Standard atomic weights (mean relative atomic masses) are here rounded up to 3 decimal places, where the accuracies of individual values make this possible. IUPAC 2001 standard atomic weights and corresponding uncertainties are reported in full in R. D. Loss, Pure Appl. Chem. 75, 1107-1122 (2003). For elements that have no stable or long-lived nuclides, the mass number of the nuclide with the longest confirmed half-life is listed between square brackets. Adapted from Periodic Table of IUPAC (International Union of Pure and Applied Chemistry: www.iupac.org), dated 4 Feb 2005. Reproduced with the permission of IUPAC.
peripheral protein a protein that is exposed on the outer or the inner surface of the plasma mem- brane and is connected to the membrane through ionic or covalent interactions with a membrane component. Peripheral proteins include many pro- teins from the membrane-supporting cytoskeleton (e.g., spectrin (q.v.)) or the extracellular matrix (e.g., fibronectin (q.v.)). Compare with integral pro- tein. See lipid bilayer model. peripherin See retinitis pigmentosum (RP). peristalsis waves of muscular contractions that pass along tubular organs and serve to move the con- tents posteriorly. perithecium the rounded or flask-shaped, fruiting body of certain ascomycete fungi and lichens. The mature fruiting body of Neurospora, for example, contains about 300 ascus sacs. peritoneal sheath a network of anastomosing muscle fibers that holds together the ovarioles of an insect ovary. peritrichous designating bacteria having flagella all over their surfaces. permeability the extent to which molecules of a given kind can pass through a given membrane.
permease a membrane-bound protein in bacteria that is responsible for transport of a specific sub- stance in or out of the cell; sometimes referred to as a transport protein. In E. coli, lactose permease ac- tively transports lactose into the cell. Permian the most recent of the Paleozoic penods. Reptiles flourished, including species with mamma- lian characteristics. Insects increased, while amphibi- ans declined. Cycads and gingkos evolved and formed forests. The Permian ended with the most severe of all mass extinctions with over 95% of all species dying off. All trilobites became extinct. See continental drift, geologic time divisions. permissible dose See maximum permissible dose. permissive cells cells in which a particular virus may cause a productive infection (i.e., the produc- tion of progeny viruses). Cells in which infection is not productive are called nonpermissive cells. Some DNA tumor viruses may cause a productive infec- tion in permissive cells of one species and a tumor in nonpermissive cells of another species. permissive conditions environmental conditions under which a conditional lethal mutant (e.g., a temperature-sensitive mutant) can survive and pro- duce wild-type phenotype.
permissive temperature See temperature-sensitive mutation. Peromyscus a genus containing about 40 species of mice native to Central and North Amenca. The genetic data accumulated so far have been primarily related to the deermouse, P. maniculatus. More lim- ited data exist for P. boylei, P. leucopus, and P. polio- notus.
Studies of biochemical variation and cytoge- netics are presently the areas of most genetical research within the genus. peroxisomes membrane-bound intracellular or- ganelles containing at least four enzymes involved in the metabolism of hydrogen peroxide. They are thought to be important in purine degradation, pho- torespiration, and the glyoxylate cycle. Peroxisomes lack DNA. See microbody, protein sorting, sorting signals. PEST sequence domains in proteins that are rich in proline, glutamic acid, serine, and threonine. The name is based on the one-letter codes for these amino acids. PEST sequences are found in short- lived proteins and are therefore thought to serve as degradation signals. pet, PET See petites. petites dwarf colonies of Saccharomyces cerevisiae.
Such yeasts are slow growing because of mutations affecting mitochondria. Segregational petites contain mutated nuclear genes that result in mitochondrial defects. The wild-type allele of a segregational petite is designated PET and the mutant allele pet. The PET gene mutations fall into more than 215 complemen- tation groups. In the case of cytoplasmic or vegetative petites, it is the mitochondrial genome that is af- fected. Wild-type strains are symbolized p+. In most mutants (p−), the mtDNA contains less than one- third of the normal genome. Some strains (p0) have lost all the mtDNA. In such cases the yeast forms promitochondria.
These have a normal outer mem- brane, but the inner membrane contains poorly de- veloped cristae. In spite of the fact that the organelle cannot function in oxidative phosphorylation, it contains nuclear-encoded proteins such as DNA and RNA polymerases, all the enzymes of the citric acid cycle, and many inner membrane proteins. See Ap- pendix C, 1949 Ephrussi et al.; Podospora anserina. pfcrt gene a gene conferring resistance in mosqui- toes to the insecticide chloroquine (q.v.). The acro- nym stands for “Plasmodium falciparum chloroquine- resistance transporter,” and the gene encodes a trans- membrane protein of the food vacuole of the mero- zoite (q.v.). Mutations in this protein reduce uptake of the insecticide. See vacuoles. petri dish a round, shallow glass or plastic dish with a loose-fitting cover in which microorganisms or dividing eukaryotic cells are cultured on a nutri- ent gel (usually agar). Richard Julius Petri, and assis- tant to Robert Koch, developed the technique around 1887.
