E

E2F:
A family of transcription factors that regulate the expression of genes involved in cell cycle progression and DNA replication.

ecdysone:
An insect steroid hormone that triggers metamorphosis.

ectoderm:
The outer germ layer; gives rise to tissues that include the skin and nervous system.

eicosanoid:
A class of lipids, including prostaglandins, prostacyclins, thromboxanes, and leukotrienes, that act in autocrine and paracrine signaling.

elaioplasts:
Plastids that store lipids.

elastic fibers:
Protein fibers that are present in the extracellular matrix of connective tissues in organs that stretch and then return to their original shape.

elastin:
The principal component of elastic fibers.

electrical synapse:
Specialized assemblies of gap junctions that allow the rapid passage of ions between nerve cells.

electrochemical gradient:
A difference in chemical concentration and electric potential across a membrane.

electron microscopy:
A type of microscopy that uses an electron beam to form an image. In transmission electron microscopy, a beam of electrons is passed through a specimen stained with heavy metals. In scanning electron microscopy, electrons scattered from the surface of a specimen are analyzed to generate a three-dimensional image.

electron tomography:
A method used to generate three-dimensional images by computer analysis of mul­-
ti­ple two-dimensional images obtained by electron microscopy.

electron transport chain:
A series of carriers through which electrons are transported from a higher to a lower energy state.

electrophoretic-mobility shift assay:
An assay for the binding of a protein to a specific DNA sequence.

electroporation:
The introduction of DNA into cells by exposure to a brief electric pulse.

Elk-1:
A transcription factor that is activated by ERK phosphorylation and induces expression of immediate-early genes.

elongation factor:
A protein involved in the elongation phase of transcription or translation.

embryonic stem (ES) cells:
Stem cells cultured from early embryos.

endocrine signaling:
A type of cell-cell signaling in which endocrine cells secrete hormones that are carried by the circulation to distant target cells.

endocytosis:
The uptake of extracellular material in vesicles formed from the plasma membrane.

endoderm:
The inner germ layer; gives rise to internal organs.

endoplasmic reticulum (ER):
An extensive network of membrane-enclosed tubules and sacs involved in protein sorting and processing as well as in lipid synthesis.

endorphin:
A neuropeptide that acts as a natural analgesic.

endosome:
A vesicular compartment involved in the sorting and transport to lysosomes of material taken up by endocytosis.

endosymbiosis:
A symbiotic relationship in which one cell resides within a larger cell.

enhancer:
A transcriptional regulatory sequence that can be located at a site distant from the promoter.

enkephalin:
A neuropeptide that acts as a natural analgesic.

entactin:
An extracellular matrix protein that interacts with laminins and type IV collagen in basal laminae.

enzymes:
Proteins or RNAs that catalyze biological reactions.

epidermal cells:
Cells forming a protective layer on the surfaces of plants and animals.

epidermal growth factor (EGF):
A growth factor that stimulates cell proliferation.

epithelial cells:
Cells forming sheets (epithelial tissue) that cover the surface of the body and line internal organs.

Epstein-Barr virus:
A human herpesvirus that causes B-cell lymphomas.

equilibrium centrifugation:
The separation of particles on the basis of density by centrifugation to equilibrium in a gradient of a dense substance.

erbA:
A proto-oncogene that encodes thyroid hormone receptor.

ErbA:
The product of the erbA proto-oncogene. The thyroid hormone receptor.

erbB-2:
A proto-oncogene encoding a receptor protein-tyrosine kinase that is frequently amplified in breast and ovarian carcinomas.

ERK:
A member of the MAP kinase family that plays a central role in growth factor-induced cell proliferation.

ERM proteins:
A family of proteins that link actin filaments to the plasma membranes of many kinds of cells.

erythrocytes:
Red blood cells.

Escherichia coli (E. coli):
A species of bacteria that has been extensively used as a model system for molecular biology.

estrogen:
A steroid hormone produced by the ovaries.

ethylene:
A plant hormone responsible for fruit ripening.

etioplast:
An intermediate stage of chloroplast development in which chlorophyll has not been synthesized.

eubacteria:
One of two major groups of prokaryotes, including most common species of bacteria.

euchromatin:
Decondensed, transcriptionally active interphase chromatin.

eukaryotic cells:
Cells that have a nuclear envelope, cytoplasmic organelles, and a cytoskeleton.

excinuclease:
The protein complex that excises damaged DNA during nucleotide-excision repair in bacteria.

exocyst:
A protein complex on the plasma membrane at which exocytosis occurs.

exon:
A segment of a gene that contains a coding sequence.

exonuclease:
An enzyme that hydrolyzes DNA molecules in either the 5' to 3' or 3' to 5' direction.

exportin:
A karyopherin that recognizes nuclear export
signals and directs transport from the nucleus to the cytosol.

expression vector:
A vector used to direct expression of a cloned DNA fragment in a host cell.

extracellular matrix:
Secreted proteins and polysaccharides that fill spaces between cells and bind cells and tissues together.

F

facilitated diffusion:
The transport of molecules across a membrane by carrier or channel proteins.

FAK (focal adhesion kinase):
A nonreceptor protein-tyrosine kinase that plays a key role in integrin signaling.

fats:
See triacylglycerols.

fatty acids:
Long hydrocarbon chains usually linked to a carboxyl group (COO-).

feedback inhibition:
A type of allosteric regulation in which the product of a metabolic pathway inhibits the activity of an enzyme involved in its synthesis.

feedback loop:
A regulatory mechanism in which a downstream element of a signaling pathway controls the activity of an upstream component of the pathway.

feedforward relay:
A regulatory mechanism in which one element of a signaling pathway stimulates a downstream component.

fertilization:
The union of a sperm and an egg.

fibroblast:
A cell type found in connective tissue.

fibronectin:
The principal adhesion protein of the extracellular matrix.

filamentous [F] actin:
Actin monomers polymerized into filaments.

filamin:
An actin-binding protein that crosslinks actin filaments into networks.

filopodium:
A thin projection of the plasma membrane supported by actin bundles.

