Take-home Midterm Exam
Please answer each of the questions (10 points each).
1. What is the structure of water at different temperatures? Why is the structure of water important in the formation of protein secondary structures and protein-protein interactions? Hydration is important for maintaining a protein soluble. How?
2. Please draw the structures of 20 L-amino acids and 4 nucleotides. Write their full names, three-letter code and one letter code. Please group amino acids according to the nature of their side chains: hydrophobic, hydrophilic, polar and nonpolar. Explain briefly each group’s tendency to interact with water. Please draw the potential hydrogen bond formations and explain how they interact with water. Draw all possible hydrogen bonds for the nucleic acid bases.
3. Describe the basic characteristic of the following secondary structures. Also, explain their function in determining the structures of protein and protein-materials.
b. 310 helix
c. p helix
f. turns and loops
g. collagen helix
4. Describe peptide bond formation and its structure in great detail. Can you deduce other structure formations based on the peptide bond structure?
5. What is characteristic of coiled-coils? Describe two, three and four strands of coiled coils. Where do you find such coiled coils in nature?
6. Explain the significance of the high-resolution crystal structure of collagen. What have we learned from the crystal structure? Explain why glycines and prolines are important in forming structure of collagen? How do collagens undergo self-assembly?
7. Describe the molecular structures of silkworm silk and the spider silk. Both proteins have high content of glycine. How are these glycine residues arranged in the silk structures?
8. Briefly explain the tool of X-ray crystallography used in determination of the molecular structure of biological materials. Briefly explain the tool of NMR in determination of the molecular structure of biological materials.
9. Describe how nature makes various types of biominerals.
10. Using the knowledge you have learned in the class to design an interesting building structural motif (hint: use various repeating sequences).
X. Alternative: You may replace a question above (1-9) with the following:
Ask a question related to the material we have covered in class that you think probes an important point. Then answer your question briefly.