GLOSSARY Abundance of an mRNA is the average number of molecules per cell. Abundant mRNAs consist of a small number of individual species, each present in a large number of copies per cell. Acceptor splicing site—see right splicing junction. Acentric fragment of a chromosome (generated by breakage) lacks a centromere and is lost cell division. Acrocentric chromosome has the centromere located nearer one end than the other. 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. Allelic exclusion describes the expression in any particular lymphocyte of only one allele coding for the expressed immunoglobulin. Allosteric control refers to the ability of an interaction at one site of a protein to influence the activity of another site. Alu family is a set of dispersed, related sequences, each~300 bp long, in the human genome. The individual members have Alu cleavage sites at each end (hence the name). Alu-equivalent family is the set of sequences in a mammalian genome that is related to the human Alu family. α-Amanitin is a bicyclic octapeptide derived from the poisonous mushroom Amanita phalloides; it inhibhits transcription by certain eukaryotic RNA polymerases, especially RNA polymerase II. Amber codon is the nucleotide triplet UAG, one of three codons that cause termination of protein synthesis. Amber mutaion 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 NH2 group of the amino acid and either 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. Amphipathic structures have two surfaces, one hydrophilic and one hydrophobic. Lipids are amphipathic; and some protein regions may form amphipathic; and some protein regions may form amphipathic helices, with one charged face and one neutral face. Amplification refers to the production of additional copies of a chromosomal sequence, found as intrachromosomal or extrachromoxomal DNA. Anchorage dependence describes the need of normal eukaryotic cells for a surface to attach to in order to grow in culture. Aneuploid chromosome constitution differes from the usal diploid constitution by loss or duplication of chromosomes or chromosomal segments. Annealing is the pairing of complementary single strands of DNA to form a double helix. Antibody is a protein (immunoglobulin) produced by B lymphocyte cells that recognizes a particular foreign ‘antigen,’and thusw triggers the immune response. Anticoding strand of duples DNA is used as a template to direct the synthesis of RNA that is complementary to it. Antigen is any molecule whose entry into an organism provokes synthesis of an antibody (immunoglobulin). Antiparallel strands of the double helix are organized in opposite orientation, so that the 5’ end of one strand is aligened with the 3’ end of the other strand. Antitermination proteins allow RNA polymerase to transcribe through certain terminator sites. Ap endonucleases make incisions in DNA on the 5’ side of either apurinic or apyrimidinc sites. Apoinducer is a protein that binds to DNA to switch on transcription by RNA polymerase. Archebacteria comprise a minor line of prokaryotes, and may have introns in the genome. Ascus of a fungus contains a tetrad or octad of the (haploid) spores, representhing the products of a sihngle meiosis. att sties are the loci on a phage and the bacterial chromosome at which recombination integrates the phage into. or excises it from , the bacterial chromosome. 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 attenuatioj occurs. Autogenous conhtrol describes the action of a gene product that either inhibits (negative autogenous control) or activates (positive autogenous control) expression of the gene coding for it. Autonomous controlling element in maize is an active transposon with the ability to transpose (cf nonautonomous controlling element). Autoradiography detects radioactively labeled molecules by their effect in creating an image on pholtographic film. Autosomes are all the chromosomes except the sex chromosomes; a diploid cell has two copies of each autosome. Blymphocytes (or B cells) are the cells responsible for synthesizing antibodies. Backcross is another (earlier) term for a testcross. Back mutation reverses the effect of a mutation that hand inactivated a gene; thus it restores wild type. Bacteriophages are viruses that infect bacteria; often abbreviated as phages. Balbaini ring is an extremely large puff at a band of a polytene chromosome. Bands of polytene chromosomes are visible as dense regions that contain the majority of DNA; bands of normal chromosomes are relatively much larger and are generated in the form of regions that retain a stain on certain chemical treatments. 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. Bivalent is the structure containing all four chromatids (two representing each homologue) at the start of meiosis. Blastoderm is a stage of insect embryogenesis in which a layer of nuclei or cells around the embryo surround an internal mass of yolk. Blocked reading frame cannot be translated into protein because it is interrupted by termination codons. 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. Branch migration describes the ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous. Breackage and reunion describes the mode of genetic recombination, in which two DNA duplex molecules are broken at corresponding points and then rejoined crosswise (involving formation of a length of heteroduplex DNA around the site of joining). Buoyant desity measures the ability of a substance to float in some standard fluid, for example, CsCl. C banding is a technique for generating stained regions around centromeres. C genes code for the constant regions of immunoglobulin protein chains. C value is the total amount of DNA in a haploid genome. CAAT box is part of a conserved sequence located upstream of the startpoints of eukaryotic transcription units; it is recognized by a large group of transcription factors. Cap is the structure at the 5’ end of eukaryotic mRNA, introduced after transcripton by linking the terminal phosphate of 5’ GTP to the terminal base of the mRNA. The added G (and sometimes some other bases) are methylated, giving a structure of the form 7MeG5’ppp 5’Np… CAP(CRP) is a positive regulator protein activated by cyclic AMP. It is needed for RNA polymerase to initiate transcription of certain (catabolitesensitive) 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 inactivates the CAP regulator. cDNA is a single-stranded DNA complementary to an RNA, synthesized from it by reverse transcription in vitro. cDNA clone is a duplex DNA sequence representing an RNA, carried in a cloning vector. Cell cycle is the period from one division to the next. Cell hybrid is a somatic cell containing chromosomes derived from parental cells of different species (e.g. a man-mouse somatic cell hybrid), generating by fusing the cells to form a heterokaryon in which the nuclei subsequently fused. Centrioles are small hollow cylinders consisting of microtubules that become located near the poles during mitosis. They reside within the centrosomes. Centromere is a constricted region of a chromosome that includes the site of attachment to the mitotic or meiotic spindle (see also kinetochore). Centrosomes are the regions from which microtubules are organized at the poles of a mitotic cell. In animal cells, each centrosome contains a pair of centrioles surrounded by a dense amorphous region to which the microtubules attach. See also MTOC. Molecular chaperone is a protein that is needed for the assembly or proper folding of some other protein, but which is not itself a component of the target complex. Chemical complexity is the amount of a DNA component measured by chemical assay. Chi sequence is an octamer that provides a hotspot for RecA-mediated genetic recombination in E. coli. Chi structure is a joint between two duplex molecules of DNA revealed by cleaving an intermediate of two joined circles to generate linear ends in each circle. It resembles a Greek chi in outline, hence the name. Chiasma (pl. chiasmata) is a site at which two homologous chromosomes appear to have exchanged material during meiosis. Chromatids are the copies of a chromosome produced by replication. The name is usually used to describe them in the period before they separate at the subsequent cell division. Chromatin is the complex of DNA and protein in the nucleus of the interphase cell. Individual chromosomes cannot be distinguished in it .It was originally recognized by its reaction with stains specific for DNA. Chromocenter is an aggregate of heterochromatin from different chromosomes. Chromomeres are densely staining granules visible in chromosomes under certain conditions, especially early in meiosis, when a chromosome may appear to consist of a series of chromomeres. Chromosome is a discrete unit of the genome carrying many genes. Each chromosome counsists of a very long molecule of duplex DNA and an approximately equal mass of proteins. It is visible as a morphological entity only during cell division. Chromosome walking describes the sequential isolation of clones carrying overlapping sequences of DNA, allowing large regions of the chromosome to be spanned. Walking is often performed in order to reach a particular locus of interest. 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-acting protein has the exceptional property of acting only on the molecule of DNA from which it was expressed. 