Biochemistry Glossary

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active site - the site on an enzyme molecule where the substrate molecule binds and where its reaction is facilitated.

active transport - transport of a substance across a membrane against an electrochemical gradient; requires the expenditure of metabolic energy.

adipocytes - specialized cells that store triacylglycerols and release fatty acids and glycerol to the bloodstream.

agonist - a substance that mimics the effects of a natural compound (such as a hormone or neurotransmitter) by binding to and activating the same cell surface receptor.

aIkaloid - one of a group of nitrogenous basic substances found in plants. It may have a taste bitter; many are pharmacologically active.

allele - a specific version of a gene that occupies a particular location in the genome. It differs in nucleotide sequence from other copies of the same gene.

allosteric - an effect that affects the activity of one part of an enzyme (such as an active site) by the binding of a molecule at a different site (regulatory site) at a different location on the enzyme.

amphipathic - having both hydrophobic and hydrophilic regions in a single molecule.

anabolism - all metabolism in which complex biomolecules are built up from simpler ones. These processes usually require cellular energy.

anomers - stereoisomers of cyclized monosaccharide molecules differing only in the configuration of the substituents on carbon 1. This carbon is a chiral center in the cyclized but not in the open-chain form of the molecule.

anticodon - the three nucleotide region of a tRNA that base pairs with the codon on mRNA during protein synthesis.

apolipoproteins - the protein portion of lipoproteins (without the lipid).

association constant - the equilibrium constant value for a chemical reaction written in terms of an association (vs. a dissociation); indicates the tendency of two chemical species to associate with each other.

asymmetric carbon - a carbon that carries four different substituents and therefore acts as a center of chirality.

attenuation - a mechanism for regulating prokaryotic gene expression in which the synthesis of a nascent RNA transcript is terminated before RNA polymerase has reached the structural genes.

B DNA - a DNA duplex with a right-hand helix structure; the usual form of DNA in vivo.

bile acids - a group of amphipathic cholesterol derivatives that are produced in the liver and excreted in the bile; they emulsify fat in the small intestine.

blood group antigens - oligosaccharides that are carried in the form of glycoproteins and glycolipids on the outside of blood cell membranes.

Bohr effect - the effect of protons on the binding of oxygen to hemoglobin; promotes both the release of oxygen from hemoglobin in the tissues and the release of carbon dioxide from the blood in the lungs.

centromere - the chromosomal region of attachment of two sister chromatids. Also the site of attachment for spindle fibers during mitosis and meiosis.

chaotropic agent - a chemical, such as urea or guanidine hydrochloride, that can disrupt the hydrogen bonding structure of water. In concentrated solutions they can denature proteins because they reduce the hydrophobic effect.

chaperonins - proteins that facilitate the proper folding of other proteins.

chiral - a molecule that is not superimposable on its mirror image. A carbon with four different substituents is called a chiral atom or center of chirality.

chromophore - a chemical group that absorbs light of characteristic wavelengths.

circular dichroism - the characteristic of certain molecules to absorb right circularly polarized light and left circularly polarized light to a different extent. Stereoisomers exhibit circular dichroism; some secondary structure s, such as alpha helices and beta pleated sheets in proteins, exhibit circular dichroism.

clone - a group of cells, organisms, or DNA sequences that are genetically identical because they are all derived from a single ancestor.

coenzyme - a small organic molecule that binds to an enzyme and is essential for its activity but is not permanently altered by the reaction. Many coenzymes are derived from vitamins.

consensus sequence - nucleotide or amino acid sequences that show significant similarity but are not identical. A sequence constructed by choosing at each position the residue that is found there most often in the group of sequen ces under consideration.

Curie - a unit of radioactivity equal to 2.22 x 1012 disintegrations per minute.

cyclic photophosphorylation - light-dependent ATP synthesis in photosynthesis that is due to the flow of electrons from photosystem II back to photosystem I.

endonucIease - an enzyme that cleaves a nucleic acid chain at an internal phosphodiester bond.

enthalpy - a thermodynamic quantity equal to the internal energy of a system plus the product of the pressure and volume. It is equal to the heat change in constant-pressure reactions (most biological reactions).

entropy - a thermodynamic quantity that expresses the degree of disorder or randomness in a system. The entropy of an open system tends to increase unless energy is expended.

episomes - plasmids that can undergo integration into the bacterial chromosome.

eukaryotes - organisms whose cells are compartmentalized by internal cellular membranes to produce a nucleus and organelles.

exon - a region in the coding sequence of a gene that is translated into protein (vs. introns which are not).

extinction coefficient - a numerical constant that indicates the ability of a particular substance in solution to absorb light of wavelength. The molar extinction coefficient is the absorbance that would be displayed by a 1.0 mol ar solution in a 1.0 cm light path.

