Glossary of biochemistry
Sumber: http://bcs.whfreeman.com/biochem6
A
acetyl CoA carboxylase An enzyme that catalyzes the ATP-dependent synthesis of
malonyl CoA from acetyl CoA and carbon dioxide, the committed step in fatty acid
synthesis.
acetylcholine receptor A ligand-gated channel that promotes a large inward
current of sodium ions and triggers an action potential; composed of a pentamer of
four kinds of polypeptide subunits, the channel opens to allow passage of sodium
and potassium ions when two acetylcholine molecules promote transient opening of
the channel.
acetylcholinesterase An enzyme in the synaptic cleft that converts acetylcholine
into choline and acetate; this enzyme promotes the closing of the acetylcholinereceptor membrane by rapidly reducing the concentration of acetylcholine in the
region between the presynaptic and the postsynaptic membranes.
acetyllysine-binding domain A domain consisting of a four-helix bundle that binds
peptides containing acetyllysine. Also called a bromodomain.
actin A highly conserved protein found in all eukaryotes; in striated muscle, it forms
the thin filaments of the sarcomere and activates the ATPase of myosin.
actinomycin A polypeptide antibiotic from Streptomyces that inhibits the elongation
phase of RNA synthesis by binding to double-helical DNA by intercalating with it,
thereby preventing the DNA from serving as a template.
action potential The increase in membrane potential and the changes in sodium
and potassium conductances that result from alterations in the permeability of the
axon membrane to those ions. Also called nerve impulse.
activated carriers Small molecules carrying activated functional groups that can be
donated to other molecules; for instance, ATP carries activated phosphate groups
and CoA carries activated acyl groups.
activated methyl cycle A series of reactions in which S-methyl groups from
methionine are converted into a biochemically reactive form through insertion into an
adenosyl group; an active S-methyl group can be transferred from Sadenosylmethionine to acceptor molecules such as norepinephrine. The remaining
part of the cycle includes the regeneration of methionine from homocysteine and N5methyltetrahydrofolate.
activation domain The structural region of a transcription factor that facilitates
transcription in some manner. See also DNA-binding domain.
active site A specific region of an enzyme that binds the substrate and carries out
catalysis.
active transport The transport of an ion or a molecule against a concentration
gradient, where DG for the transported species is positive; the process must be
coupled to an input of free energy from a source such as ATP, an electrochemical
gradient of Na+ or K+, or light.
actomyosin A complex formed in vitro between myosin and actin that displays
certain properties of muscles, such as contracting in the presence of ATP.
acyl adenylate A mixed anhydride in which the carboxyl group of a molecule is
linked to the phosphoryl group of AMP; the formation of acyl adenylates is a means
of activating carboxyl groups in biochemical reactions, such as the formation of fatty
acyl CoA molecules from a free fatty acid and coenzyme A.
acyl carrier protein A bacterial polypeptide that is linked to phosphopantetheine
and acts as a carrier of the growing fatty acyl chain during fatty acid biosynthesis.
adaptation The resetting of the sensitivity level of receptors due to the continued
presence of ligands. Also called desensitization.
addition to or formation of double bond A reaction in which a functional group is
added to a double bond or a group is removed from a molecule to form a double
bond.
adenylate cyclase An enzyme that generates cAMP, a second messenger, from
ATP.
adenylate cyclase cascade A signal-transduction pathway that employs cAMP and
a series of enzymes to convert an extracellular signal into an intracellular signal.
adipocytes Mammalian cells that are the major storage site for triacylglycerols.
A-DNA helix A right-handed double helix made up of antiparallel strands held
together by A-T and G- C base pairing; it is wider and shorter than B-DNA and is
seen in dehydrated DNA as well as in doublestranded regions of RNA and in RNADNA helices.
aerobic In the presence of oxygen.
affinity chromatography A protein-purification technique based on the high affinity
of many proteins for specific chemical groups. Such groups are attached to an inert
matrix, and the protein sample is applied; only those proteins with an affinity for the
groups will bind.
affinity labeling A means of mapping the active site of an enzyme by using a
substrate analog that binds to the active site and forms a covalent bond with a
nearby amino acid.
agonists Molecules that bind to receptor proteins and trigger signaling pathways.
alcaptonuria A relatively harmless hereditary disorder resulting from the aberrant
breakdown of tyrosine and phenylalanine.
alcoholic fermentation The anaerobic conversion of glucose into ethanol with the
concomitant production of ATP.
aldol condensation The combination of two carbonyl compounds (e.g., an aldehyde
and a ketone) to form a β-hydroxycarbonyl compound, or aldol.
aldose A monosaccharide whose C-1 carbon atom contains an aldehyde group.
alleles Alternative forms of a gene at a particular site on a chromosome.
allosteric interaction An interaction between a small molecule (a ligand) and a site
on a protein that may be some distance away from the active site; the interaction
causes a conformational change and consequent alteration in the catalytic activity of
the protein.
α helix A common structural motif in proteins, in which a polypeptide main chain
forms the inner part of a right-handed helix, with the side chains extending outward;
the helix is stabilized by intrachain hydrogen bonds between NH and CO groups of
the main chain.
α-ketoglutarate dehydrogenase A citric acid cycle enzyme that catalyzes the
oxidative decarboxylation of α-ketoglutarate to yield succinyl CoA. This enzyme,
which helps to regulate the rate of the citric acid cycle, is structurally and
mechanistically similar to the pyruvate dehydrogenase complex.
alternative splicing The generation of unique but related mRNA molecules by the
differential splicing of the pre-mRNA transcript. By allowing the synthesis of more
than one mRNA molecule from a premRNA transcript, alternative splicing increases
the encoding potential of the genome.
Amanitin A cyclic octapeptide from the mushroom Amanita phalloides (the
destroying angel) that is a potent inhibitor of the elongation phase of RNA synthesis
catalyzed by RNA polymerase II.
Ames test A simple, rapid means of detecting carcinogens by measuring a
chemical's ability to induce mutations in Salmonella bacteria.
amiloride-sensitive sodium channel A sodium channel important in the detection
of the taste of salt. Such channels are inhibited by amiloride, which also mutes the
taste of salt.
amino acid An organic acid with an α-carbon atom linked to a carboxylic acid, an
amino group, a hydrogen atom, and a side chain (the R group). Twenty different
amino acids are the building blocks of proteins.
amino sugar A sugar that contains an amino group rather than a hydroxyl group at
the C-2 position; the most common amino sugars are glucosamine and
galactosamine.
aminoacyl-tRNA An amino acid ester of transfer RNA.
aminoacyl-tRNA synthetase An enzyme that activates an amino acid and then
links it to transfer RNA. Also known as an activating enzyme, each aminoacyl-tRNA
synthetase is specific for a particular amino acid.
aminotransferase A class of enzymes that transfer an α-amino group from an αamino acid to an α- keto acid. Also called transaminases.
ammoniotelic Characteristic of organisms in which excess ammonia is directly
secreted; many aquatic animals are ammoniotelic.
AMP-dependent protein kinase A protein kinase, conserved among eukaryotes,
that is activated on binding of AMP and inhibited by ATP; consequently, it functions
as a cellular fuel gauge, inhibiting certain process by phosphorylating key enzymes
when the energy supply is low.
ampere A measure of electrical current: the flow of 6.24 × 1018 charges per second.
amphibolic reactions Metabolic reactions that can be anabolic or catabolic,
depending on the energy conditions in the cell.
amphipathic molecule A molecule, such as a membrane lipid, that contains both a
hydrophobic and a hydrophilic moiety.
amylopectin The branched form of starch, containing glucose residues in about one
α-1,6 linkage per thirty α-1,4 linkages.
amylose The unbranched form of starch, containing glucose residues in α-1,4
linkage.
amytal A barbiturate that blocks the respiratory chain by inhibiting electron transfer
in the NADH-Q reductase complex.
anabolic steroid A steroid, such as testosterone, that acts through the androgen
receptor to stimulate genes that enhance the development of lean muscle mass.
anabolism The set of metabolic reactions that require energy to syntheize
molecules from simpler precursors.
anaerobic In the absence of oxygen.
anapleurotic reaction From the Greek for "fill up," referring to a reaction that
replenishes intermediates removed from a metabolic pathway. The most common
example is the reaction catalyzed by pyruvate carboxylase, in which the
carboxylation of pyruvate produces oxaloacetate, a key component of the citric acid
cycle.
Andersen's disease A disease due to an inability to introduce α-1,6-glycosidic
bonds during the synthesis of glycogen. Glycogen is present in normal amounts but
with long outer branches; clinically, the disease is characterized by progressive
cirrhosis of the liver.
androgens A class of steroid hormones, exemplified by testosterone, that are
responsible for the development of male secondary sexual characteristics;
synthesized by the testes.
angstrom (Å) A unit of length equal to 10-10 meter.
anomers Isomers of cyclic hemiacetals or hemiketals, with different configurations
only at the carbonyl carbon atom; that carbon is known as the anomeric carbon.
antagonist A molecule that binds to a receptor protein but does not trigger the
signaling pathway. Such molecules are like competitive inhibitors for enzymes.
antibody A protein synthesized by an animal in response to the presence of a
foreign substance, or antigen; often binds to the antigen, neutralizing it or marking it
for destruction.
anticodon Three-nucleotide sequence of tRNA that base-pairs with a codon in
mRNA.
antigen A foreign substance that elicits the synthesis of an antibody.
antigenic determinant Site on an antigen to which an antibody binds. Also called
an epitope.
antimycin A An antibiotic from Streptomyces that inhibits the respiratory chain by
blocking electron transfer in the cytochrome reductase complex.
antiporter A transport system in which a molecule is carried across a membrane in
the direction opposite that of an ion, which in turn is pumped back across the
membrane through active transport linked to ATP hydrolysis.
antiserum Serum prepared from the blood of an immunized animal containing
soluble antibodies specific for a particular antigen.
apoptosis A cascade of proteolytic enzymes that results in controlled cell death in
response to significant cell damage or specific developmental programs. Also called
programmed cell death.
arachidonate Derived from linoleate, a 20:4 fatty acid that is a major precursor to
several classes of signal molecules, including prostaglandins.
arrestin A protein that plays a role in the termination of the visual signaltransduction pathway by binding to phosphorylated rhodopsin and preventing further
interaction with transducin. Arrestin may function similarly in other 7TM-dependent
signal-transduction pathways.
ascorbate (vitamin C) A water-soluble vitamin that functions as an antioxidant and
is required for the hydroxylation of collagen; scurvy results if ascorbate is deficient.
aspartyl proteases A class of protein-degrading enzymes whose activity is
dependent on an aspartate residue at the active site. An aspartyl protease is
required for HIV replication.
ATP (adenosine 5'-triphosphate) A nucleotide consisting of adenine, ribose, and
triphosphate units that serves as the cellular energy currency.
ATP-ADP translocase An adenine nucleotide carrying a transport protein that
carries ADP into the mitochondria and ATP out in a coupled fashion.
ATP-binding cassette (ABC) domain The ATP-binding domain characteristic of
specific membranetransport proteins, called ABC transporters; these transporters
also contain a membrane-spanning region.
ATP-grasp fold A protein domain that surrounds ATP and orients it for nucleophilic
attack at the ã phosphate. Enzymes with these domains catalyze the formation of
carbon-nitrogen bonds through acylphosphate intermediates.
ATP synthase Molecular assembly of the inner mitochondrial membrane responsible
for the respiratory-chain-driven synthesis of ATP. Also called Complex V,
mitochondrial ATPase, H+-ATPase, or F0F1-ATPase.
atractyloside A plant glycoside that inhibits ATP-ADP translocase.
attenuation In bacteria, a mechanism for transcriptional regulation in which a
decrease in the rate of translation of an mRNA operon reduces the rate of
transcription of that operon.
autoimmune disease A disease, such as insulin-dependent diabetes and multiple
sclerosis, that result from a failure to suppress the immune response to selfantigens.
autoradiography A means of detecting radioactive molecules immobilized in a
separation medium such as polyacrylamide; the radioactivity of the molecules will
blacken x-ray film.
autotrophs Photosynthetic organisms that synthesize glucose from carbon dioxide
and water, by using sunlight as an energy source; the glucose is then used as a fuel
for cellular metabolism.
avidity The strength of an interaction comprising multiple independent binding
interactions between partners, as would take place between an antigen and
antibody.
axoneme The fundamental design structure of cilia and flagella; it consists of a
bundle of microtubules, enclosed in a membrane, in which nine microtubule doublets
surround two microtubule singlets.
B
blymphocyte Precursors to plasma cells, which are antibody-secreting cells.
bacitracin An antibiotic that blocks the transfer of oligosaccharides from dolichol
phosphate to proteins.
bacteriorhodopsin A 26-kd integral membrane protein that absorbs light and
converts its energy into proton-motive force, which is then used to synthesize ATP.
base-excision repair A means of repairing DNA in which the damaged base is
removed and replaced by a base complementary to the undamaged DNA strand.
B-DNA helix A right-handed double helix with the following characteristics: the two
strands are antiparallel; the bases are inside the helix and the phosphates and
deoxyribose sugars are on the outside; adenine forms hydrogen bonds with thymine,
and guanine forms them with cytosine; the bases in each pair are coplanar; there
are 10.4 residues per turn, with a pitch of 35 Å.
Beer's law The relations between the absorbance of light (A) by a compound, its
extinction coefficient (å), concentration (c) and the length (l) of the light path: A =
åcl
beriberi A neurologic and cardiovascular disorder caused by a dietary deficiency of
thiamine (vitamin B1).
β sheet A common structural motif in proteins, in which two or more β strands are
associated as stacks of chains, stabilized by interchain hydrogen bonds; a number of
β strands running in the same direction form a β pleated sheet, whereas such
strands running in opposite directions form an antiparallel pleated sheet.
β-galactosidase An essential enzyme in lactose metabolism that hydrolyzes lactose
into galactose and glucose.
bifunctional enzyme An enzyme with two different, often opposing, catalytic
activities on one polypeptide chain. For instance, phosphofructokinase 2 synthesizes
fructose 2,6-bisphosphate and fructose 2,6-bisphosphatase hydrolyzes it, yet both
active sites are on the same polypeptide chain.
bile salts Polar derivatives of cholesterol that are made in the liver, stored in the
gall bladder, and released into the small intestine, where they act as detergents to
solubilize dietary lipids, facilitating their digestion and absorption.
binding energy The free energy released in the formation of the weak interactions
between enzyme and substrate.
biopterin A cofactor from which the electron carrier tetrahydrobiopterin is derived.
biotin A vitamin that plays a role in carboxylation and decarboxylation reactions.
Bohr effect The observation made by Christian Bohr that H+ and CO 2 promote the
release of oxygen from oxyhemoglobin.
bongkrekic acid An antibiotic that inhibits the action of ATP-ADP translocase.
branch migration The ability of a DNA strand partly paired with its complementary
strand to move, displacing its homologous resident strand and extending the pairing.
bromodomain A domain consisting of a four-helix bundle that binds peptides
containing acetyllysine. Also called an acetyllysine-binding domain.
C
C3 plant A plants that lacks the C4 pathway.
C4 pathway A means by which four-carbon compounds, such as oxaloacetate and
malate, carry carbon dioxide from mesophyll cells in contact with the air to bundlesheath cells, which are the major sites of photosynthesis. The pathway accelerates
photosynthesis by concentrating carbon dioxide in photosynthetic cells.
C4 plant A plant that utilizes the C4 pathway.
CAAT box A component of many eukaryotic promoters with the consensus sequence
5'-GNCAATCT- 3'.
Calcium ATPase (Ca2+ ATPase) An ATP-driven calcium pump that maintains the
large electrochemical gradient of calcium ion across the plasma membrane.
calmodulin In vertebrates, a ubiquitous protein in vertebrates that, when bound to
calcium, stimulates many enzymes and transporters.
calmodulin-dependent kinase A protein kinase that is activated by the binding of
a Ca2+-calmodulin complex.
calnexin Anchored in the endoplasmic reticulum membrane, a chaperone protein
that prevents the export of immature or defective glycoproteins by binding glucose
residues on the glycoproteins.
caloric homeostasis Maintenance of a constant body weight by a complex network
of hormonal interactions.
calorie The amount of heat required to raise the temperature of 1 gram of water
from 14.5°C to 15.5°C.
Calvin cycle In plants, a cyclic metabolic pathway in which carbon dioxide is
incorporated into ribulose 1,5-bisphosphate to give compounds that can be used for
the synthesis of glucose.
5' cap A structure at the 5' end of eukaryotic mRNA that stabilizes the mRNA and
enhances its translation. The cap contains a 7-methyl guanylate residue attached by
a triphosphate linkage to the sugar at the 5' end of the mRNA in a rare 5'-5' linkage.
capsaicin receptors Ion channels expressed in nociceptors that open in response to
noxious stimuli such as heat, acidity or chemicals such as capsaicin, the chemical
responsible for the "hot" taste of spicy food. Also called the vanilloid receptor 1
(VR1).
capsid The protein coat surrounding viral DNA or RNA.
carbamoyl phosphate synthetase An enzyme that begins the urea cycle by
catalyzing the synthesis of carbamoyl phosphate from bicarbonate, ammonium ion,
and ATP. The enzyme also catalyzes the initial reaction in pyrimidine biosynthesis.
carbohydrates Saccharides, which are aldehyde or ketone compounds with multiple
hydroxyl groups. Also defined as organic compounds with the empirical formula
(CH2O)n.
carbonium ion A carbon compound that contains a positively charged carbon atom;
a carbonium atom is critical for catalysis by lysozyme
carboxylase An enzyme that catalyzes a carboxyl transfer reaction; biotin is usually
required as a coenzyme.
carcinoembryonic antigen (CEA) A membrane glycoprotein of the fetal
gastrointestinal cells that is not significantly expressed after birth. High serum levels
of CEA are evident in many patients with colorectal cancer.
cardiotonic steroids Compounds derived from cholesterol that inhibit the Na+-K+
pump by blocking the dephosphorylation of the E2 conformation of the pump protein.
Inhibition of the pump in cardiactissue cells leads to a higher level of sodium ion in
the cells, which slows the extrusion of calcium ion and enhances cardiac muscle
contractility.
carnitine A zwitterionic compound formed from lysine that acts as a carrier of longchain fatty acids from the cytosol to the mitochondrial matrix.
carotenoids Extended polyenes that absorb light between 400 and 500 nm and
serve as accessory pigments in photosynthesis by funneling the energy to the
photosynthetic reaction center.
cascade, enzymatic A sequence of reactions, in which at each step a product
stimulates an ensuing reaction, generating an amplification of a relatively small
stimulus or signal.
caspases Cysteine proteases that participate in the proteolytic cascade in apoptosis.
catabolism The set of metabolic reactions that transform fuels into cellular energy.
catabolite activator protein (CAP) The cAMP response protein; when bound to
cAMP, CAP binds to an inverted repeated of the lac operon, near position -61 relative
to the start site of transcription, to stimulate transcription.
catabolite repression The repression by glucose of catabolic enzymes required for
the catabolism of carbohydrates other than glucose.
catalase A ubiquitous heme protein that catalyzes the dismutation of hydrogen
peroxide into molecular oxygen and water.
catalysis by approximation Enhancing the rate of a reaction by bringing multiple
substrates together along a single binding surface of an enzyme.
catalytic antibodies Antibodies generated by using transition-state analogs of a
particular reaction as antigens. Such antibodies often function as catalysts for the
reaction. Also called abzymes.
catalytic group An amino acid or cofactor at an enzymes active site that directly
participates in the making or breaking of covalent bonds.
catalytic RNA One of a class of RNA molecules that display enzymatic activity.
catalytic triad A constellation of three residues, found in many proteolytic enzymes,
in which two of the residues convert the remaining residue, usually a serine or
cysteine, into a potent nucleophile.
