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Cell_Biology_Alberts. initiator caspases Apoptotic caspases that begin the apoptotic process, activating the executioner caspases. initiator tRNA Special tRNA that intiates translation. It always carries the amino acid methionine, forming the complex MettRNAi. (Figure 6–70) innate immune response An early immune response in all organisms to a pathogen, which includes the production of antimicrobial molecules and the activation of phagocytic cells. Such a response is not specific for the pathogen, in contrast to an adaptive immune response. inner membrane Mitochondrial membrane that encloses the matrix space and forms extensive invaginations called cristae. inner mitochondrial membrane Mitochondrial membrane that encloses the matrix space and forms extensive invaginations called cristae. inner nuclear membrane One of two concentric membranes comprising the nuclear envelope; contnuous with the outer nuclear membrane; contains specific proteins as anchoring sites for chromatin and the nuclear lamina.


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Cell_Biology_Alberts. inositol 1,4,5-trisphosphate (IP3) Small intracellular signaling molecule produced during activation of the inositol phospholipid signaling pathway. Acts to release Ca2+ from the endoplasmic reticulum. (Figures 15–28 and 15–29) inositol phospholipid signaling pathway Intracellular signaling pathway that starts with the activation of phospholipase C and the generation of IP3 and diacylglycerol (DAG) from inositol phospholipids in the plasma membrane. The DAG helps to activate protein kinase C. (Figures 15–28 and 15–29) integrin Transmembrane adhesion protein that is involved in the attachment of cells to the extracellular matrix and to each other. (Figure 19–3 and Table 19–1, p. 1037) interaction domain Compact protein module, found in many intracellular signaling proteins, that binds to a particular structural motif (e.g., a short peptide sequence, a covalent modification, or another protein domain) in another protein or lipid.


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Cell_Biology_Alberts. interferon-α (IFNα) and interferon-β (IFNβ) Cytokines (type I interferons) produced by mammalian cells as a general response to a viral infection. intermembrane space Compartment of mitochondrion between by the outer and inner mitochondrial membranes. internal ribosome entry site (IRES) Specific site in a eukaryotic mRNA, other than at the 5′ end, at which translation can be initiated. (Figure 7–68) interphase Long period of the cell cycle between one mitosis and the next. Includes G1 phase, S phase, and G2 phase. (Figure 17–4) interpolar microtubule In the mitotic or meiotic spindle, a microtubule interdigitating at the equator with the microtubules emanating from the other pole. (Figure 17–23) intracellular pathogens Pathogens, including all viruses and many bacteria and protozoa, that enter and replicate inside host cells to cause disease.


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Cell_Biology_Alberts. intrinsic pathway (mitochondrial pathway) Pathway of apoptosis activated from inside the cell in response to stress or developmental signals; depends on the release into the cytosol of mitochondrial proteins normally resident in the mitochondrial intermembrane space. intron Noncoding region of a eukaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing during production of the mRNA or other functional RNA. (Figure 4–15) invadopodia Actin-rich protrusions extending in three-dimensions that are important for cells to cross tissue barriers by degrading the extracellular matrix.


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Cell_Biology_Alberts. ion channel Transmembrane protein complex that forms a water-filled channel across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients. (Figure 11–22) ion-channel-coupled receptor (transmitter-gated ion channel, ionotropic receptor) Ion channel found at chemical synapses in the postsynaptic plasma membranes of nerve and muscle cells. Opens only in response to the binding of a specific extracellular neurotransmitter. The resulting inflow of ions leads to the generation of a local electrical signal in the postsynaptic cell. (Figures 15–6 and 11–35) ion-sensitive indicators Molecules whose light emission reflects the local concentration of a particular ion; some are luminescent (emitting light spontaneously) while others are fluorescent (emitting light on exposure to light).


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Cell_Biology_Alberts. IP3-gated Ca2+-release channel (IP3 receptor) Gated Ca2+ channel in the ER membrane that opens on binding cytosolic IP3, releasing stored Ca2+ into the cytosol. (Figure 15–29) iron–sulfur cluster Electron-transporting group consisting of either two or four iron atoms bound to an equal number of sulfur atoms, found in a class of electron-transport proteins. (Figure 14–16) J gene segment Short DNA sequences that encodes part of the variable region of light and heavy immunoglobulin chains and of α and β chains of T cell receptors. (Figures 24–28 and 24–29) JAK–STAT signaling pathway Signaling pathway activated by cytokines and some hormones, providing a rapid route from the plasma membrane to the nucleus to alter gene transcription. Involves cytoplasmic Janus kinases (JAKs), and signal transducers and activators of transcription (STATs).


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Cell_Biology_Alberts. Janus kinases (JAKs) Cytoplasmic tyrosine kinases associated with cytokine receptors, which phosphorylate and activate transcription regulators called STATs. junctional diversification The random loss and gain of nucleotides at joining sites during V(D)J recombination that occurs during B and T cell development when the cells are assembling the gene segments that encode their antigen receptors. It enormously increases the diversity of V-region coding sequences. K+ leak channel K+-transporting ion channel in the plasma membrane of animal cells that remains open even in a “resting” cell. karyotype Display of the full set of chromosomes of a cell, arranged with respect to size, shape, and number. keratin Type of intermediate filament, commonly produced by epithelial cells. kinase cascade Intracellular signaling pathway in which one protein kinase, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and so on, relaying the signal onward.


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Cell_Biology_Alberts. kinesin Member of one of the two main classes of motor proteins that use the energy of ATP hydrolysis to move along microtubules. (Figure 16–56) kinesin-1 Motor protein associated with microtubules that transports cargo within the cell; also called “conventional kinesin.” kinetic proofreading A principle for increasing the specificity of catalysis. In the synthesis of DNA, RNA, and proteins, it refers to a time delay that begins with an irreversible step (such as ATP or GTP hydrolysis) and during which incorrect base pairs are more likely to dissociate than correct pairs. kinetochore Large protein complex that connects the centromere of a chromosome to microtubules of the mitotic spindle. (FIgure 17–30) kinetochore microtubule In the mitotic or meiotic spindle, a microtubule that connects the spindle pole to the kinetochore of a chromosome.


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Cell_Biology_Alberts. lagging strand One of the two newly synthesized strands of DNA found at a replication fork. The lagging strand is made in discontinuous lengths that are later joined covalently. (Figure 5–7) lamellipodium (plural lamellipodia) Flattened, sheetlike protrusion supported by a meshwork of actin filaments, which is extended at the leading edge of a crawling animal cell. (Figures 16–77 and 16–79) laminin Extracellular matrix fibrous protein found in basal laminae, where it forms a sheetlike network. (Figures 19–52 and 19–53) lampbrush chromosome Huge chromosome paired in preparation for meiosis, found in immature amphibian eggs; consisting of large loops of chromatin extending out from a linear central axis. (Figure 4–47) late endosome Compartment formed from a bulbous, vacuolar portion of early endosomes by a process called endosome maturation; late endosomes fuse with one another and with lysosomes to form endolysosomes that degrade their contents.


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Cell_Biology_Alberts. LDL-receptor-related protein (LRP) Co-receptor bound by Wnt proteins in the regulation of β-catenin proteolysis. leading strand One of the two newly synthesized strands of DNA found at a replication fork. The leading strand is made by continuous synthesis in the 5′-to-3′ direction. (Figure 5–7) lectin Protein that binds tightly to a specific sugar. Abundant lectins from plant seeds are used as affinity reagents to purify glycoproteins or to detect them on the surface of cells. Legionnaire’s disease Type of pneumonia resulting from infection with Legionella pneumophila, a parasite of freshwater amoebae that is spread to humans by air-conditioning systems that harbor infected amoebae and produce microdroplets of water that are easily inhaled. lethal factor One of the two A subunits of anthrax toxin; a protease that cleaves several activated members of the MAP kinase kinase family and causes a large fall in blood pressure and death on entry into the bloodstream of an animal.


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Cell_Biology_Alberts. leucine-rich repeat (LRR) receptor kinases Common type of receptor serine/threonine kinase in plants that contains a tandem array of leucine-rich repeat sequences in its extracellular portion. leukemia Cancer of white blood cells. leukocyte General name for all the nucleated blood cells lacking hemoglobin. Also called white blood cells. Includes lymphocytes, granulocytes, and monocytes. (Figure 22–27) ligand Any molecule that binds to a specific site on a protein or other molecule. From Latin ligare, to bind. light microscope One of a class of microscopes that uses visible light to create the image. lignin Network of cross-linked phenolic compounds that forms a supporting network throughout the cell walls of xylem and woody tissue in plants. limit of resolution In microscopy, the smallest distance apart at which two point objects can be resolved as separate. Just under 0.2 μm for conventional light microscopy, a limit determined by the wavelength of light.


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Cell_Biology_Alberts. linkage In ligand binding, the conformational coupling between two separate ligand-binding sites on a protein, such that a conformational change in the protein induced by binding of one ligand affects the binding of a second ligand. lipid bilayer (phospholipid bilayer) Thin double sheet of phospholipid molecules that forms the core structure of all cell membranes. The two layers of lipid molecules are packed with their hydrophobic tails pointing inward and their hydrophilic heads outward, exposed to water. (Figure 10–1 and Panel 2–5, pp. 98–99) lipid droplets Storage form in cells for excess lipids; comprised of a single monolayer of phospholipids and proteins that surrounds neutral lipids that can be retrieved from droplets as required by the cell.


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Cell_Biology_Alberts. lipid raft Small region of a membrane enriched in sphingolipids and cholesterol. (Figure 10–13) liposome Artificial phospholipid bilayer vesicle formed from an aqueous suspension of phospholipid molecules. (Figure 10–9) local mediator Extracellular signal molecule that acts on neighboring cells. long noncoding RNA (lncRNA) One of a large group (≈8000 in humans) of RNAs longer than 200 nucleotides and not coding for protein. The functions, if any, of most lncRNAs is unknown but individual lncRNA are known to play important roles in the cell, for example, in telomerase function and genomic imprinting. In a general sense, lncRNAs are believed to act as scaffolds, holding together proteins and nucleic acids to speed up a wide variety of reactions in the cell.


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Cell_Biology_Alberts. long-term depression (LTD) A long-lasting (hours or more) decrease in the sensitivity of certain synapses in the brain triggered by NMDA receptor activation. As the opposing process to long-term potentiation, it is thought to be involved in learning and memory. long-term potentiation (LTP) Long-lasting increase (days to weeks) in the sensitivity of certain synapses in the brain, induced by a short burst of repetitive firing in the presynaptic neurons. (Figure 11–44) loss of heterozygosity The result of errant homologous recombination that uses the homolog from the other parent instead of the sister chromatid as the template, converting the sequence of the repaired DNA to that of the other homolog.


