Birkbeck College
University of London
Crystallography Department
Advanced Certificate in Principles of Protein Structure
Thursday 18th September 1997
Answer 5 questions. If more than 5 questions are attempt, only the answers
from the 5 highest scoring questions will contribute to the final mark.
  1. Discuss several significant alternative classifications of the 20 amino acids that occur naturally in proteins. Give the names of the amino acids which fall into each class which you discuss. What modifications occur to side groups of these 20? Give an example of a protein which contains such modified residues.

2. Describe a) helix-helix packing and b) sheet-sheet packing in protein structures.

3 . The majority of known protein structures have been determined by X-ray crystallography. Discuss the strengths and weaknesses of this experimental technique.

4. Discuss the classification of b -hairpins and reverse turns in protein structures.

5 . You are interested in a protein whose co-ordinates are deposited in the Protein Data Bank. What statistics would you consider and what tests would you perform to qualitatively assess the precision and accuracy of the co-ordinates?

6. Draw the folding patterns of two a +b protein architectures. Give examples of proteins which have each type of architecture and discuss their function-structure relationships.

7. Describe the different roles which metals play in proteins, using examples to illustrate your answer.

8. Describe the 3D structure and function of one enzyme of your choice. Briefly describe, with a diagram, the structure of the active site and what this shows about its catalytic mechanism.

9. Given a small part of a DNA sequence, how would you use sequence databases and bioinformatics tools to determine whether it is part of a protein sequence and, if so, to find out as much as possible about the function of that protein?

10. Describe with the aid of a diagram, the globin fold. How does the structure of haemoglobin differ from that of myoglobin? What structural features of haemoglobin lead to its co-operative binding of oxygen?

11. What are the main classes of protein tertiary structure? Describe briefly the structures of three proteins from different classes. State, in each case, how the structure helps determine the function of the protein.

  12. Discuss quaternary structure in proteins with reference to multimeric proteins and multi-enzyme complexes.