Glossary of biochemistry

Biochemistry

iochemistry is a branch of science that explores the chemical processes and substances within and related to living organisms. By combining biology and chemistry, it plays a crucial role in understanding the molecular mechanisms of life. Biochemistry covers various fields such as molecular genetics, metabolism, enzymology, and biotechnology, providing insights into how cellular processes are regulated and how they can be manipulated for various applications.

History

The history of biochemistry can be traced back to the early 19th century with the discovery of the first enzyme, diastase, in 1833 by Anselme Payen. The term "biochemistry" itself was first used in 1882, and the discipline has since evolved to encompass a wide range of research areas, from understanding genetic codes to developing pharmaceutical drugs.

Key Concepts

• Molecular Genetics: Studies the structure and function of genes at a molecular level and how genetic information is encoded, replicated, and expressed.
• Metabolism: Involves the comprehensive study of life-sustaining chemical reactions in organisms, focusing on the processes of energy extraction, conversion, and utilization.
• Enzymology: The study of enzymes, their kinetics, structure, and function, as well as their role in catalyzing biological reactions.
• Cell Signaling: Explores how cells communicate with each other to perform complex processes, including growth, differentiation, and response to stimuli.

Applications

Biochemistry has vast applications in various fields including:

• Medicine: In developing diagnostics, therapeutics, and vaccines. Understanding biochemical pathways is essential for designing drugs that target specific metabolic processes.
• Agriculture: Enhancing crop yield, disease resistance, and nutritional value through genetic engineering and biopesticides.
• Environmental Science: In pollution control, bio-remediation, and the sustainable production of biofuels.
• Nutrition: Understanding how various nutrients affect metabolic pathways and health, leading to the development of dietary guidelines and supplements.

Challenges and Future Directions

As biochemistry continues to advance, it faces challenges such as understanding increasingly complex biological systems, ethical considerations in genetic manipulation, and the need for sustainable industrial practices. Future directions may include more personalized medicine, improvements in food security, and innovative solutions to environmental issues.

Glossary

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# - A

• 3' end - The end of a nucleic acid that lacks a nucleotide bound at the 3' position of the terminal residue.
• 5' end - The end of a nucleic acid that lacks a nucleotide bound at the 5' position of the terminal residue.
• ? stereoisomers - Compounds that have the same composition and the same order of atomic connections, but different molecular arrangements.
• A form. A duplex DNA structure with right-handed twisting in which the planes of the base pairs are tilted about 70° with respect to the helix axis.
• ADP (adenosine diphosphate) - A ribonucleoside 5'-diphosphate serving as phosphate group acceptor in the cell energy cycle.
• ATP (adenosine triphosphate) - A ribonucleoside 5'-triphosphate functioning as a phosphate group donor in the cell energy cycle; carries chemical energy between metabolic pathways by serving as a shared intermediate coupling endergonic and exergonic reactions.
• ATP synthase - An enzyme complex that forms ATP from ADP and phosphate during oxidative phosphorylation in the inner mitochondrial membrane or the bacterial plasma membrane, and during photophosphorylation in chloroplasts.
• ATPase - An enzyme that hydrolyzes ATP to yield ADP and phosphate; usually coupled to some process requiring energy.
• Acetal. The product formed by the successive condensation of two alcohols with a single aldehyde. It contains two ether-linked oxygens attached to a central carbon atom.
• Acetyl CoA. Acetyl-coenzyme A, a high-energy ester of acetic acid that is important both in the tricarboxylic acid cycle and in fatty acid biosynthesis.
• Actin. A protein found in combination with myosin in muscle and also found as filaments constituting an important part of the cytoskeleton in many eukaryotic cells.
• Actinomycin D. An antibiotic that binds to DNA and inhibits RNA chain elongation.
• Activated complex. The highest free energy state of a complex in going from reactants to products.
• Active site. The region of an enzyme molecule that contains the substrate binding site and the catalytic site for converting the substrate(s) into product(s).
• Active transport. The energy-dependent transport of a substance across a membrane.
• Adenine. A purine base found in DNA or RNA.
• Adenosine diphosphate (ADP). The nucleotide formed by adding a pyrophosphate group to the 5'-OH group of adenosine.
• Adenosine triphosphate (ATP). The nucleotide formed by adding yet another phosphate group to the pyrophosphate group on ADP.
• Adenosine. A purine nucleoside found in DNA, RNA, and many cofactors.
• Adenylate cyclase. The enzyme that catalyzes the formation of cyclic 3',5' adenosine monophosphate (cAMP) from ATP.
• Adipocyte. A specialized cell that functions as a storage depot for lipid.
• Aerobe. An organism that utilizes oxygen for growth.
• Affinity chromatography. A column chromatographic technique that employs attached functional groups that have a specific affinity for sites on particular proteins.
• Alcohol. A molecule with a hydroxyl group attached to a carbon atom.
• Aldehyde. A molecule containing a doubly bonded oxygen and a hydrogen attached to the same carbon atom.
• Alleles. Alternative forms of a gene.
• Allosteric enzyme. An enzyme whose active site can be altered by the binding of a small molecule at a nonoverlapping site.
• Ames test - A simple bacterial test for carcinogens, based on the assumption that carcinogens are mutagens.
• Angstrom (Å). A unit of length equal to 10-10 m.
• Anomers. The sugar isomers that differ in configuration about the carbonyl carbon atom. This carbon atom is called the anomeric carbon atom of the sugar.
• Antibiotic. A natural product that inhibits bacterial growth (is bacteriostatic) and sometimes results in bacterial death (is bacteriocidal).
• Antibody. A specific protein that interacts with a foreign substance (antigen) in a specific way.
• Anticodon. A sequence of three bases on the transfer RNA that pair with the bases in the corresponding codon on th messenger RNA.
• Antigen. A foreign substance that triggers antibody formation and is bound by the corresponding antibody.
• Antiparallel b-pleated sheet (b-sheet). A hydrogen bonded secondary structure formed between two or more extended polypeptide chains.
• Apoactivator. A regulatory protein that stimulates transcription from one or more genes in the presence of a coactivator molecule.
• Asexual reproduction. Growth and cell duplication that does not involve the union of nuclei from cells of opposite mating types.
• Asymmetric carbon. A carbon that is covalently bonded to four different groups.
• Attenuator. A provisional transcription stop signal.
• Autoradiography. The technique of exposing film in the presence of disintegrating radioactive particles. Used to obtain information on the distribution of radioactivity in a gel or a thin cell section.
• Autoregulation. The process in which a gene regulates its own expression.
• Autotroph. An organism that can form its organic constituents from CO2.
• Auxin. A plant growth hormone usually concentrated in the apical bud.
• Auxotroph. A mutant that cannot grow on the minimal medium on which a wild-type member of the same species can grow.
• Avogadro's number (N) - The number of molecules in a gram molecular weight (a mole) of any compound.
• Avogadro's number. The number of molecules in a gram molecular weight of any compound.

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B

• B cell. One of the major types of cells in the immune system. B cells can differentiate to form memory cells or antibody-forming cells.
• B form. The most common form of duplex DNA, containing a right-handed helix and about 10 (10.5 exactly) base pairs per turn of the helix axis.
• Base analog. A compound, usually a purine or a pyrimidine, that differs somewhat from a normal nucleic acid base.
• Base stacking. The close packing of the planes of base pairs, commonly found in DNA and RNA structures.
• Base. The adenine, guanine, cytosine or thymine group attached to a nucleotide or nucleoside. Also may be used to refer to a nucleic acid unit within a polynucleotide chain, as when a gene is said to be 2000 bases long.
• Beta-bend (b-bend) or turn. A characteristic way of turning an extended polypeptide chain in a different direction, involving the minimum number of residues, and held together by hydrogen bonding.
• Beta-oxidation (b-oxidation). Oxidative degradation of fatty acids that occurs by the successive oxidation of the b-carbon atom.
• Beta-sheet (b-sheet). A sheetlike structure formed by the interaction between two or more extended polypeptide chains.
• Bidirectional replication. Replication in both directions away from the origin, as opposed to replication in one direction only (unidirectional replication).
• Bilayer. A double layer of lipid molecules with the hydrophilic ends oriented outward, in contact with water, and the hydrophobic parts oriented inward.
• Bile salts. Derivatives of cholesterol with detergent properties that aid in the solubilization of lipid molecules in the digestive tract.
• Biochemical pathway. A series of enzyme-catalyzed reactions that results in the conversion of a precursor molecule into a product molecule.
• Bioluminescence. The production of light by a biochemical system.
• Blastoderm. The stage in embryogenesis when a unicellular layer at the surface surrounds the yolk mass.
• Bond energy. The energy required to break a bond.
• Branchpoint. An intermediate in a biochemical pathway that can follow more than one route in following steps.
• Buffer. A conjugate acid-base pair that is capable of resisting changes in pH when acid or base is added to the system. This tendency will be maximal when the conjugate forms are present in equal amounts.

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C

• CAP. The catabolite gene activator protein, sometimes incorrectly referred to as the CRP protein. The latter term, in small letters (crp), should be used to refer to the gene but not to the protein.
• Calvin cycle - The cyclic pathway used by plants to fix carbon dioxide and produce triose phosphates.
• Capping. Covalent modification involving the addition of a modified guanidine group in a 5'-5" linkage. It occurs only in eukaryotes, primarily on mRNA molecules.
• Carbohydrate. A polyhydroxy aldehyde or ketone.
• Carboxylic acid. A molecule containing a carbon atom attached to a hydroxyl group and to an oxygen atom by a double bond.
• Carcinogen. A chemical that can cause cancer.
• Carotenoids. Lipid-soluble pigments that are made from isoprene units.
• Catabolism. That part of metabolism that is concerned with degradation reactions.
• Catabolite repression. The general repression of transcription of genes associated with catabolism that is seen in the presence of glucose.
• Catalyst. A compound that lowers the activation energy of a reaction without itself being consumed.
• Catalytic site. The site of an enzyme involved in the catalytic process.
• Catenane. An interlocked pair of circular structures, such as covalently closed DNA molecules.
• Catenation. The linking of molecules without any direct covalent bonding between them, as when two circular DNA molecules interlock like the links in a chain.
• Cell commitment. That stage in a cell's life when it be comes committed to a certain line of development.
• Cell cycle. All of those stages that a cell passes through from one cell generation to the next.
• Cell line. An established clone originally derived from a whole organism through a long process of cultivation.
• Cell lineage. The pedigree of cells resulting from binary fission.
• Cell wall. A tough outer coating found in many plant, fungal, and bacterial cells that accounts for their ability to withstand mechanical stress or abrupt changes in osmotic pressure. Cell walls always contain a carbohydrate component and frequently also a peptide and a lipid component.
• Chelate. A molecule that contains more than one binding site and frequently binds to another molecule through more than one binding site at the same time.
• Chemiosmotic coupling. The coupling of ATP synthesis to an electrochemical potential gradient across a membrane.
• Chimeric DNA. Recombinant DNA whose components originate from two or more different sources.
• Chiral compound. A compound that can exist in two forms that are non-superimposable images of one another.
• Chlorophyll. A green photosynthetic pigment that is made of a magnesium dihydroporphyrin complex.
• Chloroplast. A chlorophyll-containing photosynthetic organelle, found in eukaryotic cells, that can harness light energy.
• Chromatin. The nucleoprotein fibers of eukaryotic chromosomes.
• Chromatography. A procedure for separating chemically similar molecules. Segregation is usually carried out on paper or in glass or metal columns with the help of different solvents. The paper or glass columns contain porous solids with functional groups that have limited affinities for the molecules being separated.
• Chromosome puff. A swollen region of a giant chromosome; the swelling reflects a high degree of transcription activity.
• Chromosome. A thread-like structure, visible in the cell nucleus during metaphase, that carries the hereditary information.
• Cis dominance. Property of a sequence or a gene that exerts a dominant effect on a gene to which it is linked.
• Cistron. A genetic unit that encodes a single polypeptide chain.
• Citric acid cycle. See tricarboxylic acid (TCA) cycle.
• Clone. One of a group of genetically identical cells or organisms derived from a common ancestor.
• Cloning vector. A self-replicating entity to which foreign DNA can be covalently attached for purposes of amplification in host cells.
• Coactivator. A molecule that functions together with a protein apoactivator. For example, cAMP is a coactivator of the CAP protein.
• Codon. In a messenger RNA molecule, a sequence of three bases that represents a particular amino acid.
• Coenzyme. An organic molecule that associates with enzymes and affects their activity.
• Cofactor. A small molecule required for enzyme activity. It could be organic in nature, like a coenzyme, or inorganic in nature, like a metallic cation.
• Complementary base sequence. For a given sequence of nucleic acids, the nucleic acids that are related to them by the rules of base pairing.
• Configuration. The spatial arrangement in which atoms are covalently linked in a molecule.
• Conformation. The three-dimensional arrangement adopted by a molecule, usually a complex macromolecule. Molecules with the same configuration can have more than one conformation.
• Consensus sequence. In nucleic acids, the "average" sequence that signals a certain type of action by a specific protein. The sequences actually observed usually vary around this average.
• Constitutive enzymes. Enzymes synthesized in fixed amounts, regardless of growth conditions.
• Cooperative binding. A situation in which the binding of one ligand to a macromolecule favors the binding of another. For example, DNA cooperatively binds histone molecules, and hemoglobin cooperatively binds oxygen molecules.
• Coordinate induction. The simultaneous expression of two or more genes.
• Cosmid. A DNA molecule with cos ends from lambda-bacteriophage that can be packaged in vitro into a virus for infection purposes .
• Cot curve. A curve that indicates the rate of DNA-DNA annealing as a function of DNA concentration and time.
• Cytidine. A pyrimidine nucleoside found in DNA and RNA.
• Cytochromes. Heme-containing proteins that function as electron carriers in oxidative phosphorylation and photosynthesis.
• Cytokinin. A plant hormone produced in root tissue.
• Cytoplasm. The contents enclosed by the plasma (or cytoplasmic) membrane, excluding the nucleus.
• Cytosine. A pyrimidine base found in DNA and RNA.
• Cytoskeleton. The filamentous skeleton, formed in the eukaryotic cytoplasm, that is largely responsible for controlling cell shape.
• Cytosol. The liquid portion of the cytoplasm, including the macromolecules but not including the larger structures like subcellular organelles or cytoskeleton.

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D

• D loop. An extended loop of single-stranded DNA displaced from a duplex structure by an oligonucleotide.
• DNA (deoxyribonucleic acid) - A polynucleotide having a specific sequence of deoxyribonucleotide units covalently joined through 3',5'-phosphodiester bonds; serves as the carrier of genetic informatian.
• DNA chimera - A DNA containing genetic information derived from two different species.
• DNA cloning - See cloning.
• DNA cloning. The propagation of individual segments of DNA as clones.
• DNA library - A random collection of cloned DNA fragments that includes all or most of the genome of a given organism; also called a genomic library.
• DNA library. A mixture of clones, each containing a cloning vector and a segment of DNA from a source of interest.
• DNA ligase - An enzyme that creates a phosphodiester bond between the 3' end of one DNA segment and the 5' end of another.
• DNA looping - The interaction of proteins bound at distant sites on a DNA molecule so that the intervening DNA forms a loop.
• DNA polymerase - An enzyme that catalyzes template-dependent synthesis of DNA from its deoxyribonucleoside 5'-triphosphate precursors.
• DNA polymerase. An enzyme that catalyzes the formation of 3'-5' phosphodiester bonds from deoxyribonucleotide triphosphates.
• DNA replicase system - The entire complex of enzymes and specialized proteins required in biological DNA replication. DNA supercoiling: The coiling of DNA upon itself, generally as a result of bending, underwinding, or overwinding of the DNA helix.
• DNA transposition - See transposition.
• DNA. Deoxyribonucleic acid. A polydeoxyribonucleotide in which the sugar is deoxyribose; the main repository of genetic information in all cells and most viruses.
• Dalton. A unit of mass equivalent to the mass of a hydrogen atom (1.66 x 10-24 g)
• Dark reactions. Reactions that can occur in the dark, in a process that is usually associated with light, such as the dark reactions of photosynthesis.
• De novo pathway. A biochemical pathway that starts from elementary substrates and ends in the synthesis of a biochemical.
• Deamination. The enzymatic removal of an amine group, as in the deamination of an amino acid to an alpha keto acid.
• Dehydrogenase. An enzyme that catalyzes the removal of a pair of electrons (and usually one or two protons) from a substrate molecule.
• Denaturation. The disruption of the native folded structure of a nucleic acid or protein molecule; may be due to heat, chemical treatment, or change in pH.
• Density-gradient centrifugation. The separation, by centrifugation, of molecules according to their density, in a gradient varying in solute concentration.
• Dialysis. Removal of small molecules from a macromolecule preparation by allowing them to pass across a semipermeable membrane.
• Diauxic growth. Biphasic growth on a mixture of two carbon sources in which one carbon source is used up before the other one. For example, in the presence of glucose and lactose, E. coli will utilize the glucose before the lactose.
• Difference spectra. Plots comparing the absorption spectra of a molecule or an assembly of molecules in different states, for example, those of mitochondria under oxidizing or reducing conditions.
• Differential centrifugation. Separation of molecules and/or organelles by sedimentation rate.
• Differentiation. A change in the form and pattern of a cell and the genes it expresses as a result of growth and replication, usually during development of a multicellular organism. Also occurs in microorganisms (e.g. in sporulation).
• Dimer. Structure resulting from the association of two subunits.
• Diploid cell. A cell that contains two chromosomes (2N) of each type.
• Dipole. A separation of charge within a single molecule.
• Directed mutagenesis. In a DNA sequence, an intentional alteration that can be genetically inherited.
• Dissociation constant. An equilibrium constant for the dissociation of a molecule into two parts (e.g., dissociation of acetic acid into acetate anion and a proton); Kd.
• Disulfide bridge. A covalent linkage formed by oxidation between two cysteine SH groups either in the same polypeptide chain or in different polypeptide chains. Reversible by adding reducing agents.
• Domain. A segment of a folded protein structure showing conformational integrity. A domain could include the entire protein or just a fraction of the protein. Some proteins, such as antibodies, contain many structural domains.
• Dominant. Describing an allele whose phenotype is expressed regardless of whether the organism is homozygous or heterozygous for that allele.
• Double helix. A structure in which two helically-twisted polynucleotide strands are held together by hydrogen bonding and base stacking.
• Duplex. Same as double helix.
• Dyad symmetry. Property of a structure that can be rotated by 180° to produce the same structure.

