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Cell Biology (all vocab)

Cell Biology (All Vocab)

by KirstinPereira, Dec. 2016

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	acetyl CoA (acetyl coenzyme A)	Activated carrier that donates the carbon atoms in its readily transferable acetyl group to many metabolic reactions, including the citric acid cycle and fatty acid biosynthesis; the acetyl group is linked to coenzyme A (CoA) by a thioester bond that releases a large amount of energy when hydrolyzed.
	acetyl group	Chemical group derived from acetic acid.
	acid	A molecule that releases a proton when dissolved in water; this dissociation generates hydronium (H3O+) ions, thereby lowering the pH.
	actin filament	Thin, flexible protein filament made from a chain of globular actin molecules; a major constituent of all eukaryotic cells, this cytoskeletal element is essential for cell movement and for the contraction of muscle cells.
	actin-binding protein	Protein that interacts with actin monomers or filaments to control the assembly, structure, and behavior of actin filaments and networks.
	action potential	Traveling wave of electrical excitation caused by rapid, transient, self-propagating depolarization of the plasma membrane in a neuron or other excitable cell; also called a nerve impulse.
	activated carrier	A small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic reactions. Examples include ATP, acetyl CoA, and NADH.
	activation energy	The energy that must be acquired by a molecule to undergo a chemical reaction.
	activator	A protein that binds to a specific regulatory region of DNA to permit transcription of an adjacent gene.
	active site	Region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation.
	active transport	The movement of a solute across a membrane against its electrochemical gradient; requires an input of energy, such as that provided by ATP hydrolysis.
	acyl group	Functional group derived from a carboxylic acid.
	adaptation	Adjustment of sensitivity following repeated stimulation; allows a cell or organism to register small changes in a signal despite a high background level of stimulation.
	adenylyl cyclase	Enzyme that catalyzes the formation of cyclic AMP from ATP; an important component in some intracellular signaling pathways.
	adherens junction	Cell junction that helps hold together epithelial cells in a sheet of epithelium; actin filaments inside the cell attach to its cytoplasmic face.
	ADP (Adenosine 5' diphosphate)	Nucleoside diphosphate produced by hydrolysis of the terminal phosphate of ATP. (See Figure 3–31.)
	alcohol	Organic compound containing a hydroxyl group (–OH) bound to a saturated carbon atom, for example, ethanol. (See Panel 2–1, pp. 66–67.)
	aldehyde	Reactive organic compound that contains the HC=O group, for example, glyceraldehyde. (See Panel 2–1, pp. 66–67.)
	alkyl group	Functional group consisting solely of single-bonded carbon and hydrogen atoms, such as methyl (–CH3) or ethyl (–CH2CH3) groups.
	allele	An alternative form of a gene; for a given gene, many alleles may exist in the gene pool of the species.
	allosteric	Describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; changes from one conformation to another often alter the protein’s activity or ligand affinity.
	alpha helix (? helix)	Folding pattern, common in many proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid.
	alternative splicing	The production of different mRNAs (and proteins) from the same gene by splicing its RNA transcripts in different ways.
	Alu sequence	Family of mobile genetic elements that comprises about 10% of the human genome; this short, repetitive sequence is no longer mobile on its own, but requires enzymes encoded by other elements to transpose.
	amide	Molecule containing the functional group –CONH2. (See Panel 2–1, pp. 66–67.)
	amine	Molecule containing an amino group (–NH2). (See Panel 2–1, pp. 66–67.)
	amino acid	Small organic molecule containing both an amino group and a carboxyl group; it serves as the building block of proteins. (See Panel 2–5, pp. 74–75.)
	amino acid sequence	The order of the amino acid subunits in a protein chain. Sometimes called the primary structure of a protein.
	amino group	Functional group (–NH2) derived from ammonia. Can accept a proton and carry a positive charge in aqueous solution. (See Panel 2–1, pp. 66–67.)
	amino terminus—	see N-terminus
	aminoacyl-tRNA synthetase	During protein synthesis, an enzyme that attaches the correct amino acid to a tRNA molecule to form a “charged” aminoacyl-tRNA.
	AMP (adenosine 5? monophosphate)	Nucleotide produced by the energetically favorable hydrolysis of the final two phosphate groups from ATP, a reaction that drives the synthesis of DNA and RNA. (See Figure 3–40.)
	amphipathic	Having both hydrophobic and hydrophilic regions, as in a phospholipid or a detergent molecule.
	anabolic pathway	Series of enzyme-catalyzed reactions by which large biological molecules are synthesized from smaller subunits; usually requires an input of energy.
	anabolism	Set of metabolic pathways by which large molecules are made from smaller ones.
	anaerobic	Describes a cell, organism, or metabolic process that operates in the absence of air or, more precisely, in the absence of molecular oxygen.
	anaphase	Stage of mitosis during which the two sets of chromosomes separate and are pulled toward opposite ends of the dividing cell.
	anaphase-promoting complex (APC)	A protein complex that triggers the separation of sister chromatids and orchestrates the carefully timed destruction of proteins that control progress through the cell cycle; the complex catalyzes the ubiquitylation of its targets.
	anion	Negatively charged ion, such as Cl– or CH3COO–.
	antenna complex	In chloroplasts and photosynthetic bacteria, the part of the membrane-bound photosystem that captures energy from sunlight; contains an array of proteins that bind hundreds of chlorophyll molecules and other photosensitive pigments.
	antibody	Protein produced by B lymphocytes in response to a foreign molecule or invading organism. Binds to the foreign molecule or cell extremely tightly, thereby inactivating it or marking it for destruction.
	anticodon	Set of three consecutive nucleotides in a transfer RNA molecule that recognizes, through base-pairing, the three-nucleotide codon on a messenger RNA molecule; this interaction helps to deliver the correct amino acid to a growing polypeptide chain.
	antigen	Molecule or fragment of a molecule that is recognized by an antibody.
	antiparallel	Describes two similar structures arranged in opposite orientations, such as the two strands of a DNA double helix.
	antiport	Type of coupled transporter that transfers two different ions or small molecules across a membrane in opposite directions, either simultaneously or in sequence.
	APC	—see anaphase-promoting complex
	apical	Describes the top or the tip of a cell, structure, or organ; in an epithelial cell, for example, this surface is opposite the base, or basal surface.
	apoptosis	A tightly controlled form of programmed cell death that allows cells that are unneeded or unwanted to be eliminated from an adult or developing organism.
	archaea	One of the two divisions of prokaryotes, often found in hostile environments such as hot springs or concentrated brine. (See also bacteria.)
	asexual reproduction	Mode of reproduction in which offspring arise from a single parent, producing an individual genetically identical to that parent; includes budding, binary fission, and parthenogenesis.
	aster	Star-shaped array of microtubules emanating from a centrosome or from a pole of a mitotic spindle.
	atom	The smallest particle of an element that still retains its distinctive chemical properties; consists of a positively charged nucleus surrounded by a cloud of negatively charged electrons.
	atomic mass	The mass of an atom expressed in daltons, the atomic mass unit that closely approximates the mass of a hydrogen atom.
	ATP (adenosine 5?-triphosphate)	Molecule that serves as the principal carrier of energy in cells; this nucleoside triphosphate is composed of adenine, ribose, and three phosphate groups. (See Figure 2–24.)
	ATP synthase	Membrane-associated enzyme complex that catalyzes the formation of ATP from ADP and inorganic phosphate during oxidative phosphorylation and photosynthesis.
	autophagy	Mechanism by which a cell “eats itself,” digesting molecules and organelles that are damaged or obsolete.
	Avogadro’s number	The number of molecules in a mole, the quantity of a substance equal to its molecular weight in grams; approximately 6 × 1023.
	axon	Long, thin extension that conducts electrical signals away from a nerve cell body toward remote target cells.
	bacteria	(singular bacterium) One of the two divisions of prokaryotes; some species cause disease. The term is sometimes used to refer to any prokaryotic microorganism, although the world of prokaryotes also includes archaea, which are only distantly related. (See also bacteria.)
	bacteriorhodopsin	Pigmented protein found in abundance in the plasma membrane of the salt-loving archaeon Halobacterium halobium; pumps protons out of the cell in response to light.
	basal	Situated near the base; opposite of apical.
	basal body—	see centriole
	basal lamina	Thin mat of extracellular matrix, secreted by epithelial cells, upon which the cells sit.
	base	Molecule that accepts a proton when dissolved in water; also used to refer to the nitrogen-containing purines or pyrimidines in DNA and RNA.
	base pair	Two complementary nucleotides in an RNA or a DNA molecule that are held together by hydrogen bonds— for example, G with C, and A with T or U.
	Bcl2 family	Related group of intracellular proteins that regulates apoptosis; some family members promote cell death, others inhibit it.
	beta sheet (? sheet)	Folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonds to give a rigid, flattened structure.
	bi-orientation	The symmetrical attachment of a sister chromatid pair on the mitotic spindle, such that one chromatid in the duplicated chromosome is attached to one spindle pole and the other is attached to the opposite pole.
	binding site	Region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds.
	biosynthesis	An enzyme-catalyzed process by which complex molecules are formed from simple substances by living cells; also called anabolism.
	bivalent	Structure formed when a duplicated chromosome pairs with its homolog at the beginning of meiosis; contains four sister chromatids.
	bond—	see chemical bond
	bond energy	The strength of the chemical linkage between two atoms, measured by the energy in kilocalories needed to break it.
	bond length	Average distance between two interacting atoms in a molecule, usually those linked covalently.
	buffer	Mixture of weak acids and bases that maintains the pH of a solution by releasing and taking up protons.
	C-terminus (carboxyl terminus)	The end of a polypeptide chain that carries a free carboxyl group (–COOH).
	Ca2+ pump	An active transporter that uses energy supplied by ATP hydrolysis to actively expel Ca2+ from the cell cytosol.
	Ca2+/calmodulin-dependent protein kinase (CaM kinase)	Enzyme that phosphorylates target proteins in response to an increase in Ca2+ ion concentration through its interaction with the Ca2+-binding protein calmodulin.
	cadherin	A member of a family of Ca2+-dependent proteins that mediates the attachment of one cell to another in animal tissues.
	(CaM)	Small Ca2+-binding protein that modifies the activity of many target proteins in response to changes in Ca2+ concentration.
	calorie	Unit of heat. Equal to the amount of heat needed to raise the temperature of 1 gram of water by 1°C.
	CaM—	see calmodulin
	cancer	Disease caused by abnormal and uncontrolled cell proliferation, followed by invasion and colonization of body sites normally reserved for other cells.
	carbohydrate	General term for sugars and related compounds with the general formula (CH2O)n. (See Panel 2–3, pp. 70–71.)
	carbohydrate layer	Protective layer of sugar residues, including the polysaccharide portions of proteoglycans and oligosaccharides attached to protein or lipid molecules, on the outer surface of a cell. Also called the glycocalyx.
	carbon fixation	Process by which green plants and other photosynthetic organisms incorporate carbon atoms from atmospheric carbon dioxide into sugars. The second stage of photosynthesis.
	carbonyl group	Carbon atom linked to an oxygen atom by a double bond. (See Panel 2–1, pp. 66–67.)
	carboxyl group	Carbon atom linked to an oxygen atom by a double bond and to a hydroxyl group (–COOH). In aqueous solution, acts as a weak acid. (See Panel 2–1, pp. 66–67.)
	carboxyl terminus—	see C-terminus
	cascade—	see signaling cascade
	caspase	A family of proteases that, when activated, mediates the destruction of the cell by apoptosis.
	catabolism	Set of enzyme-catalyzed reactions by which complex molecules are degraded to simpler ones with release of energy; intermediates in these reactions are sometimes called catabolites.
	catalysis	The acceleration of a chemical reaction brought about by the action of a catalyst; virtually all reactions in a cell require such assistance to occur under conditions present in living organisms.
	catalyst	Substance that accelerates a chemical reaction by lowering its activation energy; enzymes perform this role in cells.
	cation	Positively charged ion, such as Na+ or CH3NH3 +.
