CEM 882 Problem Set 1 Due Friday, January 29, 2010 in class It may be helpful to look at Voet and

d Voet or another Biochemistry text. 1. Draw the chemical structures of the following oligopeptides in their predominant ionic forms at pH 7: a. (10 points) Tyr-Gly-Arg b. (10 points) Trp-Lys-Asp c. (10 points) Glu-Leu-His-Thr 2. (20 points) Hair is composed of helical keratin protein. For hair that is growing at 15 cm/year, what is the time required to add one amino acid to the end of the keratin protein? 3. (20 points) Provide a reasoned hypothesis for why Trp rings are usually completely immobile in proteins whereas Phe and Tyr rings often rapidly flip. 4. a. (10 points) Calculate the minimum number of residues that an helix must contain in order to span the 30 -thick hydrocarbon core of a lipid bilayer. State the structural constraint for this number of residues. b. (10 points) Provide a reasoned hypothesis why the number of residues in a typical membranespanning helix of a membrane protein is larger than your a answer. Draw a picture to illustrate your hypothesis. 5. The total genome of a human contains two molecular copies of the genetic information and the two complementary copies form a double helix. The DNA is divided into 23 chromosomes each of which contains two DNA molecules in a double helix with ~1.4 108 nucleotides per molecule. a. (10 points) If the DNA was in B form structure, calculate the total length in cm of the double helix of a single chromosome. b. (5 points) What is a typical diameter in cm of a eukaryotic cell nucleus? c. (10 points) Do your answers to a and b suggest that the pure B form structure is reasonable or is not reasonable for chromosomal DNA? Provide a reasoned explanation for your choice. d. (10 points) If your answer to b was reasonable, suggest an experiment to test whether your answer is correct. If your answer to b was unreasonable, suggest how the B form structure might be modified to become reasonable. Draw a picture which qualitatively illustrates this modification.