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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 the recipient genome.
Capsid: The protein layer that encloses the nucleic acid of a phage or virus and protects it from the environment.
Carcinogen: A physical or chemical agent that causes cancer.
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.
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 protein 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 signaling the termination of polypeptide synthesis. The three standard stop codons are UAG (amber), UAA (ochre), and UGA (opal).
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. CamR encoded by many plasmids (e.g. pBR328) is due to a cytoplasmic chloramphenicol acyltransferase which inactivate s chloramphenicol by covalently acetylating it.
Chromatid: One of the two identical strands of a newly replicated chromosome.
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 are RNA.)
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.
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.
Clone: 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.
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.
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).
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.
Cold sensitive mutant: A mutation that results in a gene product that is active at a high temperature (e.g. 42°C) but inactive at low temperatures (e.g. 30°C). Cold sensitive mutations often affect hydrophobic interactions between protein complexes or between proteins and membrane components.
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.
cDNA Cloning: A technique involving reverse transcription of purified mRNA into the corresponding complementary DNA prior to insertion into a vector.
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.
Concatamer: An end-to-end (tandem) array of identical DNA molecules; 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.
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.
Constitutive gene expression: A gene or operon which is expressed at all times independent of the environmental conditions.
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.
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).
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.
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-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.
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.

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