	Cdk inhibitor protein	Regulatory protein that blocks the assembly or activity of cyclin–Cdk complexes, delaying progression primarily through the G1 and S phases of the cell cycle.
	cDNA library	Collection of DNA fragments synthesized using all of the mRNAs present in a particular type of cell as a template.
	cell	The basic unit from which a living organism is made; consists of an aqueous solution of organic molecules enclosed by a membrane.
	cell cortex	Specialized layer of cytoplasm on the inner face of the plasma membrane. In animal cells, it is rich in the actin filaments that govern cell shape and drive cell movement.
	cell cycle	The orderly sequence of events by which a cell duplicates its contents and divides into two.
	cell division	Separation of a cell into two daughter cells. In eukaryotic cells, entails the splitting of the nucleus (mitosis) closely followed by cleavage of the cytoplasm (cytokinesis).
	cell junction	Specialized region of connection between two cells or between a cell and the extracellular matrix.
	cell line	Population of cells derived from a plant or animal capable of dividing indefinitely in culture.
	cell locomotion	Active movement of a cell from one location to another.
	cell memory	The ability of differentiated cells and their descendants to maintain their identity.
	cell respiration	Process by which cells harvest the energy stored in food molecules; usually accompanied by the uptake of O2 and the release of CO2.
	cell signaling	The molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells.
	cell wall	Mechanically strong fibrous layer deposited by a cell outside its plasma membrane. Prominent in most plants, bacteria, algae, and fungi, but not present in most animal cells.
	cell-cycle control system	Network of regulatory proteins that govern the orderly progression of a eukaryotic cell through the stages of cell division.
	cellulose	Structural polysaccharide consisting of long chains of covalently linked glucose units. Provides tensile strength in plant cell walls.
	cellulose microfibril	Long, thin strand of cellulose that helps strengthen plant cell walls.
	central dogma	The principle that genetic information flows from DNA to RNA to protein.
	centriole	Cylindrical array of microtubules usually found in pairs at the center of a centrosome in animal cells. Also found at the base of cilia and flagella, where they are called basal bodies.
	centromere	Specialized DNA sequence that allows duplicated chromosomes to be separated during M phase; can be seen as the constricted region of a mitotic chromosome.
	centrosome	Microtubule-organizing center that sits near the nucleus in an animal cell; during the cell cycle, this structure duplicates to form the two poles of the mitotic spindle.
	centrosome cycle	Process by which the centrosome duplicates (during interphase) and the two new centrosomes separate (at the beginning of mitosis) to form the poles of the mitotic spindle.
	channel	A protein that forms a hydrophilic pore across a membrane, through which selected small molecules or ions can passively diffuse.
	chaperone protein	Molecule that steers proteins along productive folding pathways, helping them to fold correctly and preventing them from forming aggregates inside the cell.
	checkpoint	Mechanism by which the cell-cycle control system can regulate progression through the cycle, ensuring that conditions are favorable and each process has been completed before proceeding to the next stage.
	chemical bond	An exchange of electrons that holds two atoms together. Types found in living cells include ionic bonds, covalent bonds, and hydrogen bonds.
	chemical group	Combination of atoms, such as a hydroxyl group (–OH) or an amino group (–NH2), with distinct chemical and physical properties that influences the behavior of the molecule in which it resides.
	chemiosmotic coupling	Mechanism that uses the energy stored in a transmembrane proton gradient to drive an energyrequiring process, such as the synthesis of ATP or the transport of a molecule across a membrane.
	chiasma	(plural chiasmata) X-shaped connection between paired homologous chromosomes during meiosis; represents a site of crossing-over between two non-sister chromatids.
	chlorophyll	Light-absorbing green pigment that plays a central part in photosynthesis.
	chloroplast	Specialized organelle in algae and plants that contains chlorophyll and serves as the site in which photosynthesis takes place.
	cholesterol	Short, rigid lipid molecule present in large amounts in the plasma membranes of animal cells, where it makes the lipid bilayer less flexible.
	chromatid—	see sister chromatid
	chromatin	Complex of DNA and proteins that makes up the chromosomes in a eukaryotic cell.
	chromatin-remodeling complex	Enzyme (typically multisubunit) that uses the energy of ATP hydrolysis to alter the arrangement of nucleosomes in eukaryotic chromosomes, changing the accessibility of the underlying DNA to other proteins, including those involved in transcription.
	chromatography	Technique used to separate the individual molecules in a complex mixture on the basis of their size, charge, or their ability to bind to a particular chemical group. In a common form of the technique, the mixture is run through a column filled with a material that either binds or lets through the desired molecule.
	chromosome	Long, threadlike structure composed of DNA and proteins that carries the genetic information of an organism; becomes visible as a distinct entity when a plant or animal cell prepares to divide.
	chromosome condensation	Process by which a duplicated chromosome becomes packed into a more compact structure prior to cell division.
	cilium	(plural cilia) Hairlike structure made of microtubules found on the surface of many eukaryotic cells; when present in large numbers, its rhythmic beating can drive the movement of fluid over the cell surface, as in the epithelium of the lungs.
	cis	On the same side as.
	cis Golgi network	Section of the Golgi apparatus that receives materials from the endoplasmic reticulum.
	citric acid cycle	Series of reactions that generates large amounts of NADH by oxidizing acetyl groups derived from food molecules to CO2. In eukaryotic cells, this central metabolic pathway takes place in the mitochondrial matrix.
	classical genetic approach	Experimental techniques used to isolate the genes responsible for an interesting phenotype.
	clathrin	Protein that makes up the coat of a type of transport vesicle that buds from either the Golgi apparatus (on the outward secretory pathway) or from the plasma membrane (on the inward endocytic pathway).
	coated vesicle	Small membrane-enclosed sac that wears a distinctive layer of proteins on its cytosolic surface. It is formed by pinching-off of a protein-coated region of cell membrane.
	codon	Group of three consecutive nucleotides that specifies a particular amino acid or that starts or stops protein synthesis; applies to the nucleotides in an mRNA or in a coding sequence of DNA.
	coenzyme A	Small molecule used to carry and transfer acetyl groups needed for a variety of metabolic reactions, such as the synthesis of fatty acids. (See also acetyl CoA and Figure 3–36.)
	cohesin	Protein complex that holds sister chromatids together after DNA has been replicated in the cell cycle.
	coiled-coil	Stable, rodlike protein structure formed when two or more ? helices twist around each other.
	collagen	Triple-stranded, fibrous protein that is a major component of the extracellular matrix and connective tissues; it is the main protein in animal tissues, and different forms can be found in skin, tendon, bone, cartilage, and blood vessels.
	combinatorial control	Describes the way in which groups of transcription regulators work together to regulate the expression of a single gene.
	complementary	Describes two molecular surfaces that fit together closely and form noncovalent bonds with each other. Examples include complementary base pairs, such as A and T, and the two complementary strands of a DNA molecule.
	complementary DNA (cDNA)	DNA molecule synthesized from an mRNA molecule and therefore lacking the introns that are present in genomic DNA.
	complementation test	Genetic experiment that determines whether two mutations that are associated with the same phenotype lie in the same gene or in different genes.
	complex	A collection of macromolecules that are bound to each other by noncovalent bonds to form a large structure with a specific function.
	complex trait	A heritable characteristic whose transmission to progeny does not appear to obey Mendel’s laws. Such characteristics, for example height, usually result from the interaction of multiple genes.
	condensation—	see chromosome condensation
	condensation reaction	Chemical reaction in which a covalent bond is formed between two molecules as water is expelled; used to build polymers, such as proteins, polysaccharides, and nucleic acids.
	condensin	Protein complex that helps configure duplicated chromosomes for segregation by making them more compact.
	conformation	Precise, three-dimensional shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another.
	connective tissue	Tissues such as bone, tendons, and the dermis of the skin, in which extracellular matrix makes up the bulk of the tissue and carries the mechanical load.
	conserved synteny	The preservation of gene order and location in the genomes of different species.
	contractile ring	Structure made of actin and myosin filaments that forms a belt around a dividing cell, pinching it in two.
	copy-number variation (CNV)	Large segment of DNA, 1000 nucleotide pairs or greater, that has been duplicated or lost in an individual genome (compared to the “reference” genome sequence).
	coupled pump	Active transporter that uses the movement of one solute down its electrochemical gradient to drive the uphill transport of another solute across the same membrane.
	coupled reaction	Linked pair of chemical reactions in which free energy released by one reaction serves to drive the other reaction.
	covalent bond	Stable chemical link between two atoms produced by sharing one or more pairs of electrons.
	crossing-over	Process whereby two homologous chromosomes break at corresponding sites and rejoin to produce two recombined chromosomes that have physically exchanged segments of DNA.
	cyclic AMP (cAMP)	Small intracellular signaling molecule generated from ATP in response to hormonal stimulation of cell-surface receptors.
	cyclic-AMP-dependent protein kinase (protein kinase A, PKA)	Enzyme that phosphorylates target proteins in response to a rise in intracellular cyclic AMP concentration.
	cyclin	Regulatory protein whose concentration rises and falls at specific times during the eukaryotic cell cycle; cyclins help control progression from one stage of the cell cycle to the next by binding to cyclin-dependent protein kinases (Cdks).
	cyclin-dependent protein kinase (Cdk)	Enzyme that, when complexed with a regulatory cyclin protein, can trigger various events in the celldivision cycle by phosphorylating specific target proteins.
	cytochrome	Membrane-bound, colored, heme-containing protein that transfers electrons during cellular respiration and photosynthesis.
	cytochrome c oxidase	Protein complex that serves as the final electron carrier in the respiratory chain; removes electrons from cytochrome c and passes them to O2 to produce H2O.
	cytokine	Small signaling molecule, made and secreted by cells, that acts on neighboring cells to alter their behavior. Usually a protein, polypeptide, or glycoprotein.
	cytokinesis	Process by which the cytoplasm of a plant or animal cell divides in two to form individual daughter cells.
	cytoplasm	Contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, contained outside the nucleus.
	cytoskeleton	System of protein filaments in the cytoplasm of a eukaryotic cell that gives the cell shape and the capacity for directed movement. Its most abundant components are actin filaments, microtubules, and intermediate filaments.
	cytosol	Contents of the main compartment of the cytoplasm, excluding membrane-enclosed organelles such as endoplasmic reticulum and mitochondria. The cell fraction remaining after membranes, cytoskeletal components, and other organelles have been removed.
	dalton	Unit of molecular mass. Defined as one-twelfth the mass of an atom of carbon 12 (1.66 × 10–24 g); approximately equal to the mass of a hydrogen atom.
	dark reactions	In photosynthesis, the set of reactions that produce sugars from CO2; these reactions, also called carbon fixation, can occur in the absence of sunlight.
	denature	To cause a dramatic change in the structure of a macromolecule by exposing it to extreme conditions, such as high heat or harsh chemicals. Usually results in the loss of biological function.
	dendrite	Short, branching structure that extends from the surface of a nerve cell and receives signals from other neurons.
	deoxyribonucleic acid—	see DNA
	depolarization	A shift in the membrane potential, making it less negative.
	desmosome	Specialized cell–cell junction, usually formed between two epithelial cells, that serves to connect the ropelike keratin filaments of the adjoining cells, providing tensile strength.
	detergent	Soapy substance used to solubilize membrane proteins.
	diacylglycerol (DAG)	Small messenger molecule produced by the cleavage of membrane inositol phospholipids in response to extracellular signals. Helps activate protein kinase C.
	dideoxy sequencing or Sanger sequencing	The standard method of determining the nucleotide sequence of DNA; utilizes DNA polymerase and a set of chain-terminating nucleotides.
	differentiation	Process by which a cell undergoes a progressive, coordinated change to a more specialized cell type, brought about by large-scale changes in gene expression.
	diffusion	Process by which molecules and small particles move from one location to another by random, thermally driven motion.
	dimer	A molecule composed of two structurally similar subunits.
	diploid	Describes a cell or organism containing two sets of homologous chromosomes, one inherited from each parent. (See also haploid.)
	disulfide bond	Covalent cross-link formed between the sulfhydryl groups on two cysteine side chains; often used to reinforce a secreted protein’s structure or to join two different proteins together.
	divergence	Differences in sequence that accumulate over time in DNA segments derived from a common ancestral sequence.