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Cell_Biology_Alberts. low-density lipoprotein (LDL) Large complex composed of a single protein molecule and many esterified cholesterol molecules, together with other lipids. The form in which cholesterol is transported in the blood and taken up into cells. (Figure 13–51) lumen The space inside a hollow structure. In cells: the cavity enclosed by an organelle membrane. In tissues: the cavity enclosed by a sheet of cells. lymphocyte White blood cell responsible for the specificity of adaptive immune responses. Two main types: B cells, which produce antibody, and T cells, which interact directly with other effector cells of the immune system and with infected cells. T cells develop in the thymus and are responsible for cell-mediated immunity. B cells develop in the bone marrow in mammals and are responsible for the production of circulating antibodies.


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Cell_Biology_Alberts. lymphoid organ An organ containing large numbers of lymphocytes. Lymphocytes are produced in primary lymphoid organs and respond to antigen in peripheral lymphoid organs. (Figure 24–12) lymphoma Cancer of lymphocytes, in which the cancer cells are mainly found in lymphoid organs (rather than in the blood, as in leukemias). lysosomal storage diseases Genetic diseases resulting from defects in or a lack of one or more functional hydrolases in lysosomes of some cells, leading to accumulation of undigested substrates in lysosomes and consequent cell pathology. lysosome Membrane-enclosed organelle in eukaryotic cells containing digestive enzymes, which are typically most active at the acid pH found in the lumen of lysosomes. (Figure 13–37) lysozyme Enzyme that catalyzes the cutting of polysaccharide chains in the cell walls of bacteria.


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Cell_Biology_Alberts. M-Cdk (M-phase Cdk) Cyclin-Cdk complex formed in vertebrate cells by an M-cyclin and the corresponding cyclindependent kinase (Cdk). (Figure 17–11 and Table 17–1, p. 969) M-cyclin A cyclin found in all eukaryotic cells that promotes the events of mitosis. (Figure 17–11) M6P receptor proteins Transmembrane receptor proteins present in the trans Golgi network that recognize the mannose 6-phosphate (M6P) groups added exclusively to lysosomal enzymes, marking the enzymes for packaging and delivery to early endosomes. macromolecule Polymers constructed of long chains of covalently linked, small organic (carbon-containing) molecules. The principal building blocks from which a cell is constructed and the components that confer the most distinctive properties of living things. macrophage Phagocytic cell derived from blood monocytes, resident in most tissues but able to roam. It has both scavenger and antigen-presenting functions in immune responses.


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Cell_Biology_Alberts. macrophage Phagocytic cell derived from blood monocytes, resident in most tissues but able to roam. It has both scavenger and antigen-presenting functions in immune responses. macropinocytosis Clathrin-independent, dedicated degradative endocytic pathway induced in most cell types by cell-surface receptor activation by specific cargoes. malaria Protozoal disease caused by four species of Plasmodium, which are transmitted to humans by the bite of the female Anopheles mosquito. malignant Of tumors and tumor cells: invasive and/or able to undergo metastasis. A malignant tumor is a cancer. (Figure 20–3)


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Cell_Biology_Alberts. malignant Of tumors and tumor cells: invasive and/or able to undergo metastasis. A malignant tumor is a cancer. (Figure 20–3) MAP kinase module (mitogen-activated protein kinase module) An intracellular signaling module composed of three protein kinases, acting in sequence, with MAP kinase as the third. Typically activated by a Ras protein in response to extracellular signals. (Figure 15–49) master transcription regulator A transcription regulator specifically required for formation of a particular cell type. Artificial expression of master transcription regulators (alone or in combination with others) will often convert one cell type into another. maternal inheritance A form of inheritance observed when following mitochondria in animals and plants, where mitochondrial DNA is inherited only through the female germ line.


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Cell_Biology_Alberts. maternal inheritance A form of inheritance observed when following mitochondria in animals and plants, where mitochondrial DNA is inherited only through the female germ line. maternal-effect gene Gene that acts in the mother to specify maternal mRNAs and proteins in the egg. Maternal-effect mutations affect the development of the embryo even if the embryo itself has not inherited the mutated gene. maternal-zygotic transition (MZT) Event in animal development where the embryo’s own genome largely takes over control of development from maternally deposited macromolecules. proteolytic enzyme present in the extracellular matrix that degrades matrix proteins. Includes the collagenases. matrix space Large internal compartment of the mitochondrion. mechanosensitive channels Transmembrane ion channels that open in response to a mechanical stress on the lipid bilayer in which they are embedded.


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Cell_Biology_Alberts. mechanosensitive channels Transmembrane ion channels that open in response to a mechanical stress on the lipid bilayer in which they are embedded. megakaryocyte Large myeloid cell with a multilobed nucleus that remains in the bone marrow when mature. Buds off platelets from long cytoplasmic processes. (Figures 22–29) meiosis I The first of two rounds of chromosome segregation following meiotic chromosome duplication; segregates the homologs, each composed of a tightly linked pair of sister chromatids. meiosis II The second of two rounds of chromosome segregation following meiotic chromosome duplication; segregates the sister chromatids of each homolog.


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Cell_Biology_Alberts. membrane potential Voltage difference across a membrane due to a slight excess of positive ions on one side and of negative ions on the other. A typical membrane potential for an animal cell plasma membrane is –60 mV (inside negative relative to the surrounding fluid). (Figure 11–23) membrane protein Amphiphilic protein of diverse structure and function that associates with the lipid bilayer of cell membranes. (Figure 10–17) membrane transport protein Membrane protein that mediates the passage of ions or molecules across a membrane. The two main classes are transporters (also called carriers or permeases) and channels. (Figure 11–4) membrane-associated protein Membrane protein not extending into the hydrophobic interior of the lipid bilayer but bound to either face of the membrane by noncovalent interactions with other membrane proteins. (Figure 10–17) membrane-bending proteins Attach to specific membrane regions as needed and act to control local membrane curvature and thus


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Cell_Biology_Alberts. by noncovalent interactions with other membrane proteins. (Figure 10–17) membrane-bending proteins Attach to specific membrane regions as needed and act to control local membrane curvature and thus confer on membranes their characteristic three-dimensional shapes.


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Cell_Biology_Alberts. membrane-bound ribosome Ribosome attached to the cytosolic face of the endoplasmic reticulum. The site of synthesis of proteins that enter the endoplasmic reticulum. (Figure 12–38) memory cell In immunology: a T or B lymphocyte generated following antigen stimulation that is more easily and more quickly induced to become an effector cell or another memory cell by a later encounter with the same antigen. (Figure 24–17) mesoderm Embryonic tissue that is the precursor to muscle, connective tissue, skeleton, and many of the internal organs. (Figure 21–3) messenger RNA (mRNA) RNA molecule that specifies the amino acid sequence of a protein. Produced in eukaryotes by processing of an RNA molecule made by RNA polymerase as a complementary copy of DNA. It is translated into protein in a process catalyzed by ribosomes. (Figure 6–20) metabolism The sum total of the chemical processes that take place in living cells. All of catabolism plus anabolism. (Figure 2–14) metabotropic receptors


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Cell_Biology_Alberts. catalyzed by ribosomes. (Figure 6–20) metabolism The sum total of the chemical processes that take place in living cells. All of catabolism plus anabolism. (Figure 2–14) metabotropic receptors Neurotransmitter receptors that regulate ion channels indirectly through the activation of second-messenger molecules.


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Cell_Biology_Alberts. metaphase plate Imaginary plane at right angles to the mitotic spindle and midway between the spindle poles; the plane in which chromosomes are positioned at metaphase. (Panel 17–1, pp. 980–981) metaphase-to-anaphase transition Transition in the eukaryotic cell cycle preceding sister-chromatid separation at anaphase. If the cell is not ready to proceed to anaphase, the cell cycle is halted at this point. (Figure 17–9, and Panel 17–1, pp. 980–981) metastases Secondary tumors, at sites in the body additional to that of the primary tumor, resulting from cancer cells breaking loose, entering blood or lymphatic vessels, and colonizing separate environments. metastasis The spread of cancer cells from their site of origin to other sites in the body. (Figures 20–1 and 20–16)


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Cell_Biology_Alberts. metastasis The spread of cancer cells from their site of origin to other sites in the body. (Figures 20–1 and 20–16) MHC complex (major histocompatibility complex) Cluster of genes in one vertebrate chromosome (chromosome 6 in humans) that code for a set of highly polymorphic cell-surface glycoproteins (MHC proteins). (Figure 24–37) microbiome The combined genomes of the various species of a defined microbiota. microbiota The collective of microorganisms that reside in or on an organism. microelectrode A piece of fine glass tubing, pulled to an even finer tip, that is used to inject electric current into cells or to study the intracellular concentrations of common inorganic ions (such as H+, Na+, K+, Cl–, and Ca2+) in a single living cell by insertion of its tip directly into the cell interior through the plasma membrane.


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Cell_Biology_Alberts. microRNAs (miRNAs) Short (~21 nucleotide) eukaryotic RNAs, produced by the processing of specialized RNA transcripts coded in the genome, that regulate gene expression through base-pairing with mRNA. (Figure 7–75) microsome Small vesicle derived from endoplasmic reticulum that is produced by fragmentation when cells are homogenized. (Figure 12–34) microtubule flux Movement of individual tubulin molecules in the microtubules of the spindle toward the poles by loss of tubulin at their minus ends. Helps to generate the poleward movement of sister chromatids after they separate in anaphase. (Figure 17–35) microtubule-associated protein (MAP) Any protein that binds to microtubules and modifies their properties. Many different kinds have been found, including structural proteins, such as MAP2, and motor proteins, such as dynein. [Not to be confused with the “MAP” (mitogen-activated protein kinase) of “MAP kinase.”] microtubule-organizing center (MTOC) Region in a cell, such as a


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Cell_Biology_Alberts. as MAP2, and motor proteins, such as dynein. [Not to be confused with the “MAP” (mitogen-activated protein kinase) of “MAP kinase.”] microtubule-organizing center (MTOC) Region in a cell, such as a centrosome or a basal body, from which microtubules grow.


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Cell_Biology_Alberts. midbody Structure formed at the end of cleavage that can persist for some time as a tether between the two daughter cells in animals. (Figure 17–43) mitochondrial hsp70 Part of a multisubunit protein assembly bound to the matrix side of the TIM23 complex that acts as a motor to pull mitochondrial precursor proteins into the matrix space. mitochondrial matrix Large internal compartment of the mitochondrion. The corresponding compartment in a chloroplast is known as the stroma. mitochondrial precursor proteins Proteins first fully synthesized in the cytosol and then translocated into mitochondrial subcompartments as directed by one or more signal sequences. mitochondrion (plural mitochondria) Membrane-bounded organelle, about the size of a bacterium, that carries out oxidative phosphorylation and produces most of the ATP in eukaryotic cells. (Figure 1–28) mitogen Extracellular signal molecule that stimulates cells to proliferate.


