxidase system, is one of the most important enzymes involved in the

text: metabolism

text: of

text: xenobiotic

text: s in the body. In particular, CYP2D6 is responsible for the metabolism and

text: elimination

text: of approximately 25% of clinically used drugs, via the addition or removal of certain

text: functional group

text: s – specifically,

text: hydroxylation

text: demethylation

text: , and

text: dealkylation

text: – at various points along a substrate's core structure.  This enzyme also metabolizes several endogenous substances, such as

text: hydroxytryptamines

text: neurosteroid

text: s, and both

text: m-tyramine

text: and

text: p-tyramine

text: which CYP2D6 metabolizes into dopamine in the brain and liver.

text: Later, Green’s research extended to the RNA tumor viruses (tumor inducing viruses with an RNA genome). Before reverse transcriptase  was discovered by David Baltimore and Howard Temin in 1970 (work that earned them a Nobel Prize), Green wrote a review predicting that the enzyme must exist in the virion of retroviruses. In the early 1970s, he and his co-workers conducted important studies on the biochemical features of reverse transcriptases of avian and murine RNA tumor viruses. These studies revealed the subunit structure of the enzyme and helped define the polymerase and Ribonuclease H activities inherent with that enzyme. He coupled this basic research to the effort to detect RNA tumor viruses in human cancer. Tremendous effort was directed to the ‘simultaneous detection’ assay in which proteins are extracted from tumor samples, separated by size, and then examined for reverse transcriptase activity. There was angst associated with those studies because of the importance of the research and because the workers could occasionally detect weak activity. As was later shown, this activity was not due to infection by RNA tumor viruses, but rather to endogenous reverse transcriptase activity. These studies were negative, again arguing against a viral etiology of cancer.

text: Later, Green’s research extended to the RNA tumor viruses (tumor inducing viruses with an RNA genome). Before

text: reverse transcriptase

text: was discovered by David Baltimore and Howard Temin in 1970 (work that earned them a Nobel Prize), Green wrote a review predicting that the enzyme must exist in the virion of retroviruses. In the early 1970s, he and his co-workers conducted important studies on the biochemical features of reverse transcriptases of

text: avian

text: and

text: murine

text: RNA tumor viruses. These studies revealed the subunit structure of the enzyme and helped define the polymerase and

text: Ribonuclease H

text: activities inherent with that enzyme. He coupled this basic research to the effort to detect RNA tumor viruses in human cancer. Tremendous effort was directed to the ‘simultaneous detection’ assay in which proteins are extracted from tumor samples, separated by size, and then examined for reverse transcriptase activity. There was angst associated with those studies because of the importance of the research and because the workers could occasionally detect weak activity. As was later shown, this activity was not due to infection by RNA tumor viruses, but rather to endogenous reverse transcriptase activity. These studies were negative, again arguing against a viral etiology of cancer.

text: In line with LS9's main initiatives of using synthetic microorganisms for the production of biofuel components, LS9 has been, for a period of years (2008–2013) been pushing patents for specific enzymes involved in fatty acid synthesis and metabolism. This is of particular importance since enzymes are key regulators in metabolic pathways and the opportunity to successfully patent such an enzyme may prove of extreme value to a company vested in economic interests being generated in that area of research.

text: Ste24 endopeptidase () is an enzyme. This enzyme catalyses the following chemical reaction

text: Ste24 endopeptidase () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites.

text: An idea of the complexity of the

text: metabolic network

text: s in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more

text: holistic

text: mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on

text: gene expression

text: from

text: proteomic

text: and

text: DNA microarray

text: studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in

text: network analysis

text: , to classify human diseases into groups that share common proteins or metabolites.

text: The Yeast Metabolome Database is a freely accessible, online database of >2000 small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB contains two kinds of information: 1) chemical information and 2) biochemical information. The chemical information in YMDB includes 2027 metabolite structures with detailed metabolite descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties. It also contains nearly 4000 NMR, GC-MS and LC/MS spectra obtained from more than 500 different metabolites. The biochemical information in YMDB includes >1100 protein (and DNA) sequences and >900 biochemical reactions. The YMDB supports a wide variety of queries including text searches, chemical structure searches, sequence similarity searches and spectral similarity searches.  This makes it particularly useful for metabolomic researchers who are studying yeast as a model organism or who are looking into optimizing the production of fermented beverages (wine, beer).

text: The

text: Yeast Metabolome Database

text: is a freely accessible, online database of >2000 small molecule metabolites found in or produced by

text: Saccharomyces cerevisiae

text: Baker’s yeast

text: ). The

text: YMDB

text: contains two kinds of information: 1) chemical information and 2) biochemical information. The chemical information in YMDB includes 2027 metabolite structures with detailed metabolite descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties. It also contains nearly 4000

text: NMR

text: GC-MS

text: and

text: LC/MS

text: spectra obtained from more than 500 different metabolites. The biochemical information in

text: YMDB

text: includes >1100 protein (and DNA) sequences and >900 biochemical reactions. The

text: YMDB

text: supports a wide variety of queries including text searches, chemical structure searches, sequence similarity searches and spectral similarity searches.  This makes it particularly useful for metabolomic researchers who are studying yeast as a model organism or who are looking into optimizing the production of fermented beverages (wine, beer).

text: Glycosylation of calicheamicinone requires 4 glycosyltransferases (CalG1-4) and one acyltransferase (CalO4), each recognizing a specific sugar nucleotide or orsellinic acid substrate. Ground-breaking biochemical studies of CalG1-G4 by Thorson and coworkers revealed the reactions catalyzed by these glycosyltransferases to be highly reversible. This was a paradigm shift in the context of glycosyltransferase catalysis and Thorson and coworkers went on to demonstrate this to be a general phenomenon that could be exploited for sugar nucleotide synthesis and 'glycorandomization'. The structures of all four glycosyltransferases were also reported by the same group, revealing a conserved calicheamicin binding motif that coordinates the enediyne backbone thorough interactions with aromatic residues. The catalytic site of CalG1, CalG3, and CalG4 was shown to possess a highly conserved catalytic dyad of histidine and aspartate which promotes nucleophilic attack on the acceptor hydroxyl group of calicheamicin intermediates. Notably, this motif is absent from CalG2, suggesting a different catalytic mechanism in this enzyme.

text: Glycosylation

text: of calicheamicinone requires 4

text: glycosyltransferases

text: (CalG1-4) and one acyltransferase (CalO4), each recognizing a specific sugar nucleotide or

text: orsellinic acid

text: substrate. Ground-breaking biochemical studies of CalG1-G4 by Thorson and coworkers revealed the reactions catalyzed by these glycosyltransferases to be highly reversible. This was a paradigm shift in the context of glycosyltransferase catalysis and Thorson and coworkers went on to demonstrate this to be a general phenomenon that could be exploited for sugar nucleotide synthesis and '

text: glycorandomization

text: '. The structures of all four glycosyltransferases were also reported by the same group, revealing a conserved calicheamicin binding motif that coordinates the enediyne backbone thorough interactions with aromatic residues. The catalytic site of CalG1, CalG3, and CalG4 was shown to possess a highly conserved catalytic dyad of

text: histidine

text: and

text: aspartate

text: which promotes nucleophilic attack on the acceptor hydroxyl group of calicheamicin intermediates. Notably, this motif is absent from CalG2, suggesting a different catalytic mechanism in this enzyme.

text: In 1939, experiments using minced muscle cells demonstrated that cellular respiration using one oxygen atom can form two adenosine triphosphate (ATP) molecules, and, in 1941, the concept of the phosphate bonds of ATP being a form of energy in cellular metabolism was developed by Fritz Albert Lipmann. In the following years, the mechanism behind cellular respiration was further elaborated, although its link to the mitochondria was not known. The introduction of tissue fractionation by Albert Claude allowed mitochondria to be isolated from other cell fractions and biochemical analysis to be conducted on them alone. In 1946, he concluded that cytochrome oxidase and other enzymes responsible for the respiratory chain were isolated to the mitchondria. Eugene Kennedy and Albert Lehninger discovered in 1948 that mitochondria are the site of oxidative phosphorylation in eukaryotes. Over time, the fractionation method was further developed, improving the quality of the mitochondria isolated, and other elements of cell respiration were determined to occur in the mitochondria.

text: In 1939, experiments using minced muscle cells demonstrated that cellular respiration using one oxygen atom can form two

text: adenosine triphosphate

text: (ATP) molecules, and, in 1941, the concept of the phosphate bonds of ATP being a form of energy in cellular metabolism was developed by

text: Fritz Albert Lipmann

text: . In the following years, the mechanism behind cellular respiration was further elaborated, although its link to the mitochondria was not known. The introduction of

text: tissue fractionation

text: by

text: Albert Claude

text: allowed mitochondria to be isolated from other cell fractions and biochemical analysis to be conducted on them alone. In 1946, he concluded that

text: cytochrome oxidase

text: and other enzymes responsible for the respiratory chain were isolated to the mitchondria.

text: Eugene Kennedy

text: and

text: Albert Lehninger

text: discovered in 1948 that mitochondria are the site of

text: oxidative phosphorylation

text: in eukaryotes. Over time, the fractionation method was further developed, improving the quality of the mitochondria isolated, and other elements of cell respiration were determined to occur in the mitochondria.

text: Physical biochemistry is a branch of biochemistry that deals with the theory, techniques and methodology used to study the physical chemistry of biomolecules. It also deals with the mathematical approaches for the analysis of biochemical reaction and the modelling of biological systems. It provides insight to the structure of macromolecules, and how chemical structure influences physical properties of a biological substance.

text: Physical biochemistry is a branch of

text: biochemistry

text: that deals with the theory, techniques and methodology used to study the

text: physical chemistry

text: of

text: biomolecule

text: s. It also deals with the mathematical approaches for the analysis of

text: biochemical reaction

text: and the

text: modelling of biological systems

text: . It provides insight to the structure of macromolecules, and how chemical structure influences physical properties of a biological substance.

text: Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems.  The most common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation of RNA and DNA and peptide bond formation. Within the ribosome, ribozymes function as part of the large subunit ribosomal RNA to link amino acids during protein synthesis.  They also participate in a variety of RNA processing reactions, including RNA splicing, viral replication, and transfer RNA biosynthesis. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme, Leadzyme and the hairpin ribozyme.

text: Ribozymes (ribonucleic acid enzymes) are

text: RNA

text: molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein

text: enzymes

text: . The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like

text: DNA

text: ) and a biological

text: catalyst

text: (like protein enzymes), and contributed to the

text: RNA world hypothesis

text: , which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems.  The most common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation of RNA and DNA and peptide bond formation. Within the

text: ribosome

text: , ribozymes function as part of the large subunit ribosomal RNA to link amino acids during

text: protein synthesis

text: .  They also participate in a variety of

text: RNA processing

text: reactions, including

text: RNA splicing

text: viral replication

text: , and

text: transfer RNA

text: biosynthesis. Examples of ribozymes include the

text: hammerhead ribozyme

text: , the

text: VS ribozyme

text: Leadzyme

text: and the

text: hairpin ribozyme

text: In chemistry, initiation is a chemical reaction that triggers one or more secondary reactions. Often the initiation reaction generates a reactive intermediate from a stable molecule which is then involved in secondary reactions. In polymerisation, initiation is followed by a chain reaction and termination.

text: In

text: chemistry

text: , initiation is a

text: chemical reaction

text: that triggers one or more secondary reactions. Often the initiation reaction generates a

text: reactive intermediate

text: from a stable molecule which is then involved in secondary reactions. In

text: polymerisation

text: , initiation is followed by a

text: chain reaction

text: and

text: termination

text: Biochemically, anoxygenic photosynthesis is very different from oxygenic photosynthesis.  Cyanobacteria (and by extension, chloroplasts) use the Z scheme of electron flow in which electrons eventually are used to form NADH.  Two different reaction centers (photosystems) are used and proton motive force is generated both by using cyclic electron flow and the quinone pool.  In anoxygenic photosynthetic bacteria, electron flow is cyclic, with all electrons used in photosynthesis eventually being transferred back to the single reaction center.  A proton motive force is generated using only the quinone pool.  In heliobacteria, Green sulfur, and Green non-sulfur bacteria, NADH is formed using the protein ferredoxin, an energetically favorable reaction.  In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center.  In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase.

text: Biochemically, anoxygenic photosynthesis is very different from oxygenic photosynthesis.  Cyanobacteria (and by extension, chloroplasts) use the

text: Z scheme

text: of electron flow in which electrons eventually are used to form NADH.  Two different reaction centers (photosystems) are used and proton motive force is generated both by using cyclic electron flow and the quinone pool.  In anoxygenic photosynthetic bacteria, electron flow is cyclic, with all electrons used in photosynthesis eventually being transferred back to the single reaction center.  A proton motive force is generated using only the quinone pool.  In heliobacteria, Green sulfur, and Green non-sulfur bacteria, NADH is formed using the protein

text: ferredoxin

text: , an energetically favorable reaction.  In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center.  In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase.

text: In 2004 Syrris developed the AFRICA (Automated Flow Reaction Incubation and Control Apparatus) flow chemistry system in partnership with GlaxoSmithKline to accelerate the medicinal chemistry element of drug discovery. In 2006 Syrris launched FRX, a low-cost alternative to AFRICA, and Atlas, an automated laboratory scale batch reactor. In 2011, Syrris added 2 new products to its portfolio, the Globe chemical reactor platform and the Asia flow chemistry system, which was a recipient of an R&D100 Award in June 2012.

text: In 2004 Syrris developed the AFRICA (Automated Flow Reaction Incubation and Control Apparatus)

text: flow chemistry

text: system in partnership with

text: GlaxoSmithKline

text: to accelerate the

text: medicinal chemistry

text: element of

text: drug discovery

text: . In 2006 Syrris launched FRX, a low-cost alternative to AFRICA, and Atlas, an automated laboratory scale

text: batch reactor

text: . In 2011, Syrris added 2 new products to its portfolio, the Globe chemical reactor platform and the Asia flow chemistry system, which was a recipient of an R&D100 Award in June 2012.

text: Protein-protein interactions have been mapped, using proteins as nodes and their interactions between each other as links. These maps utilize databases such as BioGRID and the Human Protein Reference Database. The metabolic network encompasses the biochemical reactions in metabolic pathways, connecting two metabolites if they are in the same pathway. Researchers have used databases such as KEGG to map these networks. Others networks include cell signaling networks, gene regulatory networks, and RNA networks.

text: Protein-protein interaction

text: s have been mapped, using proteins as

text: node

text: s and their interactions between each other as links. These maps utilize databases such as

text: BioGRID

text: and the

text: Human Protein Reference Database

text: . The

text: metabolic network

text: encompasses the biochemical reactions in

text: metabolic pathway

text: s, connecting two

text: metabolite

text: s if they are in the same pathway. Researchers have used databases such as

text: KEGG

text: to map these networks. Others networks include

text: cell signaling

text: networks,

text: gene regulatory network

text: s, and

text: RNA

text: networks.

text: A vitamin is an organic compound needed in small quantities that cannot be made in  cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells. Nicotinamide adenine dinucleotide (NAD), a derivative of vitamin B (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD/NADH form is more important in catabolic reactions, while NADP/NADPH is used in anabolic reactions.

text: A

text: vitamin

text: is an organic compound needed in small quantities that cannot be made in  cells. In human

text: nutrition

text: , most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.

text: Nicotinamide adenine dinucleotide

text: (NAD), a derivative of vitamin B (

text: niacin

text: ), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of

text: dehydrogenase

text: s remove electrons from their substrates and

text: reduce

text: NAD into NADH. This reduced form of the coenzyme is then a substrate for any of the

text: reductase

text: s in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD/NADH form is more important in catabolic reactions, while NADP/NADPH is used in anabolic reactions.

