DNA Replication
1. Required reading: Chapter 20 pp. 666-691 & the entire Chapter 21.
2. Answer Chapter Twenty Review Questions 17 -21 & 23.
3. Answer Chapter Twenty One Review Questions 8, 14, 21 & 22.
4. Describe the Meselson & Stahl experiment.
a. What is meant by semiconservative replication?
b. Which of the three modes of replication could be ruled out after one round of replication? Explain.
c. Which of the three modes of replication could be ruled out after two rounds of replication? Explain.
5. What did the John Cairns' experiment show in regard to prokaryotic DNA replication?
6. What term is given to the region on the chromosome where DNA replication begins?
7. What did the Huberman & Tsai experiments show in regard to eukaryotic replication?
8. What is a replicon?
9. a. In prokaryotes, what occurs in the "C" period?
9. b. Which part of the eukaryotic cell cycle is synonymous to the "C" period?
10. Often the generation time in bacteria is much shorter than the DNA replication time. How is continuity between cell division & DNA replication maintained?
11. What provides the energy for DNA polymerization?
12. During DNA synthesis nucleotides are linked together by a by a ________________________ bond. What are the two specific functional groups that are joined to form this bond?
13. What is the direction of DNA synthesis? This means new nucleotides are added to the __________ end of a growing strand.
14. Compare the characteristics of DNA polymerase I, polymerase II, & polymerase III.
a. Which enzyme(s) can initiate DNA synthesis on a template?
b. Which enzyme(s) have 5' º 3' polymerization activity?
c. Which enzyme(s) have 3' º 5' exonuclease activity? What is the primary function of this activity?
d. Which enzyme(s) have 5' º 3' exonuclease activity?
e. Which enzyme is responsible for removing RNA primers & filling in the gaps caused by this removal?
f. Which enzyme is thought to be involved in repairing DNA damage, especially that caused by UV light?
g. Which enzyme is the primary enzyme involved in the polymerization reaction of DNA synthesis?
15. What direction does DNA polymerase move along the template strand?
16. Briefly describe the structural features of the DNA replication site on the Klenow fragment DNA polymerase I.
17. What term describes the most active form of DNA polymerase III? How many polypeptide subunits make up this most active form?
18. What subunits make up the "core" enzyme of DNA polymerase III?
a. Which subunit is responsible for nucleotide polymerization on the template strand?
b. Which subunit has the 3' º 5' exonuclease activity?
c. Which subunit’s function is unknown, but its presence is absolutely required for the core enzyme to function?
d. Why are dnaQ (the gene that encodes epsilon subunit) mutants called "mutator mutants"?
19. a. Which subunits make up the gamma complex of DNA polymerase III?
b. What is the function of the gamma complex?
20. a. What is the function of the beta subunit of DNA polymerase III?
b. What are two other names given to the beta subunit?
21. What is the function of the tau subunit of DNA polymerase III?
22. Discuss the composition of oriC on the E. coli chromosome.
23. a. What protein initiates the unwinding of the DNA helix?
b. Discuss the interaction of this protein with the DNA at oriC to create a replication bubble.
c. After the replication bubble is formed, further unwinding of the DNA helix occurs by the binding of what two proteins? Which of these proteins is a DNA helicase?
d. What stabilizes the open structure at the replication forks and prevents the DNA helix from reforming?
24. a. Which enzyme relaxes supercoiling ahead of the replication fork?
b. What is the basic mechanism of this enzyme?
c. What larger group of enzymes does this enzyme belong to?
25. In prokaryotes, which enzyme synthesizes the RNA primer?
26. What is meant by discontinuous synthesis?
29. a. What term is given to the strand that is synthesized continuously?
b. What term is given to the strand that is synthesized discontinuously?
30. a. What are the fragments of the discontinuous strand called?
b. Outline the sequence of events in the assembly of these fragments into a continuous strand.
31. How is it theorized that synthesis of the leading strand and lagging strand occurs simultaneously?
32. Outline the basic steps of DNA synthesis in prokaryotes.
33. Compare the rate of synthesis of eukaryotic & prokaryotic DNA polymerases.
34. a. What are the five major DNA polymerases known to exist in mammalian cells?
b. What are the two major DNA polymerases involved in nuclear DNA synthesis?
i. Which is involved in the initiation of DNA synthesis?
ii. Which enzyme has a primase activity?
iii. Which enzyme is involved in the initial phases of DNA polymerization?
iv. Which enzyme has low processivity? What does this mean?
v. Which enzyme has high processivity?
vi. Compare the rates of synthesis of these two enzymes.
c. What is meant by polymerase switching?
35. a. What term is given to the ends of eukaryotic chromosomes?
b. What is the problem encountered in replicating these regions?
c. Briefly describe the mechanism studied by Blackburn & Grieder for replicating these regions.
36. What is unique about the enzyme telomerase?
37. Compare telomerase activity in most eukaryotic somatic cells to that of malignant cells.
38. In addition to polymerization & strand separation the replication of eukaryotic DNA has two additional steps. What are they?
39. a. Are parental histone octamers conserved during DNA replication or do they dissociate?
b. Do old and new histone octamers & H1 bind specifically to the newly strand synthesized DNA strands?
40. What is a "t loop"? How is it formed? What two proteins are involved in its formation?
41. What is meant by the Hayflick limit?
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