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Cell_Biology_Alberts. mitotic chromosome Highly condensed duplicated chromosome as seen at mitosis, consisting of two sister chromatids held together at the centromere. mitotic spindle Bipolar array of microtubules and associated molecules that forms in a eukaryotic cell during mitosis and serves to move the duplicated chromosomes apart. (Figure 17–23 and Panel 17–1, pp. 980–981) model organism A species that has been studied intensively over a long period and thus serves as a “model” for deriving fundamental biological principles. molecular chaperone (chaperone) Protein that helps guide the proper folding of other proteins, or helps them avoid misfolding. Includes heat-shock proteins (hsp). monoallelic gene expression Expression of only one of the two copies of a gene in a diploid genome, occurring, for example, as a result of imprinting or X-chromosome inactivation.


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Cell_Biology_Alberts. monoallelic gene expression Expression of only one of the two copies of a gene in a diploid genome, occurring, for example, as a result of imprinting or X-chromosome inactivation. monoclonal antibody Antibody secreted by a hybridoma cell line. Because the hybridoma is generated by the fusion of a single B cell with a single tumor cell, each hybridoma produces antibodies that are all identical. (Page 444) monocyte Type of white blood cell that leaves the bloodstream and matures into a macrophage in tissues. (Figure 22–27) monomeric GTPase A single-subunit enzyme that converts GTP to GDP (also called small monomeric GTP-binding proteins). Cycles between an active GTP-bound form and an inactive GDP-bound form and frequently acts as a molecular switch in intracellular signaling pathways.


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Cell_Biology_Alberts. morphogen Diffusible signal molecule that can impose a pattern on a field of cells by causing cells in different places to adopt different fates. (Figure 21–8) morphogenesis Developmental process in which cells undergo movements and deformations in order to assemble into tissues and organs with specific shapes and sizes. motor protein Protein that uses energy derived from nucleoside triphosphate hydrolysis to propel itself along a linear track (protein filament or other polymeric molecule). mRNA degradation control Regulation by a cell of gene expression by selectively preserving or destroying certain mRNA molecules in the cytoplasm. mTOR The mammalian version of the large protein kinase called TOR, involved in cell signaling; mTOR exists in two functionally distinct multiprotein complexes.


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Cell_Biology_Alberts. mTOR The mammalian version of the large protein kinase called TOR, involved in cell signaling; mTOR exists in two functionally distinct multiprotein complexes. multidrug resistance An observed phenomenon in which cells exposed to one anticancer drug evolve a resistance not only to that drug, but also to other drugs to which they have never been exposed. multidrug resistance (MDR) protein Type of ABC transporter protein that can pump hydrophobic drugs (such as some anticancer drugs) out of the cytoplasm of eukaryotic cells. multipass transmembrane protein Membrane protein in which the polypeptide chain crosses the lipid bilayer more than once. (Figure 10–17) multivesicular bodies Intermediates in the endosome maturation process; early endosomes that are on their way to becoming late endosomes. mutation Heritable change in the nucleotide sequence of a chromosome. (Panel 8–2, pp. 486–487) mutation rate The rate at which changes (mutations) occur in DNA sequences.


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Cell_Biology_Alberts. mutation Heritable change in the nucleotide sequence of a chromosome. (Panel 8–2, pp. 486–487) mutation rate The rate at which changes (mutations) occur in DNA sequences. mutualism Ecological relationship between microbes and their host in which both the microbe and host benefit.


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Cell_Biology_Alberts. mutualism Ecological relationship between microbes and their host in which both the microbe and host benefit. Myc Transcription regulatory protein that is activated when a cell is stimulated to grow and divide by extracellular signals. It activates the transcription of many genes, including those that stimulate cell growth. (Figure 17–61) myelin sheath Insulating layer of specialized cell membrane wrapped around vertebrate axons. Produced by oligodendrocytes in the central nervous system and by Schwann cells in the peripheral nervous system. (Figure 11–33) myeloid cell Any white blood cell other than a lymphocyte. (Figure 22–31) myoblast Mononucleated, undifferentiated muscle precursor cell. A skeletal muscle cell is formed by the fusion of multiple myoblasts. (Figure 22–19) myofibril Long, highly organized bundle of actin, myosin, and other proteins in the cytoplasm of muscle cells that contracts by a sliding filament mechanism.


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Cell_Biology_Alberts. myosin Type of motor protein that uses the energy of ATP hydrolysis to move along actin filaments. Na+-K+ pump (Na+-K+ ATPase) Transmembrane carrier protein found in the plasma membrane of most animal cells that pumps Na+ out of and K+ into the cell, using energy derived from ATP hydrolysis. (Figure 11–15) NAD+/NADH (nicotinamide adenine dinucleotide/reduced nicotinamide adenine dinucleotide) Electron carrier system that participates in oxidation–reduction reactions, such as the oxidation of food molecules. NAD+ accepts the equivalent of a hydride ion (H–, a proton plus two electrons) to become the activated carrier NADH. The NADH formed donates its high-energy electrons to the ATP-generating process of oxidative phosphorylation. (Figure 2–36) NADH dehydrogenase complex First of the three electron-driven proton pumps in the mitochondrial respiratory chain, also known as Complex I. It accepts electrons from NADH and passes them to a quinone. (Figure 14–18)


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Cell_Biology_Alberts. NADP+/NADPH (nicotinamide adenine dinucleotide phosphate/reduced nicotinamide adenine dinucleotide phosphate) Electron carrier system closely related to NAD+/ NADH, but used almost exclusively in reductive biosynthetic, rather than catabolic, pathways. (Figure 2–36) naïve cell In immunology: a T or B lymphocyte that proliferates and differentiates into an effector cell or memory cell when it encounters its specific foreign antigen for the first time. (Figure 24–17) natural killer cell (NK cell) Cytotoxic cell of the innate immune system that can kill virus-infected cells and some cancer cells. natural regulatory T cell A regulatory T cell (Treg cell) that develops in the thymus and helps maintain self-tolerance. negative selection Process by which thymocytes expressing a T cell receptor with high affinity for a self peptide bound to a self-MHC protein are eliminated by undergoing apoptosis.


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Cell_Biology_Alberts. negative selection Process by which thymocytes expressing a T cell receptor with high affinity for a self peptide bound to a self-MHC protein are eliminated by undergoing apoptosis. negative staining A technique in electron microscopy enabling fine detail of isolated macromolecules to be seen. Samples are prepared such that a very thin film of heavy-metal salt covers everywhere except where excluded by the presence of macromolecules, which allow electrons to pass through, creating a reverse or negative image of the molecule. Nernst equation Equation that computes relates the electrical potential (voltage) generated by differences in ion concentrations across a membrane. Netrin Signal protein, secreted by cells of the neural tube floor plate, responsible for attracting growth cones of commissural axons toward and across the midline.


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Cell_Biology_Alberts. Netrin Signal protein, secreted by cells of the neural tube floor plate, responsible for attracting growth cones of commissural axons toward and across the midline. neural crest Collection of cells located along the line where the neural tube pinches off from the surrounding epidermis in the vertebrate embryo. Neural crest cells migrate to give rise to a variety of tissues, including neurons and glia of the peripheral nervous system, pigment cells of the skin, and the bones of the face and jaws. (Figure 19–8) neural map Regular mapping of neurons of a similar type from one territory to another, such that there are orderly projections of one array of neurons onto another.


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Cell_Biology_Alberts. neural tube Tube of ectoderm that will form the brain and spinal cord in a vertebrate embryo. (Figure 21–56) neurofilament Type of intermediate filament found in nerve cells. (Figure 16–72) neuromuscular junction Specialized chemical synapse between an axon terminal of a motor neuron and a skeletal muscle cell. (Figure 11–37) neuron (nerve cell) Impulse-conducting cell of the nervous system, with extensive processes specialized to receive, conduct, and transmit signals. (Figures 11–28 and 21–66) neuronal specificity Nonequivalence among neurons; an intrinsic characteristic that guides axons to their appropriate target sites. neurotransmitter Small signal molecule secreted by the presynaptic nerve cell at a chemical synapse to relay the signal to the postsynaptic cell. Examples include acetylcholine, glutamate, GABA, glycine, and many neuropeptides.


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Cell_Biology_Alberts. neurotrophic factor Factor released in limited amounts by a target tissue that the neurons innervating that tissue require to survive. neurotrophin Family of signal proteins that promote the survival and growth of specific classes of neurons. neutrophil White blood cell that is specialized for the uptake of particulate material by phagocytosis. Enters tissues that become infected or inflamed. (Figure 24–5) NFκB protein Latent transcription regulator that is activated by various intracellular signaling pathways when cells are stimulated during immune, inflammatory, or stress responses. Also has important roles in animal development. (Figure 15–62) nitric oxide (NO) Gaseous signal molecule that is widely used in cell–cell communication in both animals and plants. (Figure 15–40) nitrogen fixation Biochemical process carried out by certain bacteria that reduces atmospheric nitrogen (N2) to ammonia, leading eventually to various nitrogen-containing metabolites.


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Cell_Biology_Alberts. NMDA receptor Subclass of glutamate-gated ion channel in the mammalian central nervous system critical for longterm potentiation and long-term depression. NMDA-receptor channels are doubly gated, opening only when glutamate is bound to the receptor and, simultaneously, the membrane is strongly depolarized. NO synthase (NOS) Enzyme that synthesizes nitric oxide (NO) by the deamination of arginine. (Figure 15–40B) NOD-like receptors (NLRs) Large family of pattern recognition receptors (PRRs) with leucine-rich repeat motifs; they are exclusively cytoplasmic and recognize a distinct set of microbial molecules. nonclassical cadherins Large family of cadherins that are more distantly related in sequence than classical cadherins and include proteins involved in adhesion (including protocadherins, desmocollins, and desmogleins) and signaling.


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Cell_Biology_Alberts. noncoding RNA An RNA molecule that is the final product of a gene and does not code for protein. These RNAs serve as enzymatic, structural, and regulatory components for a wide variety of processes in the cell. nondisjunction Event occurring occasionally during meiosis in which a pair of homologous chromosomes fails to separate so that the resulting germ cell has either too many or too few chromosomes. nonenveloped virus Virus consisting of a nucleic acid core and a protein capsid only. (Figure 23–18C,D) nonhomologous end joining A DNA repair mechanism for double-strand breaks in which the broken ends of DNA are brought together and rejoined by DNA ligation, generally with the loss of one or more nucleotides at the site of joining.