See plaque. Pfu DNA polymerase a DNA polymerase from the bacterium Pyrococcus furiosus that possesses the lowest error rate of any commercially available ther- mostable DNA polymerase because its 3′ → 5′ exo- nuclease activity serves a proofreading function. This DNA polymerase generates amplicons with blunt ends, whereas Taq DNA polymerase (q.v.) adds an extra A residue to amplicons. See extremo- philes. pg picogram. See genome size. p53 gene See TP53. P granules polar granules (q.v.).
pH See hydrogen ion concentration. phaeomelanin one of the pigments found in the coats of mammals. It is derived from the metabolism of tyrosine and is normally yellow in color. The amount of this pigment inserted into the hairs is quantitatively and qualitatively controlled by the agouti locus. See agouti, MCIR gene, melanin. Phaeophyta a phylum that contains mostly marine species referred to as brown seaweeds (e.g., kelps).
The phylum is placed in the kingdom Protoctista (Appendix A) according to Margulis’ Five Kindom scheme. Cavalier-Smith places phaeophytes in a sixth kingdom, the Chromista (q.v.). phage an abbreviation of bacteriophage (q.v.), a virus that attacks bacteria. When referring to one or more virions of the same species, the word phage is used; thus, a cell may be infected by one or many lambda phage. Phages is used when referring to dif- ferent species; thus, lambda and T4 are both phages. phage conversion See prophage-mediated conver- sion.
phage cross a procedure requiring the multiple infection of a single bacterium with phages that dif- fer at one or more genetic sites. Upon lysis of the host, recombinant progeny phages are recovered that carry genes derived from both parental phage types. See Visconti-Delbruc¨k hypothesis. phage induction the stimulation of prophage to enter the vegetative state, accomplished by exposing lysogenic cells to ultraviolet light. Hydrogen perox-
ide, x-rays, and nitrogen mustard (q.v.) also act as inducing agents. See zygotic induction. phagocyte a cell that incorporates particles from its surroundings by phagocytosis. phagocytosis the engulfment of solid particles by cells; the ingestion of microorganisms by leukocytes. See Appendix C, 1901, Mechnikov. phagolysosome an organelle formed by the fusion of a phagosome (q.v.) and a lysosome (q.v.). phagosome a membrane-bounded cytoplasmic particle produced by the budding off of localized in- vaginations of the plasmalemma. Recently phagocy- tosed particles are segregated within the cell in phagosomes. phalloidin the most common phallotoxin pro- duced by Amanita phalloides. It is a cyclic heptapep- tide made up of (1) alanine, (2) D-threonine, (3) cysteine, (4) hydroxyproline, (5) alanine, (6) trypto- phan, and (7) γ-δ-dihydroxyleucine.
phallotoxins together with amatoxins (q.v.), the main toxic components produced by Amanita phal- loides (q.v.). Phalloidin, one of the chief phallotox- ins, forms tight complexes with filamentous actin. See rhodaminylphalloidin. phanerogam an outmoded term referring to a plant belonging to the Spermatophyta (q.v.). See cryptogam. Phanerozoic the geologic eon encompassing the Paleozoic, Mesozoic, and Cenozoic eras. During the 540-million-year interval an abundant fossil record was left in the rocks. See geologic time divisions. phantom a volume of material approximating the density and effective atomic number of tissue. Radi- ation dose measurements are made within or on a phantom as a means of determining the radiation dose within or on a body under similar exposure conditions.
pharmacogenetics the area of biochemical genet- ics dealing with genetically controlled variations in responses to drugs. pharming the genetic engineering of farm animals to produce pharmaceuticals. phase contrast microscope light rays passing through an object of high refractive index will be retarded in comparison with light rays passing through a surrounding medium with a lower refrac- tive index.
The retardation or phase change for a given light ray is a function of the thickness and the index of refraction of the material through which it passes. Thus, in a given unstained specimen, trans- parent regions of different refractive indices retard the light rays passing through them to differing de- grees. Such phase variations in the light focused on the image plane of the light microscope are not visi- ble to the observer. The phase contrast microscope is an optical system that converts such phase varia- tions into visible variations in light intensity or con- trast. The phase microscope therefore allows cytolo- gists to observe the behavior of living, dividing cells. See Appendix C, 1935, Zernicke. phaseolin a glycoprotein that constitutes up to 50% of the storage protein in the cotyledons of the bean Phaseolus vulgaris. It is encoded by a family of about 10 genes. See Appendix C, 1981, Kemp and Hall.
