1. Explain why RT has RDDP and DDDP activity.

2a. Explain the process by which RT lengthens the primer strand.

2b. In the mutagenesis HIV-1 RT paper by Harris et al,the researchers did not use the natural form of RT for their studies. What did they use instead?

3. M184V is an interesting mutation. Compare the activity of this mutation and its affect on polymerization and fidelity.

4. It seems that the RNase H activity in each of the mutants was not affected by the amino substitutions. Why do you think this is the case?

5. In the Harris et al. paper, the researchers test the pyrophosphorolysis activity of WT HIV-1 RT and its dNTP-binding pocket mutants. However, the gel products are below the primer:template, while the other gel products in the rest of the figures are above the primer:template. Explain why this is.

6. Explain how reverse transcriptase creates mutations specifically in the b3-b4 loop.

7. In the Harris et al. paper, the Y183A mutation was pretty much dead, but the Y183F mutation rescued a small amount of the activity. Explain the reasoning behind this.

8. By studying the structure of Reverse Transcriptase by Huang et al. it can easily be determined why the mutation K65R is a multi-drug resistance mutation. What is the reasoning behind this statement?

9. From the structure of the closed complex, explain the importance of the b3-b4 loop?

10. What is the importance (function) of the Y183 residue? (This question you may go out of the paper to search for. The best place to find the answer is in the primary literature like Pubmed or Google Scholar).

11. The speed at which the RT can function is limited to a specific step in the polymerization event. What step in the RT mechanism controls the rate at which RT can proceed at incorporating the dNTPs?