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Cell_Biology_Alberts. nonretroviral retrotransposons Type of transposable element that moves by being first transcribed into an RNA copy that is converted to DNA by reverse transcriptase then inserted elsewhere in the genome. The mechanism of insertion differs from that of the retroviral-like transposons. (Table 5–4, p. 288) nonsense-mediated mRNA decay Mechanism for degrading aberrant mRNAs containing in-frame internal stop codons before they can be translated into protein. (Figure 6–76) normal flora The human microbiota consisting of approximately 1014 bacterial, fungal, and protozoan cells, representing thousands of microbial species. Notch Transmembrane receptor protein (and latent transcription regulator) involved in many cell-fate choices in animal development, for example in the specification of nerve cells from ectodermal epithelium. Its ligands are cell-surface proteins such as Delta and Serrate. (Figure 15–59)


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Cell_Biology_Alberts. NSF Hexameric ATPase that disassembles a complex of a v-SNARE and a t-SNARE. (Figure 13–20) nuclear envelope Double membrane (two bilayers) surrounding the nucleus. Consists of an outer and inner membrane and is perforated by nuclear pores. The outer membrane is continuous with the endoplasmic reticulum. (Figures 4–9 and 12–7) nuclear export receptors Bind to both the export signal and nuclear pore complex proteins to guide their cargo through the nuclear pore complex to the cytosol. nuclear export signal Sorting signal contained in the structure of molecules and complexes, such as nuclear RNPs and new ribosomal subunits, that are transported from the nucleus to the cytosol through nuclear pore complexes. (Figure 12–13) nuclear import receptors Recognize nuclear localization signals to initiate nuclear import of proteins containing the appropriate nuclear localization signal. nuclear lamin Protein subunit of the intermediate filaments that form the nuclear lamina.


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Cell_Biology_Alberts. nuclear lamin Protein subunit of the intermediate filaments that form the nuclear lamina. nuclear lamina Fibrous meshwork of proteins on the inner surface of the inner nuclear membrane. It is made up of a network of intermediate filaments formed from nuclear lamins.


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Cell_Biology_Alberts. nuclear localization signal (NLS) Signal sequence or signal patch found in proteins destined for the nucleus that enables their selective transport into the nucleus from the cytosol through the nuclear pore complexes. (Figures 12–9 and 12–13) nuclear magnetic resonance (NMR) spectroscopy NMR is the resonant absorption of electromagnetic radiation at a specific frequency by atomic nuclei in a magnetic field, due to flipping of the orientation of their magnetic dipole moments. The NMR spectrum provides information about the chemical environment of the nuclei. NMR is used widely to determine the three-dimensional structure of small proteins and other small molecules. The principles of NMR are also used for medical diagnostic purposes in magnetic resonance imaging (MRI). (Figure 8–22) nuclear pore complex (NPC) Large multiprotein structure forming an aqueous channel (the nuclear pore) through the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm.


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Cell_Biology_Alberts. pore complex (NPC) Large multiprotein structure forming an aqueous channel (the nuclear pore) through the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm. (Figure 12–8) nuclear receptor superfamily Intracellular receptors for hydrophobic signal molecules such as steroid and thyroid hormones and retinoic acid. The receptor-ligand complex acts as a transcription factor in the nucleus. (Figure 15–65) nuclear transport receptor (karyopherin) Protein that escorts macromolecules either into or out of the nucleus: nuclear import receptor or nuclear export receptor. (Figure 12–13) nucleolus A prominent structure in the nucleus where rRNA is transcribed and ribosomal subunits are assembled. (Figure 4–9) nucleoporin Any of a number of different proteins that make up nuclear pore complexes.


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Cell_Biology_Alberts. nucleosome Beadlike structure in eukaryotic chromatin, composed of a short length of DNA wrapped around an octameric core of histone proteins. The fundamental structural unit of chromatin. (Figures 4–22 and 4–23) nucleotide Nucleoside with one or more phosphate groups joined in ester linkages to the sugar moiety. DNA and RNA are polymers of nucleotides. (Panel 2–6, pp. 100–101) nucleotide excision repair Type of DNA repair that corrects damage of the DNA double helix, such as that caused by chemicals or UV light, by cutting out the damaged region on one strand and resynthesizing it using the undamaged strand as template. Compare base excision repair. (Figure 5–41) O-linked glycosylation Addition of one or more sugars to a hydroxyl group on a protein. obligate pathogens Bacteria that can only replicate inside their host.


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Cell_Biology_Alberts. O-linked glycosylation Addition of one or more sugars to a hydroxyl group on a protein. obligate pathogens Bacteria that can only replicate inside their host. olfactory receptors G-protein-coupled receptors on the modified cilia of olfactory receptor neurons that recognize odors. The receptors activate adenylyl cyclase via an olfactoryspecific G protein (Golf) and resultant increases in cAMP open cyclic-AMP-gated cation channels, allowing Na+ influx and depolarization and initiation of a nerve impulse. oligodendrocyte Glial cell in the vertebrate central nervous system that forms a myelin sheath around axons. Compare Schwann cell.


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Cell_Biology_Alberts. oligodendrocyte Glial cell in the vertebrate central nervous system that forms a myelin sheath around axons. Compare Schwann cell. oncogene An altered gene whose product can act in a dominant fashion to help make a cell cancerous. Typically, an oncogene is a mutant form of a normal gene (proto-oncogene) involved in the control of cell growth or division. (Figure 20–17) open reading frame (ORF) A continuous nucleotide sequence free from stop codons in at least one of the three reading frames (and thus with the potential to code for protein). opportunistic pathogens Microbes of the normal flora that can cause disease only if the immune systems are weakened or if they gain access to a normally sterile part of the body.


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Cell_Biology_Alberts. opportunistic pathogens Microbes of the normal flora that can cause disease only if the immune systems are weakened or if they gain access to a normally sterile part of the body. optogenetics Use of genetically engineered channelrhodopsin and other light-responsive ion channels and transporters to modulate neuron function and hence analyze the neurons and circuits underlying complex functions, including behaviors in whole animals. (Figure 11–32) organelle Subcellular compartment or large macromolecular complex, often membrane-enclosed, that has a distinct structure, composition, and function. Examples are nucleus, nucleolus, mitochondrion, Golgi apparatus, and centrosomes. (Figure 1–25) Organizer Specialized tissue at the dorsal lip of the blastopore in an amphibian embryo; a source of signals that help to orchestrate formation of the embryonic body axis.


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Cell_Biology_Alberts. Organizer Specialized tissue at the dorsal lip of the blastopore in an amphibian embryo; a source of signals that help to orchestrate formation of the embryonic body axis. origin recognition complex (ORC) Large protein complex that is bound to the DNA at origins of replication in eukaryotic chromosomes throughout the cell cycle. (Figure 5–31) orthologs Genes or proteins from different species that are similar in sequence because they are descendants of the same gene in the last common ancestor of those species. Compare paralogs. (Figure 1–21) osteoblast Cell that secretes matrix of bone. (Figure 22–14) osteoclast Macrophage-like cell that erodes bone, enabling it to be remodeled during growth and in response to stresses throughout life. (Figure 22–16) osteocyte Nondividing cell in bone that develops from an osteoblast and is embedded in bone matrix. (Figure 22–14) outer membrane Mitochondrial membrane that is in contact with the cytosol.


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Cell_Biology_Alberts. outer mitochondrial membrane Membrane that separates the organelle from the cytosol. outer nuclear membrane One of two concentric membranes comprising the nuclear envelope; surrounds the inner nuclear membrane and is continuous with the inner nuclear membrane and the membrane of the endoplasmic reticulum. OXA complex Protein translocator in the inner mitochondrial membrane that mediates insertion of inner membrane proteins.


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Cell_Biology_Alberts. oxidation (verb oxidize) Loss of electrons from an atom, as occurs during the addition of oxygen to a molecule or when a hydrogen is removed. Opposite of reduction. (Figure 2–20) oxidative phosphorylation Process in bacteria and mitochondria in which ATP formation is driven by the transfer of electrons through the electron transport chain to molecular oxygen. Involves the intermediate generation of a proton gradient (pH gradient) across a membrane and a chemiosmotic coupling of that gradient to the ATP synthase. (Figures 14–12) oxidative phosphorylation Process in bacteria and mitochondria in which ATP formation is driven by the transfer of electrons through the electron-transport chain to molecular oxygen. Involves the intermediate generation of an electrochemical proton gradient across a membrane and a chemiosmotic coupling of that gradient to the ATP synthase. (Figure 14–10)


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Cell_Biology_Alberts. P-type pumps A class of ATP-driven pumps comprising structurally and functionally related multipass transmembrane proteins that phosphorylate themselves during the pumping cycle. The class includes many of the ion pumps responsible for setting up and maintaining gradients of Na+, K+, H+, and Ca2+ across cell membranes. (Figure 11–12) p53 A transcription regulatory protein that is activated by damage to DNA and is involved in blocking further progression through the cell cycle. (Figures 20–37 and 20–40) p53 Tumor suppressor gene that is mutated in about half of human cancers. Encodes a transcription regulator that is activated by damage to DNA and is involved in blocking further progression through the cell cycle. (Figure 20–27) pair-rule gene In Drosophila development, a gene expressed in a series of regular transverse stripes along the body of the embryo and which helps to determine its segments. (Figure 21–19) pairing In meiosis, the lining up of the two homologous chromosomes


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Cell_Biology_Alberts. in a series of regular transverse stripes along the body of the embryo and which helps to determine its segments. (Figure 21–19) pairing In meiosis, the lining up of the two homologous chromosomes along their length. (Figure 17–54) papillomaviruses Class of viruses responsible for human warts and a prime example of DNA tumor viruses, being a cause of cancer of the uterine cervix.


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Cell_Biology_Alberts. paracrine signaling Short-range cell–cell communication via secreted signal molecules that act on neighboring cells. (Figure 15–2) paralogs Genes or proteins that are similar in sequence because they are the result of a gene duplication event occurring in an ancestral organism. Those in two different organisms are less likely to have the same function than are orthologs. Compare orthologs. (Figure 1–21) parasitism Ecological relationship between microbes and their host in which the microbe benefits to the detriment of the host, as is often the case for pathogens. passengers Mutations that have occurred in the same cell as driver mutations, but which are irrelevant to the development of the cancer.