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E

• E. coli (Escherzchia coli) - A common bacterium found in the small intestine of vertehrates; the most well-studied organism.
• E0' - See standard reduction potential.
• Ecdysone. A hormone that stimulates the molting process in insects.
• Edman degradation. A systematic method of sequencing proteins, proceeding by stepwise removal of single amino acids from the amino terminus of a polypeptide chain.
• Eicosanoid. Any fatty acid with 20 carbons.
• Electrophoresis. The movement of particles in an electrical field. A commonly-used technique for analysis of mixtures of molecules in solution according to their electrophoretic mobilities.
• Elongation factors. Protein factors uniquely required during the elongation phase of protein synthesis. Elongation factor G (EF-G) brings about the movement of the peptidyl tRNA from the A site to the P site of the ribosome.
• Eluate. The fluid that has passed through (eluted from) a chromatographic column.
• Embryo. Plant or animal at an early stage of development.
• Enantiomorphs. Isomers that are mirror images of one another.
• End-product (feedback) inhibition. The inhibition of the first enzyme in a pathway by the end product of that pathway.
• Endergonic reaction. A reaction with a positive standard free energy change.
• Endocrine glands. Specialized tissues whose function is to synthesize and secrete hormones.
• Endonuclease. An enzyme that breaks a phosphodiester linkage at some point within a polynucleotide chain.
• Endopeptidase. An enzyme that breaks a polypeptide chain at an internal peptide linkage.
• Endoplasmic reticulum. A system of double membranes in the cytoplasm that is involved in the synthesis of transported proteins. The rough endoplasmic reticulum has ribosomes associated with it. The smooth endoplasmic reticulum does not.
• Energy charge. The fractional degree to which the AMP-ADP-ATP system is filled with high-energy phosphates (phosphoryl groups).
• Enhancer. A DNA sequence that can stimulate transcription at an appreciable distance from the site where it is located. It acts in either orientation and either upstream or downstream from the promoter.
• Entropy. The randomness of a system.
• Enzyme. A moleucle, most often a protein, that contains a catalytic site for a biochemical reaction.
• Epimers. Two stereoisomers with more than one chiral center that differ in configuration at one of their chiral centers.
• Equilibrium. The point at which the concentrations of two compounds are such that the interconversion of one compound into the other compound does not result in any change in free energy.
• Escherichia coli (E. coli). A Gram negative bacterium commonly found in the vertebrate intestine. It is the bacterium most frequently used in the study of biochemistry and genetics.
• Escherichia coli - See E. coli.
• Established cell line. A group of cultured cells derived from a single origin and capable of stable growth for many generations.
• Ether. A molecule containing two carbons linked by an oxygen atom.
• Eukaryote. A cell or organism that has a membrane-bound nucleus.
• Excision repair. DNA repair in which a damaged region is replaced.
• Excited state. An energy-rich state of an atom or a molecule, produced by the absorption of radiant energy.
• Exergonic reaction. A chemical reaction that takes place with a negative change in standard free energy.
• Exon. A segment within a gene that carries part of the coding information for a protein.
• Exonuclease. An enzyme that breaks a phosphodiester linkage at one or the other end of a polynucleotide chain so as to release single or small nucleotide residues.

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F

• F factor. A large bacterial plasmid, known as the sex-factor plasmid because it permits mating between F+ and F- bacteria.
• FAD (flavin adenine dinucleotide) - The coenzyme of some oxidation-reduction enzymes; it contains riboflavin.
• FMN (flavin mononucleotide) - Riboflavin phosphate, a coenzyme of certain oxidation-reduction enzymes.
• Facultative aerobe. An organism that can use molecular oxygen in its metabolism but that also can live anaerobically.
• Fatty acid. A long-chain hydrocarbon containing a carboxyl group at one end. Saturated fatty acids have completely saturated hydrocarbon chains. Unsaturated fatty acids have one or more carbon-carbon double bonds in their hydrocarbon chains.
• Feedback inhibition. See end-product inhibition.
• Fermentation. The energy-generating breakdown of glucose or related molecules by a process that does not require molecular oxygen.
• Fingerprinting. The characteristic two-dimensional paper chromatogram obtained from the partial hydrolysis of a protein or a nucleic acid.
• Fischer projection formulas - See projection formulas.
• Fluorescence. The emission of light by an excited molecule in the process of making the transition from the excited state to the ground state.
• Frameshift mutations. Insertions or deletions of genetic material that lead to a shift in the translation of the reading frame. The mutation usually leads to nonfunctional proteins.
• Free energy. That part of the energy of a system that is available to do useful work.
• Furanose. A sugar that contains a five-membered ring as a result of intramolecular hemiacetal formation.
• Futile cycle. See pseudocycle.

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G

• G1 phase. That period of the cell cycle in which preparations are being made for chromosome duplication, which takes place in the S phase.
• G2 phase. That period of the cell cycle between S phase and mitosis (M phase).
• Gametes. The ova and the sperm, haploid cells that unite during fertilization to generate a diploid zygote.
• Gel fitration chromatography. A technique that makes use of certain polymers that can form porous beads with varying pore sizes. In columns made from such beads, it is possible to separate molecules, which cannot penetrate beads of a given pore size, from small molecules that can. Also called gel-exclusion or molecular seive chromatography.
• Gene amplification. The duplication of a particular gene within a chromosome two or more times.
• Gene splicing. The cutting and rejoining of DNA sequences.
• Gene. A segment of the genome that codes for a functional product.
• General recombination. Recombination that occurs between homologous chromosomes at homologous sites.
• Generation time. The time it takes for a cell to double its mass under specified conditions.
• Genetic map. The arrangement of genes or other identifiable sequences on a chromosome.
• Genome. The total genetic content of a cell or a virus.
• Genotype. The genetic characteristics of an organism (distinguished from its observable characteristics, or phenotype).
• Globular protein. A folded protein that adopts an approximately globular shape. May also be called soluble proteins.
• Gluconeogenesis. The production of sugars from nonsugar precursors such as lactate or amino acids. Applies more specifically to the production of free glucose by vertebrate livers.
• Glycogen. A polymer of glucose residues in 1,4 linkage, with 1,6 linkages at branchpoints.
• Glycogenic. Describing amino acids whose metabolism may lead to gluconeogenesis.
• Glycolipid. A lipid containing a carbohydrate group.
• Glycolysis. The catabolic conversion of glucose to pyruvate with the production of ATP.
• Glycoprotein. A protein linked to an oligosaccharide or a polysaccharide. Glycosaminoglycans. Long, unbranched polysaccharide chains composed of repeating disaccharide subunits in which one of the two sugars is either N-acetylglucosamine or N-acetylgalactosamine.
• Glycosidic bond. The bond between a sugar and an alcohol. Also the bond that links two sugars in disaccharides, oligosaccharides, and polysaccharides.
• Glyoxylate cycle. A pathway that uses some of the enzymes of the TCA cycle and some enzymes whereby acetate can be converted into succinate and carbohydrates.
• Glyoxysome. An organelle containing some enzymes of the glyoxylate cycle.
• Goldman equation. An equation expressing the quantitative relationship between the concentrations of charged species on either side of a membrane and the resting transmembrane potential.
• Golgi apparatus. A complex series of double-membrane structures that interact with the endoplasmic reticulum and that serve as a transfer point for proteins destined for other organelles, the plasma membrane, or extracellular transport.
• Golgi complex - A complex membranous organelle of eukaryotic cells; functions in the posttranslational modification of proteins and their secretion from the cell or incorporation into the plasma membrane or organellar membranes.
• Gram molecular weight. For a given compound, the weight in grams that is numerically equal to its molecular weight.
• Ground state. The lowest electronic energy state of an atom or a molecule.
• Growth factor. A substance that must be present in the growth medium to permit eucaryotic cell proliferation.
• Growth fork. The region on a DNA duplex molecule where synthesis is taking place. It resembles a fork in shape, since it consists of a region of duplex DNA connected to a region of unwound single strands.
• Guanine. A purine base found in DNA or RNA.
• Guanosine. A purine nucleoside found in DNA and RNA.

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H

• Hairpin loop. A single-stranded complementary region of DNA or RNA that folds back on itself and base-pairs into a double helix.
• Half-life. The time required for the disappearance of one half of a substance.
• Haploid cell. A cell containing only one chromosome of each type.
• Haworth perspective formulas - A method for representing cyclic chemical structures so as to define the configuration of each substituent group; the method commonly used for representing sugars.
• Heavy isotopes. Forms of atoms that contain greater numbers of neutrons than the most common form (e.g., 15N, l3C).
• Helix. A spiral structure with a repeating pattern.
• Heme. An iron-porphyrin complex found in hemoglobin and cytochromes. Hemiacetal. The product formed by the condensation of an aldehyde with an alcohol; it contains one oxygen linked to a central carbon in a hydroxyl fashion and one oxygen linked to the same central carbon by an ether linkage.
• Henderson-Hasselbalch equation - An equation relating the pH, the pKa, and the ratio of the concentrations of the protonacceptor (A-) and proton-donor (HA) species in a solution.
• Henderson-Hasselbalch equation. An equation that relates the pKa, to the pH and the ratio of the proton acceptor (A-) and the proton donor (HA) species of a conjugate acid base pair.
• Heterochromatin. Highly condensed regions of chromosomes that are not usually transcriptionally active.
• Heteroduplex. An annealed duplex structure between two DNA strands that do not show perfect complementarity. Can arise by mutation, recombination, or the annealing of complementary single-stranded DNAs.
• Heteropolymer. A polymer containing more than one type of monomeric unit.
• Heterotroph. An organism that requires preformed organic compounds for growth.
• Heterozygous. Describing an organism (a heterozygote) that carries two different alleles for a given gene.
• Hexose. A sugar with a six-carbon backbone.
• High-energy compound. A compound that undergoes hydrolysis with a high negative standard free energy change.
• Hill reaction - The evolution of oxygen and the photoreduction of an artificial electron acceptor by a chloroplast preparation in the absence of carbon dioxide.
• Histones. The family of basic proteins that is normally associated with DNA in most cells of eukaryotic organisms.
• Holliday intermediate - An intermediate in genetic recombination in which two double-stranded DNA molecules are joined by virtue of a reciprocal crossover involving one strand of each molecule.
• Holoenzyme. An intact enzyme containing all of its subunits and any necessary cofactors with full enzymatic activity.
• Homologous chromosomes. Chromosomes that carry the same pattern of genes, but not necessarily the same alleles.
• Homopolymer. A polymer composed of only one type of monomeric building block.
• Homozygous. Describing an organism (a homozygote) that carries two identical alleles for a given gene.
• Hormone receptor. A protein that is located on the cell membrane or inside the responsive cell and that interacts specifically with the hormone.
• Hormone. A chemical substance made in one cell and secreted so as to influence the metabolic activity of a select group of cells located at other sites in the organism.
• Host cell. A cell used for growth and reproduction of a virus.
• Hybrid (or chimeric) plasmid. A plasmid that contains DNA from two different organisms.
• Hydrogen bond. A weak, noncovalent, attractive force between one electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom.
• Hydrolysis. The cleavage of a molecule by the addition of water. Hydrophilic. Preferring to be in contact with water.
• Hydrophobic effect. The noncovalent association of nonpolar groups with each other in aqueous solution.
• Hydrophobic. Preferring not to be in contact with water, as is the case with the hydrocarbon portion of a fatty acid or phospholipid chain.
• Hydroxyapatite. A calcium phosphate gel used, in the case of nucleic acids, to selectively absorb duplex DNA-RNA from a mixture of single-stranded and duplex nucleic acids.

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I

• Icosahedral symmetry. The symmetry displayed by a regular polyhedron that is composed of 20 equilateral triangular faces with 12 corners.
• Imine. A molecule containing a nitrogen atom attached to a carbon atom by a double bond. The nitrogen is also covalently linked to a hydrogen. Immunofluorescence. A cytological technique in which a specific fluorescent antibody is used to label an antigen. Frequently used to determine the location of an antigen in a tissue or a cell.
• Immunoglobulin. A protein made in a B plasma cell and usually secreted; it interacts specifically with a foreign agent. Synonymous with antibody. It is composed of two heavy and two light chains linked by disulfide bonds. Immunoglobulins can be divided into five classes (IgG, IgM, IgA, IgD, and IgE) based on their heavy-chain component.
• In vitro. Literally, "in glass," describing whatever happens in a test tube or other receptacle, as opposed to what happens in whole cells of the whole organism (in vivo).
• Induced fit. A change in the shape of an enzyme that results from the binding of substrate.
• Inducers. Molecules that cause an increase in a protein activity when added to cells.
• Inducible proteins. Those which are synthesized in different amounts depending on cellular signals.
• Initiation factors. Those protein factors that are specifically required during the initiation phase of protein synthesis.
• Intercalating agent. A chemical, usually containing aromatic rings, that can sandwich in-between adjacent base pairs in a DNA duplex. The intercalation leads to an adjustment in the DNA secondary structure, as adjacent base pairs are usually close-packed.
• Interferon. One of a family of proteins that are liberated by special host cells in the mammal in response to viral infection. The interferons attach to an infected cell, where they stimulate antiviral protein synthesis.
• Intervening sequence. See intron.
• Intron. A segment of the nascent transcript that is removed by splicing. Also refers to the corresponding region in the DNA. Synonymous with intervening sequence.
• Inverted repeat. A chromosome segment that is identical to another segment on the same chromosome except that it is oriented in the opposite direction.
• Ion-exchange resin. A polymeric resinous substance, usually in bead form, that contains fixed groups with positive or negative charge. An anion exchange resin has positively-charged groups and is therefore useful in exchanging the anionic groups in a test sample; a cation exchange resin is itself negatively charged, and has the opposite application. The resin is usually used in a column chromatographic procedure.
• Isoelectric point or pH. The pH at which a protein has no net charge.
• Isomerase. An enzyme that catalyzes an intramolecular rearrangement.
• Isomerization. Rearrangement of atomic groups within the same molecule without any loss or gain of atoms.
• Isozymes. Multiple forms of an enzyme that differ from one another in one or more of the properties.

