Chapter 7 Review Questions
1. Please state two different types of cues that can lead to DNA damage. Which of
these cues would spontaneous DNA damage fall under? Which of these cues would
induced DNA damage fall under? Please explain your answer in detail.
2. Please state 3 external agents that lead to DNA damage.
3. Please explain the differences in the definition of mutation for Geneticists and
Molecular Biologists. Which of these definitions is more rigorous?
4. Can mutations have a positive effects or negative effects on organisms? Please
explain your answer.
5. Please state two general regions of a gene where mutations occur. A mutation in
which of these regions will most likely result in an effect on corresponding protein
levels?
6. Please name four types of possible mutations and explain their nature in detail.
7. For each mutation below, please state whether it is a point mutation.
a. A base substitution (A  G)
b. Deletion of 20 base pairs
c. A base substitution (C  A)
d. A deletion of one base
e. A base substitution (G  C)
f. An insertion of 45 base pairs
8. For each of the possible base substitution mutations below, please state whether
there is a transition or a transversion.
a. C  T
b. G C
c. A  T
d. T  G
e. A  G
f. G  A
9. For each GENE, please explain the nature of the base substitution mutation in
detail. (i.e. also please explain why you came to your conclusions)-Please note I have
not added the complementary strand of DNA, and I will be giving you the codon
table
a. 5’ P-CTGCCCATGCCCGGGACTGAAGGGTAACCCGGGATGATAAA-OH 3’ Wild-type
5’ P-CTGCCCATGCCCGCGACTGAAGGGTAACCCGGGATGATAAA-OH 3’ Mutant
b. 5’ P-CTGCCCATGCCCGGGACTGAAGGGTAACCCGGGATGATAAA-OH 3’ Wild-type
5’ P-CTGCCCATGCCCGGGACTTAAGGGTAACCCGGGATGATAAA-OH 3’ Mutant
c. 5’ P-CTGCCCATGCCCGGGACTGAAGGGTAACCCGGGATGATAAA-OH 3’ Wild-type
5’ P-CCGCCCATGCCCGGGACTGAAGGGTAACCCGGGATGATAAA-OH 3’ Mutant
10. Please name and explain three definitions for base substitution mutations
specifically in the protein coding region.
11. Please describe in detail the mutation that leads to the development of
phenylketonuria (PKU)
12. If an insertion or deletion is also considered a point mutation, does it cause a
frameshift? Please explain your answer in as much detail as possible (including how
the corresponding protein for the mutated gene may be affected).
13. Please explain whether the following mutations will cause a frameshift. Briefly,
please explain why for each.
a. Insertions of 34 nucleotides
b. Insertion of 5 nucleotides
c. Insertion of 99 nucleotides
d. Deletion of 3 nucleotides
e. Deletion of 108 nucleotides
f. Deletion of 17 nucleotides
14. Please explain what types of mutations lead to frameshift? If there is a
frameshift, will the proper corresponding protein be produced? Please explain.
15. Under what general class of mutations does the trinucleotide expansion fall
under? If a trinucleotide expansion occurs in the protein coding region of a gene,
does it cause a frameshift? Name two disorders that are caused by trinucleotide
expansions.
16. Please state three possible classes of DNA damage.
17. Matching. For each cause of DNA damage, please explain the result
a. Deamination reaction
b. Methylation of cytosines
c Alkylation reactions
d. Oxidizing agents
18. Please explain what structural distortions in DNA are? What classes of agents
can lead to structural distortions in DNA?
19. Do thymine dimers cause structural distortions in DNA? Please explain your
answer.
20. Please explain in detail how thymine dimers in DNA are produced.
21. Please explain in detail how intercalating agents work to cause structural
distortions in DNA. Please name two chemical agents that act as intercalating
agents.
22. Please explain in detail how base analogs cause DNA damage? Please name an
agent that acts as a base analog.
23. Please explain how DNA backbone damage occurs. Which bond is usually
affected when the DNA backbone is damaged? Please discuss which two molecules
in DNA this bond links together, and why this bond can easily be damaged?
24. Please list three main categories of responses to DNA damage.
25. For each cellular response, please state which category of responses to DNA
damage it falls under.
a. Nucleotide excision repair
b. Translesion bypass
c. Photoreactivation of thymine dimers
d. Base excision repair
e. Mismatch repair
f. Removal of methyl groups
26. What type of DNA polymerases are responsible for translesion repair
synthesis? Are they more or less error prone than the replicative DNA polymerases.
27. Please briefly why a damaged lesion of DNA needs to be bypassed in translesion
synthesis (TLS)? How does translesion synthesis work?
28. Please explain how damage due to thymine dimers is reversed? Can humans
reverse damage due to thymine dimers? If not, please state how humans generally
remove thymine dimers from the DNA. Please explain briefly.
29. Please state the general paradigm behind the process of DNA damage removal.
For each of the DNA damage removal pathways, please explain how each
mechanism fits the general paradigm in detail.
a. Nucleotide excision repair (use only short patch)
b. Mismatch repair
c. Base excision repair
30. Please state which mutations result in Xeroderma pigmentosum? Which
mutations result in Hereditary Non-polyposis Colon Cancer (HNPCC)?
31 Please state two general ways by which double strand breaks can be repaired?
Which one is more regularly used by human cells?
32. Please explain how double strand break repair occurs through homologous
recombination.
33. Please explain how double strand break repair occurs through non-homologous
end joining.