final-2009sample_keys - 1/4 Part of the Final Exam...

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1/4 Part of the Final Exam questions (not included here) will be derived from your peers' HW2 presentations!! (Bis102-001) Sample Questions for Final Exam 1. The hemagglutinin protein in flu virus contains a remarkably long alpha-helix with 53 amino acids as shown in the figure above, as generated by PyMol from PDB data. (a) As we discussed in the lectures, give at least five rules (and the corresponding reasons) that the hemagglutinin protein may have to avoid in order to achieve this alpha-helix formation? (b) What would be the main stabilizing force behind this secondary structure formation? (c) How long is this alpha- helix (in Å)? (d) How many turns does this alpha- helix have? (e) Almost every individual amino acid involves in pairing two hydrogen bonds within the alpha-helix. How many hydrogen bonds are present in this alpha-helix? S HOW YOUR WORK TO RECEIVE FULL CREDIT ( USE THE BACK OF THE SHEET IF MORE SPACE IS NEEDED ). (a) 10 pts – to avoid the following property in the protein sequence - G (too flexible) / P (no H-bond at amino group, inflexible kint) / electrostatic (same-charge) repulsion of adjacent residues / series of adjacent residues with bulky R-group (phe, trp etc) to cause steric hindrance of forming helix turns / adjacent serines with water competing the H-bonds (b) H-bond between the peptide carbonyl of the n th and the peptide H of the (n+4) th residues (c) 80 Å by 53 x 1.5 Å (d) 14.7 turns by 53/3.6 (e) 49 H-bonds, as n+4 = 53, n = 49. the amide H of the first 4 residues and the carbonyl groups of the last 4 residues are not involved in the H-bonding. 2. What characteristic of proline makes it both an ! -helix breaker and a common component of " -turns Proline is an imido acid. In particiapting peptide bond, the nitrogen does not have H-bond to it (cannot be a H-bond donor). The proline stabilize the beta-turn with a cis peptide bond, there a H-bond can be formed between the the carbonyl oxygen of a peptide bond and an amide Hytrogen 3 residues away. 3. Discussed in the class, list the six major classes of enzymes accepted by the international community with one example each and their expected function. 1.
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This note was uploaded on 10/20/2009 for the course BIS 102 taught by Professor Hilt during the Summer '08 term at UC Davis.

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final-2009sample_keys - 1/4 Part of the Final Exam...

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