Citric acid cycle
citric acid cycle a cycle of enzyme-controlled re-actions by which the acetyl-coenzyme A produced by the catabolism of fats, proteins, and carbohy- drates is oxidized, and the energy released used to form ATP from ADP. The condensation of acetyl-coenzyme A with a four-carbon compound (oxalo-acetic acid) yields the six-carbon compound citric acid for which the cycle is named. Through a further series of oxidative decarboxylations, citric acid is broken down to oxaloacetic acid, and so the cycle is completed. As a result, 1 molecule of activated ace- tate is converted to 2 CO2 molecules, 8 H atoms are of ATP are formed concurrently. The enzymes are taken up and oxidized to water, and 12 molecules
localized in mitochondria (q.v.). The cycle was in- vented by prokaryotes about 2.5 billion years ago, and today virtually all organisms that use oxygen employ the citric acid cycle. The cycle is illustrated in the diagram on page 85.
The sulfur atom in coen- zyme A (q.v.) is the site where chemical groups are exchanged at various stages in the cycle. This is the reason for adding an S to the CoA-SH abbreviation. See Appendix C, 1937, Krebs; adenosine phosphate, ATP synthase, cytochrome system, glycolysis, glyoxy- late cycle, nicotine-adenine dinucleotide (NAD). citrullinuria a hereditary disease in humans arising from a deficiency of the enzyme arginosuccinate synthetase. It is caused by a recessive gene on auto- some 9. See ornithine cycle. Citrus a genus of fruit-bearing trees including C. aurantium, the Seville orange; C.
aurantifolia, the lime; C. paradisi, the grapefruit; C. limon, the lemon; C. reticulata, the tangerine; C. sinensis, the sweet or- ange. The navel orange is a cultivar (q.v.) of the last- named species. See Appendix A, Plantae, Angio- spermae, Dicotyledoneae, Sapindales. clade 1. in classification, any group of organisms that is defined by characters exclusive to all its mem- bers and that distinguish the group from all others. 2. in evolutionary studies, a taxon or other group consisting of a single species and its descendents; a holophyletic group; a set of species representing a distinct branch on a phylogenetic tree.
Graphically a clade includes the species represented by the node and all branches that spring from it. See cladogram, PhyloCode. cladistic evolution splitting of a line of descent into two species. Contrast with phyletic evolution. cladistics a method of classification that attempts to uncover the genealogic relationships between any two species by stressing only the advanced charac- teristics that they share. The graphic representation of the results of such an analysis is the cladogram (q.v.).
See Appendix C, 1950, Hennig; apomorphic. cladogenesis branching evolution; the splitting of a lineage into two or more lineages. Contrast with orthogenesis. cladogram a branching diagram that displays the relationship between taxa in terms of their shared character states and attempts to represent the true evolutionary branchings of the lineage during its evolution from the ancestral taxon. In the accompa- nying cladogram, we start with ancestral species A, which is now extinct. It is characterized by six phe- notypic characters (a-f) of taxonomic importance.
The lineage undergoes speciation events (denoted by numbers 1 to 4) to produce five extant species, B-F. Each character (except f) undergoes a single change from the ancestral (plesiomorphic) state to a derived (apomorphic) state. The time and place of the change in the lineage is marked by letters carrying primes.
Note that species E and F, which have the most recent common ancestor, share more apomor- phic characters than species with more remote com- mon ancestors. An ancestral character shared by sev- eral species is called symplesiomorphic, and a derived character shared by two or more species is called synapomorphic. Thus, character f is symple- siomorphic for the entire group, and character c is synapomorphic for species E and F. See node.
class a grouping used in the classification of organ- isms. It is a subdivision of a phylum, and it is in turn subdivided into orders. classification 1. the process of grouping organisms on the basis of features they have in common, or on the basis of their ancestry, or both. 2. the resulting arrangement of living things into groups as a conse- quence of the above process. The traditional division of living organisms into two kingdoms (Plant and Animal) dates back to Linnaeus.
This was sup- planted by a system of five kingdoms (Bacteria, Pro- tists, Fungi, Plants, and Animals) proposed by Whit- taker. An updated variant of this system is used in Appendix A. More recently, a seven-kingdom system has been proposed by T.
Cavalier-Smith. This sys- tem retains four of the five kingdoms but splits the protists into three separate kingdoms: Archaeozoa, Protozoa, and Chromista (all of which see). class switching See heavy chain class switching. clathrin See receptor-mediated endocytosis. ClB technique a technique invented by H. J. Mul- ler and used for the detection of sex-linked lethal and viable mutations in Drosophila melanogaster. The name is derived from the X chromosome used.
