Chapter 25 - DNA Replication, Repair, and Recombination Practice Quiz PDF

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This is a practice quiz for chapter 25 of biochem III. This is similar to the in class quiz. It has questions that have been used on the quiz. It can also serve as a study guide for the test. It also helps with the assignments. Some of these questions are in the assignments. Contains questions and a...

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1/9 Biochemistry III Chapter 25: DNA Replication, Repair, and Recombination Textbook: Fundamentals of Biochemistry: Life at the Molecular Level, 5th Edition. Donald Voet; Judith G. Voet Practice Quiz 1. Match each of the following: 1. The product of continuous DNA synthesis 2. Fragments of newly synthesized DNA that are the products of semidiscontinuous replication 3. Enzyme that synthesizes RNA primers for DNA replication 4. Enzymes that use single-stranded DNA as a template for synthesis of the complementary strand of DNA 5. The product of discontinuous DNA synthesis 6. A branch point in a replication eye at which DNA synthesis occurs 7. Enzyme that catalyzes the covalent joining of Okazaki fragments DNA polymerase

4

Replication fork

6

Okazaki fragments

2

Leading strand

1

Lagging strand

5

DNA ligase

7

Primase

3

2. DNA is replicated or synthesized by DNA-directed DNA polymerases.

2/9 3. Okazaki fragments are covalently joined by the enzyme ligase. 4. Okazaki fragments are initially synthesized from RNA primers. 5. True or false. DNA is synthesized by a mode of replication termed conservative. False. NOTE: It is a semiconservative mode of replication. 6. True or false. DNA replication is far more complex than the overall chemistry of the process might suggest. True. 7. True or false. DNA synthesis extends chains from a 3' end. True. 8. Match each of the following: 1. Synthesis of leading and lagging strands 2. Synthesis of lagging strand and repair 3. The larger proteolytic fragment of DNA polymerase I 4. Thought to be involved in DNA repair DNA Polymerase I (Pol I)

2

DNA Polymerase II (Pol II)

4

DNA Polymerase III (Pol III)

1

Klenow fragment

3

9. DNA polymerase I (Pol I) of E. coli is a processive enzyme, meaning that it catalyzes successive steps without releasing its template. 10. The 3' -> 5' exonuclease activity of DNA polymerase I (Pol I) is part of a proofreading mechanism. 11. True or false. Replication of the E. coli chromosome begins at multiple sites called origins of replication. False. NOTE: It begins at a single origin.

3/9 12. True or false. The replisome of E. coli contains two DNA polymerase III (Pol III) holoenzymes. True. 13. True or false. E. coli DNA ligase uses the reduction of NAD+ to drive covalent bond formation in nicked strands of DNA. False. NOTE: The hydrolysis of NAD+ is coupled to covalent bond formation in nicked strands of DNA. 14. True or false. Model-building studies indicate that the ring-like structure of the β subunit of DNA polymerase III (Pol III) fits tightly around the major and minor grooves of duplex DNA. False. NOTE: It fits loosely, so as to facilitate movement. 15. Which activities of DNA polymerase I (Pol I) of E. coli are minimally necessary for nick translation? A. 3' -> 5' exonuclease and 5' -> 3' exonuclease B. 3' -> 5' exonuclease and 5' -> 3' polymerase C. 5' -> 3' polymerase and 5' -> 3' exonuclease NOTE: 3' -> 5' exonuclease is not necessary. D. All three activities are essential.

4/9 16. Which of the following best characterizes the differences between DNA polymerase I (Pol I)and DNA polymerase III (Pol III), in E. coli? A. DNA polymerase III (Pol III) is present at lower concentration, it has a lower turnover number, and it has the same three enzyme activities as DNA polymerase I. NOTE: DNA polymease III has a higher turnover number, and it lacks the 5' -> 3' exonuclease activity of DNA polymerase I. B. DNA polymerase III (Pol III) is present at lower concentration, it has a higher turnover number, and it lacks the 5' -> 3' exonuclease activity of DNA polymerase I. C. DNA polymerase III (Pol III) is present at lower concentration, it has a higher turnover number, and it has the same three enzyme activities as DNA polymerase I. NOTE: DNA polymease III lacks the 5' -> 3' exonuclease activity of DNA polymerase I. D. DNA polymerase III (Pol III) is present at higher concentration, it has a higher turnover number, and it has the same three enzyme activities as DNA polymerase I. NOTE: DNA polymease III is present at lower concentration, and it lacks the 5' -> 3' exonuclease activity of DNA polymerase I.