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Cell_Biology_Alberts. passengers Mutations that have occurred in the same cell as driver mutations, but which are irrelevant to the development of the cancer. passive transport (facilitated diffusion) Transport of a solute across a membrane down its concentration gradient or its electrochemical gradient, using only the energy stored in the gradient. (Figure 11–4) patch-clamp recording Electrophysiological technique in which a tiny electrode tip is sealed onto a patch of cell membrane, thereby making it possible to record the flow of current through individual ion channels in the patch. (Figure 11–34) Patched Transmembrane protein predicted to cross the plasma membrane 12 times; much is in intracellular vesicles and some is on the cell surface where it binds the Hedgehog protein. pathogen (adjective pathogenic) An organism, cell, virus, or prion that causes disease.


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Cell_Biology_Alberts. pathogen (adjective pathogenic) An organism, cell, virus, or prion that causes disease. pathogen-associated molecular patterns (PAMPs) Microbe-associated molecules, either not present or sequestered in the host organism, that often occur in repeating patterns that are recognized by pattern recognition receptors (PRRs) in or on cells of the innate immune system. PAMPs are present in various microbial molecules, including nucleic acids, lipids, polysaccharides, and proteins. pattern recognition receptor (PRR) Receptor present on or in cells of the innate immune system that recognizes and is activated by microbial pathogen-associated molecular patterns (PAMPs).


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Cell_Biology_Alberts. pattern recognition receptor (PRR) Receptor present on or in cells of the innate immune system that recognizes and is activated by microbial pathogen-associated molecular patterns (PAMPs). PDZ domain Protein-binding domain present in many scaffold proteins, and often used as a docking site for intracellular tails of transmembrane proteins. (Figure 19–22) pectin Mixture of polysaccharides rich in galacturonic acid which forms a highly hydrated matrix in which cellulose is embedded in plant cell walls. (Figure 19–63) peripheral (secondary) lymphoid organ Lymphoid organ in which T cells and B cells interact and respond to foreign antigens. Examples are spleen, lymph nodes, and mucosalassociated lymphoid organs. (Figure 24–12) peroxins Form a protein translocator that participates in the import of proteins into peroxisomes.


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Cell_Biology_Alberts. peroxisome Small membrane-bounded organelle that uses molecular oxygen to oxidize organic molecules. Contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2). (Figure 12–27) pH scale Common measure of the acidity of a solution: “p” refers to power of 10, “H” to hydrogen. Defined as the negative logarithm of the hydrogen ion concentration in moles per liter (M). pH = –log [H+]. Thus a solution of pH 3 will contain 10–3 M hydrogen ions. pH less than 7 is acidic and pH greater than 7 is alkaline. phagocytosis Process by which unwanted cells, debris, and other bulky particulate material is endocytosed (“eaten”) by a cell. Prominent in carnivorous cells, such as Amoeba proteus, and in vertebrate macrophages and neutrophils. From Greek phagein, to eat.


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Cell_Biology_Alberts. phagosome Large intracellular membrane-enclosed vesicle that is formed as a result of phagocytosis. Contains ingested extracellular material. (Figure 13–61) phase variation The random switching of phenotype and expression of proteins involved in infection at frequencies much higher than mutation rates.


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Cell_Biology_Alberts. phase-contrast microscope Type of light microscope that exploits the interference effects that occur when light passes through material of different refractive indices. Used to view living cells. (Figure 9–7) phenotype The observable character (including both physical appearance and behavior) of a cell or organism. (Panel 8–2, p. 486) phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2, PIP2] Membrane inositol phospholipid (a phosphoinositide) that is cleaved by phospholipase C into IP3 and diacylglycerol at the beginning of the inositol phospholipid signaling pathway. It can also be phosphorylated by PI 3-kinase to produce PIP3 docking sites for signaling proteins in the PI-3-kinase–Akt signaling pathway. (Figures 15–28 and 15–53) phosphoglyceride Phospholipid derived from glycerol, abundant in biomembranes. (Figures 10–2 and 10–3) phosphoinositide A lipid containing a phosphorylated inositol derivative. Minor component of the plasma membrane, but important in demarking different


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Cell_Biology_Alberts. in biomembranes. (Figures 10–2 and 10–3) phosphoinositide A lipid containing a phosphorylated inositol derivative. Minor component of the plasma membrane, but important in demarking different membranes and for intracellular signal transduction in eukaryotic cells. (Figure 15–52) phosphoinositide 3-kinase (PI 3-kinase) Membrane-bound enzyme that is a component of the PI-3-kinase–Akt intracellular signaling pathway. It phosphorylates phosphatidylinositol 4,5-bisphosphate at the 3 position on the inositol ring to produce PIP3 docking sites in the membrane for other intracellular signaling proteins. (Figure 15–53) phosphoinositides (PIPs; phosphatidylinositol phosphates) A lipid containing a phosphorylated inositol derivative. Minor component of the plasma membrane, but important in demarking different membranes and for intracellular signal transduction in eukaryotic cells. (Figure 13–10) phospholipase C (PLC) Membrane-bound enzyme that cleaves inositol phospholipids to produce IP3 and


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Cell_Biology_Alberts. different membranes and for intracellular signal transduction in eukaryotic cells. (Figure 13–10) phospholipase C (PLC) Membrane-bound enzyme that cleaves inositol phospholipids to produce IP3 and diacylglycerol in the inositol phospholipid signaling pathway. PLCβ is activated by GPCRs via specific G proteins, while PLCγ is activated by RTKs. (Figure 15–55) phospholipid The main category of lipids used to construct biomembranes. Generally composed of two fatty acids linked through glycerol (or sphingosine) phosphate to one of a variety of polar groups. (FIgure 10–3, and Panel 2–5, pp. 98–99) phosphorylation Reaction in which a phosphate group is covalently coupled to another molecule.


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Cell_Biology_Alberts. photoactivation Technique for studying intracellular processes in which an inactive form of a molecule of interest is introduced into the cell, and is then activated by a focused beam of light at a precise spot in the cell. (Figure 9–28) photochemical reaction center The part of a photosystem that converts light energy into chemical energy in photosynthesis. (Figure 14–44) photosynthetic electron-transfer reactions Light-driven reactions in photosynthesis in which electrons move along an electron-transport chain in a membrane, generating ATP and NADPH. photosystem Multiprotein complex involved in photosynthesis that captures the energy of sunlight and converts it to useful forms of energy: a reaction center plus an antenna (Figure 14–45) phototropin Photoprotein associated with the plant plasma membrane that senses blue light and is partly responsible for phototropism.


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Cell_Biology_Alberts. phragmoplast Structure made of microtubules and actin filaments that forms in the prospective plane of division of a plant cell and guides formation of the cell plate. (Figure 17–49) phytochrome Plant photoprotein that senses light via a covalently attached light-absorbing chromophore, which changes its shape in response to light and then induces a change in the protein’s conformation. Plant phytochromes are dimeric, cytoplasmic serine/threonine kinases, which respond differentially and reversibly to red and far-red light to alter cell behavior.


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Cell_Biology_Alberts. PI-3-kinase–Akt pathway Intracellular signaling pathway that stimulates animal cells to survive and grow. (Figure 15–53) pinocytosis Literally, “cell drinking.” Type of endocytosis in which soluble materials are continually taken up from the environment in small vesicles and moved into endosomes along with the membrane-bound molecules. Compare phagocytosis. (Figure 13–48) piRNAs (piwi-interacting RNAs) A class of small noncoding RNAs made in the germ line that, in complex with Piwi proteins, keep in check the movement of transposable elements by transcriptionally silencing transposon genes and destroying RNAs produced by them.


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Cell_Biology_Alberts. planar cell polarity Type of cellular asymmetry seen in some epithelia, such that each cell has a polarity vector oriented in the plane of the epithelium. (Figure 21–51) plant growth regulator (plant hormone) Signal molecule that helps coordinate growth and development. Examples are ethylene, auxins, gibberellins, cytokinins, abscisic acid, and the brassinosteroids. plasma membrane The membrane that surrounds a living cell. (Figure 10–1) plasmid vector Small, circular molecules of double-stranded DNA derived from plasmids that occur naturally in bacterial cells; widely used for gene cloning. plasmodesma (plural plasmodesmata) Plant equivalent of a gap junction. Communicating cell–cell junction in plants in which a channel of cytoplasm lined by plasma membrane connects two adjacent cells through a small pore in their cell walls.


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Cell_Biology_Alberts. platelet Cell fragment, lacking a nucleus, that breaks off from a megakaryocyte in the bone marrow and is found in large numbers in the bloodstream. Helps initiate blood clotting when blood vessels are injured. (Figure 22–29) pleckstrin homology domain (PH domain) Protein domain found in some intracellular signaling proteins. Some PH domains in intracellular signaling proteins bind to phosphatidylinositol 3,4,5-trisphosphate produced by PI 3-kinase, bringing the signaling protein to the plasma membrane when PI 3-kinase is activated. pluripotent Describes a cell that has the potential to give rise to all or almost all of the cell types of the adult body. polarized In epithelia, that the basal end of a cell, adherent to the basal lamina below, differs from the apical end, exposed to the medium above; thus, all epithelia and their individual cells are structurally polarized.


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Cell_Biology_Alberts. Polycomb group Set of proteins critical for cell memory for some genes. They form complexes as part of the chromatin of the Hox complex, where they maintain a repressed state in cells where Hox genes have not been activated. polymerase chain reaction (PCR) Technique for amplifying specific regions of DNA by the use of sequence-specific primers and multiple cycles of DNA synthesis, each cycle being followed by a brief heat treatment to separate complementary strands. (Figure 8–36) polymorphisms Describes genome sequences that coexist as two or more sequence variants at high frequency in a population. polypeptide Linear polymer of amino acids. Proteins are large polypeptides, and the two terms can be used interchangeably. (Panel 3–1, pp. 112–113) polypeptide backbone Repeating sequence of atoms along the core of the polypeptide chain. polyribosome mRNA engaged with multiple ribosomes in the act of translation.


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Cell_Biology_Alberts. polyribosome mRNA engaged with multiple ribosomes in the act of translation. polytene chromosome Giant chromosome in which the DNA has undergone repeated replication and the many copies have stayed together in precise alignment. (Figures 4–50 and 4–51) porin Channel-forming proteins of the outer membranes of bacteria, mitochondria, and chloroplasts. position effect variegation Alteration in gene expression resulting from change in the position of the gene in relation to other chromosomal domains, especially heterochromatic domains. When an active gene is placed next to heterochromatin, the inactivating influence of the heterochromatin can spread to affect the gene to a variable degree, giving rise to position effect variegation. (Figure 4–31) positional value A cell’s internal record of its positional information in a multicellular organism; an intrinsic character that differs according to a cell’s location.


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Cell_Biology_Alberts. positive feedback Control mechanism whereby the end product of a reaction or pathway stimulates its own production or activation. positive selection In immunology: process of thymocyte maturation in which thymocytes expressing a T cell receptor with appropriate affinity for a self peptide bound to a self MHC protein is signaled to survive and continue development. post-transcriptional controls Any control on gene expression that is exerted at a stage after transcription has begun. (Figure 7–54) post-translational Occurring after completion of translation.


