Procaryote

1 Apr

Procaryote

a pair of labial palps which function in eating and taste. In the pb mutant (C) the proboscis has been transformed into a pair of legs. Therefore pb nor- mally functions as a segment identity gene (q.v.). See Antennapedia, Hox genes. procaryote See prokaryote. Procaryotes See Prokaryotes. processed gene an eukaryotic pseudogene (q.v.) lacking introns and containing a poly-A segment near the downstream end, suggesting that it arose by some kind of reverse copying from processed nuclear RNA into double-stranded DNA; also called retro- gene. processing 1. posttranscriptional modifications of primary transcripts. 2. antigen processing involves partial degradation by macrophages (and, in some cases, coupling with RNA) before the immunogenic units appear on the macrophage membrane in a con- dition that is stimulatory to cognate lymphocytes. processive enzyme an enzyme that remains bound to a particular substrate during repetitions of the catalytic event.

Prochlorococcus marinus a marine cyanobacter- ium that is ubiquitous in the upper 100 m of oceans that occur in a latitudinal band from 40°N to 40°S. This is the most abundant species on earth, and over half of the total chlorophyll in the ocean surface is contained in these organisms. See chlorophyll, Cya- nobacteria. Prochloron a genus of cyanobacteria whose spe- cies contain the a and b forms of chlorophyll (q.v.) found in green plants. Therefore, Prochloron is some- times called a living fossil (q.v.), a missing link in the evolution of the chloroplast (q.v.). P. didemni, the type species for this genus, lives in close association with marine ascidians. See Cyanobacteria, serial sym- biosis theory. proctodone a hormone, thought to be secreted by cells of the anterior intestine of insects, that termi- nates diapause (q.v.).

procumbent designating a plant stem that lies on the ground for all or most of its length (as in the case of vines). See runner. productive infection viral infection of a cell that produces progeny via the vegetative or lytic cycle. productivity fertility. In Drosophila the term is used specifically to refer to the number of progeny surviving to the adult stage among those produced per mated parental female in a specified time in- terval. proenzyme a zymogen (q.v.). proflavin an acridine dye (q.v.) that can function as an intercalating agent (q.v.). Treatment of T4 phage with proflavin resulted in rll mutants that had base additions or deletions. These were used to de- duce the triplet nature of the genetic code. See Ap- pendix C, 1961, Crick, Brenner et al.

progenitor a person or organism from which a person, animal, or plant is descended or originates; an ancestor or parent. progenote the hypothesized common ancestor of archaea, bacteria, and eukaryotes. See Sogin’s first symbiont. progeny the offspring from a given mating; mem- bers of the same biological family with the same mother and father; siblings. progeny test the evaluation of the genotype of a parent by a study of its progeny under controlled conditions. progeria a premature aging disease of humans. The hereditary form, Hutchinson-Gilford syndrome (q.v.) is inherited as an autosomal dominant and is caused by mutations in the lamin A gene (LMNA). Phenotypically old children usually die by age 13. Cytological studies of mutant lymphocytes show al- tered nuclear shapes and sizes, nuclear envelope in- terruptions, and chromatin extrusions. Cells have a reduced replicative life span and a reduced ability to repair damaged DNA. See lamins. progesterone a steroid hormone secreted by the corpus luteum (q.v.) to prepare the uterine lining for implantation of an ovum; also later secreted by the placenta (q.v.); essential for the maintenance of pregnancy. The structure is drawn on page 357. progestin See progestogens. progestogens a group name for substances having progesteronelike activity; also termed progestins. See progesterone.

proofreading

Progesterone

prognosis a forecast of the course and termination of a disease. programmed cell death See apoptosis. proinsulin a protein synthesized and processed by the beta cells of the pancreas. The molecule contains both the A and B peptides of insulin (q.v.) and an intervening C peptide containing 30 amino acids. Specific proteases cleave the precursor at two points, releasing the connecting peptide and the intact insu- lin molecule. prokaryon synonymous with nucleoid (q.v.). prokaryote member of the superkingdom Prokary- otes (q.v.). Prokaryotes (also Procaryotes) the superkingdom containing all microorganisms that lack a mem- brane-bound nucleus containing chromosomes. Cell division involves binary fission. Centrioles, mitotic spindles, and mitochondria are absent. Aside from pillotinas (q.v.), prokaryotes also lack microtubules. The first cells, which are thought to have evolved about 3.9 billion years ago, were chemoautotrophic prokaryotes.