CD4 A protein present on the surface of helper T cells that, along with the T-cell
receptor, binds to class II MHC proteins on antigen-presenting cells. CD4 is the
source of the specificity of helper T cells for class II MHC interactions.
CD8 A cell-surface protein expressed by cytotoxic T cells that, in conjunction with
the T cell receptor, recognizes class I MHC-peptide complexes. CD8 binds to the MHC
protein itself.
cDNA DNA complementary to an mRNA sequence.
CDP-alcohol Activated form of an alcohol that can be used in the synthesis of
phosphoglycerides by combining with diacylglycerol at the free hydroxyl group on
glycerol; for instance, CDP-choline can react with diacylglycerol to form the
phospholipid phosphatidylcholine.
CDP-diacylglycerol (cytidine diphosphodiacylglycerol) Formed from
phosphatidate and cytidine triphosphate (CTP); activated diacylglycerol used in the
synthesis of phosphoglycerides such as phosphatidyl serine.
cell type Cells within an organism that have the same genetic makeup but have
different properties owing to differences in gene expression.
cellular immune response A system for cellular recognition of foreign substances
that employs cellattached T-cell receptors to eliminate cells infected by a pathogen
or to elicit a particular antigenic response by stimulating B-lymphocyte antibody
production.
cellulose An unbranched homopolysaccharide in plants, composed of glucose
residues in α-1,4 linkage; the major structural polysaccharide in plants.
centromere The attachment site of mitotic spindles in chromosomes.
ceramide (N-acyl sphingosine) A sphingosine with a long-chain acyl group
attached to the amino group.
cerebroside A sphingolipid in which glucose or galactose is linked to the terminal
hydroxyl group of a ceramide.
cGMP phosphodiesterase An enzyme that hydrolyzes cyclic GMP to GMP; in the
visual system, this hydrolysis leads to the generation of an action potential.
cGMP-gated calcium channel A channel in rod cells that opens in response to
cGMP to allow entry of calcium and sodium ions into the cell; closing of the channel
in response to cGMP hydrolysis initiates the visual signal-transduction pathway.
channel A protein passage that is continuous and that allows ions to flow rapidly
through a eukaryotic membrane from a compartment of higher to a compartment of
lower concentration. Channels (also known as pores in bacteria) are generally
composed of four to six subunits, or domains, and are gated by membrane potential,
allosteric effectors, or covalent modification.
chaperone proteins Slow ATPases that bind newly synthesized proteins and assist
their proper folding.
chemiosmotic hypothesis The idea that electron transfer in the respiratory chain is
used to pump protons across the inner mitochondrial membrane, establishing a
proton gradient; this gradient (the proton-motive force) drives the synthesis of ATP
by ATP synthase.
chemoattractants Substances, such as glucose, that, when present in the form of a
gradient, cause bacteria to swim toward the source of the gradient.
chemorepellants Potentially harmful substances, such phenol, that, when present
in the form of a gradient, cause bacteria to swim away from the source of the
gradient.
chemotrophs Organisms that obtain energy by the oxidation of foodstuffs. See also
phototrophs.
CheY A protein in the bacterial chemotaxis signaling pathway that, when
phosphorylated, leads to clockwise rotation of the flagellum, causing tumbling, and
that, when dephosphorylated, leads to counterclockwise rotation and smooth
swimming.
chimeric DNA A recombinant DNA molecule containing unrelated genes.
chloramphenicol An antibiotic that inhibits the peptidyl transferase activity of the
prokaryotic 50S ribosomal subunit.
chlorophyll A substituted tetrapyrrole that is the principal photoreceptor in plants.
chloroplast The plant organelle in which photosynthesis takes place.
cholera toxin A toxin that consists of a catalytic domain and a membranepenetration domain; the catalytic subunit ADP-ribosylates the G stimulatory protein,
persistently activating it, leading to activation of ion pumps and subsequent efflux of
large amounts of Na+ and water into the gut.
cholesterol A sterol that is an important constituent of eukaryotic membranes as
well as lipoproteins; also a precursor of steroid hormones.
chromatin Nucleoprotein chromosomal material consisting mainly of DNA and
histones.
chromatin immunoprecipitation (ChIP) A technique for identifying the binding
sites of DNAbinding proteins. The protein is cross-linked to DNA to which it is bound
in chromatin, and the DNA is fragmented into small pieces. Antibodies to the bound
protein are used to isolate the chromatin fragments with the bound protein. The
cross-linking is reversed, and the DNA is isolated and characterized.
chromatin remodeling machine A complex of proteins that contain domains
homologous to helicases and use the energy of ATP hydrolysis to shift the positions
of nucleosomes and induce other conformational changes in chromatin.
chromophore A light-absorbing group, such as 11-cis-retinal in rhodopsin.
chromosome walking A technique for analyzing long stretches of DNA by
sequential subcloning and rescreening of overlapping segments.
chylomicrons Lipoprotein particles that transport dietary triacylglycerols from the
intestine to other tissues; apolipoprotein B-48 is a protein component of
chylomicrons.
cilia Hairlike organelles made of microtubules that protrude from the surface of the
cell and move liquid past the cell surface; responsible for movement of many singlecelled organisms.
citrate synthase An enzyme that catalyzes the condensation of acetyl CoA with
oxaloacetate to form citrate, initiating the citric acid cycle.
citric acid cycle A cyclic series of metabolic reactions that completely oxidize acetyl
units to carbon dioxide. Also known as the tricarboxylic acid cycle (after citrate) or
the Krebs cycle, after Hans Krebs, who elucidated the cyclic nature of the pathway.
class I MHC proteins Membrane proteins that tightly bind proteolytic fragments of
cellular proteins and present them to the scrutiny of T cells. A foreign protein
presented in a class I MHC protein provokes attack by killer T cells that initiate
apoptosis in the target cell.
class II MHC proteins Proteins expressed only in antigen-presenting cells; Class II
MHC proteins display peptides derived by the destruction of proteins internalized by
endocytosis.
class switching A step in the differentiation of an antibody-producing cells in which
the cells switch from producing IgM antibodies to producing one or the other classes
of antibodies while maintaining the same antigen specificity.
clathrin A protein that coats the cytosolic side of coated pits and can form a lattice
around the pit, excising it from the membrane to form a coated vesicle.
coated pits Specialized regions of the plasma membrane containing localized cellmembrane receptors. The cytosolic side of these indentations is coated with the
protein clathrin.
cobalamin (vitamin B12) A complex taking part in a number of reactions including
the formation of deoxyribonucleosides from ribonucleosides.
coding strand The strand of DNA that has the same sequence as the RNA transcript
except it contains thymine (T) in place of uracil (U).
codon Nucleotide triplet in mRNA that encodes for a particular amino acid.
coenzyme A small organic molecule required for the activity of many enzymes;
vitamins are often components of coenzymes.
coenzyme A (CoA) A coenzyme consisting of an adenine nucleotide linked to
pantothenate, which is itself linked to mercaptoethylamine; universal carrier of acyl
groups, which are bound to the mercaptoethylamine unit.
coenzyme Q A mobile electron carrier that is a component of the respiratory chain;
it shuttles between the oxidized ubiquinone form to the reduced ubiquinol form
through a semiquinone intermediate; accepts electrons from NADH-Q reductase as
well as succinate-Q reductase.
cohesive ends In double-stranded DNA molecules, complementary single-stranded
ends produced by staggered cuts. Specific cohesive ends in DNA can be produced by
certain restriction enzymes, such as EcoRI, and can then be used to join unrelated
DNA molecules by annealing and joining with DNA ligase.
colchicine An alkaloid from the autumn crocus that prevents polymerization of
tubulin to form microtubules; as a consequence, it inhibits the cell cycle at
metaphase.
combinatorial chemistry The process of producing large populations of molecules
en masse and then selecting for a particular biochemical property.
combinatorial control A means of controlling gene expression in eukaryotes in
which each transcription factor, rather than acting on its own to effect transcription,
recruits other proteins to build up large complexes that regulate the transcription
machinery.
committed step The first irreversible step in a metabolic pathway under physiologic
conditions; this step is catalyzed by an allosteric enzyme and commits the product to
a particular chemical fate.
compartmentation The location of metabolites, enzymes, or pathways in different
membrane-bound organelles in eukaryotic cells.
competitive inhibition The reduction in the rate of enzyme activity observed when
the enzyme can bind the substrate or the inhibitor but not both. Many competitive
inhibitors resemble the substrate and compete with it for binding to the active site.
Relief from inhibition by saturation with substrate is a kinetic hallmark of competitive
inhibition.
complementarity-determining region (CDR) In immunoglobulin L and H chains,
polypeptide segments that display great sequence variability and are responsible for
antigenic specificity.
concerted mechanism A model explaining the kinetics of allosteric enzymes in
which the transitions of all of the active sites between the T state and the R state
occur simultaneously.
cone A photoreceptor cell that functions in bright light and is responsible for color
vision.
consensus sequence Idealized base sequence that represents common features of
a promoter site.
conservative substitutions Mutations that replace one amino acid with another
similar in size and chemical properties.
constant region The carboxyl-terminal end of an immunoglobulin G (IgG) light
chain or an IgG heavy chain. For many antibodies, these parts of the polypeptide
chains have amino acid sequences that are very similar to one another; a light chain
has one constant region, whereas a heavy chain has three such regions, each of
which specifies a compact domain in the native immunoglobulin molecule.
constitutive genes Genes that are not subject to regulation and are constantly
transcribed.
conventional kinesin A motor protein, built around a P-loop NTPase core, that has
several structural features in common with myosin; conventional kinesin moves
toward the plus end of microtubules.
convergent evolution The process by which different evolutionary pathways arrive
at the same solution to a biochemical problem.
cooperativity A property of many allosteric enzymes in which the binding of
substrate to one active site favors the transition of all active sites from the T state to
the R state, leading to an increase in enzyme activity.
core glycosylation The addition of carbohydrates to proteins and the processing of
these carbohydrates that takes place in the endoplasmic reticulum.
core particles Particles resulting from micrococcal nuclease digestion of
nucleosomes, consisting of 140-bp DNA and the histone octamer of a nucleosome.
corepressor A small molecule that binds to a repressor protein; the corepressorrepressor complex then binds to the operator DNA of a particular operon to inhibit
transcription.
Cori cycle A cyclic metabolic pathway in which lactate from active muscle is
converted into glucose by the liver, which in turn supplies newly synthesized glucose
to muscle and other tissues.
Cori disease A disease in which the structure of liver and muscle glycogen is
abnormal and the amount is increased; it is due to an inability to hydrolyze the α1,6-glycosidic bonds in glycogen; liver function is compromised.
coupled reaction The pairing of an endergonic reaction with an exergonic reaction,
such as the hydrolysis of ATP, so that the pair of reactions will take place under
cellular conditions.
covalent catalysis Catalysis in which the active site contains a reactive group that
becomes temporarily covalently modified in the course of catalysis.
covalent intermediate In a catalytic mechanism, an intermediate comprising a
component of the substrate covalently bound to the enzyme.
covalent modification The attachment to and removal of chemical groups from an
enzyme and the consequent change in the catalytic properties of that enzyme.
Catalytic properties of many enzymes are altered by the covalent attachment and
removal of phosphoryl groups, whereas a smaller number of others undergo
reversible attachment of AMP units from ATP.
CpG islands Regions of DNA rich in the sequence CpG, usually located at the 5'
region of genes; the cytosine bases of these islands can be methylated to inhibit
transcription of the associated gene.
crassulacean acid metabolism An adaptation by plants living in arid environment;
the C4 pathway concentrates carbon dioxide at night, and vapor exchange with the
environment is curtailed during the heat of the day by closure of the stomata.
creatine phosphate (phosphocreatine) In muscle, a compound with a high
phosphoryl transfer potential that is used to regenerate ATP from ADP during the
initial seconds of muscle contraction.
critical concentration The concentration of G-actin monomers above which
polymerization occurs and below which depolymerization occurs. The critical
concentration is equal to the dissociation constant (Kd) of an actin monomer from a
filament.
cumulative feedback inhibition A regulatory strategy in which the enzyme
catalyzing the committed step common to several pathways is incrementally
inhibited by the products of each of the pathways. Thus, each inhibitor can reduce
the activity of the enzyme even if other inhibitors are bound at saturating levels.
cyclic AMP (cyclic 3', 5'-adenosine monophosphate) A cyclic nucleotide formed
from ATP and an important second messenger in a variety of signaling systems.
cyclic AMP-response element binding protein (CREB) A transcription factor that
binds to the cyclic AMP-response element in DNA and, when phosphorylated by
protein kinase A, recruits coactivators that result in the stimulation of transcription of
specific genes.
cyclic GMP (cyclic 3', 5'-guanosine monophosphate) A cyclic nucleotide formed
from GTP and an important second messenger in vision.
cyclic photophosphorylation In photosynthesis, the generation of ATP without the
concomitant formation of NADPH; electron cycling from the reaction center of
photosystem I to ferredoxin and then back to the reaction center through
cytochrome bf and plastoquinone generates a proton gradient that is used to drive
ATP formation.
cycloheximide An antibiotic that inhibits the peptidyl transferase activity of the 60S
ribosomal subunit in eukaryotes.
cyclosporin A drug that is a potent suppressor of the immune system and is used to
prevent rejection in organ transplants.
cytidine diphosphodiacylglycerol (CDP-diacylglycerol) An activated precursor
for the synthesis of many phospholipids formed by the reaction of phosphatidate with
CTP.
cytochrome An electron-transferring protein that contains a heme prosthetic group
whose iron component shuttles between the ferrous (+2) and ferric (+3) state
during electron transfer.
cytochrome bf A cytochrome complex that links photosystem II and photosystem I
in green plants; cytochrome bf contributes to the proton gradient by oxidizing
plastoquinol to plastoquinone.
cytochrome c A water-soluble, highly conserved cytochrome component of the
respiratory chain that accepts electrons from cytochrome reductase and is in turn
oxidized by cytochrome oxidase.
cytochrome c oxidase The final complex of the respiratory chain, cytochrome c
oxidase transfers electrons from cytochrome c to molecular oxygen and
concomitantly pumps protons across the inner mitochondrial membrane to generate
the proton-motive force. Also called Complex IV.
cytochrome P450 system Found in adrenal mitochondria and liver microsomes, an
electron-transport chain in which the terminal component is cytochrome P450; this
system plays a role in the detoxification of foreign substances by altering them to
increase their solubility and facilitate excretion.
cytoskeleton Internal scaffolding of cells, made up of microfilaments, intermediate
filaments, and microtubules, which enables cells to transport vesicles, change shape,
and migrate.
cytotoxic T lymphocytes T cells that trigger cell death by apoptosis in cells that
display foreign antigens on class I MHC proteins. Also called killer T cells.
D
dalton A unit of mass very nearly equal to that of a hydrogen ion and precisely
equal to 1.000 on the atomic mass scale.
dark reactions In chloroplasts, the reactions in which carbon dioxide is fixed into
organic compounds, driven by ATP and NADPH.
decarboxylase An enzyme that removes a carbon atom from a substrate in the
form of carbon dioxide.
decorated filaments A structure resulting when S1 heads are mixed with actin
filaments. Each S1 head binds to an actin filament with its long axis oriented at 45
degrees to the filament. With all S1 units similarly oriented, a structure looking like a
set of arrowheads pointing in the same direction results.
deletion A type of mutation in which one or more base pairs are left out in DNA
replication; also, the absence of one or more bases from a nucleotide sequence in a
gene.
denaturation A disruption in the native conformation of a macromolecule that
causes a loss of normal function.
de novo pathway A biosynthetic pathway that builds the final product from simple
precursors. See also salvage pathway.
density-gradient equilibrium sedimentation A centrifugal technique for
separating biological molecules according to their densities in an aqueous solution of
a salt such as cesium chloride. When such solutions are centrifuged at high speeds,
opposing forces of sedimentation and diffusion create a concentration gradient of the
salt; molecules in that gradient are driven by centrifugal force into the region where
the solution density is equal to their own.
deoxyhemoglobin A conformation of hemoglobin that is unable to bind oxygen.
Also called the T or tense form.
deoxynucleotide A nucleotide containing a purine or pyrimidine base covalently
linked to 2- deoxyribose, which is in turn linked to one or more phosphate groups.
deoxyribose A five-carbon monosaccharide (C5H9O5) that constitutes the
carbohydrate moiety of a deoxynucleotide; the deoxyribose commonly found in
deoxynucleotides is 2-deoxyribose.
desensitization The resetting of the sensitivity level of receptors due to the
continued presence of ligands. Also called adaptation.
diabetes A disease characterized by the overproduction of glucose by the liver and
its underutilization by other organs. Type I diabetes is due to an insufficiency of
insulin production, whereas type II is due to the inability of insulin receptors to
respond to the hormone.
diacylglycerol A second messenger in the phosphoinositide cascade, which leads to
the activation of protein kinase C.
diagonal electrophoresis A means of determining the location of disulfide bonds in
proteins. A mixture of proteins undergoes electrophoresis in a single lane in one
direction, disulfide bonds are irreversibly reduced, and the sample is electrophoresed
perpendicularly to the original direction. Peptides migrating as a single band in the
first direction will migrate as two bands in the second direction if they contained a
disulfide bond.
diastereoisomers A pair of molecules, each with more than one asymmetric center,
that have opposite configurations at one such center but are not mirror images of
each other; in the aldotetrose series, Derythrose and D-threose are
diastereoisomers.
dicoumarol An antagonist of vitamin K, which is a crucial factor in the carboxylation
of ã carbon atoms in glutamate residues in the amino-terminal region of
prothrombin; prothrombin synthesized in the presence of dicoumarol cannot bind
calcium ion and therefore cannot promote the blood-clotting cascade.
differential centrifugation A means of fractionating cell components by step-bystep centrifugation of increasing centrifugal force. The supernatant of each step is
centrifuged again at greater force to produce a pellet and another supernatant,
which is subsequently centrifuged at yet greater force. The starting material consists
of cells with disrupted plasma membranes.
diffusion coefficient In the context of membranes, a means of expressing the
lateral mobility of membrane constituents; for lipids, the diffusion coefficient is 2 µm 2
s-1.
digitalis A mixture of cardiotonic steroids derived from the dried leaf of the foxglove
plant; such steroids inhibit the sodium-potassium pump.
dihedral angle A measure of the rotation about a bond, usually taken to lie
between -180 and +180 degrees. Also called torsion angles.
dihydrofolate reductase An enzyme that catalyzes the regeneration of
tetrahydrofolate from dihydrofolate formed in the synthesis of thymidylate.
diphtheria toxin A toxin, produced by Corynebacterium diphtheriae, that gains
entrance to the cell by receptor-mediated endocytosis and kills the cell by ADPribosylation of protein synthesis elongation factor 2, thus inhibiting all protein
synthesis.
direct repair A means of repairing damaged DNA in which the damaged region is
corrected in place. For example, pyrimidine dimers are simply cleaved to restore the
original nucleotides.
dismutase An enzyme that catalyzes a dismutation reaction in which a single
reactant is converted into two different products.
distributive enzyme An enzyme that catalyzes the elongation or degradation of a
polymer but dissociates from the polymer after each catalytic step.
disulfide bond A covalent bond formed by the oxidation of two sulfhydryl groups;
the oxidation of cysteine residues in a polypeptide yields a disulfide bond linking the
two residues.
divergent evolution The evolutionary process by which proteins with different
properties are derived from a common ancestor.
