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Cell_Biology_Alberts. antigen A molecule that can induce an adaptive immune response or that can bind to an antibody or T cell receptor. antigen-presenting cell Cell that displays foreign antigen complexed with an MHC protein on its surface for presentation to T lymphocytes. antigenic determinant Specific region of an antigen that binds to an antibody or a complementary receptor on the surface of a B cell (BCR) or T cell (TCR). antigenic variation Ability to change the antigens displayed on the cell surface; a property of some pathogenic microorganisms that enables them to evade attack by the adaptive immune system. antiparallel Describes the relative orientation of the two strands in a DNA double helix or two paired regions of a polypeptide chain; the polarity of one strand is opposite to that of the other. antiporter Carrier protein that transports two different ions or small molecules across a membrane in opposite directions, either simultaneously or in sequence. (Figure 11–8)


Cell_Biology_Alberts

Cell_Biology_Alberts. antiporter Carrier protein that transports two different ions or small molecules across a membrane in opposite directions, either simultaneously or in sequence. (Figure 11–8) Apaf1 Adaptor protein of the intrinsic apoptotic pathway; on binding cytochrome c, oligomerizes to form an apoptosome. apical Referring to the tip of a cell, a structure, or an organ. The apical surface of an epithelial cell is the exposed free surface, opposite to the basal surface. The basal surface rests on the basal lamina that separates the epithelium from other tissue. apoptosis Form of programmed cell death, in which a “suicide” program is activated within an animal cell, leading to rapid cell death mediated by intracellular proteolytic enzymes called caspases. apoptosome Heptamer of Apaf1 proteins that forms on activation of the intrinsic apoptotic pathway; it recruits and activates initiator caspases that subsequently activate downstream executioner caspases to induce apoptosis.


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Cell_Biology_Alberts. aquaporin (water channel) Channel protein embedded in the plasma membrane that greatly increases the cell’s permeability to water, allowing transport of water, but not ions, at a high rate across the membrane. archaeon (plural arch[a]ea) (archaebacterium) Single-celled organism without a nucleus, superficially similar to bacteria. At a molecular level, more closely related to eukaryotes in genetic machinery than are bacteria. Archaea and bacteria together make up the prokaryotes. (Figure 1–17) ARF proteins Monomeric GTPase in the Ras superfamily responsible for regulating both COPI coat assembly and clathrin coat assembly. (Table 15–5, p. 854) ARP (actin-related protein) complex (Arp 2/3 complex) Complex of proteins that nucleates actin filament growth from the minus end.


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Cell_Biology_Alberts. ARP (actin-related protein) complex (Arp 2/3 complex) Complex of proteins that nucleates actin filament growth from the minus end. arrestin Member of a family of proteins that contributes to GPCR desensitization by preventing the activated receptor from interacting with G proteins and serving as an adaptor to couple the receptor to clathrin-dependent endocytosis. (Figure 15–42) astral microtubule In the mitotic spindle, any of the microtubules radiating from the aster which are not attached to a kinetochore of a chromosome. asymmetric cell division Cell division in which some important molecule or molecules are distributed unequally between the two daughter cells, causing these cells to become different from each other. ATM (ataxia telangiectasia mutated protein) Protein kinase activated by double-strand DNA breaks. If breaks are not repaired, ATM initiates a signal cascade that culminates in cell cycle arrest. Related to ATR.


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Cell_Biology_Alberts. ATP (adenosine 5′-triphosphate) Nucleoside triphosphate composed of adenine, ribose, and three phosphate groups. The principal carrier of chemical energy in cells. The terminal phosphate groups are highly reactive in the sense that their hydrolysis, or transfer to another molecule, takes place with the release of a large amount of free energy. (Figure 2–33) ATP synthase (F1Fo ATPase) Transmembrane enzyme complex in the inner membrane of mitochondria and the thylakoid membrane of chloroplasts. Catalyzes the formation of ATP from ADP and inorganic phosphate during oxidative phosphorylation and photosynthesis, respectively. Also present in the plasma membrane of bacteria. ATR (ataxia telangiectasia and Rad3 related protein) Protein kinase activated by DNA damage. If damage remains unrepaired, ATR helps initiate a signal cascade that culminates in cell cycle arrest. Related to ATM.


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Cell_Biology_Alberts. autoimmune disease Pathological state in which the body mounts a disabling adaptive immune response against one or more of its own molecules. autophagosome Organelle surrounded by a double membrane contains engulfed cytoplasmic cargo in the initial stages of autophagy. autophagy Digestion of cytoplasm and worn-out organelles by the cell’s own lysosomes. auxin Plant hormone, commonly indole-3-acetic acid, with numerous roles in plant growth and development. axon Long nerve cell projection that can rapidly conduct nerve impulses over long distances so as to deliver signals to other cells. axoneme Bundle of microtubules and associated proteins that forms the core of a cilium or a flagellum in eukaryotic cells and is responsible for their movements. bacterial artificial chromosome (BAC) Cloning vector that can accommodate large pieces of DNA, typically up to 1 million base pairs.


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Cell_Biology_Alberts. bacterial artificial chromosome (BAC) Cloning vector that can accommodate large pieces of DNA, typically up to 1 million base pairs. bacteriorhodopsin Pigmented protein found in the plasma membrane of a salt-loving archaeon, Halobacterium salinarium (Halobacterium halobium). Pumps protons out of the cell in response to light. bacterium (plural bacteria) (eubacterium) Member of the domain bacteria, one of the three main branches of the tree of life (archaea, bacteria, and eukaryotes). Bacteria and archaea both lack a distinct nuclear compartment, and together comprise the prokaryotes. (Figure 1–17) Bak A main effector Bcl2 family protein of the intrinsic pathway of apoptosis in mammalian cells that is bound to the mitochondrial outer membrane even in the absence of an apoptotic signal; activation is usually by activated pro-apoptotic BH3-only proteins. basal Situated near the base. Opposite the apical surface.


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Cell_Biology_Alberts. basal Situated near the base. Opposite the apical surface. basal lamina (plural basal laminae) Thin mat of extracellular matrix that separates epithelial sheets, and many other types of cells such as muscle or fat cells, from connective tissue. Sometimes called basement membrane. (Figure 19–51) base (1) A substance that can reduce the number of protons in solution, either by accepting H+ ions directly, or by releasing OH– ions, which then combine with H+ to form H2O. (2) The purines and pyrimidines in DNA and RNA are organic nitrogenous bases and are often referred to simply as bases. (Panel 2–2, pp. 92–93) base excision repair DNA repair pathway in which single faulty bases are removed from the DNA helix and replaced. Compare nucleotide excision repair. (Figure 5–41) base pair Two nucleotides in an RNA or DNA molecule that are held together by hydrogen bonds—for example, G paired with C, and A paired with T or U.


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Cell_Biology_Alberts. basement membrane Thin mat of extracellular matrix that separates epithelial sheets, and many other types of cells such as muscle or fat cells, from connective tissue. Also called basal lamina. (Figure 19–51) Bax A main effector Bcl2 family protein of the intrinsic pathway of apoptosis in mammalian cells; located mainly in the cytosol and translocates to the mitochondria only after activation, usually by activated pro-apoptotic BH3-only proteins. B cell receptor (BCR) The transmembrane immunoglobulin protein on the surface of a B cell that serves as its receptor for antigen. Bcl2 Anti-apoptotic Bcl2 family protein of the outer mitochondrial membrane that binds and inhibits pro-apoptotic Bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis.


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Cell_Biology_Alberts. Bcl2 family Family of intracellular proteins that either promote or inhibit apoptosis by regulating the release of cytochrome c and other mitochondrial proteins from the intermembrane space into the cytosol. BclXL Anti-apoptotic Bcl2 family protein of the outer mitochondrial membrane that binds and inhibits pro-apoptotic Bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis. benign Of tumors: self-limiting in growth, and noninvasive.


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Cell_Biology_Alberts. benign Of tumors: self-limiting in growth, and noninvasive. beta sheet (β sheet) Common structural motif in proteins in which different sections of the polypeptide chain run alongside each other, joined together by hydrogen-bonding between atoms of the polypeptide backbone. Also known as a β pleated sheet. (Figure 3–7) beta-catenin (β-catenin) Multifunctional cytoplasmic protein involved in cadherin-mediated cell–cell adhesion, linking cadherins to the actin cytoskeleton. Can also act independently as a transcription regulatory protein. Has an important role in animal development as part of a Wnt signaling pathway. BH3-only proteins The largest subclass of Bcl2 family proteins. Produced or activated in response to an apoptotic stimulus and promote apoptosis mainly by inhibiting antiapoptotic Bcl2 family proteins.


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Cell_Biology_Alberts. bi-orientation The attachment of sister chromatids to opposite poles of the mitotic spindle, so that they move to opposite ends of the cell when they separate in anaphase. binding site Region on the surface of one molecule (usually a protein or nucleic acid) that can interact with another molecule through noncovalent bonding. BiP Endoplasmic reticulum (ER)-resident chaperone protein member of the family of hsp70-type chaperone proteins. Bithorax complex One of two gene clusters in Drosophila that contain Hox genes; genes in the Bithorax complex control the differences among the abdominal and thoracic segments of the body. bivalent A four-chromatid structure formed during meiosis, consisting of a duplicated chromosome tightly paired with its homologous duplicated chromosome. blastomere One of the many cells formed by the cleavage of a fertilized egg.


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Cell_Biology_Alberts. blastomere One of the many cells formed by the cleavage of a fertilized egg. blastula Early stage of an animal embryo, usually consisting of a hollow ball of epithelial cells surrounding a fluid-filled cavity, before gastrulation begins. blebbing Membrane protrusion formed when the plasma membrane detaches locally from the underlying actin cortex, allowing cytoplasmic flow and hydrostatic pressure within the cell to push the membrane outward. bone Dense and rigid connective tissue comprising a mixture of tough fibers (type I collagen fibrils), which resist pulling forces, and solid particles (calcium phosphate as hydroxylapatite crystals), which resist compression. brassinosteroids Class of steroid signal molecules in plants that regulate the growth and differentiation of plants throughout their life cycle via binding to a cell-surface receptor kinase to initiate a signaling cascade.


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Cell_Biology_Alberts. bright-field microscope Normal light microscope in which the image is obtained by simple transmission of light through the object being viewed. buffer Solution of weak acid or weak base that resists the pH change that would otherwise occur when small quantities of acid or base are added. C3 The pivotal complement protein that is activated by the early components of all three complement pathways (the classical pathway, the lectin pathway, and the alternative pathway). (Figure 24–7) Ca2+ pump (calcium pump, Ca2+ ATPase) Transport protein in the membrane of sarcoplasmic reticulum of muscle cells (and elsewhere). Pumps Ca2+ out of the cytoplasm into the sarcoplasmic reticulum using the energy of ATP hydrolysis.