	DNA (deoxyribonucleic acid)	Double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotide units. It serves as the cell’s store of genetic information that is transmitted from generation to generation.
	DNA cloning	Production of many identical copies of a DNA sequence.
	DNA library	Collection of cloned DNA molecules, representing either an entire genome (genomic library) or copies of the mRNA produced by a cell (cDNA library).
	DNA ligase	Enzyme that reseals nicks that arise in the backbone of a DNA molecule; in the laboratory, can be used to join together two DNA fragments.
	DNA methylation	The enzymatic addition of methyl groups to cytosine bases in DNA; this covalent modification generally turns off genes by attracting proteins that block gene expression.
	DNA microarray	A surface on which a large number of short DNA molecules (typically in the tens of thousands) have been immobilized in an orderly pattern. Each of these DNA fragments acts as a probe for a specific gene, allowing the activities of thousands of genes to be monitored at the same time.
	DNA repair	Collective term for the enzymatic processes that correct deleterious changes affecting the continuity or sequence of a DNA molecule.
	DNA replication	The process by which a copy of a DNA molecule is made.
	DNA transcription—	see transcription
	domain	Small discrete region of a structure; in a protein, a segment that folds into a compact and stable structure. In a membrane, a region of the bilayer with a characteristic lipid and protein composition.
	double bond	Chemical linkage formed when two atoms share four electrons.
	double helix	The typical structure of a DNA molecule in which the two complementary polynucleotide strands are wound around each other with base-pairing between the strands.
	dynamic instability	The rapid switching between growth and shrinkage shown by microtubules.
	dynein	Motor protein that uses the energy of ATP hydrolysis to move toward the minus end of a microtubule. One form of the protein is responsible for the bending of cilia.
	electrochemical gradient	Driving force that determines which way an ion will move across a membrane; consists of the combined influence of the ion’s concentration gradient and the membrane potential.
	electron	Negatively charged subatomic particle that occupies space around an atomic nucleus (e–).
	electron acceptor	Atom or molecule that readily takes up electrons, thereby becoming reduced.
	electron carrier	Molecule capable of picking up an electron from a molecule with weak electron affinity and transferring it to a molecule with a higher electron affinity.
	electron donor	Molecule that easily gives up an electron, thereby becoming oxidized.
	electron microscope	Instrument that illuminates a specimen using beams of electrons to reveal and magnify the structures of very small objects, such as organelles and large molecules.
	electron-transport chain	A series of membrane-embedded electron carrier molecules that facilitate the movement of electrons from a higher to a lower energy level, as in oxidative phosphorylation and photosynthesis.
	electrophoresis	Technique for separating a mixture of proteins or DNA fragments by placing them on a polymer gel and subjecting them to an electric field. The molecules migrate through the gel at different speeds depending on their size and net charge.
	electrostatic attraction	Force that draws together oppositely charged atoms. Examples include ionic bonds and the attractions between molecules containing polar covalent bonds.
	element	Substance that cannot be broken down to any other chemical form; composed of a single type of atom.
	embryonic stem cell (ES cell)	An undifferentiated cell type derived from the inner cell mass of an early mammalian embryo and capable of differentiating to give rise to any of the specialized cell types in the adult body.
	endocytosis	Process by which cells take in materials through an invagination of the plasma membrane, which surrounds the ingested material in a membraneenclosed vesicle. (See also pinocytosis and phagocytosis)
	endomembrane system	Interconnected network of membrane-enclosed organelles in a eukaryotic cell; includes the endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, and endosomes.
	endoplasmic reticulum (ER)	Labyrinthine membraneenclosed compartment in the cytoplasm of eukaryotic cells where lipids and proteins are made.
	endosome	Membrane-enclosed compartment of a eukaryotic cell through which material ingested by endocytosis passes on its way to lysosomes.
	enhancer	Regulatory DNA sequence to which transcription regulators bind, influencing the rate of transcription of a gene that may be many thousands of base pairs away.
	entropy	Thermodynamic quantity that measures the degree of disorder in a system.
	enzyme	A protein that catalyzes a specific chemical reaction.
	enzyme-coupled receptor	Transmembrane protein that, when stimulated by the binding of a ligand, activates an intracellular enzyme (either a separate enzyme or part of the receptor itself).
	epigenetic inheritance	The transmission of a heritable pattern of gene expression from one cell to its progeny that does not involve altering the nucleotide sequence of the DNA.
	epithelium	(plural epithelia) Sheet of cells covering an external surface or lining an internal body cavity.
	equilibrium	State in which the forward and reverse rates of a chemical reaction are equal so that no net chemical change occurs.
	equilibrium constant (K)	For a reversible chemical reaction, the ratio of substrate to product when the rates of the forward and reverse reactions are equal. (See Table 3–1, p. 98.)
	Escherichia coli (E. coli)	Rodlike bacterium normally found in the colon of humans and other mammals and widely used in biomedical research.
	eubacteria	The proper term for the bacteria of common occurrence, used to distinguish them from archaea.
	euchromatin	One of the two main states in which chromatin exists within an interphase cell. Prevalent in generich areas, its less compact structure allows access for proteins involved in transcription. (See also heterochromatin)
	eukaryote	An organism whose cells have a distinct nucleus and cytoplasm.
	evolution	Process of gradual modification and adaptation that occurs in living organisms over generations.
	exocytosis	Process by which most molecules are secreted from a eukaryotic cell. These molecules are packaged in membrane-enclosed vesicles that fuse with the plasma membrane, releasing their contents to the outside.
	exon	Segment of a eukaryotic gene that is transcribed into RNA and dictates the amino acid sequence of part of a protein.
	exon shuffling	Mechanism for the evolution of new genes; in the process, coding sequences from different genes are brought together to generate a protein with a novel combination of domains.
	extracellular matrix	Complex network of polysaccharides (such as glycosaminoglycans or cellulose) and proteins (such as collagen) secreted by cells. A structural component of tissues that also influences their development and physiology.
	extracellular signal molecule	Any molecule present outside the cell that can elicit a response inside the cell when the molecule binds to a receptor.
	FAD—	see FADH2
	FADH2 (reduced flavin adenine dinucleotide)	A high-energy electron carrier produced by reduction of FAD during the breakdown of molecules derived from food, including fatty acids and acetyl CoA.
	fat	Type of lipid used by living cells to store metabolic energy. Mainly composed of triacylglycerols. (See Panel 2–4, pp. 72–73.)
	fatty acid	Molecule that consists of a carboxylic acid attached to a long hydrocarbon chain. Used as a major source of energy during metabolism and as a starting point for the synthesis of phospholipids. (See Panel 2–4, pp. 72–73.)
	feedback inhibition	A form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway.
	fermentation	The breakdown of organic molecules without the involvement of molecular oxygen. This form of oxidation yields less energy than aerobic cell respiration.
	fertilization	The fusion of two gametes—sperm and egg—to produce a new individual organism.
	fibroblast	Cell type that produces the collagen-rich extracellular matrix in connective tissues such as skin and tendon. Proliferates readily in wounded tissue and in tissue culture.
	fibronectin	Extracellular matrix protein that helps cells attach to the matrix by acting as a “linker” that binds to a cellsurface integrin molecule on one end and to a matrix component, such as collagen, on the other.
	fibrous protein	A protein with an elongated, rodlike shape, such as collagen or a keratin filament.
	filopodium	(plural filopodia) Long, thin, actin-containing extension on the surface of an animal cell. Sometimes has an exploratory function, as in a growth cone.
	flagellum	(plural flagella) Long, whiplike structure capable of propelling a cell through a fluid medium with its rhythmic beating. Eukaryotic flagella are longer versions of cilia; bacterial flagella are completely different, being smaller and simpler in construction.
	fluorescence microscope	Instrument used to visualize a specimen that has been labeled with a fluorescent dye; samples are illuminated with a wavelength of light that excites the dye, causing it to fluoresce.
	free energy (G)	Energy that can be harnessed to do work, such as driving a chemical reaction.
	free-energy change (?G)	“Delta G”: in a chemical reaction, the difference in free energy between reactant and product molecules. A large negative value of ?G indicates that the reaction has a strong tendency to occur. The standard freeenergy change (?G°) is the free-energy change measured at defined concentration, temperature, and pressure.
	G, ?G, ?G°—	see free energy, free-energy change
	G protein	A membrane-bound GTP-binding protein involved in intracellular signaling; composed of three subunits, this intermediary is usually activated by the binding of a hormone or other ligand to a transmembrane receptor.
	G-protein-coupled receptor (GPCR)	Cell-surface receptor that associates with an intracellular trimeric GTP-binding protein (G protein) after activation by an extracellular ligand. These receptors are embedded in the membrane by seven transmembrane ? helices.
	G1 cyclin	Regulatory protein that helps drive a cell through the first gap phase of the cell cycle and toward S phase.
	G1 phase	Gap 1 phase of the eukaryotic cell cycle; falls between the end of cytokinesis and the start of DNA synthesis.
	G1-Cdk	Protein complex whose activity drives the cell through the first gap phase of the cell cycle; consists of a G1 cyclin plus a cyclin-dependent protein kinase (Cdk).
	G1/S cyclin	Regulatory protein that helps to launch the S phase of the cell cycle.
	G1/S-Cdk	Protein complex whose activity triggers entry into S phase of the cell cycle; consists of a G1/S cyclin plus a cyclin-dependent protein kinase (Cdk).
	G2 phase	Gap 2 phase of the eukaryotic cell cycle; falls between the end of DNA synthesis and the beginning of mitosis.
	gain-of-function mutation	Genetic change that increases the activity of a gene or makes it active in inappropriate circumstances; such mutations are usually dominant.
	gamete	Cell type in a diploid organism that carries only one set of chromosomes and is specialized for sexual reproduction. A sperm or an egg; also called germ cell.
	gap junction	In animal tissues, specialized connection between juxtaposed cells through which ions and small molecules can pass from one cell to the other.
