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

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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).

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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.

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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."

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."

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answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: Digestion breaks the proteins down

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answers: Digestion breaks the proteins down for use in the metabolism

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answers: Digestion breaks the proteins down

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

text: lyase

text: , that

text: catalyzes

text: a

text: chemical reaction

text: to form a

text: cyclic compound

text: . Important cyclase enzymes include:

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answers: form a cyclic compound

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answers: catalyzes

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answers: photosynthesis

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answers: Cellular respiration

answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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

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

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 "

text: zymase

text: ". In 1907 he received the

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

text: substrate

text: (e.g.,

text: lactase

text: is the enzyme that cleaves

text: lactose

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

text: DNA polymerase

text: forms DNA polymers).

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answers: yeast cells

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answers: yeast cells

answers: NDQ_016287

answers: yeast extracts

answers: NDQ_016289

answers: cell-free fermentation

answers: NDQ_016290

answers: cell-free fermentation

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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

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

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

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.

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answers: produce sucrose

answers: NDQ_016285

answers: produce sucrose

answers: NDQ_016287

answers: no

answers: NDQ_016289

answers: It's impossible to say

answers: NDQ_016290

answers: photosynthesis

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

text: biochemical

text: process in which plants,

text: alga

text: e, and some

text: bacteria

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

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

text: protein synthesis

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

text: oxygen

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

text: photoautotroph

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

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answers: convert sunlight to chemical energy

answers: NDQ_016285

answers: protein synthesis

answers: NDQ_016287

answers: sunlight

answers: NDQ_016289

answers: protein synthesis

answers: NDQ_016290

answers: The chemical energy is used to drive reactions

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

text: metastable

text: nuclear isomer) is used in radioactive isotope

text: medical tests

text: .  For example Technetium-99m is a

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

text: keV

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

text: radiopharmaceuticals

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

text: brain

text: , heart muscle,

text: thyroid

text: lungs

text: liver

text: gall bladder

text: kidney

text: s,

text: skeleton

text: blood

text: , and

text: tumor

text: s.

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answers: metabolized

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answers: metabolized

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answers: Technetium-99m

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answers: It is well suited to the role because it emits readily detectable

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

text: acetyl

text: group to the

text: citric acid cycle

text: (Krebs cycle) to be

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).

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answers: oxidized for energy production

answers: NDQ_016285

answers: energy production

answers: NDQ_016287

answers: The acetyl group

answers: NDQ_016289

answers: The acetyl group

answers: NDQ_016290

answers: oxidized for energy production

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: protein-protein interaction

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answers: enzyme-substrate interaction

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answers: Generic biochemical reaction

answers: NDQ_016290

answers: enzyme-substrate interaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: NDQ_016284

answers: generate energy for the cell

answers: NDQ_016285

answers: generate energy

answers: NDQ_016287

answers: aerobic respiration

answers: NDQ_016289

answers: aerobic respiration

answers: NDQ_016290

answers: A series of processes and reactions that generate energy for the cell

answer: No

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: biochemical experiments

answers: NDQ_016285

answers: enzyme kinetics

answers: NDQ_016287

answers: Spectrophotometry

answers: NDQ_016289

answers: It is an inexpensive and relatively simple process

answers: NDQ_016290

answers: enzyme kinetics and biochemical analyses

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: 4: The answer has limited relevance and completeness, with noticeable gaps or inaccuracy.

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answers: peroxidases

answers: NDQ_016285

answers: peroxidase reactions

answers: NDQ_016287

answers: Peroxisomes

answers: NDQ_016289

answers: enzymes

answers: NDQ_016290

answers: Peroxisomes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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: 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.

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answers: Biochemical Technology

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answers: Biochemical Technology

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answers: Biochemical Technology

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answers: Biochemical Technology

answers: NDQ_016290

answers: Biochemical Technology

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: photosynthesis

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answers: respiration

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answers: P: R> 1

answers: NDQ_016290

answers: respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: enzymes

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answers: enzymes are protein catalysts

answers: NDQ_016287

answers: Enzymes

answers: NDQ_016289

answers: Enzymes are protein catalysts

answers: NDQ_016290

answers: Enzymes are protein catalysts

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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).

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answers: breaks down molecules into smaller units

answers: NDQ_016285

answers: breaks down large molecules

answers: NDQ_016287

answers: Catabolism

answers: NDQ_016289

answers: Catabolism

answers: NDQ_016290

answers: Catabolism

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: yeast

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answers: yeast

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answers: non-cellular fermentation

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: biochemical

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answers: biochemical

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answers: Luminescence

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answers: Luminescence

answers: NDQ_016290

answers: Luminescence

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: remove methyl (CH-) groups from nucleic acids

answers: NDQ_016285

answers: Demethylases

answers: NDQ_016287

answers: Demethylases

answers: NDQ_016289

answers: Demethylases

answers: NDQ_016290

answers: Demethylases

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

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answers: Protein function is a broad term

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answers: Biochemical reactions to transport to signal transduction

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: Nutrients

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answers: Nutrients

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answers: oxygen (O)

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answers: Biosynthesis

answers: NDQ_016290

answers: transferring energy for use by the cell

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: consume carbon dioxide

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answers: consume carbon dioxide but do not release oxygen

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answers: carbon dioxide

answers: NDQ_016289

answers: no

answers: NDQ_016290

answers: oxygenic photosynthesis

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: conversion from a substrate to a product

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answers: catalyzes

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answers: substrate

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answers: photosynthesis

answers: NDQ_016290

answers: cellular respiration

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: oxidizing nutrients and releasing waste products

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answers: obtains energy

answers: NDQ_016287

answers: ATP

answers: NDQ_016289

answers: cellular respiration

answers: NDQ_016290

answers: oxidizing nutrients and releasing waste products

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: cellular respiration

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answers: consume this oxygen through cellular respiration

answers: NDQ_016287

answers: macroalgae

answers: NDQ_016289

answers: Phytoplankton

answers: NDQ_016290

answers: Consume this oxygen through cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: carbohydrate chemistry

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answers: Glycosylation reactions

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answers: OH

answers: NDQ_016289

answers: Glycosylation reactions

answers: NDQ_016290

answers: Glycosylation reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: require significantly more energy

answers: NDQ_016285

answers: allowed if the electronic barrier is low

answers: NDQ_016287

answers: Woodward–Hoffmann rules

answers: NDQ_016289

answers: Forbidden reactions can still take place but require significantly more energy

answers: NDQ_016290

answers: Woodward–Hoffmann rules

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: light energy captured by the photosystems

answers: NDQ_016285

answers: light-driven reduction

answers: NDQ_016287

answers: oxygen

answers: NDQ_016289

answers: The water-splitting reaction

answers: NDQ_016290

answers: This oxidation of water conveniently produces the waste product O that is vital for cellular respiration

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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).

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answers: hydrolysis

answers: NDQ_016285

answers: hydrolysis of proteins, fats, oils, and carbohydrates

answers: NDQ_016287

answers: ATP hydrolysis

answers: NDQ_016289

answers: photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: ATP hydrolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: strip electrons

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answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: Metabolism

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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."

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answer: Yes

answer: Yes

answer: Yes

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answer: 1

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

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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: 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.

