Supercoiling

4 Apr

Supercoiling

Sudan black B

sulfa drugs  a group of compounds also called sul- fonamides. The simplest is sulfanilamide, and it bears a close resemblance to p-aminobenzoic acid.

Sulfanilamide and p-aminobenzoic molecules com- pete during the enzymatic synthesis of folic acid (q.v.). The bacterial enzyme dihydropteroate syn- thetase is tricked into making a dihydropteroate con- taining sulfanilamide. This product cannot be con- verted to folate, and the bacteria are starved of the folate they require to divide, and die. Humans get the folate they need in their diet and therefore are not harmed by doses of sulfanilamide that kill bacte- ria. See Prontosil. sulfatide lipidosis an autosomal-recessive disease in man due to a defect in the production of the lyso- somal enzyme arylsulfatase A.

The clinical symp- toms are paralysis, blindness, and dementia, leading to death during childhood. sulfonamides See sulfa drugs. sulfur an element universally found in small amounts in tissues. Atomic number weight 32.064; valence 2−, 4+, 6+; most abundant iso- tope 32S; radioisotope 35S (q.v.). sulfur-containing amino acids cysteine, cystine, methionine. See amino acids. sulfur-dependent thermophiles a group of pro- karyotes that generally live in sulfur-rich hot springs and generate energy by metabolizing sulfur. They are placed in the Crenarcheota of the Archaea (see Appendix A). Members of one subgroup, called eo- cytes, are thought to be immediate relatives of the first eukaryotes. Some eocyte genera are Acidianus, Desulfurococcus, Pyrodictium, Sulfolobus, and Thermo- discus.

SUMO proteins a conserved family of small ubi- quitin-like modifier proteins which become cova- lently conjugated to target proteins and modify the properties of these proteins. A SUMO protein is structurally related to ubiquitin (q.v.), and like ubi- quitin, binds by its C terminus (q.v.) end to a lysine residue in the target protein. However, protein mod- ification by SUMO does not lead to protein degra- dation; rather, the modified protein plays a role in regulating a diverse range of functions, such as nucleocytoplasmic transport, gene transcription, chromosome separation, DNA repair, and protein stability.

SUMO proteins, like those of the Poly- comb group, sometimes also silence genes by induc- ing the condensation of localized chromosomal regions. The posttranslational modification of a sub- strate protein by SUMO ligation is called sumoyla- tion. Sumoylation is a reversible, dynamic process, and many enzymes involved in SUMO activation, conjugation, and deconjugation have been identified. SUMO proteins are found in animals, fungi, and plants.

In humans there are at least four SUMO iso- forms, with distinct functions and subcellular local- ization. See Polycomb (Pc), ubiquitin-proteasome pathway (UPP). supercoiling the coiling of a covalently closed cir- cular duplex DNA molecule upon itself so that it crosses its own axis. A supercoil is also referred to as a superhelix. The B form of DNA is a right-handed double helix. Winding of the DNA duplex in the same direction as that of the turns of the double he- lix is called positive supercoiling. Twisting of a duplex DNA molecule in a direction opposite to the turns

superdominant

of the strands of the double helix is called negative supercoiling. See DNA gyrase, replisome. superdominant overdominant (q.v.). superfemale metafemale (q.v.). supergene a chromosomal segment protected from crossing over and so transmitted from genera- tion to generation as if it were a single recon. supergene family See gene superfamily. superhelix See supercoiling. superinfection the introduction of such a large number of viruses into a bacterial culture that each bacterium is attacked by several phages. supermale metamale (q.v.). Superman See cadastral genes. supernatant the fluid lying above a precipitate in a centrifuge, following the centrifugation of a sus- pension. supernumerary chromosome a chromosome pres- ent, often in varying numbers, in addition to the characteristic invariable complement of chromo- somes. See Appendix C, 1928, Randolph; B chromo- somes. superovulation the simultaneous release of more than the normal number of eggs from an ovary. This can be induced artificially by hormone treatment in cattle and other livestock for embryo transfer (q.v.) to surrogate mothers. superoxide anion a highly reactive and destruc- tive radical generated by the one electron reduction of O2. The reaction may be symbolized:

See free radical, superoxide dismutase (SOD). superoxide dismutase (SOD)  an antioxidant en- zyme (q.v.). The most common SOD in eukaryotes is a homodimeric enzyme containing one copper and one zinc atom per monomer. Prokaryotes like E. coli have SODs that contain manganese or iron. SODs remove superoxide anions from cells by catalyzing the conversion of two of these radicals to hydrogen peroxide and molecular oxygen:

