R :X 2 X R A. Inspect the figure. Draw a reaction coordinate diagram (energy vs reaction progress) that shows the enzyme- catalyzed reaction (as shown above) and uncatalyzed reaction. Make sure your sketch accurately reflects relative free energies of various species. B. What are the chemical roles of 1 and 2 in the enzyme-catalyzed reaction shown in Model 3? C. Propose specific amino acid side chains that could best serve the functions of 1 and 2 in the enzyme depicted in Model 3. Justify your choices.

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### General Method Used by Enzymes to Catalyze the First Step of a 1,4-Elimination Reaction

In the provided figure, enzymes utilize two generic proton donors and acceptors, labeled as 1 and 2, to catalyze the initial step of a 1,4-elimination reaction. These components are a part of the enzyme's active site. For clarity, the rest of the polypeptide chain that surrounds the substrate in the active site and isolates it from the bulk solvent is not depicted in the figure.

The figure shows two structural diagrams:

1. **Starting Structure:**
   - A molecule with an X group bonded to carbon (C) which is double-bonded to an oxygen (O) and single-bonded to another group (R).
   - Proton donor and acceptor sites, denoted as 1 (~ XH) and 2 (~ X), are also depicted.

2. **Reaction Intermediate:**
   - A molecule transformed to show changes in bonding, with an addition of an OH group next to the X group.
   - Proton donor and acceptor sites have facilitated the formation of the intermediate structure.

### Mandated Tasks:

**A.** Inspect the figure. Draw a reaction coordinate diagram (energy vs. reaction progress) that shows the enzyme-catalyzed reaction (as shown above) and the uncatalyzed reaction. Ensure that your sketch accurately reflects the relative free energies of various species.

**B.** What are the chemical roles of 1 and 2 in the enzyme-catalyzed reaction shown in Model 3?

**C.** Propose specific amino acid side chains that could best serve the functions of 1 and 2 in the enzyme depicted in Model 3. Justify your choices.

### Explanation of the Diagram:

- **Reactant State**: The starting structure with X group, carbon double-bonded to oxygen, single-bonded to R, and involving proton donor and acceptor sites (1 and 2).
- **Intermediate State**: The intermediate structure highlights the transformation facilitated by the enzyme.
- **Roles of Proton Donor and Acceptor Sites**:
  - **Site 1 (~ XH)**: Acts as a proton donor.
  - **Site 2 (~ X)**: Acts as a proton acceptor.

To complete these tasks, students should analyze the given reaction mechanism, draw appropriate energy diagrams showcasing the catalyzed and
Transcribed Image Text:### General Method Used by Enzymes to Catalyze the First Step of a 1,4-Elimination Reaction In the provided figure, enzymes utilize two generic proton donors and acceptors, labeled as 1 and 2, to catalyze the initial step of a 1,4-elimination reaction. These components are a part of the enzyme's active site. For clarity, the rest of the polypeptide chain that surrounds the substrate in the active site and isolates it from the bulk solvent is not depicted in the figure. The figure shows two structural diagrams: 1. **Starting Structure:** - A molecule with an X group bonded to carbon (C) which is double-bonded to an oxygen (O) and single-bonded to another group (R). - Proton donor and acceptor sites, denoted as 1 (~ XH) and 2 (~ X), are also depicted. 2. **Reaction Intermediate:** - A molecule transformed to show changes in bonding, with an addition of an OH group next to the X group. - Proton donor and acceptor sites have facilitated the formation of the intermediate structure. ### Mandated Tasks: **A.** Inspect the figure. Draw a reaction coordinate diagram (energy vs. reaction progress) that shows the enzyme-catalyzed reaction (as shown above) and the uncatalyzed reaction. Ensure that your sketch accurately reflects the relative free energies of various species. **B.** What are the chemical roles of 1 and 2 in the enzyme-catalyzed reaction shown in Model 3? **C.** Propose specific amino acid side chains that could best serve the functions of 1 and 2 in the enzyme depicted in Model 3. Justify your choices. ### Explanation of the Diagram: - **Reactant State**: The starting structure with X group, carbon double-bonded to oxygen, single-bonded to R, and involving proton donor and acceptor sites (1 and 2). - **Intermediate State**: The intermediate structure highlights the transformation facilitated by the enzyme. - **Roles of Proton Donor and Acceptor Sites**: - **Site 1 (~ XH)**: Acts as a proton donor. - **Site 2 (~ X)**: Acts as a proton acceptor. To complete these tasks, students should analyze the given reaction mechanism, draw appropriate energy diagrams showcasing the catalyzed and
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