It contains a Crossover suppressor (an inversion), a lethal, and the dominant marker Bar eye. cleavage the processes by which a dividing egg cell gives rise to all the cells of the organism. Such cleavages involve rapid cell divisions without inter- vening periods of cell growth. Therefore the embryo remains the same size, but the component cells get smaller and smaller. Cleavage in some species fol- lows a definite pattern, where it is said to be deter- minate (permitting the tracing of cell lineages); in other species the pattern is lost after the first few cell divisions.
See contractile ring, discoidal cleavage, radial cleavage, spiral cleavage. cleavage furrow See contractile ring. cleidoic egg an egg enclosed within a shell that is permeable only to gases. cleistogamous designating a plant in which fertil- ization occurs within closed flowers, and therefore where self-pollination is obligatory. See chasmoga- mous. cline a gradient of phenotypic and/or gene fre- quency change along a geographical transect of the population’s range.
See isophene. clock mutants mutants that disrupt the normal 24-hour circadian cycle of an organism. The gene pe- riod (q.v.) in Drosophila and frequency (q.v.) in Neu- rospora are the best-studied clock mutants. clomiphene any chemical that stimulates ovaries to release eggs. clonal analysis the use of mosaics generated by genetic methods or surgical operations to investigate cell-autonomous and cell-nonautonomous develop- mental processes. Cell-autonomous genetic markers are used to label cells at an early stage in develop- ment, and the subsequent morphological fates of the offspring of these cells can then be followed.
See compartmentalization. clonal selection theory a hypothesis for explain- ing the specific nature of the immune response in which the diversity among various cells for the rec- ognition of specific antigens exists prior to their ex- posure to the antigen. Subsequent exposure to a particular antigen causes the appropriate cells to un- dergo a clonal proliferation. See Appendix C, 1955, Jerne; 1959, Burnet; B lymphocyte. clone 1. a group of genetically identical cells or or- ganisms all descended from a single common ances- tral cell or organism by mitosis in eukaryotes or by binary fission in prokaryotes. 2. genetically engi- neered replicas of DNA sequences.
cloned DNA any DNA fragment that passively replicates in the host organism after it has been joined to a cloning vector. Also called passenger DNA. See recombinant DNA technology. cloned library a collection of cloned DNA se- quences representative of the genome of the organ- ism under study.
cloning in its most common usage, creating an or- ganism genetically identical to another organism. This occurs naturally in the production of monozy- gotic twins. The nine-banded armadillo regularly produces a clone of four genetically identical off- spring at each birth cycle. This type of cloning can also be done artifically by embryo splitting. For ex- ample, the eight-cell embryo of many animals can be divided in halves or quarters, and each of these portions can develop into identical twins or quadru- plets. Mitotically produced cells are (barring muta- tions) genetically identical, and thus all the somatic cells of an individual are technically a clone.
Like- wise, bacterial cells produced by binary fission from a single parent cell also form a clone (or produce a colony on solid medium). A single individual or cell may be referred to as a clone, but only with refer- ence to at least one other genetically identical indi- vidual or cell. Most plant cells are totipotent and usually are easier to clone than animal cells through asexual propagation (grafting, budding, cuttings, etc.).
In mammals, sheep, cows, goats, horses, mules, pigs, rabbits, rats, mice, cats, and dogs have been cloned experimentally. However, the rate of success in such experiments has been low. See Ap- pendix C, 1958, Steward, Mapes, and Mears; 1997, Wilmut et al.; Dasypus, Dolly, gene cloning, mosaic, nuclear reprogramming, nuclear transfer, sheep, ther- apeutic cloning, totipotency, twins. cloning vector, cloning vehicle See bacterial arti- ficial chromosomes, cosmid, DNA vector, lambda cloning vector, P1 artificial chromosomes, pBR322, plasmid cloning vector, yeast artificial chromosome.
clonogenicity the ability of cells from multicellu- lar organisms (e.g., malignant cells or stem cells) to proliferate and form colonies (or clones), each con- sisting of one or more cell types. A cell with this ability is called a clonogenic cell. clonotype the phenotype or homogenous product of a clone of cells. close pollination the pollination of a flower with pollen of another flower on the same plant. Clostridium botulinum an anaerobic, spore-form- ing, Gram-positive bacterium that is often present in
decaying food and can cause a severe type of food poisoning called botulism (q.v.). See Appendix A, Bacteria, Endospora. club wheat Triticum compactum (N = 21). See wheat. clutch a nest of eggs. cM centimorgan. See Morgan unit. C-meiosis colchicine-blocked meiosis. See meta- phase arrest. C-metaphase colchicine-blocked metaphase. See metaphase arrest. C-mitosis colchicine-blocked mitosis. See meta- phase arrest. c-myc See myc. Cnidosporidia See microsporidia.
