Study Questions for Exam 1

(revised September 17, 2016)

1. Discuss the relative strengths and other characteristics of these kinds of intermolecular bonds: hydrogen bond, Van der Waals interaction, disulfide bond, covalent bond, charge:charge interaction. Be able to recognize them in simple and complex structural models. 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 handednessof helix 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

5. Explain how protein-DNA contacts tend to differ depending on whether highly specific or nonspecific binding is required. What biological functions require specific binding? What situations require nonspecific binding?

6. In each article we read (Schwartz, Epshtein, Anson): What is the main question? Why is it important or interesting? What organism was studied, and why?

7. From your reading, cite specific examples of experiments in the categories of: biochemistry (molecular interactions in a test tube) and of structural analysis (X-ray crystallography). Cite an example of how data from two different experimental categories can complement each other.

8. Explain DNA linking number, twist, and writhe. Do these concepts differ for a circular duplex, and for a linear duplex with unrestricted ends? Can you calculate how changes in writhe compensate for changes in twist in a constrained system? 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.

11. Explain the events in each phase of transcripion: initiation, elongation, and termination. Explain the roles of each RNAP subunit and the specific intermolecular contacts for each. Explain the structural elements (and changes in their conformation) of DNA and RNA that contribute to the phases of transcription.

12. Explain why a particular operon requires both activators and repressors for regulation.

13. Explain the role of DNA bending in transcription and its regulation.

14. Why do so many control factors consist of dimers or tetramers instead of monomers? What is the advantage of a multimeric regulator that binds DNA, as compared to a monomer?

15. How do transcriptional repressors function to limit transcription initiation? What about activators? What is the difference between allosteric and recruitment mechanisms of transcritional activation? Cite an example of each and explain how it works.

16. What is transcriptional attenuation? Explain how DNA, RNA, RNA polymerase, ribosome, small molecules, and auxiliary proteins can play a role in this process. How does the mechanism of attenuation differ in the trp operon from Bacillus spp.and E. coli?

17. What are riboswitches and how do they function?

18. How do the location and nature of weak bonds differ in sequence specific DNA binding proteins and non-sequence specific DNA binding proteins?

19. The structures of amino acids and nucleotides offer great opportunities for exam questions. Know these well, both individually and in the context of macromolecules. Have a good understanding of the nature of their most common interactions within macromolecules.

20. Know your terminology. It's hard to answer questions if you don't know what the words mean.

21. Be prepared to apply the concepts, techniques, and facts you learned in novel situations or using data we have not previously examined in class.