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Unformatted text preview: Problem Set 3 BIBC 100 Spring 2008 1. For each of the following amino acid substitutions, indicate if they would be apt to cause a change or disruption of protein structure and explain your answer. Val to Leu no change likely – both are similarly sized hydrophobic residues Leu to Lys change likely –Leu is hydrophobic and Lys is large and positively charged Asp to Glu no change likely – both are similarly sized negatively charged residues Ala to Tyr change likely – Ala is small hydrophobic and tyrosine is larger and has a polar OH group 2. Which of the following peptides do you think would form a more stable alpha helix and why? #1. A – V – R – M – W – V – E – L – S #2. R – K – R – W – Q – K – R – M - H – W Peptide #1 is likely to form a more stable helix since all of the residues in helix #2 are large and bulky which could lead to steric hinderance between side chains. Furthermore, there are large residues with the same charge 3- 4 residues apart , which will lead to electrostatic repulsion of side chains. 3. You have just completed a mass spectrometry experiment and you have successfully determined the molecular mass of your 100 amino acid protein. For the experiment, you treated your protein with the enzyme trypsin, which cleaves after all Lys and Arg residues. Your protein has Lys at positions 25, 65 and 82 and Arg at positions 14, and 58. a. How many amino acids would you have in each of the resulting proteolytic fragments? Fragment # aa in fragment 1 – 14 14 15 – 25 11 26 – 58 33 59 – 65 7 66 – 82 17 83 – 100 18 b. Estimate the molecular weight of each of these fragments. (Remember that b....
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