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Cell_Biology_Alberts. preprophase band Circumferential band of microtubules and actin filaments that forms around a plant cell under the plasma membrane prior to mitosis and cell division. (Figure 17–49) prereplicative complex (preRC) Multiprotein complex that is assembled at origins of replication during late mitosis and early G1 phases of the cell cycle; a prerequisite to license the assembly of a preinitiation complex, and the subsequent initiation of DNA replication. (Figures 17–17 and 17–18) primary cell wall The first cell wall produced by a developing plant cell; it is thin and flexible, allowing room for cell growth. (Figure 19–63) primary cilium Short, single, nonmotile cilium lacking dynein that arises from a centriole and projects from the surface of many animal cell types. Some signaling proteins are concentrated in the primary cilium. (Figure 15–38) primary Ig repertoire The billions of IgM and IgD immunoglobulin molecules made by the B cells of an adaptive immune system in the absence of


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Cell_Biology_Alberts. are concentrated in the primary cilium. (Figure 15–38) primary Ig repertoire The billions of IgM and IgD immunoglobulin molecules made by the B cells of an adaptive immune system in the absence of antigen stimulation.


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Cell_Biology_Alberts. primary immune response Adaptive immune response to an antigen that is made on first encounter with that antigen. (Figure 24–16) primary pathogens Pathogens that can cause overt disease in most healthy people. Some cause acute, life-threatening epidemic infections and spread rapidly between hosts; other potential primary pathogens may persistently infect a single individual for years without causing overt disease, the host often being unaware that they are infected. primary structure Linear sequence of monomer units in a polymer, such as the amino acid sequence of a protein. primary tumor Tumor at the original site at which a cancer first arose. Secondary tumors develop elsewhere by metastasis.


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Cell_Biology_Alberts. primary tumor Tumor at the original site at which a cancer first arose. Secondary tumors develop elsewhere by metastasis. prion disease Transmissible spongiform encephalopathy— such as Kuru and Creutzfeldt–Jakob disease (CJD) in humans, scrapie in sheep, and bovine spongiform encephalopathy (BSE, or “mad cow disease”) in cows—that is caused and transmitted by an infectious, abnormally folded protein (prion). (Figure 3–33) pro-inflammatory cytokine Any cytokine that stimulates an inflammatory response. programmed cell death A form of cell death in which a cell kills itself by activating an intracellular death program.


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Cell_Biology_Alberts. prokaryote Single-celled microorganism whose cells lack a well-defined, membrane-enclosed nucleus. Either a bacterium or an archaeon. (Figure 1–17) promoter Nucleotide sequence in DNA to which RNA polymerase binds to begin transcription. (Figure 7–17) proteasome Large protein complex in the cytosol with proteolytic activity that is responsible for degrading proteins that have been marked for destruction by ubiquitylation or by some other means. (Figures 6–83 and 6–84) protein The major macromolecular constituent of cells. A linear polymer of amino acids linked together by peptide bonds in a specific sequence. (Figure 3–1) protein activity control The selective activation, inactivation, degradation, or compartmentalization of specific proteins after they have been made. One of the means by which a cell controls which proteins are active at a given time or location in the cell.


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Cell_Biology_Alberts. protein glycosylation Process of transferring a single saccharide or preformed precursor oligosaccharide to proteins. protein kinase Enzyme that transfers the terminal phosphate group of ATP to one or more specific amino acids (serine, threonine, or tyrosine) of a target protein. protein kinase C (PKC) Ca2+-dependent protein kinase that, when activated by diacylglycerol and an increase in the concentration of cytosolic Ca2+, phosphorylates target proteins on specific serine and threonine residues. (Figure 15–29) protein phosphatase Enzyme that catalyzes phosphate removal from amino acids of a target protein. protein subunit An individual protein chain in a protein composed of more than one chain. protein translocation Process of moving a protein across a membrane.


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Cell_Biology_Alberts. protein subunit An individual protein chain in a protein composed of more than one chain. protein translocation Process of moving a protein across a membrane. protein translocator Membrane-bound protein that mediates the transport of another protein across a membrane. (Figure 12–21) protein tyrosine phosphatase Enzyme that removes phosphate groups from phosphorylated tyrosine residues on proteins. proteoglycan Molecule consisting of one or more glycosaminoglycan chains attached to a core protein. (Figure 19–38) proteomics Study of all the proteins, including all the covalently modified forms of each, produced by a cell, tissue, or organism. Proteomics often investigates changes in this larger set of proteins—in “the proteome”—caused by changes in the environment or by extracellular signals. proto-oncogene Normal gene, usually concerned with the regulation of cell proliferation, that can be converted into a cancer-promoting oncogene by mutation.


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Cell_Biology_Alberts. proto-oncogene Normal gene, usually concerned with the regulation of cell proliferation, that can be converted into a cancer-promoting oncogene by mutation. protofilament Linear string of microtubule subunits joined end to end; multiple protofilaments associate with one another laterally to construct and provide strength and adaptability to microtubules. proton (H+) Positively charged subatomic particle that forms part of an atomic nucleus. Hydrogen has a nucleus composed of a single proton (H+). proton-motive force The force exerted by the electrochemical proton gradient that moves protons across a membrane. protozoan parasite Parasitic, nonphotosynthetic, single-celled, motile eukaryotic organism, for example Plasmodium. pseudogene Nucleotide sequence of DNA that has accumulated multiple mutations that have rendered an ancestral gene inactive and nonfunctional.


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Cell_Biology_Alberts. pseudogene Nucleotide sequence of DNA that has accumulated multiple mutations that have rendered an ancestral gene inactive and nonfunctional. purified cell-free system Fractionated cell homogenate that retains a particular biological function of the intact cell, and in which biochemical reactions and cell processes can be more easily studied. purifying selection Natural selection operating in a population to slow genome changes and reduce divergence by eliminating individuals carrying deleterious mutations. quantitative RT-PCR (reverse transcription–polymerase chain reaction) Technique in which a population of mRNAs is converted into cDNAs via reverse transcription, and the cDNAs are then amplified by PCR. The quantitative part relies on a direct relationship between the rate at which the PCR product is generated and the original concentration of the mRNA species of interest.


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Cell_Biology_Alberts. quaternary structure Three-dimensional relationship of the different polypeptide chains in a multisubunit protein or protein complex. quinone (Q) Small, lipid-soluble, mobile electron carrier molecule found in the respiratory and photosynthetic electron-transport chains. (Figure 14–17) Rab cascade An ordered recruitment of sequentially acting Rab proteins into Rab domains on membranes, which changes the identity of an organelle and reassigns membrane dynamics. Rab effectors Molecules that bind activated, membrane-bound Rab proteins and act as downstream mediators of vesicle transport, membrane tethering, and fusion. Rab proteins Monomeric GTPase in the Ras superfamily present in plasma and organelle membranes in its GTP-bound state, and as a soluble cytosolic protein in its GDP-bound state. Involved in conferring specificity on vesicle docking. (Table 15–5, p. 854)


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Cell_Biology_Alberts. Rac Member of the Rho family of monomeric GTPases that regulate the actin and microtubule cytoskeletons, cell-cycle progression, gene transcription, and membrane transport. Rad51 Eukaryotic protein that catalyzes synapsis of DNA strands during genetic recombination. Called RecA in E. coli. Ran (Ran protein) Monomeric GTPase of the Ras superfamily present in both cytosol and nucleus. Required for the active transport of macromolecules into and out of the nucleus through nuclear pore complexes. (Table 15–5, p. 854) rapidly inactivating K+ channel Neuronal voltage-gated K+ channel, open when the membrane is depolarized, with a specific voltage sensitivity and kinetics of inactivation that induce a reduced rate of action potential firing at levels of stimulation only just above the threshold required, thereby resulting in a firing rate proportional to the strength of the depolarizing stimulus.


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Cell_Biology_Alberts. Ras A small family of proto-oncogenes that are frequently mutated in cancers, each of which produces a Ras monomeric GTPase. Ras (Ras protein) Monomeric GTPase of the Ras superfamily that helps to relay signals from cell-surface receptor tyrosine kinase receptors to the nucleus, frequently in response to signals that stimulate cell division. Named for the ras gene, first identified in viruses that cause rat sarcomas. (Figure 3–67) Ras superfamily Large superfamily of monomeric GTPases (also called small GTP-binding proteins) of which Ras is the prototypical member. (Table 15–5, p. 854) Ras-GAPs Ras GTPase-activating proteins; increase the rate of hydrolysis of bound GTP by Ras, thereby inactivating Ras. Ras-GEFs Ras guanine nucleotide exchange factors; stimulate the dissociation of GDP and the subsequent uptake of GTP from the cytosol, thereby activating Ras.


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Cell_Biology_Alberts. Ras-GEFs Ras guanine nucleotide exchange factors; stimulate the dissociation of GDP and the subsequent uptake of GTP from the cytosol, thereby activating Ras. Ras–MAP-kinase signaling pathway Intracellular signaling pathway that relays signals from activated receptor tyrosine kinases to effector proteins in the cell including transcription regulators in the nucleus. Rb gene The gene that is defective in both copies in individuals with retinoblastoma; its protein product plays a central role in cell-cycle control. reading frame The phase in which nucleotides are read in sets of three to encode a protein. An mRNA molecule can be read in any one of three reading frames, only one of which will give the required protein. (Figure 6–49)


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Cell_Biology_Alberts. RecA (RecA protein) Prototype for a class of DNA-binding proteins that catalyze synapsis of DNA strands during genetic recombination. (Figure 5–49) receptor Any protein that binds a specific signal molecule (ligand) and initiates a response in the cell. Some are on the cell surface, while others are inside the cell. (Figure 15–3) receptor editing Process by which a developing B cell that recognizes a self molecule changes its antigen receptors so that the cell no longer does so.


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Cell_Biology_Alberts. receptor serine/threonine kinase Cell-surface receptor with an extracellular ligand-binding domain and an intracellular kinase domain that phosphorylates signaling proteins on serine or threonine residues in response to ligand binding. The TGFβ receptor is an example. (Figure 15–57) receptor tyrosine kinase (RTK) Cell-surface receptor with an extracellular ligand-binding domain and an intracellular kinase domain that phosphorylates signaling proteins on tyrosine residues in response to ligand binding. (Figure 15–43 and Table 15–4, p. 850) receptor-mediated endocytosis Internalization of receptor– ligand complexes from the plasma membrane by endocytosis. (Figure 13–52) recombinant DNA technology Collection of techniques by which DNA segments from different sources are combined to make a new DNA, often called a recombinant DNA. Recombinant DNAs are widely used in the cloning of genes, in the genetic modification of organisms, and in the production of large amounts of rare proteins.


