The following problems are to help you sharpen and deepen your understanding of DNA and DNA replication. These questions will be discussed in the recitation section on Oct. 10. Problems are not to be handed in and will not be graded.

1. Describe in words the role of each of the following in prokaryotic DNA replication:

a) the oriC region
b) dnaA protein
c) DNA helicases
d) DNA gyrase
e) single-strand binding protein
f) RNA primase
g) DNA polymerase III
h) DNA polymerase I
i) DNA ligase

2. What do you suppose are the minimum requirements for a "replicon", in terms of the structure of the DNA?

3. (Modified from Snustad & Simmons, Principles of Genetics) The nucleic acid from various viruses was extracted and the base compositions determined. What is the nature of the nucleic acid in each virus?
Virus 1) 35% A, 35% T, 15% G, 15%C; Virus 2) 35% A, 15% T, 25% G, 25% C; Virus 3) 35% A, 30% U, 30% G, 5% C; Virus 4) 20% A, 20% U, 30% G, 30% C

4. It was at first believed that DNA polymerase I (polA) was primarily responsible for nucleotide polymerization during DNA replication. However, John Cairns (1969) isolated a mutant of Escherichia coli that was deficient in polymerase I activity, and against this background it was possible to detect DNA polymerase III. It was then believed that polA was not involved in DNA replication.

Later, it was discovered that Cairns' polA-deficient mutant still retained the 5'-exonuclease activity of the polA protein and that other mutants deficient in the 5'-exonuclease activity could not replicate their DNA.

Explain these observations in terms of the multiple roles of polA in DNA replication.

5. Re-read carefully the description of the Hershey-Chase experiments on pages 208-209 of your text. Another well-known text says "The conclusion is inescapable: DNA is the hereditary material". Do you agree with this statement? If so, why? If not, why not? Can you explain the observations by an alternative model? (For the sake of humility, remember that A.D. Hershey won the Nobel Prize, largely for this famous experiment.)

6. In about 1970, I heard a seminar in which a biologist concluded that the DNA unwinding during replication would require that the entire DNA molecule rotate inside an E. coli cell at 60,000 rpm. The speaker concluded that since this was physically impossible, it was evident that E. coli did not replicate its DNA. In a purely topological sense the rotation calculation was not incorrect. What essential piece of information was missing?