CAP (Catabolite activator protein)
See CRP.

Capsduction
A DNA transfer system in Rhodobacter capsulatus where the donor DNA is carried in a phage-like structure known as a gene transfer agent (GTA). The donor DNA derived from the GTA-producing cells can enter a recipient cell and recombine with th e recipient genome.

Capsid
The protein layer that encloses the nucleic acid of a phage or virus and protects it from the environment.

Carbon source
A nutrient which provides the carbon required for cellular biosynthesis.

Carcinogen
A physical or chemical agent that causes cancer.

Cascade
A series of events that result in transmission and usually amplification of a weak signal.

Cassette
A gene fragment that can be cloned into a site to confer some property. For example, cassettes encoding antibiotic resistance are often used to disrupt a cloned gene.

Catabolite repression
A global regulatory system resulting in decreased expression of many genes due to the addition of an efficient carbon source such as glucose. Characteristically mediated by a complex between the CRP protein and cAMP in enteric bacteria.

Catenane
A circular DNA molecule with two or more interlinked rings.

CCC
An abbreviation for "circular, covalently closed" DNA molecules.

cDNA Cloning
A technique involving reverse transcription of purified mRNA into the corresponding complementary DNA prior to insertion into a vector.

Cell extract
A preparation consisting of a large number of broken cells and their released contents.

Cell-free translation system
A cell extract containing all the components required for protem synthesis (i.e. ribosomal subunits, tRNAs, amino acids, enzymes and cofactors) and able to translate added mRNA molecules.

Centromere
The region of a eukaryotic chromosome responsible for attachment to the mitotic or meiotic spindle leading to controlled partitioning of chromosomes during nuclear division.

Chain-termination ("nonsense" or "stop") codon
A codon signalling the termination of polypeptide synthesis. The three standard stop codons are UAG (amber), UAA (ochre), and UGA (opal).

Chaperone
A protein that facilitates the folding of other proteins or assembly of multi-protein complexes.

Chelator
A substance that binds particular ions, removing them from solution. Some chelators are relatively nonspecific, binding to a variety of ions with similar charge, and other chelators bind much more strongly to specific ions. A few examples include the divalent ion chelators citrate and EDTA, the calcium chelator EGTA, and the iron chelator desferrioxamine. For more about chelators, see: http://www.sigmaaldrich.com/Brands/Fluka___Riedel_Home/Bioscience/BioChemika_Ultra/Chelators.html.

Chemotaxis
A behavorial response of cells resulting in movement toward or away from to a chemical stimulus.

Chi site
An 8-nucleotide DNA sequence (5' GCTGGTGG 3') which is a hot-spot for homologous recombination. When the RecBCD exonuclease encounters a chi site the RecD subunit is released and the RecBC complex then functions as a helicase, unwinding the DNA and providing single stranded which can invade a homologous region of double-stranded DNA. Chi sites typically occur about once every 5 kb on the chromosomes of enteric bacteria and most are oriented in the same direction as DNA replication.

Chiasma
A cross-over between strands of two non-sister chromatids during recombination. The junction where two homologous chromosomes appear to exchange genetic material during recombination. (Chi is the greek letter c which resembles a genetic cross-over.)

Chimeric plasmid
A plasmid used in gene cloning and constructed from two or more different plasmids.

Chloramphenicol (Cam)
An antibiotic that inhibits protein synthesis by binding to the 50s ribosomal subunit and blocking the peptidyltransferase reaction. Chloramphenicol resistance encoded by many plasmids (e.g. pBR328) is due to a cytoplasmic chloramphenicol acyltransferase which inactivates chloramphenicol by covalently acetylating it.

Chromatid
One of the two identical strands of a newly replicated chromosome.

Chromogenic substrate
A substrate that changes color when modified by a specific enzyme.

Chromosome
A self-replicating DNA molecule that carries essential genetic information for growth and replication of a cell or virus. The DNA organized into a tightly packaged structure by associated histone-like proteins in bacteria and histones in eukaryotes. (The chromosomes of some viruses contain RNA instead of DNA.)

Chromosome walking
A technique used to identify a series of overlapping restriction fragments, often to determine the relative positions of genes on large chromosomes.

Circularly permuted DNA
A population of linear DNA molecules produced as if by breaking open circular molecules at different points.

cis
Two genes located are on the same molecule of DNA (commonly refers to genes that are located very close to each other on the same DNA molecule).

Cis-trans test
A genetic test to determine whether two mutations are in the same or in different genes.