DNA gyrase A topoisomerase that catalyzes the ATP-driven introduction of negative
supercoils into DNA. Also called topoisomerase II.
DNA ligase An enzyme that catalyzes the formation of a phosphodiester bond
between the 3'-OH group at the end of one DNA chain and the 5'-phosphate group at
the end of the other chain; it takes part in the synthesis, repair, and splicing of DNA.
DNA polymerases Enzymes that catalyze the template-directed, primer-dependent
addition of deoxynucleotide units, using deoxynucleotide triphosphates as substrates,
to the 3' end of a DNA chain; chain growth is in the 5'-to 3'-direction; such enzymes
replicate and repair DNA.
DNA probe A radioactively labeled, single-stranded specific base sequence used to
locate a complementary sequence among DNA fragments displayed on an
electrophoretic gel.
DNA-binding domain The structural region of a transcription factor that recognizes
and binds to a particular DNA sequence. See also activation domain.
dolichol phosphate A lipid, residing in the ER membrane, containing approximately
20 isoprene units that serves as a carrier of oligosaccharides destined to be attached
to a protein.
domain An independently folded unit in the tertiary structure of a polypeptide chain;
may contain a number of supersecondary structures. In multienzyme complexes,
each domain may carry out one or more catalytic reactions. In proteins, a compact
globular unit of 100 to 400 residues, possibly joined to other domains by a flexible
polypeptide segment; often encoded by a specific exon in the gene encoding the
protein.
double-displacement reaction A reaction having multiple substrates in which one
or more products are released before all substrates bind the enzyme. The defining
feature of these reactions is the formation of a substituted-enzyme intermediate.
Also called ping-pong reaction.
dynamic instability A property of microtubules such that some microtubules in a
population lengthen while other simultaneously shorten; a result of the random
fluctuations in the number of GTP- tubulin subunits or GDP-tubulin subunits at the
ends of the microtubule. GTP-tubulin polymerizes more readily.
dynein A large protein with ATPase activity that is a component of microtubules; the
ATPase activity provides the power for the movement of cilia and flagella. In
cytoplasm, a motor protein that is related to the dynein in flagella and cilia and
powers retrograde transport
E
Edman degradation The sequential removal of the N-terminal amino acid from a
protein as a phenylthiohydantoin derivative; used in sequencing proteins.
EF hand A helix-loop-helix motif that forms a binding site for calcium; found in
many calciumsensitive proteins.
eicosanoid A carbon compound containing 20 carbon atoms; prostaglandins are
examples. Eicosanoids often act as local hormones.
electrophoresis A technique used to separate charged molecules, such as proteins
and nucleic acids, that is based on the fact that such molecules will move at differing
rates in an electric field, depending on factors such as net charge, size, and shape of
the molecules.
electrospray ionization mass spectrometry A means of determining the mass of
a protein. A protein sample is sprayed into a mass spectrometer, and the mass of
the protein is determined by the mass-tocharge ratio of proteins differing in the
number of bound protons.
ELISA (enzyme-linked immunoabsorbant assay) An assay for quantifying the
presence of an antigen by using an enzyme linked to an antibody to the antigen.
elongation The second of the three stages of all biological polymerization reactions.
In this stage, polymerization is due to the repetition of a basic process characteristic
of the specific molecule being synthesized.
elongation factor One of a set of proteins that facilitate the elongation phase of
protein synthesis.
elongation factor G (EF-G) A member of the G-protein family that closely
resembles the complex between EF-Tu and tRNA. Hydrolysis of GTP by EF-G causes
the tRNAs and mRNA to move through the ribosome a distance corresponding to one
codon.
elongation factor Ts (EF-Ts) A protein that binds to the GDP-bound form of EF-Tu
and induces the release of GDP, thereby enabling EF-Tu to participate in another
elongation step.
elongation factor Tu (EF-Tu) A member of the G-protein family that delivers
aminoacyl-tRNAs to the A site of the ribosome with the concomitant hydrolysis of
GTP to GDP.
Embden-Meyerhof pathway Glycolysis.
enantiomers A pair of molecules, each with one or more chiral centers, that are
mirror images of each other.
endocytosis The process of internalization of extracellular material by invagination
and budding of the cell membrane.
endoplasmic reticulum (ER) An extensive system of cytoplasmic membranes that
comprises about half the total cell membrane. The region of the ER that binds
ribosomes is called the rough ER, and the region that is devoid of ribosomes is called
the smooth ER.
endosome A component of the receptor-mediated endocytotic pathway in which
sorting decisions about the endocytosized material are made; endosomes are derived
from coated vesicles that lose the clathrin coat.
energy charge A means of determining the energy status of the cell, equal to the
concentration of ATP plus one-half the concentration of ADP, all divided by the total
adenine nucleotide concentration.
enhancers DNA sequences that have no promoter activity themselves but that can
greatly enhance the activity of other promoters; enhancers can exert their
stimulatory effect over a distance of several thousand nucleotides.
enol phosphate A compound with a high phosphoryl transfer potential because the
phosphoryl group traps the molecule in an unstable enol form. On transfer of the
phosphate, the molecule converts into the more stable ketone form.
entropy A measure of the degree of randomness or disorder in a system; denoted
by the symbol S in thermodynamics, the change in entropy (.S) increases when a
system becomes more disordered and decreases when the system becomes more
ordered, or less random.
enzymatic cascade A sequence of reactions in which, at each step, a product
stimulates an ensuing reaction, generating an amplification of a relatively small
stimulus or signal.
enzymes Biological macromolecules that act as catalysts for biochemical reactions;
although almost all are composed of protein, catalytically active RNA molecules have
been recently discovered.
enzyme multiplicity A regulatory strategy in which the committed step common to
several pathways is catalyzed by different enzymes with the same catalytic
properties but different regulatory properties. Each enzyme thus responds to the
final product of one of the pathways having the committed step in common.
enzyme-substrate complex The product of specific binding between the active site
of an enzyme and the substrate.
epimers Pairs of molecules, each with more than one asymmetric center, that differ
in configuration at only one such center; glucose and galactose are epimers, differing
only in the configuration at C-4.
epimerases Enzymes that catalyze the interconversion of epimers of a compound.
epinephrine A catecholamine released by the adrenal medulla in response to
muscle activity or its anticipation that stimulates the breakdown of muscle glycogen.
Also called adrenaline.
epitope The specific site on an antigen that is recognized by an antibody. Also
known as the antigenic determinant.
erythromycin An antibiotic that binds to the 50S ribosomal subunit and inhibits
peptide translocation in prokaryotes.
essential amino acids Amino acids that cannot be synthesized de novo and
therefore must be acquired from the diet; in adult mammals, at least nine amino
acids are considered essential.
eubacteria The most common form of extant prokaryotes.
excinuclease uvrABC enzyme that removes thymidine dimers by hydrolyzing the
damaged DNA strand at sites on either side of the dimer site.
exons Regions of pre-mRNA that are retained in mature mRNA.
exon shuffling A hypothesis that suggests that new proteins arose in evolution by
rearranging exons that encoded discrete structural elements.
exonuclease An enzyme that digests nucleic acids from the ends of the molecule,
rather than at an internal site; exonucleases can be specific for digestion from the 3'
or 5' ends of the nucleic acid.
extinction coefficient (å) A measure of a compound's ability to absorb light, given
in units that are the reciprocals of molarity and distance in centimeters (M-1 cm-1).
extrinsic clotting pathway Blood-clotting cascade of enzyme activities that is
initiated by the activation of factor VII and the release of the lipoprotein tissue
factor, both of which are triggered by tissue trauma.
F
Fab fragment One of two 50-kd polypeptide chains produced when immunoglobulin
G is cleaved by the protease papain; Fab fragments bind antigens but cannot crosslink them, because each fragment has only one binding site for an antigen.
Fc fragment One of two 50-kd polypeptide chains produced when immunoglobulin G
(IgG) is cleaved by the protease papain; the Fc fragment of an intact IgG molecule
cannot participate in antigen binding but can mediate other important biological
activities, such as complement fixation.
facilitated diffusion Transport of an ion or a molecule down a concentration
gradient, where .G for the transported species is negative. Also called passive
transport.
F-actin A filament of G-actin monomers that is a polar, self-assembling, dynamic
polymer.
facultative anaerobes Organisms that can function aerobically in the presence of
oxygen or anaerobically, using fermentation as a source of cellular energy, in the
absence of oxygen.
FAD and FADH2 (flavin adenine dinucleotide) An important electron carrier in
the oxidation of fuel molecules; alternates between the oxidized FAD form and the
reduced FADH2 form. It consists of a flavin moiety and an AMP unit; electrons are
carried on the isoalloxazine moiety of the molecule.
familial hypercholesterolemia A disease that results from the dysfunctional
receptor-mediated endocytosis of cholesterol-bearing lipoprotein particles. With this
disease, patients have abnormally high blood levels of cholesterol, which can lead to
arterial narrowing and heart attacks at an early age.
fatty acid synthase An enzyme system that catalyzes the synthesis of saturated
long-chain fatty acids from acetyl CoA, malonyl CoA, and NADPH; in bacteria, the
constituent enzymes of the synthase complex can be dissociated when cell extracts
are prepared; in mammals, all constituent enzyme activities in fatty acid synthase
are part of the same polypeptide.
fatty acids Carboxylic acids containing long hydrocarbon chains that are an
important fuel source as well as a key component of membrane lipids.
feedback inhibition A mode of enzyme regulation in which the end product of a
biosynthetic pathway inhibits the enzyme that catalyzes the first step in that
pathway.
feedforward stimulation The activation of an allosteric enzyme in a later stage of
a pathway by the product of a reaction that takes place earlier in the reaction
pathway.
fermentation An ATP-generating process in which organic compounds act as both
donors and acceptors of electrons; fermentations can take place in the absence of
oxygen.
ferrihemoglobin Hemoglobin in which the iron component of the heme prosthetic
group is in the ferric (+3) state; ferrihemoglobin cannot bind oxygen.
ferrohemoglobin Hemoglobin in which the iron component of the heme prosthetic
group is in the ferrous (+2) state; ferrohemoglobin is capable of binding oxygen.
fertility factor A bacterial plasmid that contains genes required for conjugation.
first messengers Hormones; molecules that transduce signals from one tissue to
another tissue (the target tissue) through the blood.
Fischer projection A means of depicting the stereochemistry of a molecule. In a
Fischer projection of a molecule, atoms joined to an asymmetric carbon atom by
horizontal bonds are in front of the plane of the page, and those joined by vertical
bonds are behind.
flagella, eukaryotic Hairlike organelles made up of microtubules that protrude from
the cell surface; their movement propels the cell.
flagella, prokaryotic Extracellular appendages used to propel bacteria; the
required energy is derived directly from a proton-motive force across the cell
membrane.
flagellin The protein component of bacterial flagella.
flavins Electron carriers that use riboflavin in electron-transfer reactions; FAD,
FADH2, FMN, and FMNH2 are flavins.
flavin mononucleotide (FMN) A coenzyme for oxidation-reduction reactions
derived from the vitamin riboflavin. The electron acceptor of FMN, the isoalloxazine
ring, is identical with that of FAD, but FMN lacks the adenyl nucleotide component of
FAD.
flavoproteins Proteins tightly associated with FAD or FMN; flavoproteins play
important roles in many oxidation-reduction reactions.
FliG A bacterial flagellar protein that is part of the MS (membrane and
supramembrane) ring; FliG, in combination with flagellar proteins MotA/MotB, forms
a proton channel that drives the rotation of the flagellum.
fluid mosaic model The description of membranes as two-dimensional solutions of
oriented lipids and globular proteins.
fluorescence photobleaching recovery technique (FRAP) A technique for
measuring membrane fluidity in which a membrane component is labeled with a
fluorescent molecule that is subsequently destroyed (or bleached) by an intense
burst from a laser; fluidity is determined by the rate at which the bleached region
fills with fluorescent molecules from adjoining regions of the membrane.
fluorouracil An analog of dUMP that inhibits the methylation of dUMP to form
thymidylate; fluorouracil is used in chemotherapy.
footprinting A technique used to determine the site of a protein that binds to DNA.
DNA is digested in the presence or absence of the protein, and the sequence
protected from digestion by the protein is identified. This sequence is the "footprint"
of the protein.
free energy A form of energy capable of doing work under conditions of constant
temperature and pressure. Also, a measure of the usable energy generated in a
chemical reaction; denoted by the symbol G in thermodynamics. The change in free
energy (.G) of a system undergoing transformation at constant pressure is equal to
the change in enthalpy (.H) minus the product of the absolute temperature (T) and
the change in entropy (.S).
free energy of activation The energy required to form the transition state from the
substrate of a reaction.
frictional coefficient A characteristic of a molecule that is proportional to the shape
of the molecule. This coefficient multiplied by the velocity at which a molecule moves
through a medium constitutes viscous drag, a measure of resistance to movement of
the molecule.
functional magnetic resonance imaging (fMRI) A brain-imaging technique that
takes advantage of (1) the fact that magnetic properties of oxyhemoglobin and
deoxyhemoglobin are different and can thus be distinguished and (2) the fact that,
when a specific part of the brain is active, blood vessels relax and allow more blood
flow. Thus, a more active part of the brain will be richer in oxyhemoglobin.
furanose A five-membered heterocyclic ring formed when a monosaccharide
cyclizes to form a hemiacetal or a hemiketal; the five-membered oxygen-containing
ring is similar to that of furan.
G
G protein A guanyl nucleotide-binding protein that is a component of intracellular
signaling pathways. In the inactive state, the G protein (sometimes called a
heterotrimeric G protein) is a trimeric protein consisting of αβã subunits, with the
GDP bound to the α subunit. In the active state, the α protein exchanges GDP for
GTP and dissociates from the βã subunits. The GTP-bound α subunit propagates the
signal. Signal propagation is terminated when the α subunit hydrolyzes GTP to GDP
and reassociates with the βã subunits.
Gα The guanyl nucleotide-binding subunit of heterotrimeric G proteins.
Gβã The dimeric component of G proteins that helps to maintain the Gα component in
the inactive state. In some signal-transduction pathways, the Gβã component can
also function as a second messenger.
G(olf) An α subunit, uniquely expressed in olfactory cilia, of a G protein associated
with odorant receptors.
G-actins Actin monomers that come together to form filaments called F-actin.
galactosemia A disease characterized by vomiting, diarrhea, liver dysfunction, and
occasionally mental retardation, caused by galactose accumulation due to a
deficiency of galactose 1-phosphate uridyl transferase.
β-galactosidase In lactose metabolism, an essential enzyme that hydrolyzes
lactose into galactose and glucose.
ganglioside A ceramide, common in membranes of the nervous system, in which an
oligosaccharide is linked to the ceramide by a glucose residue.
gap junctions Passageways between the interiors of two contiguous cells. Also
known as cell-to-cell channels.
GC box A component of many eukaryotic promoters, especially those from
constitutively expressed genes. The consensus sequence for the GC box is 5'GGGCGG-3'.
gel-filtration chromatography A separation technique based on size differences. A
sample is applied to a column consisting of porous beads. Large molecules move
through the column faster than small molecules because they cannot enter the beads
and, thus, have a shorter path to travel.
gene duplication Duplication of a gene in the process of replication. One of the
duplication products may accumulate mutations and eventually evolve into a gene
with a different but related function.
general acid-base catalysis Catalysis in which a molecule other than water plays
the role of a proton donor or acceptor.
general acid catalysis Acid catalysis in which the source of the proton is a donor
group rather than a free H+.
genetic code The relation between nucleic acid sequence information and protein
sequence information.
genomic library A collection of DNA fragments, inserted into vector molecules, that
represents the entire genome of an organism.
gigaseal A high-resistance seal formed between a pipette and a small patch of
plasma membrane, required for use in the patch-clamp technique.
globin fold A folding structure of a polypeptide chain, exemplified by myoglobin and
hemoglobin subunits, that creates an environment for a heme group to reversibly
bind oxygen.
glucagon A polypeptide hormone that is secreted by the α cells of the pancreas
when the bloodglucose level is low and leads to glycogen breakdown in the liver and
the release of glucose to the blood.
glucocorticoids A class of steroid hormones, synthesized by the adrenal cortex and
exemplified by cortisol, that promote gluconeogenesis, the formation of glycogen,
and the degradation of fats and proteins.
glucogenic amino acid An amino acid whose carbon skeleton, entirely or in part,
can be converted into substrates for gluconeogenesis.
gluconeogenesis The synthesis of glucose from noncarbohydrate precursors,
including lactate, glycerol, and amino acids.
glucose homeostasis Maintenance of a constant level of glucose in the blood.
glucose 6-phosphatase A membrane protein of the lumenal side of the
endoplasmic reticulum that catalyzes the formation of free glucose from glucose 6phosphate. In the liver, the enzyme plays a key role in maintaining blood-glucose
levels.
glucose 6-phosphate A key intermediate in metabolism that can be processed to
free glucose, stored as glycogen, oxidized to produce NADPH and ribose, or
metabolized to generate cellular energy either aerobically or anaerobically.
glucose 6-phosphate dehydrogenase An enzyme that initiates the oxidative
phase of the pentose phosphate pathway by oxidizing glucose 6-phosphate to 6phosphoglucono-ä-lactone to generate one molecule of NADPH.
glucose transporter An integral membrane protein consisting of a single
polypeptide chain that has 12 transmembrane segments and facilitates the
movement of glucose across the plasma membrane into the cell.
glutamate dehydrogenase An enzyme that catalyzes the oxidative deamination of
glutamate, yielding ammonium ion and α-ketoglutarate.
glutamine phosphoryl amidotransferase An enzyme that catalyzes the
committed step in purine synthesis, which is the displacement of pyrophosphate in
5-phosphoribosyl-1-pyrophosphate by ammonia to yield 5-phosphoribosyl-1-amine
with the amine in the β configuration.
glutathione (ã-glutamylcysteinylglycine or GSH) A tripeptide playing a role in
combating oxidative stress by maintaining the reduced state of the cell. Glutathione
cycles between the reduced (GSH) and oxidized (GSSG) state.
glycerol 3-phosphate shuttle A pathway that transfers electrons from cytoplasmic
NADH into the mitochondria; dihydroxyacetone phosphate (DHAP) is reduced by
NADH to glycerol 3-phosphate, which enters the mitochondria and is oxidized to yield
FADH2 and DHAP, which leaves the mitochondria.
glyceryl ether phospholipid A phospholipid that contains an ether unit rather than
an acyl unit at C-1 and is synthesized starting with dihydroxyacetone phosphate
rather than glycerol phosphate.
glycoforms Forms of a specific protein that differ only in patterns of glycosylation.
glycogen A readily mobilized storage form of glucose in which the glucose
monomers are linked by α- 1,4-glycosidic bonds and with branches (α-1,6-glycosidic
bonds) at about every tenth residue.
glycogen degradation The cleavage of glycogen by phosphorolysis, catalyzed by
glycogen phosphorylase, to yield glucose 1-phosphate, which can be converted into
glucose 6-phosphate.
glycogen phosphorylase An enzyme that catalyzes the phosphorolysis of glycogen
to yield glucose 1- phosphate; an allosteric enzyme whose activity is further
regulated by reversible covalent modification.
glycogen storage diseases Any of a number of heritable diseases characterized by
an inability to store or utilize glycogen appropriately.
glycogen synthase An allosteric enzyme that can be reversibly covalently regulated
and is responsible for the synthesis of glycogen; it transfers glucose from UDPglucose to the hydroxyl group at a C-4 terminus of glycogen.
glycogen synthesis The synthesis of glycogen from UDP-glucose, which is
catalyzed by the enzyme glycogen synthase.
glycogenin A protein that bears an oligosaccharide of α-1,4 glucose units and is the
primer for glycogen synthase. Glycogenin uses UDP-glucose to catalyze its own
autoglycosylation.
glycolipids Sugar-containing lipids that are derived from sphingosine; the sugar
moiety is attached at the alcohol on sphingosine.
glycolysis A sequence of reactions that convert glucose into pyruvate with the
concomitant generation of energy.
glycoproteins Proteins that have a specific carbohydrate moiety attached.
glycosaminoglycan A heteropolysaccharide made of repeating disaccharide units
and containing the amino sugar glucosamine or galactosamine.
glycosidase A class of enzymes that cleave glycosidic bonds; lysozyme is a
glycosidase.
glycosidic bond A covalent bond between an aldehyde or ketone function of a
monosaccharide and an oxygen, nitrogen, or sulfur atom of another molecule. The
most common glycosidic linkages are O-links between the anomeric carbon atom of a
sugar and a hydroxyl group of another saccharide.
glycosyltransferase Any one of a number of specific enzymes that catalyze the
formation of glycosidic bonds.
glyoxylate cycle A metabolic pathway that converts two-carbon units into succinate
for energy production and biosyntheses; found primarily in bacteria and plants, the
cycle bypasses two decarboxylation steps in the citric acid cycle and allows the net
formation of glucose and other molecules through oxaloacetate from acetate or
acetyl CoA.
glyoxysomes Plant organelles in which enzymes of the glyoxylate pathway are
present.