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K - M

• Ketogenic. Describing amino acids that are metabolized to acetoacetate and acetate.
• Ketone bodies. Refers to acetoacetate, acetone, and b-hydroxybutyrate made from acetyl-CoA in the liver and used for energy in nonhepatic tissue.
• Ketone. A functional group of an organic compound in which a carbon atom is double-bonded to an oxygen. Neither of the other substituents attached to the carbon is a hydrogen. Otherwise the group would be called an aldehyde.
• Ketosis. A condition in which the concentration of ketone bodies in the blood or urine is unusually high.
• Kilobase. One thousand bases in a DNA molecule.
• Kinase. An enzyme catalyzing phosphorylation of an acceptor molecule, usually with ATP serving as the phosphate (phosphoryl) donor.
• Kinetochore. A structure that attaches laterally to the centromere of a chromosome; it is the site of chromosome tubule attachment.
• Km. See Michaelis constant.
• Krebs cycle - See citric acid cycle.
• Krebs cycle. See tricarboxylic acid (TCA) cycle.
• Lampbrush chromosome. Giant diplotene chromosome found in the oocyte nucleus. The loops that are observed are the sites of extensive gene expression.
• Law of mass action. The finding that the rate of a chemical reaction is a function of the product of the concentrations of the reacting species.
• Leader region. The region of an mRNA between the 5' end and the initiation codon for translation of the first polypeptide chain.
• Leader sequence. An N-terminal signal sequence that directs secretion and processing of proteins.
• Lectins. Agglutinating proteins usually extracted from plants.
• Ligand. A (usually small) molecule that binds to another, such as oxygen when it binds to myoglobin.
• Ligase. An enzyme that catalyzes the joining of two molecules together. In DNA it joins 5'-OH to 3' phosphates.
• Lineweaver-Burk equation - An algebraic transform of the Michaelis-Menten equation, allowing determination of Vmax and Km by extrapolation of [S] to infinity.
• Linkage. The tendency of markers to be inherited together. Linkage of two markers is an indication that they are close to one another in the genome.
• Linkers. Short oligonucleotides that can be ligated (connected) to larger DNA fragments, then cleaved (cut) to yield overlapping cohesive (sticky) ends, suitable for ligation to other DNAs that contain comparable cohesive ends.
• Linking number. The net number of times one polynucleotide chain crosses over another polynucleotide chain. By convention, right-handed crossovers are given a plus designation.
• Lipid bilayer. Model for the structure of the cell membrane based on the interaction between the hydrophobic regions of phospholipids.
• Lipid. A biological molecule that is soluble in organic solvents. Lipids include steroids, fatty acids, prostaglandins, terpenes, and waxes.
• Lipopolysaccharide. Usually refers to a unique glycolipid found in Gram negative bacteria.
• Lyase. An enzyme that catalyzes the removal of a group to form a double bond, or the reverse reaction.
• Lysogenic virus. A virus that can adopt an inactive (Iysogenic) state, in which it maintains its genome within a cell instead of entering the Iytic cycle. The circumstances that determine whether a Iysogenic (temperate) virus will adopt an inactive state or an active Iytic state are often subtle and depend upon the physiologic state of the infected cell.
• Lysosome. An organelle that contains hydrolytic enzymes designed to break down proteins that are targeted to that organelle.
• Lytic infection. A virus infection that leads to the Iysis of the host cell, yielding progeny virus particles.
• M phase. That period of the cell cycle when mitosis takes place.
• Marker. A "landmark" that can be localized to a specific region of the genome.
• Meiosis. Process in which diploid cells undergo division to form haploid sex cells.
• Membrane protein. A protein that is associated with a membrane, rather than found free in the cell. A membrane protein may be integral (embedded or buried) in the membrane, or peripheral (attached more loosely, by interactions with either lipid or intergral membrane proteins).
• Membrane transport. The facilitated transport of a molecule across a membrane.
• Membrane. A sheet-like composite of protein and lipid that is the boundary of cells and organelles.
• Merodiploid. An organism that is diploid for some but not all of its genes.
• Mesosome. An invagination of the bacterial cell membrane.
• Messenger RNA (mRNA). The template RNA carrying the message for protein synthesis.
• Metabolic turnover. A measure of the rate at which already existing molecules of the given species are replaced by newly-synthesized molecules of the same type. Usually isotopic labeling is required to measure turnover.
• Metabolism. The sum total of the enzyme-catalyzed reactions that occur in a living organism.
• Metamorphosis. A change of form, especially the conversion of a larval form to an adult form.
• Metaphase. That stage in mitosis or meiosis when all of the chromosomes are lined up on the equator (i.e., an imaginary line that bisects the cell).
• Micelle. An aggregate of lipids in which the polar head groups face outward and the hydrophobic tails face inward; no solvent is trapped in the center.
• Michaelis constant (Km). The substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half of the maximum velocity.
• Michaelis-Menten constant (Km) - The substrate concentration at which an enzyme-catalyzed reaction proceeds at onehalf its maximum velocity.
• Michaelis-Menten equation (also known as the Henri-Michaelis-Menten equation). An equation relating the reaction velocity to the substrate concentration of an enzyme.
• Michaelis-Menten equation - The equation describing the hyperbolic dependence of the initial reaction velocity, V0, on substrate concentration, [S], in many enzymecatalyzed reactions: V0 = Vmax[S] Km + [S]
• Michaelis-Menten kinetics - A kinetic pattern in which the initial rate of an enzyme-catalyzed reaction exhibits a hyperbolic dependence on substrate concentration.
• Microtubules. Thin tubules, made from globular proteins, that serve multiple purposes in eukaryotic cells.
• Mismatch repair. The replacement of a base in a heteroduplex structure by one that forms a Watson-Crick base pair.
• Missense mutation. A change in which a codon for one amino acid is replaced by a codon for another amino acid.
• Mitochondrion. An organelle, found in eukaryotic cells, in which oxidative phosphorylation takes place. It contains its own genome and unique ribosomes to carry out protein syn thesis of only a fraction of the proteins located in this organelle.
• Mitosis. The process whereby replicated chromosomes segregate equally toward opposite poles prior to cell division.
• Mobile genetic element. A segment of the genome that can move as a unit from one location on the genome to another, without any requirement for sequence homology.
• Molecular seive chromatography. See Gel filtration chromatography.
• Molecular weight. See Gram molecular weight.
• Molecularity of a reaction. The number of molecules involved in a specific reaction step.
• Monolayer. A single layer of oriented lipid molecules.
• Monomer. One unit of a protein or other structure.
• Mutagen. An agent that can bring about a heritable change (mutation) in an organism.
• Mutagenesis. A process that leads to a change in the genetic material that is inherited in later generations.
• Mutant. An organism that carries an altered gene or change in its genome.
• Mutarotation. The change in optical rotation of a sugar that is observed immediately after it is dissolved in aqueous solution, as the result of the slow approach of equilibrium of a pyranose or a furanose in its alpha and beta forms.
• Mutation. The genetically inheritable alteration of a gene or group of genes.
• Myofibril. A unit of thick and thin filaments in a muscle fiber.
• Myosin. The main protein of the thick filaments in a muscle myofibril. It is composed of two coiled subunits (Mr about 220,000) that can aggregate to form a thick filament, which is globular at each end.

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N-P

• NAD, NADP (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) - Nicotinamide-containing coenzymes functioning as carriers of hydrogen atoms and electrons in some oxidation-reduction reactions.
• Nascent RNA. The initial transcripts of RNA, before any modification or processing.
• Negative control. Repression of biological activity by the presence of a specific molecule.
• Nernst equation. An equation that relates the redox potential to the standard redox potential and the concentrations of the oxidized and reduced form of the couple.
• Nitrogen cycle. The passage of nitrogen through various valence states, as the result of reactions carried out by a wide variety of different organisms.
• Nitrogen fixation. Conversion of atmospheric nitrogen into a form that can be converted by biochemical reactions to an organic form. This reaction is carried out by a very limited number of microorganisms.
• Nitrogenous base. An aromatic nitrogen-containing molecule with basic properties. Such bases include purines and pyrimidines.
• Noncompetitive inhibitor. An inhibitor of enzyme activity whose effect is not reversed by increasing the concentration of substrate molecule.
• Nonsense mutation. A change in the base sequence that converts a sense codon (one that specifies an amino acid) to one that specifies a stop (a nonsense codon). There are three nonsense codons: amber, ochre and something I forget (let me know if you read this - S. Mowbray).
• Northern blotting. See Southern blotting.
• Nuclease. An enzyme that cleaves phosphodiester bonds of nucleic acids.
• Nucleic acids. Polymers of the ribonucleotides or deoxyribonucleotides.
• Nucleohistone. A complex of DNA and histone.
• Nucleolus. A spherical structure visible in the nucleus during interphase. The nucleolus is associated with a site on the chromosome that is involved in ribosomal RNA synthesis.
• Nucleophilic group. An electron-rich group that tends to attack an electron-deficient nucleus.
• Nucleoside. An organic molecule containing a purine or pyrimidine base and a five-carbon sugar (ribose or deoxyribose).
• Nucleosome. A complex of DNA and an octamer of histone proteins in which a small stretch of the duplex is wrapped around a molecular bead of histone.
• Nucleotide. An organic molecule containing a purine or pyrimidine base, a five-carbon sugar (ribose or deoxyribose), and one or more phosphate groups. A phosphoester of a nucleoside.
• Nucleus. In eukaryotic cells, the centrally-located organelle that encloses most of the chromosomes. Minor amounts of chromosomal substance are found in some other organelles, most notably the mitochondria and the chloroplasts.
• Okazaki fragment. A short segment of single-stranded DNA that is an intermediate in DNA synthesis. In bacteria, Okazaki fragments are 1000-2000 bases in length; in eukaryotes, 100-200 bases in length.
• Oligonucleotide. A polynucleotide containing a small number of nucleotides. The linkages are the same as in a polynucleotide; the only distinguishing feature is the small size.
• Oligosaccharide. A molecule containing a small number of sugar residues joined in a linear or a branched structure by glycosidic bonds.
• Oncogene. A gene of cellular or viral origin that is responsible for rapid, unruly growth of animal cells. A cancer-causing gene.
• Operon. A group of contiguous genes that are coordinately regulated by two cis-acting elements, a promoter and an operator. Found only in prokaryotic cells.
• Optical activity. The property of a molecule that leads to rotation of the plane of polarization of plane-polarized light when the latter is transmitted through the substance. Chirality is a necessary and sufficient property for optical activity.
• Organelle. A subcellular membrane-bounded body with a well-defined function.
• Osmotic pressure. The pressure generated by the mass flow of water to that side of a membrane-bounded structure that contains the higher concentration of solute molecules. A stable osmotic pressure is seen in systems in which the membrane is not permeable to some of the solute molecules.
• Oxidation. The loss of electrons from a compound.
• Oxidative phosphorylation. The formation of ATP as the result of the transfer of electrons to oxygen.
• Oxido-reductase. An enzyme that catalyzes oxidation-reduction reactions.
• PCR. Polymerase chain reaction. A method for amplifying DNA sequences.
• Palindrome. A sequence of bases that reads the same in both directions on opposite strands of the DNA duplex (e.g., GAATTC).
• Pentose phosphate pathway. The pathway involving the oxidation of glucose-6-phosphate to pentose phosphates and further reactions of pentose phosphates.
• Pentose. A sugar with five carbon atoms.
• Peptide mapping. Same as fingerprinting.
• Peptide. An organic molecule in which a covalent amide bond is formed between the a-amino group of one amino acid and the a-carboxyl group of another amino acid, with the elimination of a water molecule. The resulting connection is called a peptide bond.
• Peptidoglycan. The main component of the bacterial cell wall, consisting of a two-dimensional network of heteropolysaccharides running in one direction, cross-linked with polypeptides running in the perpendicular direction.
• Periplasm. The region between the inner (cytoplasmic) membrane and the cell wall or outer membrane of a bacterium.
• Permeable. The property of allowing material to pass through, as a permeable membrane.
• Permease. A protein that catalyzes the transport of a specific small molecule across a membrane.
• Peroxisomes. Subcellular organelles that contain flavin-requiring oxidases and that regenerate oxidized flavin by reaction with oxygen.
• Phenotype. The observable trait(s) that result from the genotype in cooperation with the environment.
• Phenylketonuria. A human disease caused by a genetic deficiency in the enzyme that converts phenylalanine to tyrosine. The immediate cause of the disease is an excess of phenylalanine, which can be alleviated by a diet low in phenylalanine.
• Pheromone. A hormone-like substance that acts as an attractant.
• Phosphodiester. A molecule containing two alcohols esterified to a single molecule of phosphate. For example, the backbone of nucleic acids is connected by 5'-3' phosphodiester linkages between the adjacent individual nucleotide residues.
• Phosphogluconate pathway. Another name for the pentose phosphate pathway. This name derives from the fact that 6-phosphogluconate is an intermediate in the formation of pentoses from glucose.
• Phospholipid. A lipid containing charged hydrophilic phosphate groups; a component of cell membranes.
• Phosphorylation. The formation of a phosphate derivative of a biomolecule.
• Photoreactivation. DNA repair in which the damaged region is repaired with the help of light and an enzyme. The lesion (break) is repaired without excision (cutting out) from the DNA.
• Photosynthesis. The biosynthesis that directly harnesses the chemical energy resulting from the absorption of light. Frequently used to refer to the formation of carbohydrates from CO2 that occurs in the chloroplasts of plants or the plastids of photosynthetic microorganisms.
• Pitch length (or pitch). The number of base pairs per turn of a duplex helix.
• Plaque. A circular clearing on a lawn (continuous layer) of bacterial or culture cells, resulting from cell Iysis and production of phage or animal virus progeny.
• Plasma membrane. The membrane that surrounds the cytoplasm.
• Plasmid. A circular DNA duplex that replicates autonomously in bacteria. Plasmids that integrate into the host genome are called episomes. Plasmids differ from viruses in that they never form infectious nucleoprotein particles.
• Polar group. A hydrophilic (water-loving) group.
• Polar mutation. A mutation in one gene that reduces the expression of a gene or genes distal to the promoter in the same operon.
• Polarimeter. An instrument for determining the rotation of polarization of light as the light passes through a solution containing an optically-active substance.
• Polyamine. A hydrocarbon containing more than two amino groups.
• Polycistronic messenger RNA. In prokaryotes, an RNA that contains two or more cistrons; note that only in prokaryotic mRNAs can more than one cistron be utilized by the translation system to generate individual proteins.
• Polymerase. An enzyme that catalyzes the synthesis of a polymer from monomers.
• Polynucleotide phosphorylase. An enzyme that polymerizes ribonucleotide diphosphates. No template is required.
• Polynucleotide. A chain structure containing nucleotides linked together by phosphodiester (5'-3') bonds. The polynucleotide chain has a directional sense with a 5' and a 3' end.
• Polypeptide. A linear polymer of amino acids held together by peptide linkages. The polypeptide has a directional sense, with an amino- and a carboxy-terminal end.
• Polyribosome (polysome). A complex of an mRNA and two or more ribosomes actively engaged in protein synthesis.
• Polysaccharide. A linear or branched chain structure containing many sugar molecules linked by glycosidic bonds.
• Porphyrin. A complex planar structure containing four substituted pyrroles covalently joined in a ring and frequently containing a central metal atom. For example, heme is a porphyrin with a central iron atom.
• Positive control. A system that is turned on by the presence of a regulatory protein.
• Posttranslational modification. The covalent bond changes that occur in a polypeptide chain after it leaves the ribosome and before it becomes a mature protein.
• Primary structure. In a polymer, the sequence of monomers and the covalent bonds. In proteins, it refers to the amino acid sequence.
• Primer. A structure that serves as a growing point for polymerization. Short primers of DNA are often used in sequencing and mutagenesis procedures.
• Primosome. A multiprotein complex that catalyzes synthesis of RNA primer at various points along the DNA template.
• Prochiral molecule. A nonchiral molecule that lacks handedness and is optically inactive, but would become chiral by a change in one of the substituents at the chiral center. A prochiral molecule may react with an enzyme so that two groups that have a mirror-image relationship to each other are treated differently.
• Prokaryote. A unicellular organism that contains a single chromosome, no nucleus, no membrane-bound organelles, and has characteristic ribosomes and biochemistry.
• Promoter. That region of the gene that signals RNA polymerase binding and the initiation of transcription.
• Prophage. The silent phage genome. Some prophages integrate into the host genome; others replicate autonomously. The prophage state is maintained by a phage-encoded repressor.
• Prophase. The stage in meiosis or mitosis when chromosomes condense and become visible as refractile bodies.
• Proprotein. A protein that is made in an active form, so that it requires processing to become functional.
• Prostaglandin. An oxygenated eicosanoid that has a hormonal function. Prostaglandins are unusual hormones in that they usually have effects only in that region of the organism where they are synthesized.
• Prosthetic group. Synonymous with coenzyme except that a prosthetic group is usually more firmly attached to the enzyme it serves.
• Protamines. Highly basic, arginine-rich proteins found complexed to DNA in the sperm of many invertebrates and fish.
• Protein subunit. One of the components or monomers of a multicomponent protein.
• Proteoglycan. A protein-linked heteropolysaccharide in which the heteropolysaccharide is usually the major component.
• Protist. A relatively undifferentiated organism that can survive as a single cell.
• Proto-oncogene. A cellular gene that can undergo modification to a cancer-causing gene (oncogene).
• Proton acceptor. A functional group capable of accepting a proton from a proton donor molecule.
• Proton motive force (Dp). The thermodynamic driving force for proton translocation.
• Pseudocycle. A sequence of reactions that can be arranged in a cycle but that usually do not function simultaneously in both directions. Also called a futile cycle, since the net result of simultaneous functioning in both directions would be the expenditure of energy without accomplishing any useful work.
• Pulse-chase. An experiment in which a short labeling period is followed by the addition of an excess of the same, unlabeled compound to dilute out the labeled material. Useful for observing time-dependent behavior of compounds.
• Purine. A heterocyclic ring structure with varying functional groups. The purines adenine and guanine are found in both DNA and RNA.
• Puromycin. An antibiotic that inhibits polypeptide synthesis by competing with aminoacyl-tRNA for the ribosomal binding site A.
• Pyranose. A simple sugar containing the six-membered pyran ring.
• Pyrimidine. A heterocyclic six-membered ring structure. Cytosine and uracil are the main pyrimidines found in RNA, and cytosine and thymine are the main pyrimidines found in DNA.
• Pyrophosphate. A molecule formed by two phosphates in anhydride linkage.

