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Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000.

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Molecular Cell Biology. 4th edition.

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Glossary

Boldfaced terms within a definition are also defined in this glossary. Alternative names for main entries are in italics. Figures and tables that illustrate defined terms are noted in parentheses.

A

acetyl CoA

Small, water-soluble metabolite comprising an acetyl group linked to coenzyme A (CoA); formed during oxidation of pyruvate, fatty acids, and amino acids. Its acetyl group is transferred to citrate in the citric acid cycle. (Figure 16-10)

acetylcholine (ACh)

Neurotransmitter that functions at vertebrate neuromuscular junctions and at various neuron-neuron synapses in the brain and peripheral nervous system.

acid

A compound that can donate a proton (H+). The carboxyl and phosphate groups are the primary acidic groups in biological molecules.

actin

Abundant structural protein in eukaryotic cells that interacts with many other proteins. The monomeric globular form (G actin) polymerizes to form actin filaments (F actin). In muscle cells, F actin interacts with myosin during contraction. See also microfilaments.

action potential

Rapid, transient, all-or-none electrical activity that is propagated in the plasma membrane of excitable cells such as neurons and muscle cells. Action potentials, or nerve impulses, allow long-distance signaling in the nervous system. (Figure 21-14)

activation energy

The input of energy required to (overcome the barrier to) initiate a chemical reaction. By reducing the activation energy, an enzyme increases the rate of a reaction. (Figure 2-27)

active site

Region of an enzyme molecule where the substrate binds and undergoes a catalyzed reaction.

active transport

Energy-requiring movement of an ion or small molecule across a membrane against its concentration gradient or electrochemical gradient. Energy is provided by the coupled hydrolysis of ATP or the cotransport of another molecule down its electrochemical gradient.

adenosine triphosphate

See ATP.

adenylyl cyclase

Membrane-bound enzyme that catalyzes formation of cyclic AMP (cAMP) from ATP; also called adenylate cyclase. Binding of certain ligands to their cell-surface receptors leads to activation of adenylyl cyclase and a rise in intracellular cAMP. (Figure 20-15)

aerobic

Referring to a cell, organism, or metabolic process that utilizes O2 or that can grow in the presence of O2.

aerobic oxidation

Oxygen-requiring metabolism of sugars and fatty acids to CO2 and H2O coupled to the synthesis of ATP.

allele

One of two or more alternative forms of a gene located at the corresponding site (locus) on homologous chromosomes.

allosteric transition

Change in the tertiary and/or quaternary structure of a protein induced by binding of a small molecule to a specific regulatory site, causing a change in the protein’s activity. Allosteric regulation is particularly prevalent in multisubunit enzymes.

alpha (α) helix

Common secondary structure of proteins in which the linear sequence of amino acids is folded into a right-handed spiral stabilized by hydrogen bonds between carboxyl and amide groups in the backbone. (Figure 3-6)

amino acid

An organic compound containing at least one amino group and one carboxyl group. In the 20 different amino acids that compose proteins, an amino group and carboxyl group are linked to a central carbon atom, the α carbon, to which a variable side chain is bound. (Figure 3-2)

aminoacyl-tRNA

Activated form of an amino acid, used in protein synthesis, consisting of an amino acid linked via a highenergy ester bond to the 3′-hydroxyl group of a tRNA molecule. (Figure 4-29)

amphipathic

Referring to a molecule or structure that has both a hydrophobic and a hydrophilic part.

anabolism

Cellular processes whereby energy is used to synthesize complex molecules from simpler ones. See also catabolism.

anaerobic

Referring to a cell, organism, or metabolic process that functions in the absence of O2.

anaphase

Mitotic stage during which the sister chromatids (or paired homologs in meiosis I) separate and move apart (segregate) toward the spindle poles. (Figure 19-34)

antibody

A protein that interacts with a particular site (epitope) on an antigen and facilitates clearance of that antigen by various mechanisms. See also immunoglobulin. (Figure 3-21)

anticodon

Sequence of three nucleotides in a tRNA that is complementary to a codon in an mRNA. During protein synthesis, base pairing between a codon and anticodon aligns the tRNA carrying the corresponding amino acid for addition to the growing peptide chain.

antigen

Any material (usually foreign) that elicits production of and is specifically bound by an antibody.

antiport

A type of cotransport in which a membrane protein (antiporter) transports two different molecules or ions across a cell membrane in opposite directions. See also symport.

antisense RNA

An RNA, with sequence complementary to a specific RNA transcript or mRNA, whose binding prevents processing of the transcript or translation of the mRNA. (Figure 11-46)

apoptosis

Regulated process leading to cell death via a series of well-defined morphological changes; also called programmed cell death. (Figure 23-45)

archaea

Class of prokaryotes that constitutes one of the three distinct evolutionary lineages of modern-day organisms; also called archaebacteria and archaeans. These prokaryotes are in some respects more similar to eukaryotes than to the so-called true bacteria (eubacteria). (Figure 1-5)

association constant (Ka)

See equilibrium constant.

aster

Star-shaped structure composed of microtubules (called astral fibers) that radiates outward from a centrosome during mitosis. (Figure 19-34)

asymmetric carbon atom

A carbon atom bonded to four different atoms; also called chiral carbon atom. The bonds can be arranged in two different ways producing stereoisomers that are mirror images of each other. (Figure 2-6)

ATP (adenosine 5-triphosphate)

A nucleotide that is the most important molecule for capturing and transferring free energy in cells. Hydrolysis of each of the two high-energy phosphoanhydride bonds in ATP is accompanied by a large free-energy changeG) of −7 kcal/mole. (Figure 2-24)

ATP synthase

Multimeric protein complex bound to inner mitochondrial membranes, thylakoid membranes of chloroplasts, and the bacterial plasma membrane that catalyzes synthesis of ATP during oxidative phosphorylation and photosynthesis; also called F0F1 complex. (Figure 16-28)

ATPase

One of a large group of enzymes that catalyze hydrolysis of ATP to yield ADP and inorganic phosphate with release of free energy.

autonomously replicating sequence (ARS)

Sequence that permits a DNA molecule to replicate in yeast; a yeast DNA replication origin. (Figure 9-40)

autoradiography

Technique for visualizing radioactive molecules in a sample (e.g., a tissue section or electrophoretic gel) by exposing a photographic film or emulsion to the sample. The exposed film is called an autoradiogram or autoradiograph. (Figure 3-45)

autosome

Any chromosome other than a sex chromosome.

auxotroph

A mutant cell or microorganism that grows only when the medium contains a specific nutrient or metabolite that is not required by the wild type.

axon

Long process extending from the cell body of a neuron that is capable of conducting an electric impulse (action potential) generated at the junction with the cell body (called the axon hillock) toward its distal, branching end (called the axon terminal). (Figure 21-1)

axoneme

Bundle of microtubules and associated proteins present in cilia and flagella and responsible for their movement. (Figure 19-28)

B

bacteriophage (phage)

Any virus that infects bacterial cells. Some bacteriophage are widely used as cloning vectors.

basal body

Structure at the base of cilia and flagella from which microtubules forming the axoneme radiate; structurally similar to a centriole.

basal lamina (pl. basal laminae)

A thin sheetlike network of extracellular-matrix components that underlies most animal epi-thelial layers and other organized groups of cells (e.g., muscle), separating them from connective tissue.

base

A compound, usually containing nitrogen, that can accept a proton (H+). Commonly used to denote the purines and pyrimidines in DNA and RNA.

base pair

Association of two complementary nucleotides in a DNA or RNA molecule stabilized by hydrogen bonding between their base components. Adenine pairs with thymine or uracil (A·T, A·U) and guanine pairs with cytosine (G·C). (Figure 4-4b)

benign

Referring to a tumor containing cells that closely resemble normal cells. Benign tumors stay in the tissue where they originate. See also malignant.

beta (β) sheet

A planar secondary structure of proteins that is created by hydrogen bonding between the backbone atoms in two different polypeptide chains or segments of a single folded chain. (Figure 3-8)

bilayer

See phospholipid bilayer.

biomembrane

Permeability barrier, surrounding cells or organelles, that consists of a phospholipid bilayer, associated membrane proteins, and in some cases cholesterol and glycolipids.

blastula

An early embryonic form produced by cleavage of a fertilized ovum and usually consisting of a single layer of cells surrounding a fluid-filled spherical cavity.

buffer

A solution of the acid (HA) and base (A−) form of a compound that undergoes little change in pH when small quantities of strong acid or base are added.

C

cadherin

Protein belonging to a family of Ca2-dependent cell-adhesion molecules that play roles in tissue differentiation and structure.

calmodulin

A small cytosolic protein that binds four Ca2+ ions; the Ca2+-calmodulin complex binds to and activates many enzymes. (Figure 20-40)

Calvin cycle

The major metabolic pathway that fixes CO2 into carbohydrates during photosynthesis; also called carbon fixation. It is indirectly dependent on light but can occur both in the dark and light. (Figure 16-49)

cAMP-dependent protein kinase (cAPK)

Type of cytosolic enzyme that is activated by cAMP and functions to regulate the activity of numerous cellular proteins; also called protein kinase A. Generally is activated in response to a rise in cAMP level resulting from stimulation of G protein–coupled receptors. (Figures 3-24 and 20-47)

capsid

The outer proteinaceous coat of a virus, formed by multiple copies of one or more protein subunits and enclosing the viral nucleic acid.

carbohydrate

General term for certain polyhydroxyaldehydes, polyhydroxyketones, or compounds derived from these usually having the formula (CH2O)n. Primary type of compound used for storing and supplying energy in animal cells.

carbon fixation

See Calvin cycle.

carcinogen

Any chemical or physical agent that can cause cancer when cells or organisms are exposed to it.

carcinoma

A malignant tumor derived from epithelial cells.

catabolism

Cellular processes whereby complex molecules are degraded to simpler ones and energy is released. See also anabolism.

catalyst

A substance that increases the rate of a chemical reaction without undergoing a permanent change in its structure. Enzymes are protein catalysts.

catecholamines

Group of compounds derived from tyrosine that function as neurotransmitters; include epinephrine, norepinephrine, and dopamine. (Figure 21-28)

cDNA (complementary DNA)

DNA molecule copied from an mRNA molecule by reverse transcriptase and therefore lacking the introns present in genomic DNA. Sequencing of a cDNA permits the amino acid sequence of the encoded protein to be deduced; expression of cDNAs in recombinant cells can be used to produce large quantities of their encoded proteins in vitro.

cell cycle

Ordered sequence of events in which a cell duplicates its chromosomes and divides into two. Most eukaryotic cell cycles can be commonly divided into four phases: G1 before DNA synthesis occurs; S when DNA replication occurs; G2 after DNA synthesis; and M when cell division occurs, yielding two daughter cells. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, nondividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. (Figure 13-1)

cell division

Separation of a cell into two daughter cells. In higher eukaryotes, it involves division of the nucleus (mitosis) and of the cytoplasm (cytokinesis); mitosis often is used to refer to both nuclear and cytoplasmic division.

cell fusion

Production of a hybrid cell containing two or more nuclei by various techniques that stimulate the fusion of the plasma membranes of two cells at the point of contact and intermingling of their cytoplasms. See also hybridoma.