In eukaryotes, superoxide dismutase is symbolized SOD1 to distinguish it from the SOD2 of mitochon- dria. See familial amyotrophic lateral sclerosis, free radical hypothesis of aging, indolephenoloxidase, su- peroxide anion. superrepression an uninducible state for a gene usually attributed to (1) a defective operator locus to which a functional repressor protein cannot bind, or (2) a mutant regulatory gene whose repressor protein product is insensitive to the inducer sub- stance; a phenomenon that causes a gene to be per- manently “turned off.” superspecies a complex of related allopatric spe- cies (often called a species group). Such species are grouped together because of their morphological similarities. That the superspecies constitutes a natu- ral grouping is demonstrated by finding in the genus Drosophila that whenever species hybrids are pro- duced under laboratory conditions the parents are from the same species group. supersuppressor a mutation that can suppress the expression of specific alleles of mutations at a num- ber of different chromosomal sites; usually a non- sense suppressor.

supervital mutation a mutation that increases the viability of individuals bearing it above the wild-type level. suppression 1. the restoration of a lost or aberrant genetic function (see suppressor mutation). 2. in im- munology, a specific or nonspecific state of induced nonresponsiveness in the immune system. See immu- nological suppression, suppressor T cell. suppressor-enhancing mutations genetic alter- ations that boost the activity of both temperature- sensitive as well as temperature-insensitive suppres- sors. suppressor mutation a mutation that compen- sates for some other mutation, resulting in a normal or near-normal phenotype in the double mutant. Two main types of suppressor mutations occur: in- tergenic and intragenic. An intergenic suppressor mu- tation suppresses the effect of a mutation in another gene. Some intergenic suppressors change the physi- ological conditions so that the proteins encoded by the suppressed mutants can function. Other inter- genic suppressors actually change the amino acid se- quence of the mutant protein. For example, the in- tergenic suppressor may cause a base substitution in a tRNA gene. This results in an anticodon that reads a mutated codon of the mRNA of the suppressed mutant so as to insert a functionally acceptable

symbiotic theory of the origin of undulipodia

amino acid in the protein responsible for the pheno- type. An intragenic suppressor mutation suppresses the effect of a mutation in the same gene in which it is located. Some intragenic suppressors restore the original reading frame after a frameshift. Other sup- pressor mutations produce new amino acid substitu- tions at different sites from those produced by the first mutation. However, the second changed amino acid compensates functionally for the first. Intra- genic suppressor mutations are also called second site mutations. Suppressor of variegation 205 [Su(var)205] See heterochromatin protein 1 (HP1). suppressor T cell a subpopulation of T lympho- cytes (designated Ts) whose function is to suppress the response of other lymphocytes to a particular an- tigen.

surface-dependent cells See anchorage-depen- dent cells. surrogate mother a woman (or other female mammal) that receives an embryo transplant from another donor. survival of the fittest the corollary of Darwin’s theory of natural selection; namely, that as a result of the elimination by natural selection of those indi- viduals least adapted to the environment, those that ultimately remain are the fittest. survival value the degree of effectiveness of a given phenotype in promoting the ability of that or- ganism to contribute offspring to the future popula- tions. suspension culture a type of in vitro culture in which the cells multiply while suspended in liquid medium. See anchorage-dependent cells.

Sus scrofa the pig. Domesticated pigs are gener- ally given the subspecies name domestica. The hap- loid chromosome number is 19, and about 350 genes have been mapped. Because of its anatomical and physiological similarities with humans and the ease with which it can be bred in large numbers, the do- mesticated pig is the most likely source of organs for replacement of those incapable of continued func- tion in humans. Unfortunately, pig organs trans- planted into humans are rapidly rejected by the recipient’s immune system. The generation of genet- ically engineered pigs may eventually overcome this rejection problem. See Appendix A, Chordata, Mam- malia, Artiodactyla; Appendix E; swine, transgenic animals, xenoplastic transplantation. SV 40 simian virus 40 (q.v.). Svedberg See sedimentation coefficient. sweepstakes route a potential migration pathway along which species disperse with difficulty.

Chance events play a large role in colonization of new areas along this route. For example, birds blown far out to sea by a storm may accidentally land on an oceanic island and colonize it, but it is unlikely that this will happen a second time for that species. sweet corn See corn. swine any of a number of domesticated breeds of the species Sus scrofa (q.v.). Popular breeds include Berkshire, Chester White, Duroc, Hampshire, Here- ford, Ohio Improved Chester, Poland China, Spot- ted Poland China, Tamworth, Yorkshire. switchback evolution the recurrent reversals be- tween alternative patterns of development during the evolution of particular groups of plants or ani- mals. Insect ovary types (q.v.) provide an example.

