Glossary Excerpted with modification from the Glossary in Genes V by Benjamin Lewin published by Oxford University Press, 1994. This material is limited exculsively to enrolled students in BB4592/5592! Active site is the restricted part of a protein to which a substrate binds. Allele is one of several alternative forms of a gene occupying a given locus on a chromosome. Allosteric control refers to the ability of an interaction at one site of a protein to influence the activity of another site. Amber codon is the nucleotide triplet UAG, one of three codons that cause termination of protein synthesis. Amber mutation describes any change in DNA that creates an amber codon at a site previously occupied by a codon representing an amino acid in a protein. Amber suppressors are mutant genes that code for tRNAs whose anticodons have been altered so that they can respond to UAG codons as well as or instead of to their previous codons. Aminoacyl tRNA is transfer RNA carrying an amino acid; the covalent linkage is between the amino group of the amino acideither the 3'' or 2''OH group of the terminal base of the tRNA. Aminoacyl tRNA synthetases are enzymes responsible for covalently linking amino acids to the 2'' or 3''OH position of tRNA. Annealing is the pairing of complementary single strands of DNA to form a double helix. Antiparallel strands of the double helix are organized in opposite orientation, so that the 5'' end of one strand is aligned with the 3'' end of the other strand. Antitermination proteins allow RNA polymerase to transcribe through certain terminator sites. Apoinducer is a protein that binds to DNA to switch on transcription by RNA polymerase. Attenuation describes the regulation of termination of transcription that is involved in controlling the expression of some bacterial operons. Attenuator is the terminator sequence at which attenuation occurs. Autoradiography detects radioactively labeled molecules by their effect in creating an image on photographic film. Back mutation reverses the effect of a mutation that had inactivated a gene; thus it restores wildtype. Bacteriophages are viruses that infect bacteria; often abbreviated as phages. Base pair (bp) is a partnership of A with T or of C with G in a DNA double helix; other pairs can be formed in RNA under certain circumstances. Bidirectional replication is accomplished when two replication forks move away from the same origin in different directions. Blocked reading frame cannot be translated into protein because it is interrupted by termination codons. Blunt cuts in duplex DNA are made when two strands are cleaved opposite each other. Blunt-end ligation is a reaction that joins two DNA duplex molecules directly at their ends. bp is an abbreviation for base pairs; distance along DNA is measured in bp. Buoyant density measures the ability of a substance to float in some standard fluid, for example, CsCl. CAP (CRP) is a positive regulator protein activated by cyclic AMP. It is needed for RNA polymerase to initiate transcription of certain (catabolite-sensitive) operons of E. coli. Capsid is the external protein coat of a virus particle. Catabolite repression describes the decreased expression of many bacterial operons that results from addition of glucose. It is caused by a decrease in the level of cyclic AMP, which in turn is needed to activate the CAP (CRP) regulator. cis-acting locus affects the activity only of DNA sequences on its own molecule of DNA; this property usually implies that the locus does not code for protein. cis configuration describes two sites on the same molecule of DNA. cis/trans test assays the effect of relative configuration on expression of two mutations. In a double heterozygote, two mutations in the same gene show mutant phenotype in trans configuration, wildtype in cis configuration. Cistron is the genetic unit defined by the cis/trans test; equivalent to gene in comprising a unit of DNA representing a protein. Clone describes a large number of cells or molecules identical with a single ancestral cell or molecule. Closed reading frame contains termination codons that prevent its translation into protein. Coding strand of DNA has the same sequence as mRNA. Codominant alleles both contribute to the phenotype; neither is dominant over the other. Codon is a triplet of nucleotides that represents an amino acid or a termination signal. Cognate tRNAs are those recognized by a particular aminoacyl tRNA synthetase. Cold-sensitive mutant is defective at low temperature but functional at normal temperature. Complementation refers to the ability of independent (nonallelic) genes to provide diffusible products that produce normal (wildtype) phenotype when two mutants are tested in trans configuration in a heterozygote. In vitro complementation assay consists of identifying a component of a wildtype cell that can confer activity on an extract prepared from a mutant cell. The assay identifies the component rendered inactive by the mutation. Complementation group is a series of