Example exam questions

There are examples that may or may not appear on the exam. These questions are meant to highligt important concepts that you should be familiar with after attending the course. Variations and similar (in terms of level) questions will also appear on the exam. The actual questions will obviously be based on what we have discussed during the course. However, please note that we do expect you to study the course literature - you cannot expect to pass the course with flying colors just from the lecture handouts.

Example subjects:

1. Primary/secondary/teritary structure in proteins. What does this mean for structure and function? How is it related to folding?

2. What are the different properties of amino acids, and how does it affect protein properties?

3. Proline and Glycine are a bit special. Why?

4. What is the Anfinsen Hypothesis, and Levinthal's paradox?

5. Describe the folding (and structural) properties of the secondary structure elements!

6. Describe the origin of van der Waals interactions. Why is it important in proteins?

7. Describe hydrogen bonding, and the hydrophobic effect. Why is it important in proteins?

8. What is stacking of aromatic rings?

9. What is electrostatic shielding (relative dielectric permittivity)? Can you give some examples where it occurs?

10. How strong are different interactions in nature? How stable are molecules compared to this?

11. Describe the electrostatic potential model (equation) and screening by ions!

12. Discuss protonation/deprotonation of amino acides and the relation of their charge to pH?

13. Describe some typical membrane protein structures.

14. What is an energy landscape?

15. Helix/coil transitions.

16. Protein denaturation/ reversibility

17. What is transition state theory ?

18. What are Chevron plots? When is it useful?

19. What can we learn from protein folding kinetics?

20. Describe diffusion-collision and nucleation processes.

22. What makes a membrane protein special? Compare to globular proteins.

23. Compare the role of high-throughput screening and virtual screening in drug discovery.

23. Early in the course, we spoke about Levinthal's paradox. Explain how it is resolved in practive!