cell junctions

Specialized regions on the cell surface through which cells are joined to each other or to the extracellular matrix. (Figure 15-23)

cell line

A population of cultured cells, of plant or animal origin, that has undergone a change allowing the cells to grow indefinitely, in contrast to a cell strain. Cell lines can result from chemical or viral transformation and are said to be immortal.

cell strain

A population of cultured cells, of plant or animal origin, that has a finite life span, in contrast to a cell line. (Figure 6-5)

cell wall

A specialized, rigid extracellular matrix that lies next to the plasma membrane, protecting a cell and maintaining its shape. It is prominent in most fungi, plants, and prokaryotes, but is not present in most multicellular animals. (Figures 22-29 and 22-32)

cell-adhesion molecules (CAMs)

Integral membrane proteins that mediate cell-cell binding. The five major classes are the integrins, cadherins, selectins, immunoglobulin (Ig) superfamily, and mucins. (Figure 22-1)

cellulose

A structural polysaccharide made of glucose units linked together by β(1n4) glycosidic bonds. It forms long microfibrils, which are the major component of plant cell walls. (Figure 22-31)

central nervous system (CNS)

The part of the vertebrate nervous system comprising the brain and spinal cord; the main information-processing organ.

centriole

Either of two cylindrical structures within the centrosome of animal cells and containing nine sets of triplet microtubules; structurally similar to a basal body. (Figure 19-5b)

centromere

Constricted portion of a mitotic chromosome where sister chromatids are attached and from which kinetochore fibers extend toward a spindle pole; required for proper chromosome segregation during mitosis and meiosis.

centrosome (cell center)

Organelle located near the nucleus of animal cells that is the primary microtubule-organizing center (MTOC) and contains a pair of centrioles. It divides during mitosis, forming the spindle poles.

chaperone

Collective term for two types of proteins that prevent misfolding of a target protein (molecular chaperones) or actively facilitate its proper folding (chaperonins). (Figure 3-15)

checkpoint

Any of several points in the eukaryotic cell cycle at which progression of a cell to the next stage can be halted until conditions are suitable. (Figure 13-34)

chemical equilibrium

The state of a chemical reaction in which the concentration of all products and reactants is constant and the rates of the forward and reverse reactions are equal.

chemiosmosis

Process whereby an electrochemical proton gradient (pH plus electric potential) across a membrane is used to drive an energy-requiring process such as ATP synthesis or transport of molecules across a membrane against their concentration gradient; also called chemiosmotic coupling. (Figure 16-1)

chimera

An animal or tissue composed of elements derived from genetically distinct individuals; also a protein molecule containing segments derived from different proteins.

chlorophylls

A group of light-absorbing porphyrin pigments that are critical in photosynthesis. (Figure 16-35)

chloroplast

A specialized organelle in plant cells that is surrounded by a double membrane and contains internal chlorophyll-containing membranes (thylakoids) where the light-absorbing reactions of photosynthesis occur. (Figure 16-34)

cholesterol

An amphipathic lipid containing the four-ring steroid structure with a hydroxyl group on one ring; a major component of many eukaryotic membranes and precursor of steroid hormones. (Figure 5-29)

chromatid

One copy of a duplicated chromosome, formed during the S phase of the cell cycle, that is still joined at the centromere to the other copy; also called sister chromatid. During mitosis, the two chromatids separate, each becoming a chromosome of one of the two daughter cells.

chromatin

Complex of DNA, histones, and nonhistone proteins from which eukaryotic chromosomes are formed. Condensation of chromatin during mitosis yields the visible metaphase chromosomes. (Figure 9-29)

chromatography, liquid

Group of biochemical techniques for separating mixtures of molecules based on their mass (gel-filtration chromatography), charge (ion-exchange chromatography), or ability to bind specifically to other molecules (affinity chromatography). Commonly used technique for separating and purifying proteins. (Figure 3-43)

chromosome

In eukaryotes, the structural unit of the genetic material consisting of a single, linear double-stranded DNA molecule and associated proteins. During mitosis, chromosomes condense into compact structures visible in the light microscope. In prokaryotes, a single, circular double-stranded DNA molecule constitutes the bulk of the genetic material. See also karyotype.

cilium (pl. cilia)

Membrane-enclosed motile structure extending from the surface of eukaryotic cells. Cilia usually occur in groups and beat rhythmically to move a cell (e.g., single-celled organism) or to move small particles or fluid along the surface (e.g., trachea cells). See also axoneme and flagellum.

cis-acting

Referring to a regulatory sequence in DNA (e.g., enhancer, promoter) that can control a gene only on the same chromosome. In bacteria, cis-acting elements are adjacent or proximal to the gene(s) they control, whereas in eukaryotes they may also be far away. See also trans-acting.

cisterna (pl. cisternae)

Flattened membrane-bounded compartment, as found in the Golgi complex and endoplasmic reticulum.

cistron

A genetic unit that encodes a single polypeptide.

citric acid cycle

A set of nine coupled reactions occurring in the matrix of the mitochondrion in which acetyl groups derived from food molecules are oxidized, generating CO2 and reduced intermediates used to produce ATP; also called Krebs cycle and tricarboxylic acid cycle (TCA). (Figure 16-12)

clathrin

A fibrous protein that with the aid of assembly proteins polymerizes into a lattice-like network at specific regions on the cytosolic side of a membrane, thereby forming a clathrin-coated pit, which buds off to form a vesicle. (Figures 17-53 and 17-54)

clone

A population of identical cells or DNA molecules descended from a single progenitor. Also viruses or organisms that are genetically identical and descended from a single progenitor.

cloning vector

An autonomously replicating genetic element used to carry a cDNA or fragment of genomic DNA into a host cell for the purpose of gene cloning. Commonly used vectors are bacterial plasmids and modified bacteriophage genomes. (Figures 7-3 and 7-12)

codon

Sequence of three nucleotides in DNA or mRNA that specifies a particular amino acid during protein synthesis; also called triplet. Of the 64 possible codons, three are stop codons, which do not specify amino acids. (Table 4-2)

coenzyme

Small organic molecule that associates with an enzyme and participates in the reaction catalyzed by the enzyme; also called cofactor. Some coenzymes form a transient covalent bond to the substrate; others function as carriers of electrons, acyl groups, or other activated groups. Generally, a coenzyme is bound less firmly to a protein than a prosthetic group.

coenzyme A (CoA)

See acetyl CoA.

coiled-coil

Stable rodlike quaternary protein structure formed by two or three α helices interacting with each other along their length; commonly found in fibrous proteins and certain transcription factors. (Figure 3-9a)

collagen

A triple-helical protein that forms fibrils of great tensile strength; a major component of the extracellular matrix and connective tissues. The numerous collagen subtypes differ in their tissue distribution and the extracellular components and cell-surface proteins with which they associate.

complementary

Referring to two nucleic acid sequences or strands that can form a perfect base-paired double helix with each other; also describing regions on two interacting molecules (e.g., an enzyme and its substrate) that fit together in a lock-and-key fashion.

complementary DNA (cDNA)

See cDNA.

complementation

In genetics, the restoration of a wild-type function (e.g., ability to grow on galactose) in diploid heterozygotes generated from haploids, each of which carries a mutation in a different gene whose encoded protein is required for the same biochemical pathway. If two mutants with the same mutant phenotype (e.g., inability to grow on galactose) can complement each other, then their mutations are in different genes. (Figure 8-11)

conformation

The precise shape of a protein or other macromolecule in three dimensions resulting from the spatial location of the atoms in the molecule. A small change in the conformations of some proteins affects their activity considerably.

consensus sequence

The nucleotides or amino acids most commonly found at each position in the sequences of related DNAs, RNAs, or proteins. See also homology.

constitutive

Referring to cellular production of a molecule at a constant rate, which is not regulated by internal or external stimuli.

constitutive mutant

A mutant in which a protein is produced at a constant level, as if continuously induced;

a bacterial regulatory mutant in which an operon is transcribed in the absence of inducer;

a mutant in which a regulated enzyme is in a continuously active form.

cooperativity

Property exhibited by some proteins with multiple ligand-binding sites whereby binding of one ligand molecule increases (positive cooperativity) or decreases (negative cooperativity) the binding affinity of successive ligand molecules.

cosmid

A type of vector used to clone large DNA fragments. (Figure 7-16)

cotransport

Protein-mediated transport of an ion or small molecule across a membrane against a concentration gradient driven by coupling to movement of a second molecule down its concentration gradient. See also antiport and symport.

covalent bond

Stable chemical force that holds the atoms in molecules together by sharing of one or more pairs of electrons. Such a bond has a strength of 50 – 200 kcal/mol. (Table 2-1)

crossing over

Exchange of genetic material between maternal and paternal chromatids during meiosis to produce recombined chromosomes. (Figure 8-18) See also recombination.

cyclic AMP (cAMP)

A second messenger, produced in response to hormonal stimulation of certain G protein – coupled receptors, that activates cAMP-dependent protein kinases. (Figure 20-4)

cyclin

Any of several related proteins whose concentrations rise and fall during the course of the eukaryotic cell cycle. Cyclins form complexes with cyclin-dependent kinases, thereby activating and determining the substrate specificity of these enzymes.

cyclin-dependent kinase (Cdk)

A protein kinase that is catalytically active only when bound to a cyclin. Various Cdk-cyclin complexes trigger progression through different stages of the eukaryotic cell cycle by phosphorylating specific target proteins. (Figure 13-29)

cytochromes

A group of colored, heme-containing proteins that transfer electrons during cellular respiration and photosynthesis. (Figure 16-21)

cytokine

Any of numerous secreted, small proteins (e.g., interferons, interleukins) that bind to cell-surface receptors on certain cells to trigger their differentiation or proliferation.

cytokinesis

The last stage of mitosis, where the two daughter cells separate, each with a nucleus and cytoplasmic organelles.

cytoplasm

Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus.

cytoskeleton

Network of fibrous elements, consisting primarily of microtubules, actin microfilaments, and intermediate filaments, found in the cytoplasm of eukaryotic cells. The cytoskeleton provides structural support for the cell and permits directed movement of organelles, chromosomes, and the cell itself.

cytosol

Unstructured aqueous phase of the cytoplasm excluding organelles, membranes, and insoluble cytoskeletal components.

cytosolic face

The face of a cell membrane directed toward the cytoplasm. (Figure 5-31)

D

dalton

Unit of molecular mass approximately equal to the mass of a hydrogen atom (1.66 × 10−24 g).

degenerate

In reference to the genetic code, having more than one codon specifying a particular amino acid.

denaturation

Drastic alteration in the conformation of a protein or nucleic acid due to disruption of various noncovalent bonds caused by heating or exposure to certain chemicals; usually results in loss of biological function.

dendrite

Process extending from the cell body of a neuron that is relatively short and typically branched and receives signals from axons of other neurons. (Figure 21-1)

deoxyribonucleic acid

See DNA.

depolarization

Change in the potential that normally exists across the plasma membrane of a cell at rest, resulting in a less negative membrane potential.

desmosomes

Specialized regions of the plasma membrane, consisting of dense protein plaques connected to intermediate filaments, that mediate adhesion between adjacent cells (especially epithelial cells) and between cells and the extracellular matrix. (Figure 22-6)

determination

In embryogenesis, a change in a cell that commits the cell to a particular developmental pathway.

development

Overall process involving growth and differentiation by which a fertilized egg gives rise to an adult plant or animal, including the formation of individual cell types, tissues, and organs.

diacylglycerol (DAG)

Intracellular signaling molecule produced by cleavage of phosphoinositides in response to stimulation of certain cell-surface receptors; functions as a membrane-bound second messenger in inositol-lipid signaling pathways. (Figures 20-4 and 20-37)

differentiation

Process usually involving changes in gene expression by which a precursor cell becomes a distinct specialized cell type.

diploid

Referring to an organism or cell having two full sets of homologous chromosomes and hence two copies (alleles) of each gene or genetic locus. Somatic cells contain the diploid number of chromosomes (2n) characteristic of a species. See also haploid.

disaccharide

A small carbohydrate (sugar) composed of two monosaccharides covalently joined by a glycosidic bond. Common examples are lactose (milk sugar) and sucrose, a major photosynthetic product in higher plants.

dissociation constant (KD)

See equilibrium constant.

disulfide bond (SS)

A common covalent linkage between the sulfhydryl groups on two cysteine residues in different proteins or in different parts of the same protein; generally found only in extracellular proteins or protein domains.