text: At least twenty chemical elements are known to be required to support human biochemical processes by serving structural and functional roles as well as electrolytes. However, as many as twenty-nine elements in total (including the common hydrogen, carbon, nitrogen and oxygen) are suggested to be used by mammals, as a result of studies of biochemical, special uptake, and metabolic handling studies. Many of these additional elements have no well-defined biochemical function known at present. Most of the known and suggested mineral nutrients are of relatively low atomic weight, and are reasonably common on land, or, at least, common in the ocean (iodine, sodium):

text: At least twenty chemical elements are known to be required to support human biochemical processes by serving structural and functional roles as well as

text: electrolyte

text: s. However, as many as twenty-nine elements in total (including the common hydrogen, carbon, nitrogen and oxygen) are suggested to be used by mammals, as a result of studies of biochemical, special uptake, and metabolic handling studies. Many of these additional elements have no well-defined biochemical function known at present. Most of the known and suggested mineral nutrients are of relatively low atomic weight, and are reasonably common on land, or, at least, common in the ocean (iodine, sodium):

text: In metabolism, an endergonic process is anabolic, meaning that energy is stored; in many such anabolic processes energy is supplied by coupling the reaction to adenosine triphosphate (ATP) and consequently resulting in a high energy, negatively charged organic phosphate and positive adenosine diphosphate.

text: In

text: metabolism

text: , an endergonic process is

text: anabolic

text: , meaning that energy is stored; in many such anabolic processes energy is supplied by coupling the reaction to

text: adenosine triphosphate

text: (ATP) and consequently resulting in a high energy, negatively charged organic phosphate and positive

text: adenosine diphosphate

text: The protein catalyst (enzyme) may be part of a multi-subunit complex, and/or may transiently or permanently associate with a Cofactor (e.g. adenosine triphosphate). Catalysis of biochemical reactions is vital due to the very low reaction rates of the uncatalysed reactions. A key driver of protein evolution is the optimization of such catalytic activities via protein dynamics.

text: The protein

text: catalyst

text: enzyme

text: ) may be part of a

text: multi-subunit complex

text: , and/or may transiently or permanently associate with a

text: Cofactor

text: (e.g.

text: adenosine triphosphate

text: ). Catalysis of

text: biochemical

text: reactions is vital due to the very low reaction rates of the uncatalysed reactions. A key driver of protein evolution is the optimization of such catalytic activities via

text: protein dynamics

text: Although the functions of photorespiration remain controversial, it is widely accepted that this pathway influences a wide range of processes from bioenergetics, photosystem II function, and carbon metabolism to nitrogen assimilation and respiration. The photorespiratory pathway is a major source of hydrogen peroxide () in photosynthetic cells. Through  production and pyridine nucleotide interactions, photorespiration makes a key contribution to cellular redox homeostasis. In so doing, it influences multiple signalling pathways, in particular, those that govern plant hormonal responses controlling growth, environmental and defense responses, and programmed cell death.

text: Although the functions of photorespiration remain controversial, it is widely accepted that this pathway influences a wide range of processes from bioenergetics, photosystem II function, and carbon metabolism to nitrogen assimilation and respiration. The photorespiratory pathway is a major source of

text: hydrogen peroxide

text: () in photosynthetic cells. Through  production and pyridine nucleotide interactions, photorespiration makes a key contribution to cellular redox homeostasis. In so doing, it influences multiple signalling pathways, in particular, those that govern plant hormonal responses controlling growth, environmental and defense responses, and programmed cell death.

text: Metabolic pathways are defined to mean the chemical process that occurs within an organism. L. brevis uses the glycolysis process to metabolize carbon sources by active transport, which moves material against the concentration gradient, normally this occurs is a movement from a high to low concentration. This pathway is used in probiotics and food preservation.

text: Metabolic pathways are defined to mean the chemical process that occurs within an organism. L. brevis uses the

text: glycolysis

text: process to

text: metabolize

text: carbon sources by

text: active transport

text: , which moves material against the concentration gradient, normally this occurs is a movement from a high to low concentration. This pathway is used in

text: probiotics

text: and food preservation.

text: In his profession Borodin gained great respect, being particularly noted for his work on aldehydes. Between 1859 and 1862 Borodin held a postdoctorate in Heidelberg. He worked in the laboratory of Emil Erlenmeyer working on benzene derivatives. He also spent time in Pisa, working on halocarbons. One experiment published in 1862 described the first nucleophilic displacement of chlorine by fluorine in benzoyl chloride. A related reaction known to the West as the Hunsdiecker reaction published in 1939 by the Hunsdieckers was promoted by the Soviet Union as the Borodin reaction. In 1862 he returned to the Medical–Surgical Academy, taking up a chair in chemistry, where he worked on self-condensation of small aldehydes. He published papers in 1864 and 1869, and in this field he found himself competing with August Kekulé.

text: In his profession Borodin gained great respect, being particularly noted for his work on

text: aldehyde

text: s. Between 1859 and 1862 Borodin held a postdoctorate in

text: Heidelberg

text: . He worked in the laboratory of

text: Emil Erlenmeyer

text: working on benzene derivatives. He also spent time in

text: Pisa

text: , working on

text: halocarbon

text: s. One experiment published in 1862 described the first

text: nucleophilic displacement

text: of chlorine by fluorine in

text: benzoyl chloride

text: . A related reaction known to the West as the

text: Hunsdiecker reaction

text: published in 1939 by the Hunsdieckers was promoted by the

text: Soviet Union

text: as the Borodin reaction. In 1862 he returned to the Medical–Surgical Academy, taking up a chair in chemistry, where he worked on self-condensation of small aldehydes. He published papers in 1864 and 1869, and in this field he found himself competing with

text: August Kekulé

text: For example, consider the overall reaction for aerobic cellular respiration:

text: For example, consider the overall reaction for aerobic

text: cellular respiration

text: Transphosphorylation is a chemical reaction in which a phosphate group or a phosphono group is transferred between a substrate and a receptor. There are various phosphate esters in living body including nucleic acid, and phosphorylation reaction related to their synthesis and interconversion is the basis of biochemical reaction. In most cases, ATP is the substrate of the phosphate group as a substrate and the enzyme that catalyzes these reactions is referred to as kinase.

text: Transphosphorylation is a

text: chemical reaction

text: in which a

text: phosphate

text: group or a

text: phosphono group

text: is transferred between a

text: substrate

text: and a

text: receptor

text: . There are various phosphate

text: ester

text: s in living body including

text: nucleic acid

text: , and phosphorylation reaction related to their synthesis and interconversion is the basis of biochemical reaction. In most cases,

text: ATP

text: is the substrate of the phosphate group as a substrate and the

text: enzyme

text: that catalyzes these reactions is referred to as

text: kinase

text: Vitamin B is a co-substrate of various cell reactions involved in methylation synthesis of nucleic acid and neurotransmitters. Synthesis of the trimonoamine neurotransmitters can enhance the effects of a traditional antidepressant. The intracellular concentrations of vitamin B can be inferred through the total plasma concentration of homocysteine, which can be converted to methionine through an enzymatic reaction that uses 5-methyltetrahydrofolate as the methyl donor group. Consequently, the plasma concentration of homocysteine falls as the intracellular concentration of vitamin B rises. The active metabolite of vitamin B is required for the methylation of homocysteine in the production of methionine, which is involved in a number of biochemical processes including the monoamine neurotransmitters metabolism. Thus, a deficiency in vitamin B may impact the production and function of those neurotransmitters.

text: German agricultural chemist Justus von Liebig, in his ''Organic Chemistry in Its Applications to Agriculture and Physiology'' (1840), presented the first convincing explanation of the role of soil nutrients in the growth of plants. In 1842, Liebig expanded the use of the term metabolism (Stoffwechsel), from referring to material exchanges in the body, up to the biochemical processes of natural systems.

text: German agricultural chemist

text: Justus von Liebig

text: , in his ''Organic Chemistry in Its Applications to Agriculture and Physiology'' (1840), presented the first convincing explanation of the role of soil nutrients in the growth of plants. In 1842, Liebig expanded the use of the term

text: metabolism

text: (Stoffwechsel), from referring to material exchanges in the body, up to the biochemical processes of natural systems.

text: The production of most industrially important chemicals involves catalysis. Similarly, most biochemically significant processes are catalysed.  Research into catalysis is a major field in applied science and involves many areas of chemistry, notably organometallic chemistry and materials science.  Catalysis is relevant to many aspects of environmental science, e.g. the catalytic converter in automobiles and the dynamics of the ozone hole. Catalytic reactions are preferred in environmentally friendly green chemistry due to the reduced amount of waste generated, as opposed to stoichiometric reactions in which all reactants are consumed and more side products are formed. Many transition metals and transition metal complexes are used in catalysis as well. Catalysts called enzymes are important in biology.

text: The production of most industrially important chemicals involves catalysis. Similarly, most biochemically significant processes are catalysed.  Research into catalysis is a major field in

text: applied science

text: and involves many areas of chemistry, notably

text: organometallic chemistry

text: and

text: materials science

text: .  Catalysis is relevant to many aspects of

text: environmental science

text: , e.g. the

text: catalytic converter

text: in automobiles and the dynamics of the

text: ozone hole

text: . Catalytic reactions are preferred in environmentally friendly

text: green chemistry

text: due to the reduced amount of waste generated, as opposed to

text: stoichiometric

text: reactions in which all reactants are consumed and more side products are formed. Many

text: transition metal

text: s and transition metal

text: complexes

text: are used in catalysis as well. Catalysts called

text: enzyme

text: s are important in

text: biology

text: The pyridoxal-5′-phosphate-dependent enzymes (PLP enzymes) catalyze myriad biochemical reactions. Although the scope of PLP-catalyzed reactions appears to be immensely diverse, there is a simple unifying principle: in the resting state, the co-factor (PLP) is covalently bonded to the amino group of an active site lysine, forming an internal aldimine. Once the amino substrate interacts with the active site, a new Schiff base is generated, commonly referred to as the external aldimine. After this step, the mechanistic pathway for each PLP-catalyzed reaction diverges. Density functional methods have been applied to investigate the transimination reaction, and the results have shown that the reaction involves three sequential steps: (i) formation of a tetrahedral intermediate with the active site lysine and the amino substrate bonded to the PLP co-factor; (ii) non-direct proton transfer between the amino substrate and the lysine residue; and (iii) formation of the external aldimine after the dissociation of the lysine residue. The overall reaction is exothermic (−12.0 kcal/mol), the second step being rate-limiting, with 12.6 kcal/mol for the activation energy

text: In contrast to catabolic pathways, are the anabolic pathways that require an input of energy in order to conduct the construction of macromolecules such as polypeptides, nucleic acids, proteins, polysaccharides, and lipids. The isolated reaction of anabolism is unfavorable in a cell due to a positive Gibbs Free Energy (+ΔG); thus, an input of chemical energy through a coupling with an exergonic reaction is necessary. The coupled reaction of the catabolic pathway affects the thermodynamics of the reaction by lowering the overall activation energy of an anabolic pathway and allowing the reaction to take place. Otherwise, an endergonic reaction is non-spontaneous.

text: In contrast to catabolic pathways, are the

text: anabolic pathways

text: that require an input of energy in order to conduct the construction of macromolecules such as polypeptides, nucleic acids, proteins, polysaccharides, and lipids. The isolated reaction of anabolism is unfavorable in a cell due to a positive

text: Gibbs Free Energy

text: (+ΔG); thus, an input of chemical energy through a coupling with an

text: exergonic reaction

text: is necessary. The coupled reaction of the catabolic pathway affects the thermodynamics of the reaction by lowering the overall activation energy of an anabolic pathway and allowing the reaction to take place. Otherwise, an

text: endergonic reaction

text: is non-spontaneous.

text: Some of these reactions generate a cellular energy source, ATP, in a manner similar to eukaryotic cell aerobic respiration, except the final electron acceptor is not molecular oxygen, but fumarate or nitrate. In aerobic respiration, the final oxidant is molecular oxygen (O), which accepts four electrons from an electron donor such as NADH to be converted to water. E. coli, as facultative anaerobes, can carry out both aerobic respiration and menaquinone-mediated anaerobic respiration.

text: Some of these reactions generate a cellular energy source,

text: ATP

text: , in a manner similar to

text: eukaryotic

text: cell

text: aerobic respiration

text: , except the final electron acceptor is not

text: molecular oxygen

text: , but

text: fumarate

text: or

text: nitrate

text: . In

text: aerobic respiration

text: , the final oxidant is

text: molecular oxygen

text: (O), which accepts four electrons from an electron donor such as

text: NADH

text: to be converted to

text: water

text: . E. coli, as

text: facultative anaerobe

text: s, can carry out both

text: aerobic respiration

text: and menaquinone-mediated anaerobic respiration.

text: In the 1990s, the development of effective polymerase chain reaction techniques allowed the application of cladistic methods to biochemical and molecular genetic traits of organisms, as well as to anatomical ones, vastly expanding the amount of data available for phylogenetics. At the same time, cladistics rapidly became the dominant set of methods of phylogenetics in evolutionary biology, because computers made it possible to process large quantities of data about organisms and their characteristics.

text: In the 1990s, the development of effective

text: polymerase chain reaction

text: techniques allowed the application of cladistic methods to

text: biochemical

text: and

text: molecular genetic

text: traits of organisms, as well as to anatomical ones, vastly expanding the amount of data available for phylogenetics. At the same time, cladistics rapidly became the dominant set of methods of phylogenetics in evolutionary biology, because

text: computer

text: s made it possible to process large quantities of data about organisms and their characteristics.

text: Gross primary production (GPP) is the amount of chemical energy as biomass that primary producers create in a given length of time. (GPP is sometimes confused with Gross Primary productivity, which is the rate at which photosynthesis or chemosynthesis occurs.) Some fraction of this fixed energy is used by primary producers for cellular respiration and maintenance of existing tissues (i.e., "growth respiration" and "maintenance respiration"). The remaining fixed energy (i.e., mass of photosynthate) is referred to as net primary production (NPP).

text: Gross primary production (GPP) is the amount of chemical energy as

text: biomass

text: that primary producers create in a given length of time. (GPP is sometimes confused with Gross Primary productivity, which is the rate at which photosynthesis or chemosynthesis occurs.) Some fraction of this fixed energy is used by primary producers for

text: cellular respiration

text: and maintenance of existing tissues (i.e., "growth respiration" and "

text: maintenance respiration

text: "). The remaining fixed energy (i.e., mass of photosynthate) is referred to as net primary production (NPP).

text: The term amphibolic is used to describe a biochemical pathway that involves both catabolism and anabolism.

text: The term amphibolic is used to describe a

text: biochemical

text: pathway that involves both

text: catabolism

text: and

text: anabolism

text: The compensation point is reached during early mornings and late evenings. Respiration is relatively constant, whereas photosynthesis depends on the amount of sunlight.When the rate of photosynthesis equals the rate of respiration, the compensation point occurs.

text: The compensation point is reached during early mornings and late evenings. Respiration is relatively constant, whereas photosynthesis depends on the amount of

text: sunlight

text: .When the rate of photosynthesis equals the rate of respiration, the compensation point occurs.

text: Oxygen is used in mitochondria to generate ATP during oxidative phosphorylation. The reaction for aerobic respiration is essentially the reverse of photosynthesis and is simplified as:

text: Oxygen is used in

text: mitochondria

text: to generate ATP during

text: oxidative phosphorylation

text: . The reaction for aerobic respiration is essentially the reverse of photosynthesis and is simplified as:

text: Enzyme catalysis is the increase in the rate of a chemical reaction by the active site of a protein. The protein catalyst (enzyme) may be part of a multi-subunit complex, and/or may transiently or permanently associate with a Cofactor (e.g. adenosine triphosphate). Catalysis of biochemical reactions in the cell is vital due to the very low reaction rates of the uncatalysed reactions at room temperature and pressure. A key driver of protein evolution is the optimization of such catalytic activities via protein dynamics.