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, wild-type in cis configuration. Cistron is the geneti unit defined by the cis/trans test; equivalent to gene ib comprising a unit of DNA representing a protein. Class switching is a change in the expression of the c cregion of an immunoglobulin heavy chain during lymphocyte differentiation. Clone describes a large number of cells or molecules identical with a single ancestral cell or molecule. Cloning vector is a plasmid or phage that is used to ‘carry’ inserted foreign DNA for the purposes of producing more material or a protein product. Closed reading frame contains termination codons that prevent its translation into protein. Coated vesicles are vesicles whose membrane has on its surface a layer of the protein clathrin. Coconversion is the simultaneous correction of two sites during gene conversion. Coding strand of DNA has the same sequence as mRNA. Codominant alleles both contribute to the phenotype; neither is dominant over the other. Coevolution —see concerted evolution. Cognate tRNAs are those recognized by a particular aminoacy-tRNA synthetase. Coointegrate structure is produced by fusion of two replicons, one originally possessing a transposon, the other lacking it; the cointegrate has copies of the transposon present at both junctions of the replicons, oriented as directrepeats. Cold-sensitive mutant is defective at low temperature but functional at normal temlperature. Colony hybridization is a technique for using in situ hybridization to identify bacteria carrying chimeric vectors whose inserted DNA is homologous with some particular sequence. Compatibility group of plasmids contains members unable to coexist in the same bacterial cell. Complementation refers to the ability of independent (nonallelic)genes to provide diffusible products that produce wild phenotype when two mutants are tested in trans configuration in a heterozygote. In vitro complementation assay consists of identifying a component of a wid-type 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 noncomplex mentation group. Complex locus (of D. melanogaster) has genetic properties inconsistent with the function of a gene representing a single protein. Complex loci are usually very large (>100kb) at the molecular level. Complexity is the total length of different sequences of DNA present in a given preparation. Compostie transposons have a central region flanked on each side by insertion sequences, either or both of which may enable the entire element to transpose. Concatemer of DNA consists of a series of unit genomes repeated in tandem. Concatenated circles of DNA are interlocked like rings one a chain. Concerted evolution describes the ability of two related genes to evolve together as though constituting a single locus. Condensation reaction is one in which a covalent bond is formed with loss of a water molecule, as in the addition of an amino acid to a polypeptide chain. Conditional lethal mlutations kill a cell or virus under certain (nonpermissive) conditions, but allow it to survive under other (permissive) conditions. Conjugation describes ‘mathing’ 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 most often found when many actual sequences are compared. Conservative recombination involves breakage and reunion of preexisting strands of DNA without any synthesis of new stretches of DNA. Conservative transposition refers to the movement of large elements, originally classified as transposons, but now considered to be episomes. The mechanism of movement resembles that of phage lambda. Constant regions of immunoglobulins are coded by C genes and are the parts of the chain that vary least. Those of heavy chains identify the type of immunoglobulin. 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 heterochromatin describes the inert state of permanently nonexpressed sequences, usually satellite DNA. Constitutive mutations cause genes that usually are regulated to be expressed without regulation. Contractile ring is a ring of actin filaments that forms around the equator at the end of mitosis and is responsible for pinching the daughter cells apart. Controlling elements of maize are transposable units originally identified solely by their genetic properties. They may be autonomous (able to transpose independently) or nonautonomous (able to element). Coordinate regulation refers to the common control of a group of genes. Cordycepin is 3’ deoxyadenosine, an inhibitor of polyadenylation of RNA. Core DNA is the 14.6 bp of DNA contained on a core particle. Core particle is a digestion product of the nucleosome that retains the histone octamer and has 14.6 bp of DNA; its structure appears similar to that of the nucleosome itself. Corepressor is a small molecule that triggers repression of transcription by binding to a regulator protein. Cosmids are plasmids into which phage lambda cos sites have been inserted; as a result, the plasmid DNA can be packaged in vitro in the phage coat. Cot is the product of DNA concentration and time of incubation in a reassociation reaction. Cot is the Cot required to proceed to half completion of the reaction; it is directly proportional to the unique length of reassociating DNA. Cotransfection is the simultaneous transfection of two markers. Crossing-over describes the reciprocal exchange of material between chromosomes that occurs during meiosis and is responsible for genetic recombination. Crossover fixation refers to a possible consequence of unequal crossing-over that allows a mutation in one member of a tandem cluster to spread through the whole cluster (or to be eliminated). Cruciform is the structure produced at inverted repeats of DNA if the repeated sequence pairs with its complement on the same strand (instead of with its regular partner in the other strand of the duplex). Cryptic satellite is a satellite DNA sequence not identified as such by a separate peak on a density gradient; that is, it remains present in main-band DNA. ctDNA is chloroplast DNA. Cyclic AMP (cAMP) is a molecule of AMP in which the phosphate group is joined to both the 3’ and 5’ positions of the ribose; its binding activates the CAP, a postive regulator of prokaryotic transcription. Cyclins are proteins that accumulate continuously throughout the cell cycle and are then destroyed by proteolysis during mitosis. (see also MPF). Cytokinesis is the final process involved in separation and movement apart of daughter cells at the end of mitosis. Cytological hybridization—see in situ hybridization. Cytoplasm describes the material between the plasma membrane and the nucleus. Cytoplasmic inheritance is a property of genes located in mitochondria or chloroplasts (or possibly other extranuclear organelles). Cytoplasmic protein synthesis is the ranslation of mRNAs representing nuclear genes; it occurs via ribosomes attached to the cytoskeleton. Cytoskeleton consists of networks of fibers in the cytoplasm of the eukaryotic cell. Cytosol describes the general volume of cytoplasm in which organelles ( such as the mitochondria ) are located. D loop is a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the orignal partner DNA strand in this region. The same term is used also to describe the displacement of a region of one strand of duplex DNA byu a single-stranded invader in the reaction catalyzed by RecA protein. 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. 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 singlestranded state; separation of the strands is most often accomplished by heating. Denaturation of protein describes its conversion from the physiological conformation to some other (inactive) conformation. 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. Dicentric chromosome is the product of fusing two chromosome fragments, each of which has a centromere. It is unstable and may be broken when the two centromeres are pulled to opposite poles in mitosis. Diploid set of chromosomes contains two copies of each autosome and two sex chromosome. Direct repeats are identical (or related) sequences present in two or more copies in the same orientation in the same molecule of DNA; they aer not necessarily adjacent. Discontinuous replication refers to the synthesis of DNA in short (Okazaki) fragments that are later joined into a continuous strand. Disjunction describes the movement of members of a chromosome pair to opposite poles during cell division. At mitosis and the second meiotic division, disjunction applies to sister chromatids; at first meiotic division it applies to sister chromatid pairs. 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 intitiation 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 temperature-sensitive; they cannot synthesize DNA at 42℃, but can do so at 37℃. DNAase is an enzyme that attacks bonds in DNA. DNA-driven bybridization involves the reaction of an excess of DNA with RNA. 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. Domain of a chromosome may refer either to a discrete structural entity defined as a region within which supercoiling is independent of other domains; or to an extensive region including an expressed gene that has heightened sensitivity to degradation by the enzyme DNAase I. Domain of a protein is a discrete continuous part of the amino acid sequence that can be equated with a particular function. Dominant allele determines the phenotype displayed in a heterozygote with another (recessive) allele. Donor splicing site—see left splicing junction. Down promoter mutations decrease the frequency of initiaton of transcription. Downstream identifies sequences proceeding farther in the direction of expression, for example, the conding region is downstream of the initiation condon. Early development refers to the period of a phage infection before the start of DNA replication. Extopic expression describes the expression of a gene in a tissue in which it is not usually expressed; for example, in a transgenic animal. Elongation factors (EF in prokaryotes, eEF in eukaryotes) are proteins that associate with ribosomes cyclically, during addition of each amino acid to the polypeptide chain. End labeling describes the addition of a radioactively labeled group to one end (5’ or 3’) of a DNA strand. 