DNA (deoxyribonucleic acid)

Long linear polymer, composed of four kinds of deoxyribose nucleotides, that is the carrier of genetic information. In its native state, DNA is a double helix of two antiparallel strands held together by hydrogen bonds between complementary purine and pyramidine bases. (Figure 4-6)

DNA cloning

Recombinant DNA technique in which specific cDNAs or fragments of genomic DNA are inserted into a cloning vector, which then is incorporated into cultured host cells (e.g., E. coli cells) and maintained during growth of the host cells; also called gene cloning. (Figures 7-3 and 7-15)

DNA library

Collection of cloned DNA molecules consisting of fragments of the entire genome (genomic library) or of DNA copies of all the mRNAs produced by a cell type (cDNA library) inserted into a suitable cloning vector.

DNA polymerase

An enzyme that copies one strand of DNA (the template strand) to make the complementary strand, forming a new double-stranded DNA molecule. All DNA polymerases add deoxyribonucleotides one at a time in the 5′n3′ direction to a short pre-existing primer strand of DNA or RNA.

domain

Region of a protein with a distinct tertiary structure (e.g., globular or rodlike) and characteristic activity; homologous domains may occur in different proteins.

dominant

In genetics, referring to that allele of a gene expressed in the phenotype of a heterozygote; the nonexpressed allele is recessive. Also referring to the phenotype associated with a dominant allele. (See Figure 8-1)

dorsal

Relating to the back of an animal or the upper surface of a structure (e.g., leaf, wing).

double helix, DNA

The most common three-dimensional structure for cellular DNA in which the two polynucleotide strands are anti-parallel and wound around each other with complementary bases hydrogen-bonded. (Figure 4-4a)

downstream

For a gene, the direction RNA polymerase moves during transcription, which is toward the end of the template DNA strand with a 3′ hydroxyl group. By convention, the +1 position of a gene is the first transcribed nucleotide; nucleotides downstream from the +1 position are designated +2, +3, etc. Also, events that occur later in a cascade of steps. See also upstream.

dynein

Member of a family of ATP-powered motor proteins that move toward the (−) end of microtubules by sequentially breaking and forming new bonds with microtubule proteins. Dyneins can transport vesicles and are responsible for the movement of cilia and flagella. (Figure 19-32)

E

ectoderm

Outermost of the three primary cell layers of the animal embryo; gives rise to epidermal tissues, the nervous system, and external sense organs. See also endoderm and mesoderm. (Figure 23-5)

electron carrier

Any molecule or atom that accepts electrons from donor molecules and transfers them to acceptor molecules. Most are prosthetic groups (e.g., heme, copper, iron-sulfur clusters) associated with membrane-bound proteins.

electron transport

Flow of electrons via a series of electron carriers from reduced electron donors (e.g., NADH) to O2 in the inner mitochondrial membrane, or from H2O to NADP in the thylakoid membrane of plant chloroplasts. (Figure 16-17)

electrophoresis

Any of several techniques for separating macromolecules based on their migration in a gel or other medium subjected to a strong electric field. (Figure 3-41)

electrophoretogram

An autoradiogram of a gel in which molecules have been separated by gel electrophoresis. (Figure 7-23b)

elongation factor

One of a group of nonribosomal proteins required for continued translation of mRNA following initiation. (Figure 4-39)

embryogenesis

Early development of an individual from a fertilized egg (zygote). Following cleavage of the zygote, the major axes are established during the blastula stage; in the subsequent gastrula stage, the early embryo invaginates and acquires three cell layers. (Figure 23-5)

endocytosis

Uptake of extracellular materials by invagination of the plasma membrane to form a small membrane-bounded vesicle (early endosome). (Figure 17-46)

endoderm

Innermost of the three primary cell layers of the animal embryo; gives rise to the gut and most of the respiratory tract. See ectoderm and mesoderm. (Figure 23-5)

endoplasmic reticulum (ER)

Network of interconnected membranous structures within the cytoplasm of eukaryotic cells. The rough ER, which is associated with ribosomes, functions in the synthesis and processing of secretory and membrane proteins; the smooth ER, which lacks ribosomes, functions in lipid synthesis. (Figure 5-47)

endosome, late

A sorting vesicle with an acidic internal pH in which bound ligands dissociate from their membrane-bound receptor proteins. Late endosomes participate in sorting of lysosomal enzymes and in recycling of receptors endocytosed from the plasma membrane.

endothelium

Layer of highly flattened cells that forms the lining of all blood vessels and regulates exchange of materials between the bloodstream and surrounding tissues; it usually is underlain by a basal lamina.

endothermic

Referring to a chemical reaction that absorbs heat (i.e., has a positive change in enthalpy).

enhancer

A regulatory sequence in eukaryotic DNA (rarely in prokaryotic DNA) that may be located at a great distance from the gene it controls. Binding of specific proteins to an enhancer modulates the rate of transcription of the associated gene. (Figure 10-34)

enthalpy (H)

Heat; in a chemical reaction, the enthalpy of the reactants or products is equal to their total bond energies.

entropy (S)

A measure of the degree of disorder or randomness in a system; the higher the entropy, the greater the disorder.

enzyme

A biological macromolecule that acts as a catalyst. Most enzymes are proteins, but certain RNAs, called ribozymes, also have catalytic activity.

epinephrine

A catecholamine secreted by the adrenal gland and some neurons in response to stress; also called adrenaline. It functions as both a hormone and neurotransmitter, mediating “fight or flight” responses including increased blood glucose levels and heart rate. (Figure 21-28)

epithelium

Coherent sheet comprising one or more layers of cells that covers an external body surface or lines an internal cavity. (Figure 6-4)

epitope

The part of an antigen molecule that binds to an antibody; also called antigenic determinant.

equilibrium constant (K)

Ratio of forward and reverse rate constants for a reaction. For a binding reaction, A + B 1 2 AB, it equals the association constant, Ka; the higher the Ka, the tighter the binding between A and B. The reciprocal of the Ka is the dissociation constant, KD; the higher the KD, the weaker the binding between A and B.

eubacteria

Class of prokaryotes that constitutes one of the three distinct evolutionary lineages of modern-day organisms; also called the true bacteria or simply bacteria. Phylogenetically distinct from archaea and eukaryotes. (Figure 1-5)

euchromatin

Less condensed portions of chromatin, including most transcribed regions, present in interphase chromosomes. See also heterochromatin.

eukaryotes

Class of organisms, composed of one or more cells containing a membrane-enclosed nucleus and organelles, that constitutes one of the three distinct evolutionary lineages of modern-day organisms; also called eukarya. Includes all organisms except viruses and prokaryotes.

exocytosis

Release of intracellular molecules (e.g., hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This is the process whereby most molecules are secreted from eukaryotic cells.

exon

Segments of a eukaryotic gene (or of its primary transcript) that reaches the cytoplasm as part of a mature mRNA, rRNA, or tRNA molecule. See also intron.

exoplasmic face

The face of a cell membrane directed away from the cytoplasm. The exoplasmic face of the plasma membrane faces the cell exterior, whereas the exoplasmic face of organelles (e.g., mitochondria, chloroplasts, and the endoplasmic reticulum) face their lumen. (Figure 5-31)

exothermic

Referring to a chemical reaction that releases heat (i.e., has a negative change in enthalpy).

expression

See gene expression.

expression cloning

Recombinant DNA techniques for isolating a cDNA or genomic DNA segment based on functional properties of the encoded protein and without prior purification of the protein. Also refers to techniques for producing high levels of a full-length protein once its cDNA or gene has been cloned.

expression vector

A modified plasmid or virus that carries a gene or cDNA into a suitable host cell and there directs synthesis of the encoded protein. Some expression vectors are designed for screening DNA libraries for a gene of interest (Figures 7-21 and 20-9); others, for producing large amounts of a protein from its cloned gene (Figures 7-36 and 7-37).

extracellular matrix

A usually insoluble network consisting of polysaccharides, fibrous proteins, and adhesive proteins that are secreted by animal cells. It provides structural support in tissues and can affect the development and biochemical functions of cells.

extrinsic protein

See peripheral membrane protein.

F

F0F1 complex

See ATP synthase.

facilitated transport

Protein-aided transport of an ion or molecule across a cell membrane down its concentration gradient at a rate greater than that obtained by passive diffusion; also called facilitated diffusion. Such transport exhibits ligand specificity and saturation kinetics. The glucose transporter GLUT1 is a wellstudied example of a protein that mediates facilitated diffusion. (Figure 15-7)

FAD (flavin adenine dinucleotide)

A coenzyme that participates in oxidation reactions by accepting two electrons from a donor molecule and two H+ from the solution. The reduced form, FADH2, transfers electrons to carriers that function in oxidative phosphorylation. (Figure 16-8)

fatty acid

Any hydrocarbon chain that has a carboxyl group at one end; a major source of energy during metabolism and precursors for synthesis of phospholipids. (Figure 2-18)

fertilization

Fusion of a female and male gamete (both haploid) to form a diploid zygote, which develops into a new individual.

fibroblast

A common type of connective-tissue cell that secretes collagen and other components of the extracellular matrix. It migrates and proliferates during wound healing and in tissue culture.

fibronectin

An extracellular multiadhesive protein that binds to other matrix components, fibrin, and cell-surface receptors of the integrin family. It functions to attach cells to the extracellular matrix and is important in wound healing. (Figure 22-22)

flagellum (pl. flagella)

Long locomotory structure, extending from the surface of a eukaryotic cell, whose whiplike bending propels the cell forward or backward. Usually there is only one flagellum per cell (as in sperm cells). Bacterial flagella are smaller and much simpler structures. See also axoneme and cilium.

fluorescein

See fluorescent staining.

fluorescent staining

General technique for visualizing cellular components by treating cells with a fluorescent-labeled agent that binds specifically to a component of interest and then observing the cells by fluorescence microscopy. For instance, an antibody specific for a protein of interest can be chemically linked to a fluorescent dye such as fluorescein, which emits green light, or rhodamine, which emits red light. Various fluorescent dyes that bind specifically to DNA are used to detect chromosomes or specific chromosomal regions.

footprinting

Technique for identifying protein-binding regions of DNA or RNA. A radiolabeled nucleic acid sample is digested with a nuclease in the presence and absence of a specific binding protein. Because regions of DNA or RNA with bound protein are protected from digestion, the patterns of fragment bands separated by gel electrophoresis obtained from protected and unprotected samples differ, permitting identification of the protein-binding regions. (Figure 10-6)

free energy (G)

A measure of the potential energy of a system, which is a function of the enthalpy (H) and entropy (S).

free-energy change (G)

The difference in the free energy of the product molecules and of the starting molecules (reactants) in a chemical reaction. A large negative value of ΔG indicates that a reaction has a strong tendency to occur; that is, at chemical equilibrium the concentration of products will be much greater than the concentration of reactants.

