Question

Briefly describe the role of nucleophilic catalysis in the mechanism of the chymotrypsin reaction.

Short answer

Nucleophilic catalysis in the chymotrypsin reaction involves Ser195 forming a transient covalent bond with the substrate, with His57 and Asp102 helping to stabilize the transition state and facilitate hydrolysis.

Step-by-step solution

- Identify Nucleophilic Catalysis

Nucleophilic catalysis occurs when a nucleophile forms a transient covalent bond with a substrate, thereby stabilizing the transition state and increasing the reaction rate. In the context of enzyme reactions, this often involves amino acid side chains acting as nucleophiles.

- Recognize Key Nucleophiles in Chymotrypsin

In the chymotrypsin mechanism, the key nucleophile is the serine residue (Ser195) in the enzyme's active site. This serine acts as a nucleophile, attacking the carbonyl carbon of the peptide bond being cleaved.

- Describe the Role of Histidine and Aspartate

Histidine (His57) and Aspartate (Asp102) form a catalytic triad with Ser195. Histidine acts as a base, abstracting a proton from Ser195, thereby increasing its nucleophilicity. Aspartate helps to stabilize the positive charge that develops on Histidine.

- Explain the Formation of the Acyl-Enzyme Intermediate

The nucleophilic attack by Ser195 on the peptide bond forms a covalent acyl-enzyme intermediate. This intermediate is stabilized by an oxyanion hole in the enzyme, which facilitates the progression of the reaction.

- Outline the Hydrolysis of the Acyl-Enzyme Intermediate

Water then attacks the acyl-enzyme intermediate, with His57 again playing a catalytic role by abstracting a proton from water, making it a better nucleophile. This leads to the release of the cleaved peptide fragment and regeneration of the free enzyme.

Key concepts

Nucleophilic Catalysis

In chemistry, nucleophilic catalysis is a process where a nucleophile, a molecule that donates an electron pair, temporarily binds to a substrate. This temporary bond helps to stabilize the transition state, making the reaction proceed faster.
For chymotrypsin, an enzyme, this catalytic process involves specific amino acids in its active site. These amino acids have side chains that act as nucleophiles, attacking key bonds within the substrate to facilitate its breakdown. Chymotrypsin uses the nucleophilic power of one of its amino acid residues, serine, to perform its function more efficiently.

Chymotrypsin Mechanism

Chymotrypsin is a digestive enzyme that breaks down proteins in the small intestine. Its mechanism is a beautiful example of enzymatic precision and efficiency. The process begins when the serine residue (Ser195) in the enzyme's active site attacks the carbonyl carbon of the peptide bond within a protein substrate.
This attack creates an unstable tetrahedral intermediate, which is then stabilized by other parts of the enzyme. This enzyme's catalytic steps include forming an acyl-enzyme intermediate and later hydrolyzing this intermediate to complete the protein cleavage.
Each step of the mechanism relies on careful coordination among various amino acids in the active site.

Catalytic Triad

The catalytic triad is a set of three key amino acids within the active site of chymotrypsin, which work together to make the serine residue a highly effective nucleophile. These amino acids are:

• Serine (Ser195): Acts as the primary nucleophile.


• Histidine (His57): Acts as a base, helping to abstract a proton from Ser195, increasing its nucleophilicity.


• Aspartate (Asp102): Stabilizes the positive charge that develops on Histidine during the reaction.

This triad dramatically increases the effectiveness of the nucleophilic attack performed by Ser195, making the enzyme highly efficient at breaking down proteins.

Acyl-Enzyme Intermediate

One of the critical steps in the chymotrypsin mechanism is the formation of the acyl-enzyme intermediate. After Ser195 performs the nucleophilic attack on the peptide bond, a covalent bond forms between Ser195 and the carbonyl carbon of the substrate.
This creates the acyl-enzyme intermediate, a temporary state that is essential for the reaction to proceed. The enzyme further stabilizes this intermediate through an oxyanion hole, which helps to lower the energy barrier of the reaction, facilitating a smoother progression of the catalytic steps.

Enzyme Active Site

The active site of chymotrypsin is uniquely structured to facilitate its catalytic function. It contains the catalytic triad and an oxyanion hole, both of which are critical for the enzyme's activity. The oxyanion hole stabilizes the tetrahedral transition state formed during the reaction, lowering the activation energy.
Specific pockets within the active site recognize and bind to peptide substrates with high specificity. This precise architecture ensures that the enzyme can rapidly and efficiently perform its function of protein digestion, breaking down complex peptides into simpler molecules that the body can easily absorb and use.