Prokaryotes still make up the majority of the earth’s biomass. Their total population (4-6 × 1030 cells) constitutes the largest living reservoir of the elements C, N, and P. The superkingdom Pro- karyotes contains one kingdom, the Monera (q.v.). See Appendix A, Prokaryotes; Appendix C, 1937, Chatton; 1998, Whitman, Coleman, and Wiebe; biomass, genophore; contrast with Eukaryota. prolactin See human growth hormone. proline See amino acid. promiscuous DNA DNA segments that have been transferred between organelles, such as mitochon- dria and chloroplasts, or from a mitochondrial ge- nome to the nuclear genome of the host as a result of transpositional events happening millions of years ago.

An example is a section of mitochondrial DNA present in the nuclear genome of Strongylocentrotus purpuratus (q.v.). The term is also used to refer to those plasmids that can transfer DNA horizontally between a wide variety of host species. Examples would be mariner elements and the Ti plasmid (both of which see). See Appendix C, 1983, Jacobs et al. promitochondria aberrant mitochondria charac- teristically found in yeasts grown under anaerobic conditions. Promitochondria have incomplete inner membranes and lack certain cytochromes. See pe- tites. promoter 1. a region on a DNA molecule to which an RNA polymerase binds and initiates transcrip- tion. In an operon, the promoter is usually located at the operator end, adjacent but external to the op- erator. The nucleotide sequence of the promoter de- termines both the nature of the enzyme that at- taches to it and the rate of RNA synthesis. See Appendix C, 1975, Pribnow; alcohol dehydrogenase, down promoter mutations, Hogness box, Pribnow box, regulator gene, up promoter mutations. 2. a chemical that, while not carcinogenic itself, en- hances the production of malignant tumors in cells that have been exposed to a carcinogen. promoter 35 S a promoter discovered in the Cau- liflower Mosais Virus.

CaMV is naturally transmit- ted by aphids and is world wide in its distribution. The virus occurs in broccoli, cabbage, cauliflower, and turnips. Promoter 35 S has been used to activate the expression of foreign genes in genetically engi- neered plants, including corn, cotton, potato, rice, soybean, squash, sugar beets, and tomato. The Mon- santo Company holds the patent rights to genetically modified plants and seeds that incorporate promoter 35 S. See Bt designer plants, GMO, Roundup, trans- genic plants. pronase an enzyme from Streptomyces that digests mucoproteins. Prontosil a red dye used for treating leather. It was later found to successfully combat Streptococcal in- fections. Subsequently Prontosil was shown to breakdown in vivo into its component molecules, one of which was sulfanilamide. See Appendix C, 1938, Domagk; sulfa drugs. pronucleus the haploid nucleus of an egg, sperm, or pollen grain. See Appendix A, 1877, Fol. proofreading in molecular biology, any mecha- nism for correcting errors in replication, transcrip- tion, or translation that involves monitoring of indi- vidual units after they have been added to the chain;

pro-oocyte

also called editing. See dna mutations, DNA polymer- ase, RNA editing. pro-oocyte one of the two cystocytes containing four ring canals that form synaptonemal complexes in Drosophila melanogaster. Upon entering the vitel- larium, the anterior pro-oocyte switches to the nurse cell developmental pathway, leaving the posterior cell as the oocyte. See cystocyte divisions, polyfu- some. propagule usually referring to a vegative bud or shoot from a plant which, when separated, can pro- duce a new individual and so propagate the species. More generally, any unicellular or multicellular re- productive body that can disseminate the species. properdin pathway See complement. prophage in lysogenic bacteria, the structure that carries genetic information necessary for the produc- tion of a given type of phage and confers specific hereditary properties on the host. See Appendix C, 1950, Lwoff and Gutman; cryptic prophage, lambda (λ) bacteriophage. prophage attachment site either of the two at- tachment sites flanking an integrated prophage or the nucleotide sequences in a bacterial chromosome at which phage DNA can integrate to form a pro- phage. prophage induction See induction. prophage-mediated conversion the acquisition of new properties by a bacterium once it becomes ly- sogenized.