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answer: No

answer: Yes

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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."

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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

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answers: redox reactions

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answers: take place in an electrochemical cell

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answers: true organic redox

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answers: True organic redox

answers: NDQ_016290

answers: Cellular respiration

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: absorb nutrients from the environment

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answers: absorb nutrients from the environment

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answers: Oxygen and water

answers: NDQ_016289

answers: Heterotrophs with more complex biochemical reactions

answers: NDQ_016290

answers: Heterotrophs

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

text: catabolic intermediates:

text: catabolic intermediates:

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answers: metabolize

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answers: are chemical reactions in living things that

answers: NDQ_016287

answers: oxygen and water

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answers: catabolic intermediates

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answers: cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: absorb light energy

answers: NDQ_016285

answers: absorbs a photon

answers: NDQ_016287

answers: Oxygen

answers: NDQ_016289

answers: In anoxygenic photosynthesis

answers: NDQ_016290

answers: electron acceptor

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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+.

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answers: reduced to NADH

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answers: anabolic pathways

answers: NDQ_016287

answers: NAD+

answers: NDQ_016289

answers: Anabolism

answers: NDQ_016290

answers: catabolism

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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

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answers: beta-oxidation

answers: NDQ_016289

answers: The mechanism of beta-oxidation

answers: NDQ_016290

answers: beta-oxidation

answer: No

answer: No

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: amphetamine

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answers: increase amino acid catabolism

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answers: The metabolism of glucose and insulin are also influenced

answers: NDQ_016289

answers: catabolism

answers: NDQ_016290

answers: amino acid catabolism

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: Yes

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: Gluconeogenesis

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answers: Gluconeogenesis

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answers: Gluconeogenesis

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answers: glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: interfering with native biochemical processes

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answers: bioorthogonal chemistry

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answers: bioorthogonal chemistry

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answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: elimination reactions

answers: NDQ_016285

answers: Alkylimino-de-oxo

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answers: nitrogen to oxygen

answers: NDQ_016289

answers: Alkylimino-de-oxo-bisubstitution

answers: NDQ_016290

answers: Alkylimino-de-oxo-bisubstitution

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: catabolism

answers: NDQ_016287

answers: cellular respiration

answers: NDQ_016289

answers: C4 photosynthesis

answers: NDQ_016290

answers: cellular respiration

answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: proteins/enzymes

answers: NDQ_016287

answers: biochemical reactions

answers: NDQ_016289

answers: protein biosynthesis

answers: NDQ_016290

answers: protein biosynthesis

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: biochemical pathways

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answers: greatly increases the energetic favorability

answers: NDQ_016287

answers: PPi to two phosphate ions

answers: NDQ_016289

answers: greatly increases the energetic favorability

answers: NDQ_016290

answers: hydrolysis of inorganic pyrophosphate (PPi) to two phosphate ions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: contain heterocycles

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answers: enantiomeric

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answers: oxygen and water

answers: NDQ_016289

answers: enantiomeric excesses

answers: NDQ_016290

answers: catabolic

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: cellular respiration

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answers: cellular respiration

answers: NDQ_016287

answers: It is affected by the amount and angle of solar radiation

answers: NDQ_016289

answers: Gross photosynthesis exponentially decays

answers: NDQ_016290

answers: The net growth rate equals the gross photosynthetic rate minus loss terms

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: multicomponent reactions

answers: NDQ_016285

answers: multicomponent reactions

answers: NDQ_016287

answers: Ugi reaction

answers: NDQ_016289

answers: Ugi reaction

answers: NDQ_016290

answers: Ugi reaction

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: phosphate dehydrogenase

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answers: 6-phosphate dehydrogenase

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answers: NDQ_016284

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answers: oxidation

answers: NDQ_016285

answers: Cortisone reductase

answers: NDQ_016287

answers: Cortisone reductase

answers: NDQ_016289

answers: cortisone

answers: NDQ_016290

answers: Cortisone

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: carbon fixation

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answers: synthesise polymers

answers: NDQ_016287

answers: carbon dioxide

answers: NDQ_016289

answers: Carbon fixation

answers: NDQ_016290

answers: photorespiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

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answers: biochemical reactions

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answers: biochemical reactions related to plant and animal growth

answers: NDQ_016290

answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: consumes glucose

answers: NDQ_016285

answers: produces ATP, NADH and pyruvate

answers: NDQ_016287

answers: This catabolic pathway consumes glucose

answers: NDQ_016289

answers: This catabolic pathway consumes glucose and produces ATP

answers: NDQ_016290

answers: glycolysis

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: catalyses

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answers: oxygen and water

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answers: photosynthesis

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answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answer: No

answer: Yes

answer: No

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answer: No

answer: 1

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

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answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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:

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answers: photosynthesis

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answers: oxidize carbohydrates

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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

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answers: catalyzes

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answers: formate-C-acetyltransferase

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answers: Oxygen and water

answers: NDQ_016289

answers: Photosynthesis is an anabolic reaction.

answers: NDQ_016290

answers: Cellular respiration is a catabolic reaction.

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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).

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answers: For chemistry problems involving chemical reactions

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answers: recombination of a fixed number of atoms

answers: NDQ_016290

answers: chemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: consume it

answers: NDQ_016285

answers: Metabolism

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: Metabolism

answers: NDQ_016290

answers: Metabolism

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: convert raw materials into molecules

answers: NDQ_016285

answers: cells to convert raw materials into molecules necessary for the cell’s survival

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: Metabolic engineering

answers: NDQ_016290

answers: cells to convert raw materials into molecules

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: Yes

answer: 1

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.

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracy.

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answers: Photosynthesis is an anabolic reaction.

answers: NDQ_016290

answers: Cellular respiration is a catabolic reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: Fructokinase

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answers: Fructokinase

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

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answers: thiol

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answers: Oxygen

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answers: photosynthesis

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answers: Cellular respiration

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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

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answers: respond to foods and other environmental factors

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answers: oxygen and water

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answers: Heritable (genetic) differences among humans

answers: NDQ_016290

answers: Biochemical Individuality

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

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answers: produce carbohydrates and oxygen

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answers: carbohydrates and oxygen

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answers: carbohydrates and oxygen

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answers: cellular respiration is a catabolic reaction

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: in vivo

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answers: in vivo

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answers: oxygen and water

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answers: photosynthesis

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answers: metabolism

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: autophosphorylation

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answers: autophosphorylation

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answers: NDQ_016289

answers: It's believed to be involved in the photosynthesis process and the oxidative stress management

answers: NDQ_016290

answers: autophosphorylation activity takes place from ATP

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: enzyme reactions

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answers: enzyme reactions

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: enzyme reactions

answers: NDQ_016290

answers: enzyme reactions

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: consume

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answers: produce polysaccharides

answers: NDQ_016287

answers: nucleotide sugar

answers: NDQ_016289

answers: glycosylation reactions

answers: NDQ_016290

answers: glycolysis reactions

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: 5: The answer is highly relevant, complete, and accurate.

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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.