Golgi complex In the cytoplasm, a stack of membranous sacks that constitute the
major sorting center for proteins that reside in cell membranes and the lumen of
organelles.
gout A disease characterized by inflammation of the joints and kidneys due to the
precipitation of abnormally high levels of sodium urate, a breakdown product of
purines.
G-protein-coupled receptor See seven-transmembrane-helix receptors.
granum A pile or stack of thylakoid membranes in the chloroplast.
granzymes Proteolytic enzymes secreted by activated T cells into target cells to
initiate apoptosis.
green fluorescent protein A protein isolated from the jelly fish Aequorea victoria
that fluoresces. Because the protein can be attached to other proteins by genetic
engineering techniques, it provides a means of localizing proteins in cells.
group-transfer reaction A reaction in which a chemical group is transferred from
one molecule to another.
guanylate cyclase An enzyme that catalyzes the synthesis of cGMP, a second
messenger, from GTP.
gustation The sense of taste.
gustducin An α subunit of a G protein that is primarily expressed in taste buds and
is associated with 7TM bitter and sweet receptors.
H
hair cells Specialized neurons inside the cochlea of the inner ear; hair cells use a
connected bundle of stereocilia to detect motion and initiate the hearing signaltransduction pathway.
hairpin loop A loop of nucleic acid formed by duplex formation within a single
strand.
hapten A small foreign molecule that can elicit specific antibody formation when
attached to a macromolecule. The dinitrophenyl group is effective at eliciting an
antigenic response and has been widely used as a haptenic determinant.
Haworth projection A depiction of a cyclic carbohydrate in which the plane of each
ring is perpendicular to the plane of the page and in which ring carbon atoms are not
explicitly shown.
HDL (high-density lipoprotein) A lipoprotein that collects cholesterol released into
the blood from dying cells or from membranes undergoing turnover.
heat-shock proteins A ubiquitous group of proteins that are synthesized in
response to stress, such as a heat shock, and that bind unfolded polypeptides and
assist in their refolding.
heavy (H) chain A 50-kd polypeptide that is one of two types of paired chains
found in the immunoglobulin G molecule; each heavy chain consists of a variable
region and three constant regions, and each chain is linked by a disulfide bond to a
light chain.
heavy meromyosin (HMM) Along with light meromyosin, one of the tryptic
digestion products of myosin; it retains ATPase activity and the ability to bind actin
but does not form filaments.
helicases Enzymes that catalyze the ATP-driven unwinding of nucleic acids; DNA
helicases are important in DNA replication.
helix-turn-helix A recurring motif found in many DNA-binding proteins, in which
two α-helical segments are linked by a short hairpin turn; the two segments are 34 Å
apart, which allows them to fit into adjoining major grooves in DNA.
helper T cells T cells that stimulate the proliferation of specific B lymphocytes and
cytotoxic T cells.
heme The prosthetic group of myoglobin and hemoglobin as well as other proteins;
consists of an organic constituent, protoporphyrin, and an iron atom.
hemiacetal A compound formed by the reaction of an aldehyde functional group and
a hydroxyl group; for example, the C-1 group of the open-chain form of glucose
reacts with the C-5 hydroxyl group to form an intermolecular hemiacetal.
hemiketal A compound formed by the reaction of a ketone group and a hydroxyl
group; for example, the C-2 keto group of the open-chain form of fructose reacts
with the C-5 hydroxyl group to form an intermolecular hemiketal.
hemoglobin An allosteric protein that is the primary oxygen-carrying protein in
vertebrates; it also plays a role in the transport of CO2 and H+.
hemoglobinopathy A genetic disorder resulting from any number of mutations that
produce insufficient amounts of normal hemoglobin or normal amounts of defective
hemoglobin chains.
hemophilia A general term for a number of disorders of blood clotting, in which one
or another protein in the blood-clotting pathway is defective or missing.
heptoses Monosaccharides that have seven carbon atoms.
hereditary nonpolyposis colorectal cancer (HPCC) A common form of hereditary
colon cancer due to defective correction of DNA mismatches. Also called Lynch
syndrome.
Hers disease A disease resulting from a lack of liver glycogen phosphorylase;
glycogen is present in increased amounts with mild clinical effects.
heterotrophs Organisms that obtain energy from chemical fuels only and that are
ultimately dependent on autotrophs for fuel.
heterotropic effects The effects of nonsubstrate molecules on allosteric enzymes.
hexokinase A kinase that phosphorylates six-carbon sugars, usually glucose, at the
expense of ATP.
hexoses Monosaccharides that have six carbons.
high-density lipoprotein (HDL) A lipoprotein that picks up cholesterol from dying
cells and from membranes undergoing turnover, esterifies it, and then transfers the
cholesterol esters to the liver and other steroid-synthesizing tissues.
histone acetyltransferase (HAT) An enzyme that catalyzes the attachment of
acetyl groups from acetyl CoA to specific lysine residues in the amino-terminal
domains of histones. These enzymes play crucial roles in the modification of
chromatin structure that enhances transcription.
histone deacetylase An enzyme that contributes to transcriptional repression by
deacetylation of acetylated lysine residues in histones.
histones A highly conserved group of small basic proteins found in eukaryotes in
association with DNA to form nucleosomes.
Holliday junction A crosslike structure, formed by four polynucleotide chains, that
is a key intermediate in the recombination process.
holoenzyme An enzyme that consists of the protein component forming the main
body of the enzyme (the apoenzyme) and any necessary, usually small, cofactors.
homologous recombination Recombination between homologous segments of two
DNA molecules. Also called general recombination.
Homologs Molecules that have evolved from a common ancestor. Also referred to as
homologous molecules.
homotropic effects The effects of substrate molecules on allosteric enzymes.
horizontal gene transfer The passing of pieces of DNA (plasmids) between species
that provide a selective advantage in particular environments.
hormone response elements (HREs) Specific DNA sequences that bind members
of the nuclear receptor family of transcription factors; HREs for steroid receptors are
palindromic 6-bp sequences separated by a 3-bp spacer.
hormone-binding domain A conserved 240-residue domain in members of the
nuclear receptor superfamily of transcription factors that binds a hormone or
hormonelike molecule, thus activating the factor.
human immunodeficiency virus (HIV) The cause of acquired immune deficiency
syndrome (AIDS). HIV destroys helper T cells by increasing the permeability of the T
cell membrane. Loss of the helper T cells severely cripples the immune system,
rendering the victim susceptible to many types of infection.
human leukocyte antigen (HLA) The name given to a member of the majorhistocompatibilitycomplex proteins in human beings.
humoral immune response A system for the recognition of foreign substances that
employs soluble antibodies to bind to and inactivate such substances.
hybridization A technique used to determine the relatedness of nucleic acids by
assaying the ability of single strands of one sample to form a duplex by
complementary base pairing to single stands of another sample.
hybridoma cell A cell, resulting from the fusion of an antibody-producing cell and a
tumor cell, that produces a single antibody and has an unlimited capacity for
proliferation.
hydratase An enzyme that adds the elements of water to a carbon-carbon double
bond.
hydrogen bond A bond formed when two relatively electronegative atoms, such as
oxygen or nitrogen, unequally share a hydrogen atom that is covalently bonded to
one of the electronegative atoms.
hydrolytic reactions Reactions in which bonds are cleaved by the addition of water.
hydropathy plot A means of determining transmembrane sequences in proteins by
measuring the change in free energy required to move a segment comprising 20
amino acids of a protein from a hydrophobic environment to water. The free-energy
change is plotted against the position of the amino acid sequence in the protein.
hydrophobic interactions Refers to the tendency of nonpolar molecules in water to
interact with one another; the interactions are driven by an increase in the entropy
of water when the water molecules in contact with the nonpolar molecules are
released into bulk water.
3-hydroxy-3-methylglutaryl CoA reductase (HMG-CoA reductase) A highly
regulated enzyme that catalyzes the committed step in cholesterol synthesis-the
formation of mevalonate from 3-hydroxy-3- methylglutaryl CoA.
hyperammonemia A condition characterized by high levels of ammonia in the blood
due to deficiencies in the urea cycle, which can result in brain damage and death.
hyperchromism An increase in the absorbance of light by the unstacking of base
pairs when a DNA duplex is melted into single strands.
hypersensitive sites Regions of the chromosome that are especially sensitive to
digestion by exogenous DNAses; such regions are usually located at the 5' end of
actively transcribed genes.
hyperuricemia Excessively high levels of blood urate; hyperuricemia can induce
gout.
hypervariable loop In immunoglobulin light and heavy chains, polypeptide
segments that have great sequence variability and are responsible for antigenic
specificity.
hypervariable segment In immunoglobulin light and heavy chains, polypeptide
segments that have great sequence variability and are responsible for antigenic
specificity.
hypochromism A decrease in the absorbance coefficient as DNA renatures from the
single-stranded to the double-stranded form.
Hypoxanthine A purine base that reacts with 5-phosphoribosyl-1-pyrophosphate
(PRPP) to form inosinate; the reaction is part of the salvage pathway for purine
nucleotides.
I
I-cell disease A lysosomal storage disease in which certain hydrolases are missing
from the lysosomes owing to a defect in the synthesis of the lysosomal targeting
signal, mannose 6-phosphate.
IDLs (intermediate-density lipoproteins) Lipoprotein particles that remain after
much of the triacylglycerides from VLDL are hydrolyzed and absorbed by other
tissues; can be absorbed by the liver or converted into LDL.
immunoglobulin See antibody.
immunoglobulin A (IgA) The major class of antibodies in external secretions, such
as saliva, tears, bronchial mucus and intestinal mucus.
immunoglobulin D (IgD) An antibody of unknown function.
immunoglobulin E (IgE) An antibody that confers protection against parasites; IgE
also initiates allergic reactions.
immunoglobulin fold A common structural motif for immunoglobulins, in which two
broad sheets of antiparallel β strands enclose hydrophobic side chains, and
complementarity-determining regions of variable domains pair to form an antigenbinding site.
immunoglobulin G (IgG) The major antibody in serum; IgG posses two antigenbinding sites.
immunoglobulin M (IgM) The first class of antibodies to appear in the serum after
exposure to an antigen; IgM posseses ten antigen-binding sites.
immunoreceptor tyrosine-based activation motif (ITAM) The intracellular
region of Ig-α and Ig-β membrane proteins of immature B cells; upon antigen
binding to the membrane-bound antibodies of the B cell, the ITAM regions of Ig-α
and Ig-β are phosphorylated, which initiates pathways leading to cell growth and Bcell differentiation.
in situ hybridization A technique in which cells are immobilized and their DNA is
denatured and then hybridized to radioactive RNA probes; these hybrids are then
detected by autoradiography.
induced fit The modification of the shape of an active site in an enzyme after the
substrate is bound.
inducer A small molecule that binds to a repressor and alters its interaction with an
operator.
inhibitor 1 A protein that, when phosphorylated, inhibits the activity of protein
phosphatase 1 and thereby sustains glycogen breakdown and inhibits glycogen
synthesis.
initiation The first of the three stages common to all biological polymerization
reactions; this stage establishes conditions for the beginning of the polymerization
process.
initiation complex A complex of an RNA polymerase, promoter elements, and
specific transcription factors that permits the initiation of RNA synthesis.
initiation factor One of a set of proteins that assist in the association of the
ribosome, mRNA, and initiator tRNA to initiate the process of protein synthesis.
inosinate A purine nucleotide formed by the reaction of hypoxanthine with 5phosphoribosyl-1- pyrophosphate (PRPP); a precursor to both AMP and GMP.
inositol 1,4,5-trisphosphate A second messenger of the phosphoinositide cascade
that causes an increase in intracellular calcium levels.
insertion A type of mutation in which one or more base pairs are erroneously
inserted into DNA.
insertion sequence A simple DNA transposon, composed of a kilobase sequence
that specifies a transposase and is bounded on either end by inverted terminal
repeats; an insertion sequence can insert itself into any site on a bacterial
chromosome.
insertional inactivation Gene inactivation that occurs when an unrelated DNA
fragment is inserted at a restriction site; inactivation of a gene for antibiotic
resistance in a plasmid can be used to detect those plasmids in which a DNA
fragment has been successfully inserted.
insulin A polypeptide hormone secreted by the á cells of the pancreas, that
stimulates fuel storage and protein synthesis.
integral membrane proteins Proteins found in membranes that interact
extensively with the hydrocarbon chains of the membrane lipids and usually span the
membrane.
intercalating agents Flat, aromatic compounds that can insert between adjacent
base pairs in a DNA double helix; these agents, such as ethidium bromide, can cause
insertions and deletions.
intermediate filaments Filaments ranging from approximately 7 to10 nm in
diameter that can be components of the cell cytoskeleton in epithelial cells; keratins
are intermediate filaments.
intrinsic clotting pathway The-blood clotting cascade of enzyme activities that is
initiated by the activation of factor XII through contact of activating proteins
(kininogen and kallikrein) with abnormal cell surfaces produced by injury; at least six
proteins are activated in the pathway to thrombin formation and the continuing
sequence that leads to a blood clot.
intrinsic factor A glycoprotein secreted into the gut to bind vitamin B12 and assist in
its absorption into the intestinal epithelium.
introns Regions of the primary transcript that are removed in the mature mRNA.
Also called intervening sequences.
inversion A nucleotide sequence whose normal order is reversed in a gene or in a
chromosome.
inverted region Refers to the optimal rate of electron transfer as a function of free
energy of the driving force; the rate of electron transfer increases toward the
inverted region as the free energy of the driving force increases but then decreases
with further increases in driving force.
inverted terminal repeats Sequences of 20 or so base pairs at opposite ends of a
bacterial insertion sequence.
ion channels Passive transport systems for ions capable of very high transport
rates; ion channels often display a high degree of specificity for the transported ion.
ion-exchange chromatography A protein purification technique that relies on the
charge of proteins. Proteins are applied to an inert matrix to which is attached a
charged moiety (e.g., a carboxylate group). Proteins will bind to the matrix with an
affinity proportional to their content of the counterion (i.e., positive charges in
regard to the carboxylate matrix).
IRE (iron-response amount)-binding protein An iron-sensitive protein that
regulates the translational capability of ferritin mRNA and the stability of transferrin
receptor mRNA by binding to a stem-loop structure called an iron-response element
in the mRNA molecule.
iron-response element (IRE) A stem-loop structure found in the mRNAs for
ferritin and transferrin receptor that interacts with the IRE-binding protein and
regulates the translation of the mRNAs.
iron-sulfur proteins Proteins that contain clusters of iron and sulfur that play a role
in electron transfer reactions; iron cycles between the Fe2+ and Fe3+ state. Also
called nonheme iron proteins.
irreversible inhibitor An inhibitor that binds very tightly to its target enzyme,
either covalently or noncovalently; such an inhibitor dissociates very slowly from the
enzyme.
isocitrate dehydrogenase An enzyme that catalyzes the oxidative decarboxylation
of isocitrate to form α-ketoglutarate; plays a role in controlling the rate of the citric
acid cycle.
isocitrate lyase An enzyme of the glyoxylate cycle, isocitrate lyase cleaves
isocitrate into succinate and glyoxylate.
isoelectric focusing A technique for separating proteins. A mixture of proteins is
undergoes electrophoresis in a pH gradient; each protein will migrate in the electrical
field until it reaches its isoelectric point.
isoelectric point (pI) The pH of a protein at which its net charge is equal to zero.
isomerase An enzyme that catalyzes the interconversion of isomeric forms of a
compound.
isomerization reaction A reaction in which particular atoms within a molecule are
rearranged.
Isopentenyl pyrophosphate Activated isoprene; the basic building block of
cholesterol.
3-isopentyl pyrophosphate A precursor to cholesterol as well as a large variety of
other biomolecules such as vitamin K, coenzyme Q, and the carotenoids. Isopentyl
pyrophosphate is derived from mevalonate.
isopropylthiogalactoside (IPTG) An inducer of the lac operon; ITPG binds to the
lac repressor and reduces the repressor's affinity for the operator DNA, which
permits transcription to take place.
isozymes Enzymes in an organism that catalyze the same reaction but differ in
structure; these differences may range from one to several amino acid residues. Also
called isoenzymes.
J
joule The amount of energy needed to apply a 1-newton force over a distance of 1
meter; a kilojoule (kJ) is equal to 1000 J, or to 0.239 kcal.
K
ketogenic amino acids Amino acids whose carbon skeletons, entirely or in part, are
degraded into acetyl CoA or acetoacetyl CoA; only leucine and lysine are solely
ketogenic.
α-ketoglutarate dehydrogenase A citric acid cycle enzyme that catalyzes the
oxidative decarboxylation of α-ketoglutarate to yield succinyl CoA; this enzyme,
which helps to regulate the rate of the citric acid cycle, is structurally and
mechanistically similar to the pyruvate dehydrogenase complex.
ketone body Refers to acetoacetate, β-hydroxybutyrate, and acetone, produced
when acetyl CoA is diverted from the citric acid cycle to the formation of acetoacetyl
CoA in the liver; subsequent reactions generate the three compounds, known as
ketone bodies.
ketose A monosaccharide that has a ketone group as its most oxidized carbon.
kilobase A unit of length equal to 1000 base pairs of a double-stranded nucleic acid
molecule or to 1000 bases of a single-stranded molecule.
kilocalorie (kcal) A unit of energy equal to 1000 calories, or 4.184 joules.
kinase An enzyme that catalyzes the attachment of a phosphoryl group to a
substrate by using ATP as a phosphoryl donor.
kinesin A protein with ATPase activity that moves cellular organelles along
microtubule tracks in anterograde transport.
