written_assignment_2_fall_2010 - Question 1(20 Use the...

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Question 1 (20): Use the kinemage program to answer the following questions. The link is provided in this folder. Start exercise 3. This will allow you to look at the phi and psi angles. You may also use models from organic chemistry. a) (2) What atoms overlap when phi=psi=0? b) (10) There are no ‘allowed conformations’ in which phi is between 0 and 180 degrees. What part or parts of the backbone clash in this range of phi angles? Check psi = 90 paired with phi = 0, 45, 90, 135 and 180 and psi = 45 paired with phi = 0, 45, 90, 135 and 180. State the clashes at each pair of psi phi angles. c) (2) Why does glycine have greater conformational freedom? d) (2) Start exercise 5: What are the major difference between the tuna cytC and the bacteria cytC? e) (2) What 4 residues in the tuna are protein are attached covalently to the heme? And how are they attached? f) (2) Where are the lysine residues? Buried or on the surface?
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Question 2 (20): Use this protein picture to answer the following questions a) (5) Indicate the N and C termini of this protein.
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