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answers: "damaging chemical reactions"

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answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: fix carbon dioxide and nitrogen

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answers: fix carbon dioxide and nitrogen

answers: NDQ_016287

answers: Carbon dioxide and nitrogen

answers: NDQ_016289

answers: Metabolism

answers: NDQ_016290

answers: anaeobic metabolism

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: Bioenergetics

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answers: ATP molecules

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answers: Bioenergetics

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answers: metabolic processes

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: oxidize

answers: NDQ_016285

answers: Oxidative phosphorylation

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answers: ROS

answers: NDQ_016289

answers: Fatty acids are preferentially oxidized

answers: NDQ_016290

answers: Fatty acids are preferentially oxidized

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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

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answers: cellular respiration

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answers: aerobic organisms

answers: NDQ_016287

answers: Oxygen

answers: NDQ_016289

answers: They gain the energy needed for this reaction from absorption of sunlight

answers: NDQ_016290

answers: Carbon dioxide is produced by various microorganisms from fermentation

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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).

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracies.

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answers: NDQ_016284

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answers: biocatalysis

answers: NDQ_016285

answers: steroid synthesis

answers: NDQ_016287

answers: Oxidoreductases

answers: NDQ_016289

answers: The International Union of Biochemistry and Molecular Biology (IUBMB) has developed a classification for enzymes

answers: NDQ_016290

answers: enzymes are used in the synthesis

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: Catabolic reactions

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

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answers: regulates

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answers: Free radicals

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answers: Biochemical reactions

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answers: Biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: ribozyme

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answers: catalysis

answers: NDQ_016287

answers: Catalysis

answers: NDQ_016289

answers: catalysis

answers: NDQ_016290

answers: catalysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: Bioorthogonal

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answers: Bioorthogonal

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answers: Oxygen and water

answers: NDQ_016289

answers: Bioorthogonal chemistry

answers: NDQ_016290

answers: Bioorthogonal chemistry

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: biosynthetic

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answers: biosynthetic reactions

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answers: CO and NADPH

answers: NDQ_016289

answers: NADPH is consumed during biosynthetic reactions

answers: NDQ_016290

answers: oxidative decarboxylation

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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:

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answers: oxidation

answers: NDQ_016285

answers: oxidation

answers: NDQ_016287

answers: CO and water

answers: NDQ_016289

answers: Cellular respiration

answers: NDQ_016290

answers: oxidation of glucose to CO and the reduction of oxygen to water

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: metabolism

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answers: metabolism

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answers: Oxygen

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answers: metabolism

answers: NDQ_016290

answers: metabolism

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: CAM

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answers: CAM

answers: NDQ_016289

answers: obligate CAM plants

answers: NDQ_016290

answers: CAM

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: respiration

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answers: primary production

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answers: water

answers: NDQ_016289

answers: Oxygen production

answers: NDQ_016290

answers: Oxygen consumption

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: 0: The answer is not relevant or complete at all.

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answers: 4

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answers: breaks down fatty acids

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answers: no

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answers: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: Biochemical

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answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

text: Chemiluminescent reactions

text: are widely used in

text: analytical chemistry

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answers: catabolic reactions

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answers: Chemiluminescent

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answers: Oxygen and water

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answers: [14, 15]

answers: NDQ_016290

answers: cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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:

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answers: cellular respiration

answers: NDQ_016285

answers: photosynthesis

answers: NDQ_016287

answers: Oxygen and water are the reactants of photosynthesis

answers: NDQ_016289

answers: Photosynthesis is an anabolic reaction.

answers: NDQ_016290

answers: cellular respiration is a catabolic reaction

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biosynthetic reactions

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answers: biosynthetic reactions

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answers: photophosphorylation

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answers: photophosphorylation

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answers: aerobic respiration

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: enzyme-catalyzed

answers: NDQ_016285

answers: Metabolism

answers: NDQ_016287

answers: Metabolism

answers: NDQ_016289

answers: Metabolism

answers: NDQ_016290

answers: enzyme-catalyzed reactions

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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: 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.

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answers: respiration

answers: NDQ_016285

answers: respiration

answers: NDQ_016287

answers: respiration

answers: NDQ_016289

answers: It is also lower in the winter seasons

answers: NDQ_016290

answers: respiration of phytoplankton

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: biochemical reaction

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answers: The Gray/Winkler group

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answers: ET

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answers: ET

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: alkylation reactions

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answers: alkylation

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answers: photosynthesis

answers: NDQ_016289

answers: photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: NDQ_016287

answers: RuBisCO

answers: NDQ_016289

answers: RuBisCO reaction

answers: NDQ_016290

answers: photosynthesis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: respiration

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answers: BOD

answers: NDQ_016289

answers: photosynthesis and respiration

answers: NDQ_016290

answers: Yes

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: NDQ_016284

answers: carbon dioxide (CO)

answers: NDQ_016285

answers: carbon fixation

answers: NDQ_016287

answers: sunlight

answers: NDQ_016289

answers: Carbon-fixation reaction

answers: NDQ_016290

answers: Carbon-fixation

answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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

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answers: biopolymers

answers: NDQ_016285

answers: catalyze a reaction

answers: NDQ_016287

answers: Enzymes are biological catalysts

answers: NDQ_016289

answers: Enzymes are biological catalysts

answers: NDQ_016290

answers: Enzymes are biological catalysts

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: hydrolysis reaction

answers: NDQ_016287

answers: A zymogen

answers: NDQ_016289

answers: A zymogen

answers: NDQ_016290

answers: hydrolysis reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: N- glycosylase

answers: NDQ_016285

answers: AP lyases

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: UV endonuclease

answers: NDQ_016290

answers: -elimination

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: respiration

answers: NDQ_016287

answers: respiration

answers: NDQ_016289

answers: energy stored by photosynthesis in plants

answers: NDQ_016290

answers: Respiration, or R

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: The dynamic nature of biochemistry

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answers: fermentation and respiration

answer: Yes

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: Click chemistry must run at or near biological conditions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracy.

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answers: catalyze

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answers: Anabolic reactions

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answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: Enzyme

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answers: Biochemical Society

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: Enzyme Chemistry

answers: NDQ_016290

answers: Enzyme Chemistry

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: produces the valuable byproducts

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answers: pyruvate

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answers: In aerobic conditions

answers: NDQ_016290

answers: -D-glucose-1-phosphate

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: glycogenolysis and gluconeogenesis

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: 0

answers: NDQ_016284

answers: Degradation

answers: NDQ_016285

answers: Nucleotide synthesis

answers: NDQ_016287

answers: Nucleic acids

answers: NDQ_016289

answers: No

answers: NDQ_016290

answers: Degradation

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: 4

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answers: Consumption

answers: NDQ_016285

answers: photosynthesis

answers: NDQ_016287

answers: respiration

answers: NDQ_016289

answers: This prevents the penetration of sunlight

answers: NDQ_016290

answers: Consumption

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 0

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.