Reversions from the polytrophic to the panoistic type of oogenesis have occurred within the Mecopt- era and the Neuroptera. Reversions from the telo- trophic to the panoistic type have occurred within the Megaloptera and the Thysanoptera. See Appen- dix A, Eumetazoa, Bilateria, Coelomata, Arthro- poda, Insecta. switch gene a gene that causes the epigenotype to switch to a different developmental pathway. switching sites break points at which gene seg- ments combine in gene rearrangements. swivelase See gyrase, topoisomerase. symbiogenesis the evolutionary process by which bacterial symbionts were transformed into certain of the organelles found in eukaryotic cells, such as mi- tochondria and chloroplasts. See Appendix C, 1910, Mereschkowsky; apicoplast, serial symbiosis theory. symbiont an organism living in a mutually benefi- cial relationship with another organism from a dif- ferent species: e.g., the coexistence of algae and fungi in lichens. symbiosis any interactive association between two or more species living together. See commensalism, lichen, mutualism, parasitism, serial symbiosis theory. symbiotic theory of the origin of undulipodia the theory proposed by L. Margulis that the ances- tral eukaryote acquired undulipodia (q.v.) as the re- sult of a motility symbiosis with spirochaetes.

symbols used in human cytogenetics

symbols used in human cytogenetics A-G, the chromosome groups; 1-22, the autosome numbers; X, Y, the sex chromosomes; p, the short arm of a chromosome; q, the long arm of a chromosome; ace, acentric; cen, centromere; dic, dicentric; inv, inver- sion; r, ring chromosome; t, translocation; a plus (+) or minus (−) when placed before the autosome number or group letter designation indicates that the particular chromosome is extra or missing; when placed after a chromosome arm, a plus or minus des- ignation indicates that the arm is longer or shorter than usual; a diagonal (/) separates cell lines when describing mosaicism. Examples: 45,XX, −C = 45 chromosomes, XX sex chromosomes, a missing chromosome from the C group; 46, XY, t (Bp−; Dq+) = a reciprocal translocation in a male between the short arm of a B and the long arm of a D group chromosome; inv (Dp+, q−) = a pericentric inversion involving a D chromosome; 2p+ = an increase in the length of the short arm of a chromosome 2; 46,XX, r=afemalewithoneringXchromosome;45,X/46, XY = a mosaic of two cell types, one with 45 chro- mosomes and a single X, one with 46 chromosomes and XY sex chromosomes. See human mitotic chro- mosomes. symmetrical replication bidirectional replication (q.v.). sympatric speciation in multicellular eukaryotes, an uncommon process where populations inhabiting (at least in part) the same geographic range become reproductively isolated.

However, sympatric bacte- rial speciation, defined as the origin of new bacterial species that occupy definable ecological niches, is relatively common. It occurs as a result of incorpora- tion of horizontal mobile elements (q.v.) that carry adaptive genes. It has been estimated that E. coli has received 31 kb of DNA per million years from HMEs. See Appendix C, 1997, Lawrence and Och- man; introgressive hybridization. sympatric species species whose areas of distribu- tion coincide or overlap. sympatry living in the same geographic location. Compare with allopatry. sym-plasmid a plasmid found in the symbiotic bacteria that inhabit the root nodules of legumes. One such plasmid NRG234, has had its DNA ana- lysed. It is a 536,165 bp circle, containing 416 ORFs.

Among these are symbiotic determinants, which include nodulation and nitrogen fixation genes. symplesiomorphic character an ancestral or plesi- omorphic character shared by two or more different taxa. See cladogram. synapomorphic character a derived or apomor- phic (q.v.) character shared by two or more different taxa. See cladogram. synapsis the pairing of homologous chromosomes during the zygotene state of meiosis that results from the construction of a synaptonemal complex (q.v.). See Appendix C, 1901, Montgomery. synapsis-dependent allelic complementation See transvection. synaptonemal complex a tripartite ribbon con- sisting of parallel, dense, lateral elements surround- ing a medial complex. See illustration. The lateral elements lie in the central axes of the paired homol- ogous chromosomes of a pachytene bivalent. The medial complex contains a system of interdigitating protein filaments that are oriented perpendicularly to the lateral elements and serve to maintain their parallel configuration during meiotic synapsis. See Appendix C, 1956, Moses and Fawcett; Gowen crossover suppressor, meiosis.

Synaptonemal complex
A drawing of a segment of a bivalent as seen under the electron microscope. (c) chromatin; (cs) central space; (le) lateral element; (sc) synaptonemal com- plex; (tr) transverse rods of the medial complex. syncaryon synkaryon (q.v.). syncytial blastoderm the stage during insect em- bryogenesis in which the cleavage nuclei lie at the surface of the egg in a common cytoplasm. Subse- quently the cellularization of the blastoderm occurs. In Drosophila there are 13 rapid synchronous divi- sions resulting in about 8,000 nuclei which migrate to the cortical ooplasm and then cellularize. The transition from the syncytial blastoderm to the cellu- lar blastoderm corresponds to the time the control of embryogenesis by maternal genes switches to con- trol by the zygotic genome.

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