BB481-Final-F11

BB481-Final-F11 - BB 481/581 Final Exam Biophysics Nov. 30,...

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1 BB 481/581 Biophysics Nov. 30, 2011 Final Exam Name:_____________ _ This exam is due in the Biochemistry and Biophysics office by 12:00 p.m. on Wednesday Dec. 7 th . This take-home exam is to be worked on by each student without consulting any other persons except for Dr. Karplus, who may be consulted in order to clarify the meaning of questions (karplusp@science.oregonstate.edu). Class notes, textbooks and web resources may be used. For full credit, give concise, but compete answers in the spaces provided. And remember that answers must be in your own words. The problems in this exam are largely based on the article " High resolution X-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein ” by Chiu et al (2005) Proc. Nat. Acad. Sci. 102 , 7517. Some of the figures were originally in color, but you do not need to see the colors to answer the questions. I have posted on Blackboard in the “assignments” section a PDF copy of the manuscript with color figures. I affirm that the work on this exam is my own and that I have not cheated in any way. __________________________________ signature date
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2 1. (5) Based on the first paragraph, the long-range goal of this group’s work on the villin headpiece protein HP35 is to be able to completely and realistically follow the details of the folding process of a real protein by MD simulation. For this reason the protein has to be small and the folding has to be fast. What was the main goal of the work in this paper, and how does that contribute to the long-range goal? 2. (10) The opening paragraph notes that HP35 “is the smallest naturally occurring polypeptide that folds
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BB481-Final-F11 - BB 481/581 Final Exam Biophysics Nov. 30,...

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