Final Problems - 2008SPRING

Final Problems - 2008SPRING - Name MCB C100A Chem C130...

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Name________________________ MCB C100A / Chem C130 Final Exam Spring 2008 9 pages total including cover POSSIBLY USEFUL INFORMATION: R = 8.314 J/mol/K = 1.987 cal/mol/K = 0.082 L atm/K k B = 1.38 x 10 -23 J/K N A =6.02 x 10 23 molec/mole F = 96,500 coulomb RT/F = 0.0257 1 V coulomb = 1 J properties of water: ice liquid water water vapor C p 2.1 J/K/g 4.2 J/K/g 1.8 J/K/g density of ice: 0.95 g/ml of water 1.00 g/ml of water vapor (at 1 atm) 8 x 10 -4 g/ml heat of melting of ice 333 J/g heat of vaporization of water 2216 J/g
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Problem 1. True/false or multiple choice questions, circle the correct answer for each part. a) Disulfide bonds assist in correct protein folding mainly because they make the folded state more energetically favorable relative to the unfolded state. TRUE FALSE b) Alpha helices are the most common secondary structural motif in membrane proteins. TRUE FALSE c) Loop regions in proteins are almost always unstructured and free-floating in solution. TRUE FALSE d) Which of the following amino acid best starts an alpha helix? Y P G D e) Which of the following folds commonly binds metals? i) Helix-turn-helix ii) Coiled coil iii) Rossman fold Problem 2. Briefly explain Levinthal’s paradox. What is one possible resolution of the paradox?
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Problem 3. a) Consider the reversible unfolding of a membrane protein that contains several transmembrane helices in the folded stated. Propose a model for the structure of the unfolded-state ensemble. b. β -sheets in membrane proteins do not have the same variability as β -sheets in soluble proteins. Which class of β -sheet do you think is most enriched in membrane proteins and why? Problem 4. a) Propose a possible explanation for why DNA contains thymidine and RNA contains uracil. b) What characteristic of folded RNAs aids in the prediction of RNA structure from the sequences of homologs from different organisms? c) What is an “A-minor” motif and how does it stabilize RNA structures?
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