Chapter 25 DNA Metabolism

16. Which of these enzymes is not directly involved in methyl-directed mismatch repair in E. coli? A) DNA glycosylase B) DNA helicase II C) DNA ligase D) DNA polymerase III E) Exonuclease I

A) DNA glycosylase

27. In homologous genetic recombination, RecA protein is involved in: A) formation of Holliday intermediates and branch migration. B) introduction of negative supercoils into the recombination products. C) nicking the two duplex DNA molecules to initiate the reaction. D) pairing a DNA strand from one duplex DNA molecule with sequences in another duplex, regardless of complementarity. E) resolution of the Holliday intermediate.

A) formation of Holliday intermediates and branch migration.

13. The function of the eukaryotic DNA replication factor PCNA (proliferating cell nuclear antigen) is similar to that of the β-subunit of bacterial DNA polymerase III in that it: A) facilitates replication of telomeres. B) forms a circular sliding clamp to increase the processivity of replication. C) has a 3' → 5' proofreading activity. D) increases the speed but not the processivity of the replication complex. E) participates in DNA repair.

B) forms a circular sliding clamp to increase the processivity of replication.

17. The role of the Dam methylase is to: A) add a methyl group to uracil, converting it to thymine. B) modify the template strand for recognition by repair systems. C) remove a methyl group from thymine. D) remove a mismatched nucleotide from the template strand. E) replace a mismatched nucleotide with the correct one.

B) modify the template strand for recognition by repair systems.

19. In base-excision repair, the first enzyme to act is: A) AP endonuclease. B) Dam methylase. C) DNA glycosylase. D) DNA ligase. E) DNA polymerase.

C) DNA glycosylase.

1. The Meselson-Stahl experiment established that: A) DNA polymerase has a crucial role in DNA synthesis. B) DNA synthesis in E. coli proceeds by a conservative mechanism. C) DNA synthesis in E. coli proceeds by a semiconservative mechanism. D) DNA synthesis requires dATP, dCTP, dGTP, and dTTP. E) newly synthesized DNA in E. coli has a different base composition than the preexisting DNA.

C) DNA synthesis in E. coli proceeds by a semiconservative mechanism.

11. Which of the following is not required for elongation during DNA replication in E. coli? A) DnaB (helicase) B) DnaG (primase) C) DnaC D) β-sliding clamp E) Clamp loader

C) DnaC

31. Which of the following is false about transposition of DNA? A) The diversity of immunoglobins is in part due to DNA recombination by transposition. B) Transposition occurs in both prokaryotes and eukaryotes. C) Enzymes are not required for transposition. D) The first step of transposition can be single- or double-stranded DNA cleavage. E) Transposition can lead to simple movement of a DNA region or duplication of that region in a new location.

C) Enzymes are not required for transposition.

4. Which one of the following statements about enzymes that interact with DNA is true? A) E. coli DNA polymerase I is unusual in that it possesses only a 5' → 3' exonucleolytic activity. B) Endonucleases degrade circular but not linear DNA molecules. C) Exonucleases degrade DNA at a free end. D) Many DNA polymerases have a proofreading 5' → 3' exonuclease. E) Primases synthesize a short stretch of DNA to prime further synthesis.

C) Exonucleases degrade DNA at a free end.

21. The repair of cyclobutane pyrimidine dimers by bacterial DNA photolyase involves the cofactor: A) coenzyme A. B) coenzyme Q. C) FADH-. D) pyridoxal phosphate (PLP). E) thiamine pyrophosphate (TPP).

C) FADH-.

Prokaryotic DNA polymerase III: A) contains a 5' → 3' proofreading activity to improve the fidelity of replication. B) does not require a primer molecule to initiate replication. C) has a β subunit that acts as a circular clamp to improve the processivity of DNA synthesis. D) synthesizes DNA in the 3' → 5' direction. E) synthesizes only the leading strand; DNA polymerase I synthesizes the lagging strand.

C) has a β subunit that acts as a circular clamp to improve the processivity of DNA synthesis.

5. E. coli DNA polymerase III: A) can initiate replication without a primer. B) is efficient at nick translation. C) is the principal DNA polymerase in chromosomal DNA replication. D) represents over 90% of the DNA polymerase activity in E. coli cells. E) requires a free 5'-hydroxyl group as a primer.

C) is the principal DNA polymerase in chromosomal DNA replication.

9. Which of the following is not required for initiation of DNA replication in E. coli? A) DnaB (helicase) B) DnaG (primase) C) Dam methylase D) DNA ligase E) DnaA (a AAA+ ATPase)

D) DNA ligase

22. Which mechanism is used to repair a thymidine dimer in DNA? A) Mismatch repair B) Base-excision repair C) Nucleotide-excision repair D) Direct repair E) More than one is used for this type of lesion

D) Direct repair

30. Which of the following is not a feature of site-specific recombination? A) A specific recombinase enzyme is required. B) The energy of the phosphodiester bond is preserved in covalent enzyme-DNA linkage. C) Recombination sites have non-palindromic sequences. D) Formation of Holliday intermediates is required. E) Insertions or deletions can result from site-specific recombination.

D) Formation of Holliday intermediates is required.

29. Which of the following is not a feature of homologous recombination during meiosis? A) A double strand break B) Cleavage of two crossover events C) Alignment of homologous chromosomes D) Formation of a single Holliday intermediate E) Exposed 3' ends invade the intact duplex DNA of the homolog

D) Formation of a single Holliday intermediate

26. In homologous recombination in E. coli, the protein that assembles into long, helical filaments that coat a region of DNA is: A) DNA methylase. B) DNA polymerase. C) histone. D) RecA protein. E) RecBCD enzyme.