Klenow fragment A proteolytic digestion product of DNA polymerase I that retains
the polymerase and 3'- to 5'-exonuclease activity.
Krebs cycle See citric acid cycle.
L
lac operon The operon that encodes the genes required for lactose metabolism.
lac repressor The regulator protein that binds to the operator site of the lac operon
and thereby inhibits expression of the structural genes of the operon; inhibition is
relieved when the repressor protein binds allolactose, an inducer of the lac operon.
lactic acid fermentation The anaerobic metabolism of glucose to yield lactic acid
with the concomitant production of ATP.
lagging strand A newly synthesized strand of DNA at the replication fork that is
initially synthesized as Okazaki fragments. See also leading strand.
lateral diffusion The ability of lipid and protein molecules to move laterally in the
membrane rapidly and spontaneously.
leading strand A newly synthesized strand of DNA at the replication fork that is
synthesized continuously. See also lagging strand.
Leber's hereditary optic neuropathy A maternally inherited form of blindness due
to mutations in NADH-Q reductase; one of a number of mitochondrial diseases.
lectins Plant proteins with a high affinity for specific sugar residues; as such, they
are important probes of carbohydrate-containing molecules.
leghemoglobin A homolog of hemoglobin found in leguminous plants that also
harbor symbiotic nitrogen-fixing bacteria; leghemoglobin binds oxygen, thereby
protecting nitrogenase from inactivation.
leptin A polypeptide hormone, secreted by the adipocytes in direct proportion to fat
mass, that generates satiation signals.
Lesch-Nyhan syndrome A disease resulting from the loss of a single enzyme in the
salvage pathway for purines; marked by mental retardation, extreme hostility, and
self-mutilation.
lever arm A long helix that protrudes from the S1 fragment of myosin to bind the
light chains; amplifies small structural changes at the nucleotide-binding site of
myosin to achieve 110-Å movement along an actin filament.
ligand A small molecule that binds to a protein, inducing a specific structural
change. For instance, a steroid is a ligand for a steroid-hormone receptor.
ligand-gated channel A transmembrane channel that is opened by the binding of a
one or more molecules to a ligand-binding domain of the channel protein.
ligation reactions Reactions that form bonds by using the energy of ATP hydrolysis.
light (L) chain A 25-kd polypeptide that is one of two types of chains found in
immunoglobulin G. Each L chain consists of a variable region and a constant region,
and each chain is linked by a disulfide bond to a heavy chain.
light-harvesting complex A complex of light-absorbing pigments and protein that
completely surround the reaction center of photosynthesis; funnels the energy of
absorbed light to the reaction center.
light meromyosin (LMM) Along with heavy meromyosin, one of the tryptic
digestion products of myosin; forms filaments but has no ATPase or actin-binding
activity.
light reactions In chloroplasts, the reactions in which light is used to create
reducing potential and to generate oxygen.
linking number A topological property of circular DNA, equal to the number of
times a strand of DNA winds around the helix axis.
lipid bilayer A bimolecular sheet formed by amphipathic molecules in which the
hydrophobic moieties are on the inside of the sheet and the hydrophilic ones are on
the aqueous outside.
lipoic acid (6, 8-dithiooctanoic acid) An acyl group carrier that functions as a
cofactor in dehydrogenase enzymes; linked covalently to specific lysine residues in
enzyme proteins, it can exist as the reduced open-chain form or the closed-ring
disulfide form, undergoing interconversion in a catalytic cycle.
lipolysis The enzymatic hydrolysis of triacylglycerols to free fatty acids and glycerol.
lipoprotein particles Particles, consisting of a core of hydrophobic lipids surrounded
by a shell of polar lipids and specific proteins, that play a role in the transport of
cholesterol and triacylglycerols.
liposomes Lipid vesicles having an aqueous region enclosed by a lipid bilayer
long terminal repeat A sequence that is repeated at either end of a retroviral DNA
molecule.
lovastatin A competitive inhibitor of HMG-CoA reductase, the key regulatory
enzyme in cholesterol biosynthesis; used therapeutically to lower cholesterol levels.
Also called mevinolin.
low-density lipoprotein (LDL) The major carrier of cholesterol in the blood;
consists of a core of esterified cholesterol molecules surrounded by a shell of
phospholipids, unesterified cholesterol, and apoprotein B-100; primary source of
cholesterol for cells other than the liver or intestine.
lysogenic bacteriophage A phage whose DNA is integrated into the host cell by
site-specific recombination and whose expression is repressed.
lysogenic bacterium A bacterial cell whose chromosome contains a prophage.
lytic bacteriophage A phage that replicates in its host and then lyses, or destroys,
it.
M
magnetosomes Chains of intracellular small particles containing the magnetic ore
magnetite (Fe3O4) found in some bacteria that enable the bacteria to detect Earth's
magnetic field.
main chain The regularly repeating part of the primary structure of a polypeptide;
each unit of the chain includes the α-carbon atom as well as the CO and NH groups
of an amino acid residue.
main olfactory epithelium A specific region of the nose, containing approximately
1 million sensory neurons, that detects odorants.
major groove A 12-Å-wide, 8.5-Å-deep groove in B-DNA resulting from the fact
that the glycosidic bonds of a base pair are not diametrically opposite each other.
major histocompatibility complex (MHC) Integral membrane proteins that bind
and display on a cell's surface peptides derived from the digestion of proteins from
the cytosol (class I MHC proteins) or from endosomal compartments (class II MHC
proteins). Foreign peptides bound to class I MHC proteins mark them for destruction
by killer T cells, whereas those bound to class II MHC proteins provide a signal for
helper T cells, which can in turn stimulate B-lymphocyte production.
malate-aspartate shuttle A reversible shuttle, found in the liver and heart, used to
transport electrons from cytoplasmic NADH to mitochondrial NAD+.
malate synthase An enzyme of the glyoxylate cycle that catalyzes the formation of
oxaloacetate from glyoxylate and acetyl CoA.
manganese center The site of oxygen generation in photosynthesis in green plants.
The center is a complex, which includes four manganese ions, that donates electrons
to positively charged P680. After donating four electrons, the manganese center
oxidizes two molecules of water to replenish its electrons and thus forms a single
molecule of molecular oxygen and four protons.
maple syrup disease A disease resulting from the inability to oxidatively
decarboxylate branch-chain amino acids, characterized by mental and physical
retardation and urine that smells like maple syrup.
matrix-assisted laser desorption-ionization time of flight spectrometry
(MALDI-TOF) A technique for determining a protein's mass. A protein sample is
embedded in a matrix and ionized by the application of a laser beam. An electric field
accelerates the ions through a flight tube toward a detector, with the lightest ions
arriving first.
maximal velocity The highest rate of an enzyme-catalyzed reaction, under
conditions of constant enzyme concentration and saturating amounts of substrate.
McArdle disease A disease caused by a lack of muscle glycogen phosphorylase; the
glycogen is present in increased amounts but normal structure; clinical
characteristics include an inability to perform strenuous exercise.
megasynthases A class of large, multifunctional enzymes, including fatty acid
synthase, that participate in step-by-step synthetic pathways.
melting temperature The temperature at which secondary or higher structures of a
biological molecule are lost; for a nucleic acid, the melting temperature is defined as
the temperature at which half the helical structure is lost.
membrane asymmetry Refers to the fact that the two phases of biologically
important membranes differ from each other.
membranes Sheetlike structures composed of lipids and proteins, usually only a few
molecules thick, that form closed boundaries between different compartments;
membranes separate aqueous environments
messenger RNA (mRNA) Template for protein synthesis; the base sequence of
mRNA is complementary to that of a gene in DNA.
metabolism A highly integrated network of chemical pathways that enables a cell to
extract energy from the environment and use this energy for biosynthetic purposes.
metabolon The name for large, multienzyme complexes that facilitate the
channeling of substrates between active sites.
metabotrophic glutamate receptor A 7TM receptor that binds the
neurotransmitter glutamate; a truncated version of the same protein detects the
taste, termed umami, of glutamate.
metal ion catalysis Catalysis in which a metal acts as an electrophilic catalyst by
stabilizing a negative charge on a reaction intermediate, generates a nucleophile by
increasing the acidity of nearby molecules, or increases the binding energy of the
enzyme-substrate interaction by binding to substrates.
methotrexate A competitive inhibitor of dihydrofolate reductase, an enzyme
required for the regeneration of the coenzyme tetrahydrofolate, which is necessary
for the synthesis of thymidylate; methotrexate is used as a chemotherapeutic agent.
Also called amethopterin.
mevalonate A precursor for the synthesis of cholesterol; its formation by HMG-CoA
reductase constitutes the committed step in cholesterol biosynthesis.
micelle A globular structure formed by amphipathic molecules in which the
hydrophilic part is exposed to water and the hydrophobic part is sequestered inside,
away from the water.
β2-microglobulin An immunoglobulin fold-containing subunit of human class I MHC
protein; this 12- kd polypeptide is noncovalently bound to the 44-kd α chain.
Michaelis constant The concentration of substrate at which half the active sites of
an enzyme are filled; a ratio of rate constants for the reaction model.
E + S ⇋ES → E + P
k1 k2
k-1
The constant is defined as KM = k-1+ k2/k1. Under conditions where k-1 is much
greater than k2, KM is equal to the dissociation constant of the enzyme-substrate
complex and is a measure of the affinity of the enzyme for the substrate.
Michaelis-Menten equation An equation that expresses the velocity (V) of an
enzyme-catalyzed reaction in terms of maximum velocity (V/max), substrate
concentration (S), and the Michaelis-Menten constant (KM). The equation accounts
for the hyperbolic kinetics observed when V is plotted as a function of S; the
equation is V = Vmax [S]/([S] + KM).
microfilaments Filaments of actin approximately 7 nm in diameter; filaments (Factin) are formed by the polymerization of G-actin monomers; a component of the
cytoskeleton.
microsomes Closed vesicles formed by self-annealing fragments of the endoplasmic
reticulum subsequent to following cell disruption.
microtubule A cytoskeleton element that is a major component of cilia, eukaryotic
flagella, and the mitotic spindle; composed primarily of α- and β-tubulin; capable of
rapid assembly and disassembly.
microtubule-organizing centers (MTOCs) Sites of the initiation of microtubule
growth.
mineralcorticoids A class of steroid hormones, synthesized by the adrenal cortex
and exemplified by aldosterone, that act on the kidney to increase the absorption of
Na+ and the excretion of K+ and H+.
minor groove A 6-Å-wide, 7.5-Å-deep groove in B-DNA that arises because the
glycosidic bonds of a base pair are not diametrically opposite one another.
mitochondrial diseases A set of diseases resulting from mutations in mitochondrial
DNA; most prevalent in tissues that depend heavily on oxidative phosphorylation,
such as the heart and nervous system.
mitochondrion An oval-shaped organelle, about 2 Mm in length and 0.5 Mm in
diameter, that is the site of oxidative phosphorylation, the enzymes of the citric acid
cycle, and the enzymes of fatty acid oxidation.
molecular mimicry Refers to a protein domain, such as those found in EF-G and
release factor, that mimic the structure of a tRNA molecule.
monoclonal antibody An antibody derived from a clone-a large number of cells
that are all descended from the same cell and have identical properties. Normally,
antigens with a common specificity are heterogeneous because they are produced by
a heterogeneous group of cells. Fusion of a single antigen-producing cell with an
immortal myeloma cell facilitates the production of large amounts of homogeneous
antibody protein, these antibodies are valuable analytical and preparative reagents.
monooxygenases, cytochrome P450 Enzymes that use O2 and incorporate one
atom of oxygen into a substrate and reduce the other atom to water; important in
the synthesis of steroid hormones and tyrosine, as well as the detoxification of
xenobiotic compounds.
monosaccharides Single aldehydes or ketones that have two or more hydroxyl
groups; the simplest carbohydrates.
mosaic protein A protein encoded by a gene assembled by exon shuffling; the
exons encode the structural units of the protein.
MotA and MotB A pair of bacterial proteins that form a ring around the base of the
flagellum and, in conjunction with FliG, form a proton channel that drives the
rotation of the flagellum.
multidrug resistance A phenomenon observed in cancer cells in which the
development of resistance to one drug renders the cells resistant to a range of other
drugs; due to the action of an ATP-dependent pump called the multidrug-resistance
protein (MDR), which contains an ABC domain.
multienzyme complex A polypeptide chain that contains domains for two or more
enzymatic activities.
multifunctional enzymes Functionally related enzymes that are covalently linked
in some fashion.
mutagen Perturbs to the base sequence of DNA and causes a mutation; often
chemicals but can also be energy sources such as ultraviolet light.
mutarotation For carbohydrates, the interconversion of α and β anomers through
the open-chain form; usually measured through changes in optical rotation.
mutase An enzyme that catalyzes the intramolecular shift of a chemical group.
mutations Variations that alter the meaning of the genetic message; required for
evolution.
myofibrils Fibrils inside the cytosol of vertebrate muscle cells that give such cells
their striated appearance; the functional unit of a myofibril is a sarcomere.
myoglobin A vertebrate oxygen-storage protein found in muscle; structurally similar
to an individual hemoglobin subunit.
myosin A protein that forms the thick filaments of striated muscle; displays ATPase
activity at its globular head, which, in conjunction with the ability to reversibly bind
actin at its fibrous region, provides the power stroke of muscle contraction.
N
N-acetylglutamate An allosteric activator of mammalian carbamoyl phosphate
synthetase, which catalyses the synthesis of urea.
NAD-binding domain A structural motif of NAD+-linked dehydrogenases that forms
a binding site for NAD+ and consists of four helices and six parallel β strands.
NAD+ and NADH (nicotinamide adenine dinucleotide) An important electron
carrier in the oxidation of fuel molecules; electrons are carried on the nicotinamide
moiety of the coenzyme.
NADH-Q oxidoreductase A large component of the respiratory chain that transfers
electrons from NADH to ubiquinone and in the process pumps protons across the
inner mitochondrial membrane to generate the proton-motive force. Also called
NADH dehydrogenase or Complex I.
NADP+ and NADPH (nicotinamide adenine dinucleotide phosphate) The
electron donor for reductive biosynthesis; differs from NAD+ and NADH in that a
phosphate is attached to the adenine ribose at position 3.
native form The stable, functional conformation of a biological macromolecule.
neck linker A short segment of kinesin that binds to the head domain of kinesin
when ATP is bound and is released when the nucleotide-binding site is vacant or
occupied by ADP.
negative selection A selection process in T-cell development in which T cells that
bind with high affinity to MHC complexes of antigen-presenting cells displaying selfpeptides undergo apoptosis.
nerve impulse The increase in membrane potential and the changes in sodium and
potassium conductances that result from alterations in the permeability of the axon
membrane to those ions. Also called action potential.
neurotransmitter A small, diffusible molecule, such as acetylcholine, that mediates
the passage of nerve impulses across the synapse.
nicotinate A vitamin that is a key component of the electron-transfer coenzymes
NAD+, NADH, NADP+, and NADPH. Also called niacine.
nitrogen fixation The conversion of diatomic nitrogen into ammonia; the first step
in the flow of nitrogen into amino acids, nucleotides, and other nitrogen-containing
compounds in organisms.
nitrogenase complex An enzyme complex that catalyzes the reduction of diatomic
nitrogen to ammonia; found in bacteria and the blue-green algae.
nociceptor A specialized neuron that transmits signals to pain-processing centers of
the spinal cord and brain in response to the onset of tissue damage.
nonclaret disjunctional (ncd) A member of the kinesin family of proteins that, in
contrast with most family members, moves toward the negatively charged end of
microtubules.
noncompetitive inhibition The reduction in the rate of enzyme activity observed
when an enzyme can bind its substrate and its inhibitor simultaneously.
Noncompetitive inhibitors decrease the turnover number for an enzyme but do not
diminish the proportion of enzyme molecules bound to the substrate; their effects
are not overcome by increasing substrate concentration.
nonessential amino acids Amino acids that can be synthesized by an organism
and are thus not a dietary requirement.
nonreducing sugar A sugar that is not readily converted into a form with a free
aldehyde group capable of reducing another compound. Such a conversion is
prevented because the sugar forms a glycosidic bond with another compound.
nonribosomal peptides A class of peptides, including the antibiotic penicillin,
formed by the action of specific megasynthases.
Northern blotting Analogous to Southern blotting, a technique in which a mixture
of RNA fragments is separated by electrophoresis, transferred to a nitrocellulose
sheet, hybridized to a radioactively labeled DNA probe complementary to the desired
sequence, and visualized by autoradiography; the technique can therefore be used to
locate and identify an RNA fragment containing a specific sequence.
N-terminal rule The dependency of the half-life of a cytosolic protein on the nature
of its N-terminal amino acid.
nuclear envelope A double membrane, consisting of the inner nuclear membrane
and the outer nuclear membrane, that surrounds the nucleus and is punctured with
openings called nuclear pores.
nuclear hormone receptor A member of a large family of transcription factors
that, on binding of a signal molecule such as a steroid hormone, modify the
expression of specific genes by binding to control elements in the DNA.
nuclear localization sequence An amino acid sequence that directs a protein
bearing such a sequence into the nucleus.
nuclear magnetic resonance A means of determining the structure of a protein in
solution on the basis of the ability of certain atoms in a protein to absorb
electromagnetic radiation.
nuclear Overhauser enhancement spectroscopy (NOESY) A technique that
forms the basis of NMR analysis of protein structure; NOESY displays pairs of protons
that are in close proximity in a protein even if they are not close together in primary
structure; three-dimensional structure can then be determined from such
observations.
nuclear pores A complex protein assembly that provides openings in the nuclear
membrane and permits the transit of large molecules into and out of the nucleus.
nuclear receptor superfamily A class of transcription factors that bind DNA and
activate transcription only in the presence of a specific signal molecule, such as a
hormone.
nucleoside A purine or pyrimidine base linked to a sugar.
nucleosomes The repeating unit of chromatin that consists of 200 base pairs of
DNA and two each of the histones H2A, H2B, H3, and H4.
nucleotide A nitrogenous purine or pyrimidine base linked to a sugar, which is in
turn linked to one or more phosphate groups.
nucleotide-excision repair A means of repairing DNA in which a stretch of DNA
around the site of damage is removed and replaced.
nucleotide kinases Enzymes that transfer the phosphoryl group of one nucleotide
to another nucleotide, as in the reaction of ATP with UMP to form UDP and ADP.
O
obligate anaerobes Organisms that cannot survive in the presence of oxygen and
are thus usually dependent on fermentation as an source of cellular energy.
odorants Small molecules in the air that bind to receptors in the main olfactory
epithelium to generate the perception of smell.