fimbrin:
An actin-bundling protein involved in formation of cell surface projections.

flagellum:
A microtubule-based projection of the plasma membrane that is responsible for cell movement.

flavin adenine dinucleotide (FADH₂):
A coenzyme that functions as an electron carrier in oxidation/reduction reactions.

flow cytometer:
An instrument that measures the fluoresence intensity of individual cells.

fluid mosaic model:
A model of membrane structure in which proteins are inserted in a fluid phospholipid bilayer.

fluid-phase endocytosis:
The nonselective uptake of extracellular fluids during endocytosis.

flippase:
A protein that catalyzes the translocation of lipids across the membrane of the endoplasmic reticulum.

fluorescence-activated cell sorter:
An instrument that sorts individual cells on the basis of their fluorescence intensity.

fluorescence in situ hybridization (FISH):
A method used to localize genes on chromosomes or RNAs within cells using fluorescent probes.

fluorescence microscopy:
Type of microscopy in which molecules are detected based on the emission of flourescent light.

fluorescence recovery after photobleaching (FRAP):
A method used to study the movement of proteins within living cells.

fluorescence resonance energy transfer (FRET):
A method used to study protein interactions within living cells.

focal adhesion:
A site of attachment of cells to the extracellular matrix at which integrins are linked to bundles of actin filaments.

focal complex:
A small cluster of integrins binding to the extracellular matrix that initiates the formation of a focal adhesion.

fodrin:
Nonerythroid spectrin.

footprinting:
A method used to identify the sites at which proteins bind to DNA.

formin:
An actin-binding protein that nucleates and polymerizes actin filaments.

Fos:
A transcription factor, encoded by a proto-oncogene, that is induced in response to growth factor stimulation.

freeze fracture:
Method of electron microscopy in which specimens are frozen in liquid nitrogen and then fractured to split the lipid bilayer, revealing the interior faces of cell membranes.

G

γ-tubulin ring complex:
A protein complex that nucleates the formation of microtubules.

G protein:
A family of cell signaling proteins regulated by guanine nucleotide binding.

G protein-coupled receptor:
A receptor characterized by seven membrane-spanning a helices. Ligand binding causes a conformational change that activates a &gamma protein.

G₀:
A quiescent state in which cells remain metabolically active but do not proliferate.

G₁ cyclins (Clns):
Yeast cyclins that control passage through START.

G₁ phase:
The phase of the cell cycle between the end of mitosis and the begining of DNA synthesis.

G₂ phase:
The phase of the cell cycle between the end of S phase and the begining of mitosis.

gap junction:
A plasma membrane channel forming a direct cytoplasmic connection between adjacent cells.

gel electrophoresis:
A method in which molecules are separated based on their migration in an electric field.

gene:
A segment of DNA that encodes a polypeptide chain or an RNA molecule.

gene amplification:
An increase in the number of copies of a gene resulting from the repeated replication of a region of DNA.

gene family:
A group of related genes that have arisen by duplication of a common ancestor.

gene transfer:
The introduction of foreign DNA into a cell.

general transcription factors:
Transcription factors that are part of the general transcription machinery.

genetic code:
The correspondence between nucleotide triplets and amino acids in proteins.

genomic imprinting:
The regulation of genes whose expression depends on whether they are maternally or paternally inherited, apparently controlled by DNA methylation.

genomic library:
A collection of recombinant DNA clones that collectively contain the genome of an organism.

genomics:
The systematic analysis of entire cell genomes.

genotype:
The genetic composition of an organism.

gibberellin:
A plant hormone.

Gibbs free energy (G):
The thermodynamic function that combines the effects of enthalpy and entropy to predict the energetically favorable direction of a chemical reaction.

globular [G] actin:
Monomers of actin that have not been assembled into filaments.

glucocorticoid:
A steroid produced by the adrenal gland that acts to stimulate production of glucose.

gluconeogenesis:
The synthesis of glucose.

glycerol phospholipids:
Phospholipids consisting of two fatty acids bound to a glycerol molecule.

glycocalyx:
A carbohydrate coat covering the cell surface.

glycogen:
A polymer of glucose residues that is the principal storage form of carbohydrates in animals.

glycolipid:
A lipid consisting of two hydrocarbon chains linked to a polar head group containing carbohydrates.

glycolysis:
The anaerobic breakdown of glucose.

glycoprotein:
A protein linked to oligosaccharides.

glycosaminoglycan (GAG):
A gel-forming polysaccharide of the extracellular matrix.

glycosidase:
An enzyme that removes sugar residues from its substrate.

glycosidic bond:
The bond formed between sugar residues in oligosaccharides or polysaccharides.

glycosylation:
The addition of carbohydrates to proteins.

glycosylphosphatidylinositol (GPI) anchor:
Glycolipids containing phosphatidylinositol that anchor proteins to the external face of the plasma membrane.

glycosyltransferase:
An enzyme that adds sugar residues to its substrate.

glyoxylate cycle:
The conversion of fatty acids to carbohydrates in plants.

glyoxysome:
Peroxisomes in which the reactions of the glyoxylate cycle take place.

Golgi complex:
see Golgi apparatus.

Golgi apparatus:
A cytoplasmic organelle involved in the processing and sorting of proteins and lipids. In plant cells, it is also the site of the synthesis of cell wall polysaccharides.

Golgi stack:
The compartments of the Golgi apparatus within which most metabolic animations take place.

granulocytes:
Blood cells that are involved in inflamma­tory reactions.

green fluorescent protein (GFP):
A protein from jellyfish that is commonly used as a marker for fluorescence microscopy.

growth factors:
Polypeptides that control animal cell growth and differentiation.

GTPase-activating proteins:
Proteins that stimulate GTP hydrolysis by the small GTP-binding proteins.

guanine:
A purine that base-pairs with cytosine.

guanine nucleotide exchange factor:
A protein that acts on small GTP-binding proteins to stimulate the exchange of bound GDP for GTP.

guanylyl cyclase:
An enzyme that catalyzes the formation of cyclic GMP from GTP.

guidance complex:
A protein complex that directs proteins to chloroplasts.

