Ch 11 Book Terms

Question 1

Topoisomerase

Answer 1

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.

Question 2

Initiation

Answer 2

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.

Question 3

Elongation

Answer 3

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.

Question 4

Replisome

Answer 4

The multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA. It contains DNA polymerase and other enzymes.

Question 5

Conditional Lethals

Answer 5

A mutation that is lethal under one set of conditions but not lethal under a second set of conditions, such as temperature.

Question 6

dna Mutants

Answer 6

Temperature-sensitive replication mutants in Escherichia coli that identify a set of loci called the dna genes.

Question 7

Quick-stop Mutants

Answer 7

Temperature-sensitive replication mutants that are defective in replication elongation during synthesis of DNA.

Question 8

Slow-stop Mutants

Answer 8

Temperature-sensitive replication mutants that are defective in initiation of replication.

Question 9

in vitro Complementation

Answer 9

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.

Question 10

Semiconservative Replication

Answer 10

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.

Question 11

DNA Polymerase

Answer 11

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).

Question 12

DNA Repair

Answer 12

The removal and replacement of damaged DNA by the correct sequence.

Question 13

DNA Replicases

Answer 13

“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).

Question 14

Holoenzymes

Answer 14

(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.

Question 15

Error-prone Polymerases

Answer 15

A DNA polymerase that incorporates noncomplementary bases into the daughter strand.

Question 16

Klenow Fragment

Answer 16

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.

Question 17

Nick Translation

Answer 17

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.

Question 18

Proofreading

Answer 18

A mechanism for correcting errors in DNA synthesis that involves scrutiny of individual units after they have been added to the chain.

Question 19

Processivity

Answer 19

The ability of an enzyme to perform multiple catalytic cycles with a single template instead of dissociating after each cycle.

Question 20

Mutation Hotspots

Answer 20

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.

Question 21

Leading Strand (Forward Strand)

Answer 21

The strand of DNA that is synthesized continuously in the 5′ to 3′ direction.

Question 22

Lagging Strand

Answer 22

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.

Question 23

Okazaki Fragments

Answer 23

Short stretches of 1,000 to 2,000 bases produced during discontinuous replication; they are later joined into a covalently intact strand.

Question 24

Semidiscontinuous Replication

Answer 24

The mode of replication in which one new strand is synthesized continuously while the other is synthesized discontinuously.

Question 25

Helicase

Answer 25

An enzyme that uses energy provided by ATP hydrolysis to separate the strands of a nucleic acid duplex.

Question 26

Single-Stranded Binding Protein (SSB)

Answer 26

The protein that attaches to single-stranded DNA, thereby preventing the DNA from forming a duplex.

Question 27

Primer

Answer 27

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.

Question 28

Clamp

Answer 28

A protein complex that forms a circle around the DNA. By connecting to DNA polymerase, it ensures that the enzyme action is processive.

Question 29

DNA Ligase

Answer 29

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.

Question 30

Autonomously Replicating Sequences (ARS)

Answer 30

A DNA sequence element that contains an origin of replication.

Question 31

Polymerase Switch

Answer 31

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.

Question 32

Lesion Bypass

Answer 32

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.