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Cell_Biology_Alberts. Ca2+-activated K+ channel Opens in response to the raised concentration of Ca2+ in nerve cells that occurs in response to an action potential. Increased K+ permeability makes the membrane harder to depolarize, increasing the delay between action potentials and decreasing the response of the cell to constant, prolonged stimulation (adaptation). Ca2+/calmodulin-dependent kinase (CaM-kinase) Serine/ threonine protein kinase that is activated by Ca2+/calmodulin. Indirectly mediates the effects of an increase in cytosolic Ca2+ by phosphorylating specific target proteins. (Figure 15–33) cadherin Member of the large cadherin superfamily of transmembrane adhesion proteins. Mediates homophilic Ca2+-dependent cell–cell adhesion in animal tissues. (Figure 19–3 and Table 19–1, p. 1037) cadherin superfamily Family of classical and nonclassical cadherin proteins with more than 180 members in humans.


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Cell_Biology_Alberts. calmodulin Ubiquitous intracellular Ca2+-binding protein that undergoes a large conformation change when it binds Ca2+, allowing it to regulate the activity of many target proteins. In its activated (Ca2+-bound) form, it is called Ca2+/calmodulin. (Figure 15–33) calnexin Carbohydrate-binding chaperone protein in the endoplasmic reticulum (ER) membrane that binds to oligosaccharides on incompletely folded proteins and retains them in the ER. calreticulin Carbohydrate-binding chaperone protein in the endoplasmic reticulum (ER) lumen that binds to oligosaccharides on incompletely folded proteins and retains them in the ER.


Cell_Biology_Alberts

Cell_Biology_Alberts. calreticulin Carbohydrate-binding chaperone protein in the endoplasmic reticulum (ER) lumen that binds to oligosaccharides on incompletely folded proteins and retains them in the ER. CaM-kinase II Multifunctional Ca2+/calmodulin-dependent protein kinase that phosphorylates itself and various target proteins when activated. Found in most animal cells but is especially abundant at synapses in the brain, and is involved in some forms of synaptic plasticity in vertebrates. (Figure 15–34) cancer stem cells Rare cancer cells capable of dividing indefinitely. cancer-critical genes Genes whose alteration contributes to the causation or evolution of cancer by driving tumorigenesis.


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Cell_Biology_Alberts. cancer-critical genes Genes whose alteration contributes to the causation or evolution of cancer by driving tumorigenesis. capsid Protein coat of a virus, formed by the self-assembly of one or more types of protein subunit into a geometrically regular structure. (Figure 3–27) carbohydrate layer The carbohydrate-rich zone on the eukaryotic cell surface attributable to glycoproteins, glycolipids, and proteoglycans of the plasma membrane. carbon-fixation reaction Process by which inorganic carbon (as atmospheric CO2) is incorporated into organic molecules. The second stage of photosynthesis. (Figure 14–40) carcinogenesis The generation of cancer. carcinoma Cancer of epithelial cells. The most common form of human cancer. cargo The membrane components and soluble molecules carried by transport vesicles. cartilage Form of connective tissue composed of cells (chondrocytes) embedded in a matrix rich in type II collagen and chondroitin sulfate proteoglycan.


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Cell_Biology_Alberts. cartilage Form of connective tissue composed of cells (chondrocytes) embedded in a matrix rich in type II collagen and chondroitin sulfate proteoglycan. caspase Intracellular protease that is involved in mediating the intracellular events of apoptosis. catalyst Substance that can lower the activation energy of a reaction (thus increasing its rate), without itself being consumed by the reaction. caveola (plural caveolae) Invaginations at the cell surface that bud off internally to form pinocytic vesicles. Thought to form from lipid rafts, regions of membrane rich in certain lipids. caveolins Family of unusual integral membrane proteins that are the major structural proteins in caveolae, CD4 Co-receptor protein on helper T cells and regulatory T cells that binds to a nonvariable part of class II MHC proteins (on antigen-presenting cells) outside the peptide-binding groove. (Figure 24–40)


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Cell_Biology_Alberts. CD8 Co-receptor protein on cytotoxic T cells that binds to a nonvariable part of class I MHC proteins (on antigen-presenting cells and infected target cells) outside the peptide-binding groove. (Figure 24–40) Cdc20 Activating subunit of the anaphase-promoting complex (APC/C). Cdc25 Protein phosphatase that dephosphorylates Cdks and increases their activity. Cdc42 Member of the Rho family of monomeric GTPases that regulate the actin and microtubule cytoskeletons, cell-cycle progression, gene transcription, and membrane transport. Cdc6 Protein essential in the preparation of DNA for replication. With Cdt1 it binds to an origin recognition complex on chromosomal DNA and helps load the Mcm proteins onto the complex to form the prereplicative complex. Cdh1 Activating subunit of the anaphase-promoting complex (APC/C). Cdk inhibitor protein (CKI) Protein that binds to and inhibits cyclin–Cdk complexes, primarily involved in the control of G1 and S phases.


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Cell_Biology_Alberts. Cdk inhibitor protein (CKI) Protein that binds to and inhibits cyclin–Cdk complexes, primarily involved in the control of G1 and S phases. Cdk-activating kinase (CAK) Protein kinase that phosphorylates Cdks in cyclin–Cdk complexes, activating the Cdk. cDNA clone Clone containing double-stranded cDNA molecules derived from the protein-coding mRNA molecules present in a cell. cDNA library Collection of cloned DNA molecules representing complementary DNA copies of the mRNA produced by a cell. Cdt1 Protein essential in the preparation of DNA for replication. With Cdc6 it binds to origin recognition complexes on chromosomes and helps load the Mcm proteins on to the complex, forming the prereplicative complex. cell cortex Specialized layer of cytoplasm on the inner face of the plasma membrane. In animal cells it is an actin-rich layer responsible for movements of the cell surface.


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Cell_Biology_Alberts. cell cortex Specialized layer of cytoplasm on the inner face of the plasma membrane. In animal cells it is an actin-rich layer responsible for movements of the cell surface. cell cycle (cell-division cycle) Reproductive cycle of a cell: the orderly sequence of events by which a cell duplicates its chromosomes and, usually, the other cell contents, and divides into two. (Figure 17–4) cell determination Process whereby a cell progressively loses the potential to form other cell types, as development proceeds. cell doctrine The proposal that all living organisms are composed of one or more cells and that all cells arise from the division of other living cells. cell memory Retention by cells and their descendants of persistently altered patterns of gene expression, without any change in DNA sequence. See also epigenetic inheritance.


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Cell_Biology_Alberts. cell memory Retention by cells and their descendants of persistently altered patterns of gene expression, without any change in DNA sequence. See also epigenetic inheritance. cell plate Flattened membrane-bounded structure that forms by fusing vesicles in the cytoplasm of a dividing plant cell and is the precursor of the new cell wall. cell-cycle control system Network of regulatory proteins that governs progression of a eukaryotic cell through the cell cycle. cellulose Long, unbranched chains of glucose; major constituent of plant cell walls. cellulose microfibril Highly ordered crystalline aggregate formed from bundles of about 40 cellulose chains, arranged with the same polarity and stuck together in overlapping parallel arrays by hydrogen bonds between adjacent cellulose molecules.


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Cell_Biology_Alberts. central (primary) lymphoid organ Organ in which T or B lymphocytes are produced from precursor cells. In adult mammals, these are the thymus and bone marrow, respectively. (Figure 24–12) centriole Short cylindrical array of microtubules, closely similar in structure to a basal body. A pair of centrioles is usually found at the center of a centrosome in animal cells. (Figure 16–48) centromere Constricted region of a mitotic chromosome that holds sister chromatids together. This is also the site on the DNA where the kinetochore forms so as to capture microtubules from the mitotic spindle. (Figure 4–43) centrosome Centrally located organelle of animal cells that is the primary microtubule-organizing center (MTOC) and acts as the spindle pole during mitosis. In most animal cells it contains a pair of centrioles. (Figures 16–47 and 17–24) cerebral cortex Outermost layer of the hemispheres of the brain; the most complex structure in the human body.


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Cell_Biology_Alberts. CG island Region of DNA in vertebrate genomes with a greater than average density of CG sequences; these regions generally remain unmethylated. channel (membrane channel) Transmembrane protein complex that allows inorganic ions or other small molecules to diffuse passively across the lipid bilayer. (Figure 11–3) channelrhodopsin Photosensitive protein forming a cation channel across the membrane that opens in response to light. charge separation In photosynthesis, the light-induced transfer of a high-energy electron from chlorophyll to an acceptor molecule resulting in the formation of a positive charge on the chlorophyll and a negative charge on a mobile electron carrier. chemical biology Name given to a strategy that uses large-scale screening of hundreds of thousands of small molecules in biological assays to identify chemicals that affect a particular biological process and that can then be used to study it.


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Cell_Biology_Alberts. chemical carcinogens Disparate chemicals that are carcinogenic—due to the ability to cause mutations—when fed to experimental animals or painted repeatedly on their skin. chemical group Certain combinations of atoms—such as methyl (–CH3), hydroxyl (–OH), carboxyl (–COOH), carbonyl (–C=O), phosphate (–PO32–), sulfhydryl (–SH), and amino (–NH2) groups—that have distinct chemical and physical properties and influence the behavior of the molecule in which the group occurs. chemiosmotic coupling (chemiosmosis) Mechanism in which an electrochemical proton gradient across a membrane (composed of a pH gradient plus a membrane potential) is used to drive an energy-requiring process, such as ATP production or the rotation of bacterial flagella. chemotaxis Movement of a cell toward or away from some diffusible chemical.


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Cell_Biology_Alberts. chemotaxis Movement of a cell toward or away from some diffusible chemical. chiasma (plural chiasmata) X-shaped connection visible between paired homologous chromosomes during meiosis. Represents a site of chromosomal crossing-over, a form of genetic recombination. chlorophyll Light-absorbing green pigment that plays a central part in photosynthesis in bacteria, plants, and algae. chloroplast Organelle in green algae and plants that contains chlorophyll and carries out photosynthesis. cholera toxin Secreted toxic protein of Vibrio cholerae responsible for causing the watery diarrhea associated with cholera. Comprises an A subunit with enzymatic activity and a B subunit that binds to host-cell receptors to direct subunit A to the host-cell cytosol.


