SolutionSet1 2008

SolutionSet1 2008 - BMB100B Winter 2008 Rubin Solution Set...

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BMB100B Winter 2008 Rubin Solution Set #1 1) Surveys of known protein structures have revealed that bulky aromatic sidechains (Phe, Tyr, and Trp) and glycine are underrepresented in α helices. In other word, their frequency in helices is less than what one might expect based on their frequency in protein primary sequences. Offer an explanation for why this is true. The higher the concentration of bulky aromatic sidechains in compact α helices, the more likely there would be steric hindrances between them, which are energetically unfavorable. Other conformations, such as loops and β -strands, are less compact than helices, thus there is less restriction on sidechain size. Glycine contains two C α hydrogens, and there are considerably less restrictions on its phi and psi angles (less conformations with steric hinderance between the sidechain with the peptide backbone). One reason why amino acids adopt helical conformations is this dihedral angle restriction. Glycine on the other hand is stable in many more conformations and is less likely to be found in a helix than other amino acids. 2) The exteriors of water-soluble proteins contain amino acids in loops and conformations that
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This note was uploaded on 04/07/2010 for the course BIOC 100B taught by Professor Sethrubin during the Winter '10 term at UCSC.

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SolutionSet1 2008 - BMB100B Winter 2008 Rubin Solution Set...

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