This exam covers proteins, enzymes and nucleic acids.  The following objectives are not to be considered all-inclusive, but they should give you a very good guide through the material.

Chapter 3
Differentiate between primary (1o), secondary (2o), tertiary (3o) and quaternary (4o) structure
List the forces involved in each of the levels of structure (peptide and disulfide bonds; hydrophobic effect, hydrogen bond, electrostatic interaction and metal ion coordination)
Know the kinds of functions proteins play and an example protein for each
Know the interrelation between the terms apoprotein, holoprotein, and prosthetic group
Be able to compare and contrast the a-helix and ß-sheet, as well as collagen triple helix
Know what denaturation is and how common denaturants such as acid and alcohol work
Be able to sequence a protein (on paper) given the appropriate experimental data
Be able to discuss the general process of protein purification, and how techniques such as affinity chromatogaphy are successful
Be able to discuss some ways of classifying proteins (shape, function, etc.)
Chapter 4
Be able to use the enzyme commission numbering to classify an enzyme based on seeing the reaction it catalyzes
Be able to list the vitamin form and coenzyme form of several coenzymes, as well as the type of reaction that the coenzyme is seen
Be able to identify NAD(H), NADP(H) and FAD(H2)
Know the difference between competitive, noncompetitive, and uncompetitive inhibitors in terms of:  location of binding, time of binding, effect on Km or Vmax, what a Lineweaver-Burk plot looks like ±inhibitor
Be able to discuss the lock-and-key vs. induced fit model of enzyme specificity
Be able to discuss the ways in which an enzyme can act as catalyst
Know and be able to discuss the factors that affect enzyme rate
List and discuss the means for regulating enzyme activity
Given a Lineweaver-Burk plot, be able to determine Km, Vmax and type of inhibition
Chapter 7
Be able to identify the bases, given the structures
Be able to differentiate between and describe the structure of base, nucleoside and nucleotide
Be able to indicate the base-pairing which occurs in DNA and RNA
Be able to describe the predominant physiological form of DNA (B-DNA) as well as discuss the possible existence of other forms
Be able to discuss the packing of DNA in prokaryote or eukaryote systems
Be able to describe/sketch the structures of mRNA, tRNA, and rRNA
Discuss the action of a restriction enzyme on DNA
 

Name: ___________________________
Chemistry 360, Exam 2
March 10, 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.
Answer Key
Part A. Definitions (1 point each)
1. Enzyme- Answer
2. Coenzyme-  Answer
3. Prosthetic group-  Answer
4. Monomer-  Answer
5. Edman degradation-  Answer
6. Parallel pleated sheet-  Answer
7. Active site-  Answer
8. Allosteric effector-  Answer
9. Fibrous protein-  Answer
10. Apoprotein-  Answer
11. Substrate-  Answer
12. First order reaction-  Answer
13. Competitive inhibitor-  Answer
14. Lineweaver-Burk plot- Answer
15. Nucleoside-  Answer
16. Nucleosome-  Answer
17. Bar body-  Answer
18. Denaturation-  Answer
19. Restriction enzyme-  Answer
20. Transcription-  Answer

Part B.
1. Explain the terms primary structure, secondary structure, tertiary structure, and quaternary structure. (5 points)  Answer
2. Compare and contrast the a-helix, the ß-sheet, and the collagen triple helix. (5 points)  Answer
3. From the following sequence information, deduce the sequence of the following octadecapeptide (5 points)  Answer
Fragment 1 sequence: Trp-Thr-Asn-Glu-Val-Lys
Fragment 2 sequence: Ala-Phe-Arg-Tyr-Ile-Leu-Phe-Cys
Fragment 3 sequence: Gly-Gly-Pro-Met-Ala-Phe-Arg

4. List the forces that determine protein tertiary structure and briefly discuss each with respect to amino acids involved, strength of the force, and prevalence. (5 points)  Answer
5. The golgi apparatus is an organelle bounded by a single, 5 nm thick membrane. One of the functions of the golgi is glycoprotein processing. If a sugar transport protein passes through this membrane with 12 a-helical passes, how many amino acids of this protein are required to fulfill this structural role? (5 points)  Answer
6. List four of the six functions that proteins play. (4 points)  Answer
7. Which coenzyme would be required to catalyze the following reaction? (4 points)  Answer
 

8. Identify the following coenzymes. (4 points)  Answer

9. What is the source of the following coenzymes (what is the vitamin from which they are derived) ? (4 points) Answer

Coenzyme A- ____

N5,N10-methylenetetrahydrofolate-____

Biotin- ____

Lipoic Acid- ____

10. If an enzyme has a maximal velocity (Vmax) of 75 µmol·L-1·min-1 and a Michaelis constant (Km) of 1.1 mmol·L-1, what velocity would you expect the enzyme to have at a substrate concentration of 1.9 mmol·L-1? (5 points)  Answer
11. Using the following experimental data, determine (a) the Km of the enzyme (b) the Vmax of the enzyme, assuming the experimental conditions are optimized (c) the type of inhibitor used in the study of the catalytic mechanism. (10 pts) Answer                                           

                V, µmol/min       V, µmol/min
    [S], mM   (no inhibitor)    (with inhibitor)
    0.05        0.33                0.14
    0.10        0.50                0.25
    0.20        0.67                0.40
    0.40        0.80                0.57
    0.50        0.83                0.63

12. The Enzyme Commission (EC) has classified enzymes according to the type of reaction catalyzed, substrate, product, and type of bond acted on. List the six major classes of enzymes in this system. (6 points)Answer
13. Roughly sketch a portion of a DNA molecule and indicate its important structural features. (5 points)  Answer
14. Listed below are the structures of Guanine, Adenine, Cytosine and Thymidine. Indicate the hydrogen bonding that occurs between the appropriate bases. (5 points)  Answer


15. Compare the 3 major types of RNA. (5 points)  Answer
16. List the ways in which DNA differs from RNA. (5 points)  Answer