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Cell_Biology_Alberts. cholesterol An abundant lipid molecule with a characteristic four-ring steroid structure. An important component of the plasma membranes of animal cells. (Figure 10–4) chromatin Complex of DNA, histones, and non-histone proteins found in the nucleus of a eukaryotic cell. The material of which chromosomes are made. chromatin immunoprecipitation Technique by which chromosomal DNA bound by a particular protein can be isolated and identified by precipitating it by means of an antibody against the protein. (Figures 8–66 and 8–67) chromosome Structure composed of a very long DNA molecule and associated proteins that carries part (or all) of the hereditary information of an organism. Especially evident in plant and animal cells undergoing mitosis or meiosis, during which each chromosome becomes condensed into a compact rodlike structure visible in the light microscope.


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Cell_Biology_Alberts. cilium (plural cilia) Hairlike extension of a eukaryotic cell containing a core bundle of microtubules. Many cells contain a single nonmotile cilium, while others contain large numbers that perform repeated beating movements. Compare flagellum. circadian clock Internal cyclical process that produces a particular change in a cell or organism with a period of around 24 hours, for example the sleep-wakefulness cycle in humans. cis face Face on the same or near side. cis Golgi network (CGN) Network of fused vesicular tubular clusters that is closely associated with the cis face of the Golgi apparatus and is the compartment at which proteins and lipids enter the Golgi.


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Cell_Biology_Alberts. cis-regulatory sequences DNA sequences to which transcription regulators bind to control the rate of gene transcription. In nearly all cases, these sequences must be on the same chromosome (that is, in cis) to the genes they control. (Figure 7–18) cisternal maturation model One hypothesis for how the Golgi apparatus achieves and maintains its polarized structure and how molecules move from one cisterna to another. This model views the cisternae as dynamic structures that mature from early to late by acquiring and then losing specific Golgiresident proteins as they move through the Golgi stack with cargo.


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Cell_Biology_Alberts. citric acid cycle [tricarboxylic acid (TCA) cycle, Krebs cycle] Central metabolic pathway found in aerobic organisms. Oxidizes acetyl groups derived from food molecules, generating the activated carriers NADH and FADH2, some GTP, and waste CO2. In eukaryotic cells, it occurs in the mitochondria. (Panel 2–9, pp. 106–107) clamp loader Protein complex that utilizes ATP hydrolysis to load the sliding clamp on to a primer–template junction in the process of DNA replication.


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Cell_Biology_Alberts. class I MHC protein One of two classes of major histocompatibility complex (MHC) protein. Found on the surface of almost all vertebrate cell types, where it can present foreign peptides derived from a pathogen such as a virus to cytotoxic T cells. (Figures 24–35 and 24–36A) class II MHC protein One of two classes of major histocompatibility complex (MHC) protein. Found on the surface of various antigen-presenting cells, where it presents peptides to helper and regulatory T cells. (Figures 24–35 and 24–36B) class switching Change from making one class of immunoglobulin (for example, IgM) to making another class (for example, IgG) that many B cells undergo during the course of an adaptive immune response. Involves DNA rearrangements called class-switch recombination. (Figure 24–30) class-switch recombination An irreversible change at the DNA level when a B cell switches from making IgM and IgD to making one of the secondary classes of immunoglobulin.


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Cell_Biology_Alberts. classical cadherins Family of cadherin proteins, including E-cadherin, N-cadherin, and P-cadherin, that are closely related in sequence throughout their extracellular and intracellular domains. clathrin Protein that assembles into a polyhedral cage on the cytosolic side of a membrane so as to form a clathrin-coated pit, which buds off by endocytosis to form an intracellular clathrin-coated vesicle. (Figure 13–6) clathrin-coated pits Specialized regions typically occupying about 2% of the total plasma membrane area at which the endocytic pathway often begins. clathrin-coated vesicles Coated vesicles that transport material from the plasma membrane and between endosomal and Golgi compartments. cleavage (1) Physical splitting of a cell into two. (2) Specialized type of cell division seen in many early embryos whereby a large cell becomes subdivided into many smaller cells without growth.


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Cell_Biology_Alberts. cleavage (1) Physical splitting of a cell into two. (2) Specialized type of cell division seen in many early embryos whereby a large cell becomes subdivided into many smaller cells without growth. clonal selection From a population of T and B lymphocytes with a vast repertoire of randomly generated antigen-specific receptors, a given foreign antigen activates (selects) only those lymphocyte clones that display a receptor that fits the antigen. Explains how the adaptive immune system can respond to millions of different antigens in a highly specific way. (Figure 24–15) co-receptor In immunology: an accessory receptor on B cells or T cells that does not bind antigen but binds to a co-stimulatory signal and helps activate the lymphocyte, by helping to activate an intracellular signaling pathway. co-stimulatory signal In immunology: a secreted or membrane-bound signal protein that helps activate an antigen-responding B cell or T cell.


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Cell_Biology_Alberts. co-stimulatory signal In immunology: a secreted or membrane-bound signal protein that helps activate an antigen-responding B cell or T cell. co-translational Occurring as translation proceeds. Examples include the import of a protein into the endoplasmic reticulum before the polypeptide chain is completely synthesized (co-translational translocation, Figure 12–32), and the folding of a nascent protein into its secondary and tertiary structure as it emerges from a ribosome. (Figure 6–79) coat-recruitment GTPases Members of a family of monomeric GTPases that have important roles in vesicle transport, being responsible for coat assembly at the membrane. coated vesicle Small membrane-enclosed organelle with a cage of proteins (the coat) on its cytosolic surface. Formed by the pinching off of a coated region of membrane (coated pit). Some coats are made of clathrin, others are made from other proteins.


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Cell_Biology_Alberts. codon Sequence of three nucleotides in a DNA or mRNA molecule that represents the instruction for incorporation of a specific amino acid into a growing polypeptide chain. coenzyme Small molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a covalent bond to the substrate. Examples include biotin, NAD+, and coenzyme A.


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Cell_Biology_Alberts. cohesin, cohesin complex Complex of proteins that holds sister chromatids together along their length before their separation. (Figure 17–19) coiled-coil Especially stable rodlike protein structure formed by two or more α helices coiled around each other. (Figure 3–9) collagen Fibrous protein rich in glycine and proline that is a major component of the extracellular matrix in animals, conferring tensile strength. Exists in many forms: type I, the most common, is found in skin, tendon, and bone; type II is found in cartilage; type IV is present in basal laminae. (Figures 3–23 and 19–40) collagen fibril A higher-order collagen polymer of fibrillar collagens that assemble into thin structures (10–300 nm in diameter) many hundreds of micrometers long in mature tissues. colony-stimulating factor (CSF) General name for numerous signal molecules that control differentiation of blood cells.


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Cell_Biology_Alberts. colony-stimulating factor (CSF) General name for numerous signal molecules that control differentiation of blood cells. colorectal cancer Cancer arising from the epithelium lining the colon (the large intestine) and rectum (the terminal segment of the gut). column chromatography Technique for separation of a mixture of substances in solution by passage through a column containing a porous solid matrix. Substances are retarded to different extents by their interaction with the matrix and can be collected separately from the column. Depending on the matrix, separation can be according to charge, hydrophobicity, size, or the ability to bind to other molecules. commensalism Ecological relationship between microbes and their host in which the microbe benefits but offers no benefit and causes no harm. committed precursor Cell derived from a stem cell that divides for a limited number of times before terminally differentiating; also known as a transit amplifying cell.


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Cell_Biology_Alberts. complement system System of blood proteins that can be activated by antibody–antigen complexes or pathogens to help eliminate the pathogens, by directly causing their lysis, by promoting their phagocytosis, or activating an inflammatory response. (Figure 24–7) complementary (1) Of nucleic acid sequences: capable of forming a perfect base-paired duplex with each other. (FIgure 4–4) (2) Of other interacting molecules, such as an enzyme and its substrate: having biochemical or structural features that marry up, so that noncovalent bonding is facilitated. (Figure 2–3) complementation test Test to determine whether two mutations that produce similar phenotypes are in the same or different genes. (Panel 8–2, pp. 487) complex oligosaccharides Broad class of N-linked oligosaccharides, attached to mammalian glycoproteins in the endoplasmic reticulum and modified in the Golgi apparatus, containing N-acetylglucosamine, galactose, sialic acid, and fucose residues.


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Cell_Biology_Alberts. condensin, condensin complex Complex of proteins involved in chromosome condensation prior to mitosis. Target for M-Cdk. (Figure 17–22) conditional mutation Mutation that changes a protein or RNA molecule so that its function is altered only under some conditions, such as at an unusually high or unusually low temperature. cone photoreceptor (cone) Photoreceptor cell in the vertebrate retina that is responsible for color vision in bright light. confocal microscope Type of light microscope that produces a clear image of a given plane within a solid object. It uses a laser beam as a pinpoint source of illumination and scans across the plane to produce a two-dimensional “optical section.” (Figure 9–19) conformation The folded, three-dimensional structure of a polypeptide chain.


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Cell_Biology_Alberts. connective tissue Any supporting tissue that lies between other tissues and consists of cells embedded in a relatively large amount of extracellular matrix. Includes bone, cartilage, and loose connective tissue.


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Cell_Biology_Alberts. connexin Protein component of gap junctions, a four-pass transmembrane protein. Six connexins assemble in the plasma membrane to form a connexon, or “hemichannel.” (Figure 19–25) connexon Water-filled pore in the plasma membrane formed by a ring of six connexin protein subunits. Half of a gap junction: connexons from two adjoining cells join to form a continuous channel through which ions and small molecules can pass. (Figure 19–25) consensus nucleotide sequence A summary or “average” of a large number of individual nucleotide sequences derived by comparing many sequences with the same basic function and tallying up the most common nucleotides found at each position. (Figure 6–12) consensus sequence Average or most typical form of a sequence that is reproduced with minor variations in a group of related DNA, RNA, or protein sequences. Indicates the nucleotide or amino acid most often found at each position. Preservation of a sequence implies that it is functionally important.


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Cell_Biology_Alberts. conservative site-specifc recombination A type of DNA recombination that takes place between short, specific sequences of DNA and occurs without the gain or loss of nucleotides. It does not require extensive homology between the recombining DNA molecules. constant region In immunology: region of an immunoglobulin or T cell receptor chain that has a constant amino acid sequence. constitutive secretory pathway Pathway present in all cells by which molecules such as plasma membrane proteins are continually delivered to the plasma membrane from the Golgi apparatus in vesicles that fuse with the plasma membrane. The default route to the plasma membrane if no other sorting signals are present. (Figure 13–63) contact-dependent signaling Form of intercellular signaling in which signal molecules remain bound to the surface of the signaling cell and influence only cells that contact it.


