Glossary – Biochemistry for Nurses

Glossary

A

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.

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.

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: Energy requiring transport of a solute across a membrane in the direction of increasing concentration.

Acyl Phosphate: Any molecule with the general chemical form

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 for lipid.

Adipose Tissue: Connective tissue specialized for the storage of large amounts of triacylglycerols.

Aerobe: An organism that utilizes oxygen for growth.

Aerobic: Occurring in the presence of oxygen.

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.

Aldose: A simple sugar in which the carbonylcarbonatom is an aldehyde; that is, the carbonyl carbon is at one end of the carbon chain.

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: An enzyme whose active site can be altered by the binding of a small molecule at a nonoverlapping site.

Allosteric Site: The specific site on the surface of an allosteric enzyme molecule to which the modulator or effect or molecule is bound.

Amino Acids: α–Amino substituted carboxylic acids, the building blocks of proteins.

Aminoacyl-tRNA Synthetases: Enzymes that catalyze synthesis of an aminoacyl-tRNA at the expense of ATP energy.

Aminoacyl-tRNA: An aminoacyl ester of a tRNA.

Amino-Terminal Residue: The only amino acid residue in a polypeptide chain with a free α–amino group; defines the amino terminus of the polypeptide.

Aminotransferases: Enzymes that catalyze the transfer of amino groups from α-amino to α-Keto acids; also called transaminases.

Amphibolic Pathway: A metabolic pathway used in both catabolism and anabolism.

Amphipathic: Containing both polar and nonpolar domains.

Ampholyte: A substance that can act as either a base or an acid.

Amphoteric: Capable of donating and accepting protons, thus able to serve as an acid or a base.

Anabolism: The phase intermediary metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursors.

Anaerobic: Occurring in the absence of air or oxygen.

Angstrom (Å): A unit of length equal to 10–10 m.

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: 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 defense protein synthesized by the immune system of animals. 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 animals.

Antiparallel β-pleated sheet (β-sheet): A hydrogen-bonded secondary structure formed between two or more extended polypeptide chains.

Antiparallel: Describes 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.

Apoprotein: The protein portion of a protein, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for activity.

Apoptosis (app'-a-toe'-sis): Programmed cell death, in which a cell brings about its own death and lysis, signaled from outside or programmed in its genes, by systematically degrading its own macromolecules.

Asymmetric Carbon Atom: A carbon atom to which four different atoms or groups of atom are attached is said to be asymmetric carbon atom.

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.

Autophosphorylation: Strictly, the phosphorylation of an amino acid residue in a protein, catalyzed by the same molecule. Often extended to include phosphorylation of one subunit of a humodimer by the other subunit.

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.

B

Base Pair: Two nucleotides in nucleic acid chains that are paired by hydrogen bonding of their complementary bases; for example, A with Tor U, and G with C.

Base Stacking: The close packing of the planes of base pairs, commonly found in DNA and RNA structures.

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.

Biomolecule: An organic compound normally present as an essential component of living organisms.

Biotin: A vitamin; an enzymatic cofactor involved in carboxylation reactions.

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.

β oxidation: Oxidative degradation of fatty acids into acetyl-CoA by successive oxidations at the β–carbon atom.

C

Calorie: The amount of heat required to raise the temperature of 1.0g of water from 14.5 to 15.5 °C. One calorie (cal) equals 4.18 joules (J).

Calvin Cycle: The cyclic pathway used by plants to fix carbon dioxide and produce triose phosphates.

cAMP: 3',5' cyclic adenosine monophosphate. The cAMP molecule plays a key role in metabolic regulation.

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.

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.

Carnitine Shuttle: Mechanism for moving fatty acids from the cytosol to the mitochondrial matrix as fatty esters of carnitine.

Carotenoids: It is a photosynthetic pigments made up of isoprene units.

Catabolism: That part of metabolism that is concerned with degradation reactions.

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.