Fischer projection - a way of representing stereoisomers in a plane. The tetrahedron of bonds on a carbon is represented as a plane cross, where the bonds to the right and left point toward the viewer and the bonds to the top and bot tom point away. Fischer projections of monosaccharides are oriented with the carbonyl group at the top; the chiral carbon farthest from the carbonyl group (which is the one that determines whether the sugar is the D or the L form) is then drawn wi th its hydroxyl to the right for the D form and to the left for the L form.

flavin adenine dinucleotide (FAD) - a coenzyme found in a number of enzymes that catalyze redox reactions.

fluid mosaic model - the model of membranes in which proteins are embedded in a phospholipid bilayer and are free to move in the plane of the membrane.

free energy (G) (also called Gibbs free energy) - a thermodynamic quantity that relates enthalpy and entropy. The change in free energy (delta G) for a chemical reaction indicates whether it will be thermodynamically favor ed at a given temperature.

frictional coefficient - a value that reflects the frictional force on a molecule in a moving in a particular medium.

gel electrophoresis - electrophoresis in which the supporting medium is a gel (usually agarose or acrylamide); used for separating proteins and nucleic acids base on net charge and size.

genetic code - the three-nucleotide groupings in DNA or RNA that specify the amino acid sequence of a polypeptide.

genetic recombination - any process that results in the transfer of genetic material from one DNA molecule to another. In eukaryotes, it can refer specifically to the exchange of matching segments between homologous chromosomes by the process of crossing over.

genome - all of the chromosomal DNA found in a cell; the total genetic content of a cell.

globular proteins - proteins whose three-dimensional folded shape is relatively compact.

glucogenic - compounds, such as certain amino acids, that can be used by cells for the biosynthesis of glucose.

gluconeogenesis - the processes by which glucose is synthesized from noncarbohydrate precursors, such as glycerol, lactate, some amino acids, and (in plants) acetyl-CoA.

glycosaminoglycans (also called mucopolysaccharides) - polysaccharides composed of repeating disaccharide units in which one sugar is either N-acetylgalactosamine or N-acetylglucosamine. Typically the disaccharide unit carries a c arboxyl group and often one or more sulfates, so that most glycosaminoglycans have a high density of negative charges.

G proteins - a group of membrane proteins that transduce signals from various cell-surface receptors. They are called G proteins because they bind GTP and GDP as part of their reaction cycle.

Haworth projection - a planar representation of a cyclized monosaccharide molecule. The hydroxyls that are to the right of the carbon atom in a Fischer projection are placed below the plane in a Haworth projection.

helix-loop-helix motif - a protein structural feature that consists of two a helix segments connected by a loop; found in calmodulin, some other calcium-binding proteins, and some DNA-binding proteins. .

helix-turn-helix motif - a protein structural feature that consists of two alpha helical segments connected by a beta turn; it binds DNA in a sequence-specific manner and is present in many transcription factors.

Hill coefficient - a numerical value that reflects the degree of cooperativity in protein function; it is the slope of the portion of a Hill plot that corresponds to the cooperative transition.

histones - small, basic proteins that bind DNA to form the nucleosome.

Holliday junction - a model for an intermediate formed during homologous recombination.

homologous recombination - genetic recombination that requires extensive sequence homology between the recombining DNA molecules. Meiotic recombination by crossing over in eukaryotes is an example.

hydrophilic - the property of a molecule that produces an attractive interactions with water molecules. Ionic compounds or those that can engage in hydrogen bonding are hydrophilic.

hydrophobic - the property of having no attractive interactions with water. Hydrophobic substances are nonpolar.

hydrophobic effect - the stabilization of tertiary and quaternary protein structures that results from the packing of hydrophobic side chains in the interior of the protein.

hypochromism - the reduction in the absorbance at 260 nm that accompanies the transition from random-coil DNA to a double-strand helix.