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Cell_Biology_Alberts. contractile ring Ring containing actin and myosin that forms under the surface of animal cells undergoing cell division. Contracts to pinch the two daughter cells apart. (Figure 17–42) convergent extension Rearrangement of cells within a tissue that causes it to extend in one dimension and shrink in another. (Figure 21–50) COPI-coated vesicles Coated vesicles that transport material early in the secretory pathway, budding from Golgi compartments. COPII-coated vesicles Coated vesicles that transport material early in the secretory pathway, budding from the endoplasmic reticulum. copy number variations (CNVs) A difference between two individuals in the same population in the number of copies of a particular block of DNA sequence. This variation arises from occasional duplications and deletions of these sequences. cortex The cytoskeletal network in the cortical region of the cytosol just beneath the plasma membrane.


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Cell_Biology_Alberts. cortex The cytoskeletal network in the cortical region of the cytosol just beneath the plasma membrane. coupled reaction Linked pair of chemical reactions in which the free energy released by one serves to drive the other. (Figure 2–29) covalent bond Stable chemical link between two atoms produced by sharing one or more pairs of electrons. (Panel 2–1, pp. 90–91) CRE-binding (CREB) protein Transcription regulator that recognizes the cyclic AMP response element (CRE) in the regulatory region of genes activated by cAMP. On activation by PKA, phosphorylated CREB recruits a transcriptional coactivator (CREB-binding protein; CBP) to stimulate transcription of target genes. CRISPR A defense mechanism in bacteria using small noncoding RNA molecules (crRNAs) to seek out and destroy invading viral genomes through complementary base-pairing and targeted nuclease digestion. crista (plural cristae) A specialized invagination of the inner mitochondrial membrane.


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Cell_Biology_Alberts. crista (plural cristae) A specialized invagination of the inner mitochondrial membrane. cross-linking glycan One of a heterogeneous group of branched polysaccharides that help to cross-link cellulose microfibrils into a complex network. Has a long linear backbone of one sugar type (glucose, xylose, or mannose) with short side chains of other sugars. cross-presentation A process in which extracellular proteins taken up by specialized dendritic cells can give rise to peptides that can be presented by class I MHC proteins to cytotoxic T cells. crRNAs Small noncoding RNAs (≈30 nucleotides) that are the effectors of CRISPR-mediated immunity in bacteria.


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Cell_Biology_Alberts. crRNAs Small noncoding RNAs (≈30 nucleotides) that are the effectors of CRISPR-mediated immunity in bacteria. cryoelectron microscopy Technique for examining a thin film of an aqueous suspension of biological material that has been frozen rapidly enough to create vitreous ice. The specimen is then kept frozen and transferred to the electron microscope. Image contrast is low, but is generated solely by the macromolecular structures present. cryptochrome Plant flavoprotein sensitive to blue light. Structurally related to blue-light-sensitive enzymes called photolyases (involved in the repair of ultraviolet-induced DNA damage) but do not have a role in DNA repair. Also found in animals, where they have an important role in circadian clocks. Cubitus interruptus (Ci) Latent transcription regulator that mediates the effects of Hedgehog.


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Cell_Biology_Alberts. Cubitus interruptus (Ci) Latent transcription regulator that mediates the effects of Hedgehog. cyclic AMP (cAMP) Nucleotide that is generated from ATP by adenylyl cyclase in response to various extracellular signals. It acts as a small intracellular signaling molecule, mainly by activating cAMP-dependent protein kinase (PKA). It is hydrolyzed to AMP by a phosphodiesterase. (Figure 15–25) cyclic AMP phosphodiesterase Specific enzyme that rapidly and continuously destroys cyclic AMP, forming 5′-AMP. (Figure 15–25). cyclic AMP-dependent protein kinase (protein kinase A, PKA) Enzyme that phosphorylates target proteins in response to a rise in intracellular cyclic AMP. (Figure 15–26) cyclic GMP (cGMP) Nucleotide that is generated from GTP by guanylyl cyclase in response to various extracellular signals. cyclic GMP phosphodiesterase Specific enzyme that rapidly hydrolyzes and degrades cyclic GMP.


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Cell_Biology_Alberts. cyclic GMP phosphodiesterase Specific enzyme that rapidly hydrolyzes and degrades cyclic GMP. cyclin Protein that periodically rises and falls in concentration in step with the eukaryotic cell cycle. Cyclins activate crucial protein kinases (called cyclin-dependent protein kinases, or Cdks) and thereby help control progression from one stage of the cell cycle to the next. cyclin-dependent kinase (Cdk) Protein kinase that has to be complexed with a cyclin protein in order to act. Different cyclin–Cdk complexes trigger different steps in the cell-division cycle by phosphorylating specific target proteins. (Figure 17–10) cyclin–Cdk complex Protein complex formed periodically during the eukaryotic cell cycle as the level of a particular cyclin increases. A cyclin-dependent kinase (Cdk) then becomes partially activated. (Figures 17–10 and 17–11, and Table 17–1, p. 969) cytochrome Colored heme-containing protein that transfers electrons during respiration and photosynthesis.


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Cell_Biology_Alberts. cytochrome c Soluble component of the mitochondrial electron-transport chain. Its release into the cytosol from the mitochondrial intermembrane space also initiates apoptosis. (Figure 14–26) cytochrome c oxidase complex Third of the three electron-driven proton pumps in the respiratory chain. It accepts electrons from cytochrome c and generates water using molecular oxygen as an electron acceptor. (Figure 14–18) cytochrome c reductase Second of the three electron-driven proton pumps in the respiratory chain. Accepts electrons from ubiquinone and passes them to cytochrome c. (Figure 14–18) cytokine Extracellular signal protein or peptide that acts as a local mediator in cell–cell communication.


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Cell_Biology_Alberts. cytokine receptor Cell-surface receptor that binds a specific cytokine or hormone and acts through the JAK–STAT signaling pathway. (Figure 15–56) cytokinesis Division of the cytoplasm of a plant or animal cell into two, as distinct from the associated division of its nucleus (which is mitosis). Part of M phase. (Panel 17–1, pp. 980–981) cytoplasm Contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, outside the nucleus. cytoplasmic tyrosine kinase Enzyme activated by certain cell-surface receptors (tyrosine-kinase-associated receptors) that transmits the receptor signal onward by phosphorylating target cytoplasmic proteins on tyrosine side chains. 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.


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Cell_Biology_Alberts. cytosol Contents of the main compartment of the cytoplasm, excluding membrane-bounded organelles such as endoplasmic reticulum and mitochondria. cytotoxic T cell (TC cell) Type of T cell responsible for killing host cells infected with a virus or another type of intracellular pathogen. (Figure 24–42) dark-field microscopy Type of light microscopy in which oblique rays of light focused on the specimen do not enter the objective lens, but light that is scattered by components in the living cell can be collected to produce a bright image on a dark background. (Figure 9–7) death receptor Transmembrane receptor protein that can signal the cell to undergo apoptosis when it binds its extracellular ligand. (Figure 18–5) death-inducing signaling complex (DISC) Activation complex in which initiator caspases interact and are activated following binding of extracellular ligands to cell-surface death receptors in the extrinsic pathway of apoptosis.


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Cell_Biology_Alberts. default pathway The transport pathway of proteins directly to the cell surface via the nonselective constitutive secretory pathway, entry into which does not require a particular signal. defensin Positively charged, amphipathic, antimicrobial peptide—secreted by epithelial cells—that binds to and disrupts the membranes of many pathogens. delayed K+ channel Neuronal voltage-gated K+ channel that opens following membrane depolarization but during the falling phase of an action potential due to slower activation kinetics than Na+ channels; opening permits K+ efflux, driving the membrane potential back toward its original negative value, ready to transmit a second impulse. Delta Single-pass transmembrane signal protein displayed on the surface of cells that binds to the Notch receptor protein on a neighboring cell, activating a contact-dependent signaling mechanism. dendrite Extension of a nerve cell, often elaborately branched, that receives stimuli from other nerve cells.


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Cell_Biology_Alberts. dendrite Extension of a nerve cell, often elaborately branched, that receives stimuli from other nerve cells. dendritic cell The most potent type of antigen-presenting cell, which takes up antigen and processes it for presentation to T cells. It is required for activating naïve T cells. (Figure 24–11) deoxyribonucleic acid (DNA) Polynucleotide formed from covalently linked deoxyribonucleotide units. The store of hereditary information within a cell and the carrier of this information from generation to generation. (Figure 4–3 and Panel 2–6, pp. 100–101) depolarization Deviation in the electric potential across the plasma membrane towards a positive value. A depolarized cell has a potential that is positive outside and negative inside.


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Cell_Biology_Alberts. desmosome Anchoring cell–cell junction, usually formed between two epithelial cells. Characterized by dense plaques of protein into which intermediate filaments in the two adjoining cells insert. (Figure 19–2) detergent Small amphiphilic molecule, more soluble in water than lipids, that disrupts hydrophobic associations and destroys the lipid bilayer thereby solubilizing membrane proteins. D gene segment A short DNA sequence that encodes a part of the variable region of an immunoglobulin heavy chain or the β chain of a T cell receptor (TCR).


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Cell_Biology_Alberts. D gene segment A short DNA sequence that encodes a part of the variable region of an immunoglobulin heavy chain or the β chain of a T cell receptor (TCR). diacylglycerol (DAG) Lipid produced by the cleavage of inositol phospholipids in response to extracellular signals. Composed of two fatty acid chains linked to glycerol, it serves as a small signaling molecule to help activate protein kinase C (PKC). (Figure 15–28) dideoxy sequencing The standard enzymatic method of DNA sequencing. (Panel 8–1, p. 478) differential-interference-contrast microscope Type of light microscope that exploits the interference effects that occur when light passes through parts of a cell of different refractive indices. Used to view unstained living cells. differentiation Process by which a cell undergoes a change to an overtly specialized cell type. diffusion The net drift of molecules through space due to random thermal movements.


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Cell_Biology_Alberts. differentiation Process by which a cell undergoes a change to an overtly specialized cell type. diffusion The net drift of molecules through space due to random thermal movements. Dishevelled Scaffold protein recruited to the Frizzled family of cell-surface receptors upon their activation by Wnt binding that helps relay the signal to other signaling molecules. DNA cloning (1) The act of making many identical copies (typically billions) of a DNA molecule—the amplification of a particular DNA sequence. (2) Also, the isolation of a particular stretch of DNA (often a particular gene) from the rest of the cell’s genome. DNA helicase Enzyme that is involved in opening the DNA helix into its single strands for DNA replication. DNA library Collection of cloned DNA molecules, representing either an entire genome (genomic library) or complementary DNA copies of the mRNA produced by a cell (cDNA library).


