Professor Matthew R. Pratt Professor Chao Zhang Department of Chemistry Last updated September 17, 2018 Laboratory Assignment #3:

Professor Matthew R. Pratt Professor Chao Zhang Department of Chemistry

Last updated September 17, 2018

Laboratory Assignment #3: Protein Database

Remember that each student needs to turn in their own work in their own words, even if you work together! To ensure proper ownership of ideas, you must list the full name(s) of your classmate(s) that you worked with in the appropriate field. You can use a combination of the laboratory exercise, the internet, and the AIDS Update book to answer the following questions, but be aware that your answers will be checked for plagiarism. Be sure to give references for your answers.

The HIV virus is an assembly of both proteins (viral enzymes, matrix and envelope proteins) and RNA genes. In addition to what you learned in class about proteins, mature proteins can be made up of several different chains of amino acids. If a protein is made up of only one chain, like the ones we saw in class, they are called monomers. However, if they are made of two chains, they are called dimers, and so on. The viral proteins, and possibly the genes themselves, are targets for drug design. We will learn about HIV-1 protease and the inhibitors used against it in class. In this lab, we will study the 3D structure of another HIV enzyme, HIV-1 reverse transcriptase, and examine how the structure may be used for rational drug design. You can use a combination of the laboratory exercise, the internet, and the AIDS Update book to answer the following questions, but be aware that your answers will be checked for plagiarism.

1. (5 points) HIV-1 Reverse Transcriptase Background.

What is the function of HIV-1 reverse transcriptase? Specifically, what does HIV-1 reverse transcriptase do in a biochemical sense?

2. (5 points) HIV-1 Reverse Transcriptase Structure. Using the applet supplied in this lab in the lab data link, look at the structure of HIV-1 reverse transcriptase.

(a) Is the enzyme a monomer (1 chain), a dimer (2 chains), a trimer (3 chains), etc.?

(b) Which chain is composed of greatest number of amino acids?

(c) Which chain has the greater number of alpha helix segments? (d) What is the most predominant amino acid in each chain?

3. (4 points) Reverse Transcriptase Inhibitors.

Using the applet supplied in this lab in the lab data link, look at the structure of the

HIV-1 reverse transcriptase inhibitor.

(a) Select the miscellaneous molecule (inhibitor), display it in atom and bonds format, save it as a jpg and upload it into your lab report without the enzyme subunits.

(b) How many atoms does it possess (excluding hydrogen atoms as shown)?

4. (6 points) What property of HIV-1 reverse transcriptase makes it difficult to use single drugs that remain effective in treating infection? Hint: It is a property that our DNA and RNA polymerases have evolved to avoid.