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Q-R

• Quaternary structure. In a protein, the way in which the different folded subunits interact to form the multisubunit protein.
• R group - (1) Formally, an abbreviation denoting any alkyl group. (2) Occasionally, used in a more general sense to denote virtually any organic substituent tthe R groups of amino acids, for example).
• R group. Shorthand for the side chain of an amino acid.
• R loop. A triple-stranded structure in which RNA displaces a DNA strand by DNA-RNA hybrid formation in a region of the DNA.
• RNA (ribonucleic acid) - A polyribonucleotide of a specific sequence linked by successive 3',5'-phosphodiester bonds.
• RNA polymerase - An enzyme that catalyzes the formation of RNA from ribonucleoside 5'-triphosphates, using a strand of DNA or RNA as a template.
• RNA polymerase. An enzyme that catalyzes the formation of RNA from ribonucleotide triphosphates, using DNA as a template.
• RNA splicing - Removal of introns and joining of exons in a primary transcript.
• Rapid-start complex. The complex that RNA polymerase forms at the promoter site just before initiation.
• Recombination. The transfer to offspring of genes not found together in either of the parents.
• Redox couple. An electron donor and its corresponding oxidized form.
• Redox potential (E). The relative tendency of a pair of molecules to release or accept an electron. The standard redox potential (E0) is the redox potential of a solution containing the oxidant and reductant of the couple at standard concentrations.
• Regulatory enzyme. An enzyme in which the active site is subject to regulation by factors other than the enzyme substrate. The enzyme frequently contains a nonoverlapping site for binding the regulatory factor that affects the activity of the active site.
• Regulatory gene. A gene whose principal product is a protein designed to regulate the synthesis of other genes.
• Renaturation. The process of returning a denatured structure to its original native structure, as when two single strands of DNA are reunited to form a regular duplex, or an unfolded polypeptide chain is returned to its normal folded three-dimensional structure.
• Repair synthesis. DNA synthesis following excision (cutting out) of damaged DNA.
• Repetitive DNA. A DNA sequence that is present in many copies per genome.
• Replica plating. A technique in which an impression of a culture is taken from a master plate and transferred to a fresh plate. The impression can be of bacterial clones or phage plaques.
• Replication fork. The Y-shaped region of DNA at the site of DNA synthesis; also called a growth fork.
• Replicon. A genetic element that behaves as an autonomous replicating unit. It can be a plasmid, phage, or bacterial chromosome.
• Repressor. A regulatory protein that inhibits transcription from one or more genes. It can combine with an inducer (resulting in specific enzyme induction) or with an operator element (resulting in repression).
• Resonance hybrid. A molecular structure that is a hybrid of two structures that differ in the locations of some of the electrons. For example, the benzene ring can be drawn in two ways, with double bonds in different positions. The actual structure of benzene is in-between these two equivalent structures.
• Restriction-modification system. A pair of enzymes found in most bacteria (but not eukaryotic cells). The restriction enzyme recognizes a certain sequence in duplex DNA and makes one cut in each unmodified DNA strand at or near the recognition sequence. The modification enzyme methylates (or modifies) the same sequence, thus protecting it from the action of the restriction enzyme.
• Reverse transcriptase. An enzyme that synthesizes DNA from an RNA template, using deoxyribonucleotide triphosphates.
• Rho factor. A protein involved in the termination of transcription of some messenger RNAs.
• Ribose. The five-carbon sugar found in RNA.
• Ribosomal RNA (rRNA). The RNA parts of the ribosome.
• Ribosomes. Small cellular particles made up of ribosomal RNA and protein. They are the site, together with mRNA, of protein synthesis.
• Rolling circle replication. A mechanism for the replication of circular DNA. A nick in one strand allows the 3' end to be extended, displacing the strand with the 5' end, which is also replicated, to generate a double-stranded tail that can become larger than the unit size of the circular DNA.

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S

• S phase. The period during the cell cycle when the chromosome is replicated.
• S-adenosylmethionine (adoMet) - An enzymatic cofactor involved in methyl group transfers.
• SOS response - In bacteria, a coordinated induction of a variety of genes as a response to high levels of DNA damage.
• SOS system. A set of DNA repair enzymes and regulatory proteins that regulate their synthesis so that maximum syn thesis occurs when the DNA is damaged.
• Salting in. The increase in solubility that is displayed by typical globular proteins upon the addition of small amounts of certain salts, such as ammonium sulfate.
• Salting out. The decrease in protein solubility that occurs when salts such as ammonium sulfate are present at high concentrations.
• Salvage pathway. A family of reactions that permits, for instance, nucleosides as well as purine and pyrimidine bases resulting from the partial breakdown of nucleic acids to be re-utilized in nucleic acid synthesis.
• Satellite DNA. A DNA fraction whose base composition differs from that of the main component of DNA, as revealed by the fact that it bands at a different density in a CsCI gradient. Usually repetitive DNA or organelle DNA.
• Second messenger. A diffusible small molecule, such as cAMP, that is formed at the inner surface of the plasma membrane in response to a hormonal signal.
• Secondary structure. In a protein or a nucleic acid, any repetitive folded pattern that results from the interaction of the corresponding polymeric chains. In proteins, the most common are b-strands (sheets) and a-helices.
• Semiconservative replication. Duplication of DNA in which the daughter duplex carries one old strand and one new strand.
• Semipermeable. The characteristic of allowing only some molecules, usually smaller or uncharged ones, to pass through.
• Shine-Dalgarno sequence - A sequence in an mRNA required for binding prokaryotic ribosomes.
• Sigma factor. A subunit of RNA polymerase that recognizes specific sites on DNA for initiation of RNA synthesis.
• Signal sequence. A (usually N-terminal) sequence of a protein that directs its processing or localization within the cell.
• Single-copy DNA. A region of the genome whose sequence is present only once per haploid complement.
• Site-directed mutagenesis. An intentional alteration in a DNA sequence that can be genetically inherited.
• Soluble protein. See globular protein.
• Somatic cell. Any cell of an organism that cannot contribute its genes to a later generation.
• Southern blot - A DNA hybridization procedure in which one or more specific DNA fragments are detected in a larger population by means of hybridization to a complementary, labeled nucleic acid probe.
• Southern blotting. A method for detecting a specific DNA restriction fragment, developed by Edward Southern. DNA from a gel electrophoresis pattern is blotted onto nitrocellulose paper; then the DNA is denatured and fixed on the paper. Subsequently the pattern of specific sequences in the Southern blot can be determined by hybridization to a suitable probe and autoradiography. A Northern blot is similar, except that RNA is blotted instead onto the nitrocellulose paper.
• Splicing. See RNA splicing.
• Sporulation. Formation from vegetative cells of metabolically inactive cells that can resist extreme environmental conditions.
• Stacking energy. The energy of interaction that favors the face-to-face packing of purine and pyrimidine base pairs.
• Steady state. In enzyme-kinetic analysis, the time interval when the rate of reaction is approximately constant with time. The term is also used to describe the state of a living cell where the concentrations of many molecules are approximately constant because of a balancing between their rate of synthesis and breakdown.
• Stem cell. A cell from which other cells stem or arise by differentiation.
• Stereoisomers. Isomers that are nonsuperimposable mirror images of each other.
• Steroids. Compounds that are derivatives of a tetracyclic structure composed of a cyclopentane ring fused to a substituted phenanthrene nucleus.
• Structural domain. An element of protein tertiary structure that forms an independent folding unit.
• Structural gene. A gene encoding the amino acid sequence of a polypeptide chain.
• Structural protein. A protein that serves a structural function.
• Substrate. A molecule that is acted upon, and chemically changed, by an enzyme.
• Subunit. Individual polypeptide chains in a protein.
• Supercoiled DNA. Supertwisted, covalently-closed duplex DNA.
• Suppressor gene. A gene that can reverse the phenotype of a mutation in another gene.
• Suppressor mutation. A mutation that restores a function lost by an initial mutation and that is located at a site different from the initial mutation.
• Svedberg (S) - A unit of measure of the rate at which a particle sediments in a centrifugal field.
• Svedberg unit (S). The unit used to express the sedimentation constant (S = 10-l3 sec). The sedimentation constant S is proportional to the rate of sedimentation of a molecule in a given centrifugal field and is related to the size and shape of the molecule.
• Synapse. The chemical connection for communication between two nerve cells or between a nerve cell and a target cell such as a muscle cell.
• Synapsis. The pairing of homologous chromosomes, seen during the first meiotic prophase.

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T

• TCA cycle. See tricarboxylic acid cycle.
• Tandem duplication. A duplication in which the repeated regions are immediately adjacent to one another.
• Template. A polynucleotide chain that serves as a surface for the absorption of monomers of a growing polymer and thereby dictates the sequence of the monomers in the growing chain.
• Termination factors. Proteins that are exclusively involved in the termination reactions of protein synthesis on the ribosome.
• Terpenes. A diverse group of lipids made from isoprene precursors.
• Tertiary structure. In a protein or nucleic acid, the final folded form of the polymer chain.
• Tetramer. Structure resulting from the association of four subunits.
• Thioester. An ester of a carboxylic acid with a thiol or mercaptan.
• Thymidine. One of the four nucleosides found in DNA.
• Thymine. A pyrimidine base found in DNA.
• Topoisomerase. An enzyme that changes the extent of supercoiling of a DNA duplex.
• Transamination. Enzymatic transfer of an amino group from an a-amino acid to an a-keto acid.
• Transcription. RNA synthesis that occurs on a DNA template.
• Transduction. Genetic exchange in bacteria that is mediated via phage.
• Transfection. An artificial process of infecting cells with naked viral DNA.
• Transfer RNA (tRNA). Any of a family of low-molecular weight RNAs that transfer amino acids from the cytoplasm to the template for protein synthesis on the ribosome.
• Transferase. An enzyme that catalyzes the transfer of a molecular group from one molecule to another.
• Transformation. Genetic exchange in bacteria that is mediated via purified DNA. In somatic cell genetics the term is also used to indicate the conversion of a normal cell to one that grows like a cancer cell.
• Transgenic. Describing an organism that contains transfected DNA in the germ line.
• Transition state. The activated state in which a molecule is best suited to undergoing a chemical reaction.
• Translation. The process of reading a messenger RNA sequence for the specified amino acid sequence it contains.
• Transport protein. A protein whose primary function is to transport a substance from one part of the cell to another, from one cell to another, or from one tissue to another.
• Tricarboxylic acid (TCA) cycle. The cyclical process whereby acetate is completely oxidized to CO2 and water, and electrons are transferred to NAD+ and flavine. The TCA cycle is localized to the mitochondria in eukaryotic cells and to the plasma membrane in prokaryotic cells. Also called the Krebs or citric acid cycle.
• Trypsin. A proteolytic enzyme that cleaves (cuts) peptide chains next to the basic amino acids arginine and Iysine.
• Tryptic peptide mapping. The technique of generating a chromatographic profile characteristic of the fragments resulting from trypsin enzyme cleavage of the protein.
• Tumorigenesis. The mechanism of tumor formation.
• Turnover number. The maximum number of molecules of substrate that can be converted to product per active site per unit time.

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U-Z

• UV irradiation. Electromagnetic radiation with a wavelength shorter than that of visible light (200-390 nm). Causes damage to DNA (mainly by forming pyrimidine dimers).
• Ultracentrifuge. A high-speed centrifuge that can attain speeds up to 60,000 rpm and centrifugal fields of 500,000 times gravity. Useful for characterizing and/or separating macromolecules.
• Unidirectional replication. See bidirectional replication.
• Unwinding proteins. Proteins that help to unwind double-stranded DNA during DNA replication.
• Urea cycle. A metabolic pathway in the liver that leads to the synthesis of urea from amino groups and CO2. The function of the pathway is to convert the ammonia resulting from catabolism to a nontoxic form, which is then secreted.
• Viroids. Pathogenic agents, mostly of plants, that consist of short (usually circular) RNA molecules.
• Virus. A complex of nucleic-acid and protein, that can infect and replicate inside a specific host cell to make more virus particles.
• Vitamin. A trace organic substance required in the diet of some species. Many vitamins are precursors of coenzymes.
• Vmax - The maximum velocity of an enzymatic reaction when the binding site is saturated with substrate.
• Watson-Crick base pairs. The type of hydrogen-bonded base pairs found in DNA, or comparable base pairs found in RNA. The base pairs are A-T, G-C, and A-U.
• Western blot. Similar in principle to a Southern blot, but where the species adsorbed to the nitrocellulose filter is a protein, and the detection makes use of specific antibodies.
• Wild-type gene. The form of a gene (allele) normally found in nature.
• Wobble. A proposed explanation for base pairing that is not of the Watson-Crick type and that often occurs between the 3' base in the codon and the 5' base in the anticodon.
• X-ray crystallography. A technique for determining the structure of molecules from the X-ray diffraction patterns that are produced by crystalline arrays of the molecules.
• Ylid. A compound in which adjacent, covalently-bonded atoms, both having an electronic octet, have opposite charges.
• Z form. A duplex DNA structure in which there is the usual type of hydrogen bonding between the base pairs but in which the helix formed by the two polynucleotide chains is left-handed rather than right-handed.
• Zwitterion. A dipolar ion with spatially-separated positive and negative charges. For example, most amino acids are zwitterions, having a positive charge on the a-amino group and a negative charge on the a-carboxyl group but no net charge on the overall molecule.
• Zygote. A cell that results from the union of haploid male and female sex cells. Zygotes are diploid.
• Zymogen. An inactive precursor of an enzyme. For example, trypsin exists in the inactive form trypsinogen before it is converted to its active form, trypsin.

