practice-exam1_solutions - Name:_ MCB100A/CHEM130A Practice...

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Name:_____________________________________________ MCB100A/CHEM130A Practice Exam- I 11-30-05 (Aathavan) 1. Simulate your own levels of stringency – no cheat sheets/ cheat sheets/ open book 2. DON’T PANIC if it appears difficult. Nothing in here is beyond the domain of what you already know. Just clear your heads and think 3. Remember that this may not be representative of what’ll be on the exam. 4. Have fun! I. Catalytic Triad: ( Inspired by a problem in JK’s Fall 2003 exam) (10) A. Many enzymes (proteases and lipases) use the following three amino acids in their catalytic site. Identify the three residues – A, B, C. The C-α atoms are indicated by black dots. A- Glu B- His C- Ser B. The activity of this enzyme is dependent on the formation of the pattern of hydrogen bonds shown here. The activity of the enzyme stays fairly constant as the pH of the solution is decreased from pH 9.0 to pH 6.0. When the pH of the solution is further decreased below pH 6, the activity of the enzyme drops rapidly with decreasing pH. The activity is fully regained if the pH is adjusted back up above 6.0 i) Which of these three residues is likely responsible for this behavior? His. This is the only residue that titrates in this regime ii) Write down the chemical structures of the protonated and deprotonated forms of the titrating residue indicating charges
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C. How will the pKa of A and B change if A and B are moved farther apart. Let’s look at Glutamate equilibrium. GluH <-----> Glu- + H+ If you have a positive charge next to the Glu- ,Glu- is stabilized and the reaction shifts to the right, i.e Ka (the dissociation constant for the acid) becomes higher… or the pKa = -log10Ka will become smaller. Hence moving the positive charge away will increase pKa. Similarly for His HisH+ <------> His +H+ A negative charge will stabilize HisH+ and will shift the equilibrium to the left. The Ka becomes smaller or pKa increases. So moving the –ve charge away will decrease pKa II. Designing a Coiled Coil: (10) An (exaggerated )picture of a coiled coil A. Alpha-helical segments of proteins that have a heptad repeat of leucine residues are known to form left handed super helical coils. Explain (using a wheel diagram if necessary) the driving force for the formation of this coiled-coil. It is important to first realize that a coiled-coil refers a single polypeptide strand that forms a helix whose axis itself coils up like a helix – like in the picture above. In a heptad repeat you would have a Leucine at 0 deg and 700 deg (2 x 360 – 20). The hydrophobic effect drives the supercoiling of the helix. This way all the leucines would
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This note was uploaded on 09/14/2009 for the course MCB 100A taught by Professor Kuryian during the Fall '09 term at University of California, Berkeley.

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practice-exam1_solutions - Name:_ MCB100A/CHEM130A Practice...

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