text: Enzyme catalysis is the increase in the

text: rate

text: of a

text: chemical reaction

text: by the

text: active site

text: of a

text: protein

text: . The protein

text: catalyst

text: enzyme

text: ) may be part of a

text: multi-subunit complex

text: Cofactor

text: (e.g.

text: adenosine triphosphate

text: Catalysis

text: of

text: biochemical

text: reactions in the

text: cell

text: is vital due to the very low reaction rates of the uncatalysed reactions at room temperature and pressure. A key driver of protein evolution is the optimization of such catalytic activities via

text: protein dynamics

text: Chymotrypsin C () is an enzyme. This enzyme catalyses the following chemical reaction

text: Chymotrypsin C () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: A septic tank, the septic drain field, and the associated piping compose a septic system.  The septic drain field is effective for disposal of organic materials readily catabolized by a microbial ecosystem. The drain field typically consists of an arrangement of trenches containing perforated pipes and porous material (often gravel) covered by a layer of soil to prevent animals (and surface runoff) from reaching the wastewater distributed within those trenches.  Primary design considerations are hydraulic for the volume of wastewater requiring disposal and catabolic for the long-term biochemical oxygen demand of that wastewater.

text: A

text: septic tank

text: , the septic drain field, and the associated piping compose a

text: septic system

text: .  The septic drain field is effective for disposal of organic materials readily

text: catabolized

text: by a microbial

text: ecosystem

text: . The drain field typically consists of an arrangement of trenches containing perforated pipes and porous material (often

text: gravel

text: ) covered by a layer of

text: soil

text: to prevent

text: animal

text: s (and

text: surface runoff

text: ) from reaching the

text: wastewater

text: distributed within those trenches.  Primary design considerations are hydraulic for the volume of wastewater requiring disposal and catabolic for the long-term

text: biochemical oxygen demand

text: of that wastewater.

text: Gaden spent a year as a researcher at Pfizer, Inc. before he was invited to return to Columbia University to establish its first biochemical engineering program. He twice chaired the school's Department of Chemical Engineering and Applied Chemistry. Gaden was known as a demanding teacher who expected much from the thousands of students whom he taught.

text: Gaden spent a year as a researcher at

text: Pfizer, Inc

text: . before he was invited to return to

text: Columbia University

text: to establish its first

text: biochemical

text: engineering program. He twice chaired the school's Department of Chemical Engineering and Applied Chemistry. Gaden was known as a demanding teacher who expected much from the thousands of students whom he taught.

text: The biochemical data includes 1104 protein (and DNA) sequences and more than 900 biochemical reactions (Fig. 1) that are linked to these metabolite entries. Each metabolite entry in the YMDB contains more than 80 data fields with 2/3 of the information being devoted to chemical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, Protein Data Bank, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The YMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches.

text: The biochemical data includes 1104

text: protein

text: (and

text: DNA

text: ) sequences and more than 900

text: biochemical reaction

text: s (Fig. 1) that are linked to these metabolite entries. Each metabolite entry in the YMDB contains more than 80 data fields with 2/3 of the information being devoted to chemical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (

text: KEGG

text: PubChem

text: MetaCyc

text: ChEBI

text: Protein Data Bank

text: UniProt

text: , and

text: GenBank

text: ) and a variety of structure and pathway viewing applets. The YMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches.

text: Early in his career Schultz showed that the natural molecular diversity of the immune system could be directed to generate catalytic antibodies.  This method enabled the subsequent development of many new selective enzyme-like catalysts for reactions ranging from acyl transfer and redox reactions to pericyclic and metallation reactions.  Although their catalytic activities are only rarely strong enough to be of practical use, catalytic antibodies have provided important new insights in our understanding of biocatalysis, structural plasticity of proteins, evolution of biochemical function, and the immune system itself.

text: Early in his career Schultz showed that the natural molecular diversity of the immune system could be directed to generate

text: catalytic antibodies

text: .  This method enabled the subsequent development of many new selective enzyme-like catalysts for reactions ranging from acyl transfer and redox reactions to pericyclic and metallation reactions.  Although their catalytic activities are only rarely strong enough to be of practical use, catalytic antibodies have provided important new insights in our understanding of biocatalysis, structural plasticity of proteins, evolution of biochemical function, and the immune system itself.

text: There are two different types of arthropod excretory systems. In aquatic arthropods, the end-product of biochemical reactions that metabolise nitrogen is ammonia, which is so toxic that it needs to be diluted as much as possible with water. The ammonia is then eliminated via any permeable membrane, mainly through the gills. All crustaceans use this system, and its high consumption of water may be responsible for the relative lack of success of crustaceans as land animals. Various groups of terrestrial arthropods have independently developed a different system: the end-product of nitrogen metabolism is uric acid, which can be excreted as dry material; the Malpighian tubule system filters the uric acid and other nitrogenous waste out of the blood in the hemocoel, and dumps these materials into the hindgut, from which they are expelled as feces. Most aquatic arthropods and some terrestrial ones also have organs called nephridia ("little kidneys"), which extract other wastes for excretion as urine.

text: There are two different types of arthropod excretory systems. In aquatic arthropods, the end-product of biochemical reactions that

text: metabolise

text: nitrogen

text: is

text: ammonia

text: , which is so toxic that it needs to be diluted as much as possible with water. The ammonia is then eliminated via any permeable membrane, mainly through the gills. All crustaceans use this system, and its high consumption of water may be responsible for the relative lack of success of crustaceans as land animals. Various groups of terrestrial arthropods have independently developed a different system: the end-product of nitrogen metabolism is

text: uric acid

text: , which can be excreted as dry material; the

text: Malpighian tubule system

text: filters the uric acid and other nitrogenous waste out of the blood in the hemocoel, and dumps these materials into the hindgut, from which they are expelled as

text: feces

text: . Most aquatic arthropods and some terrestrial ones also have organs called

text: nephridia

text: ("little

text: kidney

text: s"), which extract other wastes for excretion as

text: urine

text: SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database storing information about biochemical reactions and their kinetic properties.

text: SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible

text: database

text: storing information about biochemical

text: reactions

text: and their

text: kinetic

text: properties.

text: The mechanisms of enzyme-catalyzed reactions can also be studied using crossover experiments. Examples of the application of this technique in biochemistry include the study of reactions catalyzed by nucleoside diphosphohexose-4,6-dehydratases, the aconitase-catalyzed elimination of water from citrate, and various reactions catalyzed by coenzyme B-dependent enzymes, among others. Unlike isotope labeling studies in organic and organometallic chemistry, which typically use deuterium when an isotope of hydrogen is desired, biochemical crossover experiments frequently employ tritium. This is due to the fact that tritium is radioactive and can be tracked using the autoradiographs of gels in gel electrophoresis.

text: The mechanisms of enzyme-catalyzed reactions can also be studied using crossover experiments. Examples of the application of this technique in

text: biochemistry

text: include the study of reactions catalyzed by nucleoside diphosphohexose-4,6-dehydratases, the aconitase-catalyzed elimination of water from citrate, and various reactions catalyzed by coenzyme B-dependent enzymes, among others. Unlike isotope labeling studies in organic and organometallic chemistry, which typically use deuterium when an isotope of hydrogen is desired, biochemical crossover experiments frequently employ

text: tritium

text: . This is due to the fact that tritium is radioactive and can be tracked using the

text: autoradiograph

text: s of gels in

text: gel electrophoresis

text: Homocysteine and taurine are other sulfur-containing acids that are similar in structure, but not coded by DNA, and are not part of the primary structure of proteins. Many important cellular enzymes use prosthetic groups ending with -SH moieties to handle reactions involving acyl-containing biochemicals: two common examples from basic metabolism are coenzyme A and alpha-lipoic acid. Two of the 13 classical vitamins, biotin and thiamine, contain sulfur, with the latter being named for its sulfur content.

text: Homocysteine

text: and

text: taurine

text: are other sulfur-containing acids that are similar in structure, but not coded by

text: DNA

text: , and are not part of the

text: primary structure

text: of proteins. Many important cellular enzymes use prosthetic groups ending with -SH moieties to handle reactions involving acyl-containing biochemicals: two common examples from basic metabolism are

text: coenzyme A

text: and

text: alpha-lipoic acid

text: . Two of the 13 classical vitamins,

text: biotin

text: and

text: thiamine

text: , contain sulfur, with the latter being named for its sulfur content.

text: An ion-selective electrode (ISE), also known as a specific ion electrode (SIE), is a transducer (or sensor) that converts the activity of a specific ion dissolved in a solution into an electrical potential. The voltage is theoretically dependent on the logarithm of the ionic activity, according to the Nernst equation. Ion-selective electrodes are used in analytical chemistry and  biochemical/biophysical research, where measurements of ionic concentration in an aqueous solution are required.

text: An ion-selective electrode (ISE), also known as a specific ion electrode (SIE), is a

text: transducer

text: (or

text: sensor

text: ) that converts the

text: activity

text: of a specific

text: ion

text: dissolved in a

text: solution

text: into an electrical

text: potential

text: . The voltage is theoretically dependent on the

text: logarithm

text: of the ionic activity, according to the

text: Nernst equation

text: . Ion-selective electrodes are used in

text: analytical chemistry

text: and

text: biochemical

text: biophysical

text: research, where measurements of

text: ion

text: ic

text: concentration

text: in an

text: aqueous solution

text: are required.

text: Quantum tunnelling is among the central non trivial quantum effects in Quantum biology. Here it is important both as electron tunnelling and proton tunnelling. Electron tunnelling is a key factor in many biochemical redox reactions (photosynthesis, cellular respiration) as well as enzymatic catalysis while proton tunnelling is a key factor in spontaneous mutation of DNA.

text: Quantum tunnelling is among the central non trivial quantum effects in

text: Quantum biology

text: . Here it is important both as electron tunnelling and proton tunnelling. Electron tunnelling is a key factor in many biochemical redox reactions (photosynthesis, cellular respiration) as well as enzymatic catalysis while proton tunnelling is a key factor in spontaneous mutation of DNA.

text: The transfer of  in an acid–base reaction is usually referred to as "proton transfer". The acid is referred to as a proton donor and the base as a proton acceptor. Likewise, biochemical terms such as proton pump and proton channel refer to the movement of hydrated  ions.

text: The transfer of  in an

text: acid–base reaction

text: is usually referred to as "proton transfer". The

text: acid

text: is referred to as a proton donor and the

text: base

text: as a proton acceptor. Likewise,

text: biochemical

text: terms such as

text: proton pump

text: and

text: proton channel

text: refer to the movement of hydrated  ions.

text: The first issue of The Journal of Biophysical and Biochemical Cytology was published less than a year later on January 25, 1955. A subscription cost $15 per year. The list of editors comprised Richard S. Bear, H. Stanley Bennett, Albert L. Lehninger, George E. Palade, Keith R. Porter, Francis O. Schmitt, Franz Schrader, and Arnold M. Seligman. The instructions to authors described the scope of the journal, "The Journal of Biophysical and Biochemical Cytology is designed to provide a common medium for the publication of morphological, biophysical, and biochemical investigations on cells, their components, and their products. It will give special attention to reports on cellular organization at the colloidal and molecular levels and to studies integrating cytological information derived from various technical approaches." Recognizing that they needed a catchier title, the editors changed the name to The Journal of Cell Biology ("JCB") in 1962.

text: The first issue of The Journal of Biophysical and Biochemical Cytology was published less than a year later on January 25, 1955. A subscription cost $15 per year. The list of editors comprised Richard S. Bear, H. Stanley Bennett,

text: Albert L. Lehninger

text: George E. Palade

text: Keith R. Porter

text: Francis O. Schmitt

text: , Franz Schrader, and Arnold M. Seligman. The instructions to authors described the scope of the journal, "The Journal of Biophysical and Biochemical Cytology is designed to provide a common medium for the publication of

text: morphological

text: biophysical

text: , and

text: biochemical

text: investigations on cells, their components, and their products. It will give special attention to reports on cellular organization at the

text: colloidal

text: and

text: molecular

text: levels and to studies integrating cytological information derived from various technical approaches." Recognizing that they needed a catchier title, the editors changed the name to The Journal of Cell Biology ("JCB") in 1962.

text: Around 100,000 species of fungi have been formally described by taxonomists, but the global biodiversity of the fungus kingdom is not fully understood. On the basis of observations of the ratio of the number of fungal species to the number of plant species in selected environments, the fungal kingdom has been estimated to contain about 1.5 million species. A recent (2011) estimate suggests there may be over 5 million species. In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based on morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy. Species may also be distinguished by their biochemical and physiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction to chemical tests. The biological species concept discriminates species based on their ability to mate. The application of molecular tools, such as DNA sequencing and phylogenetic analysis, to study diversity has greatly enhanced the resolution and added robustness to estimates of genetic diversity within various taxonomic groups.

text: Around 100,000 species of fungi have been formally

text: described

text: by

text: taxonomists

text: , but the global biodiversity of the fungus kingdom is not fully understood. On the basis of observations of the ratio of the number of fungal species to the number of plant species in selected environments, the fungal kingdom has been estimated to contain about 1.5 million species. A recent (2011) estimate suggests there may be over 5 million species. In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based on

text: morphological

text: characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy. Species may also be distinguished by their

text: biochemical

text: and

text: physiological

text: characteristics, such as their ability to metabolize certain biochemicals, or their reaction to

entity_name: Chemical test in mushroom identification

text: chemical tests

text: . The

entity_section: The isolation species concept in more detail

text: biological species concept

text: discriminates species based on their ability to

text: mate

text: . The application of

text: molecular

text: tools, such as

text: DNA sequencing

text: and phylogenetic analysis, to study diversity has greatly enhanced the resolution and added robustness to estimates of

text: genetic diversity

text: within various taxonomic groups.

text: Two phosphoanhydride bonds (those that connect adjacent phosphates) in an ATP molecule are responsible for the high energy content of this molecule. In the context of biochemical reactions, these anhydride bonds are frequently – and sometimes controversially – referred to as high-energy bonds (despite the fact it takes energy to break bonds). Energy stored in ATP may be released upon hydrolysis of the anhydride bonds. The primary phosphate group on the ATP molecule that is hydrolyzed when energy is needed to drive anabolic reactions is the γ-phosphate group. Located the farthest from the ribose sugar, it has a higher energy of hydrolysis than either the α- or β-phosphate. The bonds formed after hydrolysis – or the phosphorylation of a residue by ATP – are lower in energy than the phosphoanhydride bonds of ATP. During enzyme-catalyzed hydrolysis of ATP or phosphorylation by ATP, the available free energy can be harnessed by a living system to do work.

text: Two

text: phosphoanhydride

text: bonds (those that connect adjacent phosphates) in an ATP molecule are responsible for the high energy content of this molecule. In the context of biochemical reactions, these anhydride bonds are frequently – and sometimes controversially – referred to as

text: high-energy bonds

text: (despite the fact it takes energy to break bonds). Energy stored in ATP may be released upon

text: hydrolysis

text: of the anhydride bonds. The primary phosphate group on the ATP molecule that is hydrolyzed when energy is needed to drive anabolic reactions is the γ-phosphate group. Located the farthest from the ribose sugar, it has a higher energy of hydrolysis than either the α- or β-phosphate. The bonds formed after hydrolysis – or the phosphorylation of a residue by ATP – are lower in energy than the phosphoanhydride bonds of ATP. During enzyme-catalyzed hydrolysis of ATP or phosphorylation by ATP, the available free energy can be harnessed by a living system to do work.

