Abortive transduction
An event where the fragment of DNA introduced by transduction fails to be recombined into the recipient chromosome and because the DNA fragment lacks an origin of replication it is only inherited by one of the daughter cells at each cell division.

Acrylamide
Used to make polyacrylamide gels for separation of macromolecules by electrophoresis. Polyacrylamide gels are produced by polymerization of acrylamide into linear chains and cross-linking the acrylamide chains with bis-acrylamide (N,N'-methylene-bis-acrylamide). Polymerization is initiated by adding ammonium persulfate and the reaction is accelerated by TEMED (N,N,N',N'-tetramethylethylenediamine) which catalyzes the formation of free radicals from ammonium persulfate. Acrylamide gels are generally poured between glass plates because oxygen inhibits the polymerization because oxygen radicals formed can interact with acrylamide and terminate chain elongation.

Activator
A gene product (usually protein) that positively regulates transcription. Activators may either increase binding of RNA polymerase to the promoter (closed complex formation) or stimulate RNA polymerase to begin transcription (open complex formation).

Active site
The region of an enzyme responsible for catalysis.

Adaption
The ability to physiologically adjust to a new environment while exposed to that particular environment. Typically cells de-adapt when transferred to different growth conditions.

Adenosine triphosphate (ATP)
A compound with high energy phosphate bonds that provide the energy for many cellular processes.

Aerobic
The presence of oxygen. Often used to describe an organism that requires oxygen for growth or growth conditions with oxygen.

Affinity
The strength of an interaction between two molecules, such as the binding of an antigen to an antibody.

Agarose
An uncharged polysaccharide purified from agar. Agarose melts when heated to 100 C and resolidifies when cooled below about 50C. When it solidifies agarose forms a matrix. The size of the pores in the gel matrix can be varied by using different concentrations of agarose: the higher the concentration of agarose, the smaller the pore size.

Alkylating agent
An organic compound able to transfer an alkyl group to nucleotides.

Alleles
Alternative forms of a gene. For example, the mutants putA601 and putA736 each have a different mutation in the putA gene.

Allele specific suppressor
A second-site mutation that repairs the mutant phenotype but only in strains with certain, specific mutations at the first-site.

Allosteric
The stereospecific modification of a protein by an effector to influence the activity of another site of the protein.

Alpha-complementation
The ability of a short N-terminal fragment of beta-galactosidase to interact with the C-terminal portion of beta-galactosidase to form a functional enzyme.

Amber codon
The UAG nonsense codon. This is one of the three normal chain termination or stop codons that does not code for any amino add in the universal code.

Amber mutation
A mutation that creats an amber codon (UAG) from a different codon.

Amber suppressor
A mutant tRNA gene that recognizes the UAG codon but is aminoacylated and inserts the amino acid at the corresponding position in the growing polypeptide.

Ames test
A genetic test for the identification of carcinogens based upon their mutagenic activity initially developed by Bruce Ames. The test relies upon the ability of a chemical or physical agent to promote the reversion of different classes of mutations that cause histidine auxotrophy.

Amino acid analog
See analog.

Ampicillin (Amp)
An antibiotic that inhibits crosslinking of peptidoglycan chains in the cell wall of eubacteria. Cells growing in the presence of ampicillin synthesize weak cell walls, causing them to burst due to the high internal osmotic pressure. Amp resistance encoded by most transposons and plasmids is due to a periplasmic Beta-lactamase that breaks the Beta-lactam ring of ampicillin. Ampicillin is a derivative of penicillin.

Anaerobic
The absence of oxygen. Often used to describe an organism that is sensitive to oxygen or growth conditions without oxygen.

Analog (or the British spelling Analogue)
A chemical that is similar, but not identical, to another chemical. For example, thioproline is an analog of the amino acid proline, and azaguanine is an analog of the nucleotide guanine. Certain analogs are toxic and can be used to select for mutants that affect the synthesis or metabolism of the corresponding compound.

Angstrom
A unit of measurement that was widely used until recently to describe molecular dimensions, but the unit nanometer (nm) is now more commonly used. One angstrom equals 10 nm.