H

haploid:
An organism or cell that has one copy of each chromosome.

hard keratin:
A keratin used for production of structures such as hair, nails, and horns.

heat-shock proteins:
A highly conserved group of chaperone proteins expressed in cells exposed to elevated temperatures or other forms of environmental stress.

Hedgehog:
A secreted signaling molecule that stimulates a pathway regulating cell fate during embryonic development.

helicase:
An enzyme that catalyzes the unwinding of DNA.

helix-loop-helix:
A transcription factor DNA-binding domain formed by the dimerization of two polypeptide chains. The dimerization domains of these proteins consist of two helical regions separated by a loop.

helix-turn-helix:
A transcription factor DNA-binding domain in which three or four helical regions contact DNA.

hemicellulose:
A polysaccharide that crosslinks cellulose microfibrils in plant cell walls.

hemidesmosome:
A region of contact between cells and the extracellular matrix at which keratin filaments are attached to integrin.

hepatitis B viruses:
A family of DNA viruses that infect liver cells and can lead to the development of liver cancer.

hepatitis C viruses:
A family of RNA viruses that infect liver cells and can lead to the development of liver cancer.

herpesviruses:
A family of DNA viruses, some members of which induce cancer.

heterochromatin:
Condensed, transcriptionally inactive chromatin.

heterophilic interaction:
An interaction between two different types of cell adhesion molecules.

heterotrimeric G protein:
A guanine nucleotide-binding protein consisting of three subunits.

high-energy bonds:
Chemical bonds that release a large amount of free energy when they are hydrolyzed.

histone acetylation:
The modification of histones by the addition of acetyl groups to specific lysine residues.

histone code:
Combinations of specific histone modifications that are thought to regulate the transcriptional activity of chromatin.

histones:
Proteins that package DNA in eukaryotic chromosomes.

HMGN proteins:
Nonhistone chromosomal proteins associated with decondensed transcriptionally active
chromatin.

Holliday junction:
The central intermediate in recombination, consisting of a crossed-strand structure formed by homologous base pairing between strands of two DNA molecules.

Holliday model:
A molecular model of genetic recombination involving the formation of heteroduplex regions.

homeobox:
Conserved DNA sequences of 180 base pairs that encode homeodomains.

homeodomain:
A type of DNA binding domain found in transcription factors that regulate gene expression during embryonic development.

homologous recombination:
Recombination between segments of DNA with homologous nucleotide sequences.

homophilic interaction:
An interaction between cell adhesion molecules of the same type.

hormones:
Signaling molecules produced by endocrine glands that act on cells at distant body sites.

hydrophilic:
Soluble in water.

hydrophobic:
Not soluble in water.

I

IAP:
Inhibitor of apoptosis. A member of a family of proteins that inhibit apoptosis by interacting with caspases.

IκB:
An inhibitory subunit of NF-κB transcription factors.

immediate-early genes:
A family of genes whose transcription is rapidly induced in response to growth factor stimulation.

immunoblotting:
A method that uses antibodies to detect proteins separated by SDS-polyacrylamide gel electrophoresis.

immunoglobulin:
See antibody.

immunoglobulin (Ig) superfamily:
A family of cell adhesion molecules containing structural domains similar to immunoglobulins.

immunoprecipitation:
The use of antibodies to isolate
proteins.

importin:
A karyopherin that recognizes nuclear localization signals and directs nuclear import.

induced fit:
A model of enzyme action in which the configurations of both the enzyme and the substrate are altered by substrate binding.

in situ hybridization:
The use of radioactive or flourescent probes to detect RNA or DNA sequences in chromosomes or intact cells.

in vitro mutagenesis:
The introduction of mutations into cloned DNA in vitro.

in vitro translation:
Protein synthesis in a cell-free extract.

initiation factor:
A protein that functions in the initiation stage of translation.

inositol 1,4,5-trisphosphate (IP₃):
A second messenger, formed from the hydrolysis of PIP₂, that signals the release of calcium ions from the endoplasmic reticulum.

insulator:
A sequence that divides chromatin into independent domains and prevents an enhancer from acting on a promoter in a separate domain.

integral membrane proteins:
Proteins embedded within the lipid bilayer of cell membranes.

integrin:
A transmembrane protein that mediates the adhesion of cells to the extracellular matrix.

intermediate filament:
A cytoskeletal filament about 10 nm in diameter that provides mechanical strength to cells in tissues. See also keratins and neurofilaments.

interphase:
The period of the cell cycle between mitoses that includes G₁, S, and G₂ phases.

intracellular signal transduction:
A chain of reactions that transmits chemical signals from the cell surface to their intracellular targets.

intron:
A noncoding sequence that interrupts exons in a gene.

ion channel:
A protein that mediates the rapid passage of ions across a membrane by forming open pores through the phospholipid bilayer.

ion pump:
A protein that couples ATP hydrolysis to the transport of ions across a membrane.

J

JAK/STAT pathway:
A signaling pathway in which STAT transcription factors are activated as a result of phosphorylation by members of the JAK family of protein kinases.

Janus kinase (JAK):
A family of nonreceptor protein-
tyrosine kinases associated with cytokine receptors.

Jun:
A transcription factor, encoded by a proto-oncogene, that is activated in response to growth factor stimulation.

junctional complex:
A region of cell-cell contact containing a tight junction, an adherens junction, and a desmosome.

K

Kaposi's sarcoma-associated herpesvirus:
A human
herpesvirus that causes Kaposi's sarcoma.

karyopherin:
A nuclear transport receptor.

keratin:
A type of intermediate filament protein of epithelial cells.

kilobase (kb):
One thousand nucleotides or nucleotide base pairs.

kinesin:
A motor protein that moves along microtubules toward the plus end.

kinetochore:
A specialized structure consisting of proteins attached to a centromere that mediates the attachment and movement of chromosomes along the mitotic spindle.

kinetochore microtubules:
Microtubules of the mitotic spindle that attach to condensed chromosomes at their centromeres.

knockout:
Inactivation of a chromosomal gene by homologous recombination with a cloned mutant allele.