More terms

• absolute configuration - The configuration of four different substituent groups around an asymmetric carbon atom, in relation to D- and L-glyceraldehyde.
• absolute configuration - The configuration of four different substituent groups around an asymmetric carbon atom, in relation to D- and L-glyceraldehyde. absolute configuration The configuration of four different substituent groups around an asymmetric carbon atom, in relation to D- and L-glyceraldehyde.
• absorption - Transport of the products of digestion from the intestinal tract into the blood.
• acceptor control - The regulation of the rate of respiration by the availability of ADP as phosphate group acceptor.
• accessory pigments - Visible lightabsorbing pigments (carotenoids, xanthophyll, and phycobilins) in plants and photosynthetic bacteria that complement chlorophylls in trapping energy from sunlight.
• acidosis - A metabolic condition in which the capacity of the body to buffer H+ is diminished; usually accompanied by decreased blood pH.
• actin - A protein making up the thin filaments of muscle; also an important component. of the cytoskeleton of many eukaryotic cells.
• activation energy (ΔG°') - The amount of energy (in joules) required to convert all the molecules in 1 mole of a reacting substance from the ground state to the transition state.
• activator - (1) A DNA-binding protein that positively regulates the expression of one or more genes; that is, transcription rates increase when an activator is bound to the DNA. (2) A positive modulator of an allosteric enzyme.
• active site - The region of an enzyme surface that binds the substrate molecule and catalytically transforms it; also known as the catalytic site.
• active transport - Energy-requiring transport of a solute across a membrane in the direction of increasing concentration.
• activity coefficient - The factor by which the numerical value of the concentration of a solute must be multiplied to give its true thermodynamic activity.
• activity - The true thermodynamic activity or potential of a substance, as distinct from its molar concentration.
• acyl phosphate - Any molecule with the general chemical form  .
• adenosine 3',5'-cyclic monophosphate - See cyclic AMP.
• adenosine diphosphate - See ADP.
• adenosine triphosphate - See ATP.
• adipocyte - An animal cell specialized for the storage of fats (triacylglycerols).
• adipose tissue - Connective tissue specialized for the storage of large amounts of triacylglycerols.
• aerobe - An organism that lives in air and uses oxygen as the terminal electron acceptor in respiration.
• aerobic - Requiring or occurring in the presence of oxygen.
• alcohol fermentation - The anaerobic conversion of glucose to ethanol via glycolysis. See also fermentation.
• aldose - A simple sugar in which the carbonyl carbon atom is an aldehyde; that is, the carbonyl carbon is at one end of the carbon chain.
• alkaloids - Nitrogen-containing organic compounds of plant origin; often basic, and having intense biological activity.
• alkalosis - A metabolic condition in which the capacity of the body to buffer OH- is diminished; usually accompanied by an increase in blood pH.
• allosteric enzyme - A regulatory enzyme, with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site.
• allosteric site - The specific site on the surface of an allosteric enzyme molecule to which the modulator or effector molecule is bound.
• amino acid activation - ATP-dependent enzymatic esterification of the carboxyl group of an amino acid to the 3'-hydroxyl group of its corresponding tRNA.
• amino acids - α-Amino-substituted carboxylic acids, the building blocks of proteins.
• amino-terminal residue - The only amino acid residue in a polypeptide chain with a free a-amino group; defmes the amino terminus of the polypeptide.
• aminoacyl-tRNA synthetases - Enzymes that catalyze synthesis of an aminoacyltRNA at the expense of ATP energy.
• aminoacyl-tRNA - An aminoacyl ester of a tRNA.
• aminotransferases - Enzymes that catalyze the transfer of amino groups from α-amino to α-keto acids; also called transaminases.
• ammonotelic - Excreting excess nitrogen in the form of ammonia.
• amphibolic pathway - A metabolic pathway used in both catabolism and anabolism.
• amphipathic - Containing both polar and nonpolar domains.
• amphoteric - Capable of donating and accepting protons, thus able to serve as an acid or a base.
• anabolism - The phase of intermediary metabolism concerned with the energyrequiring biosynthesis of cell components from smaller precursors.
• anaerobe - An organism that lives without oxygen. Obligate anaerobes die when exposed to oxygen.
• anaerobic - Occurring in the absence of air or oxygen.
• anaplerotic reaction - An enzyme-catalyzed reaction that can replenish the supply of intermediates in the citric acid cycle.
• angstrom (Å) - A unit of length (10-8 cm) used to indicate molecular dimensions.
• anhydride - The product of the condensation of two carboxyl or phosphate groups in which the elements of water are eliminated to form a compound with the general structure , where X is either carbon or phosphorus.
• anion-exchange resin - A polymeric resin with fixed cationic groups; used in the chromatographic separation of anions.
• anomers - Two stereoisomers of a given sugar that differ only in the configuration about the carbonyl (anomeric) carbon atom.
• antibiotic - One of many different organic compounds that are formed and secreted by various species of microorganisms and plants, are toxic to other species, and presumably have a defensive function.
• antibody - A defense protein synthesized by the immune system of vertebrates. See also immunoglobulin.
• anticodon - A specific sequence of three nucleotides in a tRNA, complementary to a codon for an amino acid in an mRNA.
• antigen - A molecule capable of eliciting the synthesis of a specific antibody in vertebrates.
• antiparallel - Describing two linear polymers that are opposite in polarity or orientation.
• antiport - Cotransport of two solutes across a membrane in opposite directions.
• apoenzyme - The protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity.
• apolipoprotein - The protein component of a lipoprotein.
• asymmetric carbon atom - A carbon atom that is covalently bonded to four dif ferent groups and thus may exist in two different tetrahedral configurations.
• attenuator - An RNA sequence involved in regulating the expression of certain genes; functions as a transcription terminator.
• autotroph - An organism that can synthesize its own complex molecules from very simple carbon and nitrogen sources, such as carbon dioxide and ammonia.
• auxin - A plant growth hormone.
• auxotrophic mutant (auxotroph) - A mutant organism defective in the synthesis of a given biomolecule, which must therefore be supplied for the organism's growth.
• back-mutation - A mutation that causes a mutant gene to regain its wild-type base sequence.
• bacteriophage - A virus capable of replicating in a bacterial cell.
• basal metabolic rate - The rate of oxygen consumption by an animal's body at complete rest, long after a meal.
• base pair - Tvvo nucleotides in nucleic acid chains that are paired by hydrogen bond. ing of their bases; for example, A with T or U, and G with C.
• bilayer - A double layer of oriented amphipathic lipid molecules, forming the basic structure of biological membranes. The hydrocarbon tails face inward to form a continuous nonpolar phase.
• bile salts - Amphipathic steroid derivatives with detergent properties, participating in digestion and absorption of lipids.
• binding energy - The energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand.
• biocytin - The conjugate amino acid residue arising from covalent attachment of biotin, through an amide linkage, to a Lys residue.
• biomolecule - An organic compound normally present as an essential component of living organisms.
• biopterin - An enzymatic cofactor derived from pterin and involved in certain oxidation-reduction reactions.
• biosphere - All the living matter on or in the earth, the seas, and the atmosphere.
• biotin - A vitamin; an enzymatic cofactor involved in carboxylation reactions.
• bond energy - The energy required to break a bond.
• branch migration - Movement of the branch point in branched DNA formed from two DNA molecules with identical sequences. See also Holliday intermediate.
• buffer - A system capable of resisting changes in pH, consisting of a conjugate acid-base pair in which the ratio of proton acceptor to proton donor is near unity.
• cAMP - See cyclic AMP.
• cAMP. 3',5' cyclic adenosine monophosphate. The cAMP molecule plays a key role in metabolic regulation.
• cDNA - See complementary DNA.
• cDNA. Complementary DNA, made in vitro from the mRNA by the enzyme reverse transcriptase using deoxyribonucleotide triphosphates. Unlike mRNA, cDNA can be easily propagated and sequenced.
• calorie - The amount of heat required to raise the temperature of 1.0 g of water from 14.5 to 15.5 °. One calorie (cal) equals 4.18 joules (J).
• capsid - The protein coat of a virion or virus particle.
• carbanion - A negatively charged carbon atom.
• carbocation - A positively charged carbon atom; also called a carbonium ion.
• carbon fixation reactions - In photosynthetic cells, the light-independent enzymatic reactions involved in the synthesis of glucose from CO2, ATP, and NADPH; also known as the dark reactions.
• carboxyl-terminal residue - The only amino acid residue in a polypeptide chain with a free α-carboxyl group; defines the carboxyl terminus of the polypeptide.
• carotenoids - Lipid-soluble photosynthetic pigments made up of isoprene units.
• catabolism - The phase of intermediary metabolism concerned with the energyyielding degradation of nutrient molecules.
• catabolite gene activator protein (CAP) - A specific regulatory protein that controls initiation of transcription of the genes producing the enzymes required for a bacterial cell to use some other nutrient when glucose is lacking.
• catalytic site - See active site.
• catecholamines - Hormones, such as epinephrine, that are amino derivatives of catechol.
• cation-exchange resin - An insoluble polymer with fixed negative charges; used in the chromatographic separation of cationic substances.
• central dogma - The organizing principle of molecular biology: genetic information flows from DNA to RNA to protein.
• centromere - A specialized site within a chromosome, serving as the attachment point for the mitotic or meiotic spindle.
• cerebroside - Sphingolipid containing one sugar residue as a head group.
• channeling - The direct transfer of a reaction product (common intermediate) from the active site of one enzyme to the active site of a different enzyme catalyzing the next step in a sequential pathway.
• chemiosmotic coupling - Coupling of ATP synthesis to electron transfer via an electrochemical H+ gradient across a membrane.
• chemotaxis - A cell's sensing of and movement toward, or away from, a specific chemical agent.
• chemotroph - An organism that obtains energy by metabolizing organic compounds derived from other organisms.
• chiral compound - A compound that contains an asymmetric center (chiral atom or chiral center) and thus can occur in two nonsuperimposable mirror-image forms (enantiomers).
• chlorophylls - A family of green pigments functioning as receptors of light energy in photosynthesis; magnesium-porphyrin complexes.
• chloroplasts - Chlorophyll-containing photosynthetic organelles in some eukaryotic cells.
• chromatin - A filamentous complex of DNA, histones, and other proteins, constituting the eukaryotic chromosome.
• chromatography - A process in which complex mixtures of molecules are separated by many repeated partitionings between a flowing (mobile) phase and a stationary phase.
• chromosome - A single large DNA molecule and its associated proteins, containing many genes; stores and transmits genetic information.
• chylomicron - A plasma lipoprotein consisting of a large droplet of triacylglycerols stabilized by a coat of protein and phospholipid; carries lipids from the intestine to the tissues.
• cis and trans isomers - See geometric isomers.
• cistron - A unit of DNA or RNA corresponding to one gene.
• citric acid cycle - A cyclic system of enzymatic reactions for the oxidation of acetyl residues to carbon dioxide, in which formation of citrate is the first step; also known as the Krebs cycle or tricarboxylic acid cycle.
• clones - The descendants of a single cell.
• cloning - The production of large numbers of identical DNA molecules or cells from a single ancestral DNA molecule or cell.
• closed system - A system that exchanges neither matter nor energy with the surroundings. See also system.
• cobalamin - See coenzyme B12.
• codon - A sequence of three adjacent nucleotides in a nucleic acid that codes for a specific amino acid.
• coenzyme A - A pantothenic acidcontaining coenzyme serving as an acyl group carrier in certain enzymatic reactions.
• coenzyme B12 - An enzymatic cofactor derived from the vitamin cobalamin, involved in certain types of carbon skeletal rearrangements.
• coenzyme - An organic cofactor required for the action of certain enzymes; often contains a vitamin as a component.
• cofactor - An inorganic ion or a coenzyme required for enzyme activity.
• cognate - Describing two biomolecules that normally interact; for example, an enzyme and its normal substrate, or a receptor and its normal ligand.
• cohesive ends - See sticky ends.
• cointegrate - An intermediate in the migration of certain DNA transposons in which the donor DNA and target DNA are covalently attached.
• colligative properties - Properties of solutions that depend on the number of solute particles per unit volume; for example, freezing-point depression.
• common intermediate - A chemical compound common to two chemical reactions, as a product of one and a reactant in the other.
• competitive inhibition - A type of enzyme inhibition reversed by increasing the substrate concentration; a competitive inhibitor generally competes with the normal substrate or ligand for a protein's binding site.
• complementary DNA (cDNA) - A DNA used in DNA cloning, usually made by reverse transcriptase; complementary to a given mRNA.
• complementary - Having a molecular surface with chemical groups arranged to interact specifically with chemical groups on another molecule.
• configuration - The spatial arrangement of an organic molecule that is conferred by the presence of either (1) double bonds, about which there is no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific sequence. Configurational isomers cannot be interconverted without breaking one or more covalent bonds.
• conformation, β - See β conformation.
• conformation - The spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation.
• conjugate acid-base pair - A proton donor and its corresponding deprotonated species; for example, acetic acid (donor) and acetate (acceptor).
• conjugate redox pair - An electron donor and its corresponding electron acceptor form; for example, Cu+ (donor) and Cu2+ (acceptor), or NADH (donor) and NAD+ (acceptor).
• conjugated protein - A protein containing one or more prosthetic groups.
• consensus sequence - A DNA or amino acid sequence consisting of the residues that occur most commonly at each position within a set of similar sequences.
• conservative substitution - Replacement of an amino acid residue in a polypeptide by another residue with similar properties; for example, substitution of Glu by Asp.
• constitutive enzymes - Enzymes required at all times by a cell and present at some constant level; for example, many enzymes of the central metabolic pathways. Sometimes called "housekeeping enzymes."
• corticosteroids - Steroid hormones formed by the adrenal cortex.
• cosmid - A cloning vector, used for cloning large DNA fragments; generally contains segments derived from bacteriophages and various plasmids.
• coupled reactions - Two chemical reactions that have a common intermediate and thus a means of energy transfer from one to the other.
• covalent bond - A chemical bond that involves sharing of electron pairs.
• cristae - Infoldings of the inner mitochondrial membrane.
• cyclic AMP icAMP) - A second messenger within cells; its formation by adenylate cyclase is stimulated by certain hormones or other molecular signals.
• cyclic electron flow - In chloroplasts, the light-induced flow of electrons originating from and returning to photosystem I.
• cyclic photophosphorylation - ATP synthesis driven by cyclic electron flow through photosystem I.
• cytochromes - Heme proteins serving as electron carriers in respiration, photosynthesis, and other oxidation-reduction reactions.
• cytokinesis - The final separation of daughter cells following mitosis.
• cytoplasm - The portion of a cell's contents outside the nucleus but within the plasma membrane; includes organelles such as mitochondria.
• cytoskeleton - The filamentous network providing structure and organization to the cytoplasm; includes actin filaments, microtubules, and intermediate filaments.
• cytosol - The continuous aqueous phase of the cytoplasm, with its dissolved solutes; excludes the organelles such as mitochondria.
• dalton - The weight of a single hydrogen atom (1.66 x 10 -24g).
• dark reactions - See carbon fixation reactions.
• de novo pathway - Pathway for synthesis of a biomolecule, such as a nucleotide, from simple precursors; as distinct from a salvage pathway.
• deamination - The enzymatic removal of amino groups from biomolecules such as amino acids or nucleotides.
• degenerate code - A code in which a single element in one language is specified by more than one element in a second language.
• dehydrogenases - Enzymes catalyzing the removal of pairs of hydrogen atoms from their substrates.
• deletion mutation - A mutation resulting from the deletion of one or more nucleotides from a gene or chromosome.
• denaturation - Partial or complete unfolding of the specific native conformation of a polypeptide chain, protein, or nucleic acid.
• denatured protein - A protein that has lost its native conformation by exposure to a destabilizing agent such as heat or detergent.
• deoxyribonucleic acid - See DNA.
• deoxyribonucleotides - Nucleotides containing 2-deoxy-n-ribose as the pentose component.
• desaturases - Enzymes that catalyze the introduction of double bonds into the hydrocarbon portion of fatty acids.
• desolvation - In aqueous solution, the release of bound water surrounding a solute.
• dextrorotatory isomer - A stereoisomer that rotates the plane of plane-polarized light clockwise.
• diabetes mellitus - A metabolic disease resulting from insulin deficiency; characterized by a failure in glucose transport from the blood into cells at normal glucose concentrations.
• dialysis - Removal of small molecules from a solution of a macromolecule, by allowing them to diffuse through a semipermeable membrane into water.
• differential centrifugation - Separation of cell organelles or other particles of different size by their different rates of sedimentation in a centrifugal field.
• differentiation - Specialization of cell structure and function during embryonic gnowth and development.
• diffusion - The net movement of molecules in the direction of lower concentration.
• digestion - Enzymatic hydrolysis of major nutrients in the gastrointestinal system to yield their simpler components.
• diploid - Having two sets of genetic information; describing a cell with two chromosomes of each type.
• dipole - A molecule having both positive and negative charges.
• diprotic acid - An acid having two dissociable protons.
• disaccharide - A carbohydrate consisting of two covalently joined monosaccharide units.
• dissociation constant - (1) An equilibrium constant (Kd) for the dissociation of a complex of two or more biomolecules into its components; for example, dissociation of a substrate from an enzyme. (2) The dissociation constant (Ka) of an acid, describing its dissociation into its conjugate base and a proton.
• disulfide bridge - A covalent cross link between two polypeptide chains formed by a cystine residue (two Cys residues).
• domain - A distinot structural unit of a polypeptide; domains may have separate functions and may fold as independent, compact units.
• double helix - The natural coiled conformation of two complementary, antiparallel DNA chains.
• double-reciprocal plot - A plot of 1/V0 versus I/[S], which allows a more accurate determination of Vmax and Km, than a plot of Vo versus [S]; also called the Lineweaver-Burk plot.
• electrochemical gradient - The sum of the gradients of concentration and of electric charge of an ion across a membrane; the driving force for oxidative phosphorylation and photophosphorylation.
• electrochemical potential - The energy required to maintain a separation of charge and of concentration across a membrane.
• electrogenic - Contributing to an electrical potential across a membrane.
• electron acceptor - A substance that receives electrons in an oxidation-reduction reaction.
• electron carrier - A protein, such as a ilavoprotein or a cytochrome, that can reversibly gain and lose electrons; funetions in the transfer of electrons from organic nutrients to oxygen or some other terminal acceptor.
• electron donor - A substance that donates electrons in an oxidation-reduction reaction.
• electron transfer - Movement of electrons from substrates to oxygen via the carriers of the respiratory (electron transfer) chain.
