Unit 4: DNA Repair Mechanisms and Homologous Recombination - Practice Quiz

1 Which enzyme directly reverses UV-induced pyrimidine dimers using energy from visible light?

2 The enzyme O-methylguanine-DNA methyltransferase (MGMT) repairs damage by:

3 Direct repair is characterized by:

4 Which repair pathway removes small, non-helix-distorting base lesions such as uracil or oxidized bases?

5 Which enzyme initiates base excision repair by recognizing and removing a damaged base?

6 Nucleotide excision repair (NER) is best suited to repair which type of lesion?

7 The main role of mismatch repair (MMR) is to correct:

8 In prokaryotic mismatch repair, which protein recognizes the mismatch?

9 Which two major pathways repair double-strand breaks in DNA?

10 Non-homologous end joining (NHEJ) is considered error-prone because it:

11 Homologous recombination repair of double-strand breaks is most accurate because it:

12 During which phases of the cell cycle is homologous recombination most active?

13 Homologous recombination requires which of the following between the participating DNA molecules?

14 Site-specific recombination differs from homologous recombination because it:

15 The cross-shaped intermediate structure formed during homologous recombination is known as the:

16 In the Holliday model, the movement of the crossover point along the DNA is called:

17 The final step of separating a Holliday junction into two individual DNA duplexes is called:

18 The RecBCD enzyme complex of E. coli has which combined activities?

19 The specific DNA sequence that regulates RecBCD activity and stimulates recombination is called:

20 Which protein, loaded with the help of the RecBCD pathway, promotes strand invasion during recombination?

21 A bacterial culture is exposed to UV light, forming cyclobutane pyrimidine dimers. When the cells are subsequently exposed to visible light (300–500 nm), the dimers are directly reversed. Which enzyme is responsible for this repair, and what cofactor does it use?

22 The enzyme -methylguanine-DNA methyltransferase (MGMT) is often called a 'suicide enzyme.' Why is this label appropriate?

23 In base excision repair (BER), what is the correct order of enzymatic events after a damaged base is recognized?

24 A cell has a defect in nucleotide excision repair (NER). Which type of DNA lesion would this cell be LEAST able to remove?

25 In E. coli mismatch repair, the MutH endonuclease preferentially nicks the newly synthesized daughter strand. How does the system distinguish the daughter strand from the template strand?

26 Non-homologous end joining (NHEJ) and homologous recombination (HR) both repair double-strand breaks. Which statement best distinguishes them?

27 In the initial step of homologous recombination in eukaryotes, DSB ends are processed to generate 3' single-stranded overhangs. What is this process called and why is it essential?

28 Which protein complex in eukaryotes first recognizes a double-strand break and binds the DNA ends during the NHEJ pathway?

29 Which statement correctly contrasts homologous recombination with site-specific recombination?

30 Bacteriophage integrates into the E. coli chromosome at the attB/attP sites. What type of recombination is this, and which enzyme catalyzes it?

31 In the Holliday model, the crossed-strand intermediate can move along the DNA as base pairs are broken on one duplex and reformed on the other. What is this process called?

32 A Holliday junction can be resolved in two ways depending on the orientation of the cuts. What determines whether the flanking markers are recombinant (crossover) or non-recombinant (non-crossover)?

33 In the classic Holliday model, heteroduplex DNA (a hybrid of strands from two different parental molecules) is formed. Why is heteroduplex DNA biologically significant?

34 The RecBCD enzyme of E. coli changes its behavior when it encounters a specific sequence called Chi (, 5'-GCTGGTGG-3'). What happens at the Chi site?

35 Which set of enzymatic activities does the RecBCD complex possess that makes it suited to initiate recombination at double-strand ends?

36 After RecA forms a nucleoprotein filament on single-stranded DNA generated by the RecBCD pathway, what is RecA's primary role in recombination?

37 Site-specific recombinases are grouped into two major families based on the catalytic amino acid that forms a covalent bond with DNA. What are these two families?

38 During conservative site-specific recombination, why is no DNA synthesis or high-energy cofactor (like ATP) generally required for strand exchange?

39 A researcher places two loxP sites in the same (direct/head-to-tail) orientation flanking a target gene. When Cre recombinase is expressed, what is the outcome?

40 In a conditional knockout mouse, a gene is 'floxed' and Cre expression is driven by a tissue-specific promoter. What is the main advantage of this Cre/loxP strategy?

41 The enzyme -methylguanine-DNA methyltransferase (MGMT) removes alkyl groups from guanine. Which feature of its mechanism makes it fundamentally different from a typical catalytic enzyme?

42 DNA photolyase repairs cyclobutane pyrimidine dimers using two chromophores. What is the specific role of the MTHF (or 8-HDF) chromophore relative to the FADH cofactor?

43 In base excision repair (BER), a bifunctional DNA glycosylase differs from a monofunctional one primarily because it:

44 In E. coli mismatch repair, strand discrimination relies on hemimethylation. If a mismatch lies bp from a site and MutH nicks the unmethylated strand, which activity is required to remove the intervening tract back to the mismatch?

45 Nucleotide excision repair (NER) in E. coli uses UvrABC. What is the precise nature of the dual incision made by UvrC?

46 Non-homologous end joining (NHEJ) and homologous recombination (HR) compete for double-strand break repair. Which molecular event most strongly commits a break to the HR pathway?

47 During HR, the MRN (Mre11–Rad50–Nbs1) complex initiates resection. Mre11 has a puzzling activity given its role in resection. What is it?

48 Synthesis-dependent strand annealing (SDSA) is a DSB repair sub-pathway. Why does SDSA produce exclusively non-crossover products?

49 Which statement correctly distinguishes homologous from site-specific recombination at the mechanistic level?

50 Tyrosine and serine recombinases both catalyze site-specific recombination but form different covalent intermediates. What distinguishes the tyrosine recombinase mechanism?

51 In the classical Holliday model, branch migration of the crossover point has a key consequence for the DNA involved. What is it?

52 A single Holliday junction can be resolved by cutting either of two strand pairs. How does the choice of cleavage orientation determine the outcome?

53 The double-strand-break repair (DSBR) model refined the Holliday model. Why can a single double-Holliday-junction intermediate yield either crossover or non-crossover products?

54 The RecBCD enzyme changes its behavior upon encountering a site (-GCTGGTGG-). What is the precise molecular change in its nuclease activity?

55 The RecB and RecD subunits are both motor proteins that translocate on opposite strands with opposite polarities. Before reaching , which subunit is the faster motor and what is the consequence?

56 sites are described as functionally polar hotspots for recombination in E. coli. What does 'polar' mean in this context?

57 In bacteriophage integration, Int (a tyrosine recombinase) requires the host factor IHF. What is IHF's essential structural role at ?

58 The directionality of recombination (integration vs. excision) is controlled by which factors, and why is excision not simply the reverse of integration?

59 A site is a bp sequence with two bp palindromic arms flanking an bp asymmetric spacer. Two sites in the same (head-to-tail) orientation on a single DNA molecule will be recombined by Cre to give what outcome?

60 Cre-mediated excision is intramolecular and produces a circular product plus the deletion allele, yet the reaction is reversible in principle. Why does excision dominate over reintegration in practice?