Krebs cycle:
See citric acid cycle.

L

lagging strand:
The strand of DNA synthesized opposite to the direction of movement of the replication fork by ligation of Okazaki fragments.

lamellipodium:
A broad, actin-based extension of the plasma membrane involved in the movement of fibroblasts.

laminin:
The principal adhesion protein of basal laminae.

lamins:
Intermediate filament proteins that form the nuclear lamina.

leading strand:
The strand of DNA synthesized continuously in the direction of movement of the replication fork.

leptotene:
The initial stage of the extended prophase of meiosis I during which homologous chromosomes pair before condensation.

leucine zipper:
A protein dimerization domain containing repeated leucine residues; found in many transcription factors.

leucoplast:
A plastid that stores energy sources in nonphotosynthetic plant tissues.

leukemia:
Cancer arising from the precursors of circulating blood cells.

leukotriene:
An eicosanoid synthesized from arachodonic acid.

ligand:
A molecule that binds to a receptor.

ligand-gated channels:
Ion channels that open in response to the binding of signaling molecules.

light reactions:
The reactions of photosynthesis in which solar energy drives the synthesis of ATP and NADPH.

lignin:
A polymer of phenolic residues that strengthens secondary cell walls.

LINEs (long interspersed elements):
A family of highly repeated retrotransposons in mammalian genomes.

lipid raft:
A discrete plasma membrane domain formed as a cluster of cholesterol and sphingolipids.

lipids:
Hydrophobic molecules that function as energy storage molecules, signaling molecules, and the major components of cell membranes.

liposome:
A lipid vesicle used to introduce DNA into mammalian cells.

lock-and-key model:
A model of enzyme action in which the substrate fits precisely into the enzyme active site.

long terminal repeat (LTR):
Sequences found at the ends of retroviral DNA that are direct repeats of several hundred nucleotides resulting from reverse transcriptase activity.

low-density lipoprotein (LDL):
A lipoprotein particle that transports cholesterol in the circulation.

lymphocyte:
A blood cell that functions in the immune response. B lymphocytes produce antibodies and T lymphocytes are responsible for cell mediated immunity.

lymphoma:
A cancer of lymphoid cells.

lysosomal storage diseases:
A family of diseases characterized by the accumulation of undegraded material in the lysosomes of affected individuals.

lysosome:
A cytoplasmic organelle containing enzymes that break down biological polymers.

M

M phase:
The mitotic phase of the cell cycle.

macrophage:
A type of white blood cell specialized for phagocytosis.

macropinocytosis:
The uptake of fluids in large vesicles.

malignant tumor:
A tumor that invades normal tissue and spreads throughout the body.

mannose-6-phosphate:
A modified mannose residue that targets proteins to lysosomes.

MAP kinases:
A family of mitogen-activated protein-serine/threonine kinases that are ubiquitous regulators of cell growth and differentiation.

mass spectrometry:
A method for identifying compounds based on accurate determination of their mass. Mass spectrometry is commonly used for protein identi­fication.

matrix:
The inner mitochondrial space.

matrix processing peptidase (MPP):
The protease that cleaves presequences from proteins imported to the matrix of mitochondria.

maturation promoting factor (MPF):
A complex of Cdk1 and cyclin B that promotes entry into the M phase of either mitosis or meiosis.

Mediator:
A complex of proteins that allows eukaryotic
protein-coding genes to respond to gene-specific regulatory factors.

megabase (Mb):
One million nucleotides or nucleotide base pairs.

meiosis:
The division of diploid cells to haploid progeny, consisting of two sequential rounds of nuclear and cellular division.

MEK:
MAP kinase/ERK kinase. A dual-specificity protein kinase that phosphorylates and activates members of the ERK family of MAP kinases.

membrane-anchored growth factors:
Growth factors associated with the plasma membrane that function as signaling molecules during cell-cell contact.

mesoderm:
The middle germ layer; gives rise to connective tissues and the hematopoietic system.

messenger RNA (mRNA):
An RNA molecule that serves as a template for protein synthesis.

metal shadowing:
An electron microscopic technique in which the surface of a specimen is coated with a thin layer of evaporated metal.

metaphase:
The phase of mitosis during which the chromosomes are aligned on a metaphase plate in the center of the cell.

metastasis:
Spread of cancer cells through the blood or lymphatic system to other organ sites.

7-methylguanosine cap:
A structure consisting of GTP and methylated sugars that is added to the 5' ends of eukaryotic mRNAs.

microfilament:
A cytoskeleton filament composed of actin.

microRNA (miRNA):
A naturally-occurring short noncoding RNA that acts to regulate gene expression.

microsome:
A small vesicle formed from the endoplasmic reticulum when cells are disrupted.

microspike:
See filopodium.

microtubule:
A cytoskeletal component formed by the polymerization of tubulin into rigid, hollow rods about 25 nm in diameter.

microtubule-associated proteins (MAPs):
Proteins that bind to microtubules and modify their stability.

microtubule-organizing center:
An anchoring point near the center of the cell from which most microtubules extend outward.

microvillus:
An actin-based protrusion of the plasma membrane, abundant on the surfaces of cells involved in absorption.

middle lamella:
A region of the plant cell wall that acts as a glue to hold adjacent cells together.

mineralocorticoids:
Steroid hormones produced by the adrenal gland that act on the kidney to regulate salt and water balance.

mismatch repair:
A repair system that removes mismatched bases from newly synthesized DNA strands.

mitochondria:
Cytoplasmic organelles responsible for synthesis of most of the ATP in eukaryotic cells by oxidative phosphorylation.

mitosis:
Nuclear division.

mitotic spindle:
An array of microtubules extending from the spindle poles that is responsible for separating daughter chromosomes during mitosis. See also kinetochore microtubules, polar microtubules, chromosomal microtubules, and astral microtubules.

molecular clone:
See recombinant molecule.

molecular cloning:
The insertion of a DNA fragment of interest into a DNA molecule (vector) that is capable of independent replication in a host cell.

molecular motor:
A protein that generates force and movement by converting chemical energy to mechanical energy.

monocistronic:
Messenger RNAs that encode a single polypeptide chain.

monoclonal antibody:
An antibody produced by a clonal line of B lymphocytes.

monocyte:
A type of blood cell involved in inflammatory reactions.

monosaccharides:
Simple sugars with the basic formula of (CH₂O)_n.