A prophage, for example, confers upon its bacterial host an immunity to infection by relat- ed phages. Lysogenized bacteria also often show changes in their antigenic properties or in the toxins they produce. See Appendix C, 1951, Freeman; diph- theria toxin. prophase See mitosis. propositus (female, proposita) the clinically af- fected family member through whom attention is first drawn to a pedigree of particular interest to hu- man genetics; also called proband. prosimian a member of the most primitive pri- mate suborder, the Prosimii, containing tree shrews and tarsiers. Prosobranchiata one of the three subdivisions of the mollusc class Gastropoda. See Appendix A. prospective significance the normal fate of any portion of an embryo at the beginning of develop- ment. prostaglandin a group of naturally occurring, chemically related, long-chain fatty acids that exhibit a wide variety of physiological effects (contraction of smooth muscles, lower blood pressure, antago- nism of certain hormones, etc.). The first prostaglan- din was originally isolated from the prostate gland (hence the name), but they are now known to be produced by many tissues of the body. prosthetic group that portion of a complex pro- tein that is not a polypeptide. Usually the prosthetic group is the active site of such a protein. The heme groups of hemoglobin are examples of prosthetic groups. protamines highly basic proteins that are bound to the DNA of sperm chromosomes.

During spermio- genesis (q.v.) the histones of the nucleosomes break down and are replaced by protamines. These are shorter, simpler proteins that are very rich in argi- nine and have little or no lysine. Cysteine residues are distributed at relatively conserved positions along the molecules. Protamines form an alpha helix (q.v.) when bound to DNA. Protamine genes are turned on only in males and only in the testes. Prota- mines are translated from stored mRNA during a late spermatid stage. protan See color blindness. protandry 1. the maturation of the pollen-bearing organs before the female organs on a monoecious plant. 2. sequential hermaphroditism in animals, with the male stage preceding the female stage (com- pare with protogyny). 3. the appearance of male ani- mals earlier in the breeding season than females. protanomaly See color blindness. protanopia See color blindness. protease an enzyme that digests proteins. proteasome a cylindrical, multi-subunit protein complex that recognizes and degrades many intra- cellular proteins in a highly regulated, ATP-depen- dent manner. Proteasomes have been identified in prokaryotes and eukaryotes. In mammalian cells the proteasome is a 26S complex, consisting of a 20S core complex flanked by a 19S regulatory particle, or “cap” on each end. The 19S caps serve to capture and un- fold ubiquitin-conjugated proteins and guide them into the 20S core, where polypeptides are broken down into short peptides. Proteasome complexes from prokaryotes are simpler in form than those from mammals. See calnexin, cyclins, ubiquitin, ubi- quitin-proteasome pathway (UPP).

protein structure

protein a molecule composed of one or more poly- peptide chains, each composed of a linear chain of amino acids covalently linked by peptide bonds. Most proteins have a mass between 10 and 100 kilo- daltons. A protein is often symbolized by its mass in kDa. The p53 protein is an example. See Appendix C, 1838, Mulder, Berzelius; 1902, Hofmeister and Fisher; Appendix E, Individual Databases; amino acid, insulin, peptide bond, protein structure, transla- tion. protein clock hypothesis the postulation that amino acid substitutions occur at a constant rate for a given family of proteins (e.g., cytochromes, hemo- globins) and hence that the degree of divergence be- tween two species in the amino acid sequences of the protein in question can be used to estimate the length of time that has elapsed since their diver- gence from a common ancestor. protein databases See Appendix E.

