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Head: Glossary

Acetate
A molecular ion, CH3COO-, derived from acetic acid.

Acetoacetate
A molecular ion, CH3COCH2COO-, derived from acetoacetic acid.

Acetyl phosphate
A molecular ion, CH3COPO42-, which plays a role in the synthesis of the four-carbon fatty acid, butyric acid.

Acetyl Coenzyme A (Acetyl CoA)
Originally termed "active acetate," acetyl CoA is an important metabolic intermediate, derived from various pathways, such as glycolysis, fatty-acid oxidation, and degradation of some amino acids. It also represents a key intermediate in lipid biosynthesis.

Adenosine triphosphate (ATP)
An important carrier of energy in cells, ATP is formed from adenosine diphosphate (ADP) by an oxidation reaction in mitochondria, or by a photo reaction in plants. Reactions in which it participates are often driven in the direction leading to hydrolysis (reaction with water) of ATP. The chemical energy so released may be utilized in many ways: it can be converted to mechanical energy (e.g., for muscular contraction), to light energy (for bioluminescence), or to electrical energy (in electric fish); or it may be released as heat. ATP also participates in numerous synthetic reactions in cells.

Adenylyl transferase
The generic name for numerous enzymes that are specific for the transfer of an adenylyl group (adenosine[mono]phosphor group) from a donor molecule (usually adenosine triphosphate, ATP) to an acceptor, such as a nucleotide, a protein, and a sugar.

Adenylylation
A reaction that introduces adenylyl groups into a compound generally by the action of an enzyme, adenylyl tranferase.

Aerobic degradation
Breakdown of a molecule into smaller chemical entities in the presence of oxygen.

Anaerobic bacteria
Microorganisms that exist as single cells or in clusters of single cells and are able to grow in the absence of oxygen.

Amino acid
Organic acids possessing one or more amino groups (—NH2). Proteins and peptides are polymers of amino acids, and so the biological function of amino acids is quantitatively and qualitatively important. Plants are able to synthesize all the amino acids from simple precursors. Animals, however, are able to synthesize only certain kinds of amino acids.
Amino acids that the animal can synthesize in sufficient quantities for its needs are known as nonessential, whereas those that must be supplied in diet are essential. Technically, amino acids are obtained by the hydrolysis of proteins, and by chemical and microbial synthesis.

Aspartate
A molecular ion derived from aspartic acid, an amino acid

Aspartokinase
A multifunction enzyme that catalyzes two steps in the pathway from aspartate to other amino acids, such as lysine, methionine, and isoleucine.

Butyric acid
An acid, CH3-CH2-CH2-COOH, that has four carbons in it.

Carbonyl derivative
Chemical compounds that have one or more carbonyl groups (=CO). They include aldehydes, ketones, and carboxylic acids.

Cascade system
A sequence of successive activation reactions involving either enzymes (enzyme cascades) or hormones (hormone cascades). In blood coagulation, for example, each enzyme activates the next until the final substrate is reached. In glutamine metabolism, by contrast, the activity of its key enzyme, glutamine synthetase, is regulated by the two systems of interconvertible enzyme cycles, which are tightly linked. Hence a "bicyclic cascade system." The cascade system is characterized by a series of amplifications of a weak initial stimulus, and may be activated at more than one point along the sequence.

Cell-free extract
A fluid, made by breaking open cells, that contains most of the constituents of the cells in question but no intact cells.

Cholesterol
A steroid alcohol which regulates certain cell functions and helps build cell membranes in animal fats.

Cholesterol oxidase
An enzyme that catalyzes the oxidation of cholesterol.

Coenzyme
Any of various nonprotein compounds that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.

Cortisone
A hormone from the adrenal cortex, cortisone is derived from cortisol. It stimulates the formation of carbohydrate from proteins, promotes glycogen storage in the liver, and raises the blood sugar level.

Covalent bond
A chemical bond formed between two atoms in a molecule by the sharing of electrons, usually in pairs, by the bonded atoms.

Enzyme
A complex protein which catalyzes a specific biochemical reaction without changing itself. Enzymes control digestion, muscle contraction, and many other functions of metabolism

Exudative diathesis
A tendency to pass or ooze fluids.

Fatty Acid
Any acid derived from fats by hydrolysis.

Feedback inhibition
Inhibition of the activity of an enzyme by the accumulation of a substance produced further along a metabolic pathway of which the enzyme is a constituent.

Fermentation
The decomposition of chemical substances, brought about by enzymes, that results in the production of simpler substances and, often, of energy. It often refers to the anaerobic breakdown of energy-rich carbohydrates, such as glucose, into carbon dioxide and alcohol or to an organic acid.