mutations unable to complement when tested in pairwise combinations in trans; defines a genetic unit (the cistron) that might better be called a noncomplementation group. Conditional lethal mutations kill a cell or virus under certain (nonpermissive) conditions, but allow it to survive under other (permissive) conditions. Conjugation describes ''mating'' between two bacterial cells, when (part of) the chromosome is transferred from one to the other. Consensus sequence is an idealized sequence in which each position represents the base (nucleotide) most often found when many actual sequences are compared. Constitutive genes are expressed as a function of the interaction of RNA polymerase with the promoter, without additional regulation; sometimes also called household genes in the context of describing functions expressed in all cells at a low level. Constitutive mutations cause genes that usually are regulated to be expressed without regulation. Coordinate regulation refers to the common control of a group of genes. Corepressor is a small molecule that triggers repression of transcription by binding to a regulator protein. Cyclic AMP (cAMP) is a molecule of AMP in which the phosphate group is joined to both the 3''5'' positions of the ribose; its binding activates the CAP (CRP), a positive regulator of prokaryotic transcription. Degeneracy in the genetic code refers to the lack of an effect of many changes in the third base of the codon on the amino acid that is represented; that is, many different codons specify the same amino acid. Deletions are generated by removal of a sequence of DNA, the regions on either side being joined together. Denaturation of DNA or RNA describes its conversion from the double-stranded to the single-stranded state; separation of the strands is most often accomplished by heating . Derepressed state describes a gene that is turned on. It is synonymous with induced when describing the normal state of a gene; it has the same meaning as constitutive in describing the effect of mutation. Discontinuous replication refers to the synthesis of DNA in short (Okazaki) fragments that are later joined into a continuous strand. Divergence is the percent difference in nucleotide sequence between two related DNA sequences or in amino acid sequences between two proteins. Divergent transcription refers to the initiation of transcription at two promoters facing in the opposite direction, so that transcription proceeds away in both directions from a central region. dna mutants of bacteria are temperaturesensitive; they cannot synthesize DNA at 42 degrees C, but can do so at 37 degrees C. DNAase is an enzyme that breaks bonds in DNA. DNA polymerase is an enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). May be involved in repair or replication. DNA replicase is a DNA synthesizing enzyme required specifically for replication. Dominant allele determines the phenotype displayed in a heterozygote with another (recessive) allele. Down promoter mutations decrease the frequency of initiation of transcription. Downstream identifies sequences proceeding farther in the direction of expression, for example, the coding region is downstream of the initiation codon. Elongation factors (EF in prokaryotes) are proteins that associate with ribosomes cyclically, during addition of each amino acid to the growing polypeptide chain. End product inhibition describes the ability of a product of a metabolic pathway to inhibit the activity of an enzyme that catalyzes an early step in the pathway. Endonucleases cleave bonds within a nucleic acid chain; they may be specific for RNA or for single-stranded or double-stranded DNA. Essential gene is one whose deletion is lethal to the organism (see also lethal locus). Exonucleases cleave nucleotides one at a time from the end of a polynucleotide chain; they may be specific for either the 5'' or 3'' end of DNA or RNA. F factor is a bacterial sex or fertility plasmid. Footprinting is a technique for identifying the site on DNA bound by some protein by virtue of the protection of bonds in this region against attack by nucleases. Forward mutations inactivate a wildtype gene. Frameshift mutations arise by deletions or insertions that are not a multiple of 3 bp; they change the frame in which triplets are translated into protein. Gene (cistron) is the segment of DNA involved in producing a polypeptide chain; it includes regions precedingfollowing the coding region (leadertrailer). Gene family consists of a set of related genes; the members were derived by duplicationvariation from some ancestral gene. Gene cluster is a group of adjacent genes that are identical or related. Genetic code is the correspondence between triplets in DNA (or RNA)amino acids in protein. Gyrase is a type II topoisomerase of E. coli with the ability to introduce negative supercoils into DNA. Housekeeping (constitutive) genes are those (theoretically) expressed in all cells because they provide basic functions needed for sustenance of all cell types.