Terminology

Allele - A specific version of a gene that occupies a particular location in the genome. It is distinguished from other alleles of the same gene by differences in nucleotide sequence.
Antiparallel - Arrangement of DNA strands, such that a strand running 5' to 3' forms base pairs with a strand of the opposite polarity (3' to 5').
Aphidicolin - A fungal product with a steroidlike structure that inhibits replicative DNA synthesis specifically in eukaryotes.
Apyrimidinic Endonuclease - An enzyme that recognizes an apyrimidinic site in DNA and cleaves the phosphodiester bond on the 5' side of the deoxyribose. Figure 24.35
Apyrimidinic Site - Within a DNA molecule, a sugar residue lacking an attached pyrimidine. Such sites can arise by action of uracil-DNA N-glycosylase. Figure 24.35
Bacteriocins - Proteins encoded by bacteria that are released by the organism and kill other bacteria.
-lactamase - An enzyme coded for by a plasmid in bacteria that is capable of enzymatically degrading penicillin. Bacteria carrying this gene are resistant to penicillin.
Bidirectional Replication - The mechanism of E. coli replication in which replication starts at a single origin and proceeds in both directions away from it.
Cohesive Ends - Short oligonucleotide sequences at the end of a DNA fragment that are complementary to oligonucleotide sequences at the end of another DNA fragment.
Concatemer - In replication of the T4 and T7 linear genomes, end-to-end linear aggregates of the genome that are made during replication. Figure 24.41.
Conjugation - A form of sexual reproduction in bacteria in which DNA from a donor cell is transferred to a recipient cell. Figure 24.7.
Copy Number - Number of copies per cell of a gene or DNA sequence.
Diploid - For a cell or an organism, the possession of two homologous sets of chromosomes per nucleus (with the possible exception of sex chromosomes, which may be present in only one copy).
DNA Gyrase - A type II topoisomerase from E. coli that can both relax a supercoiled DNA molecule and introduce negative superhelical turns into it. Figure 24.31.
DNA Ligase - An enzyme catalyzing covalent joining of the 5' end of one strand to the 3' end of another. The enzyme catalyes formation of phosphodiester bonds between the ends and is important for joining Okazaki fragments together. Figure 24.4, Figure 24.24.
DNA Polymerase I - A DNA polymerase in E. coli with a 5' -> 3' exonuclease activity (useful for removing Okazaki fragments), a 3' -> 5' exonuclease activity (good for proofreading), and a 5' to 3' DNA polymerase activity. Table 24.2.
DNA Polymerase II - A DNA polymerase in E. coli that probably plays a role in DNA repair and the SOS response Table 24.2
DNA Polymerase III - The DNA polymerase in E. coli responsible for most DNA synthesis. It is found at the replication fork in active E. coli DNA synthesis. Table 24.2
DNA Polymerase III Holoenzyme - A multiprotein aggregate that includes DNA polymerase III and is involved in replicating DNA in vivo.
DNA Replication - The process whereby a DNA molecule is copied by DNA polymerase and accessory proteins to make two copies where one existed originally.
dnaA - The E. coli protein that binds to oric to initiate the process of DNA replication.
dnaB - A helicase that binds to the oric complex during initiation of DNA replication in E. coli.
dnaC - An initiation protein in E. coli that binds with dnaB during initiation.
dnaG - The name of the structural gene for primase in E. coli. It binds at the oric complex during initiation.
dUTPase - An enzyme which cleaves dUTP to dUMP plus PPi. It is important in reducing the amount of dUTP in the cell so that less is available for DNA polymerase during DNA replication.
Gap - A single-strand interruption in duplex DNA, in which nucleotides are missing, as distinguished from a nick, a similar interruption with no missing nucleotides.
Genetic Map - A map that identifies the relative positions of genes on chromosomes Figure 24.8
Genome - The total genetic information contained in a cell, an organism, or a virus.
Genotype - The genetic constitution of an individual organism.
Hairpin (stem loop) - A structure in DNA (or RNA) arising from pairing of complementary sequences within a single strand.
Haploid - For a cell or an organism, the possession of only one copy of each chromosome per nucleus (or cell).
Helicases - Enzymes that catalyze the unwinding of duplex DNA strands. Figure 24.6, Figure 24.27
Integration - Insertion of one molecue of DNA into another.
Klenow Fragment - A proteolytic cleavage fragment of DNA polymerase I of E. coli that contains the DNA polymerase and 3' ->5' exonuclease activities of the enzyme.
Lagging Strand - The daughter strand during DNA replication that is extended in the direction away from the replication fork in a discontinuous manner. This strand contains the Okazaki fragments. Figure 24.3
Leading Strand - The daughter strand during DNA replication that is extended in the same direction as the replication fork and in a continuous manner. Figure 24.3
Linkage Map - A map of the genes of a genome made by measuring recombination frequencies of the genes.
Long Terminal Repeats - A feature of the retrovirus genome in which the sequence at one end of the linear chromosome is repeated at the other end.
Marker - Any allele whose frequency can be determined quantitatively.
Mismatch Repair Systems - Cellular repair system that works by scanning the newly replicated DNA, excising any residues that are not properly base-paired and replacing them with the correct nucleotides.
Nick - A single-strand interruption in duplex DNA, in which no nucleotides are missing, as distinguished from a gap, a similar interruption with one or more missing nucleotides.