Phaseolus the genus that includes P. aureus, the Mung bean; P. limensis, the lima bean; P. vulgaris, the red kidney bean. Most species are nodulating le- gumes (q.v.). See Plantae, Tracheophyta, Angio- spermae, Dicotyledoneae, Leguminales; Rhizobium. phene a phenotypic character controlled by genes. phenetic taxonomy a system of classification based upon phenotypic characteristics without regard to phylogenetic relationships; also known as numerical taxonomy. phenocopy the alteration of the phenotype, by nutritional factors or the exposure to environmental stress during development, to a form imitating that characteristically produced by a specific gene. Thus, rickets due to a lack of vitamin D would be a pheno- copy of vitamin D-resistant rickets. phenocritical period the period in the develop- ment of an organism during which an effect pro- duced by a gene can most readily be influenced by externally applied factors.
phenogenetics developmental genetics. phenogram a branching diagram linking taxons by estimates of overall similarity based on evidence from a sample of characters. Characters are not eval- uated as to whether they are primitive or derived. phenogroup any group of antigenically detectable factors of a blood group system that is inherited as a unit. Antigens in a phenogroup are encoded by alleles at a single locus. The B and C blood group systems in cattle are examples of two phenogroups. See Appendix C, 1951, Stormont et al.; haplotype. phenome the sum of all of the manifest physical and behavioral characteristics of a cell or an or- ganism. phenomic lag phenotypic lag. phenon a set of organisms grouped together by methods of numerical taxonomy (q.v.).
phenotype the observable characteristics of a cell or an organism, such as its size and shape, its meta- bolic functions, and its behavior. The genotype (q.v.) is the underlying basis of the phenotype, and the term is commonly used to describe the effect a particular gene produces, in comparison with its mutant alleles. Some genes control the behavior of the organism, which in turn generates an artefact outside the body. R. Dawkins uses the term extended phenotype to refer to the production of such an arte- fact (spider webs, bird nests, and beaver dams are examples). See Appendix C, 1909, Johannsen.
phenotypic lag the delay of the expression of a newly acquired character. Mutations may appear in a bacterial population several generations after the administration of a mutagen. Phenotypic lag may be due to any of the following reasons: (1) The muta- gen may inactivate the gene at once, but this inactiv- ity may not become apparent until the products pre- viously made by the gene are diluted to a sufficient degree. A number of cell divisions occur before the concentration of these products falls below some critical level. (2) The “mutagen” may itself be inac- tive. It may undergo a series of reactions to yield a compound that is the true mutagen. The latent pe- riod would then be the time required for those reac- tions to take place. (3) The mutagen may cause the gene to become unstable. At a later time, it will re- turn to a stable wild type or mutant state. (4) The microbe may be multinucleate, and a mutation may occur in but one nucleus. The latent period then would be the time required for nuclear segregation. See perdurance. phenotypic mixing the production of a virus with a phenotype that does not match its genotype.
Dur- ing the assembly of a virus, nucleic acid and protein components are drawn randomly from two pools. In a host infected simultaneously by mutant and wild- type viruses, progeny phages are assembled without regard to matching the coat components to the genes in the nucleic acid core. Thus, discrepancies sometimes arise, and a virus is produced with coat proteins that are not specified by its genome. See pseudovirion, reassortant virus. phenotypic plasticity a phenomenon in which a given genotype may develop different states for a character or group of characters in different environ- ments; genotype-environment interaction (q.v.). See norm of reaction. phenotypic sex determination control of gonad development by nongenetic stimuli. For example, the incubation temperature of fertilized eggs deter- mines the type of sexual development in some turtle species. phenotypic variance the total variance observed in a character.
See genetic variance, variance. phenylalanine See amino acid. phenylketonuria a hereditary disorder of amino acid metabolism in humans, inherited as an autoso- mal recessive. Homozygotes cannot convert phenyl- alanine to tyrosine due to a lack of the liver enzyme phenylalanine hydroxylase. Brain dysfunction char- acteristic of the disease can be avoided by early dietary restriction of phenylalanine. Prevalence is 1/11,000. Abbreviated PKU. Phenylketonuria is some- times called Følling disease after A. Følling, who dis- covered the underlying metabolic disorder in 1934. The PKU gene resides on the long arm of chromo- some 12 between bands 22 and 24.1. It contains 13 exons and encodes a phenylalanine hydroxylase made up of 450 amino acids. The most frequent mutant allele in Caucasians is a base substitution that causes a skipping of exon 12 during mRNA splicing. See Appendix C, 1954, Bickel, Gerrard, and Hickmans; 1961, Guthrie; gene, Guthrie test, mater- nal PKU. phenylthiocarbamide (PTC) a molecule belonging to a class of compounds called thioureas. Related compounds occur in broccoli, cabbage, kale, and turnips. PTC tastes bitter to some humans, but is tasteless to others. Human populations from various