	GDP guanosine 5? diphosphate	Nucleotide that is produced by the hydrolysis of the terminal phosphate of GTP, a reaction that also produces inorganic phosphate.
	gene	Unit of heredity containing the instructions that dictate the characteristics or phenotype of an organism; in molecular terms, a segment of DNA that directs the production of a protein or functional RNA molecule.
	gene duplication and divergence	A process by which new genes can form; involves the accidental generation of an additional copy of a stretch of DNA containing one or more genes, followed by an accumulation of mutations that over time can alter the function of either the original or its copy.
	gene expression	The process by which a gene makes a product that is useful to the cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity.
	gene family	A set of related genes that has arisen through a process of gene duplication and divergence.
	gene knockout	A genetically engineered animal in which a specific gene has been inactivated.
	gene replacement	Technique that substitutes a mutant form of a gene for its normal counterpart to investigate the gene’s function.
	general transcription factors	Proteins that assemble on the promoters of many eukaryotic genes near the start site of transcription and load the RNA polymerase in the correct position.
	genetic code	Set of rules by which the information contained in the nucleotide sequence of a gene and its corresponding RNA molecule is translated into the amino acid sequence in a protein.
	genetic engineering—	see recombinant DNA technology
	genetic instability	An increased rate of mutation often caused by defects in the systems that govern the accurate replication and maintenance of the genome; the resulting mutations sometimes drive the evolution of cancer.
	genetic map	A graphic representation of the order of genes in chromosomes spaced according to the amount of recombination that occurs between them.
	genetic screen	Experimental technique used to search through a collection of mutants for a particular phenotype.
	genetics	The study of genes, heredity, and the variation that gives rise to differences between one living organism and another.
	genome	The total genetic information carried by all the chromosomes of a cell or organism.
	genomic DNA library	Collection of cloned DNA molecules that represents the entire genome of a cell.
	genotype	The genetic makeup of a cell or organism, including which alleles (gene variants) it carries.
	germ cell	Cell type in a diploid organism that carries only one set of chromosomes and is specialized for sexual reproduction. A sperm or an egg; also called gamete.
	germ line	The lineage of reproductive cells that contributes to the formation of a new generation of organisms, as distinct from somatic cells, which form the body and leave no descendants in the next generation.
	globular protein	Any protein in which the polypeptide chain folds into a compact, rounded shape. Includes most enzymes.
	gluconeogenesis	Set of enzyme-catalyzed reactions by which glucose is synthesized from small organic molecules such as pyruvate, lactate, or amino acids; in effect, the reverse of glycolysis.
	glucose	Six-carbon sugar that plays a major role in the metabolism of living cells. Stored in polymeric form as glycogen in animal cells and as starch in plant cells. (See Panel 2–3, pp. 70–71.)
	glycocalyx	Protective layer of carbohydrates on the outside surface of the plasma membrane formed by the sugar residues of membrane glycoproteins, proteoglycans, and glycolipids.
	glycogen	Branched polymer composed exclusively of glucose units used to store energy in animal cells. Granules of this material are especially abundant in liver and muscle cells.
	glycolipid	Membrane lipid molecule that has a short carbohydrate chain attached to its hydrophilic head.
	glycolysis	Series of enzyme-catalyzed reactions in which sugars are partially degraded and their energy captured by the activated carriers ATP and NADH. (Literally, “sugar splitting.”)
	glycoprotein	Any protein with one or more covalently linked oligosaccharide chains. Includes most secreted proteins and most proteins exposed on the outer surface of the plasma membrane.
	glycosaminoglycan (GAG)	Polysaccharide chain that can form a gel that acts as a “space filler” in the extracellular matrix of connective tissues; helps animal tissues resist compression.
	Golgi apparatus	Membrane-enclosed organelle in eukaryotic cells that modifies the proteins and lipids made in the endoplasmic reticulum and sorts them for transport to other sites.
	GFP (green fluorescent protein )	Fluorescent protein, isolated from a jellyfish, that is used experimentally as a marker for monitoring the location and movement of proteins in living cells.
	group—	see chemical group
	growth factor	Extracellular signaling molecule that stimulates a cell to increase in size and mass. Examples include epidermal growth factor (EGF) and platelet-derived growth factor (PDGF).
	GTP (guanosine 5? triphosphate)	Nucleoside triphosphate used in the synthesis of RNA and DNA. Like the closely related ATP, serves as an activated carrier in some energy-transfer reactions. Also has a special role in microtubule assembly, protein synthesis, and cell signaling.
	GTP-binding protein	Intracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monomeric GTPases, such as Ras.
	haploid	Describes a cell or organism with only one set of chromosomes, such as a sperm cell or a bacterium. (See also diploid)
	haplotype block	A combination of alleles or other DNA markers that has been inherited as a unit, undisturbed by genetic recombination, across many generations.
	helix	An elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase.
	hemidesmosome	Structure that anchors epithelial cells to the basal lamina beneath them.
	heredity	The genetic transmission of traits from parents to offspring.
	heterochromatin	Highly condensed region of an interphase chromosome; generally gene-poor and transcriptionally inactive. (See also euchromatin)
	heterozygous	Possessing dissimilar alleles for a given gene.
	high-energy bond	Covalent bond whose hydrolysis releases an unusually large amount of free energy under the conditions existing in a cell. Examples include the phosphodiester bonds in ATP and the thioester linkage in acetyl CoA.
	histone	One of a group of abundant highly conserved proteins around which DNA wraps to form nucleosomes, structures that represent the most fundamental level of chromatin packing.
	histone deacetylase	Enzyme that removes acetyl groups from lysines present in histones; its action often allows chromatin to pack more tightly.
	homolog	A gene, chromosome, or any structure that has a close similarity to another as a result of common ancestry. (See also homologous chromosome)
	homologous	Describes genes, chromosomes, or any structures that are similar because of their common evolutionary origin. Can also refer to similarities between protein sequences or nucleic acid sequences.
	homologous chromosome	In a diploid cell, one of the two copies of a particular chromosome, one of which comes from the father and the other from the mother.
	homologous gene—	see homologous
	homologous recombination	Mechanism by which double-strand breaks in a DNA molecule can be repaired flawlessly; uses an undamaged, duplicated, or homologous chromosome to guide the repair. During meiosis, the mechanism results in an exchange of genetic information between the maternal and paternal homologs.
	homozygous	Possessing identical alleles for a given gene.
	horizontal gene transfer	Process by which DNA is passed from the genome of one organism to that of another, even to an individual from another species. This contrasts with “vertical” gene transfer, which refers to the transfer of genetic information from parent to progeny.
	hormone	Extracellular signal molecule that is secreted and transported via the bloodstream (in animals) or the sap (in plants) to target tissues on which it exerts a specific effect.
	hybridization	Experimental technique in which two complementary nucleic acid strands come together and form hydrogen bonds to produce a double helix; used to detect specific nucleotide sequences in either DNA or RNA.
	hydrogen bond	A weak noncovalent interaction between a positively charged hydrogen atom in one molecule and a negatively charged atom, such as nitrogen or oxygen, in another; these interactions are key to the structure and properties of water.
	hydrogen ion	Positively charged ion generated by the removal of an electron from a hydrogen atom; often used to refer to a proton (H+) in aqueous solution. Its presence is the basis of acidity. (See Panel 2–2, pp. 68–69.)
	hydrolysis	Chemical reaction that involves cleavage of a covalent bond with the accompanying consumption of water (its –H being added to one product of the cleavage and its –OH to the other); the reverse of condensation.
	hydronium ion (H3O+)	The form taken by a proton (H+) in aqueous solution.
	hydrophilic	Molecule or part of a molecule that readily forms hydrogen bonds with water, allowing it to dissolve; literally, “water loving.”
	hydrophobic	Nonpolar, uncharged molecule or part of a molecule that forms few or no hydrogen bonds with water molecules and therefore does not dissolve; literally, “water fearing.”
	hydrophobic interaction	Type of noncovalent bond that forces together the hydrophobic portions of dissolved molecules to minimize their disruption of the hydrogen-bonded network of water; helps push together membrane phospholipids and fold proteins into a compact, globular shape.
	hydroxyl (–OH)	Chemical group consisting of a hydrogen atom linked to an oxygen, as in an alcohol. (See Panel 2–1, pp. 66–67.)
	in situ hybridization	Technique in which a single-stranded RNA or DNA probe is used to locate a complementary nucleotide sequence in a chromosome, cell, or tissue; used to diagnose genetic disorders or to track gene expression.
	in vitro	Term used by biochemists to describe a process that takes place in an isolated cell-free extract. Also used by cell biologists to refer to cells growing in culture, as opposed to in an organism.
	in vivo	In an intact cell or organism. (Latin for “in life.”)
	induced pluripotent stem cell (iPS cell)	Somatic cell that has been reprogrammed to resemble and behave like a pluripotent embryonic stem (ES) cell through the artificial introduction of a set of genes encoding particular transcription regulators.
	initiation factor	Protein that promotes the proper association of ribosomes with mRNA and is required for the initiation of protein synthesis.
	initiator tRNA	Special tRNA that initiates the translation of an mRNA in a ribosome. It always carries the amino acid methionine.
	inorganic	Not composed of carbon and hydrogen.
	inositol	Sugar molecule with six hydroxyl groups that forms the structural basis for inositol phospholipids, which can act as membrane-bound signaling molecules.
	inositol 1, 4, 5-trisphosphate (IP3)	Small intracellular signaling molecule that triggers the release of Ca2+ from the endoplasmic reticulum into the cytosol; produced when a signal molecule activates a membrane-bound protein called phospholipase C.
	inositol phospholipid	Minor lipid component of plasma membranes that plays a part in signal transduction in eukaryotic cells; cleavage yields two small messenger molecules, IP3 and diacylglycerol.
	integrin	Family of transmembrane proteins present on cell surfaces that enable cells to make and break attachments to the extracellular matrix, allowing them to crawl through a tissue.
	intermediate filament	Fibrous cytoskeletal element, about 10 nm in diameter, that forms ropelike networks in animal cells; helps cells resist tension applied from outside.
	interphase	Long period of the cell cycle between one mitosis and the next. Includes G1 phase, S phase, and G2 phase.
	interphase chromosome	State in which a eukaryotic chromosome exists when the cell is between divisions; more extended and transcriptionally active than mitotic chromosomes.
	intracellular signaling molecule	Molecule that is part of the mechanism for transducing and transmitting signals inside a cell.
	intracellular signaling pathway	A set of proteins and small-molecule second messengers that interact with each other to relay a signal from the cell membrane to its final destination in the cytoplasm or nucleus.
	intrinsically disordered sequence	Region in a polypeptide chain that lacks a definite structure.
	intron	Noncoding sequence within a eukaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing to produce an mRNA.
	ion	An atom carrying an electrical charge, either positive or negative.
	ion channel	Transmembrane protein that forms a pore across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients.
	ion-channel-coupled receptor	Transmembrane receptor protein or protein complex that opens in response to the binding of a ligand to its external face, allowing the passage of a specific inorganic ion.
	ionic bond	Interaction formed when one atom donates electrons to another; this transfer of electrons causes both atoms to become electrically charged.
	iron–sulfur center	Metal complex found in electron carriers that operate early in the electron-transport chain; has a relatively weak affinity for electrons.
	isomer (stereoisomer)	One of two or more substances that contains the same atoms and has the same molecular formula (such as C6H12O6) as the other, but differs from the other in the spatial arrangement of these atoms. Optical isomers are mirror images of each other.
	isotope	A variant of an element that has the same number of protons but a different atomic weight. Some are radioactive.