Nick Translation - A process in which nucleotides in one strand of a nucleic acid duplex are replaced one by one with nucleotides complementary to the other strand. The process starts at a nick in the strand and causes the location of the nick to migrate. Figure 24.5.
Okazaki Fragments - The discontinuous stretches in which the lagging strand is initially synthesized during DNA replication. These fragments are later joined to form a continuous strand. Figure 24.3, Figure 24.6
oric - The replication origin on the E. coli chromosome.
Phenotype - The appearance and other measurable characteristics of an organism; it results from the interaction of the organism's genetic makeup with the environment.
Physical Map - A map which shows the physical locations of genes on a chromosome.
Plasmid - Small, extrachromosomal circular DNA molecules found in many bacteria. They replicate independently of the main chromosome and may occur in multiple copies per cell.
polA - The name of the structural gene for DNA polymerase I in E. coli.
polB - The name of the structural gene for DNA polymerase II in E. coli.
polC - The name of the structural gene for DNA polymerase III in E. coli.
Primase - An enzyme essential for initiating DNA replication in most cells. It is an RNA polymerase and creates a short RNA primer, which is elongated by DNA polymerase. Figure 24.4
Primer Strand - The strand being elongated in DNA replication.
Primosome - An enzyme complex that is located in the replication fork during DNA replication. It synthesizes the RNA primers on the lagging strand and also participates in unwinding the parental DNA helix.
Processivity - For a DNA or an RNA polymerase, the average number of nucleotides incorporated per event of binding between the polymerase and a 3' primer terminus. It describes the tendency of a polymerase to remain bound to a template.
Proofreading - A process in DNA replication that occurs when the 3' to 5' exonuclease activity of a DNA polymerae recognizes and excises mispaired bases in the newly replicated DNA. Such a process probably contributes to the surprisingly low error rates of DNA replication in vivo. Figure 24.44
Reconstitution - A method of studying an enzymatic process in which the individual proteins for a process are purified separately and then added back together in a test tube to perform the reaction they catalyze in vivo.
Replicase - An RNA-dependent RNA polymerase found in RNA viruses that do not go through a DNA intermediate in their life cycle.
Replication Fork - A structure occurring in DNA replication. It is the point at which replication is actually occurring. Figure 24.1
Replication Origin - A region in a DNA molecule defined by a specific nucleotide sequence where replication of DNA begins.
Replicative Form (RF) - In bacteriophages, the circular duplex form of DNA.
Replicon - The cluster of DNA that includes the sequence of nucleotides at which DNA replication begins and the structural genes for proteins whose action on the origin sequence inititates replication at that point.
Replisome - The multiprotein DNA replication complex.
Retrovirus - An RNA virus that goes through a DNA intermediate as part of its life cycle. It contains an enzyme called reverse transcriptase. Figure 24.45
Reverse Transcriptase - An enzyme, found in retroviruses, that uses RNA as a template to make DNA. Figure 24.45
Reversion - A mutation in a mutated gene which restores the wild-type genotype (and phenotype).
RFI - In bacteriophages, a covalently closed circular duplex of DNA. Figure 24.36
RFII - In bacteriophage DNA, a nicked circular form of the DNA. Figure 24.36
RNAse H - An enzyme that degrades RNA paired to DNA. Reverse transcriptase has an activity like this. Figure 24.45
Second-site Reversion (Suppression) - A mutation in a mutated gene that restores the wild-type phenotype, but which occurs at a location other than the original mutation.
Semiconservative DNA Replication - A mode of DNA replication in which each daughter duplex contains one strand from the parent duplex and one newly synthesized strand.
Silent Mutation - A mutation which occurs that does not affect the phenotype of the organism.
Single-Strand DNA-Binding Protein (SSB - also called Helix Destabilizing protein) - An E. coli protein that binds to DNA so as to stabilize a structure in which hydrogen-bonding surfaces of the DNA bases are spatially oriented toward the incoming nucleotides. Figure 24.6, Figure 24.26.
Strand Displacement - A phenomenon that occurs when replication of one DNA strand displaces a previously made DNA strand during the replication process. Figure 24.15.
Telomerase - An enzyme capable of elongating the termini of eukaryotic linear chromosomes.
Template Strand - The strand being copied in DNA replication.
Terminal Protein - In adenovirus and the 29 bacteriophage, a protein covalently attached to the 5' terminus of each strand of the linear genome that serves to initiate DNA replication.
Terminal Redundancy - Duplication of a small part of the genome at the end of a linear chromosome. Is employed by bacteriophages T4 and T7.
Structure - The appearance of the E. coli chromosome during bidirectional replication, as viewed by electron microscopy. .
Topoisomerases - Enzymes that change the supercoiling of DNA helices by either allowing the superhelical torsion to relax (thus reducing the supercoiling) or adding more twists (thus increasing the supercoiling). Figure 24.6
Transcription - The synthesis of an RNA molecule complementary to a DNA strand. The information encoded in the base sequence of the DNA is thus transcribed into the RNA version of the same code.
Translation - The synthesis of a polypeptide under the direction of an mRNA, so that the nucleotide sequence of the mRNA is translated into the amino acid sequence of the protein.
Virion - A virus particle.
Wild Type - An unaltered, unmutated form of a gene in an organism.