Chapter 35

1. Mismatches, insertions, deletions, and breaks

2. Oxidizing agents such as reactive oxygen species; deamination; alkylation; ultraviolet light; ionizing radiation

3. First, recognize the damaged base or bases. Second, remove the damaged base(s). Third, repair the gap with DNA polymerase I, and seal the deal with DNA ligase.

4. The proofreading ability of DNA polymerase; mismatch-repair systems; direct repair; base-excision repair; nucleotide-excision repair; DNA recombination.

5. The ultraviolet radiation of sunlight causes, in addition to tan lines, thymine dimers in DNA, which if not repaired, block replication and gene expression, possibly leading to a mutation.

6. The repair enzyme, AlkA in E. coli, binds the DNA and flips the base out of the helix. The enzyme cleaves the glycosidic bond to release the damaged base. The AP endonuclease nicks the backbone, and another enzyme removes the deoxyribose phosphate unit. DNA polymerase I fills in the gap, and DNA ligase seals the strand.

7. Cytosine in DNA, which pairs with guanine, sometimes undergoes deamination to form uracil, which pairs with adenine. The result would be a mutation (a U–A base pair replacing a C–G base pair). By using thymine instead of uracil, the repair machinery immediately recognizes uracil in DNA as a mistake and replaces it with cytosine.

8. 5-Methylcytosine spontaneously deaminates to form thymine. This results in a T–G base pair. Because the C → T mutation is so common, the T in a T–G pair is always treated as the incorrect base and removed by the base-excision-repair proteins. This repair system allows the methylation of cytosine to serve a role in transcription regulation without resulting in a DNA mutation.

9. A subunit of DNA polymerase III, acting as an exonuclease, removes the offending base. The polymerase activity makes the correction, and DNA ligase seals the backbone.

10. Each base pair has one purine, which can undergo spontaneous depurination at the rate 3 × 10⁻⁹ depurinations per purine per minute. The human genome contains 6 × 10⁹ base pairs, and so there must be 18 depurinations per minute. Multiplying 18 by 60 minutes in an hour and 24 hours in a day reveals that 26,000 repair events are required per day per cell.

11. Potentially deleterious side reactions are prevented. The enzyme itself might be damaged by light if it could be activated by light in the absence of bound DNA harboring a pyrimidine dimer.

12. Complete the interactive matching exercise to see answers.

13. 1. The control plate was used to determine the number of spontaneous revertants—that is, the background mutation rate.

    2. To firmly establish that the system was working. A known mutagen’s failure to produce revertants would indicate that something was wrong with the experimental system.

    3. The chemical itself has little mutagenic ability but is apparently activated into a mutagen by the liver homogenate.

    4. The cytochrome P450 system or other hepatic enzymes.

14. 1. People with xeroderma pigmentosum develop skin cancer at a much earlier age than do people without it.

    2. People with xeroderma pigmentosum lack a component of the human nucleotide-excision-repair pathway. This pathway is especially important in the repair of ultraviolet-radiation-induced DNA lesions, such as thymidine dimers. Thus, skin cancer readily develops.

    3. The late appearance of skin cancer in normal people suggests that multiple mutations in the DNA must occur before skin cancer can develop.