protein engineering any biochemical technique by which novel protein molecules are produced. These techniques fall into three categories: (1) the de novo synthesis of a protein, (2) the assembly of functional units from different natural proteins, and (3) the introduction of small changes, such as the replacement of individual amino acids, into a natu- ral protein. See Appendix C, 1965, Merrifield and Stewart. protein kinase any member of a family of proteins that transfers phosphate groups from ATP to specific serine, threonine, or tyrosine molecules in proteins. Protein kinases are activated in response to specific chemical signals such as calcium ions, cyclic AMP, or mitogens. Phosphorylation of the protein sub- strate serves to amplify the signal inside the cell. The oncogenic protein synthesized by the Rous sarcoma virus is a protein tyrosine kinase. The chloride chan- nels of epithelial cells are activated by reactions be- tween protein kinases and the cystic fibrosis trans- membrane regulator.

See Appendix C, 1959, Krebs, Graves, and Fischer; 1978, Collett and Erickson; 1991, Knighton et al.; 1992, Krebs and Fischer; Ab- elson murine leukemia virus, Bruton tyrosine kinase, cellular signal transduction, cyclins, cystic fibrosis, epi- dermal growth factor (EGF), Janus kinase 2, matura- tion promoting factor, pp60v-src, protein kinase, Src, transforming growth factor-β (TGF-β). proteinoid an amino acid polymer with a weight as high as 10,000 daltons formed under “pseudopri- meval conditions”’ by heating to 70°C a dry mixture containing phosphoric acid and 18 amino acids. Such proteinoids are acted upon by proteolytic en- zymes and have nutritive value for bacteria, but are nonantigenic. protein sorting the sorting of newly synthesized proteins into correct compartments of the eukaryo- tic cell. In the case of cotranslational sorting, the ri- bosome is associated with the membrane of the en- doplasmic reticulum via a signal recognition particle (q.v.). The protein enters the ER lumen as it is trans- lated. It may be retained there, or it may be trans- ferred via the Golgi apparatus (q.v.) to secretory vesicles, lysosomes, or the plasma membrane. In the case of posttranslational sorting, proteins begin their synthesis on ribosomes in the cytosol (q.v.). The proteins are then targeted to organelles such as mito- chondria, chloroplasts, or peroxisomes, or they may enter the nucleus through nuclear pores.

See endo- plasmic reticulum, receptor-mediated translocation, sorting signals, translation. protein splicing a phenomenon (known to occur in yeast, bacteria, and archaeons) during which a precursor protein has a segment excised from it and the N- and C-terminal fragments are subsequently spliced together. The excised segment is called an intein (internal protein sequence), and the spliced protein is composed of N- and C-exteins (external protein sequence). An intein cuts itself from its par- ent molecule and unites its former neighboring ex- teins with the usual peptide bond. Introns (q.v.) of- ten encode a “homing endonuclease” (q.v.) that can excise a DNA segment, allowing it to move to a new genomic location.

Analogously, many inteins contain a “homing endonuclease” segment in addition to a protein splicing region. This kind of intein can excise the DNA that encodes it out of a gene and allow the DNA to be transported elsewhere. A DNA poly- merase in Synechocystis (q.v.) is encoded by two gene segments sandwiched between several other genes. Each segment terminates in half of an intein gene (a “split intein”). When their protein products make contact, the intein reassembles itself and splices the two polymerase segments together. Compare with fused protein, fusion gene. See Appendix C, 1990, Kane et al.; 1997, Klenk et al.; posttranslational pro- cessing. protein structure The primary structure of a pro- tein refers to the number of polypeptide chains in it, the amino acid sequence of each, and the position of inter-and intrachain disulfide bridges. The secondary structure refers to the type of helical configuration possessed by each polypeptide chain resulting from the formation of intramolecular hydrogen bonds along its length. The tertiary structure refers to the manner in which each chain folds upon itself. The

protein tyrosine kinase
quaternary structure refers to the way two or more of the component chains may interact. See Appendix C, 1951, Pauling and Corey; 1955, Sanger et al.; 1973, Anfinsen; alpha helix, beta pleated sheet. protein tyrosine kinase See protein kinase. proteolytic causing the digestion of proteins into simpler units. proteome all of the proteins produced by a cell at any given time. Unlike the genome of a cell, which is normally invariant, the kinds or amounts of proteins produced by a cell may vary with such factors as stage of development, age, disease, drugs, and so forth.