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Cell_Biology_Alberts. recycling endosome Organelle that provides an intermediate stage on the passage of recycled receptors back to the cell membrane. Regulates plasma membrane insertion of some proteins. (Figure 13–58) red blood cell Small hemoglobin-containing blood cell of vertebrates that transports oxygen to, and carbon dioxide from, tissues. Also called an erythrocyte.


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Cell_Biology_Alberts. redox pair Pair of molecules in which one acts as an electron donor and one as an electron acceptor in an oxidation– reduction reaction: for example, NADH (electron donor) and NAD+ (electron acceptor). (Panel 14–1, p. 765) redox potential The affinity of a redox pair for electrons, generally measured as the voltage difference between an equimolar mixture of the pair and a standard reference. NADH/ NAD+ has a low redox potential and O2/H2 has a high redox potential (high affinity for electrons). (Panel 14–1, p. 765) redox reaction Reaction in which one component becomes oxidized and the other reduced; an oxidation–reduction reaction. (Panel 14–1, p. 765) reduction (verb reduce) Addition of electrons to an atom, as occurs during the addition of hydrogen to a biological molecule or the removal of oxygen from it. Opposite of oxidation. (Figure 2–20) regulated nuclear transport Mechanisms controlling export of mRNAs from the nucleus to the cytosol that can be used to regulate gene


Cell_Biology_Alberts

Cell_Biology_Alberts. removal of oxygen from it. Opposite of oxidation. (Figure 2–20) regulated nuclear transport Mechanisms controlling export of mRNAs from the nucleus to the cytosol that can be used to regulate gene expression. Also includes the selective import of proteins and RNA molecules into the nucleus.


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Cell_Biology_Alberts. regulated secretory pathway A second secretory pathway found mainly in cells specialized for secreting products rapidly on demand—such as hormones, neurotransmitters, or digestive enzymes—in which soluble proteins and other substances are initially stored in secretory vesicles for later release. (Figure 13–62) regulator of G protein signaling (RGS) A GAP protein that binds to a trimeric G protein and enhances its GTPase activity, thus helping to limit G-protein-mediated signaling. (Figure 15–8) regulatory site Region of an enzyme surface to which a regulatory molecule binds and thereby influences the catalytic events at the separate active site. regulatory T cell (Treg) A type of T cell that suppresses the development, activation, or function of other immune cells via secreted cytokines or cell-surface inhibitory proteins.


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Cell_Biology_Alberts. regulatory T cell (Treg) A type of T cell that suppresses the development, activation, or function of other immune cells via secreted cytokines or cell-surface inhibitory proteins. replication fork Y-shaped region of a replicating DNA molecule at which the two strands of the DNA are being separated and the daughter strands are being formed. (Figures 5–7 and 5–18) replication origin Location on a DNA molecule at which duplication of the DNA begins. (Figures 4–19 and 5–23) replicative cell senescence Phenomenon observed in primary cell cultures in which cell proliferation slows down and finally irreversibly halts.


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Cell_Biology_Alberts. respiratory chain (electron-transport chain) Electron-transport chain present in the inner mitochondrial membrane that generates an electrochemical gradient across the membrane that is used to drive ATP synthesis. (Figures 14–4 and 14–10) resting membrane potential Electrical potential across the plasma membrane of a cell at rest, i.e. a cell that has not been stimulated to open additional ion channels than those that are normally open.


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Cell_Biology_Alberts. restriction nuclease One of a large number of nucleases that can cleave a DNA molecule at any site where a specific short sequence of nucleotides occurs. Extensively used in recombinant DNA technology. (Figure 8–24) restriction point Important transition at the end of G1 in the eukaryotic cell cycle; commits the cell to enter S phase. The term was originally used for this transition in the mammalian cell cycle; in this book we use the term Start. (Figure 17–9) retinoblastoma A rare type of human cancer arising from cells in the retina of the eye that are converted to a cancerous state by an unusually small number of mutations. Studies of retinoblastoma led to the discovery of the first tumor suppressor gene.


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Cell_Biology_Alberts. retinoblastoma protein (Rb protein) Tumor suppressor protein involved in the regulation of cell division. Mutated in the cancer retinoblastoma, as well as in many other tumors. Its normal activity is to regulate the eukaryotic cell cycle by binding to and inhibiting the E2F proteins, thus blocking progression to DNA replication and cell division. (Figure 17–61) retroviral-like retrotransposons A large family of transposons that move themselves in and out of chromosomes by a mechanism similar to that used by retroviruses, being first transcribed into an RNA copy that is converted to DNA by reverse transcriptase then inserted elsewhere in the genome. (Table 5–4, p. 288) retrovirus RNA-containing virus that replicates in a cell by first making an RNA–DNA intermediate and then a double-strand DNA molecule that becomes integrated into the cell’s DNA. (Figure 5–62) reverse genetics Approach to discovering gene function that starts from the DNA (gene) and its protein product and then


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Cell_Biology_Alberts. DNA molecule that becomes integrated into the cell’s DNA. (Figure 5–62) reverse genetics Approach to discovering gene function that starts from the DNA (gene) and its protein product and then creates mutants to analyze the gene’s function.


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Cell_Biology_Alberts. reverse transcriptase Enzyme first discovered in retroviruses that makes a double-strand DNA copy from a single-strand RNA template molecule. RGD sequence Tripeptide sequence of arginine-glycineaspartic acid that forms a binding site for integrins; present in fibronectin and some other extracellular proteins. (Figure 19–47C) Rheb A monomeric Ras-related GTPase that in its active form (Rheb-GTP) activates mTOR, which promotes cell growth. Rho Member of the Rho family of monomeric GTPases that regulate the actin and microtubule cytoskeletons, cell-cycle progression, gene transcription, and membrane transport.


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Cell_Biology_Alberts. Rho Member of the Rho family of monomeric GTPases that regulate the actin and microtubule cytoskeletons, cell-cycle progression, gene transcription, and membrane transport. Rho family Family of monomeric GTPases within the Ras superfamily involved in signaling the rearrangement of the cytoskeleton. Includes Rho, Rac, and Cdc42. (Table 15–5, p. 854) rhodopsin Seven-span membrane protein of the GPCR family that acts as a light sensor in rod photoreceptor cells in the vertebrate retina. Contains the light-sensitive prosthetic group retinol. (Figure 15–39) ribosomal RNA (rRNA) Any one of a number of specific RNA molecules that form part of the structure of a ribosome and participate in the synthesis of proteins. Often distinguished by their sedimentation coefficient (e.g., 28S rRNA, 5S rRNA).


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Cell_Biology_Alberts. ribosome Particle composed of rRNAs and ribosomal proteins that catalyzes the synthesis of protein using information provided by mRNA. (Figure 6–64) ribozyme An RNA molecule with catalytic activity. RNA (ribonucleic acid) Polymer formed from covalently linked ribonucleotide monomers. See also messenger RNA, ribosomal RNA, transfer RNA. (Figure 6–4) RNA editing Type of RNA processing that alters the nucleotide sequence of an RNA transcript after it is synthesized by inserting, deleting, or altering individual nucleotides. RNA interference (RNAi) As originally described, mechanism by which an experimentally introduced double-stranded RNA induces sequence-specific destruction of complementary mRNAs. The term RNAi is often used to include the inhibition of gene expression by microRNAs (miRNAs) and piwi RNAs (piRNAs), which are encoded in the cell’s own genome.


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Cell_Biology_Alberts. RNA polymerase Enzyme that catalyzes the synthesis of an RNA molecule on a DNA template from ribonucleoside triphosphate precursors. (Figure 6–9) RNA primer Short stretch of RNA synthesized on a DNA template. It is required by DNA polymerases to start their DNA synthesis. RNA processing control Regulation by a cell of gene expression by controlling the processing of RNA transcripts, which includes their splicing. RNA splicing Process in which intron sequences are excised from RNA transcripts. A major process in the nucleus of eukaryotic cells leading to formation of messenger RNAs (mRNAs). RNA transport and localization control Regulation by a cell of gene expression by selecting which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localized. RNA world Hypothesis that early life on Earth was based primarily on RNA molecules that both stored genetic information and catalyzed biochemical reactions.


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Cell_Biology_Alberts. RNA world Hypothesis that early life on Earth was based primarily on RNA molecules that both stored genetic information and catalyzed biochemical reactions. RNA-seq Sequencing the entire repertoire of RNA from a cell or tissue; also known as deep RNA sequencing. robustness The ability of biological regulatory systems to function normally in the face of perturbations such as exposure to frequent and/or extreme variations in external conditions or the concentrations or activities of key components. rod photoreceptor (rod) Photoreceptor cell in the vertebrate retina that is responsible for noncolor vision in dim light. rough endoplasmic reticulum (rough ER) Endoplasmic reticulum with ribosomes on its cytosolic surface. Involved in the synthesis of secreted and membrane-bound proteins. rRNA gene Gene that specifies a ribosomal RNA (rRNA).


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Cell_Biology_Alberts. rRNA gene Gene that specifies a ribosomal RNA (rRNA). ryanodine receptor A regulated Ca2+ channel in the ER membrane that opens in response to rising Ca2+ levels and thus amplifies the Ca2+ signal. SAM complex Protein translocator that helps β-barrel proteins to fold properly in the outer mitochondrial membrane. Sar1 protein Monomeric GTPase responsible for regulating COPII coat assembly at the endoplasmic reticulum membrane. sarcoma Cancer of connective tissue. scaffold protein Protein that binds groups of intracellular signaling proteins into a signaling complex, often anchoring the complex at a specific location in the cell. (Figure 15–10) scanning electron microscope Type of electron microscope that produces an image of the surface of an object. (Figure 9–50) S-Cdk Cyclin–Cdk complex formed in vertebrate cells by an 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. S-Cdk Cyclin–Cdk complex formed in vertebrate cells by an S-cyclin and the corresponding cyclin-dependent kinase (Cdk). (Figure 17–11 and Table 17–1, p. 969) SCF Family of ubiquitin ligases formed as a complex of several different proteins. One is involved in regulating the eukaryotic cell cycle, directing the destruction of inhibitors of S-Cdks in late G1 and thus promoting the activation of S-Cdks and DNA replication. (Figures 3–71 and 17–15) Schwann cell Glial cell responsible for forming myelin sheaths in the peripheral nervous system. Compare oligodendrocyte. (Figure 11–33) S-cyclin Member of a class of cyclins that accumulate during late G1 phase and bind Cdks soon after progression through Start; they help stimulate DNA replication and chromosome duplication. Levels remain high until late mitosis, after which these cyclins are destroyed. (Figure 17–11)


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Cell_Biology_Alberts. Sec61 complex Three-subunit core of the protein translocator that transfers polypeptide chains across the endoplasmic reticulum membrane. second messenger (small intracellular mediator) Small intracellular signaling molecule that is formed or released for action in response to an extracellular signal and helps to relay the signal within the cell. Examples include cyclic AMP, cyclic GMP, IP3, Ca2+, and diacylglycerol. secondary cell wall Permanent rigid cell wall that is laid down underneath the thin primary cell wall in certain plant cells that have completed their growth. secondary Ig repertoire Immunoglobulins produced by B cells after antigenand helper-T-cell-induced somatic hypermutation and class switching. Compared to the primary Ig repertoire, these Igs have a greatly increased diversity of both Ig classes and antigen-binding sites and have increased affinity for antigen.