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. Endocytosis is a process by which proteins at the surface of the cell are internalized, being transported into the cell within membranous vesicles. Endocytic vesicles are membranous particles that transport proteins through endocytosis; also known as clathrin-coated vesicles. Endonucleases cleave bonds within a nucleic acid chain; they may be specific for RNA or for singlestranded of double-stranded DNA. Endoplasmic reticulum is a highly convoluted sheet of membranes, extending from the outer layer of the nuclear envelope into the cytoplasm. Enhancer element is a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. Envelopes surround some organelles (for example , nucleus or mitochondrion) and consist of concentric membranes, each membrane consisting of the usual lipid bilayer. Epigenetic changes influrence the phenotype without altering the genotype. They consist of changes in the properties of a cell that are inherited but that do not represent a change in genetic information. Episome is a plasmid able to integrate into bacterial DNA. Epistasis describes a situation in which expression of one gene wipes out the phenotypic effects of another gene. Essential gene is one whose deletions is lethal to the organism (see also lethal locus). Established cell lines consist of eukaryotic cells that have been adapted to indefinite growth in culture (they are said to be immortalized). Eubacteria comprise the major line of prokaryotes. Euchromatin comprises all of the genome in the interphase nucleus except for the heterochromatin. Evolutionary clock is defined by the rate at which mutations accumulate in a given gene. Excision-repair systems remove a single-stranded sequence of DNA containing damaged or mispaired bases and replace it in the duplex by synthesizing a sequence complementary to the remaining strand. Exocytosis is the process of secreting proteins from a cell into the medium, by transport in membranous vesicles from the endoplasmic reticulum, through the Golgi, to storage vesicles, and finally (upon a regulatory signal) through the plasma membrane. Exocytic vesicles (also secretory vesicles) are membranous particles that transport and store proteins during excytosis. Exon is any segment of an interrupted gene that is represented in the mature RNA product. 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. Expression vector is a cloning vector desined so that a coding sequence inserted at a particular site will be transcribed and translated into protein. Extranuclear genes reside outside the nucleus in organelles such as mitochondria and chloroplasts. F factor is a bacterial sex or fertility plasmid. F1 generation is the first generation produced by crossing two parental (homozygous) lines. Facultative heterochromatin describes the inert state of sequences that also exist in active copies—for example, one mammalian X chromosome in females. Fast component of a reassociation reaction is the first to reature and contains highly repetitive DNA. Fate map is a map of an embryo showing the adult tissues that will develop from the descendants of cells that occupy particular regions of the embryo. Figure eight describes two circles of DNA linked together by a recombination event that has not yet been completed. Filter hybridization is performed by incubating a deatured DNA preparation immobilized on a nitrocellulose filter with a solution of radioactively labeled RNA or DNA. Fingerprint of DNA is a pattern of polymorphic restriction fragments that differ between individual genomes. Fingerprint of a protein is the pattern of fragments (usually resolved on a two dimensional electrophoretic gel) generated by cleavage with an enzyme such as trypsin. Fluidity is a property of membranes; it indicates the ability of lipids to move laterally within their particular monolayer. Focus formation describes the ability of transformed eukaryotic cells to grow in dense clusters, piled up on one another. Focus forming unit (ffu) is a quantitative measure of forcus formation. Foldback DNA consists of inverted repeats that have renatured by intrastrand reassociation of denatured DNA. Foot printing 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 inatctivate a wild-type gene. Founder effect refers to the presence in a population of many individuals all with the same chromosome (or region of a chromosome) derived from a single ancestor. Frameshift mutations arise by deletions or insertions that are not a multiple of 3bp; they change the frame in which triplets are translated into protein. G banding is a technique that generates a striated pattern in metaphase chromosomes that distinguishes the members of a haploid set. G1 is the period of the eukaryotic cell cycle between the last mitosis and the start of DNA replication. G2 is the period of the eukaryotic cell cycle between the end of DNA replication and the start of the next mitosis. Gamete is either type of reproductive (germ) cell—sperm or egg—with haploid chromosome content. Gap in DNA is the absence of one or more nucleotides in one strand of the duplex. Gap (cistron) is the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). Gene conversion is the alteration of one strand of a heteroduplex DNA to make it complementary with the other strand at any position(s) where there were mispaired bases. Gene dosage gives the number of copies of a particular gene in the genome. Gene family consists of a set of genes whose exons are related; the members were derived by duplication and variation 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) and amino acids in protein. Genetic marker—see marker. Genomic (chromosomal) DNA clones are sequences of the genome carried by a cloning vector. Genotype is the genetic constitution of an organism. Golgi apparatus consists of indivivual stacks of membranes near the endoplasmic reticulum; involed in glycosylating proteins and sorting them for transport to different cellular locations. G proteins are guanine nucleotide-binding trimeric proteins that reside in the plasma membrane. When bound by GDP the trimer remains intact and is inert. When the GDP bound to the αsubunit is replaced by GTP, the αsubunit is released from the βγ dimmer. One of the separated units (either the α monomer or the βγ dimmer) then activates or represses a target protein. Gratuitous inducers resemble authentic inducers of transcription but are not substrates for the induced enzymes. GT-AG rule describes the presence of these constant dinucleotides at the first two and last two positions of introns of nuclear genes. Gyrase is a type II topoisomerase of E. coli with the ability to introduce negative supercoils into DNA. Hairpin describes a double-helical region formed by base pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA. Haploid set of chromosomes contains one copy of each autosome and one sex chromosome; the haploid number n is characteristic of gametes of diploid organisms. Haplotype is the particular combination of alleles in a defined region of some chromosome, in effect the genotype in miniature. Originally used to describe combinations of MHC alleles, it now may be used to describe particular combinations of RFLPs. Hapten is a small molecule that acts as an antigen when conjugated to a protein. Helper virus provides functions absent from a defective virus, enabling the latter to complete the infective cycle during a mixed infection. Hemizygote is a diploid individual that has lost its copy of a particular gene (for example, because a chromosome has been lost) and which therefore has only a single copy. Heterochromatin describes regions of the genome that are permanently in a highly condensed condition and are not genetically expressed. May be constitutive or facultative. Heterorduplex (hybrid) DNA is generated by hase pairing between complementary single strands derived from the different parental duplex molecules; it occurs during genetic recombination. Helerogametic sex has the diploid chromosome constitution 2A+XY. Heterogeneous nuclear (hn) RNA comprises transcripts of nuclear genes made by RNA polymerase II; it has a wide size distribution and low stability. Heteromultimeric proteins consist of nonidentical subunits (coded by different genes). Heterokaryon is a cell containing two (or more nuclei in a common cytoplasm, generate by fusing somatic cells. Heterzygote is an idividual with different alleles at some particular locus. Highly repetivive DNA is the first component to reassociate and is equated with satellite DNA. Histones are conserved DNA-binding proteins of eukaryotes that form the nucleosome, the basic subunit of chromatin. Homeobox describes the conserved sequence that is part of the coding region of D. melanogaster homeotic genes; it is also found in amphibian and mammalian genes exopressed in early embryonic development. Homeotic genes are defined by mutations that convert on body part into another; for example, an insect leg may replace an antenna. Homogametic sex has the diploid chromosome constitution 2A+XX. Homologues are chromosomes carrying the same genetic loci; a diploid cell has two copies of each homologue, one derived from each parent. Homomultimeric rotein consists of identical subunits. Homozygote is an indivivdual with the same allele at corresponding loci on the homologus chromosomes. Hotspot is site at which the frequency of mutation (or recombination) is very much increased. Hox genes are clusters of mammalian genes containing homeoboxes; the individual members are related to the genes of the complex loci ANT-C and BX-C in D. melanogaster. Housekeeping (constitutive) genes are those (theoretically) expressed in all cells because they provide basic functions needed for sustenance of all cell types. Hybrid-arrested translation in a technique that identifies the cDNA corresponding to an mRNA by relying on the ability to base pair with the RNA in vitro to inhibit translation. Hybrid dysgenesis describes the inability of certain strains of D. melanogaster to interbreed, because the hybrids are sterile (although otherwise they may be phenotypically normal). Hybrid DNA-see heteroduplex DNA. Hybridization is the pairing of complementary RNA and DNA strands to give an RNA-DNA hybrid. Hybridoma is a cell line produced by fusing a myeloma with a lymphocyte; it continues indefinitely to express the immunoglobulins of both parents. Hydrolytic reaction is one in which a covalent bond is broken with the incorporation of a water molecule. Hydropathy plot is a measure of the hydrophobicity of a protein region and therefore the likelihood that it will reside in a membrane. Hydrophilic groups interact with water, so thath hydrophilic regions of protine or the faces of a lipid bilayer reside in an aqueous environment. Hydrophobic groups repel water, so that they interact with one another to generate a nonaqueous environment. Hyperchromicity is the increase in optical bensity that occurs when DNA is denatured. DNAase I hypersensitive site is a short region of chromatin detected by its extreme sensitivity to cheavage by DNAase I and other nucleases; probably comprises an area from which nucleosome are excluded. Hypervariable regions of an immunoglobulin are the parts of the variable region that show maximum alteration when different antibodies are compared. Ideogram is a