Lecture 3: Review of DNA replication
1. Describe an experiment that was used to verify semiconservative replication of DNA.
2. DNA synthesis is a complex process:
A. How are new nucleotides added to a growing strand of DNA?B. What special problems does the pattern of growth described in part A) present for the replication of double stranded DNA? You should be able to identify at least two distinctly different problems.
C. How are the problems that you identified in part B solved during DNA replication?
D. How is the synthesis of a new strand of DNA primed and what is the nature of the primer?
E. How is the primer ultimately removed?
F. How is the problem of unidirectional synthesis of new DNA overcome?
3. What features characterize origins of replication in bacterial cells and how are they recognized by the replication machinery.
4. What role does helicase play in the replication of DNA? What problems would be encountered in its absence?
5. Distinguish between leading and lagging strands in a manner that makes it clear you know what each is and how they differ.
6. What is an Okazaki fragment and what is its biological significance?
7. Which of the bacterial DNA polymerases is believed to be responsible for the bulk of the DNA synthetic activity?
8. What enzyme is responsible for removal of the primer and its replacement with DNA? What catalytic activities are needed for these processes?
9. Why does DNA polymerase I carry the number one when it is not the enzyme that performs the bulk of the DNA synthesis?
10. What type of enzymatic activity is needed for proofreading and error correction?
11. What is a replicon and what is its significance?
12. What is telomerase and what is its primary function.
13. Why is telomerase needed for linear chromosomes, but not for circular chromosomes?
14. Identify the protein or enzyme that is needed for each of the following functions:
A. Final separation of the completely replicated bacterial chromosomes.B. Closing of the gap left after removal of the last nucleotide of the primer and its replacement with a deoxynucleotide.
C. Recognition of the bacterial origin of replication.
D. Opening of the DNA double helix after the origin has been recognized.
E. Relief from the twisting strain that develops in the double-stranded DNA as the strands are separated.
F. Preventing the separated strands of double stranded DNA from annealing (reforming a base-paired double helix) before new synthesis can begin on the separated strands.
15. Identify as many of the enzymes and other proteins that are needed for bacterial DNA synthesis as you can and describe the temporal sequence in which they function.
16. Describe the "theta" structure observed during replication of bacterial DNA and explain how it originates.
17. Explain how the leading and lagging strands can be synthesized coordinately by a polymerase dimer despite their very different patterns of synthesis.
18. What does the term "replisome" refer to? How does the replisome complex differ from the DNA polymerase holoenzyme, which is itself a complex multicomponent structure?
19. Exonuclease enzymes play major roles in DNA replication and DNA proofreading.
A. What is an exonuclease?B. Distinguish between 5' to 3' and 3' to 5' exonucleases in a manner that makes it clear that you know what each is and how they differ.
C. Describe the role(s) of 5' to 3' exonuclease activity.
D. Describe the role(s) of 3' to 5' exonuclease activity.
E. Which of the molecules in the replisome complex possess 5' to 3' exonuclease activity?
F. Which of the molecules in the replisome complex possess 3' to 5' exonuclease activity?
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