Exam 2, BICH 410 (MWF 3-3:50P), Monday October 25, 1999

Write your name on each page. Write concise answers to demonstrate effectively your mastery of the subject material. Show your work in order to receive partial credit where applicable.
gas constant R 8.315 J/mol-K

1) (10 pts) Draw the structure of 2'-deoxyguanosine triphosphate (2'-dGTP).
Answer: see hard copy answer key

2) (8 pts) Draw a Hill plot that describes the binding of oxygen to hemoglobin. Label the axes. Demonstrate how the Hill coefficient is determined from this plot.
Answer: see Fig. 7-8 in book. Note that your answer must state or portray that the axes are both log scale.

3) (12 pts) Starting with the acyl-enzyme intermediate, diagram the catalytic mechanism for phase II of the reaction catalyzed by chymotrypsin (nucleophilic attack by water and release of the carboxylate product). You need to show the roles of the catalytic triad, the transfer of electrons, and the bonds that are broken/formed.
Answer: see Fig. 11-26 in book

4) (8 pts) Draw the N-glycosidic linkage for glycoproteins demonstrating the appropriate protein side-chain and its attachment with N-acetylglucosamine (beta-D-glucose modified at C-2 with NHCOCH3).
Answer: see pg. 212 in book

5) (15 pts) Lineweaver-Burk or double-reciprocal plot
A) Starting with the Michaelis-Menten equation, show how it is rearranged to obtain the equation that describes the Lineweaver-Burk plot.
Answer: M-M eqn.: v0 = Vmax[S] / (KM + [S])
take reciprocal: 1/v0 = (KM + [S]) / Vmax[S]
rearrange terms: 1/v0 = (KM/Vmax)(1/[S]) + 1/Vmax

B) Draw a Lineweaver-Burk plot. Label the axes and show how values are obtained from the intercepts.
C) On the same plot from B), draw another line to demonstrate a situation where the same enzyme is subjected to mixed inhibition in the special case where the KM is unchanged by the inhibitor.
Answer:see Figs. 12-4 and 12-9 in text. Lines for +/- inhibitor should intersect on X-axis since the problem states that the KM is unchanged by addition of the inhibitor.

6) (6 pts) Calculate the rate enhancement (ratio of rate constants) for an enzyme catalyzed reaction when deltadeltaG(act) (difference in activation energy) is 35.6 kJ/mole. (Temp. = 37 degrees C)
Answer: rate constant (k) = Q(a constant) e-deltaG(act)/RT
rate enhancement = ratio of kcat / kuncat = Qe-deltaG(act)cat/RT / Qe-deltaG(act)uncat/RT
kcat / kuncat = e(deltaG(act)uncat - deltaG(act)cat)/RT = edeltadeltaG(act)/RT
rate enhancement = e(35.6 kJ/mole)(1000 J/kJ) / (8.315 J/mole-K)(310 K) = e13.81 = 106

7) (12 pts) Draw the structure of phosphatidyl ethanolamine (a glycerophospholipid where X = ethanolamine) that contains a 16:0 fatty acid and a 18:3delta(9,12,15) fatty acid. Show the ionization of this molecule at neutral pH. Circle the polar part of this molecule that would exist on the solvent side of a lipid bilayer.
Answer: see Table 9-2 in text; saturated fatty acid esterified to C-1 hydroxyl of glycerol (R1) and unsaturated fatty acid is R2.

8) (29 pts) Short answer
A) Name three eicosanoids:
Answer: prostaglandins, prostacyclins, thromboxanes, leukotrienes

B) The zymogen for trypsin is called ___________________________
Answer: trypsinogen

C) Write the integrated rate equation for a first-order reaction A <-> P:
Answer: ln[A] = ln[A0] - kt; or [A] = [A0]e-kt

D) Two examples of glycosaminoglycans are:
Answer: hyaluronate, chondroitin-6-sulfate, keratan sulfate, chondroitin-4-sulfate, dermatan sulfate, heparin

E) Name of an anomer for alpha-D-glucose:
Answer: beta-D-glucose

F) Name of an epimer for alpha-D-glucose:
Answer: alpha-D-mannose, alpha-D-galactose (NOT alpha-L-glucose)

G) Which fatty acid has the lowest melting point? (Circle correct answer)
18:2delta(9,12) OR 18:0
Answer: 18:2delta(9,12)

H) A positive allosteric regulator for ATCase is __________________.
Answer: ATP

I) Mathematical description (equation) that defines the fractional saturation of a protein, P, that binds a ligand, L.
theta or YO2 = [PL] / ([P] + [PL])

J) Amino acid sidechain of RNase A that acts as a general acid _____________
Amino acid sidechain of RNase A that acts as a general base_____________
Answers: histidine, histidine

K) Metal ion in the active site of human carbonic anhydrase:
Answer: Zn+2

L) Two HIV enzymes targeted by inhibitors:
Answer: protease, reverse transcriptase

M) Type of bisubstrate reaction that contains a ternary complex with the enzyme:
Answer: sequential reactions (either ordered or random mechanism)

N) Names of two nucleotides that participate in biological oxidation-reduction reactions: