Boldface terms within a definition are also defined in this glossary.

Figures and tables that illustrate defined terms are noted in parentheses.

p53 protein The product of a tumor-suppressor gene that plays a critical role in the arrest of cells with damaged DNA. Inactivating mutations in the p53 gene are found in many human cancers. (Figure 24-26)

paracrine Referring to signaling mechanism in which a target cell responds to a signaling molecule (e.g., growth factor, neurotransmitter) that is produced by a nearby cell(s) and reaches the target by diffusion.

patch clamping Technique for determining ion flow through a single ion channel or across the membrane of an entire cell by use of a micropipette whose tip is applied to a small patch of the cell membrane. (Figure 11-22)

patterning genes Genes involved in metazoan development that determine the general organization of the animal, including the major body axes and segmentation.

P body Dense cytoplasmic domain, containing no ribosomes or translation factors, that functions in repression of translation and degradation of associated mRNAs; also called cytoplasmic RNA-processing body.

PCR (polymerase chain reaction) Technique for amplifying a specific DNA segment in a complex mixture by multiple cycles of DNA synthesis from short oligonucleotide primers followed by brief heat treatment to separate the complementary strands. (Figure 6-18)

pentose A five-carbon monosaccharide. The pentoses ribose and deoxyribose are present in RNA and DNA, respectively. (Figure 2-16)

peptide A small linear polymer composed of amino acids connected by peptide bonds. The terms peptide and oligopeptide are often used interchangeably. See also polypeptide.

peptide bond The covalent amide linkage between amino acids formed between the amino group of one amino acid and the carboxyl group of another with the net release of a water molecule (dehydration). (Figure 2-13)

peptidoglycan A polysaccharide chain cross-linked by peptide cross-bridges in a bacterial cell wall that confers rigidity and helps to determine the cell’s shape.

pericentriolar material Amorphous material seen by thin-section electron microscopy surrounding the centrioles of animal cells. Pericentriolar material contains many components, including the gamma-tubulin ring complex (gamma-TuRC), which promotes nucleation of microtubule assembly. (Figure 18-6)

peripheral membrane protein Any protein that associates with the cytosolic or exoplasmic face of a membrane but does not enter the hydrophobic core of the phospholipid bilayer. See also integral membrane protein. (Figure 7-1)

perlecan A large multidomain proteoglycan component of the extracellular matrix (ECM) that binds to many ECM components, cell-surface molecules, and growth factors; a major component of the basal lamina.

peroxisome Small organelle that contains enzymes for degrading fatty acids and amino acids by reactions that generate hydrogen peroxide, which is converted to water and oxygen by catalase.

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

phagocyte Any cell that can ingest and destroy pathogens and other particulate antigens. The primary phagocytes are neutrophils, macrophages, and dendritic cells.

phagocytosis Process by which relatively large particles (e.g., bacterial cells) are internalized by certain eukaryotic cells in a process that involves extensive remodeling of the actin cytoskeleton; distinct from receptor-mediated endocytosis. (Figure 17-19)

phenotype The detectable physical and physiological characteristics of a cell or organism determined by its genotype; also, the specific trait associated with a particular allele.

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

phosphatase An enzyme that removes a phosphate group from a substrate by hydrolysis. Phosphoprotein phosphatases act with protein kinases to control the activity of many cellular proteins. (Figure 3-35)

phosphoanhydride bond A type of high-energy bond formed between two phosphate groups, such as the γ and β phosphates and the β and α phosphates in ATP. (Figure 2-31)

phosphodiester bond Chemical linkage between adjacent nucleotides in DNA and RNA; consists of two phosphoester bonds, one on the 5' side of the phosphate and another on the 3' side. (Figure 5-2)

phosphoglycerides Amphipathic derivatives of glycerol 3-phosphate that generally consist of two hydrophobic fatty acyl chains esterified to the hydroxyl groups in glycerol and a polar head group attached to the phosphate; the most abundant lipids in biomembranes. (Figures 2-20 and 10-8a)

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phosphoinositides A group of membrane-bound lipids containing phosphorylated inositol derivatives; some function as second messengers in several signal transduction pathways. (Figures 15-33 and 16-28)

phospholipase One of several enzymes that cleave various bonds in the hydrophilic end of phospholipids. (Figures 7-12)

phospholipase C (PLC) A membrane-associated phospholipase, activated by either G_αq or G_αo, that cleaves the membrane lipid phosphatidylinositol 4,5-bisphosphate to generate two second messengers, DAG and IP₃. (Figures 15-33 and 15-34a)

phospholipid The major class of lipids present in biomembranes, including phosphoglycerides and sphingolipids. (Figures 7-8a, b and 2-20)

phospholipid bilayer A two-layer, sheet-like structure in which the polar head groups of phospholipids are exposed to the aqueous media on either side and the nonpolar fatty acyl chains are in the center; the foundation for all biomembranes. (Figure 7-3a, b)

phosphorylation The covalent addition of a phosphate group to a molecule such as a sugar or a protein. The hydrolysis of ATP often accompanies phosphorylation, providing energy to drive the reaction and the phosphate group that is covalently added to the target molecule. Enzymes that catalyze phosphorylation are called kinases.