Cation-exchange Resin: An insoluble polymer with fixed negative charges; used in the chromatographic separation of cationic substances.

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.

Cerebroside: Sphingolipid containing one sugar residue as a head group.

Chiral Compound: A compound that can exist in two forms that are nonsuperimposable 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: A thread-like structure—visible in the cell nucleus during metaphase—that carries the hereditary information.

Chylomicron: A plasma lipoprotein consisting of a large droplet of triacylglycerols stabilized by a coat of protein and phospholipids; carries lipids from the intestine to the tissues.

Chymotrypsin: A well–studied protease that cleaves on the carbonyl side of amino acid residues with aromatic side chains.

Chymotrypsinogen: The zymogen precursor of chymotrypsin.

Cistron: A unit of DNA or RNA corresponding to one gene.

Citric Acid Cycle: A cycle 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 cycles or tricarboxylic acid cycle.

Codon: A sequence of three adjacent nucleotides in a nucleic acid that codes for a specific amino acid.

Coenzyme A: A pentothenic acid-containing 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 skeleton rearrangements.

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.

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 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.

Conjugate Acid–Base Pair: A proton donor and its corresponding deprotonated species; for example, acetic acid (donor) and acetate (acceptor).

Covalent Bond: A chemical bond that involves sharing of electron pairs.

Cristae: Infoldings of the inner mitochondrial membrane.

Cytidine: A pyrimidine nucleoside found in DNA and RNA.

Cytochromes: Heme-containing proteins that function as electron carriers in oxidative phosphorylation and photosynthesis.

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.

D

Dalton: A unit of mass equivalent to the mass of a hydrogen atom (1.66 × 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.

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.

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.

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.

DNA Polymerase: An enzyme that catalyzes the formation of 3'–5' phosphodiester bonds from deoxyribonucleotide triphosphates.

DNA: Deoxyribonucleic acid. A polydeoxyribonucleotide in which the sugar is deoxyribose; the main repository of genetic information in all cells and most viruses.

Double Helix: A structure in which two helically-twisted polynucleotide strands are held together by hydrogen bonding and base stacking.

E

Eicosanoid: Any fatty acid with 20 carbons.

Electron Acceptor: A substance that receives electrons in an oxidation–reduction reaction.

Electron Carrier: A protein, such as a flavoprotein or a cytochrome, that can reversibly gain and lose electrons; functions in the transfer of electrons from organic nutrients to oxygen or some other terminal acceptor.

Electron Donor: A substance that donates electron in an oxidation–reduction reaction.

Electron Transfer: Movement of electrons from substrates to oxygen via the carriers of the respiratory (electron-transfer) chain.

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: (1) Proteins that function in the elongation phase of eukaryotic transcription. (2) Specific proteins required in the elongation of polypeptide chains by ribosomes.

Enantiomorphs: Isomers that are mirror images of one another.

Endergonic Reaction: A reaction with a positive standard free energy change.

Endonuclease: An enzyme that breaks a phosphodiester linkage at some point within a polynucleotide chain.

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.

End-product (feedback) Inhibition: The inhibition of the first enzyme in a pathway by the end product of that pathway.

Energy Charge: The fractional degree to which the AMP-ADP-ATP system is filled with high-energy phosphates (phosphoryl groups).

Enzyme: A molecule, 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.

Epithelial Cell: Any cell that forms part of the outer covering of an organism or organ.

Erythrocyte: A cell containing large amounts of hemoglobin and specialized for oxygen transport; a red blood cell.

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.

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.

Ether: A molecule containing two carbons linked by an oxygen atom.

Eubacteria: One of the five kingdoms of living organisms. Eubacteria have a plasma membrane but no internal organellels or nucleus.

Eukaryote: A cell or organism that has a membrane-bound nucleus.

Exocytosis: The fusion of an intracellular vesicle with the plasma membrane, releasing the vesicle contents to the extracellular space.