• electrophile - An electron-deficient group with a strong tendency to accept electrons from an electron-rich group (nucleophile).
• electrophoresis - Movement of charged solutes in response to an electrical field; often used to separate mixtures of ions, proteins, or nucleic acids.
• elongation factors - Specific proteins required in the elongation of polypeptide chains by ribosomes.
• eluate - The effluent from a chromatographic column.
• enantiomers - Stereoisomers that are nonsuperimposable mirror images of each other.
• end-product inhibition - See feedback inhibition.
• endergonic reaetion - A chemical reaction that consumes energy (that is, for which ,ΔG is positive).
• endocrine glands - Groups of cells specialized to synthesize hormones and secrete them into the blood to regulate other types of cells.
• endocytosis - The uptake of extracellular material by its inclusion within a vesicle (endosome) formed by an invagination of the plasma membrane.
• endonuclease - An enzyme that hydrolyzes the interior phosphodiester bonds of a nucleic acid; that is, it acts at points other than the terminal bonds.
• endoplasmic reticulum - An extensive system of double membranes in the cytoplasm of eukaryotic cells; it encloses secretory channels and is often studded with ribosomes (rough endoplasmic reticulum).
• endothermic reaction - A chemical reaction that takes up heat (that is, for which ΔH is positive).
• energy charge - The fractional degree to which the ATPIADPfAMP system is filled with high-energy phosphate groups.
• energy coupling - The transfer of energy from one process to another.
• enhancers - DNA sequences that facilitate the expression of a given gene; may be located a few hundred, or even thousand, base pairs away from the gene.
• enthalpy (H) - The heat content of a system.
• enthalpy change (ΔH) - For a reaction, is approximately equal to the difference between the energy used to break bonds and the energy gained by the formation of new ones.
• entropy (S) - The extent of randomness or disorder in a system.
• enzyme - A biomolecule, either protein or RNA, that catalyzes a specific chemical reaction. It does not affect the equilibrium of the catalyzed reaction; it enhances the rate of a reaction by providing a reaction path with a lower activation energy.
• eotransport - The simultaneous transport, by a single transporter, of two solutes across a membrane. See antiport, symport.
• epimerases - Enzymes that catalyze the reversible interconversion of two epimers.
• epimers - Two stereoisomers differing in configuration at one asymmetric center, in a compound having two or more asymmetric ceuters.
• epithelial cell - Any cell that forms part of the outer covering of an organism or organ.
• epitope - An antigenic determinant; the particular chemical group or groups within a macromolecule (antigen) to which a given antibody binds.
• equilibrium constant (Keq) - A constant, characteristic for each chemical reaction; relates the specific concentrations of all reactants and products at equilibrium at a given temperature and pressure.
• equilibrium - The state of a system in which no further net change is occurring; the free energy is at a minimum.
• erythrocyte - A cell containing large amounts of hemoglobin and specialized for oxygen transport; a red blood cell.
• essential amino acids - Amino acids that cannot be synthesized by humans (and other vertebrates) and must be obtained from the diet.
• essential fatty acids - The group of polyunsaturated fatty acids produced by plants, but not by humans; required in the human diet.
• ethanol fermentation - See alcohol fermentation.
• eukaryote - A unicellular or multicellular organism with cells having a membranebounded nucleus, multiple chromosomes, and internal organelles.
• excited state - An energy-rich state of an atom or molecule; produced by the absorption of light energy.
• exergonic reaction - A chemical reaction that proceeds with the release of free energy (that is, for which ΔG is negative).
• exocytosis - The fusion of an intracellular vesicle with the plasma membrane, releasing the vesicle contents to the extracellular space.
• exon - The segment of a eukaryotic gene that encodes a portion of the final product of the gene; a portion that remains after posttranscriptional processing and is transcribed into a protein or incorporated into the structure of an RNA. See intron.
• exonuclease - An enzyme that hydrolyzes only those phosphodiester bonds that are in the terminal positions of a nucleic acid.
• exothermic reaction - A chemical reaction that releases heat (that is, for which ΔH is negative).
• expression vector - See vector.
• facilitated diffusion - Diffusion of a polar substance across a biological membrane through a protein transporter; also called passive diffusion or passive transport.
• facultative cells - Cells that can live in the presence or absence of oxygen.
• fatty acid - A long-chain aliphatic carboxylic acid found in natural fats and oils; also a component of membrane phospholipids and glycolipids.
• feedback inhibition - Inhibition of an allosteric enzyme at the beginning of a metabolic sequence by the end product of the sequence; also known as end-product inhibition.
• fermentation - Energy-yielding anaerobic breakdown of a nutrient molecule, such as glucose, without net oxidation; yields lactate, ethanol, or some other simple product.
• fibroblast - A cell of the connective tissue that secretes connective tissue proteins such as collagen.
• fibrous proteins - Insoluble proteins that serve in a protective or structural role; contain polypeptide chains that generally share a common secondary structure.
• fingerprinting - See peptide mapping.
• first law of thermodynamics - The law stating that in all processes, the total energy of the universe remains constant.
• flagellum - A cell appendage used in propulsion. Bacterial flagella have a much simpler structure than eukaryotic flagella, which are similar to cilia.
• flavin nucleotides - Nucleotide coenzymes (FMN and FAD) containing riboflavin.
• flavin-linked dehydrogenases - Dehydrogenases requiring one of the riboflavin coenzymes, FMN or FAD.
• flavoprotein - An enzyme containing a flavin nucleotide as a tightly bound prosthetic group.
• fluid mosaic model - A model describing biological membranes as a fluid lipid bilayer with embedded proteins; the bilayer exhibits both structural and functional asymmetry.
• fluorescence - Emission of light by excited molecules as they revert to the ground state.
• footprinting - A technique for identifying the nucleic acid sequence bound by a DNA- or RNA-binding protein.
• frame shift - A mutation caused by insertion or deletion of one or more paired nucleotides, changing the reading frame of codons during protein synthesis; the polypeptide product has a garbled amino acid sequence beginning at the mutated codon.
• free energy (G) - The component of the total energy of a system that can do work at constant temperature and pressure.
• [[free energy of activation (ΔG#) See activation energy.
• free radical - See radical.
• free-energy change (ΔG) - The amount of free energy released (negative ΔG) or absorbed (positive ΔG) in a reaction at constant temperature and pressure.
• functional group - The specific atom or group of atoms that confers a particular chemical property on a biomolecule.
• furanose - A simple sugar containing the five-membered furan ring.
• fusion protein - (1) A family of proteins that facilitate membrane fusion. (2) The protein product of a gene created by the fusion of two distinct genes.
• futile cycle - A set of enzyme-catalyzed cyclic reactions that results in release of thermal energy by the hydrolysis of ATP.
• gametes - Reproductive cells with a haploid gene content; sperm or egg cells.
• gangliosides - Sphingolipids, containing complex oligosaccharides as head groups; especially common in nervous tissue.
• gel flltration - A chromatographic procedure for the separation of a mixture of molecules on the basis of size; based on the capacity of porous polymers to exclude solutes above a certain size.
• gene expression - lYanscription and, in the case of proteins, translation to yield the product of a gene; a gene is expressed when its biological product is present and active.
• gene splicing - The enzymatic attachment of one gene, or part of a gene, to another.
• gene - A chromosomal segment that codes for a single functional polypeptide chain or RNA molecule.
• general acid-base catalysis - Catalysis involving proton transfer(s) to or from a molecule other than water.
• genetic code - The set of triplet code words in DNA (or mRNA) coding for the amino acids of proteins.
• genetic information - The hereditary information contained in a sequence of nucleotide bases in chromosomal DNA or RNA.
• genetic map - A diagram showirg the relative sequence and position of specific genes along a chromosome.
• genome - All the genetic information encoded in a cell or virus.
• genotype - The genetic constitution of an organism, as distinct from its physical characteristics, or phenotype.
• geometric isomers - Isomers related by rotation about a double bond; also called cis and trans isomers.
• germ-line cell - A type of animal cell that is formed early in embryogenesis and may multiply by mitosis or may produce, by meiosis, cells that develop into gametes (egg or sperm cells).
• globular proteins - Soluble proteins with a globular (somewhat rounded) shape.
• glucogenic amino acids - Amino acids with carbon chains that can be metabolically converted into glucose or glycogen via gluconeogenesis.
• gluconeogenesis - The biosynthesis of a carbohydrate from simpler, noncarbohydrate precursors such as oxaloacetate or pyruvate.
• glycan - Another term for polysaccharide; a polymer of monosaccharide units joined by glycosidic bonds.
• glycerophospholipid - An amphipathic lipid with a glycerol backbone; fatty acids are ester-linked to Gl and C-2 of glycerol, and a polar alcohol is attached through a phosphodiester linkage to C-3.
• glycolipid - A lipid containing a carbohydrate group.
• glycolysis - The catabolic pathway by which a molecule of glucose is broken down into two molecules of pyruvate.
• glycoprotein - A protein containing a carbohydrate group.
• glycosaminoglycan - A heteropolysaccharide of two alternating units: one is either N-acetylglucosamine or N-acetylgalactosamine; the other is a uronic acid (usually glucuronic acid). Formerly called mucopolysaccharide.
• glycosidic bonds - Bonds between a sugar and another molecule (typically an alcohol, purine, pyrimidine, or sugar) through an intervening oxygen or nitrogen atom; the bonds are classified as O-glycosidic or N-glycosidic, respectively.
• glyoxylate cycle - A variant of the citric acid cycle, for the net conversion of acetate into succinate and, eventually, new some
• glyoxysome - A specialized peroxisome containing the enzymes of the glyoxylate cycle; found in cells of germinating seeds.
• gram molecular weight - The weight in grams of a compound that is numerically equal to its molecular weight; the weight of 1 mole.
• grana - Stacks of thylakoids, flattened membranous sacs or discs, in chloroplasts.
• ground state - The normal, stable form of an atom or molecule; as distinct from the excited state.
• group transfer potential - A measure of the ability of a compound to donate an activated group (such as a phosphate or acyl group); generally expressed as the standard free energy of hydrolysis.
• half-life - The time required for the disappearance or decay of one-half of a given component in a system.
• haploid - Having a single set of genetic information; describing a cell with one chromosome of each type.
• helicase - An enzyme that catalyzes the separation of strands in a DNA molecule before replication.
• helix, α - See α helix.
• heme protein - A protein containing a heme as a prosthetic group.
• heme - The iron-porphyrin prosthetic group of heme proteins.
• hemoglobin - A heme protein in erythrocytes; functions in oxygen transport.
• hepatocyte - The major cell type of liver tissue.
• heteroduplex DNA - Duplex DNA containing complementary strands derived
• heterotroph - An organism that requires complex nutrient molecules, such as glucose, as a source of energy and carbon.
• heterotropic enzyme - An allosteric enzyme requiring a modulator other than its substrate.
• hexose - A simple sugar with a backbone containing six carbon atoms. high-energy compound: A compound that on hydrolysis undergoes a large decrease in free energy under standard conditions.
• high-performance liquid chromatography (HPLC) - Chromatographic procedures, often conducted at relatively high pressures, using automated equipment that permits refined and highly reproducible profiles.
• histones - The family of five basic proteins that associate tightly with DNA in the chromosomes of all eukaryotic cells.
• holoenzyme - A catalytically active enzyme including all necessary subunits, prosthetic groups, and cofactors.
• homelogous proteins - Proteins having sequences and functions similar in difierent species; for example, the hemoglobins. made up ride unit.
• homeobox - A conserved DNA sequence of 180 base pairs encoding a protein domain found in many proteins that play a regulatory role in development.
• homeodomain - The protein domain encoded by the homeobox.
• homeostasis - The maintenance of a dynamic steady state by regulatory mechanisms that compensate for changes in external circumstances.
• homeotic genes - Genes that regulate the development of the pattern of segments in the Drosophila body plan; similar genes are found in most vertebrates.
• homologous genetic recombination - Recombination between two DNA molecules of similar sequence, occurring in all cells; occurs during meiosis and mitosis in eukaryotes.
• homotropic enzyme - An allosteric enzyme that uses its substrate as a modulator.
• hormone receptor - A protein in, or on the surface of, target cells that binds a specific hormone and initiates the cellular response.
• hormone - A chemical substance synthesized in small amounts by an endocrine tissue and carried in the blood to another tissue, where it acts as a messenger to regulate the function of the target tissue or organ.
• hydrogen bond - A weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom.
• hydrolases - Enzymes (proteases, lipases, phosphatases, nucleases, for example) that catalyze hydrolysis reactions.
• hydrolysis - Cleavage of a bond, such as an anhydride or peptide bond, by the addition of the elements of water, yielding two or more products.
• hydronium ion - The hydrated hydrogen ion (H2O+).
• hydropathy index - A scale that expresses the relative hydrophobic and hydrophilic tendencies of a chemical group.
• hydrophilic - Polar or charged; describing molecules or groups that associate with (dissolve easily in) water.
• hydrophobic interactions - The association of nonpolar groups, or compounds, with each other in aqueous systems, driven by the tendency of the surrounding water molecules to seek their most stable (disordered) state.
• hydrophobic - Nonpolar; describing molecules or groups that are insoluble in water.
• hyperchromic effect - The large increase in light absorption at 260 nm occurring as a double-helical DNA is melted (unwound).
• immune response - The capacity of a vertebrate to generate antibodies to an antigen, a macromolecule foreign to the organism.
• immunoglobulin - An antibody protein generated against, and capable of binding specifically to, an antigen.
• in vitro - "In glass"; that is, in the test tube.
• in vivo - "In life"; that is, in the living cell or organism.
• induced fit - A change in the conformation of an enzyme in response to substrate binding that renders the enzyme catalytically active; also used to denote changes in the conformation of any macromolecule in response to ligand binding such that the binding site of the macromolecule better conforms to the shape of the ligand.
• inducer - A signal molecule that, when bound to a regulatory protein, produces an increase in the expression of a given gene.
• induction - An increase in the expression of a gene in response to a change in the activity of a regulatory protein.
• informational macromolecules - Biomolecules containing information in the form of specific sequences of different monomers; for example, many proteins, lipids, polysaccharides, and nucleic acids.
• initiation codon - AUG (sometimes GUG in prokaryotes); codes for the first amino acid in a polypeptide sequence: N-formylmethionine in prokaryotes, and methionine in eukaryotes.
• initiation complex - A complex of a ribosome with an mRNA and the initiating Met-tRNAMet or fMet-tRNAfMet, ready for the elongation steps.
• inorganic pyrophosphatase - An enzyme that hydrolyzes a molecule of inorganic pyrophosphate to yield two molecules of (ortho) phosphate; also known as pyrophosphatase.
• insertion mutation - A mutation caused by insertion of one or more extra bases, or a mutagen, between two successive bases in DNA.
• insertion sequence - Specific base sequences at either end of a transposable segment of DNA.
• integral membrane proteins - Proteins firmly bound to a membrane by hydrophobic interactions; as distinct from peripheral proteins.
• intercalating mutagen - A mutagen that inserts itself between two successive bases in a nucleic acid, causing a frame-shift mutation.
• intercalation - Insertion between two stacked aromatic or planar rings; for example, the insertion of a planar molecule between two successive bases in a nucleic acid.
• interferons - A class of glycoproteins with antiviral activities.
• intermediary metabolism - In cells, the enzyme-catalyzed reactions that extract chemical energy from nutrient molecules and utilize it to synthesize and assemble cell components.
• intron (intervening sequence) - A sequence of nucleotides in a gene that is transcribed but excised before the gene is translated.
• ion channel - An integral membrane protein that provides for the regulated transport of a specific ion, or ions, across a membrane.
• ion product of water (Kw) - The product of the concentrations of H+ and OH- in pure water: KW = [H+][OH-] = 1 x 10-14 at 25 °C.
• ion-exchange resin - A polymeric resin that contains fixed charged groups; used in chromatographic columns to separate ionic compounds.
• ionizing radiation - A type of radiation, such as x rays, that causes loss of electrons from some organic molecules, thus making them more reactive.
• ionophore - A compound that binds one or more metal ions and is capable of dif fusing across a membrane, carrying the bound ion.
• iron-sulfur center - A prosthetic group of certain redox proteins involved in electron transfers; Fe2+ or Fe3+ is bound to inorganic sulfur and to Cys groups in the protein.
• isoelectric focusing - An electrophoretic method for separating macromolecules on the basis of their isoelectric pH.
• isoelectric pH (isoelectric point) - The pH at which a solute has no net electric charge and thus does not move in an electric field.
• isoenzymes - See isozymes.
• isomerases - Enzymes that catalyze the transformation of compounds into their positional isomers.
• isomers - Any two molecules with the same molecular formula but a different arrangement of molecular groups.
• isoprene - The hydrocarbon 2-methyl-1,3-butadiene, a recurring structural unit of the terpenoid biomolecules.
• isothermal - Occurring at constant temperature.
• isotopes - Stable or radioactive forms of an element that differ in atomic weight but are otherwise chemically identical to the naturally abundant form of the element; used as tracers.
• isozymes - Multiple forms of an enzyme that catalyze the same reaction but differ from each other in their amino acid sequence, substrate affinity, Vmax, and/or regulatory properties; also called isoenzymes.
• keratins - Insoluble protective or structural proteins consisting of parallel polypeptide chains in α-helical or β conformations.
• ketogenic amino acids - Amino acids with carbon skeletons that can serve as precursors of the ketone bodies.
• ketone bodies - Acetoacetate, D-βhydroxybutyrate, and acetone; watersoluble fuels normally exported by the liver but overproduced during fasting or in untreated diabetes mellitus.
• ketose - A simple monosaccharide in which the carbonyl group is a ketone.
• ketosis - A condition in which the concentration of ketone bodies in the blood, tissues, and urine is abnormally high.
• kinases - Enzymes that catalyze the phosphorylation of certain molecules by ATP.
• kinetics - The study of reaction rates.
• lagging strand - The DNA strand that, during replication, must be synthesized in the direction opposite to that in which the replication fork moves.
• law of mass action - The law stating that the rate of any given chemical reaction is proportional to the product of the activities (or concentrations) of the reactants.
• leader - A short sequence near the amino terminus of a protein or the 5' end of an RNA that has a specialized targeting or regulatory function.
• leading strand - The DNA strand that, during replication, is synthesized in the same direction in which the replication fork moves.
• leaky mutant - A mutant gene that gives rise to a product with a detectable Ievel of biological activity.
• leaving group - The departing or displaced molecular group in a unimolecular elimination or a bimolecular substitution reaction.
• lethal mutation - A mutation that inactivates a biological funetion essential to the life of the cell or organism.