diagrammatic representation of the G-banding pattern of a chromosome. Idling reaction is the production of pppGpp and ppGpp by ribosomes when an uncharged tRNA is present in the A site; triggers the stringent response. Immortalization describes the acquisition by a eukaryotic cell line of the ability to grow through an indefinite number of divisions in culture. Immunity in phages refers to the ability of a prophage to prevent another phage of the same type from infecting a cell. It results from the synthesis of phage repressor by the prophage genome. Immunity in plasmids describes the ability of a plasmid to prevent another of the same type from becoming established in a cell. It results usually from interference with the ability to replicate. Immunity in transposons refers to the ability of certain transposons to prevent others of the same type from transposing to the same DNA molecule. It results from a variety of mechanisms. Imprinting describes a change in a gene that occurs during passage through the sperm or egg with the resule that the paternal and maternal alleles have different properties in the very early embryo. May be caused by methylation of DNA. In situ hybridization is performed by deaturing the DNA of cells squashed on a microscope slide so that reaction is possible with an added single-stranded RNA or DNA; the added singlestranded RNA or DNA; the added preparatin is radioactively labeled and its hybridization is followed by autoradiography. Incopmpatibility is the inability of certain bacterial plasmids to coexitst in the same cell. It is a cause of plasmid immunity. Indircet end-labeling is a technique for examining the organization of DNA by making a cut at a specific site and isolating all fragments containing the sequence adjacent to one side of the cut; it reveals the distance from the cut to the next break(s) in DNA. Induced mutations result from the addition of a mutagen. Inducer is a small molecule that triggers gene transcription by binding to a regulator protein. Induction refers to the ability of bacteria (or yeast) to synthesize certain enzymes only when their substrates are present; applied to gene expression, refers to switching on transcription as a result of interaction of the inducer with the regulator protein. Induction of prophage describes its excision from the host genome and entry into the lytic (infective) cycle as a result of destuction of the lysogenic repressor. Initiation factors (IF in prokaryotes, eIF in eukaryotes) are proteins that associate with the small subunit of the ribosome specifically at the stage of initiation of protein synthesis. Insertion sequence (IS) is a small bacterial transposon that carries only the genes needed for its own transposition. Insertions are identified by the presence of an additional stretch of base pairs in DNA. Integralmembrane protein is a protein (noncovalently) inserted into a membrane; it retains its membranous association by means of a stretch of ~25 amino acids that are uncharged and/or hydrophobic. Integration of viral or another DNA sequence is its insertion into a host genome as a region covalently linkded on either side to the host sequences. Interallelic complementation describes the change in the properties of a heteromultimeric proteinbrought about by the interaction of subunits coded by two different mutant alleles; the mixed protein may be more or less active than the protein consisting of subunits only of one or the other type. Interbands are the relatively dispersed regions of polytene chromosomes that lie between the bands. Intercistronic region is the distance between the termination condon of one gene and the initiation codon of the next gene. Intermediate component(s) of a ressociation reaction are those reacting between the fast (satellite DNA) and slow (nonrepetitive DNA) components; contain moderately repetitive DNA. Interphase is the period between mitotic cell divisions; dvivded into G1, S and G2. Intervening sequence is an intron. Intron is a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons)on either side of it. Inversion is a chromosomal change in which a segment has been rotated by 180° relative to the regions on either side and reinserted. Inverted repeats comprise two copies of the same sequence of DNA repeated in opposite orientation on the same molecule. Adjacent inverted repeats constitute a palindrome. Inverted terminal repeats are the short related or identical sequences present in reverse orientation at the ends of some transposons. IS is an abbreviation for insertion sequence, a small bacterial transposon carrying only the genetic functions involved in transposition. Isoaccepting tRNAs represent the same amino acid. Isotype is a group of closely related immunoglobulin chains. Karyotype is the entire chromosomal complement of a cell or species (as visualized during mitosis). kb is an abbreviation for 1000 base pairs of DNA or 1000 bases of RNA. Kinase is an enzyme that phosphorylates (adds a phosphat group) to a substrate; the substrates for protein kinases are amino acids in other proteins, and they are divided into those specific for tyrosine and those specific for threonine/serine. Kinetic complexity is the complexity of a DNA component measured by the kinetics of DNA reassociation. Kinetochore is the structural feature of the chromosome to which microtubules of the mitotic spindle attach (see also centromere). Lagging strand of DNA must grow overall in the 3’-5’ direcion and is synthesized discontinuously in the form of short fragments (5’-3’) that are later connected covalently. Lampbrus chromosomes are the large meiotic chromosomes found in amphibian oocytes. Lariat is an intermediate in RNA splicing in which a circular structure with a tail is created by a 5’-2’ bond. Late period of phage development is the part of infection following the start of DNA replication. Leader is the nontranslated sequence at the 5’ end of mRNA that precedes the initiation codon. Leader sequence of a protein is a short N-terminal sequence responsible for passage into or through a membrane. Leading strand or DNA is synthesized continuously in the 5’-3’ direction. Leaky mutations allow some residual level of gene expression. Left splicing junction is the boundary between the right end of an exon and the left nd of an intron. Lethal locus is and gene in which a lethal mutation can be obtained (usually by deletion of the gene). Library is a set of cloned fragments together representing the entire genome. Ligation is the formation of a phosphodiester bond to link two adjacent bases separated by a nick in one strand of a double helix of DNA.( The term can also be applied to blunt-end ligation and to joining of RNA). LINES are long period interspersed sequences in mammalian genomes that are retroposons generated from RNA polymerase II transcripts. Linkage describes the tendency of genes to be inherited together as a result of their location on the same chromosome; measured by percent recombination between loci. Linkage group includes all loci that can be connected (directly or indirectly) by linkage relationships; equivalent to a chromosome. Linkage disequilibrium describes a situation in which some combinations of genetic markers occur more of less frequently in the population than would be expected from their distance apart. It implies that group of markers has been inherited coordinately. It can result from reduced recombination in the region or from a f0under effect, in which there has been insufficient time to reach equilibrium since one of the markers was introduced into the population. Linker DNA is all DNA contained on a nucleosome in excess of the 146bp core DNA. Linker fragment is short synthetic synthetic duplex oligonucleotide containing the target sit for some restriction enzyme; may be added to ends of a DNA fragment prepared by cleavage with some other enzyme during reconstructions of recombinant DNA. Linker scanner mutations are introduced by recombining two DNA molecules in vitro at a restriction fragment added to the end of each; the result is to insert the linker sequence at the site of recombination. Linking number is the number of times the two strands of a closed DNA duplex cross over each other. Linking number paradox describes the discrepancy between the existence of –2 supercoils in the path of DNA on the nucleosome compared with the measurement of –1 supercoil released when histones are removed. Lipids have polar heads, containing phosphate (phospholipid), sterol (such as cholesterol), or saccharide (glycolipid) connected to a hydrophobic tail consisting of fatty acid(s). Lipid bilayer is the form taken by concentration of lipids in which the hydrophobic fatty acids occupy the interior and the polar heads face the exterior. Liquid (solution) hybridization is a reaction between complementary nucleic acid strands performed in solution. Locus is the position on a chromosome at which the gene for a particular trait resides; locus may be occupied by any one of the alleles for the gene. LODscore is a measure of genetic linkage, defined as the log10 ratio of the probability that the data would have arisen of the loci are linked to the probability that the data could have arisen fom unlined loci. The conventional threshold for declaring linkage is a LOD score of 3.0, that is, a 1000∶1 ratio (which must be compared with the 50∶1 probability that any random pair of loci will be unlinked). Long-period interspersion is a pattern in the genome in which long stretches of moderately repetitive and which long stretches of moderately repetitive and nonrepetitive DNA alternate. Loop in a single-stranded region at the end of a hairpin in RNA (or single-stranded DNA); corresponds to the sequence between inverted repeats in duplex DNA. LTR is an abbreviation for long-terminal repeat, a sequence directly repeated at both ends of a retroviral DNA. Lumen described the interior of a compartment bounded by membranes, usually the endoplasic reticulum or the mitochondrion. Luxury genes are those coding for specialized functions synthesized (usually) in large amounts in functions synthesized (usually) in large amounts in particular cell types. Lysis describes the death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an infecting phage. Also applies to eukaryotic cells, for example, infected cells