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Midterm 2 Problems - 2008-1

Midterm 2 Problems - 2008-1 - UC Berkeley Chem C130/MCB...

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UC Berkeley, Chem C130/MCB 100A, Fall 2008, Mid-term Exam 2. Your Name___________________________ Page 1 of 13 UNIVERSITY OF CALIFORNIA, BERKELEY CHEM C130/MCB C100A MIDTERM EXAMINATION #2 OCTOBER 17, 2008 INSTRUCTORS: John Kuriyan and Bryan Krantz 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: Jonas Lee Mark Walker Katie Thoren Kate Engel PLEASE WRITE all of your answers AS LEGIBLY AS POSSIBLE . SCORING. The exam consists of 4 questions worth 25 pts each totaling 100 pts as broken down in this table: Question Part A Part B Part C Part D Your Total Maximum Score 1. (10) (15) ------------- --------------- 25 2. (12) (13) ------------- --------------- 25 3. (12) (6) (7) --------------- 25 4. (15) (10) --------------- --------------- 25 TOTAL ! 100
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UC Berkeley, Chem C130/MCB 100A, Fall 2008, Mid-term Exam 2. Your Name___________________________ Page 2 of 13 QUESTION 1 (25 PTS TOTAL) Q1. Part A (10 points) Shown below are short segments of three proteins, containing only the amino acids D, F, G, L and K. Protein 1: DFGLLKDGG Protein 2: KFDFKDGKD Protein 3: LGLFDFLGF Protein 1 is evolutionary related to only one of the two other proteins (i.e., it is related to either protein 2 or protein 3, but not both). Using the BLOSUM substitution score matrix (given below), explain whether protein 1 is related to protein 2, or whether it is related to protein 3. Explain your reasoning completely. D F G L K D 6 -3 -1 -4 -1 F -3 6 -3 0 -3 G -1 -3 6 -4 -2 L -4 0 -4 4 -2 K -1 -3 -2 -2 5 (1) What is the relatively likelihood that protein 1 is related to protein 2 versus protein 3? That is, how much more (or less) likely is the 1-2 alignment relative to the 1-3 alignment? Explain all the steps of how you work out the answer. (8 points)
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UC Berkeley, Chem C130/MCB 100A, Fall 2008, Mid-term Exam 2. Your Name___________________________ Page 3 of 13 (2) Why is the leucine-leucine substitution score lower than all the other self-substitution scores? Explain your answer. (2 points) Q1. Part B. (15 points) The interaction between two atoms separated by a distance r is described by the following parameters: (1) F = ! k ( r ! r 0 ) (when r < 6.0 Å) (2) The bond between the atoms “breaks” when r = 6.0 Å. The force is 10.0 kJ mol -1 Å -1 when r = 6.0 Å.
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