Formate dehydrogenase
An enzyme that oxidizes formate—a molecular ion (HCOO-) derived from folic acid—by removing a hydrogen atom.

Glutamate
A molecular ion derived from glutamic acid, an amino acid.

Glutamine
An amino acid synthesized from glutamic acid. Glutamine is an important intermediate in various metabolic pathways because it is the amino group donor in the formation of many biosynthetic products as well as being a storage form of ammonia.

Glutamine synthetase
An enzyme that catalyzes the conversion of glutamate to glutamine. This is the first step in the fixation of ammonia in plants, the ATP-dependent incorporation of NH4+ into the amide position of glutamine. In E. coli, the activity of glutamine synthetase is regulated by both feedback inhibition and the bicyclic cascade system, which makes it extremely responsive to the cell's nitrogen requirements.

Glutathione peroxidase
An enzyme that catalyzes the oxidation of hydrogen peroxide (H2O2) of two molecules of glutathione to form oxidized glutathione and two molecules of H2O. It has a UGA-encoded selenocysteine residue at its active site. The main role of the enzyme is to protect hemoglobin from oxidative breakdown. The oxidized glutathione is reduced by glutathione reductase, the system thus contributing to a reduction of peroxide levels in the cell.

Glycine
An amino acid. With the formula, NH2-CH2-COOH, glycine is the simplest naturally occurring amino acid.

Glycine reductase
An enzyme that catalyzes the reductive degradation of glycine.

Hormone
A chemical substance produced in a living organism which controls the rate of biochemical processes. Hormones are transported from point to point within the organism and thus effect action at a distance from the region in which they are made. Thus, hormones are part of an information-transmission system for the organism.

Lysine
An amino acid.

Metabolism
The totality of chemical reactions within a living organism, which results in the continual turnover (degradation and renewal) of all cell components, and which generates the energy consumed by the organism. Since living organisms are open systems, metabolism consists of numerous linked reactions, which continually strive toward a fixed position of dynamic equilibrium without attaining it. Thus metabolism is a steady state, rather than an equilibrium.

Metabolic pathway
Any series of connected reactions occurring in a cell or organism. Its reactants, intermediates, and products are called metabolites. There are over 2000 known metabolic reactions, each catalyzed by a distinct enzyme. The types of enzymes and metabolites vary with the identity of the organism, the cell type, its nutritional status, and its developmental stage. Many metabolic pathways are branched and interconnected, and finding a metabolic pathway out of thousands of reactions has been one of the main research agendas of biochemistry.

Metabolic regulation (metabolic control)
A system of control mechanisms that underlies the high degree of adaptation displayed by living organisms, and guarantees the efficient and economic operation of living processes.

Methane
An odorless gas, CH4, produced by the decomposition of organic matter.

Mixed-Function Oxidation (MFO) system (Metal-Catalyzed Oxidation system)
A system that has at least three elements in it—oxygen, iron, and an electron donor—which initiates the oxidative degradation of protein.

National Cancer Institute (NCI)
Established in 1937, the National Cancer Institute began by administering a fellowship program, as well as conducting cancer research within its intramural program. It became officially part of the National Institute of Health in 1944 when the NIH was still singular. The Journal of the National Cancer Institute published its first issue in 1940. In 1972, the status of NCI was elevated to a bureau-level organization in accordance with the expanded responsibilities bestowed on it by the National Cancer Act of 1971.

National Heart Institute (NHI)
The National Heart Institute was created in 1948 as part of the National Institutes of Health. In 1969, it was renamed the National Heart and Lung Institute (NHLI), reflecting expansion of its functions. In 1972, NHLI obtained bureau status within NIH. This institute was further enlarged in 1976 to become the National Heart, Lung, and Blood Institute (NHLBI).

National Institutes of Health (NIH)
The NIH, now one of the world's foremost biomedical centers, had a humble origin. It started in 1887 as a one-room laboratory conducting bacteriological research within the Marine Hospital at Stapleton, Staten Island, New York. This laboratory, called the Laboratory of Hygiene, moved to Washington, D.C., in 1891. With the Ransdell Act of 1930, it was renamed the National Institute of Health. In 1938, construction began for NIH in Bethesda, Maryland, on the 45 acres of land donated by the Wilson family. In 1948, with the creation of the National Heart Institute, the NIH officially became plural, the National Institutes of Health, and by 1950 it had seven institutes and one division under its wing. Since then, the NIH has seen rapid growth, especially in its extramural program which administers the process of awarding grants to researchers around the world. Currently it is composed of 27 institutes and centers.

Necrosis
Localized death and degeneration of tissues in a living organism, due, e.g., to infection or injury.

Phosphotransacetylase
An enzyme that catalyzes the conversion of acetyl phosphate into acetyl CoA in the presence of coenzyme A.