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Cell_Biology_Alberts. DNA library Collection of cloned DNA molecules, representing either an entire genome (genomic library) or complementary DNA copies of the mRNA produced by a cell (cDNA library). DNA ligase Enzyme that joins the ends of two strands of DNA together with a covalent bond to make a continuous DNA strand. DNA methylation Addition of methyl groups to DNA. Extensive methylation of the cytosine base in CG sequences is used in plants and animals to help keep genes in an inactive state. DNA microarray A large array of short DNA molecules (each of known sequence) bound to a glass microscope slide or other suitable support. Used to monitor expression of thousands of genes simultaneously: mRNA isolated from test cells is converted to cDNA, which in turn is hybridized to the microarray. (Figure 8–64) DNA polymerase Enzyme that synthesizes DNA by joining nucleotides together using a DNA template as a guide.


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Cell_Biology_Alberts. DNA polymerase Enzyme that synthesizes DNA by joining nucleotides together using a DNA template as a guide. DNA primase Enzyme that synthesizes a short strand of RNA on a DNA template, producing a primer for DNA synthesis. (Figure 5–10) DNA repair A set of processes for repairing the many accidental lesions that occur continually in DNA. DNA replication Process by which a copy of a DNA molecule is made. DNA supercoiling A conformation with loops or coils that DNA adopts in response to superhelical tension; conversely, creating various loops or coils in the helix can create such tension.


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Cell_Biology_Alberts. DNA supercoiling A conformation with loops or coils that DNA adopts in response to superhelical tension; conversely, creating various loops or coils in the helix can create such tension. DNA topoisomerase (topoisomerase) Enzyme that binds to DNA and reversibly breaks a phosphodiester bond in one or both strands. Topoisomerase I creates transient single-strand breaks, allowing the double helix to swivel and relieving superhelical tension. Topoisomerase II creates transient double-strand breaks, allowing one double helix to pass through another and thus resolving tangles. (Figures 5–21 and 5–22) DNA tumor virus General term for a variety of different DNA viruses that can cause tumors. DNA-only transposon Transposable element that exists as DNA throughout its life cycle. Many move by cut-and-paste transposition. See also transposon. dolichol Isoprenoid lipid molecule that anchors the precursor oligosaccharide in the endoplasmic reticulum membrane during protein glycosylation.


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Cell_Biology_Alberts. dolichol Isoprenoid lipid molecule that anchors the precursor oligosaccharide in the endoplasmic reticulum membrane during protein glycosylation. domain (protein domain) Portion of a protein that has a tertiary structure of its own. Larger proteins are generally composed of several domains, each connected to the next by short flexible regions of polypeptide chain. Homologous domains are recognized in many different proteins. Dorsal protein Transcription regulator of the NFκB family regulating gene expression and involved in establishing the dorsoventral axis in the embryo. double helix The three-dimensional structure of DNA, in which two antiparallel DNA chains, held together by hydrogen-bonding between the bases, are wound into a helix. (Figure 4–5) drivers Mutations that are causal factors in the development of cancer.


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Cell_Biology_Alberts. dynamic instability Sudden conversion from growth to shrinkage, and vice versa, in a protein filament such as a microtubule or actin filament. (Panel 16–2, pp. 902–903) dynamin Cytosolic GTPase that binds to the neck of a clathrin-coated vesicle in the process of budding from the membrane, and which is involved in completing vesicle formation. dynein Large motor protein that undergoes ATP-dependent movement along microtubules. E2F protein Transcription regulatory protein that switches on many genes that encode proteins required for entry into the S phase of the cell cycle. early endosome Common receiving compartment with which most endocytic vesicles fuse and where internalized cargo is sorted either for return to the plasma membrane or for degradation by inclusion in a late endosome. ectoderm Embryonic epithelial tissue that is the precursor of the epidermis and nervous system.


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Cell_Biology_Alberts. ectoderm Embryonic epithelial tissue that is the precursor of the epidermis and nervous system. edema factor One of the two A subunits of anthrax toxin; an adenylyl cyclase that catalyzes production of cAMP, leading to ion imbalance and consequent edema in the skin or lung. effector Bcl2 family proteins Pro-apoptotic proteins of the intrinsic pathway of apoptosis that in response to an apoptotic stimulus become activated and aggregate to form oligomers in the mitochondrial outer membrane, inducing the release of cytochrome c and other intermembrane proteins. Bax and Bak are the main effector Bcl2 family proteins in mammalian cells. effector cell Cell that carries out the final response or function in a particular process. The main effector cells of the immune system, for example, are activated lymphocytes and phagocytes that help eliminate pathogens.


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Cell_Biology_Alberts. egg-polarity genes Genes in the Drosophila egg that define the anteroposterior and dorsoventral axes of the future embryo through the creation of landmarks (mRNA or protein) in the egg that provide signals organizing the developmental process. elastic fiber Extensible fiber formed by the protein elastin in many animal connective tissues, such as in skin, blood vessels, and lungs, which gives them their stretchability and resilience. elastin Extracellular protein that forms extensible fibers (elastic fibers) in connective tissues. electrochemical gradient Combined influence of a difference in the concentration of an ion on two sides of a membrane and the electrical charge difference across the membrane (membrane potential). Ions or charged molecules can move passively only down their electrochemical gradient. electron microscope Microscope that uses a beam of electrons to create the image.


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Cell_Biology_Alberts. electron microscope Microscope that uses a beam of electrons to create the image. electron microscope (EM) tomography Technique for viewing three-dimensional specimens in the electron microscope in which multiple views are taken from different directions by tilting the specimen holder. The views are combined computationally to give a three-dimensional image. electron-transport chain Series of reactions in which electron carrier molecules pass electrons “down the chain” from higher to successively lower energy levels. The energy released during such electron movement can be used to power various processes. Electron-transport chains present in the inner mitochondrial membrane (called the respiratory chain) and in the thylakoid membrane of chloroplasts generate a proton gradient across the membrane that is used to drive ATP synthesis. See especially Figures 14–18 and 14–52.


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Cell_Biology_Alberts. electrostatic attraction A noncovalent, ionic bond between two molecules carrying groups of opposite charge. (Panel 2–3, pp. 94–95) embryonic stem cells (ES cells) Cells derived from the inner cell mass of the early mammalian embryo. Capable of giving rise to all the cells in the body. Can be grown in culture, genetically modified, and inserted into a blastocyst to develop a transgenic animal. endocrine cell Specialized animal cell that secretes a hormone into the blood. Usually part of a gland, such as the thyroid or pituitary gland. endocytic vesicle Vesicle formed as material ingested by the cell during endocytosis is progressively enclosed by a small portion of the plasma membrane, which first invaginates and then pinches off to form the vesicle. endocytosis Uptake of material into a cell by an invagination of the plasma membrane and its internalization in a membrane-enclosed vesicle. See also pinocytosis and phagocytosis.


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Cell_Biology_Alberts. endocytosis Uptake of material into a cell by an invagination of the plasma membrane and its internalization in a membrane-enclosed vesicle. See also pinocytosis and phagocytosis. endoderm Embryonic tissue that is the precursor of the gut and associated organs. endoplasmic reticulum (ER) Labyrinthine membrane-bounded compartment in the cytoplasm of eukaryotic cells, where lipids are synthesized and membrane-bound proteins and secretory proteins are made. (Figure 12–33) endosome maturation Process by which early endosomes mature to late endosomes and endolysosomes; in the conversion process, the endosome membrane protein composition changes, the endosome moves from the cell periphery to close to the nucleus, and the endosome ceases to recycle material to the plasma membrane and irreversibly commits its remaining contents to degradation. endothelial cell Flattened cell type that forms a sheet (the endothelium) lining all blood and lymphatic vessels.


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Cell_Biology_Alberts. endothelial cell Flattened cell type that forms a sheet (the endothelium) lining all blood and lymphatic vessels. entropy (S) Thermodynamic quantity that measures the degree of disorder or randomness in a system; the higher the entropy, the greater the disorder. (Panel 2–7, pp. 102–103) enveloped virus Virus with a capsid surrounded by a lipid bilayer membrane (the envelope), which is often derived from the host-cell plasma membrane when the virus buds from the cell. (Figure 23–12) enzyme Protein that catalyzes a specific chemical reaction.


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Cell_Biology_Alberts. enzyme-coupled receptor A major type of cell-surface receptor that has a cytoplasmic domain that either has enzymatic activity or is associated with an intracellular enzyme. In either case, the enzymatic activity is stimulated by an extracellular ligand binding to the receptor. (Figure 15–6) ephrin One of a family of membrane-bound protein ligands for the Eph receptor tyrosine kinases (RTKs) that, among many other functions, stimulate repulsion or attraction responses that guide the migration of cells and nerve cell axons during animal development. epidermis Epithelial layer covering the outer surface of the body. Has different structures in different animal groups. The outer layer of plant tissue is also called the epidermis.


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Cell_Biology_Alberts. epidermis Epithelial layer covering the outer surface of the body. Has different structures in different animal groups. The outer layer of plant tissue is also called the epidermis. epigenetic inheritance Inheritance of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA. Can be due to positive feedback loops of transcription regulators or to heritable modifications in chromatin such as DNA methylation or histone modifications. (Figure 7–53) epistasis analysis Analysis to discover the order in which the genes act, by investigating if a mutation in one gene can mask the effect of a mutation in another gene when both mutations are present in the same organism or cell. epithelial tissues Tissues, such as the lining of the gut or the epidermal covering of the skin, in which cells are closely bound together into sheets called epithelia.


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Cell_Biology_Alberts. epithelial tissues Tissues, such as the lining of the gut or the epidermal covering of the skin, in which cells are closely bound together into sheets called epithelia. epithelium (plural epithelia) Sheet of cells covering the outer surface of a structure or lining a cavity. equilibrium State in a chemical reaction where there is no net change in free energy to drive the reaction in either direction. The ratio of product to substrate reaches a constant value at chemical equilibrium. (Figure 2–30) equilibrium constant (K) The ratio of forward and reverse rate constants for a reaction. Equal to the association or affinity constant (Ka) for a simple binding reaction (A + B AB). See also affinity constant, dissociation constant. (See page 62) ER lumen Space enclosed by the membrane of the endoplasmic reticulum (ER).


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Cell_Biology_Alberts. AB). See also affinity constant, dissociation constant. (See page 62) ER lumen Space enclosed by the membrane of the endoplasmic reticulum (ER). ER resident protein Protein that remains in the endoplasmic reticulum (ER) or its membranes and carries out its function there, as opposed to proteins that are present in the ER only in transit. ER retention signal Short amino acid sequence on a protein that prevents it from moving out of the endoplasmic reticulum (ER). Found on proteins that are resident in the ER and function there. ER signal sequence N-terminal signal sequence that directs proteins to enter the endoplasmic reticulum (ER). Cleaved off by signal peptidase after entry. ER tail-anchored proteins Membrane proteins anchored in the endoplasmic reticulum (ER) membrane by a single transmembrane α helix contained at their C-terminus.