F

Facilitated Diffusion: Diffusion of a polar substance across a biological membrane through a protein transporter also called passive diffusion or passive transport.

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: Allosteric enzyme Inhibition at the beginning of a metabolic sequence by the end of product of the sequence; also known as end-product inhibition.

Fermentation: The energy-generating breakdown of glucose or related molecules by a process that does not require molecular oxygen.

Fischer Projection Formulas: A method for representing molecules to show the configuration of groups around chiral centers also known as Fischer projection formulas.

Flagellum: A cell appendage used in propulsion. Bacterial flagella have a much simpler structure than eukaryotic flagella, which are similar to cilia.

Flavin-linked Dehydrogenases: Dehydrogenases requiring one of the riboflavin coenzymes, FMN or FAD.

Flavin Nucleotides: Riboflavin containing nucleotide coenzymes (FMN and FAD).

Flavoprotein: An enzyme containing a flavin nucleotide as a tightly bound prosthetic group.

Fluorescence: Emission of light by excited molecules as they revert to the ground state.

Furanose: A sugar that contains a five-membered ring as a result of intramolecular hemiacetal formation.

G

G Proteins: A family of heterotrimeric GTP-binding proteins that act in intracellular signaling pathways. Commonly, ligand binding to a serpentine receptor induces the exchange of GTP for bound GDP, enabling the G protein to activate a downstream enzyme in a signaling pathway. G proteins have intrinsic GTPase activity and therefore can self-inactivate.

Gangliosides: Sphingolipids containing complex oligosaccharides as head groups; especially common in nervous tissue.

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.

Genetic Information: The hereditary information contained in a sequence of nucleotide bases in chromosomal DNA or RNA.

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 branch points.

Glycogenesis: The process of converting glucose to glycogen.

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.

Glycosaminoglycan: A heteropolysaccharide of two alternating units: one is either N- acetyglucosamine or N-acetylgalactosamine; the other is an uronic acid (usually glucuronic acid). Formerly called mucopolysaccharide.

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.

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 post-translational modification of proteins and their secretion from the cell or incorporation into the plasma membrane or organellar membranes.

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 disks, in chloroplasts.

Guanine: A purine base found in DNA or RNA.

Guanosine: A purine nucleoside found in DNA and RNA.

H

Hairpin Loop: A single-stranded complementary region of DNA or RNA that folds back on itself and base-pairs into a double helix.

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.

Helix: A spiral structure with a repeating pattern.

Heme Protein: A protein containing a heme as a prosthetic group.

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 oneoxygen linked to a central carbon in a hydroxyl fashion and one oxygen linked to the same central carbon by an ether linkage.

Hemoglobin: A heme protein in erythrocytes; functions in oxygen transport.

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.

Hexose Monophosphate Pathway: An oxidative pathway beginning with glucose 6-phosphate and leading, via 6- phosphogluconate, to pentose phosphates and yielding NADPH. Also called the pentose phosphate pathway and the hexose monophosphate pathway.

Hexose: A sugar with a six-carbon backbone.

High-performance Liquid Chromatography (HPLC): Chromatographic procedure, often conducted at relatively high pressures, using automated equipment that permits refined and highly reproducible profiles.

Histones: The family of basic proteins that is normally associated with DNA in most cells of eukaryotic organisms.

Homopolysaccharide: A polysaccharide made up of only one type of monosaccharide unit.

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.

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: Preferring not to be in contact with water, as is the case with the hydrocarbon portion of a fatty acid or phospholipid chain.

I

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.

Immune Response: The capacity of a vertebrate to generate antibodies to an antigen, a macromolecule foreign to the organism.

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.

Intermediary Metabolism: In cells, the enzyme-catalyzed reactions that extract chemical energy from nutrient molecules and utilize it to synthesize and assemble cell components.

Ion Channel: An integral protein that provides for the regulated transport of a specific ion, or ions, across a membrane.

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.