text: The energetic requirements of a body are composed of the basal metabolic rate and the physical activity level. This caloric requirement can be met with protein, fat, carbohydrates, alcohol, or a mixture of them. Glucose is the general metabolic fuel, which can be metabolized by any cell. Fructose and some other nutrients can only be metabolized in the liver, where their metabolites are transformed either into glucose and stored as glycogen, both in the liver and in the muscles; or into fatty acids which are stored in adipose tissue.

text: The energetic requirements of a body are composed of the

text: basal metabolic rate

text: and the

text: physical activity level

text: . This caloric requirement can be met with protein, fat, carbohydrates, alcohol, or a mixture of them.

text: Glucose

text: is the general metabolic fuel, which can be metabolized by any cell.

text: Fructose

text: and some other nutrients can only be metabolized in the liver, where their metabolites are transformed either into glucose and stored as

text: glycogen

text: , both in the liver and in the muscles; or into

text: fatty acids

text: which are stored in adipose tissue.

text: Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules. Enzymes' specificity comes from their unique three-dimensional structures.

text: Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are

text: protein

text: s, although a few are

text: catalytic RNA molecules

text: . Enzymes' specificity comes from their unique

text: three-dimensional structures

text: What enables the Krebs cycle to perform metabolic changes to fats, carbohydrates, and proteins is energy, which can be defined as the ability or capacity to do work. The breakdown of large molecules into smaller molecules—associated with release of energy—is catabolism. The building up process is termed anabolism. The breakdown of proteins into amino acids is an example of catabolism, while the formation of proteins from amino acids is an anabolic process.

text: Cellular respiration is the process by which biological fuels are oxidised in the presence of an inorganic electron acceptor (such as oxygen) to produce large amounts of energy, to drive the bulk production of ATP.

text: Another important area of nuclear chemistry is the study of how fission products interact with surfaces; this is thought to control the rate of release and migration of fission products both from waste containers under normal conditions and from power reactors under accident conditions. It is interesting to note that, like chromate and molybdate, the TcO anion can react with steel surfaces to form a corrosion resistant layer. In this way, these metaloxo anions act as anodic corrosion inhibitors. The formation of TcO on steel surfaces is one effect which will retard the release of Tc from nuclear waste drums and nuclear equipment which has been lost before decontamination (e.g. submarine reactors  lost at sea). This TcO layer renders the steel surface passive, inhibiting the anodic corrosion reaction. The radioactive nature of technetium makes this corrosion protection impractical in almost all situations. It has also been shown that TcO anions react to form a layer on the surface of activated carbon (charcoal) or aluminium.. A short review of the biochemical properties of a series of key long lived radioisotopes can be read on line.

text: Another important area of nuclear chemistry is the study of how fission products interact with surfaces; this is thought to control the rate of release and migration of fission products both from waste containers under normal conditions and from power reactors under accident conditions. It is interesting to note that, like

text: chromate

text: and

text: molybdate

text: , the TcO anion can react with steel surfaces to form a

text: corrosion

text: resistant layer. In this way, these metaloxo anions act as

text: anodic

text: corrosion inhibitor

text: s. The formation of TcO on steel surfaces is one effect which will retard the release of Tc from nuclear waste drums and nuclear equipment which has been lost before decontamination (e.g.

text: submarine

text: reactors  lost at sea). This TcO layer renders the steel surface passive, inhibiting the

text: anodic

text: corrosion

text: reaction. The radioactive nature of technetium makes this corrosion protection impractical in almost all situations. It has also been shown that TcO anions react to form a layer on the surface of activated carbon (

text: charcoal

text: ) or

text: aluminium

text: .. A short review of the biochemical properties of a series of key long lived radioisotopes can be read on line.

text: Carboxypeptidase Taq () is an enzyme. This enzyme catalyses the following chemical reaction

text: Carboxypeptidase Taq () is an

text: enzyme

text: . This enzyme

text: catalyses

text: the following

text: chemical reaction

text: Biological explanations of seasonal effects on suicide rates tend to focus on seasonal variation in hormone changes and neurotransmitter levels. Chronobiological research, conducted by a team of clinical scientists in Belgium, has revealed that many “biochemical, metabolic and immune functions, which may be related to suicide, suicidal behavior or ideation or major depression, are organized along a multifrequency seasonal time-structure”. Evidence was found by calculating “serum total cholesterol concentrations to show a clear seasonality with lower levels in midyear than in winter" Similarly, medical researchers in Pennsylvania indicate that neuropeptides in normal controls have lower serum cholesterol levels and may be related to a higher occurrence of suicide. These findings clearly state that there is a relationship between summer suicide rates and biochemical (e.g., plasma L-TRP and melatonin levels, [3H]paroxetine binding to blood platelets), metabolic (serum total cholesterol, calcium and magnesium concentrations), and immune (number of peripheral blood lymphocytes and serum sIL-2R) variables.

text: Biological explanations of seasonal effects on suicide rates tend to focus on seasonal variation in

text: hormone

text: changes and

text: neurotransmitter

text: levels.

text: Chronobiological

text: research, conducted by a team of clinical scientists in Belgium, has revealed that many “biochemical, metabolic and immune functions, which may be related to suicide, suicidal behavior or ideation or major depression, are organized along a multifrequency seasonal time-structure”. Evidence was found by calculating “serum total cholesterol concentrations to show a clear seasonality with lower levels in midyear than in winter" Similarly, medical researchers in Pennsylvania indicate that

text: neuropeptides

text: in normal controls have lower serum

text: cholesterol

text: levels and may be related to a higher occurrence of suicide. These findings clearly state that there is a relationship between summer suicide rates and biochemical (e.g., plasma L-TRP and

text: melatonin

text: levels, [3H]paroxetine binding to blood platelets), metabolic (serum total cholesterol,

text: calcium

text: and

text: magnesium

text: concentrations), and immune (number of peripheral blood

text: lymphocyte

text: s and serum sIL-2R) variables.

text: BSA has numerous biochemical applications including ELISAs (Enzyme-Linked Immunosorbent Assay), immunoblots, and immunohistochemistry. It is also used as a nutrient in cell and microbial culture. In restriction digests, BSA is used to stabilize some enzymes during the digestion of DNA and to prevent adhesion of the enzyme to reaction tubes, pipet tips, and other vessels.  This protein does not affect other enzymes that do not need it for stabilization. BSA is also commonly used to determine the quantity of other proteins, by comparing an unknown quantity of protein to known amounts of BSA (see Bradford protein assay). BSA is used because of its ability to increase signal in assays, its lack of effect in many biochemical reactions, and its low cost, since large quantities of it can be readily purified from bovine blood, a byproduct of the cattle industry.

text: BSA has numerous biochemical applications including

text: ELISA

text: s (Enzyme-Linked Immunosorbent Assay), immunoblots, and

text: immunohistochemistry

text: . It is also used as a nutrient in cell and microbial culture. In

text: restriction digest

text: s, BSA is used to stabilize some enzymes during the digestion of

text: DNA

text: and to prevent adhesion of the enzyme to reaction tubes, pipet tips, and other vessels.  This

text: protein

text: does not affect other

text: enzyme

text: s that do not need it for stabilization. BSA is also commonly used to determine the quantity of other proteins, by comparing an unknown quantity of protein to known amounts of BSA (see

text: Bradford protein assay

text: ). BSA is used because of its ability to increase signal in assays, its lack of effect in many biochemical reactions, and its low cost, since large quantities of it can be readily purified from bovine blood, a byproduct of the cattle industry.

text: The theoretical oxygen demand represents the worse case scenario. The actual oxygen demand of any compound depends on the biodegradability of the compound and the specific organism metabolizing the compound. The actual oxygen demand can be measured experimentally and is called the biochemical oxygen demand (BOD).

text: The theoretical oxygen demand represents the worse case scenario. The actual oxygen demand of any

text: compound

text: depends on the

text: biodegradability

text: of the compound and the specific organism

text: metabolizing

text: the compound. The actual

text: oxygen

text: demand can be measured experimentally and is called the

text: biochemical oxygen demand

text: (BOD).

text: It publishes standards on biochemical nomenclature, including enzyme nomenclature, in some cases jointly with the International Union of Pure and Applied Chemistry (IUPAC).

text: It publishes standards on biochemical nomenclature, including

text: enzyme

text: nomenclature, in some cases jointly with the

text: (IUPAC).

text: The use of arenediazonium salts presents some advantages over traditional aryl halide electrophiles, for example, the use of phosphines as ligand are not required and thus negating the requirement for anaerobic conditions, which makes the reaction more practical and easier to handle. Additionally, the reaction can be performed with or without a base and is often faster than traditional Heck protocols.<ref>{{cite journal | last1 = Darses | first1 = Sylvain | last2 = Pucheault | first2 = Mathieu | last3 = Genêt | first3 = Jean-Pierre | title = Efficient Access to Perfluoroalkylated Aryl Compounds by Heck Reaction | journal = European Journal of Organic Chemistry | volume = 2001 | issue = 6 | pages = 1121–1128 | year = 2001 | doi = 10.1002/1099-0690(200103)2001:6

text: The use of arenediazonium salts presents some advantages over traditional aryl halide

text: electrophile

text: s, for example, the use of

text: phosphine

text: s as

text: ligand

text: are not required and thus negating the requirement for anaerobic conditions, which makes the reaction more practical and easier to handle. Additionally, the reaction can be performed with or without a base and is often faster than traditional

text: Heck protocols

text: .<ref>{{cite journal | last1 = Darses | first1 = Sylvain | last2 = Pucheault | first2 = Mathieu | last3 = Genêt | first3 = Jean-Pierre | title = Efficient Access to Perfluoroalkylated Aryl Compounds by Heck Reaction | journal = European Journal of Organic Chemistry | volume = 2001 | issue = 6 | pages = 1121–1128 | year = 2001 | doi = 10.1002/1099-0690(200103)2001:6

text: An insect uses its digestive system to extract nutrients and other substances from the food it consumes. Most of this food is ingested in the form of macromolecules and other complex substances like proteins, polysaccharides, fats and nucleic acids. These macromolecules must be broken down by catabolic reactions into smaller molecules like amino acids and simple sugars before being used by cells of the body for energy, growth, or reproduction. This break-down process is known as digestion.

text: An insect uses its digestive system to extract nutrients and other substances from the food it consumes. Most of this food is ingested in the form of

text: macromolecule

text: s and other complex substances like

text: protein

text: s,

text: polysaccharide

text: s,

text: fat

text: s and

text: nucleic acid

text: s. These macromolecules must be broken down by

text: catabolic reactions

text: into smaller molecules like

text: amino acid

text: s and

text: simple sugar

text: s before being used by cells of the body for energy, growth, or reproduction. This break-down process is known as digestion.

text: Wine (from Latin vinum) is an alcoholic beverage made from fermented grapes. These grapes are generally Vitis vinifera, or a hybrid with Vitis labrusca or Vitis rupestris. Grapes ferment without the addition of sugars, acids, enzymes, water, or other nutrients. Yeast consumes the sugar in the grapes and converts it to ethanol and carbon dioxide. Different varieties of grapes and strains of yeasts produce different styles of wine. These variations result from the complex interactions between the biochemical development of the grape, the reactions involved in fermentation, the terroir, and the production process. Many countries define legal appellations intended to define styles and qualities of wine. These typically restrict the geographical origin and permitted varieties of grapes, as well as other aspects of wine production.

text: Wine (from

text: Latin

text: vinum) is an

text: alcoholic beverage

text: made from

text: fermented

text: grape

text: s. These grapes are generally

text: Vitis vinifera

text: , or a hybrid with

text: Vitis labrusca

text: or

text: Vitis rupestris

text: . Grapes ferment without the addition of

text: sugar

text: s,

text: acid

text: s,

text: enzyme

text: s,

text: water

text: , or other

text: nutrient

text: s.

text: Yeast

text: consumes the sugar in the grapes and converts it to

text: ethanol

text: and

text: carbon dioxide

text: . Different varieties of grapes and strains of yeasts produce different styles of wine. These variations result from the complex interactions between the biochemical development of the grape, the reactions involved in fermentation, the

text: terroir

text: , and the production process. Many countries define legal

text: appellation

text: s intended to define styles and qualities of wine. These typically restrict the geographical origin and permitted varieties of grapes, as well as other aspects of wine production.

text: In biology, electron donors release an electron during cellular respiration, resulting in the release of energy. Microorganisms, such as bacteria, obtain energy in the electron transfer processes. Through its cellular machinery, the microorganism collects the energy for its use. The final result is the electron is donated to an electron acceptor. During this process (electron transport chain) the electron donor is oxidized and the electron acceptor is reduced. Petroleum hydrocarbons, less chlorinated solvents like vinyl chloride, soil organic matter, and reduced inorganic compounds are all compounds that can act as electron donors. These reactions are of interest not only because they allow organisms to obtain energy, but also because they are involved in the natural biodegradation of organic contaminants. When clean-up professionals use monitored natural attenuation to clean up contaminated sites, biodegradation is one of the major contributing processes.

text: In

text: biology

text: , electron donors release an electron during

text: cellular respiration

text: , resulting in the release of

text: energy

text: Microorganisms

text: , such as

text: bacteria

text: , obtain energy in the electron transfer processes. Through its cellular machinery, the microorganism collects the energy for its use. The final result is the electron is donated to an electron acceptor. During this process (

text: electron transport chain

text: ) the electron donor is oxidized and the electron acceptor is reduced. Petroleum

text: hydrocarbons

text: , less

text: chlorinated

text: solvents like

text: vinyl chloride

text: , soil organic matter, and reduced inorganic compounds are all compounds that can act as electron donors. These reactions are of interest not only because they allow organisms to obtain energy, but also because they are involved in the natural

text: biodegradation

text: of organic contaminants. When clean-up professionals use monitored natural attenuation to clean up contaminated sites, biodegradation is one of the major contributing processes.

text: Heterotrophs, such as animals, use light from the Sun indirectly by consuming the products of autotrophs, either by consuming autotrophs, by consuming their products, or by consuming other heterotrophs. The sugars and other molecular components produced by the autotrophs are then broken down, releasing stored solar energy, and giving the heterotroph the energy required for survival. This process is known as cellular respiration.