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Cell_Biology_Alberts. ER tail-anchored proteins Membrane proteins anchored in the endoplasmic reticulum (ER) membrane by a single transmembrane α helix contained at their C-terminus. erythrocyte Small hemoglobin-containing blood cell of vertebrates that transports oxygen to, and carbon dioxide from, tissues. Also called a red blood cell. erythropoietin A hormone produced by the kidney that stimulates the production of red blood cells in bone marrow. ESCRT protein complexes Four protein complexes (ESCRT-0, ESCRT-1, ESCRT-2, and ESCRT-3) that act sequentially to shepherd mono-ubiquitylated membrane proteins on endosomal membranes into intralumenal vesicles. ESCRT-3 complex catalyzes the pinching-off reaction. ethylene Small gas molecule that is a plant growth regulator influencing plant development in various ways including promoting fruit ripening, leaf abscission, and plant senescence and functioning as a stress signal in response to wounding, infection, and flooding.


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Cell_Biology_Alberts. euchromatin Region of an interphase chromosome that stains diffusely; “normal” chromatin, as opposed to the more condensed heterochromatin. eukaryote Organism composed of one or more cells that have a distinct nucleus. Member of one of the three main divisions of the living world, the other two being bacteria and archaea. (Figure 1–17) eukaryotic initiation factor (eIF) Protein that helps load initiator tRNA on to the ribosome, thus initiating translation. excitatory neurotransmitter Neurotransmitter that opens cation channels in the postsynaptic membrane, causing an influx of Na+, and in many cases Ca2+, that depolarizes the postsynaptic membrane toward the threshold potential for firing an action potential. executioner caspases Apoptotic caspases that catalyze the widespread cleavage events during apoptosis that kill the cell. exocytosis Excretion of material from the cell by vesicle fusion with the plasma membrane; can occur constitutively or be regulated.


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Cell_Biology_Alberts. exocytosis Excretion of material from the cell by vesicle fusion with the plasma membrane; can occur constitutively or be regulated. exon Segment of a eukaryotic gene that consists of a sequence of nucleotides that will be represented in mRNA or in a final transfer, ribosomal, or other mature RNA molecule. In protein-coding genes, exons encode the amino acids in the protein. An exon is usually adjacent to a noncoding DNA segment called an intron. (Figure 4–15) exosome Large protein complex with an interior rich in 3′-to-5′ RNA exonucleases; degrades RNA molecules to produce ribonucleotides. extracellular pathogens Pathogens that disturb host cells and can cause serious disease without replicating in host cells. extracellular signal molecule Any secreted or cell-surface chemical signal that binds to receptors and regulates the activity of the cell expressing the receptor.


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Cell_Biology_Alberts. extracellular signal molecule Any secreted or cell-surface chemical signal that binds to receptors and regulates the activity of the cell expressing the receptor. extrinsic pathway Pathway of apoptosis triggered by extracellular signal proteins binding to cell-surface death receptors. facultative pathogens Bacteria that replicate in an environmental reservoir such as water or soil and only cause disease if they happen to encounter a susceptible host. FAD/FADH2 (flavin adenine dinucleotide/reduced flavin adenine dinucleotide) Electron carrier system that functions in the citric acid cycle and fatty acid oxidation. One molecule of FAD gains two electrons plus two protons in becoming the activated carrier FADH2. (Figure 2–39) Fas (Fas protein, Fas death receptor) Transmembrane death receptor that initiates apoptosis when it binds its extracellular ligand (Fas ligand). (Figure 18–5)


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Cell_Biology_Alberts. Fas (Fas protein, Fas death receptor) Transmembrane death receptor that initiates apoptosis when it binds its extracellular ligand (Fas ligand). (Figure 18–5) Fas ligand Ligand that activates the cell-surface death receptor, Fas, triggering the extrinsic pathway of apoptosis. fat Energy-storage lipid in cells. Composed of triglycerides— fatty acids esterified with glycerol. fate map Representation showing which cell types will later derive from which regions of a tissue; e.g. from the blastula. (Figure 21–28) Fc receptor One of a family of cell-surface receptors that bind the tail region (Fc region) of an antibody molecule. Different Fc receptors are specific for different classes of antibodies, such as IgG, IgA, or IgE.


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Cell_Biology_Alberts. feedback inhibition The process in which a product of a reaction feeds back to inhibit a previous reaction in the same pathway. (Figures 3–55 and 3–56) fermentation Anaerobic energy-yielding metabolic pathway involving the oxidation of organic molecules. Anaerobic glycolysis refers to the process whereby pyruvate is converted into lactate or ethanol, with the conversion of NADH to NAD+. (Figure 2–47) fibril-associated collagen Mediates the interactions of collagen fibrils with one another and with other matrix macromolecules to help determine the organization of the fibrils in the matrix. This collagen (including types IX and XII) has a flexible triple-stranded helical structure and binds to the surface of the fibrils rather than forming aggregates.


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Cell_Biology_Alberts. fibrillar collagen Class of fibril-forming collagens (including type I collagen, the most common type and the principal collagen of skin and bone) that have long ropelike structures with few or no interruptions and which assemble into collagen fibrils. fibroblast Common cell type found in connective tissue. Secretes an extracellular matrix rich in collagen and other extracellular matrix macromolecules. Migrates and proliferates readily in wounded tissue and in tissue culture. fibronectin Extracellular matrix protein involved in adhesion of cells to the matrix and guidance of migrating cells during embryogenesis. Integrins on the cell surface are receptors for fibronectin.


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Cell_Biology_Alberts. filopodium (plural filopodia) (microspike) Thin, spike-like protrusion with an actin filament core, generated on the leading edge of a crawling animal cell. (Figure 16–21) firing rule Important principle governing synapse reinforcement and elimination during development of the nervous system: when two (or more) neurons synapsing on the same target cell fire at the same time, they reinforce their connections to that cell; when they fire at different times, they compete, so that all but one of them tend to be eliminated. flagellum (plural flagella) Long, whiplike protrusion whose undulations drive a cell through a fluid medium. Eukaryotic flagella are longer versions of cilia. Bacterial flagella are smaller and completely different in construction and mechanism of action. Compare cilium.


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Cell_Biology_Alberts. fluorescence microscope Microscope designed to view material stained with fluorescent dyes or proteins. Similar to a light microscope but the illuminating light is passed through one set of filters before the specimen, to select those wavelengths that excite the dye, and through another set of filters before it reaches the eye, to select only those wavelengths emitted when the dye fluoresces. (Figure 9–12) fluorescence recovery after photobleaching (FRAP) Technique for monitoring the kinetic parameters of a protein by analyzing how fluorescent protein molecules move into an area of the cell bleached by a beam of laser light. (Figure 9–29) fluorescence resonance energy transfer (FRET) Technique for monitoring the closeness of two fluorescently labeled molecules (and thus their interaction) in cells. Also known as Förster resonance energy transfer. (Figure 9–26) focal adhesion kinase (FAK) Cytoplasmic tyrosine kinase present at cell–matrix junctions (focal adhesions) in association


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Cell_Biology_Alberts. in cells. Also known as Förster resonance energy transfer. (Figure 9–26) focal adhesion kinase (FAK) Cytoplasmic tyrosine kinase present at cell–matrix junctions (focal adhesions) in association with the cytoplasmic tails of integrins.


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Cell_Biology_Alberts. focal adhesion kinase (FAK) Cytoplasmic tyrosine kinase present at cell–matrix junctions (focal adhesions) in association with the cytoplasmic tails of integrins. follicular helper T cell (TFH) Type of T cell located in lymphoid follicles that secretes various cytokines to stimulate B cells to undergo antibody class switching and somatic hypermutation. formin Dimeric protein that nucleates the growth of straight, unbranched actin filaments that can be cross-linked by other proteins to form parallel bundles. free energy (G) (Gibbs free energy) The energy that can be extracted from a system to drive reactions. Takes into account changes in both energy and entropy. (Panel 2–7, pp. 102–103) free ribosome Ribosome that is free in the cytosol, unattached to any membrane. free-energy change (∆G) see ΔG.


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Cell_Biology_Alberts. free-energy change (∆G) see ΔG. Frizzled Family of cell-surface receptors that are seven-pass transmembrane proteins that resemble GPCRs in structure but do not generally work through the activation of G proteins. Activated by Wnt binding to recruit the scaffold protein Dishevelled, which helps relay the signal to other signaling molecules. fungus (plural fungi) Kingdom of eukaryotic organisms that includes the yeasts, molds, and mushrooms. Many plant diseases and a relatively small number of animal diseases are caused by fungi. fusion protein Engineered protein that combines two or more normally separate polypeptides. Produced from a recombinant gene. ∆G Change in the free energy during a reaction: the free energy of the product molecules minus the free energy of the starting molecules. A large negative value of ∆G indicates that the reaction has a strong tendency to occur. (Panel 2–7, pp. 102–103)


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Cell_Biology_Alberts. G0 State of withdrawal from the eukaroytic cell-division cycle by entry into a quiescent digression from the G1 phase. A common, sometimes permanent, state for differentiated cells. G1 phase Gap 1 phase of the eukaryotic cell-division cycle, between the end of mitosis and the start of DNA synthesis. (Figure 17–4) G1-Cdk Cyclin–Cdk complex formed in vertebrate cells by a G1-cyclin and the corresponding cyclin-dependent kinase (Cdk). (Table 17–1, p. 969) G1-cyclin Cyclin present in the G1 phase of the eukaryotic cell cycle. Forms complexes with Cdks that help govern the activity of the G1/S-cyclins, which control progression to S phase. G1/S-Cdk Cyclin–Cdk complex formed in vertebrate cells by a G1/S-cyclin and the corresponding cyclin-dependent kinase (Cdk). (Figure 17–11 and Table 17–1, p. 969)


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Cell_Biology_Alberts. G1/S-Cdk Cyclin–Cdk complex formed in vertebrate cells by a G1/S-cyclin and the corresponding cyclin-dependent kinase (Cdk). (Figure 17–11 and Table 17–1, p. 969) G1/S-cyclin Cyclin that activates Cdks in late G1 of the eukaryotic cell cycle and thereby helps trigger progression through Start, resulting in a commitment to cell-cycle entry. Its level falls at the start of S phase. (Figure 17–11) G2 phase Gap 2 phase of the eukaryotic cell-division cycle, between the end of DNA synthesis and the beginning of mitosis. (Figure 17–4)


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Cell_Biology_Alberts. G2 phase Gap 2 phase of the eukaryotic cell-division cycle, between the end of DNA synthesis and the beginning of mitosis. (Figure 17–4) G2/M transition Point in the eukaryotic cell cycle at which the cell checks for completion of DNA replication before triggering the early mitotic events that lead to chromosome alignment on the spindle. (Figure 17–9) ganglioside Any glycolipid having one or more sialic acid residues in its structure. Found in the plasma membrane of eukaryotic cells and especially abundant in nerve cells. (Figure 10–16) gap gene In Drosophila development, a gene that is expressed in specific broad regions along the anteroposterior axis of the early embryo, and which helps designate the main divisions of the insect body. (Figure 21–20) gap junction Communicating channel-forming cell–cell junction present in most animal tissues that allows ions and small molecules to pass from the cytoplasm of one cell to the cytoplasm of the next.