Mos:
A protein kinase that is required for progression from meiosis I to meiosis II and maintenance of metaphase II arrest in vertebrate oocytes.

mTOR:
A protein kinase involved in regulation of protein synthesis in response to growth factors, nutrients, and energy availability.

multi-photon excitation microscopy:
A form of fluorescence microscopy in which the specimen is illuminated with a wavelength of light such that excitation of the fluorescent dye requires the simultaneous absorption of two or more photons.

muscle fibers:
The large cells of skeletal muscle, which are formed by the fusion of many individual cells during developmenht.

mutagen:
A chemical that induces a high frequency of mutations.

mutation:
A genetic alteration.

myofibril:
A bundle of actin and myosin filaments in muscle cells.

myosin:
A protein that interacts with actin as a molecular motor.

myosin I:
A type of myosin that acts to transport cargo along actin filaments.

myosin II:
The type of myosin that produces contraction by sliding actin filaments.

myosin light-chain kinase:
A protein kinase that activates myosin II by phosphorylating its regulatory light chain.

N

Na⁺-K⁺ ATPase:
See Na⁺-K⁺ pump.

Na⁺-K⁺ pump:
An ion pump that transports Na⁺ out of the cell and K⁺ into the cell.

NADP reductase:
An enzyme that transfers electrons from ferrodoxin to NADP⁺, yielding NADPH.

nebulin:
A protein that regulates the length of actin filaments in muscle cells.

nectin:
A cell adhesion molecule involved in the formation of adherens junctions.

Nernst equation:
The relationship between ion concentration and membrane potential.

nerve growth factor (NGF):
A polypeptide growth factor that regulates the development and survival of neurons.

neurofilament:
A type of intermediate filament that supports the axons of nerve cells.

neurofilament (NF) proteins:
The major intermediate filament proteins of many types of mature nerve cells.

neurohormone:
Peptides that are secreted by neurons and act on distant cells.

neuron:
A nerve cell specialized to receive and transmit signals throughout the body.

neuropeptides:
Peptide signaling molecules secreted by
neurons.

neurotransmitter:
A small, hydrophilic molecule that carries a signal from a stimulated neuron to a target cell at a synapse.

neurotrophin:
A member of a family of polypeptides that regulates neuron development and survival.

nexin:
A protein that links microtubule doublets to each other in the axoneme.

NF-κB:
A family of transcription factors that are activated in response to a variety of stimuli.

nicotinamide-adenine dinucleotide (NAD⁺):
A coenzyme that functions as an electron carrier in oxidation/reduction reactions.

nitrogen fixation:
The reduction of atmospheric nitrogen (N₂) to NH₃.

nitrosylation:
Protein modification by addition of NO groups to the side chains of cysteine residues.

N-myc:
A proto-oncogene that encodes a transcription factor and is frequently activated by amplification in neuroblastomas.

N-myristoylation:
The addition of myristic acid (a 14-carbon fatty acid) to the N-terminal glycine residue of a polypeptide chain.

nonreceptor protein-tyrosine kinase:
An intracellular protein-tyrosine kinase.

nonsense-mediated mRNA decay:
Degradation of mRNAs that lack complete open-reading frames.

Northern blotting:
A method in which mRNAs are separated by gel electrophoresis and detected by hybridization with specific probes.

Notch:
A transmembrane receptor in a signaling pathway that regulates cell fate as a result of cell-cell interactions during development.

nuclear envelope:
The barrier separating the nucleus from the cytoplasm, composed of an inner and outer membrane, a nuclear lamina, and nuclear pore complexes.

nuclear export signal:
An amino acid sequence that targets proteins for transport from the nucleus to the cytosol.

nuclear lamina:
A meshwork of lamin filaments providing structural support to the nucleus.

nuclear localization signal:
An amino acid sequence that targets proteins for transportation from the cytoplasm to the nucleus.

nuclear membranes:
Membranes forming the nuclear envelope; the outer nuclear membrane is continuous with the endoplasmic reticulum and the inner nuclear membrane is adjacent to the nuclear lamina.

nuclear pore complex:
A large structure forming a transport channel through the nuclear envelope.

nuclear receptor superfamily:
A family of transcription factors that includes the receptors for steroid hormones, thyroid hormone, retinoic acid, and vitamin D₃.

nuclear transport receptor:
A protein that recognizes nuclear localization signals and mediates transport across the nuclear envelope.

nucleic acid hybridization:
The formation of double stranded DNA and/or RNA molecules by complementary base pairing.

nucleolar organizing regions:
The chromosomal regions containing the genes for ribosomal RNAs.

nucleolus:
The nuclear site of rRNA transcription, processing, and ribosome assembly.

nucleoside:
A purine or pyrimidine base linked to a sugar (ribose or deoxyribose).

nucleosome:
The basic structural unit of chromatin consisting of DNA wrapped around a histone core.

nucleosome core particles:
Particles containing 146 base pairs of DNA wrapped around an octamer consisting of two molecules each of histones H2A, H2B, H3, and H4.

nucleosome remodeling factors:
Proteins that disrupt chromatin structure, allowing transcription factors to bind nucleosomal DNA.

nucleotide:
A phosphorylated nucleoside.

nucleotide excision repair:
A mechanism of DNA repair in which oligonucleotides containing damaged bases are removed from a DNA molecule.

nucleus:
The most prominent organelle of eukaryotic cells; contains the genetic material.