induced fit model - a model to explain enzymes catalysis. In this model, the empty active site of the enzyme only roughly fits the substrate(s), and the entry of substrate causes the enzyme to change its shape so as to both tight en the fit and cause the substrate to adopt a configuration that resembles the transition state. This is currently the most widely accepted model for enzymatic catalysis.

intercalation - refers to the inter-leafing of a small molecule between adjacent bases in a DNA helix.

internal energy - the energy contained in a chemical system. In biochemistry, this would include all the types of energy that might be change in chemical reactions, including the kinetic energy of motion and vibration and the ener gy stored in chemical bonds (covalent or noncovalent).

intron - the portion of the coding sequence of a gene that is not translated into protein.

joule (J) - a unit for energy (or work), defined as the work done by a force of 1 newton when the object it acts on moves 1 meter.

ketone bodies - the chemicals acetoacetate, beta-hydroxybutyrate, and acetone, which are produced from excess acetyl-CoA (during starvation).

lagging strand - the daughter DNA strand that is synthesized in the opposite direction to the direction of movement of the replication fork; it is synthesized as a series of fragments that are subsequently joined.

leading strand - the daughter DNA strand that is synthesized in the same direction as the direction of movement of the replication fork; it is synthesized continuously rather than in fragments.

leukotrienes - lipid molecules that are synthesized from arachidonic acid by the lipoxygenase pathway and function as local hormones, primarily to promote inflammatory and allergic reactions.

ligand - a molecule that binds specifically to a protein. The term can also be used to mean a chemical substance that forms a coordination complex with a transition metal ion.

Lineweaver-Burk plot - a graphical representation of kinetic data that permits the determination of the rate constant and the Michaelis constant for an enzyme-catalyzed reaction. It is constructed by plotting a graph of l/V versus l/[S].

lipid bilayer - a membrane structure that consists of two back-to-back layers of lipids, in each of which the polar head groups on each side face the water and the nonpolar tails lie in the center of the membrane.

messenger RNA (mRNA) - the RNA molecule that acts as template for the synthesis of polypeptides by ribosomes.

metabolism - the totality of the chemical reactions that occur in an organism.

metastability - not at thermodynamic equilibrium but stable on the time scale of interest because the rate of reaction is very slow. Kinetically stable; thermodynamically unstable.

micelles - solid spherical bodies that form when an amphipathic substance is added to water and shaken. The amphipathic molecules are arranged with their polar head groups facing out toward the water and their nonpolar tails faci ng toward the center.

microtubules - cytoplasmic fibers that consist of tubulin subunits arranged helically to form a hollow tube.

mismatch repair - system for the correction of mismatched nucleotides or single-base insertions or deletions produced during DNA replication; it scans the newly replicated DNA, and when it finds an error, it removes and replaces a stretch of the strand containing the error.

mitochondrion - an organelle involved in the synthesis of ATP via oxidative phosphorylation. It houses the enzymes for the citric acid cycle, beta-oxidation of fatty acids, the electron transport chain, and oxidative phosphorylati on

mixed-function oxidase (mono-oxygenase) - an enzyme that catalyzes a reaction between molecular oxygen and an organic compound. In this reaction one atom of oxygen is incorporated into the organic compound and the other appears in H20.

neurotransmitter - a low-molecular-weight substance that is released from an axon terminal in response to the arrival of an action potential and then diffuses across the synapse to bind to a receptor on a postsynaptic cell.

noncompetitive inhibitor - an inhibitor of an enzyme-catalyzed reaction that acts by binding to a site on the enzyme different from the active site and reducing the enzyme's catalytic efficiency (vmax).

nucleolus - the site in the nucleus where ribosomal RNAs are transcribed and processed and ribosomes are assembled.

nucleosome - a structural unit made up of 146 bp of DNA wrapped 1.75 times around a core octamer of histone proteins; aids in the compaction of eukaryotic DNA.

nucleotide - a molecule made up of a purine or pyrimidine base, a sugar, and inorganic phosphate.