photoelectron transport Light-driven electron transport that generates a charge separation across the thylakoid membrane that drives subsequent events in photosynthesis. (Figure 12-35)

photorespiration A reaction pathway that competes with CO₂ fixation (Calvin cycle) by consuming ATP and generating CO₂, thus reducing the efficiency of photosynthesis. (Figure 12-49)

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

photosystems Multiprotein complexes, present in all photosynthetic organisms, that consist of light-harvesting complexes containing chlorophylls and a reaction center where photoelectron transport occurs. (Figure 12-44a)

phragmoplast In plants, a temporary structure, formed during telophase, whose membranes become the plasma membranes of the daughter cells and whose contents develop into the new cell wall between them. (Figure 18-46)

pI See isoelectric point.

plakins A family of proteins that help attach intermediate filaments to other structures.

plaque assay Technique for determining the number of infectious viral particles in a sample by culturing a diluted sample on a layer of susceptible host cells and then counting the clear areas of lysed cells (plaques) that develop. (Figure 5-44)

plasma membrane The membrane surrounding a cell that separates the cell from its external environment; consists of a phospholipids bilayer and associated membrane lipids and proteins. (Figures 1-12a, 7-1, and 7-5)

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

plasmodesmata (sing. plasmodesma) Tube-like cell junctions that interconnect the cytoplasms of adjacent plant cells and are functionally analogous to gap junctions in animal cells. (Figure 20-41)

point mutation Change of a single nucleotide in DNA, especially in a region coding for protein; can result in formation of a codon specifying a different amino acid or a stop codon. Addition or deletion of a single nucleotide will cause a shift in the reading frame.

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

polarity In cell biology, the presence of functional and/or structural differences in distinct regions of a cell or cellular component. See also cell polarity.

polarized In cell biology, referring to any cell or subcellular structure marked by functional and structural asymmetries.

Polo kinases Family of protein kinases that are critical for many aspects of mitosis, such as centrosome duplication and cohesin removal from chromosomes.

polymer Any large molecule composed of multiple identical or similar units (monomers) linked by covalent bonds. (Figure 2-13)

polymerase chain reaction See PCR.

polypeptide Linear polymer of amino acids connected by peptide bonds, usually containing 20 or more residues. See also protein.

polyribosome A complex containing several ribosomes, all translating a single messenger RNA; also called polysome. (Figure 5-27)

polysaccharide Linear or branched polymer of monosaccharides linked by glycosidic bonds and usually containing more than 15 residues. Those with fewer than 15 residues are often called oligosaccharides.

polytene chromosome Enlarged chromosome composed of many parallel copies of itself formed by multiple cycles of DNA replication without chromosomal separation; found in the salivary glands and some other tissues of Drosophila and other dipteran insects. (Figure 8-40)

polyubiquitinylation The covalent addition of a chain of covalently linked ubiquitin molecules to a site on a target protein.

polyunsaturated Referring to a compound (e.g., fatty acid) in which two or more of the carbon-carbon bonds are double or triple bonds.

porins Class of trimeric transmembrane proteins through which small water-soluble molecules can cross the membrane; present in outer mitochondrial and chloroplast membranes and in the outer membrane of gram-negative bacteria. (Figure 7-18)

positive feedback mechanism Process where the output of a pathway promotes its own production.

potential energy Stored energy. In biological systems, the primary forms of potential energy are chemical bonds, concentration gradients, and electric potentials across cellular membranes.

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pre-mRNA Precursor messenger RNA; the primary transcript and intermediates in RNA processing. (Figures 5-15 and 10-2)

pre-rRNA Large precursor ribosomal RNA that is synthesized in the nucleolus of eukaryotic cells and processed to yield three of the four RNAs present in ribosomes. (Figures 10-40 and 10-41)

primary cilium The single nonmotile cilium present on almost all vertebrate cells that serves as a sensory organelle to detect extracellular signals.

primary structure In proteins, the linear arrangement (sequence) of amino acids within a polypeptide chain.

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

primase A specialized RNA polymerase that synthesizes short stretches of RNA used as primers for DNA synthesis. (Figure 5-30).