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answers: make

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answers: make

answers: NDQ_016287

answers: enzymes

answers: NDQ_016289

answers: no metabolic function

answers: NDQ_016290

answers: no metabolic function

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: elimination reactions

answers: NDQ_016285

answers: Organic reactions

answers: NDQ_016287

answers: organic compounds

answers: NDQ_016289

answers: Organic reactions are chemical reactions involving organic compounds

answers: NDQ_016290

answers: Organic reactions are chemical reactions involving organic compounds

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: nucleophilic

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answers: It is possible in many cases to run the reaction in water

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answers: It is possible in many cases to run the reaction in water

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: Biological energy

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answers: Biological energy

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answers: carbon dioxide

answers: NDQ_016289

answers: Biological energy is frequently stored and released

answers: NDQ_016290

answers: redox reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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

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answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: It is an anabolic reaction

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answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: consumes

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answers: provides (S)-malate and formate

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answers: carbon fixation

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answers: (S)-malate

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answers: (S)-malate and formate

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: biochemical reaction networks

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answers: biochemical reaction networks

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: The reactions involved in respiration are catabolic reactions

answers: NDQ_016290

answers: The reactions involved in respiration are catabolic reactions

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: carbon fixation

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answers: take place

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answers: carbon

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answers: Carbon fixation

answers: NDQ_016290

answers: carbon fixation

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: biochemical

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answers: oxygen and water

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answers: Biochemical

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answers: Catabolic reactions

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: carbon dioxide

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answers: Carbon dioxide is converted into sugars

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answers: Carbon dioxide is converted into sugars

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: denature

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answers: catalysed reactions

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answers: enzyme-catalysed reactions

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answers: Enzymes

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answers: Enzymes

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: substrate

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answers: anabolic reactions

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answers: substrate

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answers: How quickly the enzyme becomes saturated

answers: NDQ_016290

answers: catabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: produced from other compounds

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answers: produced from other compounds

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answers: Oxygen and water

answers: NDQ_016289

answers: Amino acid synthesis

answers: NDQ_016290

answers: Amino acid synthesis

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: 0

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracies.

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answers: oxygen and water

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answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: biochemical

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answers: Van’t Hoff relationship

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answers: Van’t Hoff relationship for monomolecular reactions

answers: NDQ_016290

answers: biochemical and physiological processes

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: Biochemical

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answers: Biochemical oxygen demand

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answers: Oxygen

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answers: Biochemical oxygen demand

answers: NDQ_016290

answers: Biochemical oxygen demand

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: catalyzed by enzymes

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answer: Yes

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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

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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.

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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:

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracies.

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answers: oxygen and water

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answers: photosynthesis

answers: NDQ_016290

answers: Cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: NDQ_016284

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answers: catalyses

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answers: catalyses

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answers: oxygen and water

answers: NDQ_016289

answers: Thermopsin

answers: NDQ_016290

answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: glycolysis

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answers: generates adenosine triphosphate

answers: NDQ_016287

answers: pyruvate dehydrogenase

answers: NDQ_016289

answers: PDH links glycolysis to the citric acid cycle

answers: NDQ_016290

answers: glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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: 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.

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answers: lose fluids

answers: NDQ_016285

answers: return to life by rapidly rehydrating in wet periods

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: biochemically inactive

answers: NDQ_016290

answers: loss of fluids

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: protein enzymes

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answers: protein enzymes

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answers: catalyze specific biochemical reactions

answers: NDQ_016289

answers: catalyze specific biochemical reactions

answers: NDQ_016290

answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: catalyzes

answers: NDQ_016285

answers: catalyze

answers: NDQ_016287

answers: Citric acid cycle

answers: NDQ_016289

answers: non competitive feedback inhibition

answers: NDQ_016290

answers: cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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

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answers: photosynthesis

answers: NDQ_016285

answers: photosynthetic

answers: NDQ_016287

answers: Förster resonance energy transfer

answers: NDQ_016289

answers: It is used by plants

answers: NDQ_016290

answers: Catabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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).

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answers: produce sugars

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answers: produce sugars

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answers: Chloroplasts

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answers: Chloroplasts

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answers: Mitochondrion

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 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: 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

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answers: metabolic rate

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answers: metabolic rate

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: dehydrogenate saturated alkanes

answers: NDQ_016285

answers: dehydrogenate saturated alkanes to form alkenes

answers: NDQ_016287

answers: hydrogen atoms from a suitable donor

answers: NDQ_016289

answers: This desaturates the donor alkane

answers: NDQ_016290

answers: This desaturates the donor alkane, forming an alkene

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: catalytic reaction

answers: NDQ_016285

answers: biochemical reactions

answers: NDQ_016287

answers: GEBIK and GEBIF equations are solved under the hypothesis of non-steady state

answers: NDQ_016289

answers: biochemical reactions

answers: NDQ_016290

answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: are determined by those causes

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answers: NDQ_016289

answers: conscious and unconscious reactions to the world

answers: NDQ_016290

answers: Humans have no free will

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: Phytepsin

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answers: cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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>

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answers: Mercury coulometer

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answers: Mercury

answers: NDQ_016289

answers: Mercury coulometer

answers: NDQ_016290

answers: Mercury coulometer

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: depends on a single reactant

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answers: first-order reactions

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answers: If a reaction rate depends on a single reactant

answers: NDQ_016289

answers: first-order reactions

answers: NDQ_016290

answers: first-order reactions

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: nucleophilic

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answers: nucleophilic

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answers: nucleophilic

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answers: nucleophilic

answers: NDQ_016290

answers: catabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: It is an anabolic reaction

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answers: It is a catabolic reaction

answer: Yes

answer: Yes

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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.

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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

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answers: to extract energy

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answers: Catabolism

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answers: monosaccharide

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answers: Catabolism

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answers: Catabolism

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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:

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracy.

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answers: cell respiration

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answers: cell respiration

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answers: The process of cell respiration

answers: NDQ_016289

answers: Photosynthesis and cellular respiration are complementary

answers: NDQ_016290

answers: cell respiration is a catabolic reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: 2-oxoglutarate

answers: NDQ_016290

answers: 2-oxoglutarate

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: NDQ_016289

answers: This includes all related topics

answers: NDQ_016290

answers: This includes all related topics

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: "S" stands for nucleophilic substitution

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: produces energy

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answers: citric acid cycle

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: carboxylic acids

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answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: import nutrients

answers: NDQ_016285

answers: import nutrients across the cell membrane

answers: NDQ_016287

answers: chlorosomes

answers: NDQ_016289

answers: import nutrients

answers: NDQ_016290

answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: catabolic reactions

answers: NDQ_016285

answers: free radical chain reaction

answers: NDQ_016287

answers: Hydrogen

answers: NDQ_016289

answers: The Addition of Hydrogen Bromide to Allyl Bromide

answers: NDQ_016290

answers: free radical chain reaction

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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: 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:

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answers: metabolites

answers: NDQ_016285

answers: catalyzed

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: catalyzed by a protein

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: uses energy from sunlight

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answers: uses energy from sunlight

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answers: The reverse of the photosynthesis

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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

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answers: decarboxylate oxaloacetate

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answers: synthesizes glycerol 3-phosphate or triglyceride

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answers: Glyceroneogenesis

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answers: Glyceroneogenesis

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answers: glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: Metabolism

answers: NDQ_016287

answers: Metab-L

answers: NDQ_016289

answers: Metabolism

answers: NDQ_016290

answers: Metabolism

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

answers: NDQ_016285

answers: biochemical reactions

answers: NDQ_016287

answers: water

answers: NDQ_016289

answers: biochemical reactions

answers: NDQ_016290

answers: Oxygen released in photosynthesis

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: Yes

answer: 1

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

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answers: breakdown of foodstuffs

answers: NDQ_016285

answers: essential for growth

answers: NDQ_016287

answers: Oxygen consumption

answers: NDQ_016289

answers: phosphate compounds acted as a link between catabolism and anabolism

answers: NDQ_016290

answers: Oxygen consumption

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: catabolic reactions

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answers: catabolic

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: catabolism

answers: NDQ_016290

answers: aerobic catabolism

answer: No

answer: No

answer: Yes

answer: No

answer: Yes

answer: 1

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

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

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracies.