• leucine zipper - A protein structural motif involved in protein-protein interactions in many eukaryotic regulatory proteins; consists of two interacting α helices in which Leu residues in every seventh position are a prominent feature of the interacting surfaces.
• leukotrienes - A family of molecules derived from arachidonate; muscle contractants that constrict air passages in the lungs and are involved in asthma.
• levorotatory isomer - A stereoisomer that rotates the plane of plane-polarized light counterclockwise.
• ligand - A small molecule that binds specifically to a larger one; for example, a hormone is the ligand for its specific protein receptor.
• light reactions - The reactions of photosynthesis that require light and cannot occur in the dark; also known as the light-dependent reactions.
• linking number - The number of times one closed circular DNA strand is wound about another; the number of topological links holding the circles together.
• lipases - Enzymes that catalyze the hydrolysis of triacylglycerols.
• lipid - A small water-insoluble biomolecule generally containing fatty acids, sterols, or isoprenoid compounds.
• lipoate (lipoic acid) - A vitamin for some microorganisms; an intermediate carrier of hydrogen atoms and acyl groups in α-keto acid dehydrogenases.
• lipoprotein - A lipid-protein aggregate that serves to carry water-insoluble lipids in the blood. The protein component alone is an apolipoprotein.
• low-energy phosphate compound - A phosphorylated compound with a relatively small standard free energy of hydrolysis.
• lyases - Enzymes that catalyze the removal of a group from a molecule to form a double bond, or the addition of a group to a double bond.
• lymphocytes - A subclass of leukocytes involved in the immune response. B lymphocytes synthesize and secrete antibodies; T lymphocytes either play a regulatory role in immunity or kill foreign and virus-infected cells.
• lysis - Destruction of a cell's plasma membrane or of a bacterial cell wall, releasing the cellular contents and killing the cell.
• lysogeny - One of two outcomes of the infection of a host cell by a temperate phage. It occurs when the phage genome becomes repressed and is replicated as part of the host DNA; infrequently it may be induced, and the phage particles so produced cause the host cell to lyse.
• lysosome - A membrane-bounded organelle in the cytoplasm of eukaryotic cells; it contains many hydrolytic enzymes and serves as a degrading and recycling center for unneeded components.
• mRNA - See messenger RNA.
• macromolecule - A molecule having a molecular weight in the range of a few thousand to many millions.
• mass-action ratio - For the reaction aA + dB  cC + dD, the ratio: [C]c[D]d [A]a[B]b
• matrix - The aqueous contents of a cell or organelle (the mitochondrion, for example) with dissolved solutes.
• meiosis - A type of cell division in which diploid cells give rise to haploid cells destined to become gametes.
• membrane transport - Movement of a polar solute across a membrane via a specific membrane protein (a transporter).
• messenger RNA (mRNA) - A class of RNA molecules, each of which is complementary to one strand of DNA; carries the genetic message from the chromosome to the ribosomes.
• metabolism - The entire set of enzymecatalyzed transformations of organic molecules in living cells; the sum of anabolism and catabolism.
• metabolite - A chemical intermediate in the enzyme-catalyzed reactions of metabolism.
• metalloprotein - A protein having a metal ion as its prosthetic group.
• metamerism - Division of the body into segments; in insects, for example.
• micelle - An aggregate of amphipathic molecules in water, with the nonpolar portions in the interior and the polar portions at the exterior surface, exposed to water.
• microbodies - Cytoplasmic, membranebounded vesicles containing peroxideforming and peroxide-destroying enzymes; include lysosomes, peroxisomes, and glyoxysomes.
• microfilaments - Thin filaments composed of actin, found in the cytoplasm of eukaryotic cells; serve in structure and movement.
• microsomes - Membranous vesicles formed by fragmentation of the endoplasmic reticulum of eukaryotic cells; recovered by differential centrifugation.
• microtubules - Thin tubules assembled from two types of globular tubulin subunits; present in cilia, flagella, centrosomes, and other contractile or motile structures.
• mitochondrion - Membrane-bounded organelle in the cytoplasm of eukaryotes; contains the enzyme systems required for the citric acid cycle, fatty acid oxidation, electron transfer, and oxidative phosphorylation.
• mitosis - The multistep process in eukaryotic cells that results in the replication of chromosomes and cell division.
• mixed-function oxidases (oxygenases) - Enzymes, often flavoproteins, that use molecular oxygen (O2) to simultaneously oxidize a substrate and a cosubstrate (commonly NADH or NADPH).
• modulator - A metabolite that, when bound to the allosteric site of an enzyme, alters its kinetic characteristics.
• molar solution - One mole of solute dissolved in water to give a total volume of 1,000 mL.
• mole - One gram molecular weight of a compound. See Avogadro's number.
• monoclonal antibodies - Antibodies produced by a cloned hybridoma cell, which therefore are identical and directed against the same epitope of the antigen.
• monolayer - A single layer of oriented lipid molecules.
• monoprotic acid - An acid having only one dissociable proton.
• monosaccharide - A carbohydrate consisting of a single sugar unit.
• mucopolysaccharide - An older name for a glycosaminoglycan.
• multienzyme system - A group of related enzymes participating in a given metabolic pathway.
• mutarotation - The change in specific rotation of a pyranose or furanose sugar or glycoside accompanying the equilibration of its α- and β-anomeric forms.
• mutases - Enzymes that catalyze the transposition of functional groups.
• mutation - An inheritable change in the nucleotide sequence of a chromosome.
• myofibril - A unit of thick and thin filaments of muscle fibers.
• myosin - A contractile protein; the major component of the thick filaments of muscle and other actin-myosin systems.
• native conformation - The biologically active conformation of a macromolecule.
• negative cooperativity - A phenomenon of some multisubunit enzymes or proteins in which binding of a ligand or substrate to one subunit impairs binding to another subunit.
• negative feedback - Regulation of a biochemical pathway achieved when a reaction product inhibits an earlier step in the pathway.
• neuron - A cell of nervous tissue specialized for transmission of a nerve impulse.
• neurotransmitter - A low molecular weight compound (usually containing nitrogen) secreted from the terminal of a neuron and bound by a specific receptor in the next neuron; serves to transmit a nerve impulse.
• nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate - See NAD, NADP.
• ninhydrin reaetion - A color reaction given by amino acids and peptides on heating with ninhydrin; widely used for their detection and estimation.
• nitrogen cycle - The cycling of various forms of biologically available nitrogen through the plant, animal, and microbial worlds, and through the atmosphere and geosphere.
• nitrogen fixation - Conversion of atmospheric nitrogen (N2) into a reduced, biologically available form by nitrogen-fixing organisms.
• nitrogenase complex - A system of enzymes capable of reducing atmospheric nitrogen to ammonia in the presence of ATP.
• noncompetitive inhibition - A type of enzyme inhibition not reversed by increasing the substrate concentration.
• noncyclic electron flow - The lightinduced flow of electrons from water to NADP+ in oxygen-evolving photosynthesis; it involves both photosystems I and II.
• nonessential amino acids - Amino acids that can be made by humans and other vertebrates from simpler precursors, and are thus not required in the diet.
• nonheme iron proteins - Proteins, usually acting in oxidation-reduction reactions, containing iron but no porphyrin groups.
• nonpolar - Hydrophobic; describing molecules or groups that are poorly soluble in water.
• nonsense codon - A codon that does not specify an amino acid, but signals the termination of a polypeptide chain.
• nonsense mutation - A mutation that results in the premature termination of a polypeptide chain.
• nonsense suppressor - A mutation, usually in the gene for a tRNA, that causes an amino acid to be inserted into a polypeptide in response to a termination codon.
• nucleases - Enzymes that hydrolyze the internucleotide (phosphodiester) linkages of nucleic acids.
• nucleic acids - Biologically occurring polynucleotides in which the nucleotide residues are linked in a specific sequence by phosphodiester bonds; DNA and RNA.
• nucleoid - In bacteria, the nuclear zone that contains the chromosome but has no surrounding membrane.
• nucleolus - A densely staining structure in the nucleus of eukaryotic cells; involved in rRNA synthesis and ribosome formation.
• nucleophile - An electron-rich group with a strong tendency to donate electrons to an electron-deficient nucleus (electrophile); the entering reactant in a bimolecular substitution reaction.
• nucleoplasm - The portion of a cell's contents enclosed by the nuclear membrane; ' also called the nuclear matrix.
• nucleoside diphosphate kinase - An enzyme that catalyzes the transfer of the terminal phosphate of a nucleoside 5'-triphosphate to a nucleoside 5'-diphosphate.
• nucleoside diphosphate sugar - A coenzymelike carrier of a sugar molecule, functioning in the enzymatic synthesis of polysaccharides and sugar derivatives.
• nucleoside monophosphate kinase - An enzyme that catalyzes the transfer of the terminal phosphate of ATP to a nucleoside 5'-monophosphate.
• nucleoside - A compound consisting of a purine or pyrimidine base covalently linked to a pentose.
• nucleosome - Structural unit for packaging chromatin; consists of a DNA strand wound around a histone core.
• nucleotide - A nucleoside phosphorylated at one of its pentose hydroxyl groups.
• nucleus - In eukaryotes, a membranebounded organelle that contains chromosomes.
• oligomer - A short polymer, usually of amino acids, sugars, or nucleotides; the definition of "short" is somewhat arbitrary, but usually less than 50 subunits.
• oligomeric protein - A multisubunit protein having two or more identical polypeptide chains.
• oligonucleotide - A short polymer of nucleotides (usually less than 50).
• oligopeptide - A few amino acids joined by peptide bonds.
• oligosaccharide - Several monosaccharide groups joined by glycosidic bonds.
• oncogene - A cancer-causing gene; any af several mutant genes that cause cells to exhibit rapid, uncontrolled proliferation. See also proto-oncogene.
• open reading frame - A group of contiguous nonoverlapping nucleotide codons in a DNA or RNA molecule that do not include a termination codon.
• open system - A system that exchanges matter and energy with its surroundings. See also system.
• operator - A region of DNA that interacts with a repressor protein to control the expression of a gene or group of genes.
• operon - A unit of genetic expression consisting of one or more related genes and the operator and promoter sequences that regulate their transcription.
• optical activity - The capacity of a substance to rotate the plane of plane-polarized light.
• optimum pH - The characteristic pH at which an enzyme has maximal catalytic activity.
• organelles - Membrane-bounded structures found in eukaryotic cells; contain enzymes and other components required for specialized cell functions.
• origin - The nucleotide sequence or site in DNA where DNA replication is initiated.
• osmosis - Bulk flow of water through a semipermeable membrane into another aqueous compartment containing solute at a higher concentration.
• osmotic pressure - Pressure generated by the osmotic flow of water through a semipermeable membrane into an aqueous compartment containing solute at a higher concentration.
• oxidation, β - See β oxidation.
• oxidation-reduction reaction - A reaction in which electrons are transferred from a donor to an acceptor molecule; also called a redox reaction.
• oxidation - The loss of electrons from a compound.
• oxidative phosphorylation - The enzymatic phosphorylation of ADP to ATP coupled to electron transfer from a substrate to molecular oxygen.
• oxidizing agent (oxidant) - The acceptor of electrons in an oxidation-reduction reaction.
• oxygen debt - The extra oxygen (above the normal resting level) consumed in the recovery period after strenuous physical exertion.
• oxygenases - Enzymes that catalyze reactions in which oxygen is introduced into an acceptor molecule.
• pH - The negative logarithm of the hydrogen ion concentration of an aqueous solution.
• pK - The negative logarithm of an equilibrium constant.
• palindrome - A segment of duplex DNA in which the base sequences of the two strands exhibit twofold rotational symmetry about an axis.
• paradigm - In biochemistry, an experimental model or example.
• partition coefficient - A constant that expresses the ratio in which a given solute will be partitioned or distributed between two given immiscible liquids at equilibrium.
• pasttranslational modification - Enzymatic processing of a polypeptide chain after translation from its mRNA.
• pathogenic - Disease-causing.
• pentose phosphate pathway - A pathway that serves to interconvert hexoses and pentoses and is a source of reducing equivalents and pentoses for biosynthetic processes; present in most organisms. Also called the phosphogluconate pathway.
• pentose - A simple sugar with a backbone containing five carbon atoms.
• peptidase - An enzyme that hydrolyzes a peptide bond.
• peptide bond - A substituted amide linkage between the α-amino group of one amino acid and the α-carboxyl group of another, with the elimination of the elements of water.
• peptide mapping - The characteristic two-dimensional pattern (on paper or gel) formed by the separation of a mixture of peptides resulting from partial hydrolysis of a protein; also known as peptide fingerprinting.
• peptide - Two or more amino acids covalently joined by peptide bonds.
• peptidoglycan - A major component of bacterial cell walls; generally consists of parallel heteropolysaccharides cross-linked by short peptides.
• peripheral proteins - Proteins that are loosely or reversibly bound to a membrane by hydrogen bonds or electrostatic forces; generally water-soluble once released from the membrane.
• permeases - See transporters. peroxisome: Membrane-bounded organelle in the cytoplasm of eukaryotic cells; contains peroxide-forming and peroxidedestroying enzymes.
• phage - See bacteriophage.
• phenotype - The observable characteristics of an organism.
• phosphodiester linkage - A chemical grouping that contains two alcohols esterified to one molecule of phosphoric acid, which thus serves as a bridge between them.
• phosphogluconate pathway - An oxidative pathway beginning with glucose-6phosphate and leading, via 6-phosphogluconate, to pentose phosphates and yielding NADPH. Also called the pentose phosphate pathway.
• phospholipid - A lipid containing one or more phosphate groups.
• phosphorolysis - Cleavage of a compound with phosphate as the attacking group; analogous to hydrolysis.
• phosphorylation potential (ΔGp) - The actual free-energy change of ATP hydrolysis under the nonstandard conditions prevailing within a cell.
• phosphorylation - Formation of a phosphate derivative of a biomolecule, usually 6y enzymatic transfer of a phosphate group from ATP.
• photochemical reaction center - The part of a photosynthetic complex where the energy of an absorbed photon causes charge separation, initiating electron transfer.
• photon - The ultimate unit (a quantum) of light energy.
• photophosphorylation - The enzymatic formation of ATP from ADP coupled to the light-dependent transfer of electrons in photosynthetic cells.
• photoreduction - The light-induced reduction of an electron acceptor in photosynthetic cells.
• photorespiration - Oxygen consumption occurring in illuminated temperate-zone plants, largely due to oxidation of phosphoglycolate.
• photosynthesis - The use of light energy to produce carbohydrates from carbon dioxide and a reducing agent such as water.
• photosynthetic phosphorylation - See photophosphorylation.
• photosystem - In photosynthetic cells, a functional set of light-absorbing pigments and its reaction center.
• phototroph - An organism that can use the energy of light to synthesize its own fuels from simple molecules such as carbon dioxide, oxygen, and water; as distinct from a chemotroph.
• plasma membrane - The exterior membrane surrounding the cytoplasm of a cell.
• plasma proteins - The proteins present in blood plasma.
• plasmalogen - A phospholipid with an alkenyl ether substituent on the C-1 of glycerol.
• plasmid - An extrachromosomal, independently replicating, small circular DNA molecule; commonly employed in genetic engineering.
• plastid - In plants, a self replicating organelle; may differentiate into a chloroplast.
• platelets - Small, enucleated cells that initiate blood clotting; they arise from cells called megakaryocytes in the bone marrow. Also known as thrombocytes.
• pleated sheet - The side-by-side, hydrogen-bonded arrangement of polypeptide chains in the extended β conformation.
• polar - Hydrophilic, or "water-loving"; describing molecules or groups that are soluble in water.
• polarity - (1) In chemistry, the nonuniform distribution of electrons in a molecule; polar molecules are usually soluble in water. (2) In molecular biology, the distinction between the 5' and 3' ends of nucleic acids.
• polyclonal antibodies - A heterogeneous pool of antibodies produced in an animal by a number of different B lymphocytes in response to an antigen. Different antibodies in the pool recognize different parts of the antigen.
• polylinker - A short, often synthetic, fragment of DNA containing recognition sequences for several restriction endonucleases.
• polymerase chain reaetion (PCR) - A repetitive procedure that results in a geometric amplification of a specific DNA sequence.
• polymorphic - Describing a protein for which amino acid sequence variants exist in a population of organisms, but the variations do not destroy the protein's function.
• polynucleotide - A covalently linked sequence of nucleotides in which the 3' hydroxyl of the pentose of one nucleotide residue is joined by a phosphodiester bond to the 5' hydroxyl of the pentose of the next residue.
• polypeptide - A long chain of amino acids linked by peptide bonds; the molecular weight is generally less than 10,000.
• polyribosome - See polysome.
• polysaccharide - A linear or branched polymer of monosaccharide units linked by glycosidic bonds.
• polysome (polyribosome) - A complex of an mRNA molecule and two or more ribo
• porphyrin - Complex nitrogenous compound containing four substituted pyrroles covalently joined into a ring; often complexed with a central metal atom.
• positive cooperativity - A phenomenon of some multisubunit enzymes or proteins in which binding of a ligand or substrate to one subunit facilitates binding to another subunit.
• posttranscriptional processing - The enzymatic processing of the primary RNA transcript, producing functional mRNA, tRNA, andJor rRNA molecules.
• primary structure - A description of the covalent backbone of a polymer (macromolecule), including the sequence of monomeric subunits and any interchain and intrachain covalent bonds.
• primary transcript - The immediate RNA product of transcription before any posttranscriptional processing reactions.
• primase - An enzyme that catalyzes the formation of RNA oligonucleotides used as primers by DNA polymerases.
• primer - A short oligomer (of sugars or nucleotides, for example) to which an enzyme adds additional monomeric subunits.
• probe - A labeled fragment of nucleic acid containing a nucleotide sequence complementary to a gene or genomic sequence that one wishes to detect in a hybridization experiment.
• processivity - For any enzyme that catalyzes the synthesis of a biological polymer, the property of adding multiple subunits to the polymer without dissociating from the substrate.
• prochiral molecule - A symmetric molecule that can react asymmetrically with an enzyme having an asymmetric active site, generating a chiral product.
• projection formulas - A method for representing molecules to show the configuration of groups around chiral centers; also known as Fischer projection formulas.
• prokaryote - A bacterium; a unicellular organism with a single chromosome, no nuclear envelope, and no membranebounded organelles.
• promoter - A DNA sequence at which RNA polymerase may bind, leading to initiation of transcription.
• prophage - A bacteriophage in an inactive state in which the genome is either integrated into the chromosome of the host cell or (sometimes) replicated autonomously.
• prostaglandins - A class of lipid-soluble, hormonelike regulatory molecules derived from arachidonate and other polyunsaturated fatty acids.
• prosthetic group - A metal ion or an organic compound (other than an amino acid) that is covalently bound to a protein and is essential to its activity.
• protein kinases - Enzymes that phosphorylate certain amino acid residues in specific proteins.
• protein targeting - The process by which newly synthesized proteins are sorted and transported to their proper locations in the cell.