D) RecA protein.

25. In homologous recombination in E. coli, the protein that moves along a double-stranded DNA, unwinding the strands ahead of it and degrading them, is: A) chi. B) DNA ligase. C) RecA protein. D) RecBCD enzyme. E) RuvC protein (resolvase).

D) RecBCD enzyme.

18. When bacterial DNA replication introduces a mismatch in a double-stranded DNA, the methyl-directed repair system: A) cannot distinguish the template strand from the newly replicated strand. B) changes both the template strand and the newly replicated strand. C) corrects the DNA strand that is methylated. D) corrects the mismatch by changing the newly replicated strand. E) corrects the mismatch by changing the template strand.

D) corrects the mismatch by changing the newly replicated strand.

14. The Ames test is used to: A) detect bacterial viruses. B) determine the rate of DNA replication. C) examine the potency of antibiotics. D) measure the mutagenic effects of various chemical compounds. E) quantify the damaging effects of UV light on DNA molecules.

D) measure the mutagenic effects of various chemical compounds.

20. The ABC excinuclease is essential in: A) base-excision repair. B) methyl-directed repair. C) mismatch repair. D) nucleotide-excision repair. E) SOS repair.

D) nucleotide-excision repair.

7. The 5' → 3' exonuclease activity of E. coli DNA polymerase I is involved in: A) formation of a nick at the DNA replication origin. B) formation of Okazaki fragments. C) proofreading of the replication process. D) removal of RNA primers by nick translation. E) sealing of nicks by ligase action.

D) removal of RNA primers by nick translation.

2. When a DNA molecule is described as replicating bidirectionally, that means that it has two: A) chains. B) independently replicating segment. C) origins. D) replication forks. E) termination points.

D) replication forks.

3. An Okazaki fragment is a: A) fragment of DNA resulting from endonuclease action. B) fragment of RNA that is a subunit of the 30S ribosome. C) piece of DNA that is synthesized in the 3' → 5' direction. D) segment of DNA that is an intermediate in the synthesis of the lagging strand. E) segment of mRNA synthesized by RNA polymerase.

D) segment of DNA that is an intermediate in the synthesis of the lagging strand.

12. In contrast to bacteria, eukaryotic chromosomes need multiple DNA replication origins because: A) eukaryotic chromosomes cannot usually replicate bidirectionally. B) eukaryotic genomes are not usually circular, like the bacterial chromosome is. C) the processivity of the eukaryotic DNA polymerase is much less than the bacterial enzyme. D) their replication rate is much slower, and it would take too long with only a single origin per chromosome. E) they have a variety of DNA polymerases for different purposes, and need a corresponding variety of replication origins.

D) their replication rate is much slower, and it would take too long with only a single origin per chromosome.

23. Which mechanism is used to repair a chemically modified base in DNA? A) Mismatch repair B) Base-excision repair C) Nucleotide-excision repair D) Direct repair E) More than one is used for this type of lesion

E) More than one is used for this type of lesion

10. At replication forks in E. coli: A) DNA helicases make endonucleolytic cuts in DNA. B) DNA primers are degraded by exonucleases. C) DNA topoisomerases make endonucleolytic cuts in DNA. D) RNA primers are removed by primase. E) RNA primers are synthesized by primase.

E) RNA primers are synthesized by primase.

15. In a mammalian cell, DNA repair systems: A) are extraordinarily efficient energetically. B) are generally absent, except in egg and sperm cells. C) can repair deletions, but not mismatches. D) can repair most types of lesions except those caused by UV light. E) normally repair more than 99% of the DNA lesions that occur.

E) normally repair more than 99% of the DNA lesions that occur.

28. Which of the following statements is false? In vitro, the strand-exchange reaction: A) can include formation of a Holliday intermediate. B) is accompanied by ATP hydrolysis. C) may involve transient formation of a three- or four-stranded DNA complex. D) needs RecA protein. E) requires DNA polymerase.

E) requires DNA polymerase.

6. The proofreading function of DNA polymerase involves all of the following except: A) a 3' → 5' exonuclease. B) base pairing. C) detection of mismatched base pairs. D) phosphodiester bond hydrolysis. E) reversal of the polymerization reaction.

E) reversal of the polymerization reaction.

24. An alternative repair system by error-prone translesion DNA synthesis can result in a high mutation rate, because: A) alternative modified nucleotides can be incorporated more readily. B) interference from the RecA and SSB proteins hinders the normal replication accuracy. C) replication proceeds much faster than normal, resulting in many more mistakes. D) the DNA polymerases involved cannot facilitate base-pairing as well as DNA polymerase III. E) the DNA polymerases involved lack exonuclease proofreading activities.

E) the DNA polymerases involved lack exonuclease proofreading activities.

48. Match the damage type or repair step at the left with a related enzyme at right. Only one answer will be the most direct for each. __e_ cytosine deamination (a) hypoxanthine-N- glycosylase __b_ base loss (b) AP endonuclease __a_ adenine deamination (c) mutH protein _c__ binds to GATC sequences (d) DNA polymerase I _f__ binds to mismatch in DNA (e) uracil N-glycosylase _d__ DNA synthesis in gaps (f) mutS-mutL complex _j__ seals nicks (g) ABC excinuclease _i__ O6-methylguanine (h) DNA photolyase _h__ direct chemical reversal (i) O6-methylguanine of pyrimidine dimer formation methyltransferase _m__ double-strand break (j) DNA ligase _g__ excision of a lesion- (k) λ integrase containing oligonucleotide (l) RecA protein (m) restriction endonuclease

e; b; a; c; f; d; j; i; h; m; g