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracies.

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answers: catalyze

answers: NDQ_016285

answers: catabolic reactions

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: Photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: Cellular respiration is a catabolic reaction.

answer: No

answer: No

answer: Yes

answer: No

answer: Yes

answer: 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.

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answers: wastefully producing

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answers: cells ramp up their production

answers: NDQ_016287

answers: cells ramp up their production

answers: NDQ_016289

answers: cells ramp up their production

answers: NDQ_016290

answers: cells ramp up their production

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: continuously passing along the peptide

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answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: The structural enzymes

answers: NDQ_016290

answers: catabolic

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: produce light by the oxidation of a pigment

answers: NDQ_016285

answers: bioluminescence

answers: NDQ_016287

answers: superoxide

answers: NDQ_016289

answers: bioluminescence

answers: NDQ_016290

answers: bioluminescence

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: Biotic metabolism

answers: NDQ_016285

answers: prefer one isotope over others

answers: NDQ_016287

answers: RuBisCO

answers: NDQ_016289

answers: Oxygenic photosynthesis

answers: NDQ_016290

answers: Oxygenic photosynthesis

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: electron acceptor

answers: NDQ_016285

answers: functions as an electron acceptor

answers: NDQ_016287

answers: electron acceptor

answers: NDQ_016289

answers: It functions as an electron acceptor

answers: NDQ_016290

answers: cellular respiration

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

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answers: oxidative rearrangement

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answers: carbon dioxide

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answers: L-carnitine

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answers: oxidative rearrangement

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: carbon dioxide

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answers: photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: transport of carbon dioxide in the opposite direction

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 0

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

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answers: synthase

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answers: NDQ_016289

answers: It is anabolic

answers: NDQ_016290

answers: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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: 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).

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answers: oxidize

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answers: form glucose and release oxygen

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answers: hydrogen from oxygen

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answers: All living cells

answers: NDQ_016290

answers: oxidize the hydrogen and carbon

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: The Petersen matrix

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answers: biochemical reactions

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answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: enzymes

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answers: Biochemical reactions

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answers: Biochemical reactions

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: It splits the CO

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: had not yet occurred

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answers: biochemical reactions

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answers: biochemical reactions

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answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: sustain the cell

answers: NDQ_016285

answers: sustain the cell

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: Th17 cells

answers: NDQ_016290

answers: glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answer: 1

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.

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answers: biochemical reactions which depend on temperature

answer: Yes

answer: Yes

answer: No

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answer: 1

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.

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answers: Enzymatic Synthesis

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answer: No

answer: No

answer: No

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answer: 1

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

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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.

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: break bonds in order to generate smaller molecules

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answers: water is removed from molecules

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answers: Without water, these particular metabolic processes could not exist

answer: No

answer: No

answer: No

answer: No

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answer: 1

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.

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answers: carbon dioxide

answers: NDQ_016289

answers: Carbon dioxide produced by respiration

answers: NDQ_016290

answers: Carbon dioxide produced by respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: remove intermediates from the cycle

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answers: Oxygen and water

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answers: anaplerotic reactions

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answers: anaplerotic reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: NDQ_016284

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answers: endothermic

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answers: endothelin

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answers: oxygen and water

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answers: photosynthesis

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answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: biochemical reactions

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answers: biochemical reactions

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answers: biochemical reactions

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answers: biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: change the nature of any nuclide

answers: NDQ_016285

answers: differ from the nuclide(s) that began the process

answers: NDQ_016287

answers: nucleus of an atom and a subatomic particle

answers: NDQ_016289

answers: nuclei

answers: NDQ_016290

answers: catabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

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answers: biochemical reactions

answers: NDQ_016287

answers: Through a chain of biochemical reactions

answers: NDQ_016289

answers: Biochemical reactions

answers: NDQ_016290

answers: Through a chain of biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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

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answers: detoxification

answers: NDQ_016285

answers: Oxygen binding

answers: NDQ_016287

answers: photosynthesis

answers: NDQ_016289

answers: ET reactions

answers: NDQ_016290

answers: ET reactions

answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: catalyzes

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answers: catalyzes

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answers: oxygen and water

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answers: catalyzes the same reaction

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answers: Cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: nourishes itself

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answers: ethanol fermentation

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answers: yeast as a living organism that nourishes itself by the sugar it ferments

answers: NDQ_016290

answers: enzyme and fermentation studies

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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: 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.

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answers: glycolysis

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answers: glycolysis

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answers: 6 carbon sugars

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answers: glycolysis

answers: NDQ_016290

answers: glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: release energy

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answers: drive desirable reactions that require energy

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answers: Enzymes

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answers: one chemical is transformed through a series of steps into another chemical

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answers: one chemical is transformed through a series of steps into another chemical

answer: Yes

answer: Yes

answer: Yes

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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.

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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

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answers: metabolize

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answers: control metabolism

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answers: oxygen and water

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answers: It helps explain how enzymes work

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answer: No

answer: Yes

answer: No

answer: No

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answer: 1

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

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answers: biochemical processes

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answers: C-H bonds

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answers: The photolabel generates a reactive carbenoid species

answers: NDQ_016290

answers: ATP transfers phosphate through a reactive monomeric metaphosphate species

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: cells

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answers: life and organization

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answers: sugar to alcohol

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answers: chemical reactions found in cells were no different in principle

answers: NDQ_016290

answers: fermentation

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: releases more oxygen

answers: NDQ_016285

answers: releases more oxygen

answers: NDQ_016287

answers: carbon

answers: NDQ_016289

answers: assimilates more carbon

answers: NDQ_016290

answers: Carbon and oxygen are released by cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: These can be identified with irreversible reactions

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answers: irreversible reactions

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answers: irreversible reactions

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: pursuing enzyme research

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answers: catabolic

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: biosynthesis

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answers: biosynthesis

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answers: acetyl CoA

answers: NDQ_016289

answers: fatty acid biosynthesis

answers: NDQ_016290

answers: metabolism of carbohydrates

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: carboxylation

answers: NDQ_016285

answers: integrates CO into organic carbon sugars

answers: NDQ_016287

answers: CO

answers: NDQ_016289

answers: The reaction that integrates CO into organic carbon sugars

answers: NDQ_016290

answers: Integrates CO into organic carbon sugars during photosynthesis

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: conversion of the carbon source (usually glucose)

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answers: glucose

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answers: macromolecular biosynthesis

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answers: conversion of the carbon source (usually glucose) into the building blocks

answer: Yes

answer: Yes

answer: Yes

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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.

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answers: Post-translational

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answers: Post-translational

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answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

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answers: biochemical ones

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answers: Biochemical reactions

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answer: No

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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.