	K+	Potassium ion—the most abundant positively charged ion in living cells.
	K+ leak channel	Ion channel permeable to K+ that randomly flickers between an open and closed state; largely responsible for the resting membrane potential in animal cells.
	karyotype	An ordered display of the full set of chromosomes of a cell arranged with respect to size, shape, and number.
	keratin filament	Class of intermediate filament abundant in epithelial cells, where it provides tensile strength; main structural component of hair, feathers, and claws.
	kilocalorie (kcal)	Unit of heat equal to 1000 calories. Often used to express the energy content of food or molecules: bond strengths, for example, are measured in kcal/ mole. An alternative unit in wide use is the kilojoule.
	kilojoule (kJ)	Standard unit of energy equal to 0.239 kilocalories.
	kinase—	see protein kinase
	kinesin	A large family of motor proteins that uses the energy of ATP hydrolysis to move toward the plus end of a microtubule.
	kinetochore	Protein complex that assembles on the centromere of a condensed mitotic chromosome; the site to which spindle microtubules attach.
	KM	The concentration of substrate at which an enzyme works at half its maximum rate. Large values of KM usually indicate that the enzyme binds to its substrate with relatively low affinity.
	knockout mouse	Genetically engineered mouse in which a specific gene has been inactivated, for example, by introducing a deletion in its DNA.
	L1 element	Type of retrotransposon that constitutes 15% of the human genome; also called LINE-1.
	lagging strand	At a replication fork, the DNA strand that is made discontinuously in short separate fragments that are later joined together to form one continuous new strand.
	lamellipodium	(plural lamellipodia) Dynamic sheetlike extension on the surface of an animal cell, especially one migrating over a surface.
	law of independent assortment	Principle that, during gamete formation, the alleles for different traits segregate independently of one another; Mendel’s second law of inheritance.
	law of segregation	Principle that the maternal and paternal alleles for a trait separate from one another during gamete formation and then reunite during fertilization; Mendel’s first law of inheritance.
	leading strand	At a replication fork, the DNA strand that is made by continuous synthesis in the 5?-to-3? direction.
	ligand	General term for a molecule that binds to a specific site on a protein.
	ligand-gated channel	An ion channel that is stimulated to open by the binding of a small molecule such as a neurotransmitter.
	ligase	Enzyme that reseals nicks that arise in the backbone of a DNA molecule; in the laboratory, can be used to join together two DNA fragments.
	light reactions	In photosynthesis, the set of reactions that converts the energy of sunlight into chemical energy in the form of ATP and NADPH.
	lipid	Organic molecule that is insoluble in water but dissolves readily in nonpolar organic solvents; typically contains long hydrocarbon chains or multiple rings. One class, the phospholipids, forms the structural basis of biological membranes.
	lipid bilayer	Thin pair of closely juxtaposed sheets, composed mainly of phospholipid molecules, that forms the structural basis for all cell membranes.
	local mediator	Secreted signal molecule that acts at a short range on adjacent cells.
	long noncoding RNA	Class of RNA molecules more than 200 nucleotides in length that does not encode proteins.
	loss-of-function mutation	A genetic alteration that reduces or eliminates the activity of a gene. Such mutations are usually recessive: the organism can function normally as long as it retains at least one normal copy of the affected gene.
	lumen	The space inside a hollow or tubular structure; can refer to the cavity in a tissue or within an organelle.
	lymphocyte	White blood cell that mediates the immune response to foreign molecules (antigens). Can be an antibodysecreting B cell type or the T cell type that recognizes and ultimately eliminates infected cells.
	lysosome	Membrane-enclosed organelle that breaks down worn-out proteins and organelles and other waste materials, as well as molecules taken up by endocytosis; contains digestive enzymes that are typically most active at the acid pH found inside these organelles.
	lysozyme	Enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears.
	M cyclin	Regulatory protein that binds to mitotic Cdk to form M-Cdk, the protein complex that triggers the M phase of the cell cycle.
	M phase	Period of the eukaryotic cell cycle during which the nucleus and cytoplasm divide.
	M-Cdk	Protein complex that triggers the M phase of the cell cycle; consists of an M cyclin plus a mitotic cyclindependent protein kinase (Cdk).
	macromolecule	Polymer built from covalently linked subunits; includes proteins, nucleic acids, and polysaccharides with a molecular mass greater than a few thousand daltons.
	macrophage	Cell found in animal tissues that defends against infections by ingesting invading microbes by a process of phagocytosis; derived from a type of white blood cell.
	MAP kinase	Mitogen-activated protein kinase. Signaling molecule that is the final kinase in a three-kinase sequence called the MAP-kinase signaling module.
	MAP-kinase signaling module	Set of three functionally interlinked protein kinases that allows cells to respond to extracellular signal molecules that stimulate proliferation; includes a mitogen-activated protein kinase (MAP kinase), a MAP kinase kinase, and a MAP kinase kinase kinase.
	mass spectrometry	Technique for determining the exact mass of every peptide present in a sample of purified protein or protein mixture.
	matrix	Large internal compartment within a mitochondrion.
	mechanically gated channel	An ion channel that allows the passage of select ions across a membrane in response to a physical perturbation.
	meiosis	Specialized type of cell division by which eggs and sperm cells are made. Two successive nuclear divisions with only one round of DNA replication generate four haploid cells from an initial diploid cell.
	membrane	Thin sheet of lipid molecules and associated proteins that encloses all cells and forms the boundaries of many eukaryotic organelles.
	membrane domain	Functionally and structurally specialized region in the membrane of a cell or organelle; typically characterized by the presence of specific proteins.
	membrane potential	Voltage difference across a membrane due to a slight excess of positive ions on one side and of negative ions on the other.
	membrane protein	A protein associated with the lipid bilayer of a cell membrane.
	membrane transport protein	Any transmembrane protein that provides a passageway for the movement of select substances across a cell membrane.
	membrane-enclosed organelle	Any organelle in a eukaryotic cell that is surrounded by a lipid bilayer, for example, the endoplasmic reticulum, Golgi apparatus, and lysosome.
	membrane-enclosed organelle	Any organelle in the eukaryotic cell that is surrounded by a lipid bilayer; for example, the endoplasmic reticulum, Golgi apparatus, and lysosome.
	messenger RNA (mRNA)	RNA molecule that specifies the amino acid sequence of a protein.
	metabolic pathway	Interconnected sequence of enzymatic reactions in which the product of one reaction is the substrate of the next.
	metabolism	The sum total of the chemical reactions that take place in the cells of a living organism.
	metaphase	Stage of mitosis in which chromosomes are firmly attached to the mitotic spindle at its equator but have not yet segregated toward opposite poles.
	metastasis	The spread of cancer cells from the initial site of the tumor to form secondary tumors at other sites in the body.
	methyl (–CH3) group	Hydrophobic chemical group derived from methane (CH4). (See Panel 2–1, pp. 66–67.)
	Michaelis constant (KM)	Concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound.
	micro-	In the metric system, prefix denoting 10–6.
	micrograph	Any photograph or digital image taken through a microscope. Can be a light micrograph or an electron micrograph, depending on the type of microscope used.
	micrometer	Unit of length equal to one millionth (10–6) of a meter or 10–4 centimeter.
	microRNA (miRNA)	Small noncoding RNA that controls gene expression by base-pairing with a specific mRNA to regulate its stability and its translation.
	microscope	Instrument for viewing extremely small objects. A light microscope utilizes a focused beam of visible light and is used to examine cells and organelles. An electron microscope utilizes a beam of electrons and can be used to examine objects as small as individual molecules.
	microtubule	Long, stiff, cylindrical structure composed of the protein tubulin. Used by eukaryotic cells to organize their cytoplasm and guide the intracellular transport of macromolecules and organelles.
	microtubule-associated protein	Accessory protein that binds to microtubules; can stabilize microtubule filaments, link them to other cell structures, or transport various components along their length.
	milli-	In the metric system, prefix denoting 10–3.
	mismatch repair	Mechanism for recognizing and correcting incorrectly paired nucleotides—those that are noncomplementary.
	mitochondrion	(plural mitochondria) Membrane-enclosed organelle, about the size of a bacterium, that carries out oxidative phosphorylation and produces most of the ATP in eukaryotic cells.
	mitogen	An extracellular signal molecule that stimulates cell proliferation.
	mitosis	Division of the nucleus of a eukaryotic cell.
	mitotic chromosome	Highly condensed duplicated chromosome in which the two new chromosomes (also called sister chromatids) are still held together at the centromere. The structure chromosomes adopt during mitosis.
	mitotic spindle	Array of microtubules and associated molecules that forms between the opposite poles of a eukaryotic cell during mitosis and pulls duplicated chromosome sets apart.
	mobile genetic element	Short segment of DNA that can move, sometimes through an RNA intermediate, from one location in a genome to another; an important source of genetic variation in most genomes. Also called a transposon.
	model organism	A living thing selected for intensive study as a representative of a large group of species. Examples include the mouse (representing mammals), the yeast Saccharomyces cerevisiae (representing a unicellular eukaryote), and Escherichia coli (representing bacteria).
	mole	The amount of a substance, in grams, that is equal to its molecular weight; this quantity will contain 6 × 1023 molecules of the substance.
	molecular mass	The weight of a molecule expressed in daltons, the atomic mass unit that closely approximates the mass of a hydrogen atom.
	molecular switch	Intracellular signaling protein that toggles between an active and inactive state in response to receiving a signal.
	molecular weight	Sum of the atomic weights of the atoms in a molecule; as a ratio of molecular masses, it is a number without units.
	molecule	Group of atoms joined together by covalent bonds.
	monomer	Small molecule that can be linked to others of a similar type to form a larger molecule (polymer).
	monomeric GTPase	Small, single-subunit GTP-binding protein. Proteins of this family, such as Ras and Rho, are part of many different signaling pathways.
	motor protein	Protein such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule.
	mutation	A randomly produced, permanent change in the nucleotide sequence of DNA.
	myofibril	Long, cylindrical structure that constitutes the contractile element of a muscle cell; constructed of arrays of highly organized bundles of actin, myosin, and other accessory proteins.
	myosin	Type of motor protein that uses ATP to drive movements along actin filaments. One subtype interacts with actin to form the thick contractile bundles of skeletal muscle.
	myosin filament	Polymer composed of interacting molecules of myosin-II; interaction with actin promotes contraction in muscle and nonmuscle cells.
	myosin-I	Simplest type of myosin, present in all cells; consists of a single actin-binding head and a tail that can attach to other molecules or organelles.
	myosin-II	Type of myosin that exists as a dimer with two actinbinding heads and a coiled-coil tail; can associate to form long myosin filaments.
	N-terminus (amino terminus)	The end of a polypeptide chain that carries a free ?-amino group.
	Na+	Sodium ion—a positively charged ion that is a major constituent of living cells.