Okazaki fragments - small fragments of DNA that are synthesized on the lagging strand during DNA replication. They are later joined to form a continuous strand by DNA polymerase I and DNA ligase.

oncogene - a gene that codes for a protein that is receptor or a part of a signal transduction pathway for a cellular growth factor. A mutated oncogene can transform a normal cell to a cancer cell.

open reading frame - an DNA sequence that is bounded by start and stop codons; it may represent the coding sequence for a polypeptide.

operator - DNA site located between a promoter site and the structural genes of an operon. A repressor protein binds to this sequence of DNA and blocks the initiation of transcription.

operon - a set of contiguous prokaryotic structural genes that are transcribed as a unit, plus the adjacent regulatory elements that control their expression.

palindrome - a sequence of DNA that is the same on one strand read right to left as on the other strand read left to right, that is, a back-to-back pair of inverted repeats.

peptide bond - the covalent bond that links successive amino acids; it consists of an amide bond between the alpha carboxyl-group of one amino acid and the alpha-amino group of the next.

phenotype - the measurable characteristic of an organism that results from the interaction of the its genetic makeup with the environment.

photoreactivation - a repair mechanism for DNA in which an enzyme uses light energy to break cyclobutane-linked pyrimidine dimers. These dimers are created by UV irradiation of DNA.

plasmid - a small, circular DNA, extrachromosomal in location, found in many bacteria; replicates independently of chromosomal DNA and may occur in multiple copies per cell.

polymer - a molecule that is made by covalently linking a number of smaller molecular units (monomers) that are similar or identical to each other.

polymerase chain reaction (PCR) - a powerful technique for synthesizing a large amount of DNA from very small amounts of DNA having a specific sequence. This is accomplished through repeated cycles of denaturation, primer anneali ng, and replication (extension) using a heat-resistant DNA polymerase. Is also used in DNA sequencing.

primary structure - the linear sequence of nucleotides or amino acids in the polynucleotide (RNA or DNA) or polypeptide (protein).

primer - a short sequence of DNA or RNA that base-pairs with a DNA template strand and provides a free 3' -OH end from which a DNA polymerase can extend a DNA strand.

processivity - the degree to which a DNA or RNA polymerase remains bound to its template during a polymerization reaction.

prokaryotes - single-celled organisms that are not compartmentalized by internal cellular membranes; includes the eubacteria and archaebacteria.

promoter - the DNA sequence to which RNA polymerase binds to initiate transcription of RNA.

prostaglandins - compounds derived from certain long-chain unsaturated fatty acids (particularly arachidonic acid) that act as local hormones. Synthesized via a cyclooxygenase reaction.

prosthetic group - a metal ion or small molecule (other than an amino acid) that associates with a protein and is essential to the its biochemical functioning; its attachment to the protein may be either covalent or noncovalent.

pseudogene - a DNA sequence that bears strong similarity to a functioning gene, but whose protein product is not very likely to be biologically active. Gene families often contain pseudogene members that may have arisen from a f unctional gene during evolution.

quaternary structure - the level of structure that results when separate, folded polypeptide chains (subunits) associate in a specific way to produce a complete oligomeric protein.

Ramachandran plot - a map of all possible angles of rotation around the two alpha carbon bonds of an amino acid that contribute to the polypeptide backbone.

random coil - a linear polymer that has no secondary or tertiary structure but instead has randomly varying geometries. This is the state of a denatured protein or nucleic acid.

rate constant - a constant numerical value that correlates the reaction rate of a particular reaction to its substrate concentrations.

receptor - a protein that upon binding a specific molecule (can be a small molecule or a macromolecule) initiates a biological response.

recombinant DNA molecule - a DNA molecule that is constructed from segments of two or more precursor DNA molecules. Used as a tool in biotechnology and in many areas of biochemistry and molecular genetics.

recombination - process in an organism in which two DNA molecules give rise to daughter DNA that combines segments from the two parent molecules. It may involve the integration of one DNA molecule into another (addition), the su bstitution of a DNA segment for a homologous segment in other DNA, or the exchange of homologous segments between two DNA molecules.

repressor - a protein that inhibits the transcription of a gene (or genes) by binding to an operator sequence of DNA.

restriction endonucleases - enzymes that catalyze the double-strand cleavage of DNA at the sites of specific sequences. These endonucleases are used extensively in molecular genetics.

reverse transcriptase - an enzyme found in retroviruses that synthesizes a double-strand DNA molecule from a single-strand RNA template. It is an important tool in molecular genetics.

ribosome - a very large protein-RNA complex that catalyzes the synthesis of polypeptides based on the sequence of a mRNA.

