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?
The reaction
  fumarate + H2O L-malate
essentially does not occur in aqueous solution because the reaction rate is near zero. In the presence of the enzyme known as fumarase, however, the reaction is so fast that its rate is limited only by how fast the substrate can diffuse to the fumarase active site.

3. What effect would fumarase have on the rate of the following reaction?
 

L-malate fumarate + H2O
no effect

Incorrect. Remember, enzymes decrease the energy of the transition state but do not change the energy of the reactants OR the products.

increases the rate

Correct! Enzymes decrease the energy of the transition state without affecting the energy of the reactants OR the products. This means the Ea for the back reaction is smaller too.

decreases the rate

Incorrect. Remember, enzymes decrease the energy of the transition state but do not change the energy of the reactants OR the products.

not enough information to answer the question

Incorrect. How is this reaction related to the given fumarate + H2O L-malate reaction?

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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.