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answers: primary metabolism

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answers: primary metabolism

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answers: BRENDA contains manually annotated data from over 130,000 different scientific articles

answers: NDQ_016289

answers: It is an anabolic reaction.

answers: NDQ_016290

answers: primary metabolism

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: decompositions impossible under ordinary conditions

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answers: catalyzed by protein enzymes

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answers: The product of one reaction is the reactant of the next reaction

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answers: chemical synthesis

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answers: Enzymes increase the rates of biochemical reactions

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: acetylacetone

answers: NDQ_016285

answers: acetylacetone

answers: NDQ_016287

answers: Oxygen and water

answers: NDQ_016289

answers: photosynthesis

answers: NDQ_016290

answers: cellular respiration

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: catabolic reactions

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answers: anabolic reactions

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answers: The mechanism can vary depending on the relative and absolute concentrations of the species involved

answers: NDQ_016289

answers: reaction progress kinetic analysis

answers: NDQ_016290

answers: reaction progress kinetic analysis

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: alter the conformation of the enzyme

answers: NDQ_016285

answers: catalytic

answers: NDQ_016287

answers: Mg

answers: NDQ_016289

answers: Mg interacts with substrates

answers: NDQ_016290

answers: catalytic reaction

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc

answers: NDQ_016285

answers: produces chemical energy

answers: NDQ_016287

answers: carbon dioxide, water, and ammonia

answers: NDQ_016289

answers: The net reaction is, therefore, thermodynamically favorable

answers: NDQ_016290

answers: Anabolism

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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

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answers: 3: The answer has limited relevance and completeness, with noticeable gaps or inaccuracies.

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answers: polyglycolide and small crystals of a salt

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answers: polyglycolide and small crystals of a salt

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answers: The salt can be conveniently removed by washing the product of the reaction with water.

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answers: polyglycolide and small crystals of a salt

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answers: A detailed characterization of polyglycolide prepared by solid-state polycondensation reaction

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

text: The reaction for biochemical oxidation may be written as:

text: The reaction for biochemical oxidation may be written as:

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answers: biochemical oxidation

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answers: anabolic

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answers: oxygen and water

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answers: photosynthesis

answers: NDQ_016290

answers: Catabolic

answer: No

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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

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answers: consumes

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answers: consumes HCO

answers: NDQ_016287

answers: CO(g)

answers: NDQ_016289

answers: by Le Châtelier's principle

answers: NDQ_016290

answers: Consumes HCO

answer: No

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: catalyse essential chemical reactions

answers: NDQ_016290

answers: essential chemical reactions

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: break down large molecules

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answers: enzymes

answers: NDQ_016287

answers: enzymes

answers: NDQ_016289

answers: Enzymes

answers: NDQ_016290

answers: Enzymes

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: metabolism

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answers: The largest number of vitamins

answers: NDQ_016289

answers: cell and tissue growth and differentiation

answers: NDQ_016290

answers: metabolism

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: photosynthesis

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answers: photosynthesis

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answers: oxygen and water

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answers: Oxygen

answers: NDQ_016290

answers: photosynthesis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

text: Biochemical kinetic reactions of type () are often catalytic reactions in which one or more substrates, <math chem>\ce{S}_j

text: Biochemical kinetic reactions of type () are often catalytic reactions in which one or more substrates, <math chem>\ce{S}_j

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answers: one or more substrates

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answers: catalytic reactions

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answers: oxygen and water

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answers: Catalytic reactions

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answers: Biochemical kinetic reactions

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: Biochemical reactions

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answers: are mainly controlled by enzymes

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answers: oxygen and water

answers: NDQ_016289

answers: photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: Biochemical reactions are mainly controlled by enzymes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: cellular automata

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answers: Belousov-Zhabotinsky

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answers: Belousov-Zhabotinsky

answers: NDQ_016290

answers: Belousov-Zhabotinsky

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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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.

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answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: phycotoxin

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answers: Biosynthesis

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answers: Metabolic

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answer: No

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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

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answers: Catalysis

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answers: Catalysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: biomolecules

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answers: Myricetin

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answers: Myricetin

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answers: Photosynthesis is an anabolic reaction.

answers: NDQ_016290

answers: Inhibition of cellular RNA polymerase

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: metabolic reaction

answers: NDQ_016285

answers: increase the rate of particular biochemical pathways by several orders of magnitude

answers: NDQ_016287

answers: photosynthesis

answers: NDQ_016289

answers: increase the rate of particular biochemical pathways by several orders of magnitude

answers: NDQ_016290

answers: metabolic reaction

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: cleavage

answers: NDQ_016285

answers: manipulation purely biochemical

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: cellular respiration

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: degrade organic matter

answers: NDQ_016285

answers: obtain higher energy

answers: NDQ_016287

answers: Oxygen, water

answers: NDQ_016289

answers: Oxygen represents the most favorable electron accepted

answers: NDQ_016290

answers: The degradation of organic matter

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 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".

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answers: biochemical processes

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answers: biochemical processes

answers: NDQ_016287

answers: Biochemical Systems Theory

answers: NDQ_016289

answers: metabolic control

answers: NDQ_016290

answers: Metabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: increase in body size

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answers: Catabolism

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answers: Anabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: oxidative catabolism

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answers: oxidative

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: COO is lost

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answers: catabolic

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answers: COO

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answers: The first reaction of the cycle

answers: NDQ_016290

answers: The Krebs Cycle

answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: PPIs

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answers: Oxygen and water

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answers: PPIs

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answers: PPIs

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: synthesis

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answers: activation of cellular cascades

answers: NDQ_016287

answers: ions

answers: NDQ_016289

answers: the synthesis of nuclear and cytoplasmic inclusion bodies

answers: NDQ_016290

answers: cellular cascades to continue cellular activity

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: produce urea

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answers: produce urea

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answers: (NH)CO

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answers: The urea cycle

answers: NDQ_016290

answers: This cycle was the first metabolic cycle discovered

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: cross-coupling reactions

answers: NDQ_016285

answers: cross-coupling reactions

answers: NDQ_016287

answers: The identity of the metal, M

answers: NDQ_016289

answers: ( )-epi-jatrophone

answers: NDQ_016290

answers: Cross-coupling reactions

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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:

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answers: biochemical compounds

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answers: biochemical reactions

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answers: mutations and other changes

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answers: mutations

answers: NDQ_016290

answers: cellular respiration

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: build up of molecules

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answers: Catabolism

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answers: Metabolism

answers: NDQ_016290

answers: the breakdown of molecules

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: substrates

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answers: biochemical pathways

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answers: metabolic

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: substrate specificity

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answers: catalytic

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answers: oxygen and water

answers: NDQ_016289

answers: Glu270 and His288

answers: NDQ_016290

answers: catalytic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

text: Subsequent biochemical analysis supports the conclusion of a ribozyme function, and determined further characteristics of the chemical reaction catalyzed by the ribozyme.

text: Subsequent biochemical analysis supports the conclusion of a ribozyme function, and determined further characteristics of the chemical reaction catalyzed by the ribozyme.

