FCH 532 Homework 6
1. Outline DNA the steps for DNA replication. List all enzymes/proteins involved
and use diagrams/pictures to explain your answer.
2. Explain how certain mutant varieties of Pol I can be nearly devoid of DNA
polymerase activity but retain almost normal levels of 5’ 3’ exonuclease
activity.
3. Why haven’t Pol I mutants been found that completely lack 5’ 3’ exonuclease
activity at all temperatures?
4. The 3’ 5’ exonuclease activity of Pol I excises only unpaired 3’-terminal
nucleotides from DNA, whereas this enzyme’s pyrophophorylysis activity
removes only properly paired 3’-terminal nucleotides. Discuss the mechanistic
significance of this phenomenon in terms of the polymerase reaction.
5. You have isolated E. coli with temperature-sensitive mutations in the following
genes. What are their phenotypes above their restrictive temperatures? Be
specific. (a) dnaB, (b) dnaE, (c) dnaG, (d) lig, (e) polA, (f) rep, (g) ssb, and (h)
recA.
6. Short answers. Define the following terms in two or three sentences. Be specific.
 Leading strand
 Lagging strand
 Primase
 Helicase
 SSB
 DnaB
 Rep
 PriA
 Ligase
 Okazaki fragment
 Theta structure
 Klenow fragment
 Gyrase
 Nucleotide excision repair
 Base excision repair
 Mismatch repair
 RecA
 Holliday junction
 Conjugation
7.
Outline the differences between the 3 main types of DNA polymerases found in
E. coli.
8. Describe an experiment to show bidirectional vs. unidirectional replication of a
circular DNA chromosome.
9. Outline mechanism for the repair of a thymine dimer in E. coli. Be specific
10. Draw the mechanism of the ligase enzyme. Show chemical structures.
11. It is generally assumed in general biochemistry that DNA replicates in the 5' 3'
direction. Why do we think this is true? Propose an experiment to prove that 3'
5' replication does not occur.
12. Why is uracil so mutagenic in DNA?
13. What is the SOS response? What proteins are involved?
14. Why is the methylation of DNA to form O6-methylguanine mutagenic?
15. A replication fork encountering a single-strand lesion may either dissociate or
leave a single-strand gap. The latter process is more likely to occur during
lagging strand synthesis than during leading strand synthesis. Explain.