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Cell_Biology_Alberts. gastrulation Important stage in animal embryogenesis during which the embryo is transformed from a ball of cells to a structure with a gut (a gastrula). gated transport Movement of proteins between the cytosol and the nucleus through nuclear pore complexes in the nuclear envelope that function as selective gates. geminin Protein that prevents the formation of new prereplicative complexes during S phase and mitosis, thus ensuring that the chromosomes are replicated only once in each cell cycle. gene Region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic, usually corresponding to (1) a single protein (or set of related proteins generated by variant post-transcriptional processing), or (2) a single RNA (or set of closely related RNAs).


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Cell_Biology_Alberts. gene control region The set of linked DNA sequences regulating expression of a particular gene. Includes promoter and cis-regulatory sequences required to initiate transcription of the gene and control the rate of transcription. (Figure 7–17) gene conversion Process by which DNA sequence information can be transferred from one DNA helix (which remains unchanged) to another DNA helix whose sequence is altered. It often accompanies general recombination events. (Figure 5–59) gene family The set of genes in an organism related in DNA sequence due to their derivation from the same ancestor.


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Cell_Biology_Alberts. gene segments In immunology: short DNA sequences that are joined together during B cell and T cell development to produce the coding sequences for immunoglobulins and T cell receptors, respectively. (Figure 24–28) general transcription factor Any of the proteins whose assembly at all promoters of a given type is required for the binding and activation of RNA polymerase and the initiation of transcription. (Table 6–3, p. 311) genetic code The set of rules specifying the correspondence between nucleotide triplets (codons) in DNA or RNA and amino acids in proteins. (Figure 6–48) genetic instability Abnormally increased spontaneous mutation rate, such as occurs in cancer cells. genetic screen Procedure for discovery of genes affecting a specific phenotype by surveying large numbers of mutagenized individuals. genetics The study of the genes of an organism on the basis of heredity and variation.


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Cell_Biology_Alberts. genetics The study of the genes of an organism on the basis of heredity and variation. genome The totality of genetic information belonging to a cell or an organism; in particular, the DNA that carries this information. genome annotation Process attempting to mark out all the genes (protein-coding and noncoding) in a genome and ascribing functions to each. genomic imprinting Phenomenon in which a gene is either expressed or not expressed in the offspring depending on which parent it is inherited from. (Figure 7–49) genomic library Collection of cloned DNA molecules representing an entire genome.


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Cell_Biology_Alberts. genotype Genetic constitution of an individual cell or organism. The particular combination of alleles found in a specific individual. (Panel 8–2, p. 486) germ cell A cell in the germ line of an organism, which includes the haploid gametes and their specified diploid precursor cells. Germ cells contribute to the formation of a new generation of organisms and are distinct from somatic cells, which form the body and leave no descendants. germ layer One of the three primary tissue layers (endoderm, mesoderm, and ectoderm) of an animal embryo. (Figure 21–3) glial cell Supporting non-neural cell of the nervous system. Includes oligodendrocytes and astrocytes in the vertebrate central nervous system and Schwann cells in the peripheral nervous system.


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Cell_Biology_Alberts. glycogen Polysaccharide composed exclusively of glucose units. Used to store energy in animal cells. Large granules of glycogen are especially abundant in liver and muscle cells. (Figure 2–51 and Panel 2–4, pp. 96–97) glycolipid Lipid molecule with a sugar residue or oligosaccharide attached. (Panel 2–5, pp. 98–99) glycolysis Ubiquitous metabolic pathway in the cytosol in which sugars are incompletely degraded with production of ATP. Literally, “sugar splitting.” (Figure 2–46 and Panel 2–8, pp. 104–105) glycoprotein Any protein with one or more saccharide or oligosaccharide chains covalently linked to amino acid side chains. Most secreted proteins and most proteins exposed on the outer surface of the plasma membrane are glycoproteins.


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Cell_Biology_Alberts. glycosaminoglycan (GAG) Long, linear, highly charged polysaccharide composed of a repeating pair of sugars, one of which is always an amino sugar. Mainly found covalently linked to a protein core in extracellular matrix proteoglycans. Examples include chondroitin sulfate, hyaluronan, and heparin. (Figure 19–32) glycosylphosphatidylinositol anchor (GPI anchor) Lipid linkage by which some membrane proteins are bound to the membrane. The protein is joined, via an oligosaccharide linker, to a phosphatidylinositol anchor during its travel through the endoplasmic reticulum. (Figure 12–52) Golgi apparatus (Golgi complex) Complex organelle in eukaryotic cells, centered on a stack of flattened, membrane-enclosed spaces, in which proteins and lipids transferred from the endoplasmic reticulum are modified and sorted. It is the site of synthesis of many cell wall polysaccharides in plants and extracellular matrix glycosaminoglycans in animal cells. (Figure 13–26)


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Cell_Biology_Alberts. GPCR kinase (GRK) Member of a family of enzymes that phosphorylates multiple serines and threonines on a GPCR to produce receptor desensitization. (Figure 15–42) G protein (trimeric GTP-binding protein) A trimeric GTP-binding protein with intrinsic GTPase activity that couples GPCRs to enzymes or ion channels in the plasma membrane. (Table 15–3, p. 846) G-protein-coupled receptor (GPCR) A seven-pass cell-surface receptor that, when activated by its extracellular ligand, activates a G protein, which in turn activates either an enzyme or ion channel in the plasma membrane. (Figures 15–6 and 15–21) Gq Class of G protein that couples GPCRs to phospholipase C-β to activate the inositol phospholipid signaling pathway. Gram negative Description for bacteria that do not stain with Gram stain as a result of having a thinner peptidoglycan cell wall outside their inner (plasma) membrane, and on an additional outer membrane.


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Cell_Biology_Alberts. Gram positive Description for bacteria that stain positive with Gram stain due to a thick layer of peptidoglycan cell wall outside their inner (plasma) membrane. Gram staining A technique for classifying bacteria based on differences in the structure of the bacterial cell wall and outer surface.


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Cell_Biology_Alberts. Gram staining A technique for classifying bacteria based on differences in the structure of the bacterial cell wall and outer surface. granulocyte Category of white blood cell distinguished by conspicuous cytoplasmic granules. Includes neutrophils, basophils, and eosinophils. Arises from a granulocyte/ macrophage (GM) progenitor cell. (Figure 22–27) granulocyte/macrophage (GM) progenitor cell Committed progenitor cell in the bone marrow that gives rise to neutrophils and macrophages. (Figure 22–31) green fluorescent protein (GFP) Fluorescent protein isolated from a jellyfish. Widely used as a marker in cell biology. (Figure 9–24) growth cone Migrating motile tip of a growing nerve cell axon or dendrite. (Figure 21–72) growth factor Extracellular signal protein that can stimulate a cell to grow. They often have other functions as well, including stimulating cells to survive or proliferate. Examples include epidermal growth factor (EGF) and platelet-derived growth factor (PDGF).


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Cell_Biology_Alberts. growth hormone (GH) Mammalian hormone secreted by the pituitary gland into the bloodstream that stimulates growth throughout the body. GTP (guanosine 5′-triphosphate) Nucleoside triphosphate produced by the phosphorylation of GDP (guanosine diphosphate). Like ATP, it releases a large amount of free energy on hydrolysis of its terminal phosphate group. Has a special role in microtubule assembly, protein synthesis, and cell signaling. (Figure 2–58) GTP-binding protein Also called GTPase; an enzyme that converts GTP to GDP.


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Cell_Biology_Alberts. GTP-binding protein Also called GTPase; an enzyme that converts GTP to GDP. GTPase An enzyme that converts GTP to GDP. GTPases fall into two large families. Large trimeric G proteins are composed of three different subunits and mainly couple GPCRs to enzymes or ion channels in the plasma membrane. Small monomeric GTP-binding proteins (also called monomeric GTPases) consist of a single subunit and help relay signals from many types of cell-surface receptors and have roles in intracellular signaling pathways, regulating intracellular vesicle trafficking, and signaling to the cytoskeleton. Both trimeric G proteins and monomeric GTPases cycle between an active GTP-bound form and an inactive GDP-bound form and frequently act as molecular switches in intracellular signaling pathways. See page 820.


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Cell_Biology_Alberts. GTPase-activating protein (GAP) Protein that binds to a GTPase and inhibits it by stimulating its GTPase activity, causing the enzyme to hydrolyze its bound GTP to GDP. (Figure 15–8) guanine nucleotide exchange factor (GEF) Protein that binds to a GTPase and activates it by stimulating it to release its tightly bound GDP, thereby allowing it to bind GTP in its place. (Figure 15–8) haplotype block Combination of alleles and DNA markers that has been inherited in a large, linked block on one chromosome of a homologous pair—undisturbed by genetic recombination—across many generations. Hedgehog protein Secreted extracellular signal molecule that has many different roles controlling cell differentiation and gene expression in animal embryos and adult tissues. Excessive Hedgehog signaling can lead to cancer.


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Cell_Biology_Alberts. helper T cell (TH cell) Type of T cell that helps activate B cells to make antibodies, cytotoxic T cells to become effector cells, and macrophages to kill ingested pathogens. They can also help activate dendritic cells. heterochromatin Chromatin that is highly condensed even in interphase; generally transcriptionally inactive. (Compare with euchromatin.) heterochronic Describes genes involved in developmental timing; mutation results in cells of a specific fate behaving as cells at a different stage of development. high-mannose oligosaccharides Broad class of N-linked oligosaccharides, attached to mammalian glycoproteins in the endoplasmic reticulum, containing two N-acetylglucosamine residues and many mannose residues. high-performance liquid chromatography (HPLC) Type of chromatography that uses columns packed with tiny beads of matrix; the solution to be separated is pushed through under high pressure.


