Download Discussion Problem Set 3 C483 Spring 2014

Discussion Problem Set 3 C483 Spring 2014
Problems from lectures 6-8. (Through Jan 31)
1. What are the two main forces that stabilize an alpha helix? Describe them. How
might you test the importance of an n-pi-star interaction?
2. What two things need to be minimized to have a stable alpha helix?
3. Which amino acid regularly adopts a cis peptide bond? Explain why this is
possible.
4. What are the two major methods for determining protein structure. Describe two
major drawbacks for each method. What is the biggest difference between the
information obtained by these two methods?
5. Describe three chromatographic techniques used to purify proteins.
6. How is the total amino acid composition of a protein determined? Which amino
acids cannot be determined in this experiment? Which amino acid reacts under
these conditions, but can still be accounted for? What amino acid is actually found
in this case?
7. What chromatographic technique separates proteins based on size? Is size
always equivalent to molecular weight?
8. Which is better for determining approximate molecular weight, PAGE, or SDS –
PAGE? Why?
9. Why are beta-strands rarely found in isolation in a protein?
10. Describe the forces that holds a beta-sandwich together.
11. Why are parallel beta-sheets relatively uncommon?
12. Describe (draw) a seven transmembrane helical protein. What is likely true
about the loops/turns in such proteins? Give an example of such a protein.
13. Describe two common DNA-binding motifs. What forces hold these structures
together? Why is every seventh amino acid a significant number in the structure of one
of these?
14. Describe how a coiled coil self-associates.