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Cell_Biology_Alberts. secondary immune response The adaptive immune response that occurs in response to a second or subsequent exposure to an antigen. The response is more rapid in onset and stronger than the primary immune response. (Figure 24–16) secondary structure Regular local folding pattern of a polymeric molecule; in proteins, α helices and β sheets. secretion system Specialized bacterial systems that secrete effector proteins that interact with host cells.


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Cell_Biology_Alberts. secretion system Specialized bacterial systems that secrete effector proteins that interact with host cells. secretory vesicle Membrane-enclosed organelle in which molecules destined for secretion are stored prior to release. Sometimes called secretory granule because darkly staining contents make the organelle visible as a small solid object. (Figures 13–65) securin Protein that binds to the protease separase and thereby prevents its cleavage of the protein linkages that hold sister chromatids together in early mitosis. Securin is destroyed at the metaphase-to-anaphase transition. (Figure 17–38) segment Divisions of an insect body along its anteroposterior axis, each forming highly specialized structures, but all built according to a similar fundamental plan.


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Cell_Biology_Alberts. segment-polarity gene In Drosophila development, a gene involved in specifying the anteroposterior organization of each body segment. (Figure 21–19) segmentation clock The gene-expression oscillator controlling regular segmentation during vertebrate embryonic development. segmentation genes Genes expressed by subsets of cells in the embryo that refine the pattern of gene expression so as to define the boundaries and ground plan of the individual body segments.


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Cell_Biology_Alberts. segmentation genes Genes expressed by subsets of cells in the embryo that refine the pattern of gene expression so as to define the boundaries and ground plan of the individual body segments. selectin Member of a family of cell-surface carbohydrate-binding proteins that mediate transient, Ca2+-dependent cell–cell adhesion in the bloodstream—for example between white blood cells and the endothelium of the blood vessel wall. (Figure 19–28) selectivity filter The part of an ion channel structure that determines which ions it can transport. (Figures 11–24 and 11–25) sensory bristles Miniature sense organs present on most exposed surfaces of Drosophila, consisting of a sensory neuron and supporting cells and responding to chemical or mechanical stimuli.


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Cell_Biology_Alberts. separase Protease that cleaves the cohesin protein linkages that hold sister chromatids together. Acts at anaphase, enabling chromatid separation and segregation. (Figure 17–38) septum Structure formed during bacterial cell division by the inward growth of the cell wall and plasma membrane and that divides the cell into two. sequential induction Development process that generates a progressively more complicated pattern. A series of local inductions whereby one of two cell types present in a developing tissue can produce a signal to induce neighboring cells to specialize in a third way; the third cell type can then signal back to the other two cell types nearby to generate a fourth and a fifth cell type, and so on. serine protease Type of protease that has a reactive serine in the active site. (Figures 3–12 and 3–39) serine/threonine kinase Enzyme that phosphorylates specific proteins on serine or threonines.


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Cell_Biology_Alberts. SH2 domain Src homology region 2, a protein domain present in many signaling proteins. Binds a short amino acid sequence containing a phosphotyrosine. (Panel 3–2, pp. 142–143) side chain The part of an amino acid that differs between amino acid types. The side chains give each type of amino acid its unique physical and chemical properties. (Panel 3–1, pp. 112–113) signal patch Protein-sorting signal that consists of a specific three-dimensional arrangement of atoms on the folded protein’s surface. (Figure 13–46) signal peptidase Enzyme that removes a terminal signal sequence from a protein once the sorting process is complete. (Figure 12–35) signal sequence Short continuous sequence of amino acids that determines the eventual location of a protein in the cell. An example is the N-terminal sequence of 20 or so amino acids that directs nascent secretory and transmembrane proteins to the endoplasmic reticulum. (Table 12–3, p. 648) signal-recognition particle (SRP)


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Cell_Biology_Alberts. is the N-terminal sequence of 20 or so amino acids that directs nascent secretory and transmembrane proteins to the endoplasmic reticulum. (Table 12–3, p. 648) signal-recognition particle (SRP) Ribonucleoprotein particle that binds an ER signal sequence on a partially synthesized polypeptide chain and directs the polypeptide and its attached ribosome to the endoplasmic reticulum. (Figure 12–36) signaling center Cluster of specialized cells in developing tissues that serves as a source of developmental signals—for example, the generation of a morphogen gradient.


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Cell_Biology_Alberts. single-nucleotide polymorphism (SNP) A variation between individuals in a population due to a relatively common difference in a specific nucleotide at a defined point in the DNA sequence.


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Cell_Biology_Alberts. single-particle reconstruction Computational procedure in electron microscopy in which images of many identical molecules are obtained and digitally combined to produce an averaged three-dimensional image, thereby revealing structural details that are hidden by noise in the original images. (Figures 9–54 and 9–55) single-pass transmembrane protein Membrane protein in which the polypeptide chain crosses the lipid bilayer only once. (Figure 10–24) single-strand DNA-binding (SSB) protein Protein that binds to the single strands of the opened-up DNA double helix, preventing helical structures from reforming while the DNA is being replicated. (Figure 5–15) sister chromatids Tightly linked pair of chromosomes that arise from chromosome duplication during S phase. They separate during M phase and segregate into different daughter cells. (Figure 17–21) sliding clamp Protein complex that holds the DNA polymerase on DNA during DNA replication. (Figure 5–17)


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Cell_Biology_Alberts. Slit Signal protein, secreted by cells of the neural tube floor plate, responsible for repelling the growth cones of commissural axons after they have crossed the midline, thereby ensuring these neurons do not re-cross the midline.


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Cell_Biology_Alberts. Smad family Latent transcription regulators that are phosphorylated and activated by receptor serine/threonine kinases and carry the signal from the cell surface to the nucleus. (Figure 15–57) small interfering RNAs (siRNAs) Short (21–26 nucleotide) double-stranded RNAs that inhibit gene expression by directing destruction of complementary mRNAs. Production of siRNAs is usually triggered by exogenously introduced double-stranded RNA. (Figure 7–77) small nuclear RNA (snRNA) Small RNA molecules that are complexed with proteins to form the ribonucleoprotein particles (snRNPs) involved in RNA splicing. (Figures 6–28 and 6–29) small nucleolar RNA (snoRNA) Small RNAs found in the nucleolus, with various functions, including guiding the modifications of precursor rRNA. (Table 6–1, p. 305, and Figure 6–41) smooth endoplasmic reticulum (smooth ER) Region of the endoplasmic reticulum not associated with ribosomes. Involved in detoxification reactions, Ca2+ storage, and lipid synthesis.


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Cell_Biology_Alberts. and Figure 6–41) smooth endoplasmic reticulum (smooth ER) Region of the endoplasmic reticulum not associated with ribosomes. Involved in detoxification reactions, Ca2+ storage, and lipid synthesis. (Figure 12–33)


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Cell_Biology_Alberts. Smoothened Seven-pass transmembrane protein with a structure very similar to a GPCR but does not seem to act as a Hedgehog receptor or as an activator of G proteins; it is controlled by the Patched and iHog proteins. SNARE proteins (SNAREs) Members of a large family of transmembrane proteins present in organelle membranes and the vesicles derived from them. SNAREs catalyze the many membrane fusion events in cells. They exist in pairs—a v-SNARE in the vesicle membrane that binds specifically to a complementary t-SNARE in the target membrane.


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Cell_Biology_Alberts. sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS-PAGE) Type of electrophoresis used to separate proteins by size. The protein mixture to be separated is first treated with a powerful negatively charged detergent (SDS) and with a reducing agent (β-mercaptoethanol), before being run through a polyacrylamide gel. The detergent and reducing agent unfold the proteins, free them from association with other molecules, and separate the polypeptide subunits. somatic cell Any cell of a plant or animal other than cells of the germ line. From Greek soma, body. somatic hypermutation In immunology: accumulation of point mutations in the assembled variable-region-coding sequences of immunoglobulin genes that occurs when B cells are activated to form memory cells. Results in the production of antibodies with altered antigen-binding sites, some of which bind antigen with increased affinity; it is responsible for affinity maturation in antibody responses.


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Cell_Biology_Alberts. somatic mutations In cancer, one or more detectable abnormalities in the DNA sequence of tumor cells that distinguish them from the normal somatic cells surrounding the tumor. somite One of a series of paired blocks of mesoderm that form during early development and lie on either side of the notochord in a vertebrate embryo. They give rise to the segments of the body axis, including the vertebrae, muscles, and associated connective tissue. (Figure 21–38) sorting signal Signal sequence or signal patch that directs the delivery of a protein to a specific location, such as a particular intracellular compartment. spectrin Abundant protein associated with the cytosolic side of the plasma membrane in red blood cells, forming a network that supports the membrane. Also present in other cells. (Figure 10–38) S phase Period of a eukaryotic cell cycle in which DNA is synthesized. (Figure 17–4) spinal cord Bundle of neurons and support cells that extends from the brain.


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Cell_Biology_Alberts. S phase Period of a eukaryotic cell cycle in which DNA is synthesized. (Figure 17–4) spinal cord Bundle of neurons and support cells that extends from the brain. spindle assembly checkpoint Regulatory system that operates during mitosis to ensure that all chromosomes are properly attached to the spindle before sister-chromatid separation starts. (Figure 17–9 and Panel 17–1, pp. 980–981) spliceosome Large assembly of RNA and protein molecules that performs pre-mRNA splicing in eukaryotic cells. Src (Src protein family) Family of cytoplasmic tyrosine kinases (pronounced “sark”) that associate with the cytoplasmic domains of some enzyme-linked cell-surface receptors (for example, the T cell antigen receptor) that lack intrinsic tyrosine kinase activity. They transmit a signal onward by phosphorylating the receptor itself and specific intracellular signaling proteins on tyrosines. (Figure 3–10)