Antigenic drift
The accumulation of mutations that modify a molecule on the cell surface of a pathogen and thereby alters recognition by the host immune system. These changes prevent preexisting antibodies from recognizing the invading pathogen. This process is most often used to describe viruses. (See Antigenic variation below)

Antigenic variation
A change in the types or amounts of a molecule on the cell surface of a pathogen that alters recognition by the host immune system. Antigenic variation can occur by altering a variety of surface molecules including proteins and carbohydrates. There are many molecular mechanisms for antigenic variation, including inversion, recombination between multiple casettes, and hypermutation. Antigenic variation occurs in eukaryotic microbes (e.g. Trypanosomes), bacteria (e.g. Neisseria gonorrhoeae, and Salmonella enterica), and viruses. The change in surface antigens due to mutation, recombination, or chromosome reassortment in viruses is called antigenic drift.

Annealing
Pairing of a single-stranded nucleic acid with the complementary strand to form a duplex.

Antibiotic
A substance that interfers with a particular step of cellular metabolism, causing either bactericidal or bacteriostatic inhibition; sometimes restricted to those having a natural biological origin.

Antibody
A protein complex that specifically interacts with an antigen.

Anticodon
The three bases in a tRNA that are complementary to those in the codon of the mRNA.

Antigen
A substance that interacts with an antibody.

Antimutator
A mutation that decreases the overall mutation rate, often by modifying DNA polymerase.

Antisense RNA
An RNA molecule that can hybridize to an mRNA molecule. Hybridization of an antisense RNA molecule to the translation start sites on an mRNA prevents the initiation of translation. For example, an antisense RNA is involved in the regulation of transposase expression from Tn10.

Anti-terminator
A protein that allows RNA polymerase to continue transcription through a transcription termination site.

AP endonuclease
An endonuclease which recognizes an AP site and cuts the defective strand on the 5' side of the missing base.

AP site
A molecule of single-stranded or double-stranded DNA missing a purine or pyrimidine base.

Aporepressor
A protein that requires binding of a small molecule co-repressor to negatively regulate gene expression.

Apurinic or apyrimidinic (AP) site
A molecule of single-stranded or double-stranded DNA missing a purine or pyrimidine base.

Apoptosis
Cell death due to a intracellular developmental program or induced by other cells.

A priori
Deduced from first principles; without prior knowledge.

Archae
One of the three domains of living organisms: Archae, Bacteria, and Eukarya. Although they share a basic morphology with bacteria and they are also prokaryotes (i.e. they lack a nuclear membrane), in many molecular details they resemble eukaryotes more than bacteria. Previously called Archaebacteria. First described by Carl Woese at the University of Illinois.

A site
The binding site for the aminoacyl-tRNA on the ribosome.

Atoll
A region of DNA that is absent on the chromosome of an organism but absent from closely related organisms (i.e., the opposite of a genetic island). The loss of such genetic material may confer a distinctive phenotype. For example, absence of certain genes from E. coli enhances virulence.

Attachment site (att)
The specific sequences on phage (attP) and bacterial (attB) chromosomes between which site-specific recombination occurs in order to integrate the phage genome into the bacterial chromosome.

Attenuation
A mechanism of regulating the level of transcription by interfering with mRNA elongation. Slowed translation through a regulatory region allows formation of a RNA secondary structure that promotes transcription termination. Requires coupled transcription and translation and thus is restricted to prokaryotes. Two examples of genes regulated by attenuation include the trp and his operons in E. coli.

Attenuator
A region of leader mRNA that can form alternative secondary structures that determine whether transcription is terminated or proceeds into downstream genes. See Attenuation.

Att site
See attachment site.

Autogenous regulation (autoregulation)
The gene product that controls its own expression. See autogenous repressor.

Autogenous repressor
The product of a regulator gene which binds to its own operator and prevents transcription of the associated structural genes.

Autoradiography
A photographic image produced exposing photographic film to a radiolabeled molecule (e.g. DNA, RNA, or protein). The emissions from the radioactive label expose the photographic film.

Autoregulation
See autogenous regulation.

Autotroph
An organism which does not require any organic carbon for its energy source or for its growth.

Auxotroph
A mutant that will only grow when a particular nutritional requirement (e.g. amino acid, nucleotide, or vitamin) is provided.

Auxotrophic requirement
A nutritional supplement required for growth of an auxotrophic strain.

Avidin
A protein that binds biotin with a very high affinity. Used for the detection of biotinylated probes.