BICH 410, section 503, EXAM 3, Monday November 14, 1994

Please write your name on each page. Write concise answers and show your work in order to receive partial credit.

1) (10 pts) Draw the structure of phosphatidylcholine (a glycerophospholipid) where one fatty acid is 16:0 and the other fatty acid is 16:2(delta9,12). You do not have to draw separately every carbon, nor show the conformation or stereochemistry of the fatty acid hydrocarbon chains.

2) (15 pts) Fill in the blanks.
A) Which amino acids form the catalytic triad for serine proteases?
____________________, ____________________, _________________
B) What amino acid of hemoglobin is coordinated to the iron of the heme group? ____________________
C) The general formula for the amino acid repeat of collagen is glycine-X-Y. Often,
X = ____________________, and Y = ___________________.
D) What is the subunit structure of adult hemoglobin? _____________________;
fetal hemoglobin? _____________________
E) Name the six classes of enzymes according to the international classification scheme.
____________________, ____________________, _________________
____________________, ____________________, _________________
F) What is the type of enzyme inhibitor that changes the Km, but not the Vmax? ______________________

3) (15 pts) Michaelis-Menten enzyme kinetics
A) Write out the equilibria for the enzymatic conversion of a single substrate, S, to a product, P. Label the arrows with the appropriate rate constants. Do not make any assumptions yet.

B) To derive the equation, what assumption is made about the rate of change of the concentration of the enzyme-substrate complex, [ES]? Write the rate equation for the overall rate of change of [ES].

C) Write the rate equation for the initial velocity of the reaction. What assumption is made here?

D) Write the Michaelis-Menten equation.

4) (10 pts) Draw the "backbone" structure of two peptide units of a protein chain, labeling the sidechains simply as R1 and R2. On your drawing, indicate every location where there is a: A) peptide bond, B) bond described by a phi angle, C) bond described by a psi angle, D) hydrogen bond donor for an alpha-helix, E) hydrogen bond acceptor for an alpha-helix.

5) (8 pts) Based on the accompanying figure, explain the strong effect of pH on the conformations of poly- glutamic acid (poly(Glu)) and polylysine (poly(Lys)). You do not need to understand specific rotation, except to know that it is a sensitive assay to detect changes in the secondary structure of a protein.
(figure is from problem 4, Chap. 7 in textbook)
B) Why does the transition occur over such a narrow range of pH?

6) (10 pts) The turnover number for an enzyme is known to be 5000 min-1. From the following set of data, (A) calculate the Km, and (B) determine the total amount of enzyme present in these experiments. For full credit, you must show your reasoning.
substrate concentration (mM)initial velocity (mmol/min)

7) (5 pts) Arrange the following fatty acids in the order of increasing melting point.
18:0, 22:0, 18:1(delta9)

8) (15 pts) Given the following hypothetical metabolic pathway:

A to B to C to D to E to F
X to Y to Z

A) What step in the top pathway might be catalyzed by an allosteric enzyme?

B) If substance F is the allosteric regulator for this step, what type of regulator is F?

C) Assume that this allosteric enzyme contains multiple binding sites for its substrate that interact cooperatively. Draw a plot of initial velocity vs. substrate concentration. Label the axes and indicate how to determine the K0.5.

D) On the same figure above, draw an initial velocity vs. substrate concentration curve in the presence of the allosteric regulator F. Assume that F does not change the Vmax.

9) (6 pts) Which is more soluble in water - a triacylglycerol or a free fatty acid? Why?

10) (6 pts) There is a class of eukaryotic proteins that dimerize (bind to each other) via a so-called leucine zipper. In these proteins a region of about 30 amino acid residues contains a leucine every seventh residue. The leucines from adjacent polypeptides interact with one another. From what you know about proteins, what might be the structure of the leucine zipper? Explain.