Study Questions for Test 1

Note: You will need to discuss Jmol structures, and gel experiment data.

1. Discuss the relative strengths and other characteristics of these kinds of intermolecular bonds: disulfide bond, hydrogen bond, salt bridge (ionic bond), Van der Waals bond. What kind of force holds the atoms together? What functions do these bonds typically serve?

2. Compare and contrast the B-form, A-form and Z-form of nucleic acid. Which forms are typical of DNA or of RNA? Which handedness does each have, and what relative dimensions? What is a typical biological function of each form?

3. Describe the types of interactions that maintain primary, secondary, tertiary, and quaternary protein structure.

4. Explain several different kinds of bond contact between a protein recognition helix and DNA. Include contacts typical of: positively charged amino acid residues; amide residues; aliphatic residues; and aromatic residues. Find examples in the articles Ha et al, 2005; Schwartz et al, 1999; Schreiter and Drennan, 2007.

5. From your reading, cite specific examples of experiments in the categories of: genetics (mutagenesis and bioinformatics); biochemistry (molecules in a test tube); and structural analysis (X-ray crystallography). Cite an example of how data from two different experimental categories complemented each other.

6. Explain three kinds of "gel blob" experiment that reveal information about structure and function of a macromolecular complex. Explain how the conditions of the experiment may or may not resemble the conditions of function in a living cell.

7. Explain the basis of crystallography data in a research article or in a PDB model. Know what components in solution were crystallized; what constitutes the unit cell; heavy atoms, if any; whether MIR or MAD was used to solve the structure; why certain parts of the structure may be "invisible"; which aspects of the unit cell are relevant to the living cell, and which aspects are mainly a function of how it crystallized.

8. Explain DNA linking number, twist, and writhe. How is linking number maintained for a circular duplex? A linear duplex? How does topoisomerase work?

9. In RNA structure, explain with a diagram (and words) the structures known as hairpin, stem-loop, and pseudoknot. Why do these form in solution?

10. Explain the structural and functional roles of the beta/beta prime complex; the alpha dimer; and sigma factor in bacterial RNA polymerases. Explain how "general transcription factors" participate in eukaryotic transcription.

11. Explain initiation, elongation, and termination of transcription. Explain how proteins interact with DNA and RNA, and how different proteins interact with each other.

12. Explain the different mechanisms by which different activators can enhance activity of RNA polymerase.