Ch 11 Book Terms Flashcards
Topoisomerase
An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other. It does this by cutting the DNA, passing DNA through the break, and resealing the DNA.
Initiation
The stages of transcription up to synthesis of the first bond in RNA. This includes binding of RNA polymerase to the promoter and melting a short region of DNA into single strands.
Elongation
The stage in a macromolecular synthesis reaction (replication, transcription, or translation) when the nucleotide or polypeptide chain is extended by the addition of individual subunits.
Replisome
The multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA. It contains DNA polymerase and other enzymes.
Conditional Lethals
A mutation that is lethal under one set of conditions but not lethal under a second set of conditions, such as temperature.
dna Mutants
Temperature-sensitive replication mutants in Escherichia coli that identify a set of loci called the dna genes.
Quick-stop Mutants
Temperature-sensitive replication mutants that are defective in replication elongation during synthesis of DNA.
Slow-stop Mutants
Temperature-sensitive replication mutants that are defective in initiation of replication.
in vitro Complementation
A functional assay used to identify components of a process. The reaction is reconstructed using extracts from a mutant cell. Fractions from wild-type cells are then tested for restoration of activity.
Semiconservative Replication
DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.
DNA Polymerase
An enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).
DNA Repair
The removal and replacement of damaged DNA by the correct sequence.
DNA Replicases
“See DNA polymerase”
An enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).
Holoenzymes
(1) The DNA polymerase complex that is competent to initiate replication.
(2) The RNA polymerase form that is competent to initiate transcription. It consists of the five subunits of the core enzyme (α2ββ′ω) and sigma factor.
Error-prone Polymerases
A DNA polymerase that incorporates noncomplementary bases into the daughter strand.
Klenow Fragment
A large protein fragment (68 kD) produced when DNA polymerase I is cleaved by a protease. It is used in synthetic reactions in vitro. It retains polymerase and proofreading 3′–5′ exonuclease activities.
Nick Translation
The ability of Escherichia coli DNA polymerase I to use a nick as a starting point from which one strand of a duplex DNA can be degraded and replaced by resynthesis of new material; it is used to introduce radioactively labeled nucleotides into DNA in vitro.
Proofreading
A mechanism for correcting errors in DNA synthesis that involves scrutiny of individual units after they have been added to the chain.
Processivity
The ability of an enzyme to perform multiple catalytic cycles with a single template instead of dissociating after each cycle.
Mutation Hotspots
A site in the genome at which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.
Leading Strand (Forward Strand)
The strand of DNA that is synthesized continuously in the 5′ to 3′ direction.
Lagging Strand
The strand of DNA that must grow overall in the 3′ to 5′ direction and that is synthesized discontinuously in the form of short fragments (5′–3′) that are later connected covalently.
Okazaki Fragments
Short stretches of 1,000 to 2,000 bases produced during discontinuous replication; they are later joined into a covalently intact strand.
Semidiscontinuous Replication
The mode of replication in which one new strand is synthesized continuously while the other is synthesized discontinuously.
Helicase
An enzyme that uses energy provided by ATP hydrolysis to separate the strands of a nucleic acid duplex.
Single-Stranded Binding Protein (SSB)
The protein that attaches to single-stranded DNA, thereby preventing the DNA from forming a duplex.
Primer
A short sequence (often of RNA) that is paired with one strand of DNA and that provides a free 3′–OH end at which a DNA polymerase starts synthesis of a deoxyribonucleotide chain.
Clamp
A protein complex that forms a circle around the DNA. By connecting to DNA polymerase, it ensures that the enzyme action is processive.
DNA Ligase
The enzyme that makes a bond between an adjacent 3′–OH and 5′–phosphate end where there is a nick in one strand of duplex DNA.
Autonomously Replicating Sequences (ARS)
A DNA sequence element that contains an origin of replication.
Polymerase Switch
The transition from initiation to elongation of DNA replication by substitution of an enzyme that will extend the chain. On the leading strand, this is DNA polymerase ε; on the lagging strand this is DNA polymerase δ.
Lesion Bypass
Replication by an error-prone DNA polymerase on a template that contains a damaged base. The polymerase can incorporate a noncomplementary base into the daughter strand.
