1. Explain the four categories of amino acid side chains. What types of interactions are the members of each of these categories likely to make?

2. Outline the four levels of protein structure, giving a specific example of each.

3. Describe the geometric features of the common secondary structure, the ? helix. Why is this structure especially common? What are the weak bonds that stabilize the ? helix?

4. You treat a protein with the denaturant urea. For each interaction or bond below, state if the interaction or bond is disrupted by the urea treatment.  

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a. Ionic bonds

b. Hydrogen bonds

c. Disulfide binds

d. Peptide bonds

e. van der Waals interactions

5. How does denaturation affect a protein’s primary, secondary, tertiary, and quaternary structures?

6. Describe the role of water in protein structure formation.