Deck 22: DNA Replication

Question 1

The individual proteins of the E. coli replisome complex dissociate and reassociate in a dynamic manner.

Answer 1

True

Question 2

The specificity of DNA polymerase activity is determined by the shapes of the substrate molecules as well as their ________ capacity.

Answer 2

hydrogen-bonding

Question 3

E. coli DNA polymerase I in vitro requires a template and primer, which must always be separate nucleic acids.

Answer 3

False

Question 4

Replication of linear genomes is problematic because primer removal at the ________ leaves a gap in the duplex.

Question 5

The initiation of DNA replication in E. coli can occur anywhere on the genome that has repeat sequence elements and requires the interaction of DnaA proteins that results in stretching and bending of DNA causing tension that leads to local unwinding.

Question 6

Eukaryotes solve the problem of replicating the ends of their linear chromosomes by:

A) terminal redundancy whereby each end of the chromosome is duplicated allowing recombination.
B) using a protein as a primer.
C) by covalently linking the two strands at each end of the linear chromosome to form a circle.
D) enzyme activity that uses an RNA template and reverse transcription in a series of repeat cycles.
E) all of the above.

Question 7

Which of the following statements about E. coli DNA polymerase I is FALSE?

A) It can copy a circular DNA template but cannot join the ends.
B) It can extend a gapped duplex from a 3'OH group and displace a preexisting 5' end.
C) The 3' exonuclease site is some distance from the polymerase active site.
D) It has 3' exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.
E) It has 5' exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.

Question 8

Okazaki fragments are initiated with ________ primers by a primase enzyme.

Question 9

Evidence supporting E.coli DNA polymerase III having the major role in nucleotide incorporation during replication includes:

A) DNA polymerase III has a high Vmax.
B) There are ten or fewer molecules of enzyme per cell.
C) Replication is blocked at high temperatures in temperature sensitive mutants with a thermolabile form of DNA polymerase III.
D) A point mutation can inactivate DNA pol III and inhibit replication.
E) All of the above.

Question 10

A null mutant in the ________ activity of DNA polymerase I will be defective in DNA replication because it will be unable to carry out primer removal.

Question 11

DNA ligase can join Okazaki fragments after activation by ________ of a lysine residue in the active site.

Question 12

Which of the following is NOT a requirement of E. coli DNA ligase?

A) A nick in the DNA strand must have a 3' OH group.
B) A nick in the DNA strand must have a 5' phosphate group.
C) The nucleotides being linked must be adjacent in the duplex structure.
D) The nucleotides being linked must be properly based-paired.
E) ATP

Question 13

The replicative E. coli DNA polymerase is a symmetrical dimer, with each part of the dimer being responsible for replicating one strand of the DNA duplex.

Question 14

DNA gyrase is able to relax supercoils as well as introduce negative supercoils in DNA.

Question 15

Fidelity of DNA replication is determined solely by the 3' exonucleolytic proofreading activity of the DNA polymerase.

Question 16

Both type I or type II topoisomerases carry out their catalytic activity via a covalent phosphodiester intermediate between a phosphate group on the DNA and a tyrosine hydroxyl group on the enzyme.

Question 17

Which of the following statement about eukaryotic DNA replication is INCORRECT?

A) Only one DNA polymerase is required to propagate a replication fork.
B) The same polymerase in humans is involved in proofreading and primer removal as well as lagging strand elongation.
C) The main DNA polymerase that elongates the leading strand has an intrinsic processivity factor.
D) Eukaryotes require two enzymes to remove RNA primers.
E) Chromatin must be dismantled in advance of replication forks and reassembled on daughter strands after the fork has passed through.

Question 18

E. coli DNA polymerase III makes extensive contacts with the ________ in duplex DNA.

Question 19

Which of the following statements about E. coli DNA replication is INCORRECT?

A) The β subunit of DNA polymerase III is the sliding clamp essential for processivity.
B) The clamp-loading complex uses exchange between ADP and ATP to eject the clamp loader and close the clamp.
C) Single-stranded DNA-binding protein promotes denaturation of DNA by lowering the melting temperature.
D) Helicases are multimeric proteins that bind preferentially to one strand and rely on ATP-hydrolysis to unwind the duplex.
E) Topoisomerases are responsible for relieving torsional stress ahead of the replication fork generated by unwinding the duplex.

Question 20

The DNA polymerase reaction is a nucleophilic substitution facilitated by:

A) the 3'OH group being a weak nucleophile.
B) the 3'OH group being a strong nucleophile.
C) the pyrophosphate being a good leaving group.
D) the reaction being irreversible.
E) none of the above.

Question 21

A single-stranded RNA virus makes a DNA copy of itself by the use of a viral multifunctional enzyme called ________.