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a. In a single sentence (but in your own words, please), summarize the point of this figure.

b. Diagram the synthesis of the genomic-length + strand DNA made from the cPPT-D mutant virus. Your diagram should include the site of initiation of this strand as well as any "jumps" or strand displacements that would be necessary.

2. (2 pts) Figure 2

a. The legend to part A states that "viral production was followed over time by RT activity in cell supernatants." Explain what is meant by the term "viral production," and why this is a measure of it.

b. Figure 2B is based on a measurement of beta-galactosidase activity. How is beta-gal being expressed in these cells, and what is this measurement designed to reflect? (You may need to consult the "Experimental procedures" section to answer this question.)

3. (2 pts) The data in figure 2 demonstrate that the cPPT-D mutant is deficient in the viral life cycle overall. Figure 3 presents experiments designed to assess particular stages of the HIV-1 life cycle. These experiments (and those in figures 4 and 5) are designed to determine the particular step at which the cPPT-D mutant is deficient.

At first glance, the experiment presented in figure 3A seems to parallel figure 2A. Both measure viral production. Yet the cPPT-D mutant is deficient in viral production as measured by the experiment in figure 2A, and proficient at it in the fig 3A experiment. Explain. (Hint: what steps of the viral life cycle are required for viral production in fig 2A, but not required in fig 3A? Why?)

4. (2 pts) The "1 LTR" and "2 LTR" circular molecules diagrammed in figure 4A are commonly observed in HIV-1-infected cells. They are only found in the nuclei of these cells, not in the cytoplasm. They appear to be "by-products" of HIV-1 infection, not directly involved in the life cycle. Neither type of circle appears to be competent for integration into the host cell genome.

What cellular mechanisms do you know about that could explain the origin of these molecules? Explain. Your explanation should include why these molecules are only found in the nucleus. (Hint: you may need to use different cellular mechanisms to explain the origin of the 1-LTR and the 2-LTR circles.)

5. (1 pt) Figure 4C includes a quantitation of "integrated" virus. Explain how these numbers were determined. (You need not explain the entire assay in detail--just explain how these particular numbers were determined, and the reasoning behind that determination.)

6. (1 pt) What is the key finding of this paper, and why is it important?

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