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answers: catalyze

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answers: catalyzed

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answers: chemical reaction

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answers: chemical reaction

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answers: chemical reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: determine the physiological and biochemical properties

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answer: Yes

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answer: Yes

answer: Yes

answer: No

answer: 1

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: 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.

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answers: perform reactions with same practical outcomes

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answers: perform reactions with same practical outcomes

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answers: tyrosine

answers: NDQ_016289

answers: reactions with same practical outcomes

answers: NDQ_016290

answers: cellular respiration

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: non-radical species

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answers: non-radical species

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answers: methylidyne

answers: NDQ_016289

answers: reactions of the quartet radical generally involves only abstraction

answers: NDQ_016290

answers: reactions of the quartet radical generally involves only abstraction

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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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

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answers: growth, development and reproduction

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answers: growth, development and reproduction

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answers: biochemicals

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answers: Allelopathy

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answer: No

answer: No

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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.

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answers: metabolize

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answers: ferrocenyl groups

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answers: 2,4-disulfides

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answers: FcPS (Fc = ferrocene)

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answers: Catabolic reactions

answer: No

answer: No

answer: No

answer: No

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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

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answers: Biochemistry

answers: NDQ_016285

answers: protein synthesis

answers: NDQ_016287

answers: The biochemistry of cell metabolism

answers: NDQ_016289

answers: protein synthesis

answers: NDQ_016290

answers: The biochemistry of cell metabolism

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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: 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:

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answers: metabolic activities

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answers: metabolic activities within an organism

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answers: chemical energy into heat and mechanical work

answers: NDQ_016289

answers: Metabolic activities within an organism

answers: NDQ_016290

answers: chemical energy into heat and mechanical work

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: clotting

answers: NDQ_016285

answers: catalyses

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: photosynthesis

answers: NDQ_016290

answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: endothermic reactions

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answers: chemical synthesis

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answers: chemical synthesis

answers: NDQ_016290

answers: chemical decomposition

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: Biochemical reactions

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answers: Biochemical reactions

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: NDQ_016290

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answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: SABIO-RK

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: take in carbon dioxide

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answers: take in carbon dioxide

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answers: Carbon dioxide

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answers: Most plants take in carbon dioxide through holes on the undersides of their leaves

answers: NDQ_016290

answers: Plant respiration is limited by the process of diffusion

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 0

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

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answers: 0

answers: NDQ_016284

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answers: enzymes

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answers: catalyses

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answers: oxygen and water

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answers: photosynthesis

answers: NDQ_016290

answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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).

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answers: catalyzed reactions

answers: NDQ_016285

answers: catalyzed reactions

answers: NDQ_016287

answers: The Hammett acidity function

answers: NDQ_016289

answers: activity coefficients

answers: NDQ_016290

answers: acid-catalyzed reactions

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: synthesize and store calcium oxalates inside the cell

answers: NDQ_016285

answers: synthesize and store calcium oxalates

answers: NDQ_016287

answers: Oxidation

answers: NDQ_016289

answers: M. bipunctata

answers: NDQ_016290

answers: cellular respiration is a catabolic reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: Photosynthesis is an anabolic reaction

answers: NDQ_016290

answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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answers: 4

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answers: synthesis of nucleic acids

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answers: GTP

answers: NDQ_016289

answers: GTP

answers: NDQ_016290

answers: synthesis of nucleic acids and proteins

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: Creatine

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answers: respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: L-xylulose

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answers: Phloroglucin reaction

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answers: L-Xylulose

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

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answers: biochemical reactions

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: hydrocarbon metathesis

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: anabolic reactions

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answers: Gluconeogenesis

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answers: Gluconeogenesis

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answers: gluconeogenesis

answers: NDQ_016290

answers: Gluconeogenesis

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: carbon dioxide fixation

answers: NDQ_016285

answers: bacteriorhodopsin

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answers: carbon dioxide

answers: NDQ_016289

answers: Carbon dioxide fixation and does not release oxygen

answers: NDQ_016290

answers: Carbon dioxide fixation and does not release oxygen

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: methanogenesis

answers: NDQ_016285

answers: methanogenesis

answers: NDQ_016287

answers: Photocyta

answers: NDQ_016289

answers: Methanobacteria

answers: NDQ_016290

answers: sulfur respiration

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: uses stored energy reserves

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answers: uses stored energy reserves

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answers: nitrogen

answers: NDQ_016289

answers: catabolic

answers: NDQ_016290

answers: An increased release of catabolic hormones

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: 0: The answer is not relevant or complete at all.

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answers: biochemical reactions

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answers: biochemical reactions

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answers: E. Coli

answers: NDQ_016289

answers: E. Coli Metabolome Database

answers: NDQ_016290

answers: E. Coli Metabolome Database (ECMDB)

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: Glycolysis

answers: NDQ_016285

answers: use the reverse reaction

answers: NDQ_016287

answers: Glycolysis

answers: NDQ_016289

answers: Glycolysis

answers: NDQ_016290

answers: Glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: catalyze the reaction

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answers: lower the activation energy of the reaction

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answers: substrates

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answers: By lowering the activation energy, the enzyme speeds up that reaction

answers: NDQ_016290

answers: enzymes recognize specific reactant molecules called substrates; they then catalyze the reaction between them

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: catalyses

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answers: catalyses

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answers: oxygen and water

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answers: photosynthesis

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answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: Glutamate synthase

answers: NDQ_016285

answers: produces two glutamate molecules

answers: NDQ_016287

answers: Glutamate synthases

answers: NDQ_016289

answers: It is anabolic

answers: NDQ_016290

answers: Catabolic reactions

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: Yes

answer: 1

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.

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answers: uncatalyzed chemistry

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answers: catalyze chemical reactions

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answers: Enzymes

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answers: Enzymes catalyze chemical reactions

answers: NDQ_016290

answers: catalyze chemical reactions

answer: Yes

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: release stored energy

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answers: release stored energy

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answers: carbon dioxide

answers: NDQ_016289

answers: The citric acid cycle

answers: NDQ_016290

answers: The citric acid cycle

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: biochemical

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answers: elongation

answers: NDQ_016287

answers: FAS I

answers: NDQ_016289

answers: FAS I

answers: NDQ_016290

answers: FAS I

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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.

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answers: biochemical

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answers: biochemical

answers: NDQ_016287

answers: O-alkyl cleavage mechanism

answers: NDQ_016289

answers: S2 reaction

answers: NDQ_016290

answers: RPE65

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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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.

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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

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answers: catabolic

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answers: metabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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 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.

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answers: aldehydes

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answers: catabolic

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answers: heterotrophic metabolism

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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

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answers: Free radical halogenation reactions

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answers: alkane substrates

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answers: auto-oxidation

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.

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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: s is of great environmental significance and involves intriguing novel biochemical reactions. In particular,

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.

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answers: biochemical reactions

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answers: catabolic

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answers: Oxygen

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answers: Catabolic

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answers: Anaerobic

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: photosynthesis

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answers: photosynthesis

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answers: Plant respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: catabolic reactions

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answers: induces an anti-inflammatory effect

answers: NDQ_016287

answers: 2-arylpropionic acid

answers: NDQ_016289

answers: AMACR

answers: NDQ_016290

answers: Human AMACR 1A

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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: 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.