• protein - A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds.
• proteoglycan - A hybrid macromolecule consisting of a heteropolysaccharide joined to a polypeptide; the polysaccharide is the major component.
• proto-oncogene - A cellular gene, usually encoding a regulatory protein, that can be converted into an oncogene by mutation.
• proton acceptor - An anionic compound capable of accepting a proton from a proton donor; that is, a base.
• proton donor - The donor of a proton in an acid-base reaction; that is, an acid.
• proton-motive force - The electrochemical potential inherent in a transmembrane gradient of H+ concentration; used in oxidative phosphorylation and photophosphorylation to drive ATP synthesis.
• protoplasm - A general term referring to the entire contents of a living cell.
• purine - A nitrogenous heterocyclic base found in nucleotides and nucleic acids; containing fused pyrimidine and imidazole rings.
• puromycin - An antibiotic that inhibits polypeptide synthesis by being incorporated into a growing polypeptide chain, causing its premature termination.
• pyranose - A simple sugar containing the six-membered pyran ring.
• pyridine nucleotide - A nucleotide coenzyme containing the pyridine derivative nicotinamide; NAD or NADP.
• pyridoxal phosphate - A coenzyme containing the vitamin pyridoxine (vitamin B6); functions in reactions involving amino group transfer.
• pyrimidine dimer - A covalently joined dimer of two adjacent pyrimidine residues in DNA, induced by absorption of ITV light; most commonly derived from two adjacent thymines (a thymine dimer).
• pyrimidine - A nitrogenous heterocyclic base found in nucleotides and nucleic acids.
• pyrophosphatase - See inorganic pyrophosphatase.
• quantum - The ultimate unit of energy.
• quaternary structure - The three-dimensional structure of a multisubunit protein; particularly the manner in which the subunits fit together.
• rRNA - See ribosomal RNA.
• racemic mixture tracemate) - An equimolar mixture of the D and L stereoisomers of an optically active compound.
• radical - An atom or group of atoms possessing an unpaired electron; also called a free radical.
• radioactive isotope - An isotopic form of an element with an unstable nucleus that stabilizes itself by emitting ionizing radiation.
• radioimmunoassay - A sensitive and quantitative method for detecting trace amounts of a biomolecule, based on its capacity to displace a radioactive form of the molecule from combination with its specific antibody.
• rate-limiting step - (1) Generally, the step in an enzymatic reaction with the greatest activation energy or the transition state of highest free energy. (2) The slowest step in a metabolic pathway.
• reaction intermediate - Any chemical species in a reaction pathway that has a finite chemical lifetime.
• reading frame - A contiguous and nonoverlapping set of three-nucleotide codons in DNA or RNA.
• recombinant DNA - DNA formed by the joining of genes into new combinations.
• redox pair - An electron donor and its corresponding oxidized form; for example, NADH and NAD+.
• redox reaction - See oxidation-reduction reaction.
• reducing agent (reductant) - The electron donor in an oxidation-reduction reaction.
• reducing end - The end of a polysaccharide having a terminal sugar with a free anomeric carbon; the terminal residue can act as a reducing sugar.
• reducing equivalent - A general or neutral term for an electron or an electron equivalent in the form of a hydrogen atom or a hydride ion.
• reducing sugar - A sugar in which the carbonyl (anomeric) carbon is not involved in a glycosidic bond and can therefore undergo oxidation.
• reduction - The gain of electrons by a compound or ion.
• regulatory enzyme - An enzyme having a regulatory function through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification.
• regulatory gene - A gene that gives rise to a product involved in the regulation of the expression of another gene; for example, a gene coding for a repressor protein.
• regulatory sequence - A DNA sequence involved in regulating the expression of a gene; for example, a promoter or operator.
• regulon - A group of genes or operons that are coordinately regulated even though some, or all, may be spatially distant within the chromosome or genome.
• release factors - See termination factors.
• releasing factors - Hypothalamic hormones that stimulate release of other hormones by the pituitary gland.
• renaturation - Refolding of an unfolded (denatured) globular protein so as to restore native structure and protein function.
• replication - Synthesis of a daughter duplex DNA molecule identical to the parental duplex DNA.
• replisome - The multiprotein complex that promotes DNA synthesis at the replication fork.
• repressible enzyme - In bacteria, an enzyme whose synthesis is inhibited when its reaction product is readily available to the cell.
• repression - A decrease in the expression of a gene in response to a change in the activity of a regulatory protein.
• repressor - The protein that binds to the regulatory sequence or operator for a gene, blocking its transcription.
• residue - A single unit within a polymer; for example, an amino acid within a polypeptide chain. The term reflects the fact that sugars, nucleotides, and amino acids lose a few atoms (generally the elements of water) when incorporated in their respective polymers.
• respiration - The catabolic process in which electrons are removed from nutrient molecules and passed through a chain of carriers to oxygen.
• respiratory chain - The electron transfer chain; a sequence of electron-carrying proteins that transfer electrons from substrates to molecular oxygen in aerobic cells.
• restriction endonucleases - Site-specific endodeoxyribonucleases causing cleavage of both strands of DNA at points within or near the specific site recognized by the enzyme; important tools in genetic engineering.
• restriction fragment length polymorphisms (RFLPs) - Variations, among individuals in a population, in the length of certain restriction fragments within which certain genomic sequences occur. These variations result from rare sequence changes that create or destroy restriction sites in the genome.
• restriction fragment - A segment of double-stranded DNA produced by the action of a restriction endonuclease on a larger DNA.
• retrovirus - An RNA virus containing a reverse transcriptase.
• reverse transcriptase - An RNA-directed DNA polymerase in retroviruses; capable of making DNA complementary to an RNA.
• ribonuclease - A nuclease that catalyzes the hydrolysis of certain internucleotide linkages of RNA.
• ribonucleic acid - See RNA.
• ribonucleotide - A nucleotide containing n-ribose as its pentose component.
• ribosomal RNA (rRNA) - A class of RNA molecules serving as components of ribosomes.
• ribosome - A supramolecular complex of rRNAs and proteins, approximately 18 to 22 nm in diameter; the site of protein synthesis.
• ribozymes - Ribonucleic acid molecules with catalytic activities; RNA enzymes.
• salvage pathway - Synthesis of a biomolecule, such as a nucleotide, from intermediates in the degradative pathway for the biomolecule; a recycling pathway, as distinct from a de novo pathway.
• saponification - Alkaline hydrolysis of triacylglycerols to yield fatty acids as soaps.
• sarcomere - A functional and structural unit of the muscle contractile system.
• satellite DNA - Highly repeated, nontranslated segments of DNA in eukaryotic chromosomes; most often associated with the centromeric region. Its function is not clear.
• saturated fatty acid - A fatty acid containing a fully saturated alkyl chain.
• second law of thermodynamics - The law stating that in any chemical or physical process, the entropy of the universe tends to increase.
• second messenger - An effector molecule synthesized within a cell in response to an external signal (first messenger) such as a hormone.
• secondary metabolism - Pathways that lead to specialized products not found in every living cell.
• secondary structure - The residue-byresidue conformation of the backbone of a polymer.
• sedimentation coefficient - A physical constant specifying the rate of sedimentation of a particle in a centrifugal field under specified conditions.
• shuttle vector - A recombinant DNA vector that can be replicated in two or more different host species. See also vector.
• sickle-cell anemia - A human disease characterized by defective hemoglobin molecules; caused by a homozygous allele coding for the β chain of hemoglobin.
• sickle-cell trait - A human condition recognized by the sickling of erythrocytes when exposed to low oxygen tension; occurs in individuals heterozygous for the allele responsible for sickle-cell anemia.
• signal sequence - An amino-terminal sequence that signals the cellular fate or destination of a newly synthesized protein.
• signal transduction - The process by which an extracellular signal (chemical, mechanical, or electrical) is amplified and converted to a cellular response.
• silent mutation - A mutation in a gene that causes no detectable change in the biological characteristics of the gene product.
• similar sequences, often as a product of genetic recombination. heteropolysaccharide - A polysaccharide containing more than one type of sugar.
• simple diffusion - The movement of solute molecules across a membrane to a region of lower concentration, unassisted by a protein transporter.
• simple protein - A protein yielding only amino acids on hydrolysis.
• site-directed mutagenesis - A set of methods used to create specific alterations in the sequence of a gene.
• site-specific recombination - A type of genetic recombination that occurs only at specific ssquences.
• small nuclear RNA (snRNA) - Any of several small RNA molecules in the nucleus; most have a role in the splicing reactions that remove introns from mRNA, tRNA, and rRNA molecules.
• somatic cells - All body cells except the germ-line cells.
• specific activity - The number of micromoles (μmol) of a substrate transformed by an enzyme preparation per minute per milligram of protein at 25°C; a measure of enzyme purity.
• specific heat - The amount of energy (in joules or calories) needed to raise the temperature of 1 g of a pure substance by 1 °C.
• specific rotation - The rotation, in degrees, of the plane of plane-polarized light (D-line of sodium) by an optically active compound at 25 °C, with a specified concentration and light path.
• specificity - The ability of an enzyme or receptor to discriminate among competing substrates or ligands.
• sphingolipid - An amphipathic lipid with a sphingosine backbone to which are attached a long-chain fatty acid and a polar alcohol.
• splicing - See gene splicing; RNA splicing.
• standard free-energy change (ΔG°) - The free-energy change for a reaction occurring under a set of standard conditions : temperature, 298 K; pressure, 1 atm or 101.3 kPa; and all solutes at 1 ni concentration. ΔG°' denotes the standard free-energy change at pH 7.0.
• standard reduction potential (E0') - The electromotive force exhibited at an electrode by 1 M concentrations of a reducing agent and its oxidized form at 25 °C and pH 7.0; a measure of the relative tendency of the reducing agent to lose electrons.
• steady state - A nonequilibrium state of a system through which matter is flowing and in which all components remain at a constant concentration.
• stem cells - The common, self regenerating cells in bone marrow that give rise to differentiated blood cells such as erythrocytes and lymphocytes.
• sterols - A class of lipids containing the steroid nucleus.
• sticky ends - Two DNA ends in the same DNA molecule, or in different molecules, with short overhanging single-stranded segments that are complementary to one another, facilitating ligation of the ends; also known as cohesive ends.
• stop codons - See termination codons.
• stroma - The space and aqueous solution enclosed within the inner membrane of a chloroplast, not including the contents within the thylakoid membranes.
• structural gene - A gene coding for a protein or RNA molecule; as distinct from a regulatory gene.
• substitution mutation - A mutation caused by the replacement of one base by another.
• substrate-level phosphorylation - Phosphorylation of ADP or some other nucleoside 5'-diphosphate coupled to the dehydrogenation of an organic substrate; independent of the electron transfer chain.
• substrate - The specific compound acted upon by an enzyme.
• suicide inhibitor - A relatively inert molecule that is transformed by an enzyme, at its active site, into a reactive substance that irreversibly inactivates the enzyme.
• suppressor mutation - A mutation that totally or partially restores a function lost by a primary mutation; located at a site different from the site of the primary mutation.
• symbionts - Two or more organisms that are mutually interdependent; usually Iiving in physical association.
• symport - Cotransport of solutes across a membrane in the same direction.
• synthases - Enzymes that catalyze condensation reactions in which no nucleoside triphosphate is required as an energy source.
• synthetases - Enzymes that catalyze candensation reactions using ATP or another nucleoside triphosphate as an energy source.
• system - An isolated collection of matter; all other matter in the universe apart from the system is called the surroundings.
• tRNA - See transfer RNA.
• telomere - Specialized nucleic acid structure found at the ends of linear eukaryotic chromosomes.
• temperate phage - A phage whose DNA may be incorporated into the host-cell genome without being expressed; as distinct from a virulent phage, which destroys the host cell.
• template - A macromolecular mold or pattern for the synthesis of an informational macromolecule.
• terminal transferase - An enzyme that catalyzes the addition of nucleotide residues of a single kind to the 3' end of DNA chains.
• termination codons - UAA, UAG, and UGA; in protein synthesis, signal the termination of a polypeptide chain. Also known as stop codons.
• termination factors - Protein factors of the cytosol required in releasing a completed polypeptide chain from a ribosome; also known as release factors.
• termination sequence - A DNA sequence that appears at the end of a transcriptional unit and signals the end of transcription.
• terpenes - Organic hydrocarbons or hydrocarbon derivatives constructed from recurring isoprene units. They produce some of the scents and tastes of plant products; for example, the scents of geranium leaves and pine needles.
• tertiary structure - The three-dimensional conformation of a polymer in its native folded state.
• tetrahydrobiopterin - The reduced coenzyme form of biopterin.
• tetrahydrofolate - The reduced, active coenzyme form of the vitamin folate.
• thiamine pyrophosphate - The active coenzyme form of vitamin Bl; involved in aldehyde transfer reactions.
• thioester - An ester of a carboxylic acid with a thiol or mercaptan.
• thrombocytes - See platelets.
• thromboxanes - A class of molecules derived from arachidonate and involved in platelet aggregation during blood clotting.
• thylakoid - Closed cisterna, or disc, formed by the pigment-bearing internal membranes of chloroplasts.
• thymine dimer - See pyrimidine dimer.
• tissue culture - Method by which cells derived from multicellular organisms are grown in liquid media.
• titration curve - A plot of the pH versus the equivalents of base added during titration of an acid.
• tocopherols - Forms of vitamin E.
• topoisomerases - Enzymes that introduce positive or negative supercoils in closed, circular duplex DNA.
• topoisomers - Different forms of a covalently closed, circular DNA molecule that differ only in their linking number.
• toxins - Proteins produced by some organisms and toxic to certain other species.
• trace element - A chemical element required by an organism in only trace amounts.
• transaminases - See aminotransferases.
• transamination - Enzymatic transfer of an amino group from an α-amino acid to an α-keto acid.
• transcription - The enzymatic process whereby the genetic information contained in one strand of DNA is used to specify a complementary sequence of bases in an mRNA chain.
• transcriptional control - The regulation of a protein's synthesis by regulation of the formation of its mRNA.
• transduction - (1) Generally, the conversion of energy or information from one form to another. (2) The transfer of genetic information from one cell to another by means of a viral vector.
• transfer RNA (tRNA) - A class of RNA molecules (Mr. 25,000 to 30,000), each of which combines covalently with a specific amino acid as the first step in protein synthesis.
• transformation - Introduction of an exogenous DNA into a cell, causing the cell to acquire a new phenotype.
• transgenic - Describing an organism that has genes from another organism incorporated within its genome as a result of recombinant DNA procedures.
• transition state - An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate.
• translation - The process in which the genetic information present in an mRNA molecule specifies the sequence of amino acids during protein synthesis.
• translational control - The regulation of a protein's synthesis by regulation of the rate of its translation on the ribosome.
• translational repressor - A repressor that binds to an mRNA, blocking translation.
• translocase - (1) An enzyme that catalyzes membrane transport. (2) An enzyme that causes a movement, such as the movement of a ribosome along an mRNA.
• transpiration - Passage of water from the roots of a plant to the atmosphere via the vascular system and the stomata of the leaves.
• transporters - Proteins that span a membrane and transport specific nutrients, metabolites, ions, or proteins across the membrane; sometimes called permeases.
• transposition - The movement of a gene or set of genes from one site in the genome to another.
• transposon (transposable element) - A segment of DNA that can move from one position in the genome to another.
• triacylglycerol - An ester of glycerol with three molecules of fatty acid; also called a triglyceride or neutral fat.
• tricarboxylic acid cycle - See citric acid cycle.
• triose - A simple sugar with a backbone containing three carbon atoms.
• tropic hormone (tropin) - A peptide hormone that stimulates a specific target gland to secrete its hormone; for example, thyrotropin produced by the pituitary stimulates secretion of thyroxine by the thyroid.
• turnover number - The number of times an enzyme molecule transforms a substrate molecule per unit time, under conditions giving maximal activity at substrate concentrations that are saturating.
• ultraviolet (UV) radiation - Electromagnetic radiation in the region of 200 to 400 nm.
• uncoupling agent - A substance that uncouples phosphorylation of ADP from electron transfer; for example, 2,4-dinitrophenol.
• uniport - A transport system that carries only one solute, as distinct from cotransport.
• unsaturated fatty acid - A fatty acid containing one or more double bonds.
• urea cycle - A metabolic pathway in vertebrates, for the synthesis of urea from amino groups and carbon dioxide; occurs in the liver.
• ureotelic - Excreting excess nitrogen in the form of urea.
• uricotelic - Excreting excess nitrogen in the form of urate (uric acid).
• van der Waals forces. Refers to the combined effect of two types of interactions, one attractive and one repulsive. The attractive forces are due to favorable interactions among the induced instantaneous dipole moments that arise from fluctuations in the electron charge densities of neighboring nonbonded atoms. Repulsive forces arise when noncovalently bonded atoms come too close together.
• vector - A DNA molecule known to replicate autonomously in a host cell, to which a segment of DNA may be spliced to allow its replication; for example, a plasmid or a temperate-phage DNA.
• viral vector - A viral DNA altered so that it can act as a vector for recombinant DNA.
• virion - A virus particle.
• virus - A self replicating, infectious, nucleic acid-protein complex that requires an intact host cell for its replication; its genome is either DNA or RNA.
• vitamin - An organic substance required in small quantities in the diet of some species; generally functions as a component of a coenzyme.
• wild type - The normal (unmutated) phenotype.
• wobble - The relatively loose base pairing between the base at the 3' end of a codon and the complementary base at the 5' end of the anticodon.
• x-ray crystallography - The analysis of x-ray diffraction patterns of a crystalline compound, used to determine tha molecule's three-dimensional structure.
• zinc finger - A specialized protein motif involved in DNA recognition by some DNA-binding proteins; characterized by a single atom of zinc coordinated to four Lys residues or to two His and two Lys residues.
• zwitterion - A dipolar ion, with spatially separated positive and negative charges.
• zymogen - An inactive precursor of an enzyme; for example, pepsinogen, the precursor of pepsin.
• ΔG°' - See standard free-energy change.
• α helix - A helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; one of the most common secondary structures in proteins.
• β conformation - An extended, zigzag arrangement of a polypeptide chain; a common secondary structure in proteins.
• β oxidation - Oxidative degradation of fatty acids into acetyl-CoA by successive oxidations at the β-carbon atom.

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