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bcmb8190_problemSet3 - approximate the effect of the...

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BCMB/CHEM 8190 PROBLEM SET 3 1) Couplings between 5' and 5'' protons and the phosphate phosphorus in a 5' nucleotide are observed to be 6.0 and 8.0 Hz, respectively. Using the formula J PH = 21 x cos( θ ) 2 -2.25, and assuming idealized rotomer geometries about the C5 - O5 bond, calculate the rotamer populations for this molecule. 2) An adenine in a bulge of a poly A – poly U nucleic acid helix is said to be flipped out in solution instead of being stacked between adenine rings of adjacent base pairs. Assume the six membered rings of adenine act like benzene rings and the H2 proton of the adenine in question is above and below the center of rings before and after the central adenine by 3Å. In the flipped out position assume the distance to the center of the other adenine rings is large. Using the remote group model for benzene to
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Unformatted text preview: approximate the effect of the adenine rings, what would you expect for the chemical shift of the H2 proton of the flipped out adenine compared to other adenine H2s? 3) What would you expect for the alpha carbon chemical shift of an alanine when it was in an alpha helix of a protein as compared to a beta sheet? 4) Write down a Hamiltonian for a pair of spin 1/2 spins in a static B field using the z component spin operators Iz 1 , Iz 2 , their coupling constant J 12 , and their chemical shieldings, σ 1 and σ 2 . Make an energy level diagram showing the positions of levels for the four simple product spin functions. Show the allowed one quantum transitions and calculate the energy differences associated with them. Sketch and label the corresponding lines in a frequency resolved spectrum....
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