Terminology

5,10-Methenyltetrahydrofolate - A molecule that acts like 8-hydroxy-5-deazaflavin in DNA photolyases. It acts as a light harvesting factor.

5-Methylcytosine - The only methylated base found in eukaryotic DNA

6-4 Photoproduct - A structure in DNA of a covalent link made between carbon #4 of the 3' pyrimidine and carbon #6 of an adjacent 5' pyrimidine. It occurs as a result of exposure to UV light. It can lead to mutation during replication. Figure 25.9.

8-Hydroxy-5-deazaflavin - A molecule that acts like 5,10-methenyltetrahydrofolate in DNA photolyases. It acts as a light harvesting factor.

8-Oxoguanine - An oxidized form of guanine arising from oxidative damage.

attB - A locus in the E. coli chromosome targeted by the bacteriophage for site-specific recombination. Figure 25.31.

attP The site on the chromosome involved in site-specific recombination with the E. coli chromosome. Figure 25.31.

Base Excision Repair - Cellular DNA repair system that cleaves the glycosidic bond connecting a damaged base to the DNA sugar-phosphate backbone.

BRCA-1 - A gene associated with an increased risk of breast and ovarian cancer that is involved in transcription-coupled excision repair.

Chi - An octanucleotide sequence in E. coli (5'-GCTGGTCC-3') recognized by exonuclease V. At this sequence, the exonuclease switches strands and its preferred polarity of DNA degradation. This facilitates the loading of RecA to a free 3' end and initiates strand invasion of a nearby duplex. Figure 25.28

Chromophore - A structural moiety that absorbs light of characteristic wavelengths. Figure 25.10

Clonal Expansion - A mechanism by which large-scale production of specific antibodies occurs. The B and T cells produced by the body have randomly generated antigen specificities. When a particular antigen enters the body, it induces proliferation only in B and T cells that happen to be specific for it. Thus, the antigen selects the cells that will mount an immune response against it and stimulates them to undergo clonal proliferation.

Cyclobutane Pyrimidine Dimer - A structure in DNA of two covalent bonds made between adjacent pyrimidine residues as a result of exposure to UV light. The two new bonds form a four-membered ring and can lead to mutation during replication if not repaired. Figure 25.9

DNA Photolyase - An enzyme that repairs cyclobutane pyrimidine dimers in the presence of visible light. Figure 25.10.

Excinuclease - A term used to describe the enzymatic cutting of DNA by the uvrABC system.

Exonuclease V (also called RecBCD nuclease) - A protein in E. coli recombination that binds at a double-strand break on duplex DNA and uses a helicase activity to unwind and partially degrade the DNA. It helps to load RecA to a 3' end. Figure 25.28

Gene Amplification - Selective amplification of a specific region of a genome

Heteroduplex - A double stranded DNA in which the two strands were not made from each other and came from other molecules. Figure 25.19

Holliday Junction - An intermediate during homologous recombination; a four-armed structure in which each of the participating DNA duplexes has exchanged one strand with the other duplex. Figure 25.20

Holliday Model - A model for homologous recombination involving alignment of homologous sequences, nicking, strand invasion, ligation, migration of the cross point (Holliday Junction), isomerization, breaking of strands, and rejoining. A variation of the model was proposed by Meselson and Radding. Figure 25.20

Homogeneously Staining Region - A region of a chromosome that lacks the typical chromosome banding pattern. It can be produced by gene amplification.

Homologous Recombination - Genetic recombination that requires extensive sequence homology between the recombining DNA molecules. Meiotic recombination by crossing over in eukaryotes is an example.

Illegitimate Recombination - An extremely rare type of recombination that possibly occurs by chance. It involves neither sequence homology nor the action of any known protein.

Immunoglobulin G (IgG) - An antibody of class 'G' containing two heavy chains and two light chains.

Maintenance Methylase - A eukaryotic enzyme that ensures that all of the methylated sites in the parental DNA are also methylated in the progeny DNA. Figure 25.3

Meselson -Radding Model - A proposed model for homologous recombination involving alignment of homologous sequences, nicking, strand displacement synthesis, strand invasion, loop cleavage, ligation of the displaced strand, isomerization, branch migration and ligation of the invading 'A' strand, and resolution as in the Holliday model. Figure 25.22

Microsatellite Instability - Mutations consisting of repeats of single, double, and triple-nucleotide sequences which probably arise by 'slipping' of strands during DNA polymerization.

Mismatch Repair - Cellular DNA repair system that recognizes DNA mismatches created either by replication errors, non-homologous recombination, or damage to one DNA base, and corrects the error.