Isomers: Any two molecules with the same molecular formula but a different arrangement of molecular groups.

Isoprenoid: Any of a large number of natural products synthesized by enzymatic polymerization of two or more isoprene units: also called terpenoids.

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.

K

Keratins: Insoluble protective or structural proteins consisting of parallel polypeptide chains in α-helical or β conformations.

Ketogenic: Describing amino acids that are metabolized to acetoacetate and acetate.

Ketone Bodies: Refers to acetoacetate, acetone and β-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.

Km: See Michaelis constant.

Krebs cycle: A cycle 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 cycles or tricarboxylic acid cycle.

L

Lectins: Agglutinating proteins usually extracted from plants.

Leukocyte: White blood cell; involved in the immune response in mammals.

Leukotrienes: A family of molecules derived from arachidonate; muscle contractants that constrict air passages in the lungs and are involved in asthma.

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.

Lipases: Enzymes that catalyze the hydrolysis of triacylglycerols.

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.

Lipoate (lipoic acid): A vitamin for some microorganisms; an intermediate carrier of hydrogen atoms and acyl groups in α-keto acid dehydrogenases.

Lipopolysaccharide: Usually refers to a unique glycolipid found in Gram negative bacteria.

Lipoprotein: A lipid protein aggregate that serves to carry water-insoluble lipids in the blood. The protein component alone is an apolipoprotein.

Liposome: A small, spherical vesicle composed of a phospholipid bilayer, which forms spontaneously when phospholipids are suspended in an aqueous buffer.

Lyase: An enzyme that catalyzes the removal of a group to form a double bond, or the reverse reaction.

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.

Lysosome: An organelle that contains hydrolytic enzymes designed to break down proteins that are targeted to that organelle.

M

Membrane: A sheet-like composite of protein and lipid that is the boundary of cells and organelles.

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 integrral membrane proteins).

Membrane Transport: The facilitated transport of a molecule across a membrane.

Mesosome: An invagination of the bacterial cell membrane.

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 equation (also known as the Henri-Michaelis-Menten equation): An equation relating the reaction velocity to the substrate concentration of an enzyme.

Microtubules: Thin tubules, made from globular proteins, that serve multiple purposes in eukaryotic cells.

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 synthesis of only a fraction of the proteins located in this organelle.

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.

Monolayer: A single layer of oriented lipid molecules.

Monomer: One unit of a protein or other structure.

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 gamestes.

Membrane Transport: Movement of a polar solute across a membrane via a specific membrane protein (a transportor).

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 enzyme-catalyzed transformations of organic molecules in living cells; the sum of anabolism and catabolism.

Microsomes: Membranous vesicles formed by fragmentation of the endoplasmic reticulum of eukaryotic cells; recovered by differential centrifugation.

N

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.

Negative Feedback: Regulation of a biochemical pathway achieved when a reaction product inhibits an earlier step in the pathway.

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.

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; describes molecules or groups that are poorly soluble in water.

Nuclease: An enzyme that cleaves phosphodiester bonds of nucleic acids.

Nucleic Acids: Polymers of the ribonucleotides or deoxyribonucleotides.

Nucleoid: In bacteria, the nuclear zone that contains the chromosome but has no surrounding membrane.

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.

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.

O

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.

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.

Osmosis: Bulk flow of water through a semi-permeable membrane into another aqueous compartment containing solute at a higher concentration.

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.

Oxidation–reduction Reaction: A reaction in which electrons are transferred from a donor to an acceptor molecule; also called a redox reaction.

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.

P

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 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: An organic molecule in which a covalent amide bond is formed between the α-amino group of one amino acid and the α-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.

pH: The negative logarithm of the hydrogen ion concentration of an aqueous solution.

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.

Phosphatases: Enzymes that hydrolyze a phosphate ester or anhydride, releasing inorganic phosphate, Pi.

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.

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.

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.

Plasma Membrane: The membrane that surrounds the cytoplasm.