	Na+ pump (sodium pump)	Transporter found in the plasma membrane of most animal cells that actively pumps Na+ out of the cell and K+ in using the energy derived from ATP hydrolysis.
	NAD+ nicotine adenine dinucleotide	Activated carrier that accepts a hydride ion (H–) from a donor molecule, thereby producing NADH. Widely used in the energy-producing breakdown of sugar molecules. (See Figure 3–34.)
	NADH	Activated carrier widely used in the energy-producing breakdown of sugar molecules. (See Figure 3–34.)
	NADPH )(nicotine adenine dinucleotide phosphate)	Activated carrier closely related to NADH and used as an electron donor in biosynthetic pathways. In the process it is oxidized to NADP+. (See Figure 3–35.)
	nanometer	Unit of length that represents 10–9 (one billionth of a) meter; commonly used to measure molecules and organelles.
	Nernst equation	An equation that relates the concentrations of an inorganic ion on the two sides of a permeable membrane to the membrane potential at which there would be no net movement of the ion across the membrane.
	nerve terminal	Structure at the end of an axon that signals to another neuron or target cell.
	neuron	An electrically excitable cell that integrates and transmits information as part of the nervous system; a nerve cell.
	neurotransmitter	Small signaling molecule secreted by a nerve cell at a synapse to transmit information to a postsynaptic cell. Examples include acetylcholine, glutamate, GABA, and glycine.
	nitric oxide (NO)	Locally acting gaseous signal molecule that diffuses across cell membranes to affect the activity of intracellular proteins.
	nitrogen fixation	Conversion of nitrogen gas from the atmosphere into nitrogen-containing molecules by soil bacteria and cyanobacteria.
	noncovalent bond	Chemical association that does not involve the sharing of electrons; singly are relatively weak, but can sum together to produce strong, highly specific interactions between molecules. Examples are hydrogen bonds and van der Waals attractions.
	nonhomologous end joining	A quick-and-dirty mechanism for repairing doublestrand breaks in DNA that involves quickly bringing together, trimming, and rejoining the two broken ends; results in a loss of information at the site of repair.
	nonpolar	Describes a molecule that lacks a local accumulation of positive or negative charge; generally insoluble in water.
	nuclear envelope	Double membrane surrounding the nucleus. Consists of outer and inner membranes, perforated by nuclear pores.
	nuclear lamina	Fibrous layer on the inner surface of the inner nuclear membrane formed as a network of intermediate filaments made from nuclear lamins.
	nuclear magnetic resonance (NMR) spectroscopy	Technique used for determining the threedimensional structure of a protein in solution.
	nuclear pore	Channel through which selected large molecules move between the nucleus and the cytoplasm.
	nuclear receptor	Protein inside a eukaryotic cell that, on binding to a signal molecule, enters the nucleus and regulates transcription.
	nucleic acid	Macromolecule that consists of a chain of nucleotides joined together by phosphodiester bonds; RNA or DNA.
	nucleolus	Large structure within the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled.
	nucleoside	Molecule made of a nitrogen-containing ring compound attached to a sugar, either ribose (in RNA) or deoxyribose (in DNA).
	nucleosome	Beadlike structural unit of a eukaryotic chromosome composed of a short length of DNA wrapped around a core of histone proteins; includes a nucleosomal core particle (DNA plus histone protein) along with a segment of linker DNA that ties the core particles together.
	nucleotide	Basic building block of the nucleic acids, DNA and RNA; includes a nucleoside with a series of one or more phosphate groups linked to its sugar.
	nucleus	In biology, refers to the prominent, rounded structure that contains the DNA of a eukaryotic cell. In chemistry, refers to the dense, positively charged center of an atom.
	Okazaki fragment	Short length of DNA produced on the lagging strand during DNA replication. Adjacent fragments are rapidly joined together by DNA ligase to form a continuous DNA strand.
	oligo-	Prefix that denotes a short polymer (oligomer). May be made of amino acids (oligopeptide), sugars (oligosaccharide), or nucleotides (oligonucleotide).
	oncogene	A gene that, when activated, can potentially make a cell cancerous. Typically a mutant form of a normal gene (proto-oncogene) involved in the control of cell growth or division.
	open reading frame (ORF)	Long sequence of nucleotides that contains no stop codon; used to identify potential protein-coding sequences in DNA.
	optogenetics	Technique that uses light to control the activity of neurons into which light-gated ion channels have been artificially introduced.
	organelle	A discrete structure or subcompartment of a eukaryotic cell that is specialized to carry out a particular function. Examples include mitochondria and the Golgi apparatus.
	organic chemistry	The branch of chemistry concerned with compounds made of carbon. Includes essentially all of the molecules from which living cells are made, apart from water and metal ions such as Na+.
	organic molecule	Chemical compound that contains carbon and hydrogen.
	origin recognition complex (ORC)	Assembly of proteins that is bound to the DNA at origins of replication in eukaryotic chromosomes throughout the cell cycle.
	osmosis	Passive movement of water across a cell membrane from a region where the concentration of water is high (because the concentration of solutes is low) to a region where the concentration of water is low (and the concentration of solutes is high).
	oxidation	Removal of electrons from an atom, as occurs during the addition of oxygen to a carbon atom or when a hydrogen is removed from a carbon atom. The opposite of reduction. (See Figure 3–11.)
	oxidative phosphorylation	Process in bacteria and mitochondria in which ATP formation is driven by the transfer of electrons from food molecules to molecular oxygen.
	p53	Transcription regulator that controls the cell’s response to DNA damage, preventing the cell from entering S phase until the damage has been repaired or inducing the cell to commit suicide if the damage is too extensive; mutations in the gene encoding this protein are found in many human cancers.
	pairing	In meiosis, the process by which a pair of duplicated homologous chromosomes attach to one another to form a structure containing four sister chromatids.
	passive transport	The spontaneous movement of a solute down its concentration gradient across a cell membrane via a membrane transport protein, such as a channel or a transporter.
	patch-clamp recording	Technique used to monitor the activity of ion channels in a membrane; involves the formation of a tight seal between the tip of a glass electrode and a small region of cell membrane, and manipulation of the membrane potential by varying the concentrations of ions in the electrode.
	pedigree	Chart showing the line of descent, or ancestry, of an individual organism.
	peptide bond	Chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid. (See Panel 2–5, pp. 74–75.)
	peroxisome	Small membrane-enclosed organelle that contains enzymes that degrade lipids and destroy toxins.
	pH scale	Concentration of hydrogen ions in a solution, expressed as a logarithm. Thus, an acidic solution with pH 3 will contain 10–3 M hydrogen ions.
	phagocytic cell	A cell such as a macrophage or neutrophil that is specialized to take up particles and microorganisms by phagocytosis.
	phagocytosis	The process by which particulate material is engulfed (“eaten”) by a cell. Prominent in predatory cells, such as Amoeba proteus, and in cells of the vertebrate immune system such as macrophages.
	phenotype	The observable characteristics of a cell or organism.
	phosphatidylcholine	Common phospholipid present in abundance in most cell membranes; uses choline attached to a phosphate as its head group.
	phosphodiester bond	Strong covalent bond that forms the backbone of DNA and RNA molecules; links the 3? carbon of one sugar to the 5? carbon of another. (See Figure 2–26.)
	phosphoinositide 3-kinase (PI 3-kinase)	Enzyme that phosphorylates inositol phospholipids in the plasma membrane, which generates docking sites for intracellular signaling proteins that promote cell growth and survival.
	phospholipase C	Enzyme associated with the plasma membrane that generates two small messenger molecules in response to activation.
	phospholipid	A major type of lipid molecule in many cell membranes. Generally composed of two fatty acid tails linked to one of a variety of phosphate-containing polar groups.
	phosphorylation—	see protein phosphorylation
	photosynthesis	The process by which plants, algae, and some bacteria use the energy of sunlight to drive the synthesis of organic molecules from carbon dioxide and water.
	photosystem	Large multiprotein complex containing chlorophyll that captures light energy and converts it into chemical energy; consists of a set of antenna complexes and a reaction center.
	phragmoplast	In a dividing plant cell, structure made of microtubules and membrane vesicles that guides the formation of a new cell wall.
	phylogenetic tree	Diagram or “family tree” showing the evolutionary history of a group of organisms or proteins.
	pinocytosis	Type of endocytosis in which soluble materials are taken up from the environment and incorporated into vesicles for digestion. (Literally, “cell drinking.”)
	plasma membrane	The protein-containing lipid bilayer that surrounds a living cell.
	plasmid	Small circular DNA molecule that replicates independently of the genome. Used extensively as a vector for DNA cloning.
	plasmodesma	(plural plasmodesmata) Cell–cell junction that connects one plant cell to the next; consists of a channel of cytoplasm lined by membrane.
	pluripotent	Capable of giving rise to any type of cell or tissue.
	pluripotent stem cell	Cell capable of giving rise to any of the specialized cell types in the body.
	point mutation	Change in a single nucleotide pair in a DNA sequence.
	polar	In chemistry, describes a molecule or bond in which electrons are distributed unevenly.
	polarity	An inherent asymmetry that allows one end of an object to be distinguished from another; can refer to a molecule, a polymer (such as an actin filament), or even a cell (for example, an epithelial cell that lines the mammalian small intestine).
	polyadenylation	The addition of multiple adenine nucleotides to the 3? end of a newly synthesized mRNA molecule.
	polymer	Long molecule made by covalently linking multiple identical or similar subunits (monomers).
	polymerase	General term for an enzyme that catalyzes addition of subunits to a nucleic acid polymer. DNA polymerase, for example, makes DNA, and RNA polymerase makes RNA.
	polymerase chain reaction (PCR)	Technique for amplifying selected regions of DNA by multiple cycles of DNA synthesis; can produce billions of copies of a given sequence in a matter of hours.
	polymorphism	DNA sequence for which two or more variants are present at high frequency in the general population.
	polynucleotide	A molecular chain of nucleotides chemically linked by a series of phosphodiester bonds. A strand of RNA or DNA.
	polypeptide backbone	Repeating sequence of atoms (–N–C–C–) that forms the core of a protein molecule and to which the amino acid side chains are attached.
	polypeptide; polypeptide chain	Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.
	polyribosome	Messenger RNA molecule to which multiple ribosomes are attached and engaged in protein synthesis.
	polysaccharide	Linear or branched polymer composed of sugars. Examples are glycogen, hyaluronic acid, and cellulose.
	positive feedback loop	An important form of regulation in which the end product of a reaction or pathway stimulates continued activity; controls a variety of biological processes, including enzyme activity, cell signaling, and gene expression.
	post-transcriptional control	Regulation of gene expression that occurs after transcription of the gene has begun; examples include RNA splicing and RNA interference.
	primary structure	The amino acid sequence of a protein.
	primary transcript—	see transcription
	primase	An RNA polymerase that uses DNA as a template to produce an RNA fragment that serves as a primer for DNA synthesis.
	primer	In DNA replication, a short length of RNA made at the beginning of the synthesis of each DNA fragment; these RNA segments are subsequently removed and filled in with DNA.
	processive	Describes an ability to catalyze consecutive reactions or undergo multiple conformational changes without releasing a substrate. Examples include replication by DNA polymerase or the movement of motor proteins involved in transport, such as kinesin.
	programmed cell death	A tightly controlled form of cell suicide that allows cells that are unneeded or unwanted to be eliminated from an adult or developing organism; also called apoptosis.