text: Heterotroph

text: s, such as animals, use light from the Sun indirectly by consuming the products of autotrophs, either by consuming autotrophs, by consuming their products, or by consuming other heterotrophs. The sugars and other molecular components produced by the autotrophs are then broken down, releasing stored solar energy, and giving the heterotroph the energy required for survival. This process is known as

text: cellular respiration

text: C-terminus - C4 photosynthesis - cadherin - calbindin -calcitonin - calcitonin gene-related peptide - calcitonin gene-related peptide receptor - calcitonin receptor - calcitriol receptor - calcium channel - calcium signaling - calcium-binding protein - Calmodulin - calmodulin-binding protein - Calvin cycle - CAM photosynthesis - CAM plants - cancer - capsid - Carbohydrate - Carbon - Carbon fixation - Carboxylic acid - carcinoembryonic antigen - carrier - carrier protein - CAS registry number - casein - catabolism - catalyst - catalytic domain - CCR5 receptor - CD4 antigen - CD45 antigen - CD95 antigen - CDC28 protein kinase - cell - cell adhesion molecule - Cell biology - cell cycle protein - cell membrane - cell membrane transport - cell nucleus - cell surface receptor - cellular respiration - cellulose - centriole - centromere - centrosome - Chaperone - Chelation - Chemical bond - Chemical compound - Conformation - chemical element - Chemical equilibrium - Chemical formula - Chemical nomenclature - Chemical property - Chemical reaction - Chemical series - Chemical thermodynamics - Cheminformatics - chemiosmosis - chemiosmotic hypothesis - chemiosmotic potential - Chemist - Chemistry - Chemistry basic topics - chemotroph - chemokine receptor - chemoreceptor - chiasma - Chimera (protein) - chimeric protein - Chirality - chloride channel - chlorophyll - chloroplast - chloroplast membrane - cholecystokinin receptor - cholesterine - cholinergic receptor - chorionic gonadotropin - chromatid - chromatin - ciclosporin - Chromatography - Chromosomal crossover - chromosome - chromosome walking - cilium - circular dichroism -  - cis face - Citric acid - Citric acid cycle - cladistics - cloning - coenzyme - cofactor (biochemistry) - colchicine - collagen - colloid - colony-stimulating factor - Colony stimulating factor 1 receptor - Colorimeter - comparative biochemistry - competitive inhibition - complement 3A - complement 5A - complement factor B - complement membrane attack complex - complement receptor - complex - computational biology - computational chemistry - computational genomics - concanavalin A - Concentration - concentration gradient - consensus sequence - conserved sequence - Cooperative - Cooperative binding - Cooperativity - cooperativity cellular respiration - corticotropin - corticotropin receptor - corticotropin-releasing hormone - corticotropin-releasing hormone receptor - cotransport metabolism - covalent bond - Covalent radius - CpG island - cristae - cryptobiology - Crystal structure - Crystallography - cuticula - CXCR4 receptor - cyclic AMP receptor - cyclic AMP receptor protein - cyclic AMP-responsive DNA-binding protein - cyclic electron flow - Cyclic nucleotide - cyclic peptide - cyclin - cyclin A - cyclin B - cyclin E - cyclin-dependent kinase - cycloleucine - cyclosporin - cyclosporine - cystatin - cysteine - cystic fibrosis transmembrane conductance regulator - cytochrome B - cytochrome C - cytochrome P-450 - cytochrome P-450 CYP1A1 - cytochrome C oxidase - cytokine receptor - cytoplasm - cytoplasmic and nuclear receptor - Cytosine - cytoskeletal protein - cytoskeleton - cytosol - cytotoxic T cell -

text: C-terminus

text: C4 photosynthesis

text: cadherin

text: calbindin

text: calcitonin

text: calcitonin gene-related peptide

text: calcitonin gene-related peptide receptor

text: calcitonin receptor

text: calcitriol receptor

text: calcium channel

text: calcium signaling

text: calcium-binding protein

text: Calmodulin

text: calmodulin-binding protein

text: Calvin cycle

text: CAM photosynthesis

text: CAM plants

text: cancer

text: capsid

text: Carbohydrate

text: Carbon

text: Carbon fixation

text: Carboxylic acid

text: carcinoembryonic antigen

text: carrier

text: carrier protein

text: CAS registry number

text: casein

text: catabolism

text: catalyst

text: catalytic domain

text: CCR5 receptor

text: CD4 antigen

text: CD45 antigen

text: CD95 antigen

text: CDC28 protein kinase

text: cell

text: cell adhesion molecule

text: Cell biology

text: cell cycle protein

text: cell membrane

text: cell membrane transport

text: cell nucleus

text: cell surface receptor

text: cellular respiration

text: cellulose

text: centriole

text: centromere

text: centrosome

text: Chaperone

text: Chelation

text: Chemical bond

text: Chemical compound

text: Conformation

text: chemical element

text: Chemical equilibrium

text: Chemical formula

text: Chemical nomenclature

text: Chemical property

text: Chemical reaction

text: Chemical series

text: Chemical thermodynamics

text: Cheminformatics

text: chemiosmosis

text: chemiosmotic hypothesis

text: chemiosmotic potential

text: Chemist

text: Chemistry

text: Chemistry basic topics

text: chemotroph

text: chemokine receptor

text: chemoreceptor

text: chiasma

text: Chimera (protein)

text: chimeric protein

text: Chirality

text: chloride channel

text: chlorophyll

text: chloroplast

text: chloroplast membrane

text: cholecystokinin receptor

text: cholesterine

text: cholinergic receptor

text: chorionic gonadotropin

text: chromatid

text: chromatin

text: ciclosporin

text: Chromatography

text: Chromosomal crossover

text: chromosome

text: chromosome walking

text: cilium

text: circular dichroism

text: cis face

text: Citric acid

text: Citric acid cycle

text: cladistics

text: cloning

text: coenzyme

text: cofactor (biochemistry)

text: colchicine

text: collagen

text: colloid

text: colony-stimulating factor

text: Colony stimulating factor 1 receptor

text: Colorimeter

text: comparative biochemistry

text: competitive inhibition

text: complement 3A

text: complement 5A

text: complement factor B

text: complement membrane attack complex

text: complement receptor

text: complex

text: computational biology

text: computational chemistry

text: computational genomics

text: concanavalin A

text: Concentration

text: concentration gradient

text: consensus sequence

text: conserved sequence

text: Cooperative

text: Cooperative binding

text: Cooperativity

text: cooperativity cellular respiration

text: corticotropin

text: corticotropin receptor

text: corticotropin-releasing hormone

text: corticotropin-releasing hormone receptor

text: cotransport metabolism

text: covalent bond

text: Covalent radius

text: CpG island

text: cristae

text: cryptobiology

text: Crystal structure

text: Crystallography

text: cuticula

text: CXCR4 receptor

text: cyclic AMP receptor

text: cyclic AMP receptor protein

text: cyclic AMP-responsive DNA-binding protein

text: cyclic electron flow

text: Cyclic nucleotide

text: cyclic peptide

text: cyclin

text: cyclin A

text: cyclin B

text: cyclin E

text: cyclin-dependent kinase

text: cycloleucine

text: cyclosporin

text: cyclosporine

text: cystatin

text: cysteine

entity_name: Cystic fibrosis transmembrane conductance regulator

text: cystic fibrosis transmembrane conductance regulator

text: cytochrome B

text: cytochrome C

text: cytochrome P-450

text: cytochrome P-450 CYP1A1

text: cytochrome C oxidase

text: cytokine receptor

text: cytoplasm

text: cytoplasmic and nuclear receptor

text: Cytosine

text: cytoskeletal protein

text: cytoskeleton

text: cytosol

text: cytotoxic T cell

text: ACADs are an important class of enzymes in mammalian cells because of their role in metabolizing fatty acids present in ingested food materials.  This enzyme's action represents the first step in fatty acid metabolism (the process of breaking long chains of fatty acids into acetyl CoA molecules). Deficiencies in these enzymes are linked to genetic disorders involving fatty acid oxidation (i.e. metabolic disorders).

text: ACADs are an important class of

text: enzymes

text: in

text: mammalian

text: cells

text: because of their role in metabolizing

text: fatty acids

text: present in ingested food materials.  This

text: enzyme's

text: action represents the first step in

text: fatty acid

text: metabolism

text: (the process of breaking long chains of fatty acids into acetyl CoA molecules). Deficiencies in these

text: enzymes

text: are linked to

text: genetic

text: disorders involving

text: fatty acid

text: oxidation

text: (i.e. metabolic disorders).

text: Sedoheptulose 7-phosphate, a pentose phosphate pathway intermediate, is a common precursor of C7N aminocyclitol moiety of natural products, such as acarbose, validamycin A, salbostatin, cetoniacytone A, and pyralomicin 1a. 2-epi-5-epi-valiolone synthase (EEVS), one of the sugar phosphate cyclase family enzyme and which is a homolog of 3-dehydroquinate synthase in shikimate pathway, catalyzes the formation of a common intermediate, 2-epi-5-epi-valiolone from sedoheptulose 7-phosphate. After multiple enzyme reaction steps, which include phosphorylation, epimerization, dehydration, and keto-reduction reactions, valienol, an important core structure is formed which leads to the formation of C7N aminocyclitol containing natural products. In validamycin biosynthesis, the C-N linkage which connect the C7 cyclitol moiety to the other was found to be formed by unprecedented actions of nucleotidyltransferase and glycosyltransferase-like enzymes (which is termed pseudoglycosyltransferase).

text: Sedoheptulose 7-phosphate

text: , a

text: pentose phosphate pathway

text: intermediate, is a common precursor of C7N aminocyclitol moiety of natural products, such as

text: acarbose

text: validamycin

text: A, salbostatin, cetoniacytone A, and pyralomicin 1a. 2-epi-5-epi-valiolone synthase (EEVS), one of the sugar phosphate cyclase family enzyme and which is a homolog of

text: 3-dehydroquinate synthase

text: in

text: shikimate pathway

text: , catalyzes the formation of a common intermediate, 2-epi-5-epi-valiolone from

text: sedoheptulose 7-phosphate

text: . After multiple enzyme reaction steps, which include

text: phosphorylation

text: epimer

text: ization,

text: dehydration

text: , and keto-reduction reactions,

text: valienol

text: , an important core structure is formed which leads to the formation of C7N aminocyclitol containing natural products. In

text: validamycin

text: biosynthesis, the C-N linkage which connect the C7 cyclitol moiety to the other was found to be formed by unprecedented actions of

text: nucleotidyltransferase

text: and

text: glycosyltransferase

text: -like enzymes (which is termed pseudoglycosyltransferase).

text: In March 1989 he was elected a Fellow of the Royal Society. The citation on his application read: "Distinguished for his contributions to analytical atomic and molecular spectroscopy. His early work at Birmingham on molecular spectroscopic studies of analytical chelate chemistry was of great importance and included his interpretation of the only known positive colour reaction of the fluoride ion. This reaction has replaced all other spectrophotometric reactions for fluoride. His evolution of the unique conditionally specific reaction between calcium and a new specially synthesised trihydroxytrisazo clathrate cage dyestuff molecule was also outstanding. His work on quartz fibre torsion ultramicrobalances and thereafter on a complete system of ultramicroscopic organic elemental and functional group analysis is also notable. At Imperial College, he created a new research group to work on analytical atomic absorption and atomic fluorescence spectroscopy. Under West's leadership this group very quickly became established as a leading centre of research in these fields. His many contributions included those to electrothermal methods of atomisation, microwave-excited atomic spectral lamps, low-luminosity flames, and atom-trapping techniques. At Aberdeen he has continued work in these fields. He has also contributed to the use of piezo-electric crystal sensor systems for the measurement of minute traces of airborne pollutants. He has collaborated in work on bio-significant and toxic trace elements in the soil-plant ecosystem and on acidification phenomena. West has served widely on many national and international committees and is at present Secretary-General of the International Union of Pure and Applied Chemistry."

text: In March 1989 he was elected a

text: Fellow of the Royal Society

text: The first step in the process is to identify a desired goal to achieve through the improvement or modification of an organism's metabolism.  Reference books and online databases are used to research reactions and metabolic pathways that are able to produce this product or result. These databases contain copious genomic and chemical information including pathways for metabolism and other cellular processes.  Using this research, an organism is chosen that will be used to create the desired product or result. Considerations that are taken into account when making this decision are how close the organism's metabolic pathway is to the desired pathway, the maintenance costs associated with the organism, and how easy it is to modify the pathway of the organism.  Escherichia coli (E. coli) is widely used in metabolic engineering to synthesize a wide variety of products such as amino acids because it is relatively easy to maintain and modify.  If the organism does not contain the complete pathway for the desired product or result, then genes that produce the missing enzymes must be incorporated into the organism.

text: Anabolism (from , "upward" and βάλλειν, "to throw") is the set of metabolic pathways that construct molecules from smaller units. These reactions require energy, known also as an endergonic process. One way of categorizing metabolic processes, whether at the cellular, organ or organism level, is as "anabolic", or as "catabolic" which is the opposite and thus the separation of a macromolecule. Anabolism is powered by catabolism, where large molecules are broken down into smaller parts and then used up in cellular respiration. Many anabolic processes are powered by the hydrolysis of adenosine triphosphate (ATP).

text: Anabolism (from , "upward" and βάλλειν, "to throw") is the set of

text: metabolic pathway

text: s that construct molecules from smaller units. These reactions require

text: energy

text: , known also as an

text: endergonic

text: process. One way of categorizing

text: metabolic

text: processes, whether at the

text: cell

text: ular, organ or organism level, is as "anabolic", or as "

text: catabolic

text: " which is the opposite and thus the separation of a macromolecule. Anabolism is powered by catabolism, where large molecules are broken down into smaller parts and then used up in

text: cellular respiration

text: . Many anabolic processes are powered by the

text: hydrolysis of adenosine triphosphate (ATP)

text: In biochemistry differences between the isotopomers of biochemicals such as starches is of practical importance in archaeology. They offer clues to the diet of prehistoric humans that lived as long ago as paleolithic times. This is because naturally occurring carbon dioxide contains both C and C. monocots, such as rice and oats, differ from dicots, such as potatoes and tree fruits, in the relative amounts of CO and CO that they incorporate into their tissues as products of photosynthesis. When tissues of such subjects are recovered, usually tooth or bone, the relative isotopic content can give useful indications of the main source of the staple foods of the subjects of the investigations.

text: In biochemistry differences between the isotopomers of biochemicals such as starches is of practical importance in archaeology. They offer clues to the diet of prehistoric humans that lived as long ago as paleolithic times. This is because naturally occurring

text: carbon dioxide

text: contains both C and C.

text: monocots

text: , such as

text: rice

text: and

text: oat

text: s, differ from

text: dicots

text: , such as

text: potato

text: es and

text: tree fruit

text: s, in the relative amounts of CO and CO that they incorporate into their tissues as products of

text: photosynthesis

text: . When tissues of such subjects are recovered, usually tooth or bone, the relative isotopic content can give useful indications of the main source of the

text: staple food

text: s of the subjects of the investigations.

text: Post-mortem chemistry, also called necrochemistry or death chemistry is a subdiscipline of chemistry in which the chemical structures, reactions, processes and parameters of a dead organism is investigated. Post-mortem chemistry plays a significant role in forensic pathology. Biochemical analyses of vitreous humor, cerebrospinal fluid, blood and urine  is important in determining the cause of death or in elucidating forensic cases.

text: Post-mortem chemistry, also called necrochemistry or death chemistry is a subdiscipline of

text: chemistry

text: in which the

text: chemical structure

text: s,

text: reactions

text: processes

text: and parameters of a

text: dead

text: organism

text: is investigated. Post-mortem chemistry plays a significant role in

text: forensic pathology

text: Biochemical analyses

text: of vitreous humor, cerebrospinal fluid, blood and urine  is important in determining the cause of death or in elucidating forensic cases.

text: By the end of the 19th century all of the major pathways of drug metabolism had been discovered, along with the outlines of protein and fatty acid metabolism and urea synthesis. In the early decades of the 20th century, the minor components of foods in human nutrition, the vitamins, began to be isolated and synthesized. Improved laboratory techniques such as chromatography and electrophoresis led to rapid advances in physiological chemistry, which—as biochemistry—began to achieve independence from its medical origins. In the 1920s and 1930s, biochemists—led by Hans Krebs and Carl and Gerty Cori—began to work out many of the central metabolic pathways of life: the citric acid cycle, glycogenesis and glycolysis, and the synthesis of steroids and porphyrins. Between the 1930s and 1950s, Fritz Lipmann and others established the role of ATP as the universal carrier of energy in the cell, and mitochondria as the powerhouse of the cell. Such traditionally biochemical work continued to be very actively pursued throughout the 20th century and into the 21st.

text: By the end of the 19th century all of the major pathways of

text: drug metabolism

text: had been discovered, along with the outlines of protein and fatty acid metabolism and urea synthesis. In the early decades of the 20th century, the minor components of foods in human nutrition, the

text: vitamins

text: , began to be isolated and synthesized. Improved laboratory techniques such as

text: chromatography

text: and

text: electrophoresis

text: led to rapid advances in physiological chemistry, which—as biochemistry—began to achieve independence from its medical origins. In the 1920s and 1930s, biochemists—led by

text: Hans Krebs

text: and

text: Carl

text: and

text: Gerty Cori

text: —began to work out many of the central

text: metabolic pathways

text: of life: the

text: citric acid cycle

text: glycogenesis

text: and

text: glycolysis

text: , and the synthesis of

text: steroid

text: s and

text: porphyrin

text: s. Between the 1930s and 1950s,

text: Fritz Lipmann

text: and others established the role of

text: ATP

text: as the universal carrier of energy in the cell, and

text: mitochondria

text: as the powerhouse of the cell. Such traditionally biochemical work continued to be very actively pursued throughout the 20th century and into the 21st.