Mutagenesis - The process of creating mutations.

mutT - An E. coli gene that catalyzes the following reaction: 8-oxo-dGTP + H2O <=> 8-oxo-dGMP + PPi

Nucleotide Excision Repair - A process whereby a damaged section of a DNA chain is cut out, or excised, followed by the action of DNA polymerase and then DNA ligase to regenerate a covalently closed duplex at the site of the original damage.

O⁶-Alkylguanine Alkyltransferase - An unusual repair enzyme that transfers a methyl or ethyl group from an O⁶-methylguanine or O⁶-ethylguanine to a cysteine residue in the active site of the protein. It can thus, only function once.

Oncogenic Transformation - Conversion of a normal cell to a cancerous one.

Photoproducts - The products that result when light energy causes a chemical reaction to occur in a substance. With respect to DNA, the term refers to the types of damaged DNA that can be caused by uv irradiation.

Plaque - A cleared area on a Petri dish on a plate of bacteria arising from growth of a bacteriophage in that region.

Postreplication Repair - Processes that attempt to fix mismatches, gaps, or damage to DNA that escapes the repair process that occurs during replication

Prophage - The integrated, inactive chromosome in the E. coli genome.

Provirus - With respect to a retrovirus, a virus integrated into the host genome.

RecA - A multifunctional protein with Mr of about 38,000. In recombination it promotes the pairing of homologous strands. In the SOS response it also plays a role in gene activation. Figure 25.23

Recombination - A process in an organism in which two parent DNA molecules give rise to daughter DNA that combines segments from both parent molecules. It may involve the integration of one DNA molecule into another, the substitution of a DNA segment for a homologous segment on another DNA molecule, or the exchange of homologous segments between two DNA molecules.

Recombinational Repair - Cellular DNA repair system in which newly replicated DNA duplexes undergo genetic recombination, with ultimate removal of the damaged DNA segment.

Resolvase - An enzyme found in class II and class III type transposons that catalyzes site-specific recombination between the two elements of the transposon created by replicative transposition.

Restriction Endonucleases - Enzymes that catalyze the double-strand cleavage of DNA at specific base sequences.

Restriction/Modification - A defense system common in bacteria involving a restriction endonuclease and a site-specific methylase that methylates the same sequence the restriction endonuclease cuts at. Normally, the host DNA is methylated, which protects against the action of the restriction endonuclease, but invading viral DNA is not methylated, and is cut. Figure 25.5

Retrotransposon - A transposable element which goes through an RNA stage.

Retroviruses - A family of RNA viruses that possess reverse transcriptase. After the virus infects a cell, this enzyme transcribes the RNA genome into a double-strand DNA version, which integrates into a host chromosome. Human immunodeficiency virus (HIV) is an example.

ruvA - A protein involved in E. coli recombination. It is a DNA binding protein, whose specificity directs it toward the four-stranded Holliday structure

ruvB A protein involved in E. coli recombination. It is an ATP-requiring motor protein, which binds to two opposed arms of the Holliday junction and rotates them in opposite directions, forcing branch migration by driving the rotational movement of the other two strands toward the junction.

ruvC A protein involved in E. coli recombination. It begins resolution of the Holliday structure by nicking two strands.

Site-specific Recombination - Recombination that involves only limited sequence homology between recombining partners. Sites of breaking and joining are determined by specific DNA-protein interactions. Figure 25.17

Somatic Mutations - Mutations that occur in non-germline cells.

SOS Response - A bacterial response to various potentially lethal stresses, including severe UV irradiation. It involves the coordinated expression of a set of proteins that carry out survival maneuvers, including an error-prone type of repair for thymine dimers in DNA.

Strand Invasion - A process that is postulated to occur in homolous recombination in which an unpaired part of a strand of DNA invades a duplex region of another DNA.

Thymine Glycol - An oxidized form of thymine arising from oxidative damage.

Transition Mutation - A mutation that changes a purine-pyrimidine base pair to a different purine-pyrimidine base pair. An example is a transition from G-C to A-T.

Transposable Genetic Elements - DNA fragments containing genes that do not have a fixed location in a genome but can move from place to place within the genome, albeit with low frequency. Figure 25.34.

Transposase - An enzyme involved in movement of a transposon from one DNA to another. It can make a staggered cut in a specific sequence in a target DNA into which the transposon moves.

Transposition - A type of recombination which involves neither sequence homology nor the RecA protein (in E. coli) but does require a special sequence on the donor DNA.

Tranverse Mutation - A mutation that changes a purine-pyrimidine base pair to a different pyrimidine-purine base pair. An example is a transition from G-C to T-A.

Unequal Crossing Over - A recombinational process that can lead to multiple copies of a gene. It may be important in gene amplification.

uvrD - A helicase component of the E. coli nucleotide excision repair system.

Xis - A protein required in addition to Int and IHF to reverse the process by which was integrated into the E. coli genome.