O

Okazaki fragments:
Short DNA fragments that are joined to form the lagging strand of DNA.

oligonucleotide:
A short polymer of only a few nucleotides.

oligosaccharide:
A short polymer of only a few sugars.

oncogene:
A gene capable of inducing one or more characteristics of cancer cells.

oncogene addiction:
The dependence of cancer cells on the continuing activity of oncogenes.

one gene-one enzyme hypothesis:
The hypothesis, based on analysis of nutritional mutants of Neurospora crassa in the 1940s, that a gene specifies the structure of a single enzyme. The current statement of this hypothesis is that a gene specifies the structure of a single polypeptide chain.

open-reading frame:
A stretch of nucleotide sequence that does not contain stop codons and can encode a poly­peptide.

operator:
A regulatory sequence of DNA that controls transcription of an operon.

operon:
A group of adjacent genes transcribed as a single mRNA.

origin of replication:
A specific DNA sequence that serves as a binding site for proteins that initiate replication.

origin recognition complex (ORC):
A protein complex that initiates DNA replication at eukaryotic origins.

oxidative metabolism:
The use of molecular oxygen as an electron acceptor in the breakdown of organic molecules.

oxidative phosphorylation:
The synthesis of ATP from ADP coupled to the energetically favorable transfer of electrons to molecular oxygen as the final acceptor in an electron transport chain.

P

P1 artificial chromosome (PAC):
A vector used for cloning large fragments of DNA in E. coli.

p53:
A transcription factor (encoded by the p53 tumor suppressor gene) that arrests the cell cycle in G₁ in response to damaged DNA and is required for apoptosis induced by a variety of stimuli.

pachytene:
The stage of meiosis I during which recombination takes place between homologous chromosomes.

palmitoylation:
The addition of palmitic acid (a 16-carbon fatty acid) to cysteine residues of a polypeptide chain.

papillomavirus:
A member of a family of DNA viruses, some of which cause cervical and other anogenital cancers in humans.

paracrine signaling:
Local cell-cell signaling in which a molecule released by one cell acts on a neighboring target cell.

parenchyma cell:
A type of plant cell responsible for most metabolic animations.

passive diffusion:
The diffusion of small hydrophobic molecules through a phospholipid bilayer.

passive transport:
The transport of molecules across a membrane in the energetically favorable direction.

patch clamp technique:
A method used to isolate and study the activity of single ion channels.

pectin:
A gel-forming polysaccharide in plant cell walls.

peptide bond:
The bond joining amino acids in polypeptide chains.

peptide hormone:
A signaling molecule composed of amino acids.

peptidoglycan:
The principal component of bacterial cell walls consisting of linear polysaccharide chains crosslinked by short peptides.

peptidyl prolyl isomerase:
An enzyme that facilitates protein folding by catalyzing the cis-trans isomerization of prolyl peptide bonds.

pericentriolar material:
The material in the centrosome that initiates microtubule assembly.

peripheral membrane proteins:
Proteins indirectly associated with cell membranes by protein-protein interactions.

peroxin:
A protein present in peroxisomes.

peroxisome:
A cytoplasmic organelle specialized for carrying out oxidative reactions.

phagocytosis:
The uptake of large particles, such as bacteria, by a cell.

phagolysosome:
A lysosome that has fused with a phagosome or autophagosome.

phagosome:
A vacuole containing a particle taken up by phagocytosis.

phalloidin:
A drug that binds to actin filaments and prevents their disassembly.

phase-contrast microscopy:
A type of microscopy in which variations in density or thickness between parts of the cell are converted to differences in contrast in the final image.

phenotype:
The physical appearance of an organism.

phosphatidylcholine:
A glycerol phospholipid with a head group formed from choline.

phosphatidylethanolamine:
A glycerol phospholipid with a head group formed from ethanolamine.

phosphatidylinositide 3-kinase (PI 3-kinase):
An enzyme that phosphorylates PIP₂, yielding the second messenger phosphatidylinositol 3,4,5-trisphosphate (PIP₃).

phosphatidylinositol:
A glycerol phospholipid with a head group formed from inositol.

phosphatidylinositol 3,4,5-triphosphate (PIP₃):
A second messenger formed by phosphorylation of PIP₂.

phosphatidylinositol 4,5-bisphosphate (PIP₂):
A minor phospholipid component of the inner leaflet of the plasma membrane. Hormones and growth factors stimulate its hydrolysis by phospholipase C, yielding the second messengers diacylglycerol and inositol trisphosphate.

phosphatidylserine:
A glycerol phospholipid with a head group formed from serine.

phosphodiester bond:
A bond between the 5'-phosphate of one nucleotide and the 3'-hydroxyl of another.

phospholipase C:
An enzyme that hydrolyzes PIP₂ to form the second messengers diacylglycerol and inositol trisphosphate.

phospholipid bilayer:
The basic structure of biological membranes in which the hydrophobic tails of phospholipids are buried in the interior of the membrane and their polar head groups are exposed to the aqueous solution on either side.

phospholipid transfer protein:
A protein that transports phospholipid molecules between cell membranes.

phospholipids:
The principal components of cell membranes, consisting of two hydrocarbon chains (usually fatty acids) joined to a polar head group containing phosphate.

phosphorylation:
The addition of a phosphate group to a molecule.

photocenter:
An assembly of photosynthetic pigments in the thylakoid membrane of chloroplasts.

photoreactivation:
A mechanism of DNA repair in which solar energy is used to split pyrimidine dimers.

photorespiration:
A process that metabolizes a by-product of photosynthesis.

photosynthesis:
The process by which cells harness energy from sunlight and synthesize glucose from CO₂ and water.

photosynthetic pigments:
Molecules that capture energy from sunlight by absorbing photons.

photosystem I:
A protein complex in the thylakoid membrane that uses energy absorbed from sunlight to synthesize NADPH.

photosystem II:
A protein complex in the thylakoid membrane that uses energy absorbed from sunlight to synthesize ATP.

pinocytosis:
The uptake of fluids or molecules into a cell by small vesicles.

plakin:
A member of a family of proteins that link intermediate filaments to other cellular structures.

plant hormones:
A group of small molecules that coordinate the responses of plant tissues to environmental signals.

plasma membrane:
A phospholipid bilayer with associated proteins that surrounds the cell.

plasmalogens:
A family of phospholipids that have an ether bond and an ester bond.

plasmid:
A small, circular DNA molecule capable of independent replication in a host cell.

plasmodesma:
A cytoplasmic connection between adjacent plant cells formed by a continuous region of the plasma membrane.

plastids:
A family of plant organelles including chloroplasts, chromoplasts, leucoplasts, amyloplasts, and elaioplasts.

platelet-derived growth factor (PDGF):
A growth factor released by platelets during blood clotting to stimulate the proliferation of fibroblasts.