5/9 17. Match each of the following: 1. Nuclear polymerase, with 3' -> 5' exonuclease activity 2. Nuclear polymerase with a tightly primase 3. Nuclear polymerase that is highly processive in the absence of PCNA 4. Mitochondrial polymerase DNA polymerase α

2

DNA polymerase δ

1

DNA polymerase ε

3

DNA polymerase χ

4

18. DNA polymerase delta is essentially infinitely processive when it is in contact with PCNA. 19. Eukaryotic chromosomes contain multiple origins of replication. 20. True or false. A leading strand DNA polymerase will generally have much greater processivity than a lagging strand polymerase. True. 21. True or false. Telomerase is structurally and functionally similar to reverse transcriptase. True.

6/9 22. What is the role of PCNA in DNA replication? A. It forms a trimeric ring structure that is essential for high processivity by DNA polymerase delta. B. It inititates rolling-circle DNA replication. C. It forms a DNA-binding cleft that is essential for DNA replication by DNA polymerase delta. D. It forms a trimeric ring structure that is essential for primase activity in leading strand DNA synthesis. 23. Match each of the following: 1. Point mutations in which a purine is replaced by a pyrimidine (or vice versa) 2. Substances that induce mutations 3. Substances that are also often mutagens 4. Point mutations in which one purine (or pyrimidine) is replaced by another 5. Product of uv radiation 6. Substances that may cause insertions or deletions during replication of DNA Thymine dimer

5

Transitions

4

Transversions

1

Chemical mutagens

2

Intercalating agents

6

Carcinogens

3

24. Thymine is the base most likely to form uv-induced dimers. 25. Oxidative deamination of adenine leads to formation of hypoxanthine.

7/9 26. In the Ames test, a substance is tested for its frequency of generating mutations in a bacterial strain. 27. True or false. Mutations in somatic cells are not passed on to the offspring of the organism. True. 28. True or false. An example of an insertion mutation is when a pyrimidine is replaced by a purine. False. NOTE: That is an example of a transversion. 29. That is an example of a transversion. 1. A class of DNA repair enzymes that absorb radiation and restore modified molecules to their original state 2. Nuclease that repairs helix distortion by nucleotide excision 3. A class of enzymes that excise damaged bases from the sugar backbone 4. A DNA-binding protein involved in both the SOS response and in genetic recombination DNA photolyases

1

UvrABC endonuclease

2

DNA glycosylases

3

RecA protein

4

30. DNA photolyases are DNA repair enzymes that contain a light absorbing cofactor and FADH-. 31. Pyrimidine dimers can be removed and replaced by nucleotide excision repair. 32. Replication or postreplication repair occurs when damaged DNA undergoes replication before it has been repaired.

8/9 33. True or false. Defective nucleotide excision repair in humans is associated with two diseases, xerderma pigmentosum and Cockayne syndrome. True. 34. True or false. Apurinic or apyrimidinic sites are sometimes generated by glycosylases, but never occur under other circumstances. False. NOTE: Occasionally they arise from failures in nucleotide synthesis. 35. True or false. The SOS response is a DNA repair mechanism in E. coli that restores extensively-damaged DNA to its original state. False. NOTE: Extensively-damaged DNA cannot usually be repaired completely, but the SOS system limits the damage. 36. Match each of the following: 1. Insertion sequences that make up the simplest transposons 2. Mobile genetic elements 3. Proteins that bind to Holliday junctions and drive branch migration 4. The crossover section of a four-stranded DNA structure 5. Unwinds the double helix and nicks the resulting single-stranded DNA 6. Transposon derived from a retroviral genome Transposon

2

Holliday junction

4

RecBCD protein

5

RuvA and RuvB proteins

3

IS elements

1

Retrotransposon

6

37. RecA is a protein that promotes recombination by polymerizing on DNA that contains a single-strand gap.

9/9 38. During recombination in E. coli, the RecBCD protein makes single-stranded nicks to which RecA binds. 39. True or false. RecA can partially unwind duplex DNA, and in a reaction driven by ATP hydrolysis, it can cause single-stranded DNA to be exchanged. True. 40. True or false. Transposons can carry genes that provide antibiotic resistance or genes of many types. True. 41. The RuvA protein, which binds to Holliday junctions and to RuvB, and is the motor that drives branch migration during recombination, has what type of symmetry? A. It is a trimer with threefold rotational symmetry. B. It is a tetramer with fourfold rotational symmetry. C. It is a dimer with twofold rotational symmetry. D. It is a tetramer with dihedral symmetry. 42. Which of the following is NOT a step of recombination repair? A. RecA activates LexA to cleave itself, and thereby inactivate itself. NOTE: This is part of the SOS response. B. Recombination allows the gapped strand to be exchanged with its intact sister strand. NOTE: This is a step in recombination repair. C. The gapped strand can be filled in according to an undamaged template. NOTE: This is a step in recombination repair. D. The replication machinery stops when it encounters a pyrimidine dimer and resumes polymerization at some point past the dimer site, leaving a gap in one strand. NOTE: This is a step in recombination repair....