that are attacked by the immune system. Lysogen is a bacterium that possesses a repressed prophage as part of its genome. Lysogenic immunity is the ability of a prophage to prevent another phage genome of the same type from becoming established in the bacterium. Lysogenic repressor is the protein responsible for preventing a prophage form reenterin the lytic cycle. Lysogeny describes the ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome. Lysosomes are small bodies, enclosed by membranes, that contain hydrolytic enzymes. Lytic infection of bacteria by a phage ends in destruction of bacteria and release of progeny phage. Main band of genomic DNA consists of a broad peak on a density gradient, excluding any visible satellite DNAs that form separate bands. Major histocompatibility locus is a large chromosomal region containing a gaint cluster of genes that code for transplantation anticgenes and other proteins found on the surfaces of lymphocytes. Map distance is measured as cM (centiMorgans)= percent recombination (sometimes subject to adjustments). MAR (matrix attachment site; also known as SAR for scaffold attachment site) is a region of DNA that attaches to the nuclear matrix. Marker (DNA) is a fragment of known size used to calibrate an electrophoretic gel. Marker (genetic) is any allele of interest in an experiment. Maternal inheritance describes the preferential survival in the progeny of genetic markers provided by one parent. Meisosis occurs by two successive ,divisions (meiosis I and II) that reduce the starting number of (meiosis I and II) that reduce the strting number of 4n chromosomes to 1n in each of four product ells. products may mature to germ cell (sperm or eggs.) Melting of DNA means its denaturation. Melting temperature (Tm) is the midpoint of the temperature range over which DNA is denatured. Membranes consist of an asymmetrical lipid bilaryer that has lateral fluidity and contains proteins. Membrane proteins have hydrophobic regions that allow part or all of the protein structure to reside within the membrane; the bonds involved in this association are usually noncovalent. Metastasis describes the ability of tumor cells to leave their site of origin and migrate to other locations in the body, where a new colony is established. Micrococcal nuclease is an endonuclease that cleaves DNA; in chromatin, DNA is cleaved preferentially between nucleosomes. Microsomes are fragmented pieces of endoplasmic reticulum associated with ribosomes. Microtubules are filaments consisting of dimmers of tubulin; interphase microtubules are reorganized into spindle fibers at mitosis, when they are responsible for chromosome movement. Microtubule associated proteins (MAPs) are proteins associated with microtubules and responsible for influnencing ther stability and organization. Microtubule organizing center (MTOC) is a structure from which microtubules may be extended. Minicell is an anucleate bacterial (E. coli) cell produced by a division that generates cytoplasm without a nucleus. Minichromosome of SV40 or polyoma is the numcleosomal form of the viral circular DNA. Mitosis is the division of a eukaryotic somatic cell. Modification of DNA or RNA includes all changes made to the nucleotides after their initial incorporation into the polynucleotide chain. Modififed bases are all those except the usual four from which DNA (T, C, A, G) or RNA (U, C, A, G) are synthesized; they result from postsynthetic changes in the nucleic acid. Monocistronic mRNA condes for one protein. Monolayer describes the growth of eukaryotic cells in culture as a layer only one cell deep. Morphogen is a factor that induces development of particular cell types in a manner that depends on its concentration. MPF (maturaton-or M phase-promoting factor) is a dimeric kinase, containing the p34, catalytic subunit and a cyclin regulatory subunit, whose activation triggers the onset of mitosis. mtDNA is mitochondrial DNA. MTOC (microtubule organizing center) is a region from which microtubules emanate. The major MTOCs in a mitotic cell are the centrosomes. Nyktuciot okasnuds are present in bacteria at amounts greater than one per chromosome. Multiforked chromosome (in bacterium) has more than one replication fork, because a second initiation has occurred before the first cycle of replication has been completed. Multimeric proteins consist of more than one subunit. Mutagens increase the rate of mutation by inducing changes in DNA. Mutation describes any change in the sequence of genomic DNA. Mutation frequency is the frequency at which a particular mutant is found in the population. Mutation rate is the rate at which a particular mutation occurs, usually given as the nuber of events per gene per generation. Myeloma is a tumor cell line derived from a lymphocyte; usually produces a single type of immunoglobulin. Begative complementation occurs when interallelic complementation allow a mutant subuntit to suppress the activity of a wild-type subunit in a multimeric protein. Negative regulators function by switching of transcription or translation. Negative regulators function by switching off transcription or translation. Negative supercoiling comprises the twisting of a duplex of DNA in space in the opposite sense to the turns of the strands in the double helix. Neutral substitutions in a protein are those changes of amino acids that do not affect activity. Nick in duplex DNA is the absence of a phosphodiester bond between two adjacent nucleotides on one strand. Nick trandslation describes the ability of E. Coli DNA polymerase I to use a nick as a starting point from which one strand of a duplex DNA and be degraded and replaced by resynthesis of new material; is used to introduce radioactively labeled nucleotides into DNA in vitro. Nonautonomous controlling elements are defective transposons that can transpose only when assisted by an autonomous controlling element of the same type. Nondisjunction describes failure of chromatids (duplicate chromosomes) to move to opposite poles during mitosis or meiosis. Nonpermissive conditions do not allow conditional lethal muants to survive. Nonrepetitive DNA shows reassociation kinetics expected of unique sequences. Nornreplicative transposition describes the movement of a transposon that leave a donor site (usually generating a double strand break) and moves to a new site. Nosense codon is any one of three triplets (UAG, UAA, UGA) that cause termination of protein synthesis. (UAG is know as amber; UAA as ochre.) Nonsense mutation is any change in DNA that causes a (termination) codon to replace a codon representing an amino acid. Nonsense suppressor is a gene coding for a mutant tRNA able to respond to one of more of the termination codons. Nontranscribed spacer is the region between transcription units in a tandem gene cluster. Northern blotting is a technique for transferring RNA from an agarose gel to a nitrocellulose filter on which it can be hybridized to a complementary DNA. Nuclear envelope is a layer of two membranes surrounding the nucleus. It is penetrated by nuclear pores and bounded on the interior by the nuclear laminim. Nuclear lamina consists of a proteiaceous layer on the inside of the nuclear envelope. It consists of (upto) three lamin proteins. Nuclear matrix is a network of fibers surrounding and penetrating the nucleus. Nuclear pores represent holes in the nuclear envelope and are presumed to be used for transport of macromolecules. Nucleolar organizer is the region of a chromosome carrying genes coding for rRNA. Nucleoid is the compact body that contains the genome in a bacterium. Nucleoid is a discrete region of the nucleus crdeated by the transcription of rRNA genes. Nucleosome is the basic structural subunit of chromatin, consisting of ~200 bp of DNA and an octamer of histone proteins. Nucleolytic reactions involve the hydrolysis of a phosphodiester bond in a nucleic acid. Null mutation completely eliminates the function of a gene, usually because it has been physically deleted. Ochre codon is the triplet UAA, one of three codons that cause termination of protein synthesis. Ochre mutation is any change in DNA that creates a USS condon at a site previously occupied by another codon. Ochre suppressor is a gene coding for a mutant tRNA able to respond to the UAA codon to allow continuation of protein synthesis; ochre suppressors also suppress amber codons. Okazaki fragments are the short stretches of 1000-2000 bases produced during discontinuous replication; they are later joined into a covalently intact strand. Oncogenes are genes whose products have the ability to transform eukaryotic cells so that they grow in a manner analogous to tumor cells. Oncogenes carried by retroviruses have names of the form v-onc. See also proto-oncogene. Open reading frame (ORF) contains a series of triplets coding for amino acids without any termination codons; sequence is (potentially) translatable into protein. Operator is the site on DNA at which a repressor protein binds to preven transcription from initiating at the adjacent promoter. Operon is a unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulator gene product(s). Organelles is a unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulator gene product(s). Organelles are compartments located in the cytoplasm and surrounded by a membrane. Origin (ori) is a sequence of DNA at which replications is initiated. Orphons are isolated individual genes found in isolated locations, but related to members of a gene cluster. Overwinding of DNA is caused by positive supercoiling (which applies further tension in the direction of winding of the two strands about each other in the duplex). Packing ratio is the ratio of the length of DNA to the unit length of the fiber containing it. Pairing of chromosomes –see synapsis. Palindrome is a sequence of DNA that is the same when one strand is read left to right or the other is read right to left; consists of adjacent inverted repeats. Palindrome is a sequence of DNA that is the same when one strand is read left to right or the other is read right to left; consists of adjacent inverted repeats. Papovaviruses are a class of animal viruses with small genomes, including SV40 and polyoma. Parnemic joint describes a region in which two complementary sequences of DNA are associated side by side instead