Welcome to the Enzymes debriefing.

Answer the questions below. If necessary click on the Check buttons when you are finished with each question.

1. Proline racemase is an enzyme that alters the stereochemistry of the amino acid proline at its a carbon. Click on the molecule you think would be the strongest competitive inhibitor of proline racemase.

Correct! Pyrrole 2-carboxylate mimics the transition state of the substrate proline. Therefore it can fit into the active site of the enyzme and prevent the substrate from binding.
Pyrrole 2-carboxylate mimics the transition state of the substrate proline. Therefore it can fit into the active site of the enyzme and prevent the substrate from binding.

Pyrrole might compete with proline, but is there another molecule that looks more like proline?

Pyrrole 3-carboxylate has all the same function groups as proline, but not in the same positions.

While 4-butyl pyrrole 2-carboxylate has all the same functional groups in the same positions as proline, the butyl group might prevent it from fitting into the enzyme's active site.

Before there were computer programs that fit curves to experimental data, scientists usually had to manipulate their data algebraically to give straight-line plots that were easier to interpret. One way to do this with Michaelis-Menten kinetics is to plot the data as 1 / V vs. 1 / [S]. This yields a Lineweaver-Burke plot, which can be used to determine Vmax and Km, as well as the type of inhibition seen in a particular system. The y-intercept of a Lineweaver-Burke plot equals 1 / Vmax, while the x-intercept equals -1 / Km.

2. Click on the graph below to see Lineweaver-Burke plots of an uninhibited and an inhibited enzyme reaction. What kind of inhibition is going on?

Competitive
Noncompetitive
Mixed
1 / Vmax is larger, which implies that Vmax is smaller. What sort of competition is this a feature of?
Correct! 1 / Vmax is larger, which implies that Vmax is smaller. This is a feature of noncompetitive inhibition.
1 / Vmax is larger, which implies that Vmax is smaller. This is a feature of noncompetitive inhibition.
Notice that the x-intercept is unchanged, while the y-intercept is larger. What does this say about Km and Vmax?

3. From the following list of reactions and their DGs, select the one(s) that an enzyme might be able to catalyze.

A. fructose-6-phosphate + H3PO4 fructose-1,6-bisphosphate + H2O
DG = +16.7 kJ/mol
B. fumarate + H2O L-malate
DG = -0.418 kJ/mol
C. 4 cytochrome c-Fe3+ + 2 H2O 4 cytochrome c-Fe2+ + 4 H+ + O2
DG = +232 kJ/mol
D. 2-phosphoglycerate 3-phosphoglycerate
DG = -4.60 kJ/mol
Correct! Enzymes can only catalyze reactions that are favorable thermodynamically, i.e., that have a negative DG.
Correct! But is there another?
Remember, enzymes cannot catalyze a reaction that is not thermodynamically favorable.
Please make a selection from the choices above.

Note that the reactions written in A and C do occur in living systems, but not as written. They need continuous outside intervention, usually in the form of a coupled reaction that releases energy, in order to go forward.

Congratulations!

You have completed the Enzymes module.

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References

Mariusz Jaskolski, Alfredo G. Tomasselli, Tomi K. Sawyer, Douglas G. Staples, Robert L. Heinrikson, Jens Schneider, Stephen B.H. Kent, and Alexander Wlodawer. "Structure at 2.5-Å Resolution of Chemically Synthesized Human Immunodeficiency Virus Type I Protease Complexed with a Hydroxyethylene-Based Inhibitor." Biochemistry (1991) 30: 1600-1609.

Jun Ohkawa, Tetsuhiko Koguma, Takeo Kohda, and Kazunari Taira. "Ribozymes: From Mechanistic Studies to Applications In Vivo." Journal of Biochemistry (1995) 118: 251-258.

William G. Scott, James B. Murray, John R.P. Arnold, Barry L. Stoddard, and Aaron Klug. "Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme." Science (1996) 274: 2065-2069.

William G. Scott and Aaron Klug. "Ribozymes: Structure and Mechanism in RNA Catalysis." Trends in Biochemical Sciences (1996) 21: 220-223.