This exam is to be worked on independently. You may not discuss any aspect of this exam with anyone except Professor Martin - not other students, not other faculty, no one.

Backbone views:

Question 3

a) Explain the role and interactions within this structure of of chain D
Answer: (15 points) Show me the . We can see that Glu 41 interacts with G32 and the 2'-OH of G43 via H-bonds, while simultaneously interacting with Arg 36, which in turn contacts a DNA backbone phosphate. Thus each amino acid "buttresses" the other, with the aid of the two DNA contact points - cute.
Note that all of these interactions are not equivalent. Indeed, while the 3 contents made by OE1 of Glu41 are all of about the same distance, the angles are better for 2 of the 3. Can you discern the differences? A similar story exists for contacts made by OE2.

b) Explain the role and interactions within this structure of of chain E.
Answer: (15 points) Show me the answer and
His 270 stacks onto A39, stabilizing an otherwise exposed hydrophobic end of the DNA. It also makes H-bonds to the 2' hydroxyl of A39 and to a DNA backbone phosphate.
Some of you noted H-bonds from His270 to A39. While potential dononr-acceptor distances are acceptable, the angles are terrible. His270 can make no reasonable H-bonds to any atom in A39. Think about where the orbitals are, and then think about orbital overlap.