Plasma Proteins: The proteins present in blood plasma.

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.

Polar Group: A hydrophilic (water-loving) group.

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.

Primary Structure: In a polymer, the sequence of monomers and the covalent bonds. In proteins, it refers to the amino acid sequence.

Projection Formulas: A method for representing molecules to show the configuration of groups around chiral centers; also known as Fischer projection formulas.

Prokaryote: A unicellular organism that contains a single chromosome, no nucleus, no membrane-bound organelles, and has characteristic ribosomes and biochemistry.

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.

Protein Kinases: Enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to a Ser, Thr, Tyr, Asp, or His side chain in a target protein, thereby regulating the activity or other properties of that protein.

Protein: A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds.

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.

Proton Acceptor: A functional group capable of accepting a proton from a proton donor molecule.

Protoplasm: A general term referring to the entire contents of a living cell.

Purine: A heterocyclic ring structure with varying functional groups. The purines adenine and guanine are found in both DNA and RNA.

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 reaction involving amino group transfer.

Pyrimidine Dimer: A covalently joined dimer of two adjacent pyrimidine residues in DNA, induced by absorption of UV light; most commonly derived from two adjacent thymines (a thymine dimer).

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.

Pyrophosphatase: An enzyme that hydrolyzes a molecule of inorganic pyrophosphate to yield two molecules of (ortho) phosphate; also known as pyrophosphatase.

Pyrophosphate: A molecule formed by two phosphates in anhydride linkage.

Q

Quantum: The ultimate unit of energy.

Quaternary Structure: In a protein, the way in which the different folded subunits interact to form the multisubunit protein.

R

R group: Shorthand for the side chain of an amino acid.

Racemic Mixture (racemate): An equimolar mixture of the D and L stereoisomers of an optically active compound.

Radioimmunoassay (RIA): 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.

Reducing Agent (reductant): The election donor in an oxidation–reduction reaction.

Reducing Sugar: A sugar in which the carbonyl (anomeric) carbon is not involved in a glycosidic bond and can therefore undergo oxidation. .

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.

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.

Ribozymes: Ribonucleic acid molecules with catalytic activities; RNA enzymes.

RNA (ribonucleic acid): A polynucleotide in which the sugar is ribose.

RNA polymerase: An enzyme that catalyzes the formation of RNA from ribonucleotide triphosphates, using DNA as a template.

S

S-adenosylmethionine (adoMet): An enzymatic cofactor involved in methyl group transfers.

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.

Saponification: Alkaline hydrolysis of triacylglycerols to yield fatty acids as soaps.

Saturated Fatty Acid: A fatty acid containing a fully saturated alkyl chain.

Secondary Metabolism: Pathways that lead to specialized products not found in every living cell.

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 β-strands (sheets) and α-helices.

Semipermeable: The characteristic of allowing only some molecules, usually smaller or uncharged ones, to pass through.

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.

Sterols: A class of lipids containing the steroid nucleus.

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 –l3sec). 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.

T

TCA Cycle: See tricarboxylic acid cycle.

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.

Thromboxanes: A class of molecules derived from arachidonate and involved in platelet aggregation during blood clotting.

Thylakoid: Closed cisterna, or disk, formed by the pigment–bearing internal membranes of chloroplasts.

Thymidine: One of the four nucleosides found in DNA.

Thymine: A pyrimidine base found in DNA.

Transamination: Enzymatic transfer of an amino group from an α-amino acid to an α-keto acid.

Transfection: An artificial process of infecting cells with naked viral DNA.

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.

U

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.

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.

V

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.

W

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.

Wild Type: The normal (unimutated) phenotype.

X

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.

Z

Zwitterion: A dipolar ion with spatially-separated positive and negative charges. For example, most amino acids are zwitterions, having a positive charge on the α-amino group and a negative charge on the α-carboxyl group but no net charge on the overall molecule.

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.

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.