Okazaki fragments Small fragments of DNA (approximately 1000 nucleotides) that
are formed on the lagging strand at the replication fork of DNA synthesis and later
joined; enable 5' . 3' polymerization at the nucleotide level while overall growth is in
the 3' . 5'direction.
olfaction The sense of smell.
oligomycin An antibiotic that blocks ATP synthesis (and consequently the
respiratory chain) by interfering with proton flow through the ATP synthase complex.
oligosaccharides Carbohydrates composed of 2 to 12 monosaccharide units.
oncogene A gene whose expression contributes to the development of cancer.
one-carbon metabolism Biochemical reactions in which tetrahydrofolate
derivatives serve as donors of a variety of one-carbon units, ranging from the
oxidation level of a methyl group to a formyl group; also includes reactions involving
the fully oxidized carbon unit, carbon dioxide, and its carrier, biotin.
operator A DNA segment that is adjacent to a group of structural genes and is the
target sequence for a repressor protein; a unit of gene regulation and expression
that includes structural genes and regulatory elements recognized by one or more
regulatory gene products.
operon model A model of prokaryotic gene regulation that consists of an operator
sequence and its associated structural genes.
opsin A 7TM receptor of rod cells that, when bound to 11-cis-retinal to form
rhodopsin, absorbs visible light to initiate the visual signal-transduction pathway.
optical rotation The change in direction of polarization of linearly polarized light on
passing through an optically active solution; can be used as an indicator of the mainchain conformation of a protein.
optical trap A means of measuring the force exerted by a single myosin molecule
on an actin filament. In this device, a laser beam is focused on a bead, which is
attached to an actin filament. The laser holds or traps the bead at the center of the
beam. The strength of the force holding the beam may be adjusted by altering the
intensity of the laser beam. The force exerted by a myosin molecule on the actin
filament is measured as the force required to hold the bead in the optical trap.
organic fluorophosphates Compounds such as diisopropylfluorophosphate, which
inhibits acetylcholinesterase by forming a stable phosphoryl enzyme complex at a
serine residue in the active site.
orotidylate A nucleotide precursor to uridylate and cytidylate formed by the
reaction of orotate with 5- phosphoribosyl-1-pyrophosphate (PRPP).
orthologs Homologous molecules that are present within different species and have
similar or identical functions.
osmosis The movement of a solvent across a membrane in the direction that tends
to equalize concentrations of solute on the two sides of the membrane.
osteomalacia A clinical condition in adults that is due to vitamin D deficiency and is
characterized by softening and weakening of the bones.
overlap peptides Peptides resulting from the degradation of a protein by two
different procedures that are subsequently sequenced; the sequence of a peptide
from one degradation procedure frequently overlaps the sequences of two or more
peptides of the other degradation procedure, thereby establishing the order of the
peptides.
β-oxidation Oxidation of the C-3 carbon atom that is β to a functional group; in the
degradation of a fatty acyl CoA molecule, the sequence of oxidation, hydration, and
oxidation reactions that converts a methylene group at C-3 into a β-keto group.
oxidation-reduction reaction A reaction that transfers electrons.
oxidative phosphorylation The process in which ATP is formed as a result of the
transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers.
oxyanion hole A region on certain proteolytic enzymes that stabilizes the oxyanion
constituent of the tetrahedral intermediate of the reaction.
oxygen-dissociation curve A plot of the oxygen-binding capacity of a protein
versus the partial pressure of oxygen.
P
P680 A special pair of molecules in photosystem II in green plants; absorption of
light by P680 results in the transfer of electrons from water to plastoquinone, which
generates a proton gradient.
P700 A special pair of molecules in photosystem I in green plants; absorption of
light by P700 results in the transfer of electrons that generates ferredoxin and,
ultimately, NADPH.
P960 A dimer of bacterial chlorophyll-b molecules, called the special pair, that
absorbs light maximally at 960 nm; initiates charge separation in bacterial
photosynthesis.
packing ratio The degree of condensation of DNA in chromatin; the ratio of linear
DNA to the length of the packaged DNA; the packing ratio of metaphase human
chromosomes is 104.
palindrome A word, sentence, or verse that reads the same from right to left as it
does from left to right; an example is "radar." By extension to biochemistry, a
sequence of double-stranded DNA that is the same in each strand when the strands
are read in the same direction; that is, it displays a twofold rotational symmetry-for
example, 3'-CCTAGG-5'/5'-GGATCC-3'.
pantothenate A vitamin that is a key component of coenzyme A.
paralogs Homologous molecules that are present within one species; often differ in
their detailed biochemical functions.
passive transport Transport of an ion or a molecule down a concentration gradient,
where .G for the transported species is negative. Also called facilitated diffusion.
Pasteur effect The inhibition of glycolysis by respiration, discovered by Louis
Pasteur; the rate of glycolysis is lower in the presence of oxygen than under
anaerobic conditions, a phenomenon largely due to the inhibition of
phosphofructokinase by ATP and citrate.
patch-clamp technique A method for studying ion channels in which a highresistance seal is formed between a pipette and a small patch of plasma membrane,
allowing the monitoring of the flow of ions through a single channel with high time
resolution.
pellagra A disease caused by dietary deficiencies of tryptophan and nicotinate and
characterized by dermatitis, diarrhea, and dementia.
pentoses Monosaccharides that have five carbon atoms.
pentose phosphate pathway A metabolic pathway that generates NADPH and fivecarbon sugars such as ribose 5-phosphate from glucose 6-phosphate; it includes
oxidative reactions that produce NADPH and ribose 5-phosphates as well as
nonoxidative reactions that together convert five-carbon sugar phosphates into
gluconeogenic precursors of glucose 6-phosphate. Also referred to as the hexose
monophosphate shunt or the phosphogluconate pathway.
peptide Two or more amino acids joined by peptide bonds.
peptide bond A covalent linkage formed between the α-carboxyl group of one
amino acid and the α- amino group of another. Also known as an amide bond.
peptidoglycan A macromolecule that consists of linear polysaccharides cross-linked
by short peptides; often found in bacterial cell walls, peptidoglycans confer
mechanical support and protect bacterial cells from disruption by osmotic pressure.
peptidyl transferase center A region of the large ribosomal subunit that catalyzes
peptide-bond formation between the aminoacyl (or peptidyl) tRNA in the P site and
the aminoacyl tRNA in the A site.
perforin A protein secreted by activated T cells that renders target cells permeable
by forming 10-nm pores in the target-cell membranes; pores allow entry of
granzymes.
peripheral membrane protein A protein associated with the surface of a
membrane by electrostatic and hydrogen-bond interactions.
pernicious anemia A disease in which vitamin B12 absorption is impaired, owing to
a deficiency of intrinsic factor, which results in an inability to synthesize thymine and
purines.
peroxidases Heme enzymes catalyzing the reduction of an alkyl peroxide to
produce an alcohol and water.
peroxisomes Small membrane-bounded organelles that are present in most
eukaryotes and play a role in detoxification, the synthesis of plasmalogens and bile
salts, and β-oxidation of long-chain fatty acids.
phenylketonuria A disease caused by the inability to convert phenylalanine into
tyrosine, which results in excess phenylalanine and its secondary metabolites; the
disease is characterized by severe retardation.
phorbol esters Polycyclic alcohol derivatives of croton oil that resemble
diacylglycerol and inappropriately stimulate protein kinase C; phorbol esters are
tumor promoters.
phosphatase An enzyme that catalyzes the removal of a phosphoryl group from a
substrate by hydrolysis.
phosphatidate (diacylglycerol 3-phosphate) A precursor to triacylglycerols as
well as many phospholipids.
phosphodiesterase An enzyme that converts cyclic nucleotides (e.g., cAMP) into
the noncyclic form (e.g., AMP).
phosphofructokinase A kinase that phosphorylates fructose 6-phosphate to
fructose 1,6-bisphosphate; phosphofructokinase, an allosteric enzyme, is the major
control point for flux through the glycolytic pathway.
phosphoinositide cascade A set of reactions that convert an extracellular signal
into an intracellular one; the conversion entails the cleavage of the phospholipid
phosphatidyl inositol 4,5-bisphosphate into two second messengers, inositol 1,4,5trisphosphate and diacylglycerol.
phospholipases A class of enzymes of varying specificity that catalyze the
degradation of phospholipids; can function as digestive enzymes as well as
components of signal-transduction pathways.
phospholipids Important constituents of membranes and composed of three
components: a backbone (usually glycerol or sphingosine), two fatty acid chains, and
a phosphorylated alcohol.
phosphorolysis The cleavage of a bond by orthophosphate, as in the degradation of
glycogen to glucose 1-phosphate.
phosphoryl transfer potential A measure of the tendency of a phosphorylated
compound to transfer a phosphate to another compound; presented as the .G°' of
hydrolysis of the phosphate compound; the more negative the .G°' of hydrolysis, the
greater the phosphoryl transfer potential.
phosphorylation potential A means of measuring the energy status of a cell that is
derived by dividing the concentration of ATP by the product of the concentrations of
ADP and Pi.
photoinduced charge separation The excitation of an electron from its ground
state to a higher energy level by light absorption and the subsequent movement of
the excited electron from the initial molecule to an acceptor, resulting in a positive
charge on the initial molecule and a negative charge on the acceptor molecule.
photoreceptors Membrane proteins that can convert light into to atomic motion and
then into a chemical signal.
photorespiration The conversion of organic carbon into carbon dioxide without the
production of energy-rich metabolites; the result of the oxygenase reaction catalyzed
by rubisco and the subsequent regeneration of glucose from two molecules of
glycolate, with the release of carbon dioxide and ammonia and the consumption of
ATP.
photosynthetic unit A light-harvesting complex that includes about 2500 antenna
chlorophyll molecules and a reaction-center chlorophyll pair, all in the thylakoid
membrane.
photosystem I In chloroplasts, a photosynthetic unit that includes a lightharvesting complex, a reaction center, and an electron-transport chain. The system
catalyzes the light-driven transfer of electrons from reduced plastoquinone to
ferredoxin, which in turn drives the formation of NADPH; it requires light of
wavelength shorter than 700 nm.
photosystem II In chloroplasts, a photosynthetic unit that includes a lightharvesting complex, a reaction center, and an electron-transport chain. The system
catalyzes the light-driven transfer of electrons from water to plastoquinone, with the
concomitant generation of oxygen; it requires light of wavelength shorter than 680
nm.
phototrophs Organisms that can meet their energy needs by converting light
energy into chemical energy.
phycobilisome A large assembly of phycobiliproteins, which contain the lightabsorbing compound bilin, that harvests light for organisms, such as red algae and
cyanobacteria, living at a depth of a meter or more in seawater.
plasmalogens Phospholipids containing an α,β-unsaturated ether at the C-1
position of glycerol; abundant in phospholipids of the nervous system.
plasmids Circular duplex DNA molecules that replicate autonomously and act as
accessory chromosomes in bacteria; they carry useful genes but are disposable
under certain conditions.
P-loop A component, characteristic of nucleotide-binding proteins, of the NTPbinding domain that interacts with the phosphoryl groups of a bound nucleotide.
poly(A) tail A long (as many as 250 nucleotides) polyadenylate segment added
posttranscriptionally to the 3' end of most eukaryotic mRNA.
polycistronic message Refers to an mRNA molecule that encodes for more than
one protein.
polyclonal antibodies Antibodies that are the products of many different
populations of antibodyproducing cells.
polyketides A class of compounds, including the antibiotic erythromycin, formed by
the action of specific megasynthases.
polymerase An enzyme that catalyzes the step-by-step addition of ribo- or
deoxyribonucleotide units to a polynucleotide chain.
polymerase chain reaction A method for amplifying DNA sequences by using DNA
polymerase; a series of three-step cycles is employed, in which parental DNA strands
are separated by heating, primers to flanking regions of the target sequence are
annealed to the separated strands, and the primers are then extended by DNA
synthesis.
polypeptide A series of amino acids, each connected to the next in the series by a
peptide bond.
polysaccharides Carbohydrates composed of large numbers of linear or branched
monosaccharide units; homopolysaccharides are composed of large numbers of one
type of sugar, whereas heteropolysaccharides contain more than one type.
polysome A group of ribosomes bound to an mRNA molecule and simultaneously
carrying out translation. Also called polyribosome.
Pompe disease A disease that affects all tissues and is due to a lack of a lysosomal
glycogen-degrading enzyme; the glycogen is structurally normal but present in
abnormally large amounts; death results at an early age from cardiovascular failure.
porin A transmembrane protein that forms channels in the outer mitochondrial
membrane, permitting the passage of small molecules and ions to the inner
membrane space.
porphyrias Inherited or acquired metabolic disorders caused by an enzyme
deficiency in the biosynthetic pathway for heme; often characterized by the
accumulation of one or more pathway intermediates in blood or other tissues, as well
as their excretion in urine.
positive selection A selection process in T cell development in which T cells that
can bind to MHC molecules survive, whereas those that cannot undergo apoptosis.
power stroke The conformational change in myosin heads powered by phosphate
release as myosin binds to actin and pulls the actin filament, with the resulting
displacement of the myosin heads.
pregnenolone A steroid formed by the removal of the six-carbon side chain from
cholesterol; steroid hormones are synthesized from pregnenolone.
pre-mRNA The unspliced, immediate product of RNA polymerase II in eukaryotes.
Pribnow box A promoter component of prokaryotic genes that has the consensus
sequence 5'- TATAAA-3' located 10 base pairs downstream from the transcription
start site.
primary messenger The information embodied in the interaction of ligand with its
receptor molecule.
primary structure Usually refers to the linear sequence of amino acids in a protein;
more generally, the linear sequence of units that form a polymer.
primase A specialized RNA polymerase that synthesizes the RNA primers for DNA
synthesis.
primer In the elongation of polymers, the initial segment of the polymer that is to
be extended; elongation depends on the primer.
primosome A complex of proteins that facilitate the unwinding of DNA and the
synthesis of RNA primers, thus initiating DNA synthesis.
processivity A property of an enzyme that enables it to catalyze multiple rounds of
elongation or the digestion of a polymer while the polymer stays bound to the
enzyme.
proenzyme A zymogen, or a catalytically inactive precursor of an enzyme; a
proenzyme can be converted into the active form by the hydrolysis of one or a few
peptide bonds.
progestagen A class of steroid hormone, exemplified by progesterone, that
prepares the uterus for implantation of the ovum; synthesized by the corpus luteum
of the ovary.
programmed cell death Refers to a cascade of proteolytic enzymes that result in
controlled cell death in response to significant cell damage or specific development
programs. Also called apoptosis.
promoter sites A specific sequence of DNA, usually just upstream of a gene, that
specifies the site and extent of transcription of the associated gene.
propeller twisting The twisting of base pairs in crystals of DNA from the coplanar
conformation; enhances the stacking of bases within a strand.
prostaglandins A class of short-lived signal molecules that are 20-carbon fatty
acids containing a fivemembered ring.
proteases Enzymes that degrade proteins by cleaving peptide bonds.
proteasomes Large protein complexes that carry out routine degradation of
ubiquitinated cellular proteins as well as of those from pathogens.
protein A biological macromolecule composed of a linear array of amino acids joined
by peptide bonds; roles of proteins in biological processes include catalysis, transport
and storage, motion, mechanical support, immune protection, the generation and
transmission of nerve impulses, and the control of growth and differentiation.
Protein Data Bank (PDB) A Web storage site for the coordinates of protein
structures that have been solved by x-ray crystallography and NMR analysis. With
the use of the coordinates, the structures can be accessed for visualization and
analysis.
protein disulfide isomerase An enzyme that catalyzes the formation of correct
disulfide pairings in nascent proteins; preferentially reacting with peptides that
contain cysteine residues but otherwise undiscriminating, the enzyme speeds up the
disulfide shuffling required for a protein to find the most thermodynamically stable
disulfide pairings among those that can be formed.
protein kinase A A protein kinase that consists of two catalytic subunits and two
regulatory subunits that inhibit the catalytic subunits; on binding of cAMP, the
regulatory subunits dissociate from the catalytic subunits, which then become active.
protein kinase C A protein kinase that is activated by the binding of diacylglycerol.
protein kinases A class of enzymes that transfer a phosphoryl group from ATP to
proteins; protein kinases are frequently found in regulatory pathways.
protein phosphatase 1 A protein phosphatase stimulated by insulin that inhibits
glycogen degradation and stimulates glycogen synthesis.
protein phosphatase 2A An insulin-responsive phosphatase that activates acetyl
CoA carboxylase to stimulate fatty acid synthesis.
protein phosphatases Enzymes that hydrolyze phosphorylated serine and
threonine residues in other proteins; protein phosphatase 1 reverses the regulatory
effects of kinases on glycogen metabolism.
proteoglycans Proteins containing one or more covalently linked glycosaminoglycan
chains; cartilage proteoglycan contains keratan sulfate and chondroitin chains linked
to a polypeptide backbone.
proteome The functional representation of the genome that includes the types,
functions, and interactions of proteins that are present in a cell; the proteome is not
a fixed characteristic of a cell but will vary, depending on such factors as
developmental stage or hormonal status.
proton gradient The unequal distribution of protons across a proton-impermeable
membrane; such gradients can be used to power various biochemical processes,
such as the synthesis of ATP.
proton-motive force The energy inherent in the proton gradient established during
the functioning of the respiratory chain; consists of a membrane potential as well as
a chemical gradient.
proto-oncogene A signal transduction protein that usually regulates cell growth in
some fashion; when proto-oncogenes mutated, they become oncogenes and
contribute to the development of cancer.
protoporphyrin An organic constituent of the heme prosthetic group; consists of
four pyrrole rings joined by methylene bridges and contains various side chains.
pseudogenes Sequences of DNA that resemble actual genes but do not encode
functional products.
pseudosubstrate An amino acid sequence that resembles the actual substrate for
an enzyme except that a crucial amino acid has been changed, converting the
sequence into an inhibitor; the regulated binding of pseudosubstrates is sometimes
used to control enzyme activity.
P-type ATPases A family of enzymes that use the energy of hydrolysis to move ions
across membranes; called "P-type ATPases" because the reaction mechanism
includes a phosphoaspartate intermediate.
pulsed-field electrophoresis An electrophoretic technique for separating large
DNA molecules. Electric fields, oriented at 120 degrees to each other, are applied in
an alternating fashion. Large molecules reorient more slowly than small ones and
hence cannot follow the electric field as rapidly.
pump A protein passage in a membrane that can transport a molecule from one
compartment to another against a concentration gradient; pumps undergo a cycle of
conformational changes that alter the affinity of the binding site for the transported
molecule, and the eversion of the molecule during the cycle is driven by expenditure
of free energy. Also called active transporters.
pur repressor A protein regulator of the pur operon, which encodes genes taking
part in purine biosynthesis; the pur repressor binds to operator DNA only when
bound to a small molecule (guanine or hypoxanthin) called a corepressor.
purine A nitrogenous base that includes a pyrimidine ring fused with a fivemembered imidazole ring; the purine derivatives adenine and guanine are found in
nucleotides and nucleic acids.
puromycin An antibiotic that is an analog of the terminal aminoacyl-adenosine part
of aminoacyltRNA; in translation, it causes premature chain termination when its
amino group joins the carboxyl group of the growing polypeptide chain and the
resulting adduct dissociates from the ribosomal complex.
pyranose A six-membered heterocyclic ring formed when a monosaccharide cyclizes
to form a hemiacetal or a hemiketal; the six-membered, oxygen-containing ring is
similar to that of pyran.
pyridine nucleotides Nucleotides, such as NAD+, NADH, NADP+, and NADPH, that
are employed in redox reactions; the functional group is nicotinamide, a derivative of
pyridine.
pyridoxal phosphate A prosthetic group derived from vitamin B6 (pyridoxine) that
plays a key role in transamination reactions.
pyrimidine A nitrogenous base that is a six-membered heterocyclic ring containing
two nitrogen atoms and four carbon atoms; the pyrimidine derivatives cytosine,
uracil, and thymine are found in nucleotides and nucleic acids.
pyrimidine dimers Refers to a mutation in which exposure to ultraviolet light
causes the covalent linkage of two adjacent pyrimidine residues.
pyrrole A five-membered heterocyclic diene ring compound in which the hetero
atom is nitrogen; a building block of the heme group.
pyruvate A prominent intermediate in metabolism; a precursor for alanine and
glucose and can be converted into lactate in anaerobic glycolysis; can also be
oxidized to acetyl CoA, which can be further oxidized to yield energy aerobically,
converted into fats, or used to synthesize cholesterol and other steroids.
pyruvate carboxylase A biotin-dependent enzyme that catalyzes the formation of
oxaloacetate from pyruvate and CO2 at the expense of ATP; important in
gluconeogenesis as well as in the replenishment of the citric acid cycle.
pyruvate dehydrogenase complex A large, complex mitochondrial enzyme that
catalyzes the oxidative decarboxylation of pyruvate to form acetyl CoA; this
irreversible reaction is the link between glycolysis and the citric acid cycle.
