Name: ___________________________
Chemistry 562/762, Exam 1
October 1, 1997
General Instructions. Read each question carefully. Show your setup for all calculation problems so I can give partial credit if necessary. Include units of measurement on all answers. If you need a calculator, pencil, eraser, more paper, etc., ask.
Part A. Definitions (1 point each)
1. Dipeptide-
2. ____________________________ is an organism whose DNA is bounded by a membrane.
3. Aerobic organism-
4. ____________________________ is an organelle whose function is energy production.
5. Functional group-
6. ____________________________ is a compound that resists changes in pH even if small amounts of acid or base are added.
7. Chiral center-
8. ____________________________ is the pH at which an amino acid has no net charge.
9. Zwitterion-
10. ____________________________ is an enzyme which fragments proteins.
11. Sangers reagent-
12. ____________________________ is a protein lacking it's prosthetic group.
13. Metalloprotein-
14. ____________________________ is the number of units of protein per mg total protein.
15. Denaturation-
16. ____________________________ is separation of protein based on its charge.
17. Hemoglobin S-
18. ____________________________ is when an amino acid at the same position in a protein is identical from species to species.
19. Salting out-
20. ____________________________ is when salt is removed from a protein by placing the mixture in a semipermeable membrane bag into a buffer solution.
21. Macromolecule-
22. Chemoheterotroph-

Part B. Concepts
1. Diagram the structure of an animal cell. (10 points)

2. What, if any, organelles would you leave out of a bacterial cell? What, if any, organelles would you include in a plant cell? (5 points)

3. Draw the structure, at physiological pH, of (a) alanine (b) an acidic amino acid (c) a basic amino acid, (d) an aromatic amino acid, and (e) a polar amino acid. Include the name or 3-letter abbreviation of the amino acid you have drawn. (10 points)

4. What is the formula of the Henderson-Hasselbach equation? (2 points)

5. Draw the general form of a tripeptide. (5 points)

6. There are many forces which act in concert to determine the threee-dimensional shape of a protein molecules. List two of these strong forces and two weak forces. (4 points)

7. Indicate the location of cleavage of the following peptide by cyanogen bromide. (3 points)
        Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val-Gly-Lys

8. Indicate the location of cleavage of the following peptide by trypsin. (3 points)
        Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val-Gly-Lys

9. Using the accompanying table of amino acid pK values, indicate the identity of the amino acid which displays the following titration curve. (6 points)
        (A) ____________     (B) ____________     (C) ____________
 

Part C. Application of concepts
10. Complete the following purification table. (10 points)
                        Total protein,     Activity,         Specific                               Fold
Step                     mg                     U               Activity     Yield             Purification
Crude extract     20,000             400,000
Salt precipitation   5,000            300,000
ion-exchange
chromatography     2,000            200,000
gel filtration
chromatography     1,000             100,000
affinity
chromatography         10                 90,000

11. As a professional biochemist, what recommendation would you have for improving the above purification procedure? (5 points)

12. Compute the number of amino acid residues that must be present in an alpha-helix in order to span a cell membrane (5.0 nm thick) one time. (5 points)

13. From the buffers in the accompanying table, choose a buffer you could use if you wanted to make an artificial system to study protein degradation at pH 4.3? (2 points)

14. Suppose you make a buffer system by dissolving 58.0 g of Na2HPO4 and 63.0 g NaH2PO4 in 100 mL of water. What would the pH be? (5 points)

15. In what pH range(s) would arginine make a good buffer? (3 points)

Bonus question (5 points)
For the alpha-helix in question 12, which amino acids would you expect to be used, and why?