of being intertwined in a double helical structure. pBR322 is one of the standard plasmid cloning vectors. PCR (polymerase chain reaction) describes a tenchnique in which cycles of denaturation, annealing with primer, and extension with DNA polymerase, are used to amplify the number of copies of a target DNA sequence by >106 times. Perinuclear space lies between the inner and outer membranes of the nuclear envelope. Periodicity of DNA is the number of base pairs per turn of the double helix. Permissive conditions allow conditional lethal mutants to survive. Petite strains of yeast lack mitochondrial function. Phage (bacteriophage) is a bacterial virus. Phase variation describes an alternation in the type of flagella produced by a bacterium. Phenotype is the appearance or other characteristics of an organism, resulting from the interaction of its genetic constitution with the environment. Phosphatase is an enzyme that removes phosphate groups from substrates. Plasma membrane is the continuous membrane defining the boundary of every cell. Plasmid is an autonomous self-replicating extrachromosomal circular DNA. Playback experiment describes the retrieval of DNA that has hybridized with RNA to check that it is nonrepetitive by a further reassociation reaction. Plectonemic winding describes the intertwining of the two strands in the classical double helix of DNA. Pleiotropic gene affects more than one (apparently unrelated) characteristic of the phenotype. Ploidy refers to the number of copies of the chromosome set present in a cell; a haploid has one copy, a diploid has two copies, etc. Point mutations are changes involving single base pairs. Polarity refers to the effect of a mutation in one gene in influencing the expression (at transcription or translation) of subsequent genes in the same transcription unit. Polyadenylation is tha addition of a sequence of polyadenylic acid to the 3’ end of a eukaryotic RNA after its transcription. Polycistronic mRNA includes conding regions representing more than one gene. Polymorphism refers to the simultaneous occurrence in the population of genomes showing allelic variations (as seen either in alleles producing different phenotypes or—for example—in changes in DNA affecting the restriction pattern.) Polyploid cell has more than two sets of the haploid genome. Polyprotein is a gene product that is cleaved into several independent proteins. Polysome (polyribosome) is an mRNA associated with a series of ribosomes engaged in translation. Polytene chromosomes are generated by successive replications of a chromosome set without separation of the replicas. Position effect refers to a change in the expression of a gene brought about by its translocation to a new site in the genome; for example, a previously active gene may become inactive if placed near heterochromatin. Kpositive regulator proteins are required for the activation of a transcription unit. Positive supercoiling describes the coiling of the double helix in space in the same direction as the winding of the two strands of the double helix itself. Postmeitotic segregation describes the segregation of two strands of a duplex DNA that bear different information (created by heteroduplex formation during meiosis) when a subsequent replication allows the strands to separate. Primary cells are eukaryotic cels taken into culture directly from the animal. Primary transcript is the original unmodified RNA product corresponding to a transcription unit. Primer is a short sequence (often of RNA) that is paired with one strand of DNA and provides a free 3’-OH end at which a DNA polymerase starts synthesis of a deoxyrigonucleotide chain. Primosome describes the complex of proteins involved in the priming action that initiates synthesis of each Okazaki fragment during discontinuous DNA replication; the primosome may move alon DNA to engage in successive priming events. Procentriole is an immature centriole, formed in the vicinity of a mature centriole. Processed pseudogene is an inactive gene copy that lacks introns, contrasted with the interrupted structure of the active gene. Such genes presumably originate by reverse transcription of mRNA and insertion of a duplex copy into the genome. Processive enzymes continue to act on a particular substrate, that is, do not dissociate between repetitions of the catalytic event. Prokaryotic organisms (bacteria ) lack nuclei. Promoter is a region of DNA involved in binding of RNA polymerase to initiate transcription. -10 sequence is the consensus sequence TATAATG centered about 10 bp before the startpoint of a bacterial gene. It is involed in the initial melting of DNA by RNA polymerase. -35 sequence is the consensus sequence centered about 35 bp before the startpoint of a bacterial gene. It is involved in initial recognition by RNA polymerase. Proofreading refers to any mechanism for correcting errors in protein or nuclei acid synthesis that involves scrutiny of individual units after they have been added to the chain. Prophage is a phage genome covalently integrated as a linear part of the bacterial chromosome. Proteolytic reactions comprise the hydrolysis of peptide bonds in protein. proto-oncogenes are the normal counterparts in the eukaryotic genome to the oncogenes carried by some retroviruses. They are given names of the form c-onc. Provirus is a duplex DNA sequence in the eukaryotic chromosome corresponding to the genome of an RNA retrovirus. Pseudogenes are inactive but stable components of the genome derived by mutaion of an ancestral active gene. Puff is an expansion of a band of a polytene chromosome associated with the synthesis of RNA at some locus in the band. Pulse-chase experiment are performed by incubating cells very briefly with a radioactively labeled precursor (of some pathway or macromolecule); then the fate of the label is followed during a subsequent incubation with a nonlabeled precursor. Quaternary structure of a protein refers to its multimeric constitution. Quick-stop dna mutants of E. coli cease replication immediately when the temperature is increased to 42℃. R loop is the structure formed when an RNA strand hybridizes with its complementary strand in a DNA duplex, thereby displacing the original strand of DNA in the form of a loop extending over the region of hybridization. Rapid lysis (r) mutants display a change in the pattern of lysis of E. coli at the end of an infection by a T-even phage. Reading frame is one of three possible ways of reading a nucleotide sequences as a series of triplets. Reassociation of DNA describes the pairing of complementary single strands of torm a double helix. Rec A is the product of the recA locus of E. coli; a protein with dual activities, activating proteases and also able to exchange single strands of DNA molecules. The protease-activating activity controls the SOS response; the nucleic acid handling facility is involved in recombinationrepair pathways. Receptor is a transmembrane protein, located in the plasma membrane, that binds a ligand in a domain on the extracellular side, and as a result has a change in activity of the cytoplasmic domain. (The same term is sometimes used also for the steroid receptors which are transcription factors that are cativated by binding ligands that a steroids or other small molecules.) Recesssive allele is obscured in the phenotype of a heterozygote by the dominant allele, often due to inactivity or absence of the product of the recessive allele. Recessive lethal is an allele that is lethal when the cell is homozygous for it. Reciprocal recombination is the production of new genotypes with the reverse arrangements of alleles according to maternal and paternal origin. Reciprocal translocation exchanges part of one chromosome with part of another chromosome. Recombinant progeny have a different genotype from that of either partne. Recombinant joint is the point at which two recombining molecules of duplex DNA are connected (the edge of the heteroduplex region). Recombination nodules (nodes) are dense objects present on the synaptonemal complex; could be involved in crossing-over. Recombination-repair is a mode of filling a gap in one strand of duplex DNA by retrieving a homlogous single strand from another duplex. Regulatory gene codes for an RNA or protein product whose function is to control the expression of other genes. Relaxed mutants of E. coli do not display the stringent response to starvation for amino acids (or other nutritional deprivation). Relaxed replication control refers to the ability of some plasmids to continue replicatin after bacteria cease dividing. Release (termination) factors respond to termination codons to cause release of the completed polypeptide chain and the ribosme from mRNA. Renaturation is the reassociaition of deatured complementary single strands of a DNA double helix. Repeating unit in a tandem cluster is the length of the sequence that is repeated ;appears circular on a restriction map. Repetition frequency is the (integral) number of copies of a given sequence present in the haploid genome; equals 1 for nonrepetitive DNA, >2 for repetitive DNA. Repetitive DNA behaves in a reassociation reaction as though many (related or identical) sequences are present in a component, allowing any pair of complementary sequences to reassociate. Replacement sites in a gene are those at which mutations alter the amino acid that is coded. Replication-defective virus has lost one or more genes essential for completing the infective cycle. Replication eye is region in which DNA has been replicated within a longer, unreplicated region. Replication fork is the point at which strands of parental duplex DNA are separated so that replication can procedd. Replicative transpostition describes the movement of a transposon by a mechanisim in which first it is replicated, and then one copy is transferred to a new site. Replicon is a unit of the genome in which DNA is replicated; contains an origin for intitiation of replication. Replisome is the multiprotin structure that assemble at the bacterial replicating fork to undertake synthesis of DNA. Contains DNA polymerase and other enzymes. Reporter gene is a coding unit whose product is easily assayed (such as chloramphenicol transacetylase); it may be connected to any promoter of interest so that expression of the gene can be used