Q
Q cycle A set of reactions in which coenzyme Q cycles between the fully reduced
state and the fully oxidized state through one-electron transfer reactions in which
one of the electrons is temporarily stored in cytochrome b; provides a means of
passing the two electrons of coenzyme Q to the single-electron carrier cytochrome c,
one electron at a time.
Q-cytochrome c oxidoreductase A component of the respiratory chain, this
oxidoreductase carries electrons from coenzyme Q to cytochrome c and, in the
process, pumps protons out of the mitochondrial matrix to generate the protonmotive force. Also called cytochrome reductase or Complex III.
quaternary structure In proteins containing more than one polypeptide chain, the
spatial arrangements of those chains (subunits) and the nature of contacts among
them.
R
Ramachandran plot A steric contour diagram that depicts allowed ranges of the
angles Ö and Ø for amino acid residues in polypeptide chains; for each residue, its
conformation in the main chain of a polypeptide can be completely defined by Ö (the
degree of rotation at the bond between the nitrogen atom and the α-carbon atom)
and Ø (the degree of rotation at the bond between the α-carbon atom and the
carbonyl carbon atom).
random-coil conformation The disordered, unfolded structure of a denatured
macromolecule; many proteins that are not cross-linked lose their native threedimensional structure as well as their biological function in the presence of unfolding
agents such as urea.
reaction center In a photosynthetic unit, a specialized chlorophyll molecule that
collects excitation energy from other chlorophyll molecules and mediates the
transformation of light into chemical energy.
reading frame A group of three nonoverlapping nucleotides that is read as a codon
during protein synthesis; the reading frame begins with the initiator codon AUG.
receptor-mediated endocytosis A means of importing specific proteins into a cell
by their binding to plasma-membrane receptors and their subsequent endocytosis
and inclusion into vesicles.
receptor tyrosine kinases Transmembrane receptor proteins that, when bound to
the appropriate signal molecules, display intracellular protein kinase activity,
phosphorylating proteins at tyrosine residues.
recombinant DNA technology An array of techniques used to analyze and
manipulate DNA; these methods include the specific modification of genes as well as
the construction of new ones, gene cloning and amplification, and the expression of
new and modified genes to yield protein products.
recombinase An enzyme that catalyzes the exchange of genetic material when two
DNA molecules recombine.
recombination The formation of new arrangements of genes or gene sequences by
movement of DNA.
recombination synapse The initial stage in the recombination process in which four
molecules of recombinase and their associated DNA molecules come together.
reducing sugars Sugars that convert into a form with a free aldehyde group that is
readily oxidized and can thus reduce another compound.
reductase An enzyme that catalyzes the reduction of a functional group, often using
NADPH as an electron donor; a type of oxidoreductase.
reductive biosynthesis Refers to anabolic pathways that require hydride ion
donors to reduce carbon atoms in metabolic intermediates; NADPH serves as an
electron donor in many such pathways, including the biosynthesis of palmitoyl CoA.
regulatory proteins Proteins that bind to enzymes and regulate their catalytic
activity.
relaxed DNA A circular DNA molecule that has no superhelical turns.
relay helix A long helix that connects the switch regions of the S1 fragment to the
lever arm; the nature of the nucleotide in the S1 fragment (ATP or ADP) allows the
relay helix to change position, resulting in a reorientation of the lever arm.
release factor One of a set of proteins that recognize stop codons on mRNA at the
A site on the ribosome, which leads to the release of the completed protein from the
tRNA in the P site of the ribosome.
repair The restoration of the normal structure and sequence of a gene after damage
from ultraviolet light or chemical agents.
replication fork The site of DNA synthesis where the parental strands are separated
and daughter strands complementary to each parent are synthesized.
replicon A segment of DNA that carries its own origin of replication and can
replicate autonomously; bacterial plasmids are replicons.
repressor A protein that binds to an operator sequence and inhibits the
transcription of the structural genes in the operon.
resistance transfer factor A DNA sequence that allows a plasmid carrying genes
for drug resistance to be transferred to other bacteria by conjugation.
resonance structures Alternative covalent bonding patterns for a molecule that are
equally likely or nearly so.
respiration An ATP-generating process in which an inorganic compound, such as O2,
serves as the ultimate electron acceptor; the electron donor can be either an organic
compound or an inorganic one.
respiratory chain The path that electrons travel in going from NADH or FADH2 to
O2; consists of three complexes that pump protons as a result of the electron
transport and two mobile electron carriers. Also called the electron transport
chain.
respiratory control Tight coupling or coordination of the oxidation of reduced
cofactors (NADH and FADH2) in the electron-transport chain and the phosphorylation
of ADP to yield ATP in the mitochondrion; such control ensures that the rate of the
citric acid cycle, where reduced cofactors are generated, corresponds to the demand
for ATP.
restriction enzymes Endonuclease enzymes that recognize specific base sequences
in double-stranded DNA and cleave both strands of the duplex at specific places.
restriction-fragment-length polymorphism (RFLP) The genetic diversity within
a population indicated by mutations within specific sites in DNA; such mutations alter
the position of restriction fragments in electrophoretic gel analysis.
restriction-modification system A system such that, for each restriction enzyme
that a prokaryote produces, the cell also produces a corresponding methylase that
marks the host DNA and prevents its degradation.
retinal The prosthetic group of rhodopsin that, upon absorbing light, undergoes an
isomerization from 11-cis-retinal to all-trans-retinal, initiating the visual signal
transduction pathway.
retrograde transport The cytoplasmic dynein-driven transport of organelles from
the periphery to the center of a cell.
retrovirus A virus that contains an RNA genome but that replicates through the
intermediacy of double-stranded DNA that is integrated into the host-cell genome.
reverse transcriptase An enzyme that synthesizes DNA by using an RNA template.
rho protein An ATP-dependent bacterial helicase that breaks the RNA-DNA hybrid at
the transcription bubble, and thereby terminates transcription.
rhodopsin The photoreceptor of rod cells. It is composed of the protein opsin and
the prosthetic group 11-cis-retinal.
rhodopsin kinase An enzyme that phosphorylates activated rhodopsin at multiple
serine and threonine residues to provide a binding site for the inhibitory protein
arrestin.
riboflavin A vitamin component of the electron-transfer coenzymes FAD, FADH2,
FMN, and FMNH2. Also called vitamin B2.
ribonucleoproteins Macromolecular complexes whose optimal activity depends on
the presence of specific RNAs and proteins; ribosomes are ribonucleoproteins.
ribonucleotide A nucleotide that contains a purine or pyrimidine base covalently
linked to a ribose, which is in turn linked to one or more phosphate groups.
ribonucleotide reductase An enzyme that catalyzes the reduction of all four
ribonucleotides to deoxyribonucleotides.
ribose A five-carbon monosaccharide (C5H10O5) that constitutes the carbohydrate
moiety of ATP, other ribonucleosides and ribonucleotides, and cofactors such as NAD
and coenzyme A.
ribosomal RNA The RNA component of a ribosome, the site of protein synthesis.
ribosome A large ribonucleoprotein assembly that catalyzes the formation of
peptide bonds; a molecular machine that coordinates protein synthesis.
ribozymes RNA molecules that display enzymatic activity.
rickets A disease caused by the insufficient formation of vitamin D, resulting in the
inadequate calcification of cartilage and bone.
Rieske center An unusual 2Fe-2S center in that one of the iron ions is coordinated
by two histidine residues rather than by two cysteine residues.
rifamycin An antibiotic isolated from Streptomyces that inhibits the initiation of RNA
synthesis by blocking the formation of the first phosphodiester bond.
RNA editing A change, after transcription, in the information content of RNA by
processes other than RNA splicing.
RNA enzymes RNA molecules that act as enzymes. Also called ribozymes.
RNA polymerases A class of enzymes that synthesize RNA molecules
complementary to a DNA template.
RNA primers Small pieces of RNA that base-pair with the template strand of DNA
and serve as primers for primer-dependent DNA synthesis; the RNA is later removed
and replaced by DNA.
RNA processing Any alteration of a precursor RNA molecule, such as splicing or
polyadenylation, that yields a mature RNA molecule.
RNA world A theoretical time early in evolution in which RNA molecules served both
as the genetic material and as catalysts for biochemical reactions.
rod A long, slender photoreceptor cell that functions in dim light but does not
perceive color.
rotenone A plant toxin that inhibits electron transfer in the NADH-Q reductase
complex; used as a fish and insect poison.
rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) An enzyme that
catalyzes the reaction of carbon dioxide with ribulose 1,5-bisphosphate to form two
molecules of 3-phosphoglycerate.
S
S1 fragments Proteolytic digestion products of myosin that are the force-generating
units of the intact myosin molecule; the S1 fragment contains the ATPase and actinbinding sites.
S1 heads Proteolytic digestion products of myosin that are the force-generating
units of the intact myosin molecule; contain the ATPase and actin-binding sites; S1
heads are smaller than heavy meromyosin.
S-adenosylmethionine An activated methyl donor that consists of an adenosyl
group linked to the sulfur atom of methionine.
salting out A protein purification technique based on the fact that the solubility of
most proteins is lowered at higher salt concentrations; consequently, different
proteins will precipitate at varying salt concentrations.
salvage pathway In general, a pathway that synthesizes the final product from
preformed components; nucleotides can be synthesized in a salvage pathway by
attaching purine bases to PRPP.
Sanger dideoxy method A DNA-sequencing technique that employs controlled
interruption of enzymatic replication of the molecule to be analyzed. DNA polymerase
I is used with a primer, the four deoxynucleoside triphosphates, and a 2',3'-dideoxy
analog of one of them. Fragments of various lengths are produced in which the
dideoxy analog is at the 3' end. Four sets of chain-terminated fragments (one for
each analog) are then displayed by electrophoresis and autoradiography, and the
base sequence can be read from the four lanes of the gel.
sarcomere The functional unit of a myofibril; its distinct repeating structure is due
to the overlapping of thick protein filaments, composed of myosin, and thin
filaments, composed of actin and other proteins, which contract through the use of a
sliding-filament method.
sarcoplasmic reticulum An extensive intracellular compartment in muscle cells
that sequesters Ca2+ and releases it in response to a nerve impulse, thereby
initiating muscle contraction.
Schiff base An intermediate formed when an amine reacts with an aldehyde or a
ketone from a nitrogen compound analogous to a carbonyl compound; Schiff bases
are intermediates in a number of enzymecatalyzed reactions.
scissile bond The bond in a substrate molecule that is cleaved by the enzyme.
scurvy A disease caused by a deficiency of ascorbate (vitamin C), which results in
the formation of unstable collagen.
SDS-polyacrylamide gel electrophoresis The electrophoresis of proteins in a
polyacrylamide medium; the detergent SDS renders the movement of the proteins
inversely proportional to molecular weight (see also electrophoresis).
second messenger A small signal molecule whose concentration changes in
response to a primary messenger.
secondary structure In a protein, the spatial arrangement of amino acid residues
that are relatively close to one another in the linear sequence; the α helix and the β
strand are both elements of primary structure.
secondary transporter A transporter that uses the energy of the downhill
(exergonic) flow of one ion or molecule to power the uphill (endergonic) flow of
another. Also called cotransporter.
sedimentation coefficient The velocity at which a macromolecule moves in a
centrifugal field divided by the strength of the centrifugal field; usually expressed in
Svedberg units.
sedimentation-equilibrium centrifugation An ultracentrifugation technique that
can be used to determine the mass of a protein; centrifugation is at a relatively slow
speed so that sedimentation is counterbalanced by diffusion.
segmental flexibility Mobility imparted to IgG antibodies by a flexible polypeptide
that joins the Fc and the two Fab units. Such mobility enhances the formation of
antibody-antigen complexes.
selectins Carbohydrate-binding proteins that constrain immune-system cells to the
site of injury in an inflammatory response.
selectivity filter A region of ion-channel proteins that determines the specificity of a
particular channel.
self-diagonal plot A tool used to search for amino acid sequence repeats within a
protein. The protein sequence is displayed on both the vertical and the horizontal
axes, running from amino to carboxyl terminis. A dot is placed at each point at which
the amino acid along the horizontal axis is the same as that on the vertical axis.
Internal repeats are seen as lines parallel to the central diagonal line, which
represents the sequence aligned with itself.
self-splicing RNA Refers to introns that have the ability to remove themselves from
the precursor RNA and assist in the splicing of exons to form mature RNA.
semiconservative replication In the duplication of DNA, one of the strands of each
daughter molecule is newly synthesized, whereas the other is unchanged from the
parental DNA double helix.
sequence templates Conserved residues that are structurally and functionally
important and are characteristic of particular families of proteins.
sequential displacement reaction A reaction having multiple reactants, in which
all substrates bind to the enzyme before any product is released. Thus, in a reaction
with two substrates, a ternary complex of the enzyme and both substrates forms.
sequential model A model for explaining allosteric enzymes in which the binding of
one substrate influences the substrate affinity of neighboring active sites without
necessarily inducing a transition encompassing the entire enzyme.
serine proteases A class of protein-degrading enzymes whose activity depends on
the presence of serine at the active site; chymotrypsin and trypsin are examples.
seven-transmembrane-helix (7TM) receptors A class of integral membrane
proteins typified by transducin in which the intramembrane part consists of seven
helical regions; these receptors are always coupled to G proteins.
SH2 domain (Src homology domain) A domain of approximately 100 amino acids
that binds to phosphotyrosine residues.
SH3 domain (Src homology domain) A domain that binds proline-rich stretches
of polypeptide.
sheet, β A common structural motif in proteins, in which two or more β strands are
associated as stacks of chains, stabilized by interchain hydrogen bonds; several β
strands running in the same direction form a β pleated sheet, whereas such strands
running in opposite directions form an antiparallel pleated sheet.
Shine-Dalgarno sequence In messenger RNA, a purine-rich region about 10
nucleotides on the 5' side of an initiator codon that pairs with the 3' end of 16S RNA
in the 30S ribosomal subunit; helps to determine where translation is initiated on an
mRNA molecule.
side chain The distinctive R group bonded to the á-carbon atom of an amino acid.
siemen The reciprocal of an ohm, which is a measure of resistance to the flow of
electrical charge.
sigma subunit A component of bacterial RNA polymerase that enables the core RNA
polymerase to recognize promoter sites.
signal sequences A sequence of amino acid residues ranging in size from 13 to 36
residues, usually at the amino terminus of the nascent polypeptide chain, that marks
the protein for translocation across the rough endoplasmic reticulum.
site-specific mutagenesis The use of recombinant DNA technology to create
specific deletions, insertions, or substitutions in vitro in a particular gene; this
technique allows the production of proteins having any desired amino acid at any
position.
site-specific recombination The exchange of two specific but not always
homologous DNA sequences.
small G protein A monomeric guanyl nucleotide binding protein that is active when
bound to GTP and inactive when bound to GDP; has inherent GTPase activity.
small nuclear RNAs (snRNAs) A class of small RNAs confined to the nucleus;
some play a role in splicing.
snRNA See small nuclear RNAs.
sodium-potassium pump An enzyme that uses the energy of ATP hydrolysis to
pump sodium out of the cell and potassium into the cell. Also called sodiumpotassium ATPase.
solid-phase method A means of synthesizing discrete peptides in which amino
acids are added step-bystep to a growing peptide chain that is anchored to an
insoluble matrix.
somatic mutation Refers to the introduction of a mutation after V-D-J
recombination to further increase antibody diversity.
Southern blotting A technique used to locate and identify a DNA fragment
containing a specific sequence; a mixture of fragments is separated by
electrophoresis, transferred to a nitrocellulose sheet, hybridized to a radioactively
labeled DNA probe complementary to the desired sequence, and visualized by
autoradiography.
special pair In a photosynthetic reaction center, the pair of chlorophyll molecules
that collect excitation energy from antenna chlorophyll molecules and then transfer
high-energy electrons to other electron acceptors.
specific activity A measure of the activity of a protein sample relative to the
amount of protein present in the sample, usually presented as activity units per
milligram of protein; assessed at each step of a protein purification procedure as a
measure of the effectiveness of the purification.
sphingomyelin Common in brain tissue, a sphingolipid in which the terminal
hydroxyl group of ceramide has a phosphorylcholine substituent.
sphingosine An amino alcohol containing a long, unsaturated hydrocarbon chain
that is a component of the phospholipid sphingomyelin as well as glycolipids; serves
a role analogous to that of glycerol in phosphoglycerides.
spliceosome An assembly of proteins and small nuclear RNAs that splices primary
transcripts to form mature mRNA.
splicing The removal of introns and the ligation of exons from precursors of RNA to
form mature RNA.
spontaneous reaction A process that proceeds irreversibly toward equilibrium and
is accompanied by an increase in disorder, or entropy.
stage 1 metabolism A stage in which large molecules are broken into smaller
units; glycogen, for instance, is converted into glucose.
stage 2 metabolism A stage in which small molecules are degraded to a few key
intermediates, such as acetyl CoA, in metabolism.
stage 3 metabolism A stage consisting of the citric acid cycle and oxidative
phosphorylation; the final common pathway for the oxidation of fuel molecules.
standard free-energy change The free-energy change of a reaction, when it takes
place under standard conditions, in which each of the reactants is present at a
concentration of 1.0 M.
starch A homopolysaccharide that is a storage form of glucose in plant chloroplasts;
amylopectin, the branched form of starch, has approximately one α-1,6 linkage per
thirty α-1,4 linkages, whereas amylose is unbranched, composed of glucose residues
in α-1,4 linkage.
start codon The first codon to be translated, usually AUG.
starved-fed cycle In animals, the biochemical changes that take place in the
postabsorptive state, a prolonged fast and a refed state, such as would take place
between an evening meal and breakfast.
statins Inhibitors of HMG-CoA reductase that are used to lower the plasma
cholesterol level of people with atherosclerosis.
stem-loop structure The simplest and most common structural motif found in
single-stranded nucleic acids, formed when two complementary sequences within a
single strand come together to yield a double-helical structure with an unpaired loop
at the end of the helical region.
stereocilium One of a bundle of 20 to 300 hairlike projections that protrude from
hair cells; movements of a stereocilia initiate the hearing signal-transduction
pathway by altering the polarization of hair cells.
steroid hormones Hormones, such as androgen and estrogen, derived from
cholesterol.
sterol regulatory element binding protein (SREBP) A transcription factor that
binds to the sterol regulatory element of the HMG-CoA reductase gene and other
genes in cholesterol metabolism to stimulate their transcription.
stop codons A set of codons that are recognized by release factors and mark the
end of translation.
strand, β An extended polypeptide chain, with an axial distance of 3.5 Å between
adjacent amino acids, often found in a β pleated sheet.
streptomycin A highly basic trisaccharide antibiotic that causes both the inhibition
of translational initiation and the misreading of mRNA in prokaryotes.
stringent response In bacteria, a decrease in the rate of ribosomal and transfer
RNA synthesis in response to a scarcity of amino acids.
stroma The matrix of the chloroplast; contains thylakoids as well as soluble
enzymes and is enclosed by the inner membrane of the chloroplast.
substitution matrix A tool for determining evolutionary relationships between
amino acid sequences. When two sequences are compared, each substitution is
assigned a score based on the matrix. A large positive score corresponds to a
substitution that occurs frequently, whereas a negative score corresponds to a
substitution that occurs only rarely.
substrate A reactant in a chemical reaction. An enzyme catalyzes a single chemical
reaction or set of closely related reactions, and the components of those reactions
are called substrates.
substrate channeling A property of multienzyme complexes in which the product
of one reaction is routed directly to the active site of the next enzyme in the
complex, for which it is a substrate; substrate channeling enhances catalytic rate by
preventing the loss of intermediates in the overall reaction.
substrate cycle A pair of thermodynamically irreversible biochemical reactions that
simultaneously produce and consume a pair of metabolic intermediates; these paired
pathways may amplify metabolic signals and in some cases can also generate heat
for the maintenance of temperature in tissues. Also called futile cycle.
substrate-level phosphorylation The formation of ATP from ADP in which the
phosphate donor is a substrate with high phosphoryl transfer potential.
subunit Any of the polypeptide chains in a protein that contains more than one of
such chains.
subunit, 30S The small subunit of the bacterial 70S ribosome; composed of 21
different proteins and a 16S RNA molecule.
subunit, 50S The large subunit of the bacterial 70S ribosome; the site of peptidebond synthesis, it contains 34 different proteins, a 5S RNA species, and a 23S RNA
species.
succinate-Q reductase An integral membrane protein complex of the inner
mitochondrial membrane that transfers electrons from FADH 2 formed in the citric
acid cycle to coenzyme Q. Also called Complex II.
sucrose A disaccharide of glucose and fructose (commonly known as table sugar)
that is readily transportable and stored in many plant cells.
suicide (mechanism-based) inhibition Inhibition that results when an enzyme
converts a pseudosubstrate into a reactive inhibitor that immediately inactivates its
catalytic activity.
supercoil A structure formed by closed, circular DNA in which the DNA is more
compact than the relaxed circular DNA; the circular DNA helix twists upon itself to
form a superhelix.
supercoiling Refers to the ability of closed, circular DNA to coil upon itself.
superhelix The coil of a double-stranded DNA that forms when it is twisted so as to
cross over its own axis.
superoxide dismutase An enzyme that scavenges superoxide radicals by
catalyzing the conversion of two of these radicals into hydrogen peroxide and
molecular oxygen; protects against damage by reactive oxygen species.