sarcoplasmic reticulum - a network of membranous tubules that surrounds each myofibril in a skeletal muscle cell. It sequesters and then releases the calcium ions that trigger muscle contraction.

secondary structure - the first level of actual folding of the backbone of a linear polymer to form a regular, repeating structure. Examples are the B- and Z-helical forms of DNA and the alpha-helix and beta-sheet structures of polypeptides.

second law of thermodynamics - a statement that the entropy in a closed system never decreases, or alternatively, that processes that free energy must decrease if a change is to be thermodynamically favorable at constant tempera ture and pressure.

second-order reaction - a reaction in which two reactant molecules must come together for the reaction to occur. The reaction is called second-order because the reaction rate depends on the product of two reactant concentrations.

sedimentation coefficient (S) - a measure of the velocity at which a particular particle will sediment during centrifugation; it depends on the density of the medium and the size, shape, and mass of the particle.

signal recognition particles (SRPs) - proteins that bind to a specific N-terminal signal sequence on nascent polypeptides being formed on ribosomes; they assist in docking these ribosomes on the surface of the endoplasmic reticul um.

Southern blotting - a hybridization technique for detecting the presence of a specific DNA sequence in a genome. The DNA is extracted, cleaved into fragments, separated by gel electrophoresis, denatured, and blotted onto a nitroc ellulose filter. The filter is incubated under annealing conditions with a radiolabeled DNA probe, and the presence of bands of DNA containing the sequence of interest is detected by radioautography.

standard state - a set of specific chemical conditions (for substances in solution, standard state is 1 M concentration at 1 atm pressure and 250C) that create a reference point from which thermodynamic quantities can be d efined.

stop codons - triplets of nucleotides in RNA (normally UAG, UGA, and UAA) that signal a ribosome to stop translating an mRNA and to release the completed polypeptide.

supercoiling - turns of the two helical DNA strands around each other that either larger or smaller than the number of turns in the most stable linear helical conformation that would occur in free solution. Only a helix that is circular or else bound at both ends can maintain supercoiling.

suppression - a mutation that restores the wild-type phenotype, but it occurs at a second site on the DNA that is outside of the gene containing the original mutation,

Svedberg unit (S) - the unit of the sedimentation coefficient, which is equal to 10-13 seconds.

symport - a membrane transport process that couples the transport of a substrate in one direction across a membrane (down it electrochemical gradient) to the transport of a different substrate in the same direction (up its electr ochemical gradient).

telomerase - a DNA polymerase that adds a short repeating sequence to the 3' strand at either end of a linear chromosomal DNA molecule, thereby creating a single-strand overhang. This permits DNA replication of the full length o f the chromosome.

tertiary structure - the folding of the elements of secondary structure, such as alpha helices and beta-sheet.

topoisomerase - an enzymes that change the supercoiling of DNA helices by either allowing the superhelical torsion to relax (reducing the supercoiling) or adding more twists and increasing the supercoiling.

transcription - synthesis of a messenger RNA molecule that has a sequence complementary to that of a strand of DNA.

transition state - the highest energy state (and the molecular configuration that corresponds to it) that exists between reactant and product in a chemical reaction.

translation - synthesis of a sequence of amino acids in a polypeptide based on the sequence information in mRNA.

turnover number - the number of substrate molecules one enzyme molecule can convert to product (turn over) per second when the enzyme is saturated with substrate.

twist - the total number of times the two strands of a DNA helix cross over each other, excluding writhing.

van der Waals radius - radius of the electron cloud of an atom or a molecule; defines how close other atoms or molecules can approach.

vector - a DNA molecule that can be used to introduce a DNA sequence into a cell. The vector, which is usually plasmid or viral DNA, must be capable of being replicated by the cell.

writhe - the number of times the DNA double helix crosses over itself; the number of superhelical turns that are present.

x-ray diffraction - a technique used to determine the three-dimensional structure of molecules, including macromolecules. A crystal of the substance is illuminated with a beam of x-rays, and the repeating elements of the crystal scatter the x-rays to form a diffraction pattern that gives information on the location of atoms in the molecule (requires resolution of the phase problem).

Z-DNA - a duplex of DNA with a specific left-hand helical structure.

created by John Brabson and Adrienne Enfield on 6/2/97
maintained by
last revised on 8/30/97