G

G protein

Any of numerous heterotrimeric GTP-binding proteins that function in intracellular signaling pathways; usually activated by ligand binding to a coupled seven-spanning receptor on the cell surface. See also GTPase superfamily. (Table 20-5)

G protein–coupled receptor (GPCR)

Member of an important class of cell-surface receptors that have seven transmembrane α helices and are directly coupled to a trimeric G protein. (Figure 20-16)

G0, G1, G2phase

See cell cycle.

gamete

Specialized haploid cell (in animals either a sperm or an egg) produced by meiosis of germ cells; in sexual reproduction, union of a sperm and an egg initiates the development of a new individual.

ganglion (pl. ganglia)

Collection of neuron cell bodies located outside of the central nervous system.

ganglioside

Any glycolipid containing one or more N-acetylneuraminic acid (sialic acid) residues in its structure. Gangliosides are found in the plasma membrane of eukaryotic cells and confer a net negative charge on most animal cells.

gap junction

Protein-lined channel between adjacent cells that allows passage of ions and small molecules between the cells. (Figure 22-8)

gastrula

An early embryonic form subsequent to the blastula characterized by invagination of the cells to form a rudimentary gut cavity and development of three cell layers.

gene

Physical and functional unit of heredity, which carries information from one generation to the next. In molecular terms, it is the entire DNA sequence — including exons, introns, and noncoding transcription-control regions — necessary for production of a functional protein or RNA. See also cistron and transcription unit.

gene cloning

See DNA cloning.

gene control

All of the mechanisms involved in regulating gene expression. Most common is regulation of transcription, although mechanisms influencing the processing, stabilization, and translation of mRNAs help control expression of some genes.

gene conversion

Phenomenon in which one allele of a gene is converted to another during meiotic recombination.

gene expression

Overall process by which the information encoded in a gene is converted into an observable phenotype (most commonly production of a protein).

genetic code

The set of rules whereby nucleotide triplets (codons) in DNA or RNA specify amino acids in proteins. (See Table 4-2)

genome

Total genetic information carried by a cell or organism.

genomic DNA

All the DNA sequences composing the genome of a cell or organism. See also cDNA.

genomics

Comparative analysis of the complete genomic sequences from different organisms; used to assess evolutionary relations between species and to predict the number and general types of proteins produced by an organism.

genotype

Entire genetic constitution of an individual cell or organism; also, the alleles at one or more specific loci.

germ cell

Any precursor cell that can give rise to gametes. See also somatic cell.

germ line

Lineage of germ cells, which give rise to gametes and thus participate in formation of the next generation of organisms; also the genetic material transmitted from one generation to the next through the gametes.

glial cells

Nonexcitable supportive cells in the nervous system; also called neuroglial cells. Include astrocytes and oligodendrocytes in the vertebrate central nervous system and Schwann cells in the peripheral nervous system.

glucagon

A peptide hormone produced in the α cells of the pancreas that triggers the conversion of glycogen to glucose by the liver; acts with insulin to control blood glucose levels. (Figure 20-45)

glucose

Six-carbon monosaccharide (sugar) that is the primary metabolic fuel in most cells. The large glucose polymers, glycogen and starch, are used to store energy in animal cells and plant cells, respectively.

glycocalyx

Carbohydrate-rich layer covering the outer surface of the plasma membrane of eukaryotic cells; composed of membrane glycolipids, the oligosaccharide side chains of integral membrane proteins, and absorbed peripheral membrane proteins.

glycogen

A very long, branched polysaccharide, composed exclusively of glucose units, that is the primary storage carbohydrate in animal cells. It is found primarily in liver and muscle cells.

glycogenolysis

Breakdown of glycogen to glucose 6-phosphate; stimulated by a rise in cAMP following epinephrine stimulation of cells and, in muscle, by a rise in Ca2+ following neuronal stimulation. (Figure 20-43)

glycolipid

Any lipid to which a short carbohydrate chain is covalently linked; commonly found in the plasma membrane.

glycolysis

Metabolic pathway whereby sugars are degraded anaerobically to lactate or pyruvate in the cytosol with the production of ATP; also called Embden-Meyerhof pathway. (Figure 16-3)

glycoprotein

Any protein to which one or more oligosaccharide chains are covalently linked. Most secreted proteins and many membrane proteins are glycoproteins.

glycosaminoglycan (GAG)

A long, linear, highly charged polymer of a repeating disaccharide in which one member of the pair usually is a sugar acid (uronic acid) and the other is an amino sugar and many residues are sulfated. Generally are covalently bound to core proteins forming proteoglycans, which are major components of the extracellular matrix. (Figure 22-24)

glycosidic bond

The covalent linkage between two monosaccharide residues formed by a condensation reaction in which one carbon, usually carbon #1, of one sugar reacts with a hydroxyl group on a second sugar with the loss of a water molecule. (Figure 2-10)

glycosyl transferase

An enzyme that forms a glycosidic bond between a sugar residue (monosaccharide) and an amino acid side chain of a protein or a residue in an existing carbohydrate chain.

Golgi complex

Stacks of membranous structures in eukaryotic cells that function in processing and sorting of proteins and lipids destined for other cellular compartments or for secretion; also called Golgi apparatus. (Figure 5-49)

growing fork

Site in double-stranded DNA at which the template strands are separated and addition of deoxyribonucleotides to each newly formed chain occurs; also called replication fork. (Figure 12-9)

growth factor

An extracellular polypeptide molecule that binds to a cell-surface receptor triggering an intracellular signaling pathway leading to proliferation, differentiation, or other cellular response.

GTP (guanosine 5-triphosphate)

A nucleotide that is a precursor in RNA synthesis and also plays a special role in protein synthesis, signal-transduction pathways, and microtubule assembly.

GTPase superfamily

Group of GTP-binding proteins that cycle between an inactive state with bound GDP and an active state with bound GTP. These proteins — including G proteins, Ras proteins, and certain polypeptide elongation factors — function as intracellular switch proteins. (Figure 20-22)

H

haploid

Referring to an organism or cell having only one member of each pair of homologous chromosomes and hence only one copy (allele) of each gene or genetic locus. Gametes and bacterial cells are haploid. See also diploid.

HeLa cell

Line of human epithelial cells, derived from a human cervical carcinoma, that grows readily in culture and is widely used in research.

helicase

Any enzyme that moves along a DNA duplex using the energy released by ATP hydrolysis to separate (unwind) the two strands. Required for the replication and transcription of DNA.

helix-loop-helix

A conserved structural motif found in many monomeric Ca2+-binding proteins and dimeric eukaryotic transcription factors. (Figure 3-9b)

helix-turn-helix

A DNA-binding motif found in most bacterial DNA-binding proteins.

heterochromatin

Regions of chromatin that remain highly condensed and transcriptionally inactive during interphase.

heteroduplex

A double-stranded DNA molecule containing one or more mispaired bases.

heterokaryon

Cell with more than one functional nucleus produced by the fusion of two or more different cells.

heterozygous

Referring to a diploid cell or organism having two different alleles of a particular gene.

hexose

A six-carbon monosaccharide.

high-energy bond

Covalent bond that releases a large amount of energy when hydrolyzed under the usual intracellular conditions. Examples include the phosphoanhydride bonds in ATP, thioester bond in acetyl CoA, and various phosphate ester bonds. (Table 2-7)

histones

A family of small, highly conserved basic proteins, found in the chromatin of all eukaryotic cells, that associate with DNA in the nucleosome.

Holliday structure

Intermediate structure in recombination between homologous chromosomes. (Figures 12-29 and 12-30)

homeobox

Conserved DNA sequence that encodes a DNAbinding domain (homeodomain) in a class of transcription factors encoded by certain homeotic genes.

homeodomain

A conserved DNA-binding motif found in many developmentally important transcription factors. See also homeobox.

homeosis

Transformation of one body part into another arising from mutation in or misexpression of certain developmentally critical genes.

homeotic gene

A gene in which mutations cause cells in one region of the body to act as though they were located in another, giving rise to conversions of one cell, tissue, or body region into another.

homologous chromosome

One of the two copies of each morphologic type of chromosome present in a diploid cell; also called homologue. Each homologue is derived from a different parent.

homologue

See homologous chromosome.

homology

Similarity in the sequence of a protein or nucleic acid or in the structure of an organ that reflects a common evolutionary origin. Molecules or sequences that exhibit homology are referred to as homologs. In contrast, analogy is a similarity in structure or function that does not reflect a common evolutionary origin.

homozygous

Referring to a diploid cell or organism having two identical alleles of a particular gene.

hormone

General term for any extracellular substance that induces specific responses in target cells. Hormones coordinate the growth, differentiation, and metabolic activities of various cells, tissues, and organs in multicellular organisms.

Hox complex

Clusters of homologous selector genes, which help determine the body plan in animals.

hyaluronan

A large, highly hydrated polysaccharide that is a major component of the extracellular matrix; also called hyaluronic acid and hyaluronate. It imparts stiffness and resilience as well as a lubricating quality to many types of connective tissue.

hybridization

Association of two complementary nucleic acid strands to form double-stranded molecules, which can contain two DNA strands, two RNA strands, or one DNA and one RNA strand. Used experimentally in various ways to detect specific DNA or RNA sequences.

hybridoma

A clone of hybrid cells that are immortal and produce monoclonal antibodies; formed by fusion of normal antibody-producing B lymphocytes with myeloma cells. (Figure 6-10)

hydrogen bond

A noncovalent bond between an electronegative atom (commonly oxygen or nitrogen) and a hydrogen atom covalently bonded to another electronegative atom. Particularly important in stabilizing the three-dimensional structure of proteins and formation of base pairs in nucleic acids.

hydrolysis

Reaction in which a covalent bond is cleaved with addition of an H from water to one product of the cleavage and of an OH from water to the other.

hydrophilic

Interacting effectively with water. See also polar.

hydrophobic

Not interacting effectively with water; in general, poorly soluble or insoluble in water. See also nonpolar.

hydrophobic bond

The force that drives nonpolar molecules or parts of molecules to associate with each other in aqueous solution. A type of noncovalent bond that is particularly important in stabilization of the phospholipid bilayer.

hypertonic

Referring to an external solution whose solute concentration is high enough to cause water to move out of cells due to osmosis.

hypotonic

Referring to an external solution whose solute concentration is low enough to cause water to move into cells due to osmosis.

