practice-exam1 - Name MCB100A/CHEM130A Practice Exam...

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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. 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? 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. 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.
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B. Let us say that you are designing your own coiled-coil and wanted it to have a right- handed twist instead of a left handed twist. What should be the spacing between the
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