Svedberg unit A unit for measuring the sedimentation of a macromolecule; 1
Svedberg unit (S) is equal to 10-13 seconds.
symporter A transport system in which a molecule is carried across a membrane in
the same direction as an ion, which in turn is pumped back across the membrane
through active transport linked to ATP consumption.
synthase An enzyme catalyzing a synthetic reaction in which two units are joined
without the direct participation of a nucleotide triphosphate.
synthetase An enzyme catalyzing a synthetic reaction in which two units are joined
with the direct participation of ATP or another nucleoside triphosphate.
T
TATA box Found in nearly all eukaryotic genes, a promoter element giving rise to
mRNA. The TATA box is centered between 30 and 90 residues downstream of the
transcription start site and has the consensus sequence 5'-TATAAAA-3'.
TATA-box-binding protein associated factor (TAF) One of a group of proteins,
many of which contain bromodomains, that bind to the TATA-box-binding protein to
form a complex required for RNA transcription.
taxol A chemical isolated from the Pacific yew tree that stabilizes tubulin in
microtubules and promotes polymerization; used in chemotherapy to interfere with
the proliferation of rapidly dividing cells.
Tay-Sachs disease A heritable disorder caused by the accumulation of gangliosides
due to the lack of an enzyme (α-N-acetylhexosaminidase) responsible for their
degradation; clinical characteristics include weakness, mental retardation, dementia,
blindness, and death by age 3.
T cell A lymphocyte that has receptors (T cell receptors) that recognize antigens
only if bound to MHC proteins; two major types of T cells exist: cytotoxic T
lymphocytes (killer T cells) and helper T cells.
T-cell-mediated immunity One of the recognition systems of the immune
response, in which T cells scan the surfaces of all cells and kill those that exhibit
foreign proteins synthesized by intercellular pathogens.
T-cell receptor A receptor that recognizes peptides displayed by MHC proteins on
target cells; the receptor consists of two different 43-kd chains joined by a disulfide
bond and spanning the plasma membrane; the combination of constant and variable
regions among various T-cell receptors allows T cells to recognize a large number of
different epitopes.
telomerase A reverse transcriptase that contains its own template; a highly
processive enzyme that elongates the 3'-ending strand of a telomere.
telomeres Ends of chromosomes; the DNA at the telomere consists of hundreds of
repeats of a hexanucleotide sequence characteristic of the organism.
template In DNA or RNA, a sequence that directs the production of a
complementary sequence.
template strand The strand of DNA that is complementary to the RNA transcript.
terminal glycosylation The addition of carbohydrates to proteins and the
processing of these carbohydrates that takes place in the Golgi complex.
termination The final state common to all biological polymerization reactions; the
polymerization process is halted in response to a set of termination signals specific
for the type of biological molecule being synthesized.
tertiary structure In proteins, the spatial arrangement of amino acid residues that
are far from each other in the linear sequence, as well as the pattern of disulfide
bonds.
tetracycline An antibiotic that binds to the prokaryotic 30S ribosomal subunit and
inhibits the binding of aminoacyl-tRNA molecules to the ribosomal complex.
tetrahydrofolate (tetrahydropteroylglutamate) A highly versatile carrier of
activated one-carbon units.
tetrodotoxin A highly potent poison from the fugu (puffer) fish that blocks the
conduction of nerve impulses along axons and excitable membranes in nerve fibers,
leading to respiratory paralysis.
tetroses Monosaccharides that have four carbon atoms.
thalassemias Genetic disorders characterized by the defective synthesis of one or
more hemoglobin chains.
thermogenesis The regulated uncoupling of oxidative phosphorylation as a means
of generating heat to maintain body temperature.
thermogenin A mitochondrial membrane protein (an uncoupling protein) that plays
a role in thermogenesis by forming a pathway for the flow of protons into the
mitochondria, thereby generating heat without synthesizing ATP.
thiamine The vitamin component of the coenzyme thiamine pyrophosphate. Also
called vitamin B1.
thiamine pyrophosphate The coenzyme form of thiamine (vitamin B1), composed
of a modified thiazole ring linked by a methylene bridge to a substituted pyrimidine;
a cofactor in enzymatic reactions in which bonds to carbonyl carbon atoms are
cleaved or synthesized.
thioester intermediate An ester in which the noncarbonyl oxygen atom is replaced
by a sulfur atom; thioesters are energy-rich intermediates in a number of
biochemical reactions.
thiol proteases A class of protein-degrading enzymes whose activity depends on
the presence of a cysteine residue at the active site; papain is a thiol protease.
thioredoxin A protein with exposed cysteines that can be reversibly oxidized and
reduced; an important electron carrier in the reduction of ribonucleotides and in
photosynthesis.
3-hydroxy-3-methylglutaryl CoA reductase (HMG-CoA reductase) A highly
regulated enzyme that catalyzes the committed step in cholesterol synthesis-the
formation of mevalonate from 3-hydroxy-3- methylglutaryl CoA.
3-isopentyl pyrophosphate A precursor to cholesterol as well as a large variety of
other biomolecules such as vitamin K, coenzyme Q, and the carotenoids; derived
from mevalonate.
thylakoid In chloroplasts, a membranous sac, or vesicle, that contains the energytransducing machinery of photosynthesis, including light-harvesting proteins,
reaction centers, electron-transport chains, and ATP synthase.
thymidylate synthase An enzyme that catalyzes the methylation of deoxyuridylate
(dUMP) to form thymidylate (TMP).
tip link A filament that links adjacent stereocilia; in the membrane of sterocilia, tip
links are coupled to ion channels that are gated by stress; mechanical movement
alters the current flow across a hair-cell membrane, which may initiate or terminate
the hearing signal-transduction pathway.
topoisomerases Enzymes that catalyze the interconversion of topoisomers of DNA;
can relax supercoiled DNA.
topoisomerase II (DNA gyrase) A topoisomerase that catalyzes the ATP-driven
introduction of negative supercoils into DNA.
topoisomers Molecules of DNA that differ from one another only in their linking
number.
transaldolase An enzyme that transfers a three-carbon dihydroxyacetone unit from
a ketose to an aldose acceptor; one of the enzymes in the nonoxidative part of the
pentose phosphate pathway.
transamination The transfer of an α-amino group from an amino acid to an αketoacid.
transcription DNA-directed synthesis of RNA catalyzed by RNA polymerase.
transcription bubble The site of RNA synthesis or transcription; it contains RNA
polymerase, a locally melted "bubble" of DNA, and helix consisting of the template
strand and the newly synthesized RNA.
transcription factor A protein that assists RNA polymerase in the initiation of RNA
synthesis; binds to a specific promoter element.
transducin G protein that is the signal-coupling protein of visual excitation;
activated by rhodopsin, it leads to the activation of cGMP phosphodiesterase, which
in turn leads to a nerve impulse.
transfer RNA The adaptor molecule in protein synthesis; contains an amino acid
recognition site as well as a template-recognition site, or anticodon.
transferase An enzyme that catalyzes group transfer, often employing a cofactor.
transformation The incorporation of intact foreign DNA into a cell.
transgenic animal An animal that harbors and expresses a foreign gene that has
been inserted into the germ line; experiments with such animals and their offspring
show that a foreign gene under the control of a new promoter can be efficiently
integrated, expressed, and transmitted.
transition A mutation that results from the substitution of one pyrimidine for
another or one purine for another.
transition state A chemical species that has the highest free energy and the lowest
concentration of those on the pathway from a substrate to a product.
transition-state analog A compound resembling the transition state of a catalyzed
reaction; such compounds are often potent inhibitors of enzyme-catalyzed reactions.
transketolase An enzyme that transfers an activated aldehyde unit from a ketose to
an aldose acceptor; one of the enzymes in the nonoxidative part of the pentose
phosphate pathway.
translation Cellular protein synthesis, so named because the four-letter alphabet of
nucleic acids is translated into the different amino acids that make up proteins.
translational repressor A mechanism for transcriptional regulation in which a
protein encoded by an operon binds to an mRNA near the initiation site for its own
synthesis and blocks the synthesis of several proteins encoded by that polygenic
message; the synthesis of the 50 or so ribosomal proteins is subject to control by
translational repression.
translocase An enzyme that carries a molecule from one cellular compartment to
another; the ATPADP translocase facilitates the exchange of ATP and ADP between a
mitochondrion and the cytosol.
transport antibiotics Antibiotics that exert their effect by rendering the
membranes abnormally permeable.
transport vesicles Membrane-bounded compartments that mediate the transfer of
proteins between the endoplasmic reticulum and the Golgi complex, and between the
Golgi complex and subsequent destinations.
transposase A nuclease enzyme encoded by an insertion sequence (IS) or
transposon; makes staggered cuts in donor and recipient sites, facilitating IS
insertion into a bacterial gene.
transposition The movement of a gene from one chromosome to another or from
one location to another on the same chromosome.
transposons Mobile bacterial genetic elements that enable genes to be transferred
among nonhomologous sequences.
transversion A mutation in which a purine is replaced by a pyrimidine or vice versa.
triacylglycerols Glycerols that have fatty acyl chains esterified to each of their
hydroxyl groups; storage form of fats. Also known as neutral fats or triglycerides.
trimethoprim A competitive inhibitor of dihydrofolate reductase, like methotrexate
but specific for bacterial and protozoan enzymes.
trinucleotide repeats Stretches of DNA in which a trinucleotide sequence is
repeated many times; these segments of DNA can expand in the course of DNA
replication, causing such genetic diseases as Huntington disease.
trioses Monosaccharides that have three carbon atoms.
tropomyosin Located in the thin filaments of a sarcomere, a protein that plays a
role in the regulation of muscle contraction by blocking the interaction of myosin with
actin at low Ca2+ concentrations; regulated by troponin.
troponin complex Located in the thin filaments of the sarcomeres, that regulate
muscle contraction through allosteric interactions with tropomyosin in response to
changes in Ca2+ concentrations.
TRP (transient receptor potential) channels A family of ion channels whose
properties are altered in response to motion.
tubulin The major microtubule protein component that exists in two forms, α- and
β-tubulin; tubulins display GTPase activity that is vital for the assembly and
disassembly of microtubules.
tumor promoters Chemicals that promote the proliferation of carcinogenic cells;
phorbol esters are tumor promoters.
tunicamycin An antibiotic inhibitor of N-glycosylation that is a hydrophobic analog
of UDP-Nacetylglucosamine; blocks the first step in core oligosaccharide synthesis.
turn, β In proteins, a structural element composed of four amino acids, in which the
CO and NH groups of residue 1 are hydrogen bonded to the NH and CO groups of
residue 4, respectively; such a structure forms a hairpin turn, allowing polypeptide
chains to reverse their direction.
turnover number The number of substrate molecules converted into product by an
enzyme molecule in a unit time when the enzyme is fully saturated with substrate;
equal to the kinetic constant k2 (see Michaelis constant).
two-dimensional gel electrophoresis A means of analyzing a protein sample in
which the sample is initially fractionated in one dimension by isoelectric focusing and
is subsequently fractionated in a second dimension, perpendicular to the first, by
SDS-polyacrylamide gel electrophoresis.
U
ubiquinone and ubiquinol See coenzyme Q.
ubiquitin Present in all eukaryotes, a small, highly conserved protein that, when
attached to another protein, targets it for proteolytic destruction.
ultracentrifugation High-speed centrifugation used to separate biomolecules and
determine their masses.
uncoupling protein A mitochondrial membrane protein that plays a role in
thermogenesis by forming a pathway for the flow of protons into the mitochondria,
thereby generating heat without synthesizing ATP. Also called thermogenin.
urea cycle A cyclic pathway that converts excess ammonia into urea for secretion;
the first metabolic pathway to be discovered.
ureotelic Refers to organisms in which excess ammonia is converted into urea and
then excreted; most terrestrial vertebrates are ureotelic.
uricotelic Refers to organisms in which excess ammonia is converted into the purine
uric acid for secretion; birds and terrestrial reptiles are uricotelic.
uridine diphosphate glucose (UDP-glucose) The activated form of glucose used
in the synthesis of glycogen; formed from glucose 1-phosphate and UTP.
V
van der Waals interaction The attraction between two molecules based on
transient electron asymmetry around an atom that induces a complementary
asymmetry in a nearby molecule.
variable region The 108-residue amino acid sequence found at the N-terminal end
of both the light and heavy chains of immunoglobulin G; the sequence in this region
varies for every antibody type known; parts of these segments (the hypervariable
regions) form the antigen-binding site of the immunoglobulin.
V-D-J recombination A means to increase antibody diversity by recombining
different variable (V) genes, joining (J) genes, and diversity (D) genes to generate
the entire variable regions of antibody chains; the D genes undergo recombination
only in antibody heavy chains.
virilization An inherited disorder of steroid-hormone synthesis due to abnormally
high levels of androgen; clinical characteristics include early sexual development in
males, masculinization of external female genitalia, and persistent loss of Na+,
leading to dehydration and hypotension.
virion The complete extracellular form of a virus consisting of DNA or RNA
surrounded by a coat.
virus A complex of protein and nucleic acid that can penetrate a cell and replicate
itself by co-opting the host's metabolism and employing its own as well as the host's
gene products; the smallest organism known.
vitamin A A fat-soluble vitamin that is the precursor of the light-sensitive pigment
retinal and the signal molecule retinoic acid, an activator of certain transcription
factors. Also called retinol.
vitamin B12 A prosthetic group, consisting of a cobalt atom, a corrin ring, and
deoxyadenosine, that plays a role in intramolecular rearrangements, methylations,
and reductions of ribonucleotides to deoxyribonucleotides. Also called cobalamin.
vitamin D A fat-soluble vitamin that plays a role in the regulation of calcium and
phosphorus metabolism; deficiencies in vitamin D lead to the impairment of bone
formation.
vitamin E Protects unsaturated membrane lipids from oxidation. Also called αtocopherol.
vitamin K A fat-soluble vitamin required for blood coagulation.
vitamins Organic substances required in trace amounts for a number of essential
biochemical reactions.
VLDLs (very low density lipoproteins) Lipoprotein particles, stabilized by
apolipoproteins B-100 and E, that transport excess endogenous triacylglycerides and
cholesterol from the liver to other tissues.
voltage-gated channel A transmembrane channel that is opened by membrane
depolarization; the sodium and potassium channels of axon membranes are good
examples.
von Gierke disease A disease resulting from defective glucose 6-phosphatase that
affects the liver and kidneys; glycogen is normal in structure but present in
abnormally large amounts and so there is a massive increase in liver size with
resulting damage to liver functions.
W
Watson-Crick helix See B-DNA helix.
Western blotting An immunoassay technique used to detect a specific protein in a
cell or in body fluid. A sample undergoes electrophoresis in an SDS-polyacrylamide
gel, the resolved proteins are transferred to a polymer sheet, and then an antibody
specific for the protein of interest is incubated with the blotted sample; other
antibodies or radioactive markers may then be used to help visualize the desired
antigen-antibody complex.
wobble hypothesis The notion that steric freedom in the pairing of the third base
of an mRNA codon with the anticodon of a transfer RNA molecule allows more than
one codon to be recognized by a particular tRNA molecule.
X
xeroderma pigmentosa A rare skin disorder, characterized by sensitivity to
ultraviolet light and a propensity for skin cancers, caused by a defect in excinuclease,
which plays a role in the removal of pyrimidine dimers.
x-ray crystallography A technique for determining the three-dimensional structure
of protein crystals at atomic resolution by examining the diffraction pattern of x-rays
striking the crystal.
Y
yeast artificial chromosome (YAC) A DNA molecule that can be used to clone
DNA inserts ranging from 100 to 1000 kb in length; contains a centromere, an
autonomously replicating sequence, a pair of telomeres, selectable marker genes,
and an insertion site for the sequence to be cloned.
Z
Z scheme of photosynthesis The pathway of electron flow between photosystem I
and II; so called because the redox diagram from P680 to P700+ looks like the letter
Z.
Z-DNA A left-handed double helix in which the backbone phosphates zigzag; can be
formed by oligonucleotides with alternating sequences of purines and pyrimidines.
zinc clusters Found in pairs in the nuclear receptor superfamily of proteins, a DNAbinding motif in which a zinc ion is coordinated to four cysteine side chains.
zinc finger A conserved sequence-specific DNA-binding domain, found in members
of the nuclear hormone-receptor family, that consists of eight cysteine residues: the
first four bind one zinc ion and the second four bind another.
zinc proteases A class of protein-degrading enzymes whose catalytic activity
depends on a zinc ion; carboxypeptidase A is a zinc protease.
zonal centrifugation An ultracentrifugation technique in which the sample is
centrifuged through a gradient of increasing density and the components are
separated on the basis of differing sedimentation coefficients.
zwitterion A dipolar ion (from the German zwitter, "between"); at neutral pH,
amino acids have a protonated amino group and a dissociated carboxyl group and
are therefore zwitterions.
zymogen A catalytically inactive precursor of an enzyme.