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Copyright © UC Regents Davis campus, 2005-12. All Rights Reserved. May not be re-distributed without prior written consent of course instructor. 1of3 BIS 102 Name Kew Summer} 2012 Last ~ First K. Hilt Second Midterm Score (100): Equations: pH = pK, + log {{bVal} (K)(Ki)= 1x10" Ky=x/ 0-0) Ky=x'y-x) pH=(PKg,+pKy,V2 F=(@q'q)/er AG=AH-TAS pX,’s of amino acid side chains: D (3.9), E (4.2), H (6.0), C (8.3), Y (10.1), K (10.5), R (12.5) pK, of amino acid a-COOH (2.1); pK, of amino acid a-NH;* (9.6) pK, of oligopeptide N-terminus (7.4); pK, of oligopeptide C-terminus (3.6) 1. A peptide portion in a protein is 36 amino acid residues long and forms an a-helix. (3 pts.) a) How many hydrogen bonds will be present in this a-helix? Show your calculations and/or reasoning. n-Y= a oof H- bdo Be-4 = (3 pts.) b) How many turns will there be in this a-helix? Be aa/tun 2, Be ae 1D turns 3.6 a.¢/turn (10 pts.) c) In the space below, draw two tums of this a-helix, using a line (—-) to indicate the peptide backbone. Clearly indicate one hydrogen bond in this a-helix, drawing in chemical structures and circling the atoms that are making up this bond. In addition, indicate clearly the position of R-groups in this portion of the a-helix. ek, eh (5 pts.) d) Do you think a glycine residue would be part of this a-helix? Explain. No. Slycine 1S tye small ond Llevible + be aumstrained. to the - 6d", -50° ¢, VY values of on ahelix . 2. A B-pleated sheet is a form of secondary protein structure. (5 pts.) a) Using the cartoon representations of B-pleated sheets that we discussed in class, draw a B-pieated sheet that is composed of five strands, the first three of which are parallel and the last two are antiparallel. Draw in the hydrogen bonds for all five strands (dots representing the H-bonds are fine). (3 pts.) b) A glycine residue can be a part of this five-stranded B-pleated sheet structure. Explain why. the glycine is surrounded by a netwerk at H-bada stabilizn, ' his structure and hence reduel lycine's Y cho write ettuckim is Aifferest fram a oe 6, pices, j 