I

immunoglobulin (Ig)

Any protein that functions as an antibody. The five major classes of vertebrate immunoglobulins (IgA, IgD, IgE, IgG, and IgM) differ in their specific functions in the immune response.

in vitro

Denoting a reaction or process taking place in an isolated cell-free extract; sometimes used to distinguish cells growing in culture from those in an organism.

in vivo

In an intact cell or organism.

induction

In embryogenesis, a change in the developmental fate of one cell or tissue caused by direct interaction with another cell or tissue or with an extracellular signaling molecule; in metabolism, an increase in the synthesis of an enzyme or series of enzymes mediated by a specific molecule (inducer).

initiation factor

One of a group of proteins that promote the proper association of ribosomes and mRNA and are required for initiation of protein synthesis. (Figure 4-37)

initiator

A eukaryotic promoter sequence for RNA polymerase II that specifies transcription initiation within the sequence.

insulin

A protein hormone produced in the β cells of the pancreas that stimulates uptake of glucose into muscle and fat cells and with glucagon helps to regulate blood glucose levels (Figure 20-45). Insulin also functions as a growth factor for many cells.

integral membrane protein

Any membrane-bound protein all or part of which interacts with the hydrophobic core of the phospholipid bilayer and can be removed from the membrane only by extraction with detergent; also called intrinsic membrane protein. (Figure 3-32)

integrins

A large family of heterodimeric transmembrane proteins that promote adhesion of cells to the extracellular matrix or to the surface of other cells.

interferons (IFNs)

Small group of cytokines that bind to cell- surface receptors on target cells inducing changes in gene expression leading to an antiviral state or other cellular responses important in the immune response.

intermediate filaments

Cytoskeletal fibers (10 nm in diameter) formed by polymerization of several classes of cell-specific subunit proteins including keratins, lamins, and vimentin. They constitute the major structural proteins of skin and hair; form the scaffold that holds Z disks and myofibrils in place in muscle; and generally function as important structural components of many animal cells and tissues.

interphase

Long period of the cell cycle, including the G1, S, and G2 phases, between one M (mitotic) phase and the next. (Figure 13-1)

intrinsic protein

See integral membrane protein.

intron

Part of a primary transcript (or the DNA encoding it) that is removed by splicing during RNA processing and is not included in the mature, functional mRNA, rRNA, or tRNA; also called intervening sequence.

ion channel

Any transmembrane protein complex that forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient. See also ion pump.

ion pump

Any transmembrane ATPase that couples hydrolysis of ATP to the transport of a specific ion across the phospholipid bilayer against its electrochemical gradient. (Table 15-2)

ionic bond

A noncovalent bond between a positively charged ion (cation) and negatively charged ion (anion).

isoelectric focusing

Technique for separating molecules by gel electrophoresis in a pH gradient subjected to an electric field. A protein migrates to the pH at which its overall net charge is zero.

isoelectric point (pI)

The pH of a solution at which a dissolved protein or other potentially charged molecule has a net charge of zero and therefore does not move in an electric field.

isoform

One of several forms of the same protein whose amino acid sequences differ slightly but whose general activity is identical.

isotonic

Referring to a solution whose solute concentration is such that it causes no net movement of water in or out of cells.

K

karyotype

Number, sizes, and shapes of the entire set of metaphase chromosomes of a eukaryotic cell. (Figure 9-33)

kinase

An enzyme that transfers the terminal (γ) phosphate group from ATP to a substrate. Protein kinases, which phosphorylate specific serine, threonine, or tyrosine residues in target proteins, play a critical role in regulating the activity of many cellular proteins. See also phosphatases.

kinesin

Member of a family of motor proteins that use energy released by ATP hydrolysis to move toward the (+) end of a microtubule, transporting vesicles or particles in the process. (Figure 19-24)

kinetochore

A three-layer protein structure located at or near the centromere of each mitotic chromosome from which microtubules (kinetochore fibers) extend toward the spindle poles of the cell; plays an active role in movement of chromosomes toward the poles during anaphase.

Km

A parameter that describes the affinity of an enzyme for its substrate and equals the substrate concentration that yields the half-maximal reaction rate; also called the Michaelis constant. A similar parameter describes the affinity of a transport protein for the transported molecule or the affinity of a receptor for its ligand. (Figure 3-26)

knockin, gene

Technique in which the coding sequences of one gene are replaced by those of another.

knockout, gene

Technique for selectively inactivating a gene by replacing it with a mutant allele in an otherwise normal organism.

Krebs cycle

See citric acid cycle.

L

label

A fluorescent chemical group or radioactive atom incorporated into a molecule in order to spatially locate the molecule or follow it through a reaction or purification scheme. As a verb, to add such a group or atom to a cell or molecule.

lagging strand

Newly synthesized DNA strand formed at the growing fork as short, discontinuous segments, called Okazaki fragments, which are later joined by DNA ligase. Although overall lagging-strand synthesis occurs in the 3′→5′ direction, each Okazaki fragment is synthesized in the 5′→3′ direction. See also leading strand. (Figure 12-9)

laminin

A component of the extracellular matrix that is found in all basal laminae and has binding sites for cell-surface receptors, collagen, and heparan sulfate proteoglycans. (Figure 22-19)

lamins

A group of intermediate filament proteins that form the fibrous network (nuclear lamina) on the inner surface of the nuclear envelope. (Figure 13-15)

leading strand

Newly synthesized DNA strand formed by continuous synthesis in the 5′n3′ direction at the growing fork. The direction of leading-strand synthesis is the same as movement of the growing fork. See also lagging strand. (Figure 12-9)

lectin

Any protein that binds tightly to specific sugars. Lectins can be used in affinity chromatography to purify glycoproteins or as reagents to detect them in situ.

leucine zipper

Common structural motif in some dimeric eukaryotic transcription factors characterized by a C-terminal coiled-coil dimerization domain and N-terminal DNA-binding domain. (Figure 10-43)

leukemia

Cancer of white blood cells and their precursors.

library

See DNA library.

ligand

Any molecule, other than an enzyme substrate, that binds tightly and specifically to a macromolecule, usually a protein, forming a macromolecule-ligand complex.

ligase

An enzyme that links together the 3′ end of one nucleic acid strand with the 5′ end of another, forming a continuous strand.

linkage

In genetics, the tendency of two different loci on the same chromosome to be inherited together. The closer two loci are, the greater their linkage and the lower the frequency of recombination between them.

lipid

Any organic molecule that is insoluble in water but is soluble in nonpolar organic solvents. Lipids contain covalently linked fatty acids and are found in fat droplets and, as phospholipids, in biomembranes.

lipophilic

See hydrophobic.

liposome

Spherical phospholipid bilayer structure with an aqueous interior that forms in vitro from phospholipids and may contain protein. (Figure 15-4)

locus

In genetics, the specific site of a gene on a chromosome. All the alleles of a particular gene occupy the same locus.

lymphocytes

Two classes of white blood cells that can recognize foreign molecules (antigens) and mediate immune responses. B lymphocytes are responsible for production of antibodies; T lymphocytes are responsible for destroying virus- and bacteria-infected cells, foreign cells, and cancer cells.

lysogenic cycle

Series of events in which a bacterial virus (bacteriophage) enters a host cell and its DNA is incorporated into the host-cell genome in such a way that the virus (the prophage) lays dormant. The association of a prophage with the host-cell genome is called lysogeny. By various mechanisms, the prophage can be activated so that it enters the lytic cycle. (Figure 6-19.)

lysogeny

See lysogenic cycle.

lysosome

Small organelle having an internal pH of 4–5 and containing hydrolytic enzymes.

lytic cycle

Series of events in which a virus enters and replicates within a host cell to produce new viral particles eventually causing lysis of the cell. See also lysogenic cycle. (Figure 6-17)

M

M (mitotic)

phase See cell cycle.

macromolecule

Any large, usually polymeric molecule (e.g., a protein, nucleic acid, polysaccharide) with a molecular mass greater than a few thousand daltons.

malignant

Referring to a tumor or tumor cells that can invade surrounding normal tissue and/or undergo metastasis. See also benign.

MAP kinase

Protein kinase that is activated in response to cell stimulation by many different growth factors and that mediates cellular responses by phosphorylating specific target proteins.

mapping

Various techniques for determining the relative order of genes on a chromosome (genetic map), the absolute position of genes (physical map), or the relative position of restriction sites (restriction map).

meiosis

In eukaryotes, a special type of cell division that occurs during maturation of germ cells; comprises two successive nuclear and cellular divisions with only one round of DNA replication resulting in production of four genetically nonequivalent haploid cells (gametes) from an initial diploid cell. (Figure 8-2)

membrane

See biomembrane.

membrane potential

Voltage difference across a membrane due to the slight excess of positive ions (cations) on one side and negative ions (anions) on the other.

mesenchyme

Embryonic mesoderm tissue in animals from which are formed the connective tissues, blood vessels, and lymphatic vessels.

mesoderm

The middle of the three primary cell layers of the animal embryo, lying between the ectoderm and endoderm; gives rise to the notochord, connective tissue, muscle, blood, and other tissues.

messenger RNA

See mRNA.

metabolism

The sum of the chemical processes that occur in living cells; includes anabolism and catabolism.

metaphase

Mitotic stage at which chromosomes are fully condensed and attached to the mitotic spindle at its equator but have not yet started to segregate toward the opposite spindle poles. (Figure 19-34)

metastasis

Spread of tumor cells from their site of origin and establishment of areas of secondary growth.

Michaelis constant

See Km.

microfilaments

Cytoskeletal fibers (≈7 nm in diameter) that are formed by polymerization of monomeric globular (G) actin; also called actin filaments. Microfilaments play an important role in muscle contraction, cytokinesis, cell movement, and other cellular functions and structures. (Figure 18-2)

microtubule-associated protein (MAP)

Any protein, including motor proteins, that binds to microtubules in a constant ratio and determines the unique properties of different types of microtubules.

microtubules

Cytoskeletal fibers (24 nm in diameter) that are formed by polymerization of α,β-tubulin monomers and exhibit structural and functional polarity. They are important components of cilia, flagella, the mitotic spindle, and other cellular structures. (Figure 19-2)

microvillus (pl. microvilli)

Small, membrane-covered projection on the surface of an animal cell containing a core of actin filaments. Numerous microvilli are present on the absorptive surface of intestinal epithelial cells, increasing the surface area for transport of nutrients. (Figure 18-10)

mitochondrion (pl. mitochondria)

Large organelle that is surrounded by two phospholipid bilayer membranes, contains DNA, and carries out oxidative phosphorylation, thereby producing most of the ATP in eukaryotic cells. (Figures 5-45 and 16-7)

mitogen

Any extracellular substance, such as a growth factor, that promotes cell proliferation.

mitosis

In eukaryotic cells, the process whereby the nucleus is divided to produce two genetically equivalent daughter nuclei with the diploid number of chromosomes. See also cytokinesis and meiosis. (Figure 19-34)

mitotic apparatus

A specialized temporary structure, present in eukaryotic cells only during mitosis, that captures the chromosomes and then pushes and pulls them to opposite sides of the dividing cell. Consists of a central bilaterally symmetric bundle of microtubules with the overall shape of a football (the mitotic spindle) and two star-shaped tufts of microtubules (the asters), one at each pole of the spindle. (Figure 19-36)

mitotic spindle

See mitotic apparatus.

mobile DNA element

Any DNA sequence that is not present in the same chromosomal location in all individuals of a species.

monoclonal antibody

Antibody produced by the progeny of a single B cell and thus a homogeneous protein exhibiting a single antigen specificity. Experimentally, it is produced by use of a hybridoma. (Figure 6-10)

monomer

Any small molecule that can be linked with others of the same type to form a polymer. Examples include amino acids, nucleotides, and monosaccharides.

monomeric

For proteins, consisting of a single polypeptide chain.

monosaccharide

Any simple sugar with the formula (CH2O)n where n = 3 – 7.

morphogen

A molecule that specifies cell identity during development as a function of its concentration.

motif

In proteins, a structural unit exhibiting a particular three-dimensional architecture that is found in a variety of proteins and usually is associated with a particular function. (Figure 3-9)

motor protein

Any member of a special class of enzymes that use energy from ATP hydrolysis to walk or slide along a microfilament (myosin) or a microtubule (dynein and kinesin).