text: Groups A–C are physiologically similar; S. sonnei (group D) can be differentiated on the basis of biochemical metabolism assays. Three Shigella groups are the major disease-causing species: S. flexneri is the most frequently isolated species worldwide, and accounts for 60% of cases in the developing world; S. sonnei causes 77% of cases in the developed world, compared to only 15% of cases in the developing world; and S. dysenteriae is usually the cause of epidemics of dysentery, particularly in confined populations such as refugee camps.

text: Photosynthesis is not quite as simple as adding water to  to produce sugars and oxygen. A complex chemical pathway is involved, facilitated along the way by a range of enzymes and co-enzymes. The enzyme RuBisCO is responsible for "fixing"  – that is, it attaches it to a carbon-based molecule to form a sugar, which can be used by the plant, releasing an oxygen molecule along the way. However, the enzyme is notoriously inefficient, and just as effectively will also fix oxygen instead of  in a process called photorespiration. This is energetically costly as the plant has to use energy to turn the products of photorespiration back into a form that can react with .

text: Photosynthesis

text: is not quite as simple as adding water to  to produce sugars and oxygen. A complex chemical pathway is involved, facilitated along the way by a range of

text: enzymes

text: and co-enzymes. The

text: enzyme

text: RuBisCO

text: is responsible for "fixing"  – that is, it attaches it to a carbon-based molecule to form a sugar, which can be used by the plant, releasing an oxygen molecule along the way. However, the enzyme is notoriously inefficient, and just as effectively will also fix oxygen instead of  in a process called

text: photorespiration

text: . This is energetically costly as the plant has to use energy to turn the products of photorespiration back into a form that can react with .

text: Many catabolic biochemical processes, such as glycolysis, the citric acid cycle, and beta oxidation, produce the reduced coenzyme NADH. This coenzyme contains electrons that have a high transfer potential; in other words, they will release a large amount of energy upon oxidation. However, the cell does not release this energy all at once, as this would be an uncontrollable reaction. Instead, the electrons are removed from NADH and passed to oxygen through a series of enzymes that each release a small amount of the energy. This set of enzymes, consisting of complexes I through IV, is called the electron transport chain and is found in the inner membrane of the mitochondrion. Succinate is also oxidized by the electron transport chain, but feeds into the pathway at a different point.

text: Many

text: catabolic

text: biochemical processes, such as

text: glycolysis

text: , the

text: citric acid cycle

text: , and

text: beta oxidation

text: , produce the reduced

text: coenzyme

text: NADH

text: . This coenzyme contains electrons that have a high

text: transfer potential

text: ; in other words, they will release a large amount of energy upon oxidation. However, the cell does not release this energy all at once, as this would be an uncontrollable reaction. Instead, the electrons are removed from NADH and passed to oxygen through a series of enzymes that each release a small amount of the energy. This set of enzymes, consisting of complexes I through IV, is called the electron transport chain and is found in the inner membrane of the mitochondrion.

text: Succinate

text: is also oxidized by the electron transport chain, but feeds into the pathway at a different point.

text: Plants use carbon dioxide gas in the process of photosynthesis, and exhale oxygen gas as waste. The chemical equation of photosynthesis is 6 CO (carbon dioxide) and 6 HO (water) and that makes 6 O (oxygen) and CHO (glucose). What is not expressed in the chemical equation is the capture of energy from sunlight which occurs. Photosynthesis uses electrons on the carbon atoms as the repository for that energy. Respiration is the opposite of photosynthesis. It reclaims the energy to power chemical reactions in cells. In so doing the carbon atoms and their electrons are combined with oxygen forming a gas which is easily removed from both the cells and the organism. Plants use both processes, photosynthesis to capture the energy and respiration to use it.

text: Plant

text: s use

text: carbon dioxide

text: gas in the process of

text: photosynthesis

text: , and exhale

text: oxygen

text: gas as waste. The chemical equation of photosynthesis is 6 CO (carbon dioxide) and 6 HO (water) and that makes 6 O (oxygen) and CHO (glucose). What is not expressed in the chemical equation is the capture of energy from sunlight which occurs. Photosynthesis uses electrons on the carbon atoms as the repository for that energy. Respiration is the opposite of photosynthesis. It reclaims the energy to power chemical reactions in cells. In so doing the carbon atoms and their electrons are combined with oxygen forming a gas which is easily removed from both the cells and the organism. Plants use both processes, photosynthesis to capture the energy and respiration to use it.

text: Public availability of biological network data makes the process of searching for new drug targets easier than it was before. By using the available metabolic networks, it is possible to find important nodes with link analysis algorithms, like PageRank. In a recently published paper, biochemical reactions are treated as nodes of the metabolic network. In this directed network, reaction A has a directed edge towards reaction B if the product of the former enters the latter reaction as a substrate or co-factor.

text: Dihydrolipoyl transacetylase participates in the pyruvate decarboxylation reaction that links glycolysis to the citric acid cycle. These metabolic processes are important for cellular respiration—the conversion of biochemical energy from nutrients into adenosine triphosphate (ATP) which can then be used to carry out numerous biological reactions within a cell. The various parts of cellular respiration take place in different parts of the cell. In eukaryotes, glycolysis occurs in the cytoplasm, pyruvate decarboxylation in the mitochondria, the citric acid cycle within the mitochondrial matrix, and oxidative phosphorylation via the electron transport chain on the mitochondrial cristae. Thus pyruvate dehydrogenase complexes (containing the dihydrolipoyl transacetylase enzymes) are found in the mitochondria of eukaryotes (and simply in the cytosol of prokaryotes).

text: Dihydrolipoyl transacetylase participates in the pyruvate decarboxylation reaction that links glycolysis to the citric acid cycle. These metabolic processes are important for cellular respiration—the conversion of biochemical energy from nutrients into

text: adenosine triphosphate

text: (ATP) which can then be used to carry out numerous biological reactions within a cell. The various parts of cellular respiration take place in different parts of the cell. In eukaryotes, glycolysis occurs in the cytoplasm, pyruvate decarboxylation in the mitochondria, the citric acid cycle within the mitochondrial matrix, and

text: oxidative phosphorylation

text: via the

text: electron transport chain

text: on the mitochondrial

text: cristae

text: . Thus pyruvate dehydrogenase complexes (containing the dihydrolipoyl transacetylase enzymes) are found in the mitochondria of eukaryotes (and simply in the cytosol of prokaryotes).

text: The types and sizes of the substituents in the vicinity of the enol and enolate (e.g., R, R, and R in the image above), and the particulars of reaction solvent, additives, and temperature contribute to the stability of the enol-type isomer, and fix the point at which an equilibrium lies, and for enols, the ability of the enol's hydroxyl group to hydrogen bond with an adjacent group can make it the preponderant isomer in solution (e.g., 3:1 and more over the keto form). Moreover, the substituents and conditions determine the preponderant conformations of these reactive species, and therefore dictate the stereochemical outcomes of their reactions. In biochemical transformations, the control of such reactions has been understood as exquisite for as long as the reactions have been studied, and in modern  chemical syntheses the same control is increasingly being achieved by man. Likewise, more complex substituents contribute to further unique reactivities, such as in enediols, alkenes with two hydroxyl groups, one on each end of the double bond, which appear in such structures as that of vitamin C, and contribute to its important redox properties.

text: The types and sizes of the substituents in the vicinity of the enol and enolate (e.g., R, R, and R in the image above), and the particulars of reaction solvent, additives, and temperature contribute to the stability of the enol-type

text: isomer

text: , and fix the point at which an equilibrium lies, and for enols, the ability of the enol's

text: hydroxyl group

text: to

text: hydrogen bond

text: with an adjacent group can make it the preponderant isomer in solution (e.g., 3:1 and more over the keto form). Moreover, the substituents and conditions determine the preponderant

text: conformations

text: of these reactive species, and therefore dictate the

text: stereochemical

text: outcomes of their reactions. In biochemical transformations, the control of such reactions has been understood as exquisite for as long as the reactions have been studied, and in modern

text: chemical syntheses

text: the same control is increasingly being achieved by man. Likewise, more complex substituents contribute to further unique reactivities, such as in

text: enediol

text: s, alkenes with two

text: hydroxyl group

text: s, one on each end of the double bond, which appear in such structures as that of

text: vitamin C

text: , and contribute to its important

text: redox

text: properties.

text: Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. In animals these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.

text: Catabolism

text: is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their

text: primary nutritional groups

text: ), as shown in the table below. Organic molecules are used as a source of energy by

text: organotroph

text: s, while

text: lithotroph

text: s use inorganic substrates and

text: phototroph

text: s capture sunlight as

text: chemical energy

text: . However, all these different forms of metabolism depend on

text: redox

text: reactions that involve the transfer of electrons from reduced donor molecules such as

text: organic molecule

text: s, water,

text: ammonia

text: hydrogen sulfide

text: or

text: ferrous ions

text: to acceptor molecules such as

text: oxygen

text: nitrate

text: or

text: sulfate

text: . In animals these reactions involve complex

text: organic molecule

text: s that are broken down to simpler molecules, such as

text: carbon dioxide

text: and water. In

text: photosynthetic

text: organisms such as plants and

text: cyanobacteria

text: , these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.

text: The dismutation of pyruvic acid in other small organic molecules (ethanol + CO, or lactate and acetate, depending on the environmental conditions) is also an important step in fermentation reactions. Fermentation reactions can also be considered as disproportionation or dismutation biochemical reactions. Indeed, the donor and acceptor of electrons in the redox reactions supplying the chemical energy in these complex biochemical systems are the same organic molecules simultaneously acting as reductant or oxidant.

text: The dismutation of pyruvic acid in other small organic molecules (ethanol + CO, or lactate and acetate, depending on the environmental conditions) is also an important step in

text: fermentation

text: reactions. Fermentation reactions can also be considered as disproportionation or dismutation

text: biochemical reaction

text: s. Indeed, the

text: donor

text: and

text: acceptor

text: of electrons in the

text: redox reaction

text: s supplying the

text: chemical energy

text: in these complex biochemical systems are the same organic molecules simultaneously acting as

text: reductant

text: or

text: oxidant

text: In molecular biology, acetate kinase (), which is predominantly found in micro-organisms, facilitates the production of acetyl-CoA by phosphorylating acetate in the presence of ATP and a divalent cation. Short-chain fatty acids (SCFAs) play a major role in carbon cycle and can be utilized as a source of carbon and energy by bacteria. Salmonella typhimurium propionate kinase (StTdcD) catalyzes reversible transfer of the γ-phosphate of ATP to propionate during l-threonine degradation to propionate. Kinetic analysis revealed that StTdcD possesses broad ligand specificity and could be activated by various SCFAs (propionate>acetate≈butyrate), nucleotides (ATP≈GTP>CTP≈TTP; dATP>dGTP>dCTP) and metal ions (Mg(2+)≈Mn(2+)>Co(2+)). Inhibition of StTdcD by tricarboxylic acid (TCA) cycle intermediates such as citrate, succinate, α-ketoglutarate and malate suggests that the enzyme could be under plausible feedback regulation. Crystal structures of StTdcD bound to PO4 (phosphate), AMP, ATP, Ap4 (adenosine tetraphosphate), GMP, GDP, GTP, CMP and CTP revealed that binding of nucleotide mainly involves hydrophobic interactions with the base moiety and could account for the broad biochemical specificity observed between the enzyme and nucleotides. Modeling and site-directed mutagenesis studies suggest Ala88 to be an important residue involved in determining the rate of catalysis with SCFA substrates. Molecular dynamics simulations on monomeric and dimeric forms of StTdcD revealed plausible open and closed states, and also suggested role for dimerization in stabilizing segment 235-290 involved in interfacial interactions and ligand binding. Observation of an ethylene glycol molecule bound sufficiently close to the γ-phosphate in StTdcD complexes with triphosphate nucleotides supports direct in-line phosphoryl transfer. The enzyme is important in the process of glycolysis, enzyme levels being increased in the presence of excess glucose. The growth of a bacterial mutant lacking acetate kinase has been shown to be inhibited by glucose, suggesting that the enzyme is involved in excretion of excess carbohydrate. A related enzyme, butyrate kinase, facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate.

text: In molecular biology, acetate kinase (), which is predominantly found in micro-organisms, facilitates the production of

text: acetyl-CoA

text: by

text: phosphorylating

text: acetate

text: in the presence of ATP and a

text: divalent

text: cation

text: enzyme

text: is important in the process of

text: glycolysis

text: , enzyme levels being increased in the presence of excess

text: glucose

text: . The

text: growth

text: of a

text: bacteria

text: l

text: mutant

text: lacking acetate

text: kinase

text: has been shown to be inhibited by glucose, suggesting that the enzyme is involved in

text: excretion

text: of excess

text: carbohydrate

text: . A related enzyme,

text: butyrate kinase

text: , facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl

text: phosphate

text: The antenna pigments are predominantly chlorophyll b, xanthophylls, and carotenes. Chlorophyll a is known as the core pigment. Their absorption spectra are non-overlapping in order to broaden the range of light that can be absorbed in photosynthesis. The carotenoids have another role as an antioxidant to prevent photo-oxidative damage of chlorophyll molecules. Each antenna complex has between 250 and 400 pigment molecules and the energy they absorb is shuttled by resonance energy transfer to a specialized chlorophyll-protein complex known as the reaction center of each photosystem. The reaction center initiates a complex series of chemical reactions that capture energy in the form of chemical bonds.

text: The

text: antenna pigments

text: are predominantly

text: chlorophyll b

text: xanthophylls

text: , and

text: carotene

text: s.

text: Chlorophyll a

text: is known as the core pigment. Their absorption spectra are non-overlapping in order to broaden the range of light that can be absorbed in photosynthesis. The carotenoids have another role as an antioxidant to prevent photo-oxidative damage of chlorophyll molecules. Each antenna complex has between 250 and 400 pigment molecules and the energy they absorb is shuttled by

text: resonance energy transfer

text: to a specialized chlorophyll-protein complex known as the

text: reaction center

text: of each

text: photosystem

text: . The reaction center initiates a complex series of chemical reactions that capture energy in the form of chemical bonds.

text: Since all natural waterways contain bacteria and nutrient, almost any waste compounds introduced into such waterways will initiate biochemical reactions (such as shown above).  Those biochemical reactions create what is measured in the laboratory as the biochemical oxygen demand (BOD).

text: Since all natural waterways contain bacteria and nutrient, almost any waste compounds introduced into such waterways will initiate biochemical reactions (such as shown above).  Those biochemical reactions create what is measured in the laboratory as the

text: biochemical oxygen demand

text: (BOD).

text: Using this measure of investment in carnivory, a model can be proposed. Above is a graph of carbon dioxide uptake (potential for growth) against trap respiration (investment in carnivory) for a leaf in a sunny habitat containing no soil nutrients at all. Respiration is a straight line sloping down under the horizontal axis (respiration produces carbon dioxide). Gross photosynthesis is a curved line above the horizontal axis: as investment increases, so too does the photosynthesis of the trap, as the leaf receives a better supply of nitrogen and phosphorus. Eventually another factor (such as light intensity or carbon dioxide concentration) will become more limiting to photosynthesis than nitrogen or phosphorus supply. As a result, increasing the investment will not make the plant grow better. The net uptake of carbon dioxide, and therefore, the plant's potential for growth, must be positive for the plant to survive. There is a broad span of investment where this is the case, and there is also a non-zero optimum. Plants investing more or less than this optimum will take up less carbon dioxide than an optimal plant, and hence growing less well. These plants will be at a selective disadvantage. At zero investment the growth is zero, because a non-carnivorous plant cannot survive in a habitat with absolutely no soil-borne nutrients. Such habitats do not exist, so for example, Sphagnum absorbs the tiny amounts of nitrates and phosphates in rain very efficiently and also forms symbioses with diazotrophic cyanobacteria.