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Cell_Biology_Alberts. high-performance liquid chromatography (HPLC) Type of chromatography that uses columns packed with tiny beads of matrix; the solution to be separated is pushed through under high pressure. histone One of a group of small abundant proteins, rich in arginine and lysine, that combine to form the nucleosome cores around which DNA is wrapped in eukaryotic chromosomes. (Figure 4–24) histone chaperone (chromatin assembly factor) Protein that binds free histones, releasing them once they have been incorporated into newly replicated chromatin. (Figure 4–27) histone H1 “Linker” (as opposed to “core”) histone protein that binds to DNA where it exits from a nucleosome and helps package nucleosomes into the 30-nm chromatin fiber. (Figure 4–30)


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Cell_Biology_Alberts. Holliday junction (cross-strand exchange) X-shaped structure observed in DNA undergoing recombination, in which the two DNA molecules are held together at the site of crossing-over, also called a cross-strand exchange. (Figure 5–55) homeotic selector gene In Drosophila development, a gene that defines and preserves the differences between body segments. homolog One of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene. The term covers both orthologs and paralogs. (Figure 1–21) See homologous chromosomes. homologous Genes, proteins, or body structures that are similar as a result of a shared evolutionary origin. homologous chromosomes (homologs) The maternal and paternal copies of a particular chromosome in a diploid cell.


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Cell_Biology_Alberts. homologous chromosomes (homologs) The maternal and paternal copies of a particular chromosome in a diploid cell. homologous recombination (general recombination) Genetic exchange between a pair of identical or very similar DNA sequences, typically those located on two copies of the same chromosome. Also a DNA repair mechanism for double-strand breaks. (Figures 5–48, 5–50, and 5–54) homophilic Binding between molecules of the same kind, especially those involved in cell–cell adhesion. (Figure 19–5) horizontal gene transfer Gene transfer between bacteria via natural transformation by released naked DNA, transduction by bacteriophages, or sexual exchange by conjugation. hormone Signal molecule secreted by an endocrine cell into the bloodstream, which can then carry the signal to distant target cells. Hox complex A gene complex consisting of a series of Hox genes


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Cell_Biology_Alberts. hormone Signal molecule secreted by an endocrine cell into the bloodstream, which can then carry the signal to distant target cells. Hox complex A gene complex consisting of a series of Hox genes Hox genes Genes coding for transcription regulators, each gene containing a homeodomain, and specifying body-region differences. Hox mutations typically cause homeotic transformations. Hox proteins Transcription regulator proteins encoded by Hox genes; possess a highly conserved, 60-amino-acid-long DNA-binding homeodomain. HPV Human papillomavirus; infects the cervical epithelium and is important as a cause of carcinoma of the uterine cervix.


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Cell_Biology_Alberts. hyaluronan (hyaluronic acid) Type of nonsulfated glycosaminoglycan with a regular repeating sequence of up to 25,000 identical disaccharide units, not linked to a core protein. Found in the fluid lubricating joints and in many other tissues. (Figures 19–33 and 19–34) hybridization In molecular biology, the process whereby two complementary nucleic acid strands form a base-paired duplex DNA-DNA, DNA-RNA, or RNA-RNA molecule. Forms the basis of a powerful technique for detecting specific nucleotide sequences. (Figures 5–47 and 8–33) hybridoma Hybrid cell line generated by fusion of a tumor cell and another cell type. Monoclonal antibodies are produced by hybridoma lines obtained by fusing antibody-secreting B cells with cells of a B lymphocyte tumor. (Figure 8–4) hydrogen bond Noncovalent bond in which an electropositive hydrogen atom is partially shared by two electronegative atoms. (Panel 2–3, pp. 94–95) hydronium ion (H3O+) Water molecule associated with an additional proton. The


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Cell_Biology_Alberts. bond in which an electropositive hydrogen atom is partially shared by two electronegative atoms. (Panel 2–3, pp. 94–95) hydronium ion (H3O+) Water molecule associated with an additional proton. The form generally taken by protons in aqueous solution.


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Cell_Biology_Alberts. hydrophilic Dissolving readily in water. Literally, “water loving.” hydrophobic (lipophilic) Not dissolving readily in water. Literally, “water-fearing.” hydrophobic force Force exerted by the hydrogen-bonded network of water molecules that brings two nonpolar surfaces together by excluding water between them. (Panel 2–3, pp. 94–95) hypervariable region In immunology: any of the three small parts of the variable region of an immunoglobulin or T cell receptor chain that show the highest variability from molecule to molecule and contribute to the antigen-binding site. (Figure 24–26) hypoxia-inducible factor 1α (HIF1α). Transcription regulator, the intracellular levels of which increase in response to a shortage of oxygen, that stimulates transcription of the VEGF gene to promote angiogenesis. IκB Inhibitory proteins that bind tightly to NFκB dimers and hold them in an inactive state within the cytoplasm of unstimulated cells.


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Cell_Biology_Alberts. IκB Inhibitory proteins that bind tightly to NFκB dimers and hold them in an inactive state within the cytoplasm of unstimulated cells. Ig superfamily Large and diverse family of proteins that contain immunoglobulin or immunoglobulin-like domains. Most are involved in cell–cell interactions or antigen recognition. (Figure 24–48) IgA Immunoglobulin A; the principal class of antibody in secretions, including saliva, tears, milk, and respiratory and intestinal secretions. IgD Immunoglobulin D; produced by immature naïve B cells after leaving the bone marrow. Transmembrane IgD and IgM proteins, with the same antigen-binding site, form the B cell receptors (BCRs) on these cells.


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Cell_Biology_Alberts. IgE Immunoglobulin E; binds with high affinity via its tail region to a class of Fc receptors on the surface of mast cells (tissues) or basophils (blood), where it acts as an antigen receptor; antigen binding stimulates the secretion of cytokines and biologically active amines, which help attract white blood cells, antibodies, and complement proteins to the site of activation. IgG Immunoglobulin G; the major antibody class in the blood, produced in especially large quantities during secondary antibody responses. The tail region of some IgG subclasses can bind to specific Fc receptors on macrophages and neutrophils. Antigen–IgG complexes can activate complement.


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Cell_Biology_Alberts. IgM Immunoglobulin M; the first class of immunoglobulin that a developing B cell in the bone marrow makes, forming B-cell receptors on its surface. IgM antibodies are the major class of antibody secreted into the blood in the early stages of a primary antibody response on first exposure to an antigen, where their pentameric structure (with 10 antigen-binding sites) allows strong binding to pathogens. When bound to antigen, it is highly efficient activation of complement. iHog Protein with four or five immunoglobulin-like domains and two or three fibronectin-type-III-like domains; located on the cell surface and thought to serve as co-receptors for Hedgehog proteins.


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Cell_Biology_Alberts. image processing Computer based techniques in microscopy that process digital images in order to extract latent information. Enables compensation for some optical faults in microscopes, enhanced contrast to improve detection of small differences in light intensity, and subtraction of background irregularities in the optical system. imaginal disc Group of cells that are set aside, apparently undifferentiated, in the Drosophila embryo and which will develop into an adult structure, e.g., eye, leg, wing. Overt differentiation occurs at metamorphosis. (Figure 21–60) immunization Method of inducing adaptive immune responses to pathogens or foreign molecules, usually involving the co-injection of an adjuvant, a molecule (often of microbial origin) that helps activate innate immune responses required for the adaptive responses.


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Cell_Biology_Alberts. immunoglobulin (Ig) superfamily Large and diverse family of proteins that contain immunoglobulin domains or immunoglobulin-like domains. Most are involved in cell–cell interactions or antigen recognition. (Figure 24–48) immunoglobulin domain (Ig domain) Characteristic protein domain of about 100 amino acids that is found in immunoglobulin light and heavy chains. Similar domains, known as immunoglobulin-like (Ig-like) domains, are present in many other proteins, which, together with Igs, constitute the Ig superfamily. (Figure 24–27) immunogold electron microscopy Method to localize specific macromolecules using a primary antibody that binds to the molecule of interest and is then detected with a secondary antibody to which a colloidal gold particle has been attached. The gold particle is electron-dense and can be seen as a black dot in the electron microscope. (Figure 9–45) immunological memory Long-lived property of the adaptive immune system that follows a primary immune response


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Cell_Biology_Alberts. electron-dense and can be seen as a black dot in the electron microscope. (Figure 9–45) immunological memory Long-lived property of the adaptive immune system that follows a primary immune response to many antigens, such that a subsequent encounter with the same antigen will provoke a more rapid and stronger secondary immune response. (Figure 24–16) immunological self-tolerance The lack of response of the adaptive immune system to an antigen. Tolerance to self molecules is crucial to avoid autoimmune diseases. (Figure 24–21) immunological synapse The highly organized interface that develops between a T cell and an antigen-presenting cell (APC) or target cell it is in contact with, formed by T-cell receptors binding to antigen–MHC complexes on the APC and cell-adhesion proteins binding to their counterparts on the APCs.


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Cell_Biology_Alberts. induced fit A principle for increasing the specificity of substrate recognition by proteins and RNAs. In protein synthesis, a ribosome, or enzyme folds around a codon– anticodon interaction and only when the match is correct is the subsequent reaction allowed to proceed. induced pluripotent stem cells (iPS cells) Cells that are induced by artificial expression of specific transcription regulators to look and behave like the pluripotent embryonic stem cells that are derived from embryos. induced regulatory T cell A regulatory T cell (Treg cell) that develops from naive helper T cells when they are activated in the presence of TGFβ in the absence of IL6. inflammasome Intracellular protein complex formed after activation of cytoplasmic NOD-like receptors with adaptor proteins. It contains a caspase enzyme that cleaves pro-inflammatory cytokines from their precursor proteins.


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Cell_Biology_Alberts. inflammatory response Local response of a tissue to injury or infection—characterized clinically by redness, swelling, heat, and pain. Caused by invasion of white blood cells, which are attracted by and secrete various cytokines. inhibitors of apoptosis (IAPs) Intracellular protein inhibitors of apoptosis. inhibitory G protein (Gi) Trimeric G protein that can regulate ion channels and inhibit the enzyme adenylyl cyclase in the plasma membrane. See also G protein. (Table 15–3, p. 846) inhibitory neurotransmitter Neurotransmitter that opens transmitter-gated Cl– or K+ channels in the postsynaptic membrane of a nerve or muscle cell and thus tends to inhibit the generation of an action potential. initial segment Specialized membrane region at the base of a nerve axon (adjacent to the cell body) that is rich in voltage-gated Na+ channels plus other classes of ion channels that all contribute to the encoding of membrane depolarization into action potential frequency.