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answers: biochemical

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answers: prolonged his life

answers: NDQ_016287

answers: biochemical

answers: NDQ_016289

answers: biochemical explosive reaction

answers: NDQ_016290

answers: Biochemical

answer: Yes

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: 0: The answer is not relevant or complete at all.

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answers: 1: The answer is not relevant or complete at all.

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answers: cellular respiration

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answers: cellular respiration

answers: NDQ_016287

answers: Two water molecules are oxidized

answers: NDQ_016289

answers: Oxygen is a waste product of light-dependent reactions

answers: NDQ_016290

answers: Oxygen is a waste product

answer: No

answer: Yes

answer: Yes

answer: No

answer: No

answer: 1

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.""

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answers: catalyse unusual reactions

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answers: work vigorously in anhydrous organic media

answers: NDQ_016287

answers: small molecules of a solvent

answers: NDQ_016289

answers: anabolic

answers: NDQ_016290

answers: The ability to catalyse unusual reactions

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: take place

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answers: CBB

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answers: light-independent reactions

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answers: reductive pentose phosphate cycle

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: excrete material

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answers: An animal that eats food with high values

answers: NDQ_016287

answers: marine photosynthetic organisms

answers: NDQ_016289

answers: It is an anabolic reaction

answers: NDQ_016290

answers: Cellular respiration

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

text: On this track, students are introduced to the fundamental reaction mechanisms in the field of chemical and biochemical engineering.

text: On this track, students are introduced to the fundamental reaction mechanisms in the field of chemical and biochemical engineering.

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answers: biochemical

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answers: biochemical

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answers: oxygen and water

answers: NDQ_016289

answers: photosynthesis

answers: NDQ_016290

answers: Catabolic

answer: No

answer: No

answer: Yes

answer: No

answer: Yes

answer: 1

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.

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answers: respiration

answers: NDQ_016285

answers: cellular respiration

answers: NDQ_016287

answers: Enzymes

answers: NDQ_016289

answers: cellular respiration

answers: NDQ_016290

answers: cellular respiration

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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

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answers: catabolic reactions are chemical reactions in living things

answers: NDQ_016285

answers: Anabolic reactions are chemical reactions in living things

answers: NDQ_016287

answers: Click reactions are, by definition, rapid, spontaneous, selective, and high-yielding.

answers: NDQ_016289

answers: Click reactions are, by definition, rapid, spontaneous, selective, and high-yielding.

answers: NDQ_016290

answers: Cellular respiration is a catabolic reaction.

answer: Yes

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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.

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answers: metabolites

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answers: Secondary plant metabolites

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answers: Secondary plant metabolites

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answers: Secondary plant metabolites

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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)

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answers: The metabolism of a cell

answers: NDQ_016290

answers: breakdown of molecules

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: Potassium

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answers: Potassium serves as an activator of enzymes

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answers: Potassium

answer: No

answer: No

answer: No

answer: No

answer: No

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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

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answers: catalyze

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answers: RNA could play an active role in cellular processes

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answers: It was believed that biological catalysis was solely the realm of protein enzymes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: catabolic metabolism

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answers: GTP or ATP

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answers: GTP or ATP

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answers: tissue typically involved in anabolic metabolism

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answers: tissue involved in catabolic metabolism

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: uses metal ions

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answers: metal-promoted

answers: NDQ_016287

answers: metal ions

answers: NDQ_016289

answers: metal-promoted functionalization

answers: NDQ_016290

answers: Catabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: utilizes highly reduced chemical compounds

answers: NDQ_016285

answers: anaerobic

answers: NDQ_016287

answers: ADP and inorganic phosphate

answers: NDQ_016289

answers: ATP synthesis

answers: NDQ_016290

answers: Oxygen (in aerobic respiration) or another chemical substance

answer: No

answer: No

answer: Yes

answer: No

answer: No

answer: 1

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.

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answers: products

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answers: increase the yield

answers: NDQ_016287

answers: oxygen and water

answers: NDQ_016289

answers: Product inhibition

answers: NDQ_016290

answers: metabolism

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: Yes

answer: 1

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

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answers: catabolic reactions

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answers: catabolic

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answers: Catabolism

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answers: Catabolism

answers: NDQ_016290

answers: cell respiration is a catabolic reaction

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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: 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.

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answers: catalysed

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answers: oxygen and water

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answers: NDQ_016290

answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: respiration

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answers: photosynthesis

answers: NDQ_016287

answers: carbon dioxide

answers: NDQ_016289

answers: A colour change to purple

answers: NDQ_016290

answers: carbon dioxide is being liberated

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical transformations

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answers: Calcium absorption and bone formation

answers: NDQ_016287

answers: pyrophosphate

answers: NDQ_016289

answers: Calcium absorption and bone formation

answers: NDQ_016290

answers: This is a highly exergonic reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answers: aerobic digestion

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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: 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.

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answers: enzymatic synthetase

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answers: enzymatic synthetase reaction

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answers: acetic acid

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answers: photosynthesis

answers: NDQ_016290

answers: catabolic

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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

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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

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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.

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answers: Oxidative metabolism

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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

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answers: Glycolysis

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answers: Glycolysis

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: Formaldehyde

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answers: Formaldehyde

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answers: Formaldehyde is believed to be the primary precursor for most of the complex organic material

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: biochemical reactions

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answers: biochemical reactions

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answers: photosynthesis

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answers: Michaelis–Menten

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answers: biochemical reactions

answer: No

answer: Yes

answer: No

answer: No

answer: No

answer: 1

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: processes that occur in living organisms. The first is

text: anabolism

text: , which refers to the buildup 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.

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answers: breakdown of molecules

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answers: buildup of molecules

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answers: Catabolism

answers: NDQ_016289

answers: Metabolism

answers: NDQ_016290

answers: the breakdown of molecules

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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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.

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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 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.

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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.

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answers: photosynthesis

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answers: water (HO)

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answers: It is an anabolic reaction.

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answers: The inequality is balanced by photosynthesis

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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.

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answers: break down of complex molecules by releasing energy

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answers: synthesize molecules

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answers: Catabolic pathway

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answers: synthesize molecules with the utilization of energy

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answers: break down of complex molecules by releasing energy in the process

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

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:

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answers: 2: The answer has limited relevance and completeness, with significant gaps or inaccuracies.

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answers: oxidize

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answers: oxidized

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answers: oxygen and water

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answers: photosynthesis

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answers: catabolic

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: No

answer: 1

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.

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answer: Yes

answer: Yes

answer: No

answer: Yes

answer: No

answer: 1

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

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answers: catalyses

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answers: catalyses

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answers: Cellular respiration

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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.

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answers: anabolic

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answers: AAS

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answers: protein synthesis

answers: NDQ_016290

answers: Anabolic

answer: No

answer: No

answer: No

answer: No

answer: No

answer: 1

text: Bioluminescence is light resulting from biochemical reaction by a living organism.

text: Bioluminescence is light resulting from biochemical reaction by a living organism.

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answers: biochemical reaction

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answers: Bioluminescence

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answers: biochemical reaction

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answers: biochemical reaction

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: Yes

answer: 1

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 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  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.

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answers: endothermic

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answers: carbon dioxide

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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:

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