PML/RARα:
An oncogene formed by translocation of the retinoic acid receptor in acute promyelocytic leukemia.

polar body:
A small cell formed by asymmetric cell division following meiosis of oocytes.

polar microtubules:
Microtubules of the mitotic spindle that overlap in the center of the cell and push the spindle poles apart.

Polo-like kinase:
A protein kinase involved in mitotic spindle formation, kinetochore function, and cytokinesis.

poly-A tail:
A tract of about 200 adenine nucleotides added to the 3' ends of eukaryotic mRNAs.

polyadenylation:
The process of adding a poly-A tail to a pre-mRNA.

polycistronic:
Messenger RNAs that encode multiple polypeptide chains.

polymerase chain reaction (PCR):
A method for amplifying a region of DNA by repeated cycles of DNA synthesis in vitro.

polynucleotide:
A polymer containing up to millions of nucleotides.

polyomavirus:
A widely-studied DNA tumor virus.

polyp:
A benign tumor projecting from an epithelial surface.

polypeptide:
A polymer of amino acids.

polysaccharide:
A polymer containing hundreds or thousands of sugars.

polysome:
A series of ribosomes translating a messenger RNA.

polytene chromosome:
A giant chromosome found in some tissues of Drosophila that arises from repeated replication of DNA strands that fail to separate from each other.

porin:
A member of a class of proteins that cross membranes as b-barrels and form channels in the outer membranes of some bacteria, mitochondria, and chloroplasts.

pre-mRNA:
The primary transcript, which is processed to form messenger RNA in eukaryotic cells.

pre-rRNA:
The primary transcript, which is cleaved to form individual ribosomal RNAs (the 28S, 18S, and 5.8S rRNAs of higher eukaryotic cells).

pre-tRNA:
The primary transcript, which is cleaved to form transfer RNAs.

prenylation:
The addition of specific types of lipids (prenyl groups) to C terminal cysteine residues of a polypeptide chain.

presequence:
An amino-terminal sequence that targets proteins to mitochondria.

primary cell walls:
The walls of growing plant cells.

primary cultures:
Cell cultures established from a tissue.

primary structure:
The sequence of amino acids in a polypeptide chain.

primase:
An RNA polymerase used to intiate DNA synthesis.

processed pseudogene:
A pseudogene that has arisen by reverse transcription of mRNA.

procollagens:
Soluble precursors to the fibril-forming collagens.

product:
A compound formed as a result of an enzymatic reaction.

profilin:
An actin-binding protein that stimulates the assembly of actin monomers into filaments.

progesterone:
A steroid hormone produced by the ovaries.

programmed cell death:
A normal physiological form of cell death characterized by apoptosis.

prokaryotic cells:
Cells lacking a nuclear envelope, cytoplasmic organelles, and a cytoskeleton (bacteria).

prometaphase:
A transition period between prophase and metaphase during which the microtubules of the mitotic spindle attach to the kinetochores and the chromosomes shuffle until they align in the center of the cell.

promoter:
A DNA sequence at which RNA polymerase binds to initiate transcription.

pronuclei:
Two haploid nuclei in a newly fertilized egg.

proplastid:
A small undifferentiated organelle that can develop into different types of mature plastids.

proofreading:
The selective removal of mismatched bases by DNA polymerase.

prophase:
The beginning phase of mitosis, marked by the appearance of condensed chromosomes and the development of the mitotic spindle.

prostacyclin:
An eicosanoid formed from prostaglandin H₂.

prostaglandin:
A family of eicosanoid lipids involved in signaling inflammation.

prosthetic groups:
Small molecules bound to proteins.

proteasome:
A large protease complex that degrades proteins tagged by ubiquitin.

protein disulfide isomerase (PDI):
An enzyme that catalyzes the formation and breakage of disulfide (S-S) linkages.

protein kinase:
An enzyme that phosphorylates proteins by transferring a phosphate group from ATP.

protein kinase A:
A protein kinase regulated by cyclic AMP.

protein kinase C:
A family of protein-serine/threonine kinases that are activated by diacylglycerol and Ca²⁺ and function in intracellular signal transduction.

protein phosphatase:
An enzyme that reverses the action of protein kinases by removing phosphate groups from phosphorylated amino acid residues.

protein-serine/threonine kinase:
A protein kinase that phosphorylates serine and threonine residues.

protein-tyrosine kinase:
A protein kinase that phosphorylates tyrosine residues.

protein-tyrosine phosphatase:
An enzyme that removes the phosphate groups from phosphotyrosine residues.

proteins:
Polypeptides with a unique amino acid sequence.

proteoglycan:
A protein linked to glycosaminoglycans.

proteolysis:
Degradation of polypeptide chains.

proteome:
All of the proteins expressed in a given cell.

proteomics:
Large scale analysis of cell proteins.

proto-oncogene:
A normal cell gene that can be converted into an oncogene.

pseudogene:
A nonfunctional gene copy.

pseudopodium:
An actin-based extension of the plasma membrane responsible for phagocytosis and amoeboid movement.

PTB domain:
A protein domain that binds phosphotyrosine-containing peptides.

PTEN:
A lipid phosphatase that dephosphorylates PIP₃ and acts as a tumor suppressor.

purine:
One of the types of bases present in nucleic acids. The purines are adenine and guanine.

pyrimidine:
One of the types of bases present in nucleic acids. The pyrimidines are cytosine, thymine, and uracil.

pyrimidine dimer:
A common form of DNA damage caused by UV light in which adjacent pyrimidines are joined to form a dimer.