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

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

progenitor cells A type of undifferentiated cell that, when provided with the appropriate signals, will divide and differentiate into one or a few cell types.

programmed cell death See apoptosis.

prokaryotes Class of organisms, including the bacteria (eubacteria) and archaea, that lack a true membrane-limited nucleus and other organelles. See also eukaryotes. (Figure 1-1)

prolactin A cytokine released during pregnancy of mammals that induces the development of mammary glands to produce and secrete milk proteins.

prometaphase Second stage in mitosis, during which the nuclear envelope and nuclear lamina break down and microtubules assembled from the spindle poles “capture” chromosome pairs at specialized structures called kinetochores. (Figure 18-37)

promoter DNA sequence that determines the site of transcription initiation for an RNA polymerase. (Figure 5-11)

promoter-proximal element Any regulatory sequence in eukaryotic DNA that is located within ∼200 base pairs of the transcription start site. Transcription of many genes is controlled by multiple promoter-proximal elements. (Figure 9-23)

prophase Earliest stage in mitosis, during which the chromosomes condense, the duplicated centrosomes separate to become the spindle poles, and the mitotic spindle begins to form. (Figure 18-37)

protease Any enzyme that cleaves one or more peptide bonds in target proteins.

proteasome Large multifunctional protease complex in the cytosol that degrades intracellular proteins marked for destruction by attachment of multiple ubiquitin molecules. (Figure 3-31)

protein A macromolecule composed of one or more linear polypeptide chains and folded into a characteristic three-dimensional shape (conformation) in its native, biologically active state.

protein family Set of homologous proteins encoded by a gene family.

protein domain Distinct regions of a protein’s three-dimensional structure. A functional domain exhibits a particular activity characteristic of the protein; a structural domain is ≈40 or more amino acids in length, arranged in a distinct secondary or tertiary structure; a topological domain has a distinctive spatial relationship to the rest of the protein.

protein kinase A (PKA) Cytosolic enzyme that is activated by cyclic AMP (cAMP) and functions to phosphorylate and thus regulate the activity of numerous cellular proteins; also called cAMP-dependent protein kinase. (Figure 15-29)

protein kinase B (PKB) Cytosolic enzyme that is recruited to the plasma membrane by signal-induced phosphoinositides and subsequently activated; also called Akt. (Figure 16-29)

protein kinase C (PKC) Cytosolic enzyme that is recruited to the plasma membrane in response to signal-induced rise in cytosolic Ca²⁺ level and is activated by membrane-bound diacylglycerol (DAG). (Figure 15-34a)

protein kinase G (PKG) A cytosolic protein kinase activated by cyclic GMP.

proteoglycans A group of glycoproteins (e.g., perlecan and aggrecan) that contain a core protein to which is attached one or more glycosaminoglycan (GAG) chains. They are found in nearly all animal extracellular matrices, and some are integral membrane proteins. (Figure 20-32)

proteome All the proteins in a cellular compartment, intact cell, organ, or organism.

proteomics The systematic study of the amounts, modifications, interactions, localization, and functions of all or subsets of proteins at the whole-organism, tissue, cellular, and subcellular levels.

proton-motive force The energy equivalent of the proton (H⁺) concentration gradient and electric potential gradient across a membrane; used to drive ATP synthesis by ATP synthase, transport of molecules against their concentration gradient, and movement of bacterial flagella. (Figure 12-2)

proto-oncogene A normal cellular gene that encodes a protein usually involved in regulation of cell growth or differentiation and that can be mutated into a cancer-promoting oncogene, either by changing the protein-coding segment or by altering its expression. (Figure 24-15)

protostomes A group of bilaterally symmetric animals whose mouth develops close to the blastopore and has a ventral nerve cord. This group includes worms, insects, and mollusks.

provirus The DNA of an animal virus that is integrated into a host-cell genome; during replication of the cell, the proviral DNA is replicated and appears in both daughter cells. Activation of proviral DNA leads to production and release of progeny virions.

pseudogene DNA sequence that is similar to that of a functional gene but does not encode a functional product; probably arose by sequence drift of duplicated genes.

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pseudosubstrate domain A protein domain whose sequence or structure resembles that of an enzyme’s substrate and thus binds to the enzyme’s active site, but which cannot be modified by the enzyme (i.e., phosphorylated), resulting in inhibition of the enzyme.

pulse-chase A type of experiment in which a radioactive small molecule is added to a cell for a brief period (the pulse) and then is replaced with an excess of the unlabeled form of the same small molecule (the chase). Used to detect changes in the cellular location of a molecule or its metabolic fate over time. (Figure 3-42)

pump See ATP-powered pump.

purines A class of nitrogenous compounds containing two fused heterocyclic rings. Two purines, adenine (A) and guanine (G), are base components of nucleotides found in DNA and RNA. See also base pair. (Figure 2-17)

pyrimidines A class of nitrogenous compounds containing one heterocyclic ring. Two pyrimidines, cytosine (C) and thymine (T), are base components of nucleotides found in DNA; in RNA, uracil (U) replaces thymine. See also base pair. (Figure 2-17)