	prokaryote	Major category of living cells distinguished by the absence of a nucleus. Prokaryotes include the archaea and the eubacteria (commonly called bacteria).
	prometaphase	Stage of mitosis in which the nuclear envelope breaks down and duplicated chromosomes are captured by the spindle microtubules; precedes metaphase.
	promoter	DNA sequence that initiates gene transcription; includes sequences recognized by RNA polymerase.
	proofreading	The process by which DNA polymerase corrects its own errors as it moves along DNA.
	prophase	First stage of mitosis, during which the duplicated chromosomes condense and the mitotic spindle forms.
	protease	Enzyme that degrades proteins by hydrolyzing their peptide bonds.
	proteasome	Large protein machine that degrades proteins that are damaged, misfolded, or no longer needed by the cell; its target proteins are marked for destruction primarily by the attachment of a short chain of ubiquitin.
	protein	Polymer built from amino acids that provides cells with their shape and structure and performs most of their activities.
	protein complex—	see complex
	protein domain	Segment of a polypeptide chain that can fold into a compact stable structure and that usually carries out a specific function.
	protein family	A group of polypeptides that shares a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. Individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins.
	protein kinase	Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.
	protein kinase C (PKC)	Enzyme that phosphorylates target proteins in response to a rise in diacylglycerol and Ca2+ ions.
	protein machine	Large assembly of protein molecules that operates as a unit to perform a complex series of biological activities, such as replicating DNA.
	protein phosphatase	Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site.
	protein phosphorylation	The covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alters the activity or properties of the target protein.
	proteoglycan	Molecule consisting of one or more glycosaminoglycan chains attached to a core protein; these aggregates can form gels that regulate the passage of molecules through the extracellular medium and guide cell migration.
	proteolysis	Degradation of a protein by means of a protease.
	proteomics	The large-scale study of the structure and function of proteins.
	proto-oncogene	Gene that when mutated or overexpressed can transform a normal cell into a cancerous one.
	proton	Positively charged particle found in the nucleus of every atom; also, another name for a hydrogen ion (H+).
	proton (H+) pump	A transporter that actively moves H+ across a cell membrane, thereby generating a gradient that can be used by the cell, for example, to import other solutes.
	protozoan	(plural protozoa) A free-living, nonphotosynthetic, single-celled, motile eukaryote.
	pump	Transporter that uses a source of energy, such as ATP hydrolysis or sunlight, to actively move a solute across a membrane against its electrochemical gradient.
	purifying selection	Preservation of a specific nucleotide sequence driven by the elimination of individuals carrying mutations that interfere with its functions.
	purine	A double-ringed, nitrogen-containing compound found in DNA and RNA. Examples are adenine and guanine. (See Panel 2–6, pp. 76–77.)
	pyrimidine	A nitrogen-containing, six-membered ring compound found in DNA and RNA. Examples are thymine, cytosine, and uracil. (See Panel 2–6, pp. 76–77.)
	pyruvate	Three-carbon metabolite that is the end product of the glycolytic breakdown of glucose; provides a crucial link to the citric acid cycle and many biosynthetic pathways.
	quaternary structure	Complete structure formed by multiple, interacting polypeptide chains within a protein molecule.
	quinone	Small, lipid-soluble, mobile electron carrier molecule found in the respiratory and photosynthetic electrontransport chains. (See Figure 14–23.)
	Rab protein	A family of small GTP-binding proteins present on the surfaces of transport vesicles and organelles that serves as a molecular marker to help ensure that transport vesicles fuse only with the correct membrane.
	Ras	One of a large family of small GTP-binding proteins (the monomeric GTPases) that helps relay signals from cell-surface receptors to the nucleus. Many human cancers contain an overactive mutant form of the protein.
	reaction center	In photosynthetic membranes, a protein complex that contains a specialized pair of chlorophyll molecules that performs photochemical reactions to convert the energy of photons (light) into high-energy electrons for transport down the photosynthetic electrontransport chain.
	reading frame	One of the three possible ways in which a set of successive nucleotide triplets can be translated into protein, depending on which nucleotide serves as the starting point.
	receptor	Protein that recognizes and responds to a specific signal molecule.
	receptor serine/threonine kinase	Enzyme-coupled receptor that phosphorylates target proteins on serine or threonine.
	receptor tyrosine kinase (RTK)	Enzyme-coupled receptor in which the intracellular domain has a tyrosine kinase activity, which is activated by ligand binding to the receptor’s extracellular domain.
	receptor-mediated endocytosis	Mechanism of selective uptake of material by animal cells in which a macromolecule binds to a receptor in the plasma membrane and enters the cell in a clathrin-coated vesicle.
	recombinant DNA molecule	A DNA molecule that is composed of DNA sequences from different sources.
	recombinant DNA technology	The collection of techniques by which DNA segments from different sources are combined to make new DNA. Recombinant DNAs are widely used in the cloning of genes, in the genetic modification of organisms, and in molecular biology generally.
	recombination	Process in which an exchange of genetic information occurs between two chromosomes or DNA molecules. Enzyme-mediated recombination can occur naturally in living cells or in a test tube using purified DNA and enzymes that break and re-ligate DNA strands.
	redox pair	Two molecules that can be interconverted by the gain or loss of an electron; for example, NADH and NAD+.
	redox potential	A measure of the tendency of a given redox pair to donate or accept electrons.
	redox reaction	A reaction in which electrons are transferred from one chemical species to another. An oxidation– reduction reaction.
	reduction	Addition of electrons to an atom, as occurs during the addition of hydrogen to a carbon atom or the removal of oxygen from it. The opposite of oxidation. (See Figure 3–11.)
	regulatory DNA sequence	DNA sequence to which a transcription regulator binds to determine when, where, and in what quantities a gene is to be transcribed into RNA.
	regulatory RNA	RNA molecule that plays a role in controlling gene expression.
	replication fork	Y-shaped junction that forms at the site where DNA is being replicated.
	replication origin	Nucleotide sequence at which DNA replication is initiated.
	reporter gene	Gene encoding a protein whose activity is easy to monitor experimentally; used to study the expression pattern of a target gene or the localization of its protein product.
	repressor	A protein that binds to a specific regulatory region of DNA to prevent transcription of an adjacent gene.
	reproductive cloning	The artificial production of genetically identical copies of an animal by, for example, the transplantation of a somatic cell nucleus into an enucleated fertilized egg.
	respiration	General term for any process in a cell in which the uptake of molecular oxygen (O2) is coupled to the production of CO2.
	respiratory enzyme complex	Set of proteins in the inner mitochondrial membrane that facilitates the transfer of high-energy electrons from NADH to water while pumping protons into the intermembrane space.
	resting membrane potential	Voltage difference across the plasma membrane when a cell is not stimulated.
	restriction nuclease	Enzyme that can cleave a DNA molecule at a specific, short sequence of nucleotides. Extensively used in recombinant DNA technology.
	retrotransposon	Type of mobile genetic element that moves by being first transcribed into an RNA copy that is reconverted to DNA by reverse transcriptase and inserted elsewhere in the chromosomes.
	retrovirus	RNA-containing virus that replicates in a cell by first making a double-stranded DNA intermediate that becomes integrated into the cell’s chromosome.
	reverse transcriptase	Enzyme that makes a double-stranded DNA copy from a single-stranded RNA template molecule. Present in retroviruses and as part of the transposition machinery of retrotransposons.
	Rho protein family	Family of small, monomeric GTPases that controls the organization of the actin cytoskeleton.
	ribosomal RNA (rRNA)	RNA molecule that forms the structural and catalytic core of the ribosome.
	ribosome	Large macromolecular complex, composed of ribosomal RNAs and ribosomal proteins, that translates messenger RNA into protein.
	ribozyme	An RNA molecule with catalytic activity.
	RNA (ribonucleic acid)	Molecule produced by the transcription of DNA; usually single-stranded, it is a polynucleotide composed of covalently linked ribonucleotide subunits. Serves a variety of structural, catalytic, and regulatory functions in cells.
	RNA capping	The modification of the 5? end of a maturing RNA transcript by the addition of an atypical nucleotide.
	RNA interference (RNAi)	Cellular mechanism activated by double-stranded RNA molecules that results in the destruction of RNAs containing a similar nucleotide sequence. It is widely exploited as an experimental tool for preventing the expression of selected genes (gene silencing).
	RNA polymerase	Enzyme that catalyzes the synthesis of an RNA molecule from a DNA template using nucleoside triphosphate precursors.
	RNA primer—	see primer
	RNA processing	Broad term for the modifications that a precursor mRNA undergoes as it matures into an mRNA. It typically includes 5? capping, RNA splicing, and 3? polyadenylation.
	RNA splicing	Process in which intron sequences are excised from RNA molecules in the nucleus during the formation of a mature messenger RNA.
	RNA transcript	RNA molecule produced by transcription that is complementary to one strand of DNA.
	RNA world	Hypothetical period in Earth’s early history in which life-forms were thought to use RNA both to store genetic information and to catalyze chemical reactions.
	RNA-Seq	Sequencing technique used to determine directly the nucleotide sequence of a collection of RNAs.
	rough endoplasmic reticulum	Region of the endoplasmic reticulum associated with ribosomes and involved in the synthesis of secreted and membrane-bound proteins.
	S cyclin	Regulatory protein that helps to launch the S phase of the cell cycle.
	S phase	Period during a eukaryotic cell cycle in which DNA is synthesized.
	S-Cdk	Protein complex whose activity initiates DNA replication; consists of an S cyclin plus a cyclindependent protein kinase (Cdk).
	sarcomere	Highly organized assembly of actin and myosin filaments that serves as the contractile unit of a myofibril in a muscle cell.
	saturated	Describes an organic molecule that contains a full complement of hydrogen; in other words, no double or triple carbon–carbon bonds.
	second messenger	Small intracellular signaling molecule generated or released in response to an extracellular signal. Examples include cAMP, IP3, and Ca2+.
	secondary structure	Regular local folding pattern of a polymeric molecule. In proteins, it refers to ? helices and ? sheets.
	secretion	Production and release of a substance from a cell.
	secretory vesicle	Membrane-enclosed organelle in which molecules destined for secretion are stored prior to release. Sometimes called a secretory granule because darkly staining contents make the organelle visible as a small solid object.
	segregation	During cell division, the process by which duplicated chromosomes are organized and then separated into the chromosome sets that will be inherited by each of the daughter cells.
	sequence	The linear order of monomers in a large molecule, for example amino acids in a protein or nucleotides in DNA; encodes information that specifies a macromolecule’s precise biological function.
	serine/threonine kinase	Enzyme that phosphorylates target proteins on serines or threonines.
	sex chromosome	Type of chromosome that determines the sex of an individual and directs the development of sexual characteristics. In mammals, the X and Y chromosomes.
	sexual reproduction	Mode of reproduction in which the genomes of two individuals are mixed to produce an individual that is genetically distinct from its parents.
	side chain	Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid its unique properties.
	signal sequence	Amino acid sequence that directs a protein to a specific location in the cell, such as the nucleus or mitochondria.
	signal transduction	Conversion of an impulse or stimulus from one physical or chemical form to another. In cell biology, the process by which a cell responds to an extracellular signal.
	signaling cascade	Sequence of linked reactions, often including phosphorylation and dephosphorylation, that carries information within a cell, often amplifying an initial signal.
	single-nucleotide polymorphism (SNP)	Form of genetic variation in which one portion of the population differs from another in terms of which nucleotide is found at a particular position in the genome.
	sister chromatid	Copy of a chromosome, produced by DNA replication, that remains bound to the other copy.
	site-directed mutagenesis	Technique by which a mutation can be made at a particular site in DNA.
	site-specific recombination	Type of genetic exchange in which one segment of DNA is inserted into another at a particular nucleotide sequence; does not require extensive similarity between the two participating DNA sequences, which can be on different DNA molecules or within a single DNA molecule.
	small interfering RNA (siRNA)	Short length of RNA produced from double-stranded RNA during the process of RNA interference. It basepairs with identical sequences in other RNAs, leading to the inactivation or destruction of the target RNA.
	small intracellular signaling molecule	Nucleotide, lipid, ion, or other small molecule generated or released in response to an extracellular signal. Examples include cAMP, IP3, and Ca2+. Also called second messengers.
	small messenger—	see second messenger
	small nuclear ribonucleoprotein (snRNP)	Complex made of RNA and protein that recognizes RNA splice sites and participates in the chemistry of splicing; together these complexes form the core of the spliceosome.
	small nuclear RNA (snRNA)	RNA molecule of around 200 nucleotides that participates in RNA splicing.
	smooth endoplasmic reticulum (SER0	Region of the endoplasmic reticulum not associated with ribosomes; involved in the synthesis of lipids.