Cis-dominance
A mutation that prevents the expression of downstream genes. Polar mutations in an operon are typically cis-dominant.

Cistron
An obsolete term for a gene. Often used to refer to the number of genes encoded by a single transcript; monocistronic refers to a transcript that encodes one gene, and polycistronic refers to a transcript that encodes multiple genes.

Cleared lysate
A cell extract that has been centrifuged to remove cell debris, subcellular particles, and much of the chromosomal DNA.

Clonal
A population of cells derived from a single cell and thus expected to be genetically identical. Genetic differences in a "clonal" population may arise from random spontaneous mutations during growth of the cells.

Clone
Cells derived from a single cell and thus expected to be genetically identical.

Cloning
The production of multiple, genetically identical molecules of DNA, cells, or organisms.

Cloning vector
A DNA molecule that is capable of replication in a suitable host cell, that has suitable site(s) for the insertion of DNA fragments by recombinant DNA techniques, and that has genetic markers that allow selection for the vector in a host cell.

Coding region
A sequence of DNA that encodes a polypeptide.

Codominance
The observation of a phenotype caused by independent expression of both alleles of a gene in a diploid.

Codon
The three consecutive nucleotides (triplets) in DNA or RNA that encode a particular amino acid or signal the termination of polypeptide synthesis.

Cohesive ends
Single-stranded complementary sequences at two ends of a DNA molecule (examples include the ends of the linear phage lambda chromosome, and the ends resulting from digestion of DNA with many restriction endonucleases).

Coinheritance frequency
The ratio of recombinants that acquire both the selected and unselected marker vs the total number of recombinants.

Cointegrate
A circular molecule of DNA formed during replicative transposition by joining two separate circular replicons. The resulting structure has two copies of the transposon, one at each junction point, orientated in direct repeats.

Colinearity
The linear correspondance between the nucleotide sequence and the order of amino acids in a polypeptide chain.

Cold sensitive mutant
A mutation that results in a gene product that is active at a high temperature (e.g. 42C) but inactive at low temperatures (e.g. 30C). Cold sensitive mutations often affect hydrophobic interactions between protein complexes or between proteins and membrane componants.

Cold spot
Sites within a gene (or genome)at which mutations occur with much lower frequency than at other sites.

Colicin
A polypeptide secreted by bacteria which inhibit or prevent the growth of related bacteria which lack the corresponding colicin immunity proteins. Colicins are encoded by a group of naturally occurring plasmids first found in E. coli (e.g., the Col E1 plasmid). Colicins kill other bacteria by a variety of mechanisms depending on the type of colicin -- some colicins block protein synthesis, some colicins induce the degradation of chromosomal DNA, some colicins form transmembrane holes in the cytoplasmic membrane, etc.

Colinear
Markers that occur in a sequential order in a DNA or protein sequence.

Coliphage
A phage that infects Escherichia coli.

Colony
A visible group of cells arising from a single cell plated on solid medium.

Colony blots
See Colony hybridization.

Colony hybridization
Use of in situ hybridization with a labeled nucleotide probe to identify bacterial colonies that contain DNA sequences homologous to a probe.

Colony PCR
Use of a bacterial colony for direct polymerase chain reaction to amplify a specific nucleotide sequence.

Coorperativity
For DNA binding proteins, cooperativity generally refers to the increased binding of a protein to a DNA site due to the prior binding of another protein nearby. (Note that more rigorous definations of cooperativity are sometimes used in biochemistry to refer to binding of small molecules, that can result in positive cooperativity (enhanced binding) and negative cooperativity (poorer binding) of a second molecule following binding of a first molecule.)

Coordinate gene expression
Transcription of a group of genes at the same time due to a common regulatory mechanism.

Compatibility
The ability of two different types of plasmid to coexist in the same cell.

Competence
The transient physiological state required for a bacterial cell to take up transforming DNA.

Complementary
Two polynucleotide chains that can base-pair to form a double-stranded molecule.

Complementation
The ability of a gene to produce a functional gene product which compensates for the mutant phenotype caused by a mutation in another gene. Typically, the complementing gene produces a gene product (e.g. a repressor protein or an enzyme for synthesis of a metabolite) that is diffusible and thus functions in trans.

Complex
Containing multiple macromolecules in an organized structure. For example, the RecBCD proteins form a complex that functions as an exonuclease and this activity requires all three of the proteins to function together.

Composite transposon
A transposible element flanked by two copies of an IS element.

Concatamer
An end-to-end (tandem) array of identical DNA rnolecules; a repeated polymer of DNA.