Q

quaternary structure:
The interactions between polypeptide chains in proteins consisting of more than one polypeptide.

R

Rab:
A family of small GTP-binding proteins that play key roles in vesicular transport.

Rac:
A small GTP-binding protein involved in regulation of the actin cytoskeleton.

Rad51:
A eukaryotic protein that functions similarly to RecA in homologous recombination.

raf:
Gene encoding Raf proteins.

Raf:
A protein-serine/threonine kinase (encoded by the raf oncogene) that is activated by Ras and leads to activation of the ERK MAP kinase.

Ran:
A small GTP-binding protein involved in nuclear import and export.

ras:
Gene encoding Ras proteins

Ras:
A family of small GTP binding proteins (encoded by the ras oncogenes) that couple growth factor receptors to intracellular targets, including the Raf protein-serine/
threonine kinase and the ERK MAP kinase pathway.

Rb:
A transcriptional regulatory protein that controls cell cycle progression and is encoded by a tumor suppressor gene that was identified by the genetic analysis of retinoblastoma.

RecA:
A protein that promotes the exchange of strands between homologous DNA molelcules during recombination.

receptor down-regulation:
The loss of receptors from the cell surface as a result of their internalization by endocytosis following ligand binding.

receptor-mediated endocytosis:
The selective uptake of macromolecules that bind to cell surface receptors that concentrate in clathrin-coated pits.

receptor protein-tyrosine kinase:
Membrane-spanning protein-tyrosine kinases that are receptors for extracellular ligands.

recessive:
An allele that is masked by a dominant allele.

recombinant DNA library:
A collection of genomic or cDNA clones.

recombinant molecule:
A DNA insert joined to a vector.

recombination:
The exchange of genetic material.

recombinational repair:
The repair of damaged DNA by recombination with an undamaged homologous DNA molecule.

release factor:
A protein that recognizes stop codons and terminates translation of mRNA.

replication fork:
The region of DNA synthesis where the parental strands separate and two new daughter strands elongate.

repressor:
A regulatory molecule that blocks transcription.

reproductive cloning:
The use of nuclear transfer to create a cloned organism.

resolution:
The ability of a microscope to distinguish objects separated by small distances.

restriction endonuclease:
An enzyme that cleaves DNA at a specific sequence.

restriction map:
The locations of restriction endonuclease cleavage sites on a DNA molecule.

restriction point:
A regulatory point in animal cell cycles that occurs late in G₁. After this point, a cell is committed to entering S and undergoing one cell division cycle.

retinoic acid:
A signaling molecule synthesized from
vitamin A.

retinoid:
A molecule related to retinoic acid.

retrotransposon:
A transposable element that moves via reverse transcription of an RNA intermediate.

retrovirus:
A virus that replicates by making a DNA copy of its RNA genome by reverse transcription.

retrovirus-like element:
A retrotransposon that is structurally similar to a retrovirus.

reverse genetics:
Analysis of gene function by introducing mutations into a cloned gene.

reverse transcriptase:
A DNA polymerase that uses an RNA template.

reverse transcription:
Synthesis of DNA from an RNA
template.

Rho:
A family of small GTP-binding proteins involved in regulation of the cytoskeleton.

rhodopsin:
A G protein-coupled photoreceptor in retinal rod cells that activates transducin in response to light absorption.

ribonucleic acid (RNA):
A polymer of ribonucleotides.

ribose:
The five-carbon sugar found in RNA.

ribosomal RNA (rRNA):
The RNA component of ribosomes.

ribosomes:
Particles composed of RNA and proteins that are the sites of protein synthesis.

ribozyme:
An RNA enzyme.

RNA editing:
RNA processing events other than splicing that alter the protein coding sequences of mRNAs.

RNA interference (RNAi):
The degradation of mRNAs by short complementary double-stranded RNA molecules.

RNA polymerase:
An enzyme that catalyzes the synthesis of RNA.

RNA splicing:
The joining of exons in a precursor RNA molecule.

RNase H:
An enzyme that degrades the RNA strand of RNA-DNA hybrid molecules.

RNase P:
A ribozyme that cleaves the 5' end of pre-tRNAs.

RNA world:
An early stage of evolution based on self-replicating RNA molecules.

rough endoplasmic reticulum (ER):
The region of the endoplasmic reticulum covered with ribosomes and involved in protein metabolism.

Rous sarcoma virus (RSV):
An acutely transforming retrovirus in which the first oncogene was identified.

ryanodine receptors:
Calcium channels in muscle and nerve cells that open in response to changes in membrane potential.

S

S phase:
The phase of the cell cycle during which DNA replication occurs.

Saccharomyces cerevisiae:
A frequently studied budding yeast.

sarcoma:
A cancer of cells of connective tissue.

sarcomere:
The contractile unit of muscle cells composed of interacting myosin and actin filaments.

sarcoplasmic reticulum:
A specialized network of membranes in muscle cells that stores a high concentration of Ca²⁺.

satellite DNA:
Simple-sequence repetitive DNA with a buoyant density differing from the bulk of genomic DNA.

scaffold proteins:
Proteins that bind to components of signaling pathways, leading to their organization in specific signaling cassettes.

scanning electron microscopy:
See electron microscopy.

sclerenchyma cells:
Plant cells characterized by thick cell walls that provide structural support to the plant.

SDS-polyacrylamide gel electrophoresis (SDS-PAGE):
A commonly used method to separate proteins by gel electrophoresis on the basis of size.

second messenger:
A compound whose metabolism is modified as a result of a ligand-receptor interaction; it functions as a signal transducer by regulating other intracellular processes.

secondary cell wall:
A thick cell wall laid down between the plasma membrane and the primary cell wall of plant cells that have ceased growth.

secondary response gene:
A gene whose induction following growth factor stimulation of a cell requires protein synthesis.

secondary structure:
The regular arrangement of amino acids within localized regions of a polypeptide chain. See a helix and b sheet.