See metabolic control levels, serial analysis of gene expression (SAGE), transcriptome. proteomics the large-scale study of all the ex- pressed proteins, particularly their structures, func- tions, and interactions. Proteomics utilizes a diverse range of technologies, from genetic analysis and two- dimensional gel electrophoresis (q.v.) to x-ray chrys- tallography (q.v.), NMR spectroscopy (q.v.), and se- quence alignment searches using advanced computer programs. See Appendix E, Individual Databases. proter the anterior daughter organism produced by the transverse division of a protozoan. Proterozoic the more recent of the two eras mak- ing up the Precambrian eon. Stromatolites (q.v.) oc- cur in early Proterozoic strata, and by the end of the era animals as advanced as coelenterates and annelids were present. The origin of eukaryotes presumably occurred midway through the era. See Appendix C, 1954, Barghoorn and Tyler; geologic time divisions. prothallus (prothalium) the independent gameto- phyte of a horsetail or fern. See Appendix A, Plantae, Tracheophyta.

prothetely an experimentally induced abnormality in which an organ appears in advance of the normal time because of a partially inhibited metamorphosis; for example, the formation of pupal antennae on a caterpillar. prothoracic gland a gland located in the protho- rax of insects that secretes ecdysone (q.v.). See ring gland. prothoracicotropic hormone (PTTH) a peptide hormone produced by neurosecretory cells in the dorsum of the insect brain that stimulates the pro- thoracic gland (q.v.) to synthesize and secrete ecdy- sones. prothrombin an inactive form of thrombin. See blood clotting. protist an informal term used to refer to any sin- gle-celled (usually eukaryotic) organism. protocooperation population or species interac- tion favorable to both, but not obligatory for either one. Protoctista five kingdoms of living organisms. It contains the eukaryotic microorganisms and their immediate de- scendants, i.e., the nucleated algae, flagellated water molds, slime molds, and protozoa. See Appendix A, Superkingdom Eukaryotes. protogyny sequential hermaphroditism with the ovary functioning before the testis. Compare with protandry. protomers single polypeptide chains (either iden- tical or nonidentical) of a multimeric protein. protomitochondria See petites.

proton an elementary particle of the atomic nu- cleus with a positive electric charge (equal numeri- cally to the negative charge of the electron) and a mass of 1.0073 mass units. proto-oncogene a cellular gene that functions in controlling the normal proliferation of cells and ei- ther (1) shares nucleotide sequences with any of the known viral onc genes, or (2) is thought to represent a potential cancer gene that may become carcino- genic by mutation, or by overactivity when coupled to a highly efficient promoter. Some proto-onco- genes (e.g., c-src) encode protein kinases that phos- phorylate tyrosines in specific cellular proteins. Oth- ers (e.g., c-ras) encode proteins that bind to guanine nucleotides and possess GTPase activity. Still other oncogenes encode growth factors or growth factor receptors. See maturation promoting factor, Philadel- phia (Ph1) chromosome, platelet-derived growth factor. protoplasm the substance within the plasma membrane of a cell; the nucleus and surrounding cy- toplasm. See Appendix C, 1839, Purkinje. protoplast the organized living unit of a plant or bacterial cell consisting of the nucleus (or nucleoid), cytoplasm, and surrounding plasma membrane, but with the cell wall left out of consideration. Proto- plasts can be generated experimentally; e.g., the walls of E. coli cells can be removed by lysozyme treatment. Aphragmabacteria (see Mycoplasma) lack cell walls and in this sense are protoplasts.

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