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Midterm 2 Problems - 2009

Midterm 2 Problems - 2009 - UC Berkeley Chem C130/MCB 100A...

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UNIVERSITY OF CALIFORNIA, BERKELEY CHEM C130/MCB C100A MIDTERM EXAMINATION #2 October 15, 2009 INSTRUCTORS: John Kuriyan and David Wemmer THE TIME LIMIT FOR THIS EXAMINATION: 1 HOUR 20 MINUTES SIGNATURE: ________________________________________________________________ Please SIGN your name on the line above in INDELIBLE INK . YOUR NAME: ________________________________________________________________ PLEASE PRINT your name ( IN INDELIBLE INK ) on the line above (& on the top right hand corner of every page). PLEASE CIRCLE the name of your GSI: Anna Asmundson Geo rey Feld Zhijuan Gao Patrick Visperas PLEASE WRITE all of your answers AS LEGIBLY AS POSSIBLE . SCORING. The exam consists of 4 questions worth 25 points each totaling 100 points as broken down in this table: Question Part A Part B Part C Part D Your Total Maximum Score 1. [12] [13] ---------------- --------------- 25 2. [9] [16] ---------------- ---------------- 25 3. [8] [6] [11] --------------- 25 4. [15] [10] --------------- --------------- 25 TOTAL ! 100 UC Berkeley, Chem C130/MCB 100A, Fall 2009, Mid-term Exam 2. Your Name___________________________ Page 1 of 14
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Q1 25 points Shown below is a block of aligned sequences from a family of related proteins. Assume that amino acid substitutions occur independently in this block. Q1A (12 points) (i) (3 points) Based on the amino acid abundances seen in this block, what is the probability of finding Trp (W) at any position in the block? Show how you work out the answer. Q1A (ii) (3 points) What is the probability of finding Phe (F) at any position in the block? Q1A (iii) (6 points) If the sequence block were random and uncorrelated, but with the same amino acid composition (i.e., same numbers of each amino acids), what is the probability of seeing a Phe-Trp substitution? Show the steps of how you do the calculation. UC Berkeley, Chem C130/MCB 100A, Fall 2009, Mid-term Exam 2. Your Name___________________________ Page 2 of 14
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Q1 B. (13 points) Q1B (i) (4 points) How many Phe-Trp substitutions are actually there in this block? Show the steps of how you calculate the answer. Q1 B (ii) (6 points) What is the observed probability of Phe-Trp substitutions? That is, calculate the ratio: number of observed Phe-Trp substitutions number of all possible substitutions . Explain your answer. Q1B (iii) (3 points) Briefly explain why the substitution score is expressed in terms of the logarithm of the likelihood of a substitution. UC Berkeley, Chem C130/MCB 100A, Fall 2009, Mid-term Exam 2. Your Name___________________________ Page 3 of 14
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Q2. (25 points) (A) (9 points) The diagrams below show the heat capacity as a function of temperature for two proteins, Protein A and Protein B. The temperature scale on the horizontal axis is the same on both graphs. The sequences of Protein A and Protein B are the same, except that a scientist introduced mutations so that many of the leucine residues in Protein A are replaced with arginine in Protein B.
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