text: Using this measure of investment in carnivory, a model can be proposed. Above is a graph of carbon dioxide uptake (potential for growth) against trap respiration (investment in carnivory) for a leaf in a sunny habitat containing no soil nutrients at all. Respiration is a straight line sloping down under the horizontal axis (respiration produces carbon dioxide). Gross photosynthesis is a curved line above the horizontal axis: as investment increases, so too does the photosynthesis of the trap, as the leaf receives a better supply of nitrogen and phosphorus. Eventually another factor (such as light intensity or

text: carbon dioxide

text: concentration) will become more limiting to photosynthesis than nitrogen or phosphorus supply. As a result, increasing the investment will not make the plant grow better. The net uptake of carbon dioxide, and therefore, the plant's potential for growth, must be positive for the plant to survive. There is a broad span of investment where this is the case, and there is also a non-zero

text: optimum

text: . Plants investing more or less than this optimum will take up less carbon dioxide than an optimal plant, and hence growing less well. These plants will be at a selective disadvantage. At zero investment the growth is zero, because a non-carnivorous plant cannot survive in a habitat with absolutely no soil-borne nutrients. Such habitats do not exist, so for example,

text: Sphagnum

text: absorbs the tiny amounts of nitrates and phosphates in rain very efficiently and also forms symbioses with diazotrophic

text: cyanobacteria

text: Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays. In 1913 Leonor Michaelis and Maud Leonora Menten proposed a quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics. The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis-Menten complex in their honor. The enzyme then catalyzes the chemical step in the reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane, who derived kinetic equations that are still widely used today.

text: Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from

text: enzyme assay

text: s. In 1913

text: Leonor Michaelis

text: and

text: Maud Leonora Menten

text: proposed a quantitative theory of enzyme kinetics, which is referred to as

text: Michaelis–Menten kinetics

text: . The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis-Menten complex in their honor. The enzyme then catalyzes the chemical step in the reaction and releases the product. This work was further developed by

text: G. E. Briggs

text: and

text: J. B. S. Haldane

text: , who derived kinetic equations that are still widely used today.

text: An amphibolic pathway is one that can be either catabolic or anabolic based on the availability of or the need for energy. The currency of energy in a biological cell is adenosine triphosphate (ATP), which stores its energy in the phosphoanhydride bonds. The energy is utilized to conduct biosynthesis, facilitate movement, and regulate active transport inside of the cell. Examples of amphibolic pathways are the citric acid cycle and the glyoxylate cycle. These sets of chemical reactions contain both energy producing and utilizing pathways. To the right is an illustration of the amphibolic properties of the TCA cycle.

text: An

text: amphibolic pathway

text: is one that can be either catabolic or anabolic based on the availability of or the need for energy. The currency of energy in a biological cell is

text: adenosine triphosphate (ATP)

text: , which stores its energy in the

text: phosphoanhydride bonds

text: . The energy is utilized to conduct biosynthesis, facilitate movement, and regulate active transport inside of the cell. Examples of amphibolic pathways are the citric acid cycle and the glyoxylate cycle. These sets of chemical reactions contain both energy producing and utilizing pathways. To the right is an illustration of the amphibolic properties of the TCA cycle.

text: Since both the oxidized and reduced forms of nicotinamide adenine dinucleotide are used in these linked sets of reactions, the cell maintains significant concentrations of both NAD and NADH, with the high NAD/NADH ratio allowing this coenzyme to act as both an oxidizing and a reducing agent. In contrast, the main function of NADPH is as a reducing agent in anabolism, with this coenzyme being involved in pathways such as fatty acid synthesis and photosynthesis. Since NADPH is needed to drive redox reactions as a strong reducing agent, the NADP/NADPH ratio is kept very low.

text: Since both the oxidized and reduced forms of nicotinamide adenine dinucleotide are used in these linked sets of reactions, the cell maintains significant concentrations of both NAD and NADH, with the high NAD/NADH ratio allowing this coenzyme to act as both an oxidizing and a reducing agent. In contrast, the main function of NADPH is as a reducing agent in

text: anabolism

text: , with this coenzyme being involved in pathways such as

text: fatty acid synthesis

text: and

text: photosynthesis

text: . Since NADPH is needed to drive redox reactions as a strong reducing agent, the NADP/NADPH ratio is kept very low.

text: Each metabolic pathway consists of a series of biochemical reactions that are connected by their intermediates: the products of one reaction are the substrates for subsequent reactions, and so on. Metabolic pathways are often considered to flow in one direction. Although all chemical reactions are technically reversible, conditions in the cell are often such that it is thermodynamically more favorable for flux to flow in one direction of a reaction. For example, one pathway may be responsible for the synthesis of a particular amino acid, but the breakdown of that amino acid may occur via a separate and distinct pathway. One example of an exception to this "rule" is the metabolism of glucose. Glycolysis results in the breakdown of glucose, but several reactions in the glycolysis pathway are reversible and participate in the re-synthesis of glucose (gluconeogenesis).

text: Each metabolic pathway consists of a series of biochemical reactions that are connected by their intermediates: the products of one reaction are the

text: substrates

text: for subsequent reactions, and so on. Metabolic pathways are often considered to flow in one direction. Although all chemical reactions are technically reversible, conditions in the cell are often such that it is

text: thermodynamically

text: more favorable for

text: flux

text: to flow in one direction of a reaction. For example, one pathway may be responsible for the synthesis of a particular amino acid, but the breakdown of that amino acid may occur via a separate and distinct pathway. One example of an exception to this "rule" is the metabolism of

text: glucose

text: Glycolysis

text: results in the breakdown of glucose, but several reactions in the glycolysis pathway are reversible and participate in the re-synthesis of glucose (

text: gluconeogenesis

text: In addition to his academic duties, Cameron also served as Chairman of the Fisheries Research Board of Canada from 1934–1947, a role for which he was awarded a C.M.G. in 1946. At various stages of his career, he was a Fellow of the Royal Society of Canada, the President of the Canadian Institute of Chemistry, an original member of the Biochemical Society, and Secretary for the Scientific Club of Winnipeg.

text: In addition to his academic duties, Cameron also served as Chairman of the Fisheries Research Board of Canada from 1934–1947, a role for which he was awarded a

text: C.M.G.

text: in 1946. At various stages of his career, he was a Fellow of the

text: Royal Society of Canada

text: , the President of the Canadian Institute of Chemistry, an original member of the

text: Biochemical Society

text: , and Secretary for the Scientific Club of Winnipeg.

text: If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.

text: If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-

text: keto acid

text: . Enzymes called

text: transaminase

text: s can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via

text: transamination

text: . The amino acids may then be linked together to make a protein.

text: Usually, in the presence of NADPH dehydrogenase or NADH dehydrogenase as the enzyme, NADPH or NADH is the reductant that converts resazurin to resorufin. Hence the resazurin/diaphorase/NADPH system can be used to detect NADH, NADPH, or diaphorase level, and any biochemical or enzyme activity that is involved in a biochemical reaction generating NADH or NADPH.

text: Usually, in the presence of

text: NADPH dehydrogenase

text: or

text: NADH dehydrogenase

text: as the enzyme,

text: NADPH

text: or

text: NADH

text: is the reductant that converts resazurin to resorufin. Hence the resazurin/diaphorase/NADPH system can be used to detect NADH, NADPH, or diaphorase level, and any biochemical or enzyme activity that is involved in a biochemical reaction generating NADH or NADPH.

text: Aldol condensations are important in organic synthesis, because they provide a good way to form carbon–carbon bonds. For example, the Robinson annulation reaction sequence features an aldol condensation; the Wieland-Miescher ketone product is an important starting material for many organic syntheses. Aldol condensations are also commonly discussed in university level organic chemistry classes as a good bond-forming reaction that demonstrates important reaction mechanisms.In its usual form, it involves the nucleophilic addition of a ketone enolate to an aldehyde to form a β-hydroxy ketone, or "aldol" (aldehyde + alcohol), a structural unit found in many naturally occurring molecules and pharmaceuticals.

text: Aldol condensations are important in

text: organic synthesis

text: , because they provide a good way to form

text: carbon–carbon bond

text: s. For example, the

text: Robinson annulation

text: reaction sequence features an aldol condensation; the

text: Wieland-Miescher ketone

text: product

text: is an important starting material for many organic syntheses. Aldol condensations are also commonly discussed in university level

text: organic chemistry

text: classes as a good bond-forming reaction that demonstrates important

text: reaction mechanism

text: s.In its usual form, it involves the

text: nucleophilic

text: addition of a

text: ketone

text: enolate

text: to an

text: aldehyde

text: to form a β-hydroxy ketone, or "aldol" (aldehyde + alcohol), a

text: structural

text: unit found in many naturally occurring

text: molecules

text: and

text: pharmaceuticals

text: tert-Butyl hydroperoxide is a common oxidant in the Sharpless epoxidation, which is used for the stereoselective synthesis of epoxides. Karl Barry Sharpless was awarded the 2001 Nobel prize in Chemistry for this reaction.

text: tert-Butyl hydroperoxide

text: is a common

text: oxidant

text: in the

text: Sharpless epoxidation

text: , which is used for the

text: stereoselective

text: synthesis of epoxides.

text: Karl Barry Sharpless

text: was awarded the 2001 Nobel prize in Chemistry for this reaction.

text: A catalyst is a substance that alters the rate of a chemical reaction but remains chemically unchanged afterwards. The catalyst increases the rate of the reaction by providing a different reaction mechanism to occur with a lower activation energy. In autocatalysis a reaction product is itself a catalyst for that reaction leading to positive feedback. Proteins that act as catalysts in biochemical reactions are called enzymes. Michaelis–Menten kinetics describe the rate of enzyme mediated reactions. A catalyst does not affect the position of the equilibrium, as the catalyst speeds up the backward and forward reactions equally.

text: A

text: catalyst

text: is a substance that alters the rate of a chemical reaction but remains

text: chemically

text: unchanged afterwards. The catalyst increases the rate of the reaction by providing a different

text: reaction mechanism

text: to occur with a lower

text: activation energy

text: . In

text: autocatalysis

text: a reaction product is itself a catalyst for that reaction leading to

text: positive feedback

text: . Proteins that act as catalysts in biochemical reactions are called

text: enzyme

text: s.

text: Michaelis–Menten kinetics

text: describe the

text: rate of enzyme mediated reactions

text: . A catalyst does not affect the position of the equilibrium, as the catalyst speeds up the backward and forward reactions equally.

text: Cellular respiration takes place in the cristae of the mitochondria within cells.  Depending on the pathways followed, the products are dealt with different ways.

text: Cellular respiration takes place in the

text: cristae

text: of the

text: mitochondria

text: within cells.  Depending on the pathways followed, the products are dealt with different ways.

text: In heterocyclic chemistry, organic reactions are classified by the type of heterocycle formed with respect to ring-size and type of heteroatom. See for instance the chemistry of indoles. Reactions are also categorized by the change in the carbon framework. Examples are ring expansion and ring contraction, homologation reactions, polymerization reactions, insertion reactions, ring-opening reactions and ring-closing reactions.

text: In

text: heterocyclic chemistry

text: , organic reactions are classified by the type of heterocycle formed with respect to ring-size and type of heteroatom. See for instance the chemistry of

text: indole

text: s. Reactions are also categorized by the change in the carbon framework. Examples are

text: ring expansion and ring contraction

text: homologation reaction

text: s,

text: polymerization reaction

text: s,

text: insertion reaction

text: s,

text: ring-opening reaction

text: s and

text: ring-closing reaction

text: s.

text:
Cortisone reductase deficiency is caused by dysregulation of the 11β-hydroxysteroid dehydrogenase type 1 enzyme (11β-HSD1), otherwise known as cortisone reductase, a bi-directional enzyme, which catalyzes the interconversion of cortisone to cortisol in the presence of NADH as a co-factor. If levels of NADH are low, the enzyme catalyses the reverse reaction, from cortisol to cortisone, using NAD+ as a co-factor.
Cortisol is a glucocorticoid that plays a variety of roles in many different biochemical pathways, including, but not limited to: gluconeogenesis, suppressing immune system responses and carbohydrate metabolism.
One of the symptoms of cortisone reductase deficiency is hyperandrogenism, resulting from activation of the Hypothalamic–pituitary–adrenal axis.The deficiency has been known to exhibit symptoms of other disorders such as Polycystic Ovary Syndrome in women. Cortisone Reductase Deficiency alone has been reported in fewer than ten cases in total, all but one case were women. Elevated activity of 11β-HSD1 can lead to obesity or Type II Diabetes, because of the role of cortisol in carbohydrate metabolism and gluconeogenesis.

text: Cortisone reductase deficiency is caused by dysregulation of the

text: 11β-hydroxysteroid dehydrogenase type 1

text: enzyme (11β-HSD1), otherwise known as

text: cortisone reductase

text: , a bi-directional enzyme, which catalyzes the interconversion of

text: cortisone

text: to

text: cortisol

text:
in the presence of NADH as a co-factor. If levels of NADH are low, the enzyme catalyses the reverse reaction, from cortisol to cortisone, using NAD+ as a co-factor.
Cortisol is a glucocorticoid that plays a variety of roles in many different biochemical pathways, including, but not limited to: gluconeogenesis, suppressing immune system responses and carbohydrate metabolism.
One of the symptoms of cortisone reductase deficiency is

text: hyperandrogenism

text: , resulting from activation of the

text: Hypothalamic–pituitary–adrenal axis

text: .The deficiency has been known to exhibit symptoms of other disorders such as

text: Polycystic Ovary Syndrome

text: in women. Cortisone Reductase Deficiency alone has been reported in fewer than ten cases in total, all but one case were women. Elevated activity of 11β-HSD1 can lead to obesity or Type II Diabetes, because of the role of cortisol in carbohydrate metabolism and gluconeogenesis.

text: The biochemical reactions that occur in living organisms are collectively known as metabolism. Among the most important of its mechanisms is the anabolism, in which different DNA and enzyme-controlled processes result in the production of large molecules such as proteins and carbohydrates from smaller units. Bioenergetics studies the sources of energy for such reactions. An important energy source is glucose, which can be produced by plants via photosynthesis or assimilated from food. All organisms use this energy to produce adenosine triphosphate (ATP), which can then be used to energize other reactions.

text: The biochemical reactions that occur in living organisms are collectively known as

text: metabolism

text: . Among the most important of its mechanisms is the

text: anabolism

text: , in which different

text: DNA

text: and enzyme-controlled processes result in the production of large molecules such as

text: protein

text: s and

text: carbohydrates

text: from smaller units.

text: Bioenergetics

text: studies the sources of energy for such reactions. An important energy source is

text: glucose

text: , which can be produced by plants via

text: photosynthesis

text: or assimilated from food. All organisms use this energy to produce

text: adenosine triphosphate

text: (ATP), which can then be used to energize other reactions.

text: Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes.

text: functional group

text: s. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes.

text: All four stay in a small home and the house owner Malaysia Vasudevan advises them to go for some job instead of following their dream so that they can earn some money and improve their living condition. He also scolds Ganesh for spending all the hard earned money for the sake of his friends. But Ganesh remains positive about his friends’ talent and believes that they will succeed one day in life.

