Chymotrypsin Mechanism | Biochemistry

Summary

Chymotrypsin is a digestive enzyme that cleaves peptide bonds following aromatic residues like phenylalanine, tyrosine, and tryptophan. The mechanism involves a catalytic triad of aspartate, histidine, and serine, which work together in the active site to facilitate cleavage. The process begins with substrate binding and an induced fit that alters the pKa of histidine, allowing it to abstract a proton from serine. This leads to the formation of unstable tetrahedral intermediates, ultimately resulting in the release of two products while regenerating the enzyme for subsequent reactions. Chymotrypsin exemplifies efficient enzymatic action through precise molecular interactions.

Takeaways

• 😀 Chymotrypsin is an enzyme that cleaves peptide bonds after aromatic residues like phenylalanine, tyrosine, or tryptophan.
• 😀 The active site of chymotrypsin contains a hydrophobic pocket, an oxyanion hole, and a catalytic triad consisting of aspartate (102), histidine (57), and serine (195).
• 😀 The numbers in parentheses represent the position of the amino acids in the protein sequence.
• 😀 The hydrophobic pocket accommodates the bulky, hydrophobic side chains of the aromatic amino acids to stabilize the substrate during cleavage.
• 😀 The enzyme undergoes a conformational change (induced fit) upon substrate binding, compressing the bond between aspartate and histidine.
• 😀 This compression raises the pKa of histidine from 6 to over 12, making it a better proton acceptor.
• 😀 Histidine abstracts a proton from serine, enabling serine to nucleophilically attack the carbon of the peptide bond, leading to the formation of a tetrahedral intermediate.
• 😀 The tetrahedral intermediate is short-lived and unstable, with stabilization provided by interactions in the oxyanion hole.
• 😀 The reaction proceeds through the acyl-enzyme intermediate, where water is introduced, allowing for further cleavage and release of the second product.
• 😀 After releasing the second product, chymotrypsin returns to its original state, ready for another catalytic cycle, demonstrating that enzymes are not consumed in reactions.

Q & A

What is chymotrypsin and its primary function?

Chymotrypsin is a serine protease enzyme that primarily functions to cleave peptide bonds in proteins, specifically after aromatic amino acids such as phenylalanine, tyrosine, and tryptophan.

What are the main structural components of the chymotrypsin active site?

The active site of chymotrypsin contains a hydrophobic pocket, an oxyanion hole, and a catalytic triad consisting of three amino acids: aspartate (102), histidine (57), and serine (195).

What role does the hydrophobic pocket play in the chymotrypsin mechanism?

The hydrophobic pocket accommodates bulky aromatic side chains of substrate amino acids, helping to stabilize the polypeptide in place during the cleavage process.

What is the significance of the catalytic triad in chymotrypsin?

The catalytic triad, made up of aspartate, histidine, and serine, works together to facilitate the cleavage of peptide bonds. Each amino acid plays a specific role in the reaction mechanism.

What happens during the substrate binding step of chymotrypsin's mechanism?

During substrate binding, the substrate enters the active site and induces a conformational change in chymotrypsin, optimizing the positioning of the substrate for effective cleavage.

How does histidine function in the mechanism of chymotrypsin?

Histidine acts as a base, abstracting a proton from serine, which allows serine's oxygen to nucleophilically attack the carbon of the peptide bond, facilitating cleavage.

What is a tetrahedral intermediate and why is it important?

The tetrahedral intermediate is a short-lived and unstable structure formed during the cleavage process when carbon has four bonds. It is critical as it represents a key transition state in the reaction.

What occurs during the release of the first product in the chymotrypsin mechanism?

As the tetrahedral intermediate collapses, the carbonyl bond reforms, leading to the release of the first product and the formation of an acyl-enzyme intermediate.

What role does water play in the second half of the chymotrypsin mechanism?

Water acts as a nucleophile, with its oxygen attacking the carbon of the acyl-enzyme intermediate after histidine abstracts a proton from water, leading to the formation of another tetrahedral intermediate.

How does chymotrypsin regenerate after the reaction?

Chymotrypsin regenerates its active site by releasing the second product and returning to its original state, allowing it to catalyze another round of peptide bond cleavage.