Conditional lethal mutant
A mutant that can grow under one set (permissive) of environmental conditions but dies under different (restrictive or nonpermissive) conditions.

Conditional mutant
A mutant that can grow under one set (permissive) of environmental conditions but cannot grow under different (restrictive or nonpermissive) conditions. Some conditional mutants survive under the nonpermissive conditions but others (conditional lethal mutants) die under the nonpermissive conditions.

Congenic
Strains that are identical except for a small region of the chromosome.

Congression
The uptake of more than one transforming DNA fragment by a single competent cell (occurs most often when a high concentration of transforming DNA is available).

Conjugation
The establishment of a bridge between a donor and a recipient cell and the transfer of DNA from one cell to the other. Conjugation is mediated by certain plasmids and transposons. Conjugation requires direct contact between the donor and recipient cells.

Conjugative plasmid
A bacterial plasmid that encodes functions required for conjugation.

Conjugative transposon
A transposon that encodes functions required for conjugation.

Consensus sequence
A idealized nucleotide sequence that represents a sequence that serves some particular function (e.g. a promoter) at multiple places in a genome. Each position of the consensus sequence represents the nucleotide most often found at that position in the real sequences. The precise sequence will vary from site to site, but they all are similar to the consensus sequence.

Conservative (nonreplicative) transposition
A transposition event where the transposable element is lost from its original location and inserted at a new location.

Conserved sequence
A nucleotide or protein sequence which is shared between different regions or organisms, typically because the sequence fulfills an important function (e.g. a DNA-binding site or protein motif) and thus is retained during evolution.

Constitutive gene expression
A gene or operon which is expressed at all times independant of the environmental conditions.

Contig
A set of DNA fragments that overlap to yield a continuous sequence without gaps.

Continuous culture
The culture of microorganisms in liquid medium under controlled conditions, with regular additions of depleted nutrients and removal of excreted metabolites from the medium over a lengthy period of time.

Copy number
The number of molecules of a particular plasmid present in a bacterium.

Co-repressor
A small molecule that binds to an aporepressor protein, producing a conformational change that causes it to function as a transcriptional repressor.

Cos site
The sequence that is cut to produce the cohesive, single-stranded extensions located at the ends of the linear DNA molecules of certain phages (e.g. lambda).

Cosanguine
Related by a common ancestor.

Cosmid
A cloning vector consisting of the phage lambda cos site inserted into a plasmid. Such vectors can be packaged into lambda phage or maintained as plasmids. Cosmids are often used to clone large DNA fragments (up to about 40 kilobases).

Cotransduction
Homologous recombination of two closely linked genes or two mutations within the same gene and brought into a cell on the same fragment of transducing DNA.

Cotransformation
The simultaneous uptake of two genetic markers via transformation. Cotransformation of two markers occurs at a frequency greater than 50 percent indicates that the two markers are genetically linked.

Counterselection
A condition that prevents growth of the donor in a genetic cross.

Covalently closed-circular (CCC)
A completely double-stranded circular DNA molecule, with no nicks or discontinuities, usually with a supercoiled conformation.

CRM
Cross reacting material. A molecule that reacts with an antibody. A common test for the presence of an inactive protein in cells.

Cross-feeding
Growth of a mutant stimulated by metabolites released by another cell.

Cross-over
The site where two homologous DNA strands originating from homologous chromosomes are resealed to form the recombinant chromosome. The reciprocal exchange of genetic material to produce genetic recombinants. Sometimes abbreviated as X-over.

Cross reacting material
See CRM.

CRP
Catabolite receptor protein, also called CAP or catabolite activator protein. The interaction of CRP with cAMP modulates many aspects of catabolite repression in enteric bacteria.

Cryptic
A function that is silent. For example, a cryptic gene may have an intact coding sequence but lack an active promoter. Cryptic functions can be turned on by an appropriate mutation.

C-terminus
The end of a polypeptide chain that has a free carboxylic acid (-COOH) group.

Curing
A treatment that promotes the loss of a resident prophage or plasmid from a cell. For example, acridine orange is sometimes used to cure bacteria of a plasmid.

Cut and paste
Jargon for the excision of a DNA fragment from one molecule and insertion into another DNA molecule. Commonly used to describe cloning a DNA fragment by cleavage with a restriction enzyme and ligation into a vector. Also used to describe transposition mechanisms where the transposon is excised from one DNA molecule and inserted into a second DNA molecule without replication of the transposon.

Cyclic AMP (cAMP)
An adenosine monophosphate molecule with the phosphate covalently attached to both the 3' and 5' carbons of the ribose.