text: Peter Walker Quote December 1975 technical paper in ‘Wireless World’ magazine

text: Young Stars Football Academy is a South African development association football club based in Pollack Park, Springs, Gauteng, that plays in the Eastern Springs Local Football Association League, the top flight of Springs development football.

text: Young Stars Football Academy is a

text: South African

text: development

text: association football

text: club based in Pollack Park,

text: Springs

text: , Gauteng, that plays in the

entity_section: Eastern Springs Local Football Association League

text: Eastern Springs Local Football Association League

text: , the top flight of Springs development football.

text: Hadratusy Syaikh KH.Hasyim Asy'ari (February 14, 1871July 25, 1947) was an Indonesian ulama and founder of Nahdatul Ulama.

text: Hadratusy Syaikh KH.Hasyim Asy'ari (February 14, 1871July 25, 1947) was an Indonesian

text: ulama

text: and founder of

text: Nahdatul Ulama

text: Films with live action and animation such as Disney's Mary Poppins, Pete's Dragon, Enchanted and the Robert Zemeckis film Who Framed Roger Rabbit are also fantasy films although are more often referred to as Live action/animation hybrids (2 of those are also classified as musicals).

text: Films with live action and animation

text: such as

text: Disney

text: 's

text: Mary Poppins

text: Pete's Dragon

text: Enchanted

text: and the

text: Robert Zemeckis

text: film

text: Who Framed Roger Rabbit

text: are also fantasy films although are more often referred to as Live action/animation hybrids (2 of those are also classified as musicals).

text: Aequorin is a photoprotein isolated from the bioluminescent jellyfish Aequorea victoria.  Upon addition of calcium ions (Ca2+) and coelenterazine, a reaction occurs whose end result is the generation of blue light in the 460 - 470 nm range.  Aequorin has been incorporated into human B cell lines for the detection of pathogenic bacteria and viruses in what is referred to as the Cell CANARY assay (Cellular Analysis and Notification of Antigen Risks and Yields).  The B cells are genetically engineered to produce aequorin.  Upon exposure to antigens of different pathogens, the recombinant B cells emit light as a result of activation of an intracellular signaling cascade that releases calcium ions inside the cell.

text: Aequorin

text: is a photoprotein isolated from the bioluminescent jellyfish

text: Aequorea victoria

text: .  Upon addition of

text: calcium

text: ions (Ca2+) and coelenterazine, a reaction occurs whose end result is the generation of blue light in the 460 - 470 nm range.  Aequorin has been incorporated into human

text: B cell

text: lines for the detection of

text: pathogenic

text: bacteria and viruses in what is referred to as the

text: Cell CANARY

text: assay (Cellular Analysis and Notification of Antigen Risks and Yields).  The B cells are genetically engineered to produce aequorin.  Upon exposure to antigens of different pathogens, the recombinant B cells emit light as a result of activation of an intracellular signaling cascade that releases calcium ions inside the cell.

text: Enjolras is featured in the Les Misérables stage musical. The musical omits much of the political background of the Friends of the ABC and the June Rebellion; it also presents Marius and Enjolras as being much closer friends than they are in the novel. Though many of the events at the barricade feature in the musical, Enjolras is often shown as dying while raising the red flag atop the barricade, a conflation of his death with the death of Mabeuf. In the 2012 film adaptation, his death is similar to that in the book.

text: Enjolras is featured in the

text: Les Misérables stage musical

text: . The musical omits much of the political background of the Friends of the ABC and the June Rebellion; it also presents Marius and Enjolras as being much closer friends than they are in the novel. Though many of the events at the barricade feature in the musical, Enjolras is often shown as dying while raising the red flag atop the barricade, a conflation of his death with the death of Mabeuf. In the

text: 2012 film adaptation

text: , his death is similar to that in the book.

text: 1 John 3:1

text: 1 John 3:1

text: He then linked up with Nigel Worthington during the final weeks of the 2006–07 season as assistant to Worthington in his role as caretaker manager of Leicester City. The pair steered Leicester to survival in the Football League Championship but were not rewarded with long term contracts and left the club.

text: He then linked up with

text: Nigel Worthington

text: during the final weeks of the

text: 2006–07 season

text: as assistant to Worthington in his role as caretaker manager of

text: Leicester City

text: . The pair steered Leicester to survival in the

text: Football League Championship

text: but were not rewarded with long term contracts and left the club.

text: Also, the provincial capitals of these provinces listed below(Guangzhou, Shenyang, Jinan, Hangzhou) are themselves sub-provincial cities (even before 1997 when Chongqing is a sub-provincial city of Sichuan province, since Chengdu is sub-provincial) except Fuzhou, Fujian.

text: These different types of social support have different patterns of correlations with health, personality, and personal relationships.  For example, perceived support is consistently linked to better mental health whereas received support and social integration are not. In fact, research indicates that perceived social support that is untapped can be more effective and beneficial than utilized social support. Some have suggested that invisible support, a form of support where the person has support without his or her awareness, may be the most beneficial. As of yet, there is no universally agreed upon definition of social support among researchers in the field, but these distinctions are all key in understanding what exactly researchers are examining in studies.

text: These different types of social support have different patterns of correlations with

text: health

text: personality

text: , and

text: personal relationships

text: .  For example, perceived support is consistently linked to better mental health whereas received support and social integration are not. In fact, research indicates that perceived social support that is untapped can be more effective and beneficial than utilized social support. Some have suggested that

text: invisible support

text: , a form of support where the person has support without his or her awareness, may be the most beneficial. As of yet, there is no universally agreed upon definition of social support among researchers in the field, but these distinctions are all key in understanding what exactly researchers are examining in studies.

text: HLCS (holocarboxylase synthetase (biotin-(propionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)) is a human gene that provides instructions for making an enzyme called holocarboxylase synthetase (). This enzyme is important for the effective use of biotin, a B vitamin found in foods such as liver, egg yolks, and milk. In many of the body's tissues, holocarboxylase synthetase activates other specific enzymes (called biotin-dependent carboxylases) by attaching biotin to them. These carboxylases are involved in many critical cellular functions, including the production and breakdown of proteins, fats, and carbohydrates.

text: HLCS (holocarboxylase synthetase (biotin-(propionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)) is a

text: human

text: gene

text: that provides instructions for making an enzyme called holocarboxylase synthetase (). This enzyme is important for the effective use of

text: biotin

text: , a B vitamin found in foods such as

text: liver

text: egg yolk

text: s, and

text: milk

text: . In many of the body's tissues, holocarboxylase synthetase activates other specific enzymes (called biotin-dependent carboxylases) by attaching biotin to them. These carboxylases are involved in many critical cellular functions, including the production and breakdown of proteins, fats, and carbohydrates.

text: Before the correlation between fold type and reaction correlation of proteins were understood, Harmon C. Dunathan, a chemist at Haverford College proposed that the bond that is cleaved using pyridoxal is perpendicular to the system. Though an important concept in bioorganic chemistry, it is now known that enzyme conformations play a critical role in the final chemical reaction.

text: Before the correlation between fold type and reaction correlation of

text: proteins

text: were understood, Harmon C. Dunathan, a

text: chemist

text: at

text: Haverford College

text: proposed that the bond that is cleaved using

text: pyridoxal

text: is perpendicular to the system. Though an important concept in

text: bioorganic chemistry

text: , it is now known that enzyme conformations play a critical role in the final chemical reaction.

text: Cells use the monomers released from breaking down polymers to either construct new polymer molecules, or degrade the monomers further to simple waste products, releasing energy. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia, and urea. The creation of these wastes is usually an oxidation process involving a release of chemical free energy, some of which is lost as heat, but the rest of which is used to drive the synthesis of adenosine triphosphate (ATP). This molecule acts as a way for the cell to transfer the energy released by catabolism to the energy-requiring reactions that make up anabolism. (Catabolism is seen as destructive metabolism and anabolism as constructive metabolism). Catabolism therefore provides the chemical energy necessary for the maintenance and growth of cells. Examples of catabolic processes include glycolysis, the citric acid cycle, the breakdown of muscle protein in order to use amino acids as substrates for gluconeogenesis, the breakdown of fat in adipose tissue to fatty acids, and oxidative deamination of neurotransmitters by monoamine oxidase.

text: Cells use the monomers released from breaking down polymers to either construct new polymer molecules, or degrade the monomers further to simple waste products, releasing energy. Cellular wastes include

text: lactic acid

text: acetic acid

text: carbon dioxide

text: ammonia

text: , and

text: urea

text: . The creation of these wastes is usually an

text: oxidation

text: process involving a release of chemical free energy, some of which is lost as

text: heat

text: , but the rest of which is used to drive the synthesis of

text: adenosine triphosphate

text: (ATP). This molecule acts as a way for the cell to transfer the energy released by catabolism to the energy-requiring reactions that make up

text: anabolism

text: . (Catabolism is seen as destructive

text: metabolism

text: and anabolism as constructive metabolism). Catabolism therefore provides the chemical energy necessary for the maintenance and growth of cells. Examples of catabolic processes include

text: glycolysis

text: , the

text: citric acid cycle

text: , the breakdown of muscle protein in order to use amino acids as

text: substrate

text: s for

text: gluconeogenesis

text: , the breakdown of

text: fat

text: in

text: adipose tissue

text: to

text: fatty acid

text: s, and

text: oxidative deamination

text: of neurotransmitters by

text: monoamine oxidase

text: Piano ballads have been written since the 19th century; several have been composed in the 20th century (see below).

text: After moving Washington, D.C. in 1977, Barton was hired as an arts administrator at the Glen Echo Park Arts Center. The Writers’ Center, a resident organization formed by graduates of Visual Studies Workshop in Rochester, New York, presented Barton’s first exposure to the book arts. When The Writers’ Center received a grant from the National Endowment for the Arts to produce twenty artists’ books, Barton was invited as a participant in the project. She welcomed the opportunity to explore the book form as an artistic medium.

text: After moving

text: Washington, D.C.

text: in 1977, Barton was hired as an arts administrator at the Glen Echo Park Arts Center. The Writers’ Center, a resident organization formed by graduates of

text: Visual Studies Workshop

text: in

text: Rochester

text: New York

text: , presented Barton’s first exposure to the book arts. When The Writers’ Center received a grant from the

text: National Endowment for the Arts

text: to produce twenty artists’ books, Barton was invited as a participant in the project. She welcomed the opportunity to explore the book form as an artistic medium.

text: DNA is the seventh studio album by the American rock band Trapt, released on August 19, 2016. The album's recording was partly funded by a 2014 campaign on Indiegogo. The band was originally set to release the album in 2015. Best Buy offered a Limited Edition, which included the 2 bonus track "Panic Room" and "Chasing Highs", as well as the front cover of the insert sleeve being autographed by the band.

text: There is also a specificity element of biochemical interactions to create synaptic plasticity, namely the importance of location. Processes occur at microdomains – such as exocytosis of AMPA receptors is spatially regulated by the t-SNARE STX4.Specificity is also an important aspect of CAMKII signaling involving nanodomain calcium.The spatial gradient of PKA between dendritic spines and shafts is also important for the strength and regulation of synaptic plasticity.  It is important to remember that the biochemical mechanisms altering synaptic plasticity occur at the level of individual synapses of a neuron.  Since the biochemical mechanisms are confined to these "microdomains," the resulting synaptic plasticity affects only the specific synapse at which it took place.

text: There is also a specificity element of biochemical interactions to create synaptic plasticity, namely the importance of location. Processes occur at microdomains – such as

text: exocytosis

text: of AMPA receptors is spatially regulated by the

text: t-SNARE

text: .Specificity is also an important aspect of CAMKII signaling involving nanodomain calcium.The spatial gradient of PKA between dendritic spines and shafts is also important for the strength and regulation of synaptic plasticity.  It is important to remember that the biochemical mechanisms altering synaptic plasticity occur at the level of individual synapses of a neuron.  Since the biochemical mechanisms are confined to these "microdomains," the resulting synaptic plasticity affects only the specific synapse at which it took place.

text: -2-amino-4-pentynoic acid (0.257% w/w); and

text: -2-amino-4-pentynoic acid (0.257%

text: w/w

text: ); and

text: Hill reaction of photosynthesis was discovered by Robin Hill (1937). He found that isolated chloroplasts from plants can release oxygen when they are illuminated by sunlight in the presence of a suitable electron acceptor such as ferricyanide. To demonstrate the Hill reaction in the laboratory dichlorophenolindophenol (DCPIP) was used as the terminal electron acceptor, replacing NADP which was not available due to the extraction of the chloroplasts from the plant cellular environment. The ferrocyanide is reduced (just as NADP is when the chloroplast is in vivo) while water (HO) is oxidized into oxygen (O) and hydrogen cations during the reaction. By using this technique to observe the reaction, Hill revealed a variety of valuable facts about photosynthesis. The Hill reaction confirms that oxygen (O) is produced by a reaction that is separate from carbon dioxide (CO) fixation.  The reaction in which oxygen is released requires light; therefore the Hill reaction can be described as the light dependent reaction of photosynthesis. The reaction in which oxygen is released takes place within the chloroplast of plants and the Hill reaction demonstrated that the release of oxygen (O) is only a partial reaction which requires one step of photosynthesis.

text: Hill reaction of photosynthesis was discovered by

text: Robin Hill

text: (1937). He found that isolated chloroplasts from

text: plant

text: s can release oxygen when they are illuminated by sunlight in the presence of a suitable

text: electron acceptor

text: such as

text: ferricyanide

text: . To demonstrate the Hill reaction in the laboratory

text: dichlorophenolindophenol

text: (DCPIP) was used as the terminal electron acceptor, replacing NADP which was not available due to the extraction of the chloroplasts from the plant cellular environment. The ferrocyanide is reduced (just as NADP is when the chloroplast is in vivo) while water (HO) is oxidized into oxygen (O) and hydrogen cations during the reaction. By using this technique to observe the reaction, Hill revealed a variety of valuable facts about photosynthesis. The Hill reaction confirms that oxygen (O) is produced by a reaction that is separate from carbon dioxide (CO) fixation.  The reaction in which oxygen is released requires light; therefore the Hill reaction can be described as the

text: light dependent reaction

text: of photosynthesis. The reaction in which oxygen is released takes place within the chloroplast of plants and the Hill reaction demonstrated that the release of oxygen (O) is only a partial reaction which requires one step of photosynthesis.

text: Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.

text: Classically, metabolism is studied by a

text: reductionist

text: approach that focuses on a single metabolic pathway. Particularly valuable is the use of

text: radioactive tracer

text: s at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be

text: purified

text: and their

text: kinetics

text: and responses to

text: inhibitors

text: investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the

text: metabolome

text: . Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.

text: ALOX12 is also distinguished from arachidonate 12-lipoxygenase, 12R type (ALOX12B), which metabolizes arachidonic acid to the R stereoisomer of 12(S)-HpETE viz., 12(R)-hydroperoxy-5Z,8Z,10E,14Z-icosatetraenoic acid (12(R)-HpETE), a product with very different pathophysiological roles than that of 12(S)-HpETE (see ALOX12B).

text: ALOX12 is also distinguished from arachidonate 12-lipoxygenase, 12R type (ALOX12B), which metabolizes arachidonic acid to the R

text: stereoisomer

text: of 12(S)-HpETE viz., 12(R)-hydroperoxy-5Z,8Z,10E,14Z-icosatetraenoic acid (12(R)-HpETE), a product with very different pathophysiological roles than that of 12(S)-HpETE (see

text: Factors that affect an enzyme-mediated chemical reaction would naturally affect a ligation reaction, such as the concentration of enzyme and the reactants, as well as the temperature of reaction and the length of time of incubation.  Ligation is complicated by the fact that the desired ligation products for most ligation reactions should be between two different DNA molecules and the reaction involves both inter- and intra-molecular reactions, and that an additional annealing step is necessary for efficient ligation.