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Chem237Fall2011Midterm1October12,2011 Name:_____________________________________________ID#:_______________________________________

Hi. I do not know how to answer question 1.b. and 2.
Chem 237 Fall 2011 Midterm 1 October 12, 2011 Name: _____________________________________________ ID#: _______________________________________ Useful pK a information: Tris base (8.1) acetic acid (4.76) HEPES (7.55) phosphate (6.8) 1. a. 4 marks. Write a coupled reaction using the 2 following hydrolysis reactions. What is ΔG o’ of this coupled reaction? Δ G o (kJ/mol) acetylphosphate + H 2 O acetate + P i ‐40 glycerol‐3‐phosphate + H 2 O glycerol + P i ‐9 b. 4 marks Can these following reactions be coupled to form a thermodynamically favorable reaction ? Support your answer. (Hint: consider the type of bonds being formed and broken—see the figures) glucose‐6‐P + H 2 O glucose + P i fructose‐6‐P + H 2 O fructose + P i 2 . BUFFER HORROR STORY. 10 marks Once upon a time, I was working with a fellow graduate student “Minnie” (not her real name). She made a buffer for our purification, 50 mM HEPES, pH 6.8. On a hunch, I checked the pH of the buffer before using it, and it was about pH 4. a. What Minnie’s mistake? How could this error be corrected? b. Had she made the buffer correctly , would this buffer been optimal at pH 6.8? If the intended buffer (50 mM HEPES, pH 6.8) is NOT an optimal buffer, how would you make it a usable buffer? Support your answer. 3. 6 X 1.5 marks. Draw the following amino acids in the predominant form found at pH 7. a. Phe b. Leu c. Ser d. Arg e. Gln f. Met 4. 3 X 5 marks. Explain the following statements, in terms of what we discussed in class. I will count the best 3 of 4. a. A mutant protein, A, that has a Pro substituted for a Glu is found to fold very slowly and denatures at a very low temperature, compared to the non‐mutant protein. b. Another protein, B, does not form 4 o structure until after it has been processed by GroEL, and then it forms an α 2 dimer. c. Different proteins have different, characteristic pI values, ranging, typically, from about 4 to 9. d. Only certain ψ and φ angles in the peptide bond are allowed in protein structures. OVER
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5. a. 10 marks. Draw the following peptide in the fully protonated form. Indicate the N‐ and C‐ terminals, and the peptide bonds. Cys‐Pro‐Trp‐Lys b. 8 marks Draw a titration curve for this peptide, using base to titrate it. Be sure to label the axes properly and indicate the pK a values of the groups titrating and the titration endpoints. c. 4 marks. What is the pI of the peptide? Show your reasoning. 6. The figure here is of the “prion” protein that causes Mad Cow Disease; the first structure is of the abnormal prion protein, and the second structure is of the normal form of the prion protein. You do not need to know any details of the physiology of this disease to answer this question. [Abnormal] [Normal] a. 5 marks What is primary structure? Do these proteins have primary structure? If so, where in the structure is it found? What holds primary structure together? In the abnormal form, indicate the N‐ and C‐termini of the proteins on this page. b. 10 marks What is secondary structure? Do either of these proteins have secondary structure? If so, describe the types of secondary structure that are found in the structures. A complete answer would include the dimensions of the different 2 o structures. Where in the structures is it (are they) found? What holds secondary structure together? c. 5 marks. Does this protein have tertiary structure? If so, where in the structure is it found? What forces hold tertiary structure together? d. 2 marks Do either of these proteins have quaternary structure? Why or why not? e. 5 marks. Qualitatively, what is the difference between the abnormal and normal structures of the prion protein? What structural changes would need to take place for the normal form to convert into the abnormal form? Which level(s) of protein structure are affected? The End
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