MPF (mitosis-promoting factor)

A heterodimeric protein, composed of a cyclin and cyclin-dependent kinase (Cdk), that triggers entrance of a cell into mitosis by inducing chromatin condensation and nuclear-envelope breakdown; originally called maturation-promoting factor.

mRNA (messenger RNA)

Any RNA that specifies the order of amino acids in a protein. It is produced by transcription of DNA by RNA polymerase and, in RNA viruses, by transcription of viral RNA. In eukaryotes, the initial RNA product (primary transcript) undergoes processing to yield functional mRNA, which is transported to the cytoplasm. See also translation.

MTOC (microtubule-organizing center)

General term for any structure (e.g., the centrosome) that organizes microtubules in nonmitotic (interphase) cells. (Figure 19-5)

multiadhesive matrix proteins

Group of long flexible proteins that bind to other components of the extracellular matrix (collagen, polysaccharides) and to cell-surface receptors, thereby cross-linking the matrix to the cell membrane.

multimeric

For proteins, containing several polypeptide chains (or subunits).

mutagen

A chemical or physical agent that induces mutations.

mutation

In genetics, a permanent, heritable change in the nucleotide sequence of a chromosome, usually in a single gene; commonly leads to a change in or loss of the normal function of the gene product.

myelin sheath

Stacked specialized cell membrane that forms an insulating layer around vertebrate axons and increases the speed of impulse conduction. (Figures 21-15 and 21-16)

myofibril

Long, highly organized bundle of actin and myosin filaments and other proteins that constitute the basic structural unit of muscle cells (myofibers) (Figure 22-26)

myosin

One of a family of motor proteins with a globular head region and coiled-coil tail region that has actin-stimulated ATPase activity; drives movement along actin filaments during muscle contraction and cytokinesis (myosin II) and mediates vesicle translocation (myosins I and V). (Figure 18-20)

N

NAD+ (nicotinic adenine dinucleotide)

A widely used coenzyme that participates in oxidation reactions by accepting two electrons from a donor molecule and one H+ from the solution. The reduced form, NADH, transfers electrons to carriers that function in oxidative phosphorylation. (Figure 16-4)

NADP+ (nicotinic adenine dinucleotide phosphate)

Phosphorylated form of NAD+, which is used extensively as an electron carrier in biosynthetic pathways and during photosynthesis.

Nernst equation

Mathematical expression that defines the electric potential E across a membrane as directly proportional to the logarithm of the ratio of the ion concentrations on either side of the membrane and inversely proportional to the valency of the ions.

neuron (nerve cell)

Any of the impulse-conducting cells of the ner-vous system. A typical neuron contains a cell body; several short, branched processes (dendrites); and one long process (axon). (Figure 21-1)

neuropeptide

A peptide secreted by neurons that functions as a signaling molecule either at a synapse or elsewhere. These molecules have diverse, often long-lived effects in contrast to neurotransmitters.

neurotransmitter

Extracellular signaling molecule that is released by the presynaptic neuron at a chemical synapse and relays the signal to the postsynaptic cell. The response elicited by a neurotransmitter, either excitatory or inhibitory, is determined by its receptor on the postsynaptic cell. Examples include acetylcholine, dopamine, GABA (γ-aminobutyric acid), and serotonin. (Figure 21-28)

noncovalent bond

Any relatively weak chemical bond that does not involve an intimate sharing of electrons. Multiple noncovalent bonds often stabilize the conformation of macromolecules and mediate highly specific interactions between molecules.

nonpolar

Referring to a molecule or structure that lacks any net electric charge or asymmetric distribution of positive and negative charges. Nonpolar molecules generally are insoluble in water.

Northern blotting

Technique for detecting specific RNAs separated by electrophoresis by hybridization to a labeled DNA probe. See also Southern blotting.

nuclear envelope

Double-membrane structure surrounding the nucleus; the outer membrane is continuous with the endoplasmic reticulum and the two membranes are perforated by nuclear pores. (Figures 5-42 and 5-50)

nuclear lamina

Fibrous network on the inner surface of the inner nuclear membrane composed of lamin filaments. (Figure 13-15)

nuclear pore complex (NPC)

Large, multiprotein structure in the nuclear envelope through which ions and small molecules can diffuse and which mediates the active transport of ribonucleoproteins and large proteins between the nucleus and cytoplasm. (Figure 11-28)

nuclear receptor

General term for intracellular receptors that bind lipid-soluble hormones (e.g., steroid hormones); also called steroid receptor superfamily. Following ligand binding, the hormonereceptor complex translocates to the nucleus and functions as a transcription factor. (Figure 10-67)

nucleic acid

A polymer of nucleotides linked by phosphodiester bonds. DNA and RNA are the primary nucleic acids in cells.

nucleocapsid

A viral capsid plus the enclosed nucleic acid.

nucleolus

Large structure in the nucleus of eukaryotic cells where rRNA synthesis and processing occurs and ribosome subunits are assembled.

nucleoside

A small molecule composed of a purine or pyrimidine base linked to a pentose (either ribose or deoxyribose). (Table 4-1)

nucleosome

Small structural unit of chromatin consisting of a disk-shaped core of histone proteins around which a ≈146-bp segment of DNA is wrapped. (Figure 9-31)

nucleotide

A nucleoside with one or more phosphate groups linked via an ester bond to the sugar moiety. DNA and RNA are polymers of nucleotides. (Figure 4-1a and Table 4-1)

nucleus

Large membrane-bounded organelle in eukaryotic cells that contains DNA organized into chromosomes; synthesis and processing of RNA and ribosome assembly occur in the nucleus.

O

Okazaki fragments

Short (<1000 bases), single-stranded DNA fragments that are formed during synthesis of the lagging strand in DNA replication and are rapidly joined by DNA ligase to form a continuous DNA strand. (Figure 12-9)

oncogene

A gene whose product is involved either in transforming cells in culture or in inducing cancer in animals. Most oncogenes are mutant forms of normal genes (proto-oncogenes) involved in the control of cell growth or division.

oocyte

Developing egg cell.

operator

Short DNA sequence in a bacterial or viral genome that binds a repressor protein and controls transcription of an adjacent gene. (Figure 10-2)

operon

In bacterial DNA, a cluster of contiguous genes transcribed from one promoter that gives rise to a polycistronic mRNA.

organelle

Any membrane-limited structure found in the cytoplasm of eukaryotic cells.

osmosis

Net movement of water across a semipermeable membrane from a solution of lesser to one of greater solute concentration. The membrane must be permeable to water but not to solute molecules.

osmotic pressure

Hydrostatic pressure that must be applied to the more concentrated solution to stop the net flow of water across a semipermeable membrane separating solutions of different concentrations. (Figure 15-30)

oxidation

Loss of electrons from an atom or molecule as occurs when hydrogen is removed from a molecule or oxygen is added. The opposite of reduction.

oxidation potential

The voltage change when an atom or molecule loses an electron.

oxidative phosphorylation

The phosphorylation of ADP to form ATP driven by the transfer of electrons to oxygen (O2) in bacteria and mitochondria. This process involves generation of a proton-motive force during electron transport, and its subsequent use to power ATP synthesis. (Figure 16-9)

P

passive (simple)

diffusion Net movement of a molecule across a membrane down its concentration gradient at a rate proportional to the gradient and the permeability of the membrane.

patch clamping

Technique for determining ion flow through a single ion channel or across the membrane of an entire cell by use of a micropipette whose tip is applied to a small patch of the cell membrane. (Figures 21-19 and 21-20)

PCR (polymerase chain reaction)

Technique for amplifying a specific DNA segment in a complex mixture by multiple cycles of DNA synthesis from short oligonucleotide primers followed by brief heat treatment to separate the complementary strands. (Figure 7-38)

pentose

A five-carbon monosaccharide. The pentoses ribose and deoxyribose are present in RNA and DNA, respectively.

peptide

A small polymer usually containing fewer than 30 amino acids connected by peptide bonds.

peptide bond

Covalent bond that links adjacent amino acid residues in proteins; formed by a condensation reaction between the amino group of one amino acid and the carboxyl group of another with release of a water molecule. (Figure 3-3)

peripheral membrane protein

Any protein that associates with the cytosolic or exoplasmic face of a membrane but does not enter the hydrophobic core of the phospholipid bilayer; also called extrinsic protein. See also integral membrane protein. (Figure 3-32)

peroxisome

Small organelle in eukaryotic cells whose functions include degradation of fatty acids and amino acids by means of reactions that generate hydrogen peroxide, which is converted to water and oxygen by catalase.

pH

A measure of the acidity or alkalinity of a solution defined as the negative logarithm of the hydrogen ion concentration in moles per liter: pH=−log [H+]. Neutrality is equivalent to a pH of 7; values below this are acidic and those above are alkaline. (Table 2-3)

phage

See bacteriophage.

phagocytosis

Process by which relatively large particles (e.g., bacterial cells) are internalized by certain eukaryotic cells.

phenotype

The observable characteristics of a cell or organism as distinct from its genotype.

pheromone

A signaling molecule released by an individual that can alter the behavior or gene expression of other individuals of the same species. The yeast α and a mating-type factors are well-studied examples.

phosphatase

An enzyme that removes a phosphate group from a substrate by hydrolysis. Phosphoprotein phosphatases act with protein kinases to control the activity of many cellular proteins.

phosphoanhydride bond

A type of high-energy bond formed between two phosphate groups, such as the γ and β phosphates and the β and α phosphates in ATP. (Figure 2-24)

phosphodiester bond

A covalent bond in which two hydroxyl groups form ester linkages to the same phosphate group; joins adjacent nucleotides in DNA and RNA.

