University of California, Santa Barbara MCDB 108A Midterm1 11-ALL ANSWERS CORRECT
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Course
MCDB 108A BIOCHEMISTRY
Institution
University Of California, Santa Barbara
Biochemistry, MCDB 108A Your Name_______________________________
Prof. Duane Sears Neatly print YOUR FULL NAME HERE
Midterm Exam #1, Oct. 28, 2011
F11‐108A‐MT Page 1 of 7 Pages
INSTRUCTIONS
LEGIBLY PRINT your name on the top of all 7 pages, including the last page with the scoring grid...
Biochemistry, MCDB 108A Your Name_______________________________
Prof. Duane Sears Neatly print YOUR FULL NAME HERE
Midterm Exam #1, Oct. 28, 2011
INSTRUCTIONS
LEGIBLY PRINT your name on the top of all 7 pages, including the last page with the scoring grid.
Answer all 3 questions for a maximum score of 100 points. The point value for each question is
shown in parentheses next to the question number.
Where appropriate, clearly show your reasoning in order to optimize your partial credit.
No partial credit will be given for ambiguous or vague answers or reasoning.
PLEASE KEEP YOUR EYES ON YOUR OWN EXAM AND MATERIALS AT ALL TIMES.
QUESTION 1 (50 points)
From the amino acid (AA) sequencing steps listed below, write correct amino acid sequence in the
answer box on the next page for a polypeptide chain that would generate the following cleavage
products.
INSTRUCTIONS:
The AA compositions for each peptide are listed in alphabetical order in the parentheses. Any number
preceding an AA corresponds to its relative molar ratio compared to the other AAs.
The numbered reaction products are listed from smallest to largest in size.
For full credit, clearly indicate to the right of each step any sequence information you can deduce from
a step: For example,. “N‐terminal peptide” or “D‐F‐(S,A)‐P ” with the order of S & A not yet specified.
For full credit, clearly note as instructed on the next page, the sequence step or steps that helped
identify the position of a given AA: For example, “B.5” or “A.2” written below the amino acid letter.
Hints: For this question, use the same format as used for the sequencing problems of Ch. 3 of WWBH
(in the Course Supplement) where the peptide amino acid compositions, free amino acids, and amino
acids derivatives are all listed for each product generated in a given cleavage step.
Also, assume that each peptide is fully homogeneous and its exact AA composition has been determined.
Finally, assume the specificity of each cleavage reagent is exactly as shown in the slides for LECTURE 8.
A. Chemical cleavage with CNBr Sequence deductions you can make:
1. (M, Q, R)
2. (A, C, 2E, I, 2N, P, 2R, 2Y)
B. Proteolytic cleavage with V8 Protease Sequence deductions you can make:
3. (E, P, Y)
4. (E, M, N, Q, R)
5. (A, C, I, N, 2R, Y)
C. Proteolytic cleavage with THERMOLYSIN Sequence deductions you can make:
6. (I, N)
F11‐108A‐MT1.docx Page 1 of 7 Pages
, Biochemistry, MCDB 108A Your Name______________________________
Prof. Duane Sears Neatly print YOUR FULL NAME HERE
Midterm Exam #1, Oct. 28, 2011
QUESTION 1 (cleavage with THERMOLYSIN continued)
7. (A, C, Y)
8. (E, P, 2R, Y)
9. (E, M, N, Q, R)
D. Aminoethylation by ethyleneimine followed by TRYPSIN proteolysis Sequence deductions:
10. 2 R (relative moles of free amino acid)
11. (C, Y)
12. (A, I, N)
13. (2E, M, N, P, Q, R, Y)
E. Proteolytic cleavage with CHYMOTRYPSIN Sequence deductions you can make:
14. (A, C, I, N)
15. (2E, M, N, P, Q, 3R, 2Y)
Using one‐letter AA abbreviations and the accepted ordering convention for AA residues in a polypeptide
sequence, write your predicted polypeptide sequence in the answer box below. For full credit, clearly
show your deductions for each site. No credit given for just writing a sequence.
On the lines provided below, use the 1‐letter abbreviations for standard amino acids to predict the
amino acid sequence of a polypeptide that yields the cleavage fragments listed above, where the bolded
numbers below the lines correspond to the numbered residues of the polypeptide chain.
Also, indicate your justifications for placing particular residues at the numbered positions by noting (in the
spaces below the numbers) which fragmentation step or combinations of steps above (e.g. B.6, C.4, etc.)
led you to make those selections.
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