to assay promoter function. Repression is the ability of bacteria to prevent synthesis of certain enzymes when their products are present; more generally, refers to inhibition of transcription (or translation) by bhinding of repressor protein to a specific site on DNA (or mRNA). Repressor protein binds to operator on DNA or RNA to prevnt transcription or translation, respectively. Resolvase is enzyme activity involved in sitespecific recombination between two transposons present as direct repeats in a cointegrate structure. Restriction enzymes recognize specific short sequences of (usually) unmethylated DNA and cleave the duplex (sometimes at target site, sometimes elsewhere, depending on type). Restriction fragment length poymorphism (RFLP) refers to inherited differences in sites for restriction enzymes (for example, caused by base changes in the target site) that result in differences in the lengths of the fragments produced by cleavage with the relevant restriction enzyme. RFLPs are used for genetic mapping to link the genome directly to a converntional genetic marker. Restriction map is a linear array of sites on DNA cleaved by various restriction enzymes. Retroposon is a transposon that mobilizes via an RNA form; the DNA element is transcribed into RNA, and then reverse-transcribed into DNA, which is inserted at a new site in the genome. Retroregulation describes the ability of a sequence downstream to regulate translation of an mRNA. Retrovirus is an RNA virus that propagates via conversion into duplex DNA. Reverse transcription is synthesis of DNA on a template of RNA; accomplished by reverse transcriptase enzyme. Reverse translation is a technique for isolating genes (or mRNAs ) by their ability to bybridize with a short oligonucleotide sequence prepared by predicting the nucleic acid sequence from the known protin sequence. Reversion of mutation is a change in DNA that either reverses the original alteration (true reversion) or compensates for it (second site reversion in the same gene). Revertants are derived by reversion of a mutant cell or orgaism. Rho factor is a protein involved in assisting E. coli RNA polymerase to terminate transcription at certain (rho-dependedt) sites. Rho-independent terminators are sequences of DNA that cause E. coli RNA polymerase to terminate in vitro in the absence of rho factor. Rifamycins (including rifampicin) inhibit transcription in bacteria. Right splicing junction is the boundary between the right end of an intron and the left end of the adjacent exon. RNAase is an enzyme whose substrate is RNA. RNA-driven hybridization reactions use an excess of RNA to react with all complementary sequences in a single-stranded preparation of DNA. RNA polymerase is an enzyme that synthesizes RNA using a DNA template (formally described as DNA-dependent RNA polymerase). RNA replicase is an enzyme that synthesizes RNA using an RNA template (used for replication by RNA viruses). Rolling circle is a mode of replication in which a replication fork proceeds around a circular template for an indefinite number of revolutions; ;the DNA strand newly synthesized in each revolution displaces the strand synthesized in the previous revolution, giving a tail containing a linear series of sequences complementary toe the circular template strand. Rot is the product of RNA concentration and time of incubation in an RNA-driven hybridization reaction. Rought ER consists of endoplasmic reticulum associated with rigosomes. S phase is the restricted part of the eukaryotic cell cycle during which synthesis of DNA occurs. S1 nuclease is an enzyme that specifically degrades unpaired (single-stranded) sequences of DNA. Saltatory replication is a sudden lateral amplification to produce a large number of copies of some sequence. Satellite DNA contsists of many tandem repeats (identical or related) of a short basic repeating unit. Saturation desity is the density to which cultured eukaryotic cells grow in vitro before division is inhibited by cell-cell contacts. Saturation bybridization experiment has a large excess of one component, causing all complementary sequences in the other component to enter a duplex form. Scaffold of a chromosome is a proteinaceous structure in the shape of a sister chromatid pair, generated when chromosomes are depleted of histones. Scare (complex) mRNA comsists of a large number of individual mRNA species, each present in very few copies per cell. scRNA is any one of several small cytoplasmic RNAs, molecules present in the cytoplasm and (sometimes) nucleus. scRNPs are small cytoplasmic ribonucleoprotein (scRNAs associated with proteins). Segmentations genes are concerned with controlling the number or polarity of body segments in insects. Selection describes the use of particular conditions to allow survival only of cells with a particular phenotype. Semiconservative replication is accomplished by separation of the strands of a parental duplex each then acting as a template for synthesis of a complementary strand. Semidiscontinuous replication is mode in which one new strand is synthesized continuously while the other is synthesized discontinuously. Sepum constitutes the material that forms in the center of a bacterium to divide it into twi daughter cells at the end of a division cycle. Serum dependence describes the need of eukaryotic cells for factors contained in serum in order to grow in culture. Sex chromosomes are those whose contents are different in the two sexes; usually labeled X and Y (or W and Z), one sex has XX (or WW), the other sex has YX (or WZ). Sex linkage is pattern of inheritance shown by genes carried on a sex chromosome (usually the X). Sex plasmid is actually an episome; it is able to intitiate the process of conjugation, by which chromosomal material is transferred from one bacterium to another. Shine-Dalgarno sequence is part or all of the polypurine sequence AGGAGG located on bacterial mRNA just prior to an AUG initiation condon; is complementary to the sequence at the 3’ end of 16S rRNA; involved in binding of rigosome to mRNA. Short-period interspersion is a parttern in a genome in which moderately repetitive DNA sequences of ~300 bp alternate with nonrepetitive sequences of ~1000bp. Shotgun experiment is cloning of an entire genome in the form of randomly generated fragments. Shuttle vector is a plamid construdcted to have origins for replication for two hosts (for example, E. coli and S. cerevisiae) so that it can be used to carry a foreign sequence in either prokaryotes or eukaryotes. Sigma factor is the subunit of bacterial RNA polymerase needed for initiation; is the major influence on selection of binding sites (promoters). Signal hypothesis describes the role of the N-termainal sequence of a secreted protein in attaching nascent polypeptide to membrane; that is, mRNA and ribosome are attached to membrne via the N-terminal end of the protein under synthesis. Signal sequence is the region of a protein (usually N-termainal) responsible for co-translational insertion into membranes of the endoplasmic reticulum. Signal transduction describes the process by which a receptor interacts with a ligand at the surface of the cell and then transmits a signal to trigger a pathway within the cell. Silent muations do not change the product of a gene. Silent sites in a gene describe those positions at which mutations do not alter the product. Simple-sequence DNA equals satellite DNA. SINES are a class of retroposons found as short interspersed repeats in mammalian genomes; derived form transcripts of RNA polymerase III. Single-copy plasmids are maintained in bacteria at a ratio of one plasmid for very host chromosome. Single-strand assimilation describes the ability of Rec A protein to cause a single strand of DNA to displace its homologous strand in a duplex; that is the single strand is assimilated into the duplex. Single-strand exchange is a reaction in which one of the strands of a duplex of DNA leaves its former partner and instead pairs with the complementary strand in another molecule, displacing its homologue in the second duplex. Sister chromatids are the copies of a chromosome produced by its replication. Site-specific recombination occurs between two specific (not necessarily homologous) sequences. as in phage integration/excision or resolution of cointegrate structures during transposition. Slow component of a reassociation reaction is the last to reassociate; usually consists of nonrepetivive DNA. Slow-stop dna mutants of E. coli complete the current round of bacterial replication but cannot initiate another at 42℃. Smooth ER consists of a regions of endoplasmic reticulum devoid of ribosomes. snRNA (small nuclear RNA) is any one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions. snRNPs are small nuclear ribonucleoproteins (snRNAs associated with proteins). Solution hybridization is the same as liquid hybridization. Somatic cells are all the cells of an organism except those of the germ line. Somatic mutation is a mutation occurring in a somatic cell, and therefore affecting only its descendants; it is not inherited. SOS box is the DNA sequence (operator) of ~20 bp recognized by LexA repressor protein. SOS response in E. coli describes the coordinate induction of many enzymes, including repair activities, in response to irradiation or other damage to DNA; results from activation of protease activit by RecA to cleave LexA repressor. Southern blotting describes the procedure for transferring denatured DNA from an agarose gel to a nitrocellulose filter where it can be by bridized with a complementary nucleic acid. Spheroplast is a bacterial or yeast cell whose wall has been largely or entirely removed. Spindle describes the reorganized structure of a eukaryotic cell passing though division; the nucleus has been dissolved and chromosomes are attached to the spindle by microtubules. Splicing describes the removal of introns and joining of exons in RNA; thus introns are spliced out while exons are spliced together. Splicing junctions are the sequences immediately surrounding the exon-intron boundaries. Spontaneous mutations are those that occur in the absence of any added reagent to increase the mutation rate. Sporulation is thegeneration of a spore by a bacterium (by morphological conversion) or by a yeast (as the product of meiosis). SSB