phosphoinositides

A family of membrane-bound lipids containing phosphorylated inositol derivatives that are important in signal-transduction pathways in eukaryotic cells. (Figure 20-29)

phospholipid bilayer

A symmetrical two-layer structure, found in all biomembranes, in which the polar head groups of phospholipids are exposed to the aqueous medium, while the nonpolar hydrocarbon chains of the fatty acids are in the center. (Figure 5-30)

phospholipids

The major class of lipids present in biomembranes, usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, with the phosphate esterified to one of various polar groups. (Figure 5-27)

photosynthesis

Complex series of reactions occurring in some bacteria and plant chloroplasts whereby light energy is used to generate carbohydrates from CO2, usually with the consumption of H2O and evolution of O2.

pI

See isoelectric point.

pinocytosis

The nonspecific uptake of small droplets of extracellular fluid into endocytic vesicles.

plaque assay

Technique for determining the number of infectious viral particles in a sample by culturing a diluted sample on a layer of susceptible host cells and then counting the clear areas of lysed cells (plaques) that develop. (Figure 6-14)

plasma membrane

The membrane surrounding a cell that separates the cell from its external environment, consisting of a phospholipid bilayer and associated proteins. (Figure 3-32)

plasmid

Small, circular extrachromosomal DNA molecule capable of autonomous replication in a cell. Commonly used as a cloning vector.

plasmodesmata (sing. plasmodesma)

Tubelike cell junctions that interconnect the cytoplasm of adjacent plant cells and are functionally analogous to gap junctions in animal cells. (Figure 22-36)

point mutation

Change of a single nucleotide in DNA, especially in a region coding for protein; can result in formation of a codon specifying a different amino acid or a stop codon, or a shift in the reading frame. (Figure 8-4)

polar

Referring to a molecule or structure with a net electric charge or asymmetric distribution of positive and negative charges. Polar molecules are usually soluble in water.

polarity

Presence of functional and/or structural differences in distinct regions of a cell or cellular component.

polymer

Any large molecule composed of multiple identical or similar units (monomers) linked by covalent bonds.

polymerase chain reaction

See PCR.

polypeptide

Linear polymer of amino acids connected by peptide bonds. Proteins are large polypeptides, and the two terms commonly are used interchangeably.

polyribosome

A complex containing several ribosomes all translating a single messenger RNA; also called polysome.

polysaccharide

Linear or branched polymer of monosaccharides, linked by glycosidic bonds, usually containing more than 15 residues. Examples include glycogen, cellulose, and glycosaminoglycans.

positional cloning

Isolation and cloning of the normal form of a mutation-defined gene (i.e., a gene identified by genetic analysis of mutants).

pre-mRNA

Precursor messenger RNA; the primary transcript and intermediates in RNA processing.

pre-rRNA

Large precursor ribosomal RNA that is synthesized in the nucleolus of eukaryotic cells and processed to yield three of the four RNAs present in ribosomes. (Figure 11-50)

primary structure

In proteins, the linear arrangement (sequence) of amino acids and the location of covalent (mostly disulfide) bonds within a polypeptide chain.

primary transcript

Initial RNA product, containing introns and exons, produced by transcription of DNA. Many primary transcripts must undergo RNA processing to form the physiologically active RNA species.

primase

A specialized RNA polymerase that synthesizes short stretches of RNA used as primers for DNA synthesis.

primer

A short nucleic acid sequence containing a free 3′ hydroxyl group that forms base pairs with a complementary template strand and functions as the starting point for addition of nucleotides to copy the template strand.

probe

Defined RNA or DNA fragment, radioactively or chemically labeled, that is used to detect specific nucleic acid sequences by hybridization.

prokaryotes

Class of organisms, including the eubacteria and archaea, that lack a true membrane-limited nucleus and other organelles. See also eukaryotes.

promoter

DNA sequence that determines the site of transcription initiation for an RNA polymerase.

promoter-proximal element

Any regulatory sequence in eukaryotic DNA that is located within ≈200 base pairs of the transcription start site. Transcription of many genes is controlled by multiple promoter-proximal elements. (Figure 10-34)

prophase

Earliest stage in mitosis during which the chromosomes condense and the centrioles begin moving toward the spindle poles. (Figure 19-34)

prosthetic group

A nonpeptide organic molecule or metal ion that binds tightly and specifically with a protein and is required for its activity, such as heme in hemoglobin. See also coenzyme.

proteasome

Large multifunctional protease complex in the cytosol that degrades intracellular proteins marked for destruction by attachment of multiple ubiquitin molecules. (Figure 3-18)

protein

A linear polymer of amino acids linked together in a specific sequence and usually containing more than 50 residues. Proteins form the key structural elements in cells and participate in nearly all cellular activities.

proteoglycans

A group of glycoproteins that contain a core protein to which is attached one or more glycosaminoglycans. They are found in nearly all extracellular matrices, and some are attached to the plasma membrane. (Figures 22-26 and 22-27)

proton-motive force

The energy equivalent of the proton (H+) concentration gradient and electric potential gradient across a membrane; used to drive ATP synthesis by ATP synthase, transport of molecules against their concentration gradient, and movement of bacterial flagella.

proto-oncogene

A normal cellular gene that encodes a protein usually involved in regulation of cell growth or proliferation and that can be mutated into a cancer-promoting oncogene, either by changing the protein-coding segment or by altering its expression.

pulse-chase

A type of experiment in which a radioactive small molecule is added to a cell for a brief period (the pulse) and then is replaced with an excess of the unlabeled form of same small molecule (the chase). Used to detect changes in the cellular location of a molecule or its metabolic fate over time.

pump

Any transmembrane protein that mediates the active transport of an ion or small molecule across a biomembrane. (Table 15-2)

purines

A class of nitrogenous compounds containing two fused heterocyclic rings. Two purines, adenine and guanine, commonly are found in DNA and RNA. (Figure 4-2)

pyrimidines

A class of nitrogenous compounds containing one heterocyclic ring. Two pyrimidines, cytosine and thymine, commonly are found in DNA; in RNA, uracil replaces thymine. (Figure 4-2)

Q

quaternary structure

The number and relative positions of the polypeptide chains in multisubunit proteins.

quiescent

Referring to a cell that has exited the cell cycle and is in the G0 state.

R

radioisotope

Unstable form of an atom that emits radiation as it decays. Several radioisotopes are commonly used experimentally as labels in biological molecules.

Ras protein

A monomeric GTP-binding protein that functions in intracellular signaling pathways and is activated by ligand binding to receptor tyrosine kinases and other cell-surface receptors. See also GTPase superfamily. (Figure 20-23)

reading frame

The sequence of nucleotide triplets (codons) that runs from a specific translation start codon in a mRNA to a stop codon. Some mRNAs can be translated into different polypeptides by reading in two different reading frames. (Figure 4-21)

receptor

Any protein that binds a specific extracellular signaling molecule (ligand) and then initiates a cellular response. Receptors for steroid hormones, which diffuse across the plasma membrane, are located within the cell; receptors for water-soluble hormones, peptide growth factors, and neurotransmitters are located in the plasma membrane with their ligand-binding domain exposed to the external medium.

receptor tyrosine kinase (RTK)

Member of an important class of cell-surface receptors whose cytosolic domain has tyrosine-specific protein kinase activity. Ligand binding activates this kinase activity and initiates intracellular signaling pathways. (Figure 20-23)

recessive

In genetics, referring to that allele of a gene that is not expressed in the phenotype when the dominant allele is present. Also refers to the phenotype of an individual (homozygote) carrying two recessive alleles. (Figure 8-1)

recombinant DNA

Any DNA molecule formed by joining DNA fragments from different sources. Commonly produced by cutting DNA molecules with restriction enzymes and then joining the resulting fragments from different sources with DNA ligase.

recombination

Any process in which chromosomes or DNA molecules are cleaved and the fragments are rejoined to give new combinations. Occurs naturally in cells as the result of the exchange (crossing over) of DNA sequences on maternal and paternal chromatids during meiosis; also is carried out in vitro with purified DNA and enzymes.

reduction

Gain of electrons by an atom or molecule as occurs when hydrogen is added to a molecule or oxygen is removed. The opposite of oxidation.

reduction potential

The voltage change when an atom or molecule gains an electron.

replication fork

See growing fork.

replication origin

Unique DNA segments present in an organism’s genome at which DNA replication begins. Eukaryotic chromosomes contain multiple origins, whereas bacterial chromosomes and plasmids often contain just one.

replicon

Region of DNA served by one replication origin.

resolution

The minimum distance that can be distinguished by an optical apparatus; also called resolving power.

respiration

General term for any cellular process involving the uptake of O2 coupled to production of CO2.

restriction enzyme (endonuclease)

Any enzyme that recognizes and cleaves a specific short sequence, the restriction site, in double-stranded DNA molecules. These enzymes are widespread in bacteria and are used extensively in recombinant DNA technology. (Table 7-1 and Figure 7-5)

restriction fragment

A defined DNA fragment resulting from cleavage with a particular restriction enzyme. These fragments are used in the production of recombinant DNA molecules and DNA cloning.

restriction point

The point in late G1 of the cell cycle at which mammalian cells become committed to entering the S phase and completing the cycle even in the absence of growth factors.

retrotransposon

Type of eukaryotic mobile DNA element whose movement in the genome is mediated by an RNA intermediate and involves a reverse transcription step. See also transposon.

retrovirus

A type of eukaryotic virus containing an RNA genome that replicates in cells by first making a DNA copy of the RNA. This proviral DNA is inserted into cellular chromosomal DNA, and gives rise to further genomic RNA as well as the mRNAs for viral proteins. (Figure 6-22)

reverse transcriptase

Enzyme found in retroviruses that catalyzes synthesis of a double-stranded DNA from a single-stranded RNA template. (Figure 9-16)

ribosomal RNA

See rRNA.

ribosome

A large complex comprising several different rRNA molecules and more than 50 proteins, organized into a large subunit and small subunit; the site of protein synthesis. (Figures 4-32 and 4-34)

ribozyme

An RNA molecule or segment with catalytic activity.

RNA (ribonucleic acid)

Linear, single-stranded polymer, composed of ribose nucleotides, that is synthesized by transcription of DNA or by copying of RNA. The three types of cellular RNA — mRNA, rRNA, and tRNA — play different roles in protein synthesis.

RNA editing

Unusual type of RNA processing in which the sequence of a pre-mRNA is altered.

RNA polymerase

An enzyme that copies one strand of DNA or RNA (the template strand) to make the complementary RNA strand using as substrates ribonucleoside triphosphates.

RNA processing

Various modifications that occur to many but not all primary transcripts to yield functional RNA molecules.

RNA splicing

A process that results in removal of introns and joining of exons in RNAs. See also spliceosome. (Figure 11-16)

rRNA (ribosomal RNA)

Any one of several large RNA molecules that are structural and functional components of ribosomes. Often designated by their sedimentation coefficient: 28S, 18S, 5.8S, and 5S rRNA in higher eukaryotes.