CNS abbreviation for central nervous system (the brain and spinal cord). coadaptation the selection process that tends to accumulate harmoniously interacting genes in the gene pool of a population. coated pit, vesicle See receptor-mediated endocy- tosis.
coat protein the structural protein making up the external covering of a virus. cobalamin vitamin B12, a coenzyme for a variety of enzymes. It is essential for deoxyribose synthesis. The vitamin is characterized by a tetrapyrole ring system similar to that of heme (q.v.).
The molecule contains a central cobalt atom linked to four pyrrole nitrogens. The vitamin is unique in being synthe- sized only by microorganisms. See Appendix C, 1964, Hodgkin. cobalt a biological trace element. Atomic number 27; atomic weight 58.9332; valence 2, 3+; most abundant isotope Co59; radioisotope Co60, half-life 5.2 years, radiation emitted—beta and gamma rays (used extensively as a gamma-ray source).
coconversion the concurrent correction of two sites during gene conversion. cocoon 1. a covering of silky strands secreted by the larva of many insects in which it develops as a pupa. Commercial silk is derived from the cocoon of Bombyx. 2. a protective covering of mucus se- creted about the eggs of some species. code for the genetic code dictionary, see amino acid, start codon, stop codon. code degeneracy See degenerate code. coding strand See strand terminologies. coding triplet codon. See amino acid. CODIS the acronym for the Combined DNA In- dex System operated by the Federal Bureau of Inves- tigation.
This is a national DNA databank which uti- lizes computer and DNA technologies to match DNA profiles developed from crime scene evidence against the profiles of individuals convicted of felony sex offenses and other violent crimes. The profiles stored in CODIS are generated using STR analysis (q.v.). All 50 states have laws requiring that DNA profiles of violent criminals be sent to CODIS, where they are stored in its Convicted Offender Index.
codominant designating genes when both alleles of a pair are fully expressed in the heterozygote. For example, the human being of AB blood group is showing the phenotypic effect of both IA and IB co- dominant genes. See semidominance. codon (also coding triplet) the nucleotide triplet in messenger RNA that specifies the amino acid to be inserted in a specific position in the forming poly- peptide during translation.
A complementary codon resides in the structural gene specifying the mRNA in question. The codon designations are listed in the amino acid and genetic code entries. See start codon; synonymous codons, termination codon. codon bias the nonrandom use of synonymous co- dons. Such biases have been observed in genes from both prokaryotes and eukaryotes. For example, 90% of the leucines in the outer membrane protein of E.
coli are encoded by one of the six synonymous leu- cine codons. There seems to be a positive correlation between the relative frequencies of the synonymous codons in the genes of a given species and the rela- tive abundances of their cognate tRNAs. So codon usage may be determined by translational efficiency. See genetic code, transfer RNA.
coefficient of coincidence See coincidence. coefficient of consanguinity the probability that two homologous genes drawn at random, one from each of the two parents, will be identical and there- fore be homozygous in an offspring. The inbreeding coefficient of an individual is the same as the coeffi- cient of consanguinity of its parents. See Wright’s in- breeding coefficient. coefficient of inbreeding Wright’s inbreeding co- efficient.
coefficient of kinship coefficient of consanguinity (q.v.). coefficient of parentage coefficient of consan- guinity (q.v.). coefficient of relationship (r) the proportion of alleles in any two individuals that are replicas inher- ited from a common ancestor. coefficient of selection (s) See selection coeffi- cient. coelacanth See living fossil. coelenterate referring to a marine organism char- acterized by radial symmetry, a simple diploblastic body, a gastrovascular cavity, and usually showing metagenesis (q.v.).
See Appendix A, Animalia, Eu- metazoa, Radiata, Cnidaria. coelomate referring to animals having a coelom or body cavity formed in and surrounded by meso- derm. See Appendix A, Animalia, Eumatozoa, Bilat- eria, Protostomia, Coelomata. coenobium a colony of unicellular eukaryotes sur- rounded by a common membrane. coenzyme an organic molecule that must be loosely associated with a given enzyme in order for it to function. Generally, the coenzyme acts as a do- nor or acceptor of groups of atoms that have been added or removed from the substrate. Well-known coenzymes include NAD, NADP, ATP, FAD, FMN, and coenzyme A.
Some coenzymes are derivatives of vitamins. coenzyme A a coenzyme made up of adenosine di- phosphate, pantothenic acid, and mercaptoethylam- ine. The acetylated form of the coenzyme plays a central role in the citric acid cycle (q.v.). See formula illustrated on page 90. coenzyme Q a molecule (illustrated on page 90) that functions as a hydrogen acceptor and donor in the electron transport chain (q.v.). See cytochrome system (Q and QH2).