Genetics

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Ames test

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An assay that measures the ability of chemicals to cause mutations in certain bacteria. It can identify potential carcinogens

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base analog

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A chemical whose molecular structure is very similar to that of one of the bases normally found in DNA. Some chemical mutagens, such as 5bromouracil (5BU), are base analogs

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bacterial artificial chromosome (BAC)

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A vector for cloning DNA fragments up to about 200 kb long in E. coli. A BAC contains the origin of replication of the F factor, a multiple cloning site, and a selectable marker.

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chromosome walking

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A method for analyzing long segments of DNA by sequentially identifying adjacent, overlapping clones in a genomic library.

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cloning vector

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A double-stranded DNA molecule that is able to replicate autonomously in a host cell and into which a DNA fragment (or fragments) can be inserted to form a recombinant DNA molecule for cloning.

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conditional mutation

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A mutation that results in a wild-type phenotype under one set of conditions but a mutant phenotype under other conditions. Temperature-sensitive mutations are a common type of conditional mutation.

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cDNA library

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Collection of cloned complementary DNAs (cDNAs) produced from the entire mRNA population of a cell.

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DNA microarray

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An ordered grid of DNA molecules of known sequence—probes—fixed at known positions on a solid substrate, either a silicon chip, glass, or, less commonly, a nylon membrane. Labeled free DNA molecules—targets—are added to the fixed probes to analyze identities or quantities of target molecules. DNA microarrays allow for the simultaneous analysis of thousands of DNA target molecules.

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depurination

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depurination
Loss of a purine base (adenine or guanine) from a nucleotide in DNA.

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genomic library

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Collection of cloned DNA fragments in which every DNA sequence in the genome of an organism is represented at least once.

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intergenic suppressor

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A mutation whose effect is to suppress the phenotypic consequences of another (primary) mutation in a different gene.

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intragenic suppressor

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A mutation whose effect is to suppress the phenotypic consequences of another (primary) mutation within the same gene.

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LINEs (long interspersed elements)

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One class of dispersed repeated DNA consisting of repetitive sequences that are several thousand base pairs in length. LINEs can move in the genome by retrotransposition.

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mutation

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Any detectable and heritable change in the genetic material not caused by genetic recombination; Mutations may occur within or between genes and are the ultimate source of all new genetic variation.

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missense mutation

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A point mutation in a gene that changes one codon in the corresponding mRNA so that it specifies a different amino acid than the one specified by the wild-type codon.

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nonsense mutation

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A point mutation in a gene that changes an amino acid-coding codon in the corresponding mRNA to a stop codon.

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positional cloning

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The isolation of a gene associated with a genetic disease on the basis of its approximate chromosomal position.

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plasmid

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An extrachromosomal circular, double-stranded DNA molecule that replicates autonomously from the host chromosome. Plasmids occur naturally in many bacteria and can be engineered for use as cloning vectors.

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proteome

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The complete set of proteins in a cell.

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point mutation

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A heritable alteration of the genetic material in which one base pair is changed to another.

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restriction mapping

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Procedure for locating the relative positions of restriction enzyme cleavage sites in a cloned DNA fragment, yielding a restriction map of the fragment.

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retrotransposon

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A type of mobile genetic element, found only in eukaryotes, that encodes reverse transcriptase and moves in the genome via an RNA intermediate.

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retrovirus

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A virus with a single-stranded RNA genome that replicates via a double-stranded DNA intermediate produced by reverse transcriptase, an enzyme encoded in the viral genome. The DNA integrates into the host’s chromosome where it can be transcribed.

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restriction fragment length polymorphism (RFLP)

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Variation in the lengths of fragments generated by treatment of DNA with a particular restriction enzyme. RFLPs result from point mutations that create or destroy restriction enzyme cleavage sites.

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SINEs (short interspersed elements)

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One class of dispersed repeated DNA consisting of sequences that are 100 to 400 bp in length. SINEs can move in the genome by retrotransposition.

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RNA editing

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Unusual type of RNA processing in which the nucleotide sequence of a pre-mRNA is changed by the posttranscriptional insertion or deletion of nucleotides or by conversion of one nucleotide to another.

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shuttle vector

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A cloning vector that can be introduced into and replicate in two or more host organisms (e.g., E. coli and yeast).

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single nucleotide polymorphism (SNP)

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A difference in one base pair at a particular site (SNP locus) within coding or noncoding regions of the genome. SNPs that affect restriction sites cause restriction fragment length polymorphisms (RFLPs).

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transposase

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An enzyme encoded by many types of mobile genetic elements that catalyzes the movement (transposition) of these elements in the genome.

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transcriptome

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The set of mRNA transcripts in a cell.

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yeast artificial chromosome (YAC)

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A vector for cloning large DNA fragments, several hundred kilobase pairs long, in yeast. A YAC is a linear molecular with a telomere at each end, a centromere, an autonomously replicating sequence (ARS), a selectable marker, and a polylinker.

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auxotroph

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A mutant strain of an organism that cannot synthesize a molecule required for growth and therefore must have the molecule supplied in the growth medium for it to grow. Also called auxotrophic mutant or nutritional mutant.

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bacteriophages

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Viruses that attack bacteria. Also called phages.

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base excision repair

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An enzyme-catalyzed process for repairing damaged DNA by removal of the altered base, followed by excision of the baseless nucleotide. The correct nucleotide then is inserted in the gap.

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bidirectional replication

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Synthesis of DNA in both directions away from an origin of replication.

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carcinogen

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Any physical or chemical agent that increases the frequency with which cells become cancerous.

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transversion mutation

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A type of base pair substitution mutation that involves a change of a purine-pyrimidine base pair to a pyrimidine-purine base pair (e.g., A-T to T-A or G-C to T-A) at a particular site in the DNA.

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transition mutation

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A type of base pair substitution mutation that involves a change of one purine-pyrimidine base pair to the other purine-pyrimidine base pair (e.g., AT to GC). at a particular site in the DNA.

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silent mutation

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A point mutation in a gene that changes a codon in the mRNA to another codon for the same amino acid, resulting in no change in the amino acid sequence or function of the encoded protein.

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synonymous

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Referring to nucleotides in a gene that when mutated do not result in a change in the amino acid sequence of the encoded wild-type protein.

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replica plating

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Procedure for transferring the pattern of colonies from a master plate to a new plate. In this procedure, a velveteen pad on a cylinder is pressed lightly onto the surface of the master plate, thereby picking up a few cells from each colony to inoculate onto the new plate.

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transposable element

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A DNA segment that can move from one position in the genome to another (nonhomologous) position; also called mobile genetic element. Transposable elements are found in both prokaryotes and eukaryotes.

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transposon (Tn)

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A mobile genetic element that contains a gene for transposase, which catalyzes transposition, and genes with other functions such as antibiotic resistance.

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retrotransposon

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A type of mobile genetic element, found only in eukaryotes, that encodes reverse transcriptase and moves in the genome via an RNA intermediate.