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ProbSet4_solutions - Problem Set 4 Chem C130/MCB C100A UC...

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Hand in your answers to the 4 questions marked with a * on Thursday, September 23 . This is the last problem set due before the midterm exam on Tuesday, September 28. A. Multiple choice, True/False or Fill in the Blanks. Q1. The BLOSUM scoring matrix gives a measure of how conservative a mutation is. For substitutions of aspartic acid (ASP, D), which of the following orderings correctly places the amino acids from most conservative to least conservative: A) K,L,A,C,E,S B) E,S,K,A,C,L C) L,C,A,K,S,E D) A,C,E,K,L,S Answer: E,S,K,A,C,L Q2. An environment profile in the 3D-1D profile method compares: I) the stability of the amino acid in varying solvents II) the burial of each amino acid in the structure III) the hydrophobicity of surrounding each amino acid IV)type of secondary structure element containing each amino acid Which of the following combinations A) I,II,III,IV B) I,IV C) II,III,IV D) II,IV Answer: C) II,III,IV Q3. Protein domains can be assembled together in many different ways, because surface sidechains can mutated easily without losing protein stability TRUE /FALSE Q4. In contrast to ribonuclease, some proteins cannot fold without the assistance of proteins known as molecular chaperones. This means the thermodynamic hypothesis of protein folding does not apply to these proteins. TRUE/ FALSE ( The thermodynamic hypothesis reflects the idea that the protein sequence determines its structure. Even though chaperones prevent off-pathway events, the structure is still determined by the sequence. ) Q5. Two proteins that share more than 50% sequence identity over a 100 residue stretch are likely to have the same three dimensional fold TRUE /FALSE Q6. Fill in the blank The hydrophobic portion of a lipid bilayer is approximately _35______ Å thick. Problem Set 4. Chem C130/MCB C100A. UC Berkeley Fall 2010 Page 1 of 14
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The packing of alpha-helices against each within the lipid bilayer is mainly stabilized by _van der Waals_________ interactions. ( Because the helices are in a hydrophobic environment, their interactions are not determined by the hydrophobic effect . Occasionally such helices may also be stabilized by hydrogen bonds, but this is rarer ). The process by which proteins use energy to move molecules across the membrane is known as _active transport_________. Two common reversible chemical denaturants of proteins are guanidinium and _urea______. Refer to the BLOSUM substitution matrix. The most conservative substitution of Tryptophan (W) other than itself, is __Y____, which has a score of ___+2___. Q7. Molecular chaperones are proteins that help globular protein molecules to fold up properly. Many molecular chaperones work by preventing protein aggregation. They do this by repeatedly binding to and releasing unfolded proteins. Since chaperones help many different kinds of globular proteins to fold properly they must recognize features that are common to all unfolded globular proteins. Which of the following features are likely to be the most important targets of chaperones?
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