Polypeptide chain
Any chain of peptide comprising 10 to 20 amino-acid residues connected by peptide linkages. Unlike a protein, it usually lacks appreciable tertiary structure in solution and is not liable to irreversible denaturation.

Protease (Proteinase)
Enzymes that hydrolyze (breaks down in the presence of water) peptide bonds in proteins and peptides.

Protein
A major macromolecular constituent of living organisms. All enzymes are proteins. A protein is a linear polymer of amino acids linked by peptide bonds in a specific sequence. In the biosynthesis of the polypeptide chain, any of twenty different amino acids may be incorporated, according to the genetic instruction of the cell.

Protein turnover (Protein degradation)
Like other components of living cells constantly turning over, proteins have lifetimes that range from as short as a few minutes to weeks or more. In any case, cells continuously synthesize proteins from and degrade them to amino acids. This seemingly wasteful process has three functions: (1) to store nutrients in the form of proteins and to break them down in times of metabolic need; (2) to eliminate abnormal proteins whose accumulation would be harmful to the cell; and (3) to permit the regulation of cellular metabolism by eliminating superfluous enzymes and regulatory proteins. Controlling the rate of protein turnover is therefore as important to the cellular and organismal economy as is controlling its rate of synthesis.

Radical
Any molecular entity, charged or uncharged, that possesses an unpaired electron (but normally excluding any paramagnetic metal ion). A radical is usually very unstable and thus highly reactive. Radical character is indicated in a formula by a centered dot symbolizing the unpaired electron. The term "free radical" is now preferably restricted to any radical that does not form part of a radical pair, that is, two radicals in close proximity in liquid solution. "Radical scavenger" refers to any substance that can readily bind with, and thereby eliminate, radicals.

Radioactive tracer (Radiotracer)
A radioactive substance that is added to a metabolic system in quantities too small to perturb the system. It is used to follow, by isolating the radioactive intermediates formed, the sequence of transformations undergone normally by the same (nonradioactive) molecule under similar conditions.

Selenium
A metallic element whose atomic number is 34. It occurs in various colors (gray, red, black). Selenium is an essential trace element, required for the formation of selenoproteins, notably glutathione peroxidase. Measurement of red-cell glutathione peroxidase activity gives an index of selenium status. The most distinctive clinical feature of dietary selenium deficiency is myopathy, a disorder of muscle tissue.

Selenocysteine
An amino acid in which selenium takes the place of sulfur in the amino acid cysteine. Its formula is H-Se-CH2-CH(NH2)-COOH. It is an essential component of selenium-containing proteins, or selenoproteins.

Steroid
A general class of substances widely found in nature, characterized by the presence of a molecular part called the cyclopentano-phenanthrene ring. The steroid includes substances which are normal constituents of animal structure, such as cholesterol, and many other substances possessing various specific physiological actions in the animal organism.

Stop codon
Any of the trinucleotide codons, UGA, UAG, and UAA, that signal the termination of translation of a messenger RNA molecule and the release of the nascent polypeptide chain. A codon is a group of three consecutive nucleotide bases (base triplet) in a given messenger RNA molecule that specifies the synthesis of a particular amino acid in the polypeptide chain or signals the beginning or the end of the message.

Tyrosine
An amino acid.

Uridine monophosphate (UMP)
A molecular ion derived from uridylic acid. It has a uracil as its base.

Vitamin B12
The existence of vitamin B12 came to light in 1926 when George Minot and William Murphy discovered that pernicious anemia, an often fatal disease of the elderly characterized by decreased numbers of red blood cells, low hemoglobin levels, and progressive neurological deterioration, could be treated by the daily consumption of large amounts of raw liver. Vitamin B12 was not isolated until 1948. This vitamin is synthesized neither by plants nor animals but only by a few species of bacteria. Humans obtain almost all of their vitamin B12 directly from their diet, particularly from meat.

References
Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer, Biochemistry, 5th ed. New York: W. H. Freeman, 2002.

Paul Singleton and Diana Sainsbury, eds. Dictionary of Microbiology and Molecular Biology, 2nd ed. New York: John Wiley & Sons, 1996.

A. D. Smith, et al., eds. Oxford Dictionary of Biochemistry and Molecular Biology. Oxford and New York: Oxford University Press, 1997.

Friedrich W. Stöcker, Gerhard Dietrich, and VEB E. A. Brockhaus, eds. Concise Encyclopedia of Biology, translated and revised by Thomas A. Scott. Berlin and New York: Walter de Gruyter & Co, 1996.

Donald Voet, Judith G. Voet, and Charlotte W. Pratt, Fundamentals of Biochemistry. New York: Wiley, 2002.

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