BIOCHEMISTRY Question: Please write neatly and answer Question 3 parts A-F, each
ID: 195006 • Letter: B
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BIOCHEMISTRY Question: Please write neatly and answer Question 3 parts A-F, each part requires an appropriate enzyme followed by a brief explanation for that answer. Immediate thumbs up and write consistently!! Thank you!
3) Your research advisor asks you to rank four different enzymes that catalyze conversion of your lab's favorite substrate S into its product P. The free energy diagram for the uncatalyzed reaction is shown on the left in black. Each of the graphs depict the free energy diagram for the catalyzed reaction (dashed line) compared to the uncatalyzed reaction (gray). Answer the following questions using the graphs below to select the appropriate enzyme. Explain your logic for each answer with one sentence. In the case of a tie, name both enzymes. uncatalyzed enzyme #4 ES enzyme #1 enzyme #2 enzyme #3 ESt ESt E+S ES ES, Reaction coordinate Reaction coordinate Reaction coordinate Reaction coordinate Reaction coordinate a) Which enzyme has the smallest Km? b) Which enzyme has the largest Km? c) Which enzyme binds the transition state with the lowest affinity? d) Which enzyme results in the greatest rate enhancement relative to the uncatalyzed reaction? e) Which enzyme results in the poorest rate enhancement? f) List the rank order of enzymes from the lowest to highest Vmax. In the case of a tie, indicate it with a symbol.Explanation / Answer
Before answering this question, two important facts need to be revised.
1) Michaelis-Menten constant Km is inversely proportional to the affinity of the enzyme for its substrate. More the affinity, lower the Km.
2) A favorable interaction in an enzyme-substrate complex or a high affinity complex will always lower the Gibb's free energy, G. More the affinity, lower the G content.
3a) Enzyme #1 has the smallest Km, therefore highest affinity for its substrate. Thus the enzyme-substrate ES complex will have lowest free energy among the four ES complexes.
3b) Enzyme #4 has the largest Km, therefore the lowest affinity for its substrate. Thus the ES complex will have the highest free energy among the four ES complexes.
3c) Both Enzymes #1 and #4 bind the transition state with lowest affinity. The free energy of the enzyme-transition state complex ES# for these enzymes is the highest compared to the remaining two.
Rate enhancement of an enzyme catalyzed reaction will be dependent on both the following factors:
i) affinity of the enzyme-substrate complex: the affinity of this complex should be intermediate such that the it easily attains the transition state. If affinity of the ES complex is high, then the free energy will be further lowered and it will take time to attain the transition state complex.
ii) affinity of the enzyme towards transition state: This affinity component should be low, i.e. the free energy of the transition state should be high, such that it easily breaks up to form the products.
3d) Enzyme #3 will achieve the greatest rate enhancement. Enzymes #1 and #2 have very high affinities for the substrate, as they lower the free energies maximally, making it difficult to attain the transition state complex. On the other hand, even though its transition state complex has high free energy, Enzymes #4 has very low affinity for its substrate, so the initial binding to the substrate will slow the rate of the reaction. Enzyme #3 has intermediate affinity for the substrate, which will fasten the formation of the transition state complex, which will eventually form products.
3e) Enzyme #2 has the poorest rate enhancement as it binds to the substrate with very high afffinity (lowest free energy of the ES complex) like enzyme #1, but unlike enzyme #1, the E2-transition state complex is fairly stable (lower free energy of TS complex compared to E1-TS complex) slowing down the formation of products.
3f) Km= 1/2 Vmax or Vmax= 2Km
highest affinity is proportional to lowest Km (or lowest 2Km= lowest Vmax).
The order of enzymes from lowest to highest Vmax should be
Enzyme #1 = Enzyme #2 < Enzyme #3 < Enzyme 4
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