S

S (synthesis) phase

See cell cycle.

sarcoma

A malignant tumor derived from connective tissue.

sarcomere

Repeating unit of a myofibril in striated muscle that extends from one Z disk to an adjacent one and shortens during contraction. (Figure 18-27)

sarcoplasmic reticulum

Network of membranes that surrounds each myofibril in a muscle cell and sequesters Ca2 ions. Stimulation of a muscle cell induces release of Ca2 ions into the cytosol, triggering coordinated contraction along the length of the cell. (Figure 18-31)

Schwann cell

Type of glial cell that forms the myelin sheath around axons in the peripheral nervous system.

second messenger

An intracellular signaling molecule whose concentration increases (or decreases) in response to binding of an extracellular ligand to a cell-surface receptor. Examples include cAMP, Ca2, diacylglycerol (DAG), and inositol 1,4,5-trisphosphate (IP3). (Figure 20-4)

secondary structure

In proteins, local folding of a polypeptide chain into regular structures including the α helix, β sheet, and U-shaped turns and loops.

secretory vesicle

Small membrane-bound organelle containing molecules destined to be released from the cell.

segregation

In genetics, the process that distributes an equal complement of chromosomes to daughter cells during mitosis and meiosis.

seven-spanning receptor

See G protein–coupled receptor (GPCR).

signal sequence

A relatively short amino acid sequence that directs a protein to a specific location within the cell; also called signal peptide and targeting sequence.

signal transduction

Conversion of a signal from one physical or chemical form into another. In cell biology commonly refers to the sequential process initiated by binding of an extracellular signal to a receptor and culminating in one or more specific cellular responses.

signaling molecule

General term for any extracellular or intracellular molecule involved in mediating the response of a cell to its external environment or other cells.

silencer sequence

A sequence in eukaryotic DNA that promotes formation of condensed chromatin structures in a localized region, thereby blocking access of proteins required for transcription of genes within several hundred base pairs of the silencer sequence.

simple-sequence DNA

Short, tandemly repeated sequences that are found in centromeres and telomeres as well as at other chromosomal locations and are not transcribed.

somatic cell

Any plant or animal cell other than a germ cell or germ-cell precursor.

Southern blotting

Technique for detecting specific DNA sequences separated by electrophoresis by hybridization to a labeled nucleic acid probe. (Figure 7-32)

SPF (S phasepromoting factor)

A heterodimeric protein, composed of a cyclin and cyclin-dependent kinase (Cdk), that triggers entrance of a cell into the S phase of the cell cycle by inducing expression of proteins required for DNA replication and passage through the S phase.

spliceosome

Large ribonucleoprotein complex that assembles on a pre-mRNA and carries out RNA splicing. (Figures 11-18 and 11-19)

starch

A very long, branched polysaccharide, composed exclusively of glucose units, that is the primary storage carbohydrate in plant cells.

start

A point in the G1 stage of the yeast cell cycle that controls entry of cells into the S phase. Passage of a cell through start commits a cell to proceed through the remainder of the cell cycle.

stem cell

A self-renewing cell that divides to give rise to a cell with an identical developmental potential and/or one with a more restricted developmental potential.

stereoisomers

Two compounds with identical molecular formulas whose atoms are linked in the same order but in different spatial arrangements. In optical isomers, designated d and l, the atoms bonded to an asymmetric carbon atom are arranged in a mirror-image fashion. Geometric isomers include the cis and trans forms of molecules containing a double bond.

steroid

A group of four-ring hydrocarbons including cholesterol and related compounds. Many important hormones (e.g., estrogen and progesterone) are steroids.

substrate

Molecule that undergoes a change in a reaction catalyzed by an enzyme.

substrate-level phosphorylation

Formation of ATP from ADP and Pi catalyzed by cytosolic enzymes in reactions that do not depend on a proton-motive force.

sulfhydryl group (SH)

A hydrogen atom covalently bonded to a sulfur atom; also called a thiol group. A substituent group present in the amino acid cysteine and other molecules.

supercoils, DNA

Regions of DNA in which the double helix is twisted on itself.

suppressor mutation

A mutation that reverses the phenotypic effect of a second mutation. Suppressor mutations are frequently used to identify genes encoding interacting proteins.

symport

A type of cotransport in which a membrane protein (symporter) transports two different molecules or ions across a cell membrane in the same direction. See also antiport.

synapse

Specialized region between an axon terminus of a neuron and an adjacent neuron or other excitable cell (e.g., muscle cell) across which impulses are transmitted. At a chemical synapse, the impulse is conducted by a neurotransmitter; at an electric synapse, impulse transmission occurs via gap junctions connecting the cyto-plasms of the pre- and postsynaptic cells. (Figures 21-4 and 21-35)

syncytium

A multinucleated mass of cytoplasm enclosed by a single plasma membrane.

T

TATA box

A conserved sequence in the promoter of many eukaryotic protein-coding genes where the transcription-initiation complex assembles (Figure 10-50)

telomere

End region of a eukaryotic chromosome containing characteristic telomeric (TEL) sequences that are replicated by a special process, thereby counteracting the tendency of a chromosome to be shortened during each round of replication. (Figure 12-13)

telophase

Final mitotic stage during which the nuclear-envelope re-forms around the two sets of separated chromosomes; the chromosomes decondense; and division of the cytoplasm (cytokinesis) is completed. (Figure 19-34)

temperature-sensitive (ts) mutant

A cell or organism with a mutant gene encoding an altered protein that functions normally at one temperature (the permissive temperature) but is nonfunctional at another temperature (the nonpermissive temperature).

template

A molecular “mold” that dictates the structure of another molecule; most commonly, one strand of DNA that directs synthesis of a complementary DNA strand during DNA replication or of an RNA during transcription.

termination factor

One of several proteins that acts to terminate protein synthesis by recognizing a stop codon in mRNA and causing release of the ribosomal subunits. (Figure 4-40)

tertiary structure

In proteins, overall three-dimensional form of a polypeptide chain, which is stabilized by multiple noncovalent interactions between side chains.

thylakoids

Flattened membranous sacs in a chloroplast that are arranged in stacks forming the grana and contain the photosynthetic pigments. (Figure 16-34)

tight junction

Ribbon-like bands connecting adjacent epithelial cells that prevent leakage of fluid across the cell layer. (Figure 15-28)

topoisomerase

Class of enzymes that control the number and topology of supercoils in DNA. Type I enzymes cut one DNA strand, rotate it about the other, and reseal the ends. Type II enzymes cut and reseal both DNA strands.

trans-acting

Referring to DNA sequences encoding diffusible proteins (e.g., transcription activators and repressors) that control genes on the same or different chromosomes. See also cis-acting.

transcript

See primary transcript.

transcription

Process whereby one strand of a DNA molecule is used as a template for synthesis of a complementary RNA by RNA polymerase. (Figure 4-15)

transcription factor (TF)

General term for any protein, other than RNA polymerase, required to initiate or regulate transcription in eukaryotic cells. General factors, required for transcription of all genes, participate in formation of the transcription-initiation complex near the start site. Specific factors stimulate (or repress) transcription of particular genes by binding to their regulatory sequences.

transcription unit

A region in DNA, bounded by an initiation (start) site and termination site, that is transcribed into a single primary transcript.

transcription-control region

Collective term for all the cis-acting DNA regulatory sequences that regulate transcription of a particular gene.

transfection

Experimental introduction of foreign DNA into cells in culture, usually followed by expression of genes in the introduced DNA.

transfer RNA

See tRNA.

transformation

Permanent, heritable alteration in a cell resulting from the uptake and incorporation of a foreign DNA. Also, conversion of a “normal” mammalian cell into a cell with cancer-like properties usually induced by treatment with a virus or other cancer-causing agent.

transgene

A cloned gene that is introduced and stably incorporated into a plant or animal and is passed on to successive generations.

transgenic

Referring to any plant or animal carrying a transgene.

translation

The ribosome-mediated production of a polypeptide whose amino acid sequence is specified by the nucleotide sequence in an mRNA.

translocon

Multiprotein complex in the membrane of the rough endoplasmic reticulum through which a nascent secretory protein enters the ER lumen as it is being synthesized. (Figure 17-16)

transport vesicles

Small membrane-bounded organelles that carry secretory and membrane proteins in both directions between the rough endoplasmic reticulum (ER) and the Golgi complex, and from the Golgi to the cell surface or other destination. Form by budding off from the donor organelle and release their contents by fusion with the target membrane.

transposon

A relatively long mobile DNA element, in prokaryotes and eukaryotes, that moves in the genome by a mechanism involving DNA synthesis and transposition. See also retrotransposon.

tricarboxylic acid cycle

See citric acid cycle.

tRNA (transfer RNA)

A group of small RNA molecules that function as amino acid donors during protein synthesis. Each tRNA becomes covalently linked to a particular amino acid, forming an aminoacyl-tRNA. (Figure 4-26)

tubulin

A family of globular cytoskeletal proteins that polymerize to form microtubules.

tumor

A mass of cells, generally derived from a single cell, that is not controlled by normal regulators of cell growth.

tumor-suppressor gene

Any gene whose encoded protein directly or indirectly inhibits progression through the cell cycle and in which a loss-of-function mutation is oncogenic. Inheritance of a single mutant allele of many tumor-suppressor genes (e.g., RB, APC, and BRCA1) greatly increases the risk for developing certain types of cancer.

U

ubiquitin

A small, highly conserved protein that becomes covalently linked to lysine residues in other intracellular proteins. Proteins to which a chain of ubiquitin molecules is added usually are degraded in a proteasome.

uncoupler

An agent that dissipates the proton-motive force across the inner mitochondrial membrane and thylakoid membrane of chloroplasts, thereby inhibiting ATP synthesis.

upstream

The direction on a DNA opposite to the direction RNA polymerase moves during transcription. By convention, the +1 position in a gene is the first transcribed base; nucleotides upstream from the +1 position are designated −1, −2, etc. See also downstream.

upstream activating sequence (UAS)

Any protein-binding regulatory sequence in the DNA of yeast and other simple eukaryotes that is necessary for maximal gene expression; equivalent to an enhancer or promoter-proximal element in higher eukaryotes. (Figure 10-34)

V

van der Waals interaction

A weak noncovalent attraction due to small, transient asymmetric electron distributions around atoms (dipoles).

vector

In cell biology, an agent that can carry DNA into a cell or organism. See also cloning vector and expression vector.

ventral

Relating to the front of an animal or lower surface of a structure (e.g., wing or leaf).

virion

An individual viral particle.

virus

A small parasite consisting of nucleic acid (RNA or DNA) enclosed in a protein coat that can replicate only in a susceptible host cell; widely used in cell biology research. (Table 6-3)

Vmax

Parameter that describes the maximal velocity of an enzyme-catalyzed reaction or other process such as protein-mediated transport of molecules across a membrane. (Figure 3-26)

W

Western blotting

Technique for detecting specific proteins separated by electrophoresis by use of labeled antibodies. (Figure 3-44)

wild type

Normal, nonmutant form of a macromolecule, cell, or organism.

X

x-ray crystallography

Most commonly used technique for determining the three-dimensional structure of macromolecules (particularly proteins and nucleic acids) by passing x-rays through a crystal of the purified molecules and analyzing the diffraction pattern of discrete spots that results.

Z

zinc finger

Several types of conserved DNA-binding motifs composed of protein domains folded around a zinc ion; present in several types of eukaryotic transcription factors. (Figure 10-41)

zygote

A fertilized egg; diploid cell resulting from fusion of a male and female gamete.

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