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Biochemistry 2/28/17 Chantel Acevero

4. What is the explanation for the effect of the pH changes on the conformations of poly (Glu)
and poly(Lys)? Why does the transition occur over such a narrow range of pH?

Answer: Effect of pH on the conformation of poly (Glu) and poly(Lys):

Poly-glutamate has an α helical conformation at pH 3. When the pH is raised to 7, there is a large
decrease in the specific rotation of the solution due to the carboxyl groups of poly (Glu) being
fully deprotonated. This results in the unfolding of the α helix. Similarly, poly-lysine, an α helix
at pH 10, can unfold due to the protonation of the amino groups of poly (Lys). A repulsion is
formed among these positively charged groups. This narrow transition occurs because
deprotonation of only a few of each of the amino acids donate charge to the helix. This small
charge can lead to repulsion and evidently rapid unfolding of the α helix.

7. Our growing understanding of how proteins fold allows researchers to make predictions
about protein structure based on primary amino acid sequence data.
a. In the amino acid sequence above, where would you predict that bends or  turns
would occur?
Bends and turns have the highest possibility of forming at Pro residues 7 & 19. Bends
or turns are may also occur at the Thr residue (residue 4) or the Ile residue (residue 1).

b. Where intra-chain di-sulfide cross-linkages might be formed?
Formed between Cys residues 13 and 24.

c. Assuming that this sequence is part of a larger globular protein, indicate the probable
location (the external surface or interior of the protein) of the following amino acid
residues: Asp, Ile, Thr, Ala, Gln, Lys. Explain your reasoning.
Amino acids with ionic (charged) or strongly polar neutral groups (Asp, Gln, and
Lys) would be located on the external surface, where they interact with water.
Residues with nonpolar side chains (such as Ala and Ile) are hydrophobic and would
be located in the interior of the cell. Thr is of intermediate polarity and could be found
either in the interior or on the exterior surface of the protein.

8. Under the proper environmental conditions, the salt-loving bacterium Halobacterium
halobium synthesizes a membrane protein (Mr 26,000) known as bacteriorhodopsin, which is
purple because it contains retinal. Molecules of this protein aggregate into “purple patches”
in the cell membrane. Bacteriorhodopsin acts as a light-activated proton pump that provides
energy for cell functions. X-ray analysis of this protein reveals that it consists of seven
parallel -helical segments, each of which traverses the bacterial cell membrane (thickness
45 Å). Calculate the minimum number of amino acid residues necessary for one segment of
-helix to traverse the membrane completely. Estimate the fraction of the bacteriorhodopsin
protein that is involved in membrane-spanning helices. (Use an average amino acid residue
weight of 110.)

a helix of length 45 Å requires a minimum of (45 Å) (0. Of these. Thus. of the protein . Thus the protein contains 26.4 Å/turn). there are 0.000/110 ± 240 AA. which is 210/240 ± 0.87.6 AA/turn.67 AA/Å along the axis of a helix.000 and average AA M r of 110. The membrane protein has an Mr of 26. or 87%.67 AA/Å) ± 30 amino acid residues. 5.Biochemistry 2/28/17 Chantel Acevero Using the parameters from Problem 3 (3. (30 AA/helix)(7 helices) ± 210 AA are involved in membrane-spanning helices.