is the single-strand protein of E. coli, a protein that binds to single-stranded DNA. Staggered cuts in duplex DNA are made when two strands are cleaved at different points near each other. Startpoint (startsite) refers to the position on DNA corresponding to the first base incorporated into RNA. Stem is the base-paired segment of a hairpin. Sticky ends are complementary single strands of DNA that protrude from opposite ends of a duplex or from ends of different duplex molecules; can be generated by staggered cuts in duplex DNA. Stop codons are the three triplets (UAA, UAG, UGA) which terminate protein synthesis. Strand displacement is a mode of replication of some viruses in which a new DNA strand grows by displacing the previous (homologous) strand of the duplex. Streptolydigins inhibit the elongation of transcription by bacterial RNA polymerase. Stingent replication describes the limitation of single-copy plasmids to replication pari passu with the bacterial chromosome. Stringent response refers to the ability of a bacterium to shut down synthesis of tRNA and rigosomes in a poor-growth medium. Structural gene codes for any RNA or protein product other than a regulator. Supercoiling dexcribes the coiling of a closed duplex DNA in space so that it crosses over its own axis. Superrepressed means the same as uninducible. Suppression describes the occurrence of changes that eliminate the effects of a mutation without reversing the original change in DNA. Suppressor (extragenic) is usually a gene coding a mutant tRNA that reads the mutated codon eigher in the sense of the original condon or to give an acceptable substitute for the original meaning. Suppressor (intragenic) is a compensating mutation that restores the original reading frame after a frameshift. Synapsis describes the association of the two pairs of sister chromatids representing homologous chromosomes that occurs at the start of meiosis; resulting structure is called a bivalent. Synaptonemal complex describes the morphological structure of synapsed chromosomes. Syntenic genetic loci lie on the same chromosome. T Cells are lymphocytes of the T (thymic) lineage; may be subdivived into several functional types. They carry TcR (T cell receptor) and are involved in the cell-mediated immune response. Tm is the abbreviation for melting temperature. Tandem repeats are multiple copies of the same sequence lying in series. TATA box is a conserved A?T-rich septamer found about 25 bp bdfore the startpoint of each eukaryotic RNA polymerase II transcription unit; may be involved in positioning the enzyme for correct intitiation. Telomerase is the ribonucleoprotein enzyme that creates repeating units of one strand at the telomere, by adding individual bases. Telomere is the natural end of a chromosome; the DNA sequence consists of a simple repeating unit with a protruding single-stranded end that may fold into a hairpin. Temperature-sensitive mutation creates a gene product that is functional at low temperature but inactive at higher temperature (the reverse relationship is usually called cold- sensitive). Termainal redundancy describes the repetition of the same sequence at both ends of (for example) a phage genome. Termination condon is one of three triplet sequences, UAG (amber), UAA (ochre), or UGA that cause termination of protein synthesis; they are also called ‘nonsense’ codons. terminator is a sequence of DNA. represented at the end of the transcript, that causes RNA polymerase to terminate transcription. Tertiary structure of a protein describes the organization in space of its polypeptide chain. Testcross involves crossing an unknown genotype to a recessive homozygote so that the phenotypes of the progeny correspond directly to the chromosomes carried by the parent of unknown genotype. Thalassemia is diease of red blood cells resulting from lack of either α or βglogin. Thymine dimmer comprises a chemically crosslinked pair of adjacent thymine residues in DNA, a result of damage induced by ultraviolet irradiation. Topoisomerase is an enzyme that can change the likning number of DNA (in steps of 1by type I; in steps of 2 by type II). Topological isomers are molecules of DNA that are identical except for a difference in linking number. Tracer is a radioactively labeled nucleic acid component included in a reassociation reaction in amounts too small to influence the progress of reaction. Trailer is a nontranslated sequence at the 3’ end of an mRNA following the termination condon. Trans configuration of two sites refers to their presence on two different molecules of DNA (chromosomes). Transcribed spacer is the part of an rRNA transcription unit that is transcribed but discarded during maturation; that is, it does not give rise to part of rRNA. Transcription is synthesis of RNA on a DNA template. Transcription unit is the distance between sites of initiation and termination by RNA polymerase; may include more than one gene. Transduction refers to the transfer of a bacterial gene from one bacterium to another by a phage; a phage carrying host as well as its own genes is station and transfer of eukaryotic cellular sequences by retroviruses. Transfection of eukaryotic cells is the acquistion of new genetic markers by incorporation of added DNA. Transformation of bacteria describes the qcquisition of new genetic markers by incorporation of added DNA. Transformation of eukaryotic cells refers to their conversion to a state of unrestrained growth in culture, resembling or identical with the tumorigenic condition. Transgenic animals are created by introducing new DNA sequences into the germ line via addition to the egg. Transit peptide is the short leader sequence cleaved from proteins that are imported into cellular organelles by post-translational passage of the membrane. Transition is a mutation in which one pyrimidine is substituted by the other or in which one purine is substituted for the other. Translation is synthesis of protein on the mRNA template. Translocation of a chromosome describes a rearrangement in which part of chromosome is detached by breakage and then becomes attached to some other chromosome. Translocaation of a gene refers to the appearance of a new copy at location in the genome elsewhere from the original copy. Translocation of a protein refers to its movement across a membrane. Translocation of the rigbosome is its movement one codon along mRNA after the addition of each amino acid to the polypeptide chain. Transmembrane protein is a component of a membrance; a hydrophobic region of regions of the protein resides in the membrane, and hydrophilic regions are exposed on one or both sides of the membrane. Transplantation antigen is protein coded by a major histocompatibility locus, presuent on all mammalian cells, involved in interactions between lymphocytes. Transposaes is the enzyme activity involved in insertion of transposon at a new site. Transpostion immunity refers to the ability of certain transposons to prevent others of the same type from transposing to the same DNA molecule. Transposon is a DNA sequence able to insert itself at a new location in the genome (without any sequence relationship with the target locus). Transpostion refers to the movement of a transposon to a new site in the genome. See also nonreplicative transposition, replicative transposition, and conservative transposition. Transvection describes the ability of a locus to influence activeity of an allele on the other homoloue only when two chromosomes are synapsed. Transversion is a mutation in which a purine is replaced by a pyrimidine or vice versa. True-breeding organisms are homozygous for the trait under consideration. Twisting number of a DNA is the number of base pairs divided by the number of base pairs per turn of the double helix. Underwinding of DNA is produced by negative supercoiling (because the double helix is itself coiled in the opposite sense from the intertwining of the strands). Unequal crossing-over describes a recombination event in which the two recombining sites lie at nonidentical locations in the two parental DNA molecules. Unidirectional replication refers to the movement of a single replication fork from a given origin. Uninducible mutants cannot be induced. Unscheduled DNA synthesis is any DNA synthesis occurring outside the S phase of the euikaryotic cell. Up promoter mutations increase the frequency of initiation of transcription. Upstream identifies sequences proceeding in the opposite direction from expression; for example, the bacterial promoter is upstream from the transcription unit, the initiation codon is upstream of the coding region. URF is an open (unidentified) reading frame, presumed to code for protein, but for which no product has been found. V gene is sequence coding for the major part of the variable (N-termainal) region of an immunoglobulin chain. Variable region of an immunoglobulin chain is conded by the V gene and varies extensively when different chains are compared, as the result of multiple (different) genomic copies and changes introduced during construction of an active immunoglobulin. Variegation of phenotype is produced by a change in genotype during somatic development. Vector—see cloning vector. Vesicles are small bodies bounded by membrane, derived by budding from one membrane, often able to fuse with another membrane. Virion is the physical virus particle (irrespective of its ability to infect cells and reproduce). Virulent phage mutants are unable to establish lysogeny. Wobble hypotheis accounts for the ability of a tRNA to recognize more than one condon by unusual (non-G·C,A·T) pairing with the third base of a codon. Writhing number is the number of times a duplx axis crosses over itself in space. Zero time-binding DNA enters the duplex form at the start of a reassociation reaction; results from intramolecular reassociation of inverted repeats. Zinc finger protein has a repeated motif of amino acids with characteristic spacing of cysteines that may be invoved in binding ainc; is characteristic of some proteins that bind DNA and /or RNA. Zoo blot describes the use of Southern blotting to test the ability of a DNA probe from one species to hybridize with the DNA from the genomes of a variety of other species. Zygote is produced by fusion of two gametes—that is, it is a fertilized egg.