	SNARE	One of a family of membrane proteins responsible for the selective fusion of vesicles with a target membrane inside the cell.
	sodium pump—	see Na+ pump
	solute	Any substance that is dissolved in a liquid. The liquid is called the solvent.
	somatic cell	Any cell that forms part of the body of a plant or animal that is not a germ cell or germ-line precursor.
	specificity	Selective affinity of one molecule for another that permits the two to bind or react, even in the presence of a vast excess of unrelated molecular species.
	spindle pole	Centrosome from which microtubules radiate to form the mitotic spindle.
	spliceosome	Large assembly of RNA and protein molecules that splices introns out of pre-mRNA in the nucleus of eukaryotic cells.
	starch	Polysaccharide composed exclusively of glucose units, used as an energy store in plant cells.
	stem cell	Relatively undifferentiated, self-renewing cell that produces daughter cells that can either differentiate into more specialized cell types or can retain the developmental potential of the parent cell.
	steroid hormone	Hydrophobic signal molecule related to cholesterol; can pass through the plasma membrane to interact with intracellular receptors that affect gene expression in the target cell. Examples include estrogen and testosterone.
	stroma	In a chloroplast, the large interior space that contains the enzymes needed to incorporate CO2 into sugars during the carbon-fixation stage of photosynthesis; equivalent to the matrix of a mitochondrion.
	substrate	A molecule on which an enzyme acts.
	substratum	Solid surface to which a cell adheres.
	subunit	A monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. Can also refer to a complete molecule that forms part of a larger molecule. Many proteins, for example, are composed of multiple polypeptide chains, each of which is called a protein subunit.
	sugar	A substance made of carbon, hydrogen, and oxygen with the general formula (CH2O)n. A carbohydrate or saccharide. The “sugar” of everyday use is sucrose, a sweet-tasting disaccharide made of glucose and fructose.
	sulfhydryl group (SH-)thiol	Chemical group containing sulfur and hydrogen found in the amino acid cysteine and other molecules. Two can join together to produce a disulfide bond.
	survival factor	Extracellular signal molecule that must be present to suppress apoptosis.
	symbiosis	Intimate association between two organisms of different species from which both derive a long-term selective advantage.
	symport	A transporter that transfers two different solutes across a cell membrane in the same direction.
	synapse	Specialized junction where a nerve cell communicates with another cell (such as a nerve cell, muscle cell, or gland cell), usually via a neurotransmitter secreted by the nerve cell.
	synaptic plasticity	The ability of a synapse to adjust its strength for a prolonged period, either up or down, depending on its use; thought to play an important role in learning and memory.
	synaptic vesicle	Small membrane-enclosed sac filled with neurotransmitter that releases its contents by exocytosis at a synapse.
	telomerase	Enzyme that elongates telomeres, synthesizing the repetitive nucleotide sequences found at the ends of eukaryotic chromosomes.
	telomere	Repetitive nucleotide sequence that caps the ends of linear chromosomes. Counteracts the tendency of the chromosome otherwise to shorten with each round of replication.
	telophase	Final stage of mitosis in which the two sets of separated chromosomes decondense and become enclosed by a nuclear envelope.
	template	A molecular structure that serves as a pattern for the production of other molecules. For example, one strand of DNA directs the synthesis of the complementary DNA strand.
	tertiary structure	Complete three-dimensional structure of a fully folded protein.
	therapeutic cloning	Procedure that uses nuclear transplantation to generate cells for tissue repair and other such purposes, as opposed to producing whole multicellular individuals.
	thioester bond	High-energy bond formed by a condensation reaction between an acid (acyl) group and a thiol group (–SH); seen, for example, in acetyl CoA and in many enzyme–substrate complexes.
	thylakoid	In a chloroplast, the flattened disclike sac whose membranes contain the proteins and pigments that convert light energy into chemical energy during photosynthesis.
	tight junction	Cell–cell junction that seals adjacent epithelial cells together, preventing the passage of most dissolved molecules from one side of the epithelial sheet to the other.
	tissue	Cooperative assembly of cells and matrix woven together to form a distinctive multicellular fabric with a specific function.
	trans	Beyond, or on the other side.
	trans Golgi network (TGN)	Portion of the Golgi apparatus furthest from the endoplasmic reticulum and from which proteins and lipids leave for lysosomes, secretory vesicles, or the cell surface.
	transcription	Process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence.
	transcription factor	Term loosely applied to any protein required to initiate or regulate transcription in eukaryotes. Includes transcription regulators as well as the general transcription factors.
	transcription regulator	Protein that binds specifically to a regulatory DNA sequence and is involved in controlling whether a gene is switched on or off.
	transcriptional activator	A protein that binds to a specific regulatory region of DNA to permit transcription of an adjacent gene.
	transcriptional repressor	A protein that binds to a specific regulatory region of DNA to prevent transcription of an adjacent gene.
	transfer RNA (tRNA)	Small RNA molecule that serves as an adaptor that “reads” a codon in mRNA and adds the correct amino acid to the growing polypeptide chain.
	transformation	Process by which cells take up DNA molecules from their surroundings and then express genes on that DNA.
	transgenic organism	A plant or animal that has stably incorporated into its genome one or more genes derived from another cell or organism.
	transition state	Structure that forms transiently during the course of a chemical reaction; in this configuration, a molecule has the highest free energy, and is no longer a substrate, but is not yet a product.
	translation	Process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into protein.
	translation initiation factor	Protein that promotes the proper association of ribosomes with mRNA and is required for the initiation of protein synthesis.
	transmitter-gated ion channel	Transmembrane receptor protein or protein complex that opens in response to the binding of a neurotransmitter, allowing the passage of a specific inorganic ion; its activation can trigger an action potential in a postsynaptic cell.
	transport vesicle	Membrane vesicle that carries proteins from one intracellular compartment to another, for example, from the endoplasmic reticulum to the Golgi apparatus.
	transporter	Membrane transport protein that moves a solute across a cell membrane by undergoing a series of conformational changes.
	transposon	General name for short segments of DNA that can move from one location to another in the genome. Also known as mobile genetic elements.
	triacylglycerol	Compound made of three fatty acid tails covalently attached to glycerol. A storage form of fat, the main constituent of fat droplets in animal tissues (in which the fatty acids are saturated) and of vegetable oil from plants (in which the fatty acids are mainly unsaturated).
	tryptophan repressor	In bacteria, a transcription regulator that, in the presence of tryptophan, shuts off production of the tryptophan biosynthetic enzymes by binding to the promoter region that controls expression of those genes.
	tubulin	Protein from which microtubules are made.
	?-tubulin ring	Protein complex in centrosomes from which microtubules grow.
	tumor suppressor gene	A gene that in a normal tissue cell inhibits cancerous behavior. Loss or inactivation of both copies of such a gene from a diploid cell can cause it to behave as a cancer cell.
	turgor pressure	Force exerted on a plant cell wall when water enters the cell by osmosis; keeps plant from wilting.
	turnover number	The number of substrate molecules an enzyme can convert into product per second.
	tyrosine kinase	Enzyme that phosphorylates target proteins on tyrosines.
	unfolded protein response (UPR)	Molecular program triggered by the accumulation of misfolded proteins in the endoplasmic reticulum. Allows cells to expand the endoplasmic reticulum and produce more of the molecular machinery needed to restore proper protein folding and processing.
	unsaturated	Describes an organic molecule that contains one or more double or triple bonds between its carbon atoms.
	valence	The number of electrons an atom must gain or lose (either by electron sharing or electron transfer) to achieve a filled outer shell. For example, Na must lose one electron, and Cl must gain one electron. This number is also equal to the number of single bonds that the atom can form.
	van der Waals attraction	Weak noncovalent interaction, due to fluctuating electrical charges, that comes into play between two atoms within a short distance of each other.
	vector	DNA molecule that is used as a vehicle to carry a fragment of DNA into a recipient cell for the purpose of gene cloning; examples include plasmids, engineered viruses, and artificial chromosomes.
	vesicle	Small, membrane-enclosed, spherical sac in the cytoplasm of a eukaryotic cell.
	vesicular transport	Movement of material between organelles in the eukaryotic cell via membrane-enclosed vesicles.
	virus	Particle consisting of nucleic acid (RNA or DNA) enclosed in a protein coat and capable of replicating within a host cell and spreading from cell to cell. Often the cause of disease.
	Vmax	The maximum rate of an enzymatic reaction, reached when the active sites of the enzyme molecules in a sample are fully occupied by substrate.
	voltage-gated channel	Channel protein that permits the passage of selected ions, such as Na+, across a membrane in response to changes in the membrane potential. Found primarily in electrically excitable cells such as nerve and muscle.
	voltage-gated ion channel	Protein that selectively allows particular ions to cross a membrane in response to a change in membrane potential. Found mainly in electrically excitable cells such as nerve and muscle cells.
	voltage-gated Na+ channel	Protein in the plasma membrane of electrically excitable cells that opens in response to membrane depolarization, allowing Na+ to enter the cell. It is responsible for action potentials in these cells.
	wild type	Typical non-mutant form of a species, gene, or characteristic as it occurs in nature.
	Wnt protein	Member of a family of extracellular signal molecules that regulates cell proliferation and migration during embryonic development and that maintains stem cells in a proliferative state.
	X chromosome	Larger of the two sex chromosomes in mammals. The cells of males contain one, and females possess two.
	X-ray crystallography	Technique used to determine the three-dimensional structure of a protein molecule by analyzing the pattern produced when a beam of X-rays is passed through an ordered array of the protein.
	Y chromosome	Smaller of the two sex chromosomes of mammals. Present in a single copy only in the cells of males, contains genes that direct the development of male sex organs and characteristics.
	yeast	Common term for several families of eukaryotic unicellular fungi used as model organisms. Includes species used for brewing beer and making bread, as well as species that cause disease.
	zygote	Diploid cell produced by fusion of a male and a female gamete. A fertilized egg.

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