Question

Which amide bonds in the following polypeptide are cleaved by trypsin? By chymotrypsin? Phe-Leu-Met-Lys-Tyr-Asp-Gly-Gly-Arg-Val-Ile-Pro-Tyr

Short answer

Trypsin cleaves after Lys and Arg; Chymotrypsin cleaves after Phe and the two Tyr residues.

Step-by-step solution

Understanding Trypsin's Cleavage Specificity

Trypsin is an enzyme that cleaves peptide bonds on the carboxyl side of lysine (Lys) and arginine (Arg) residues. This means trypsin recognizes these amino acids and cuts the peptide bond directly after them.

Identifying Trypsin Cleavage Sites

In the given polypeptide, look for lysine (Lys) and arginine (Arg) residues. The sequence is Phe-Leu-Met-Lys-Tyr-Asp-Gly-Gly-Arg-Val-Ile-Pro-Tyr, which includes Lys at position 4 and Arg at position 9. Therefore, trypsin will cleave at the following bonds: after Lys (Lys-Tyr) and after Arg (Arg-Val).

Understanding Chymotrypsin's Cleavage Specificity

Chymotrypsin is an enzyme that cleaves peptide bonds on the carboxyl side of aromatic amino acids like phenylalanine (Phe), tryptophan (Trp), and tyrosine (Tyr). It may also cleave at methionine (Met) under certain circumstances.

Identifying Chymotrypsin Cleavage Sites

In the sequence Phe-Leu-Met-Lys-Tyr-Asp-Gly-Gly-Arg-Val-Ile-Pro-Tyr, aromatic residues include Phe at position 1, Tyr at position 5 and 13. Thus, chymotrypsin will cleave after the following bonds: after Phe (Phe-Leu), after Tyr (Tyr-Asp), and after the Tyr at the end (since there is no following residue, it just cuts the bond).

Key concepts

Trypsin Specificity

Trypsin is a special enzyme known for its ability to target and cleave specific bonds in proteins. It is highly specific and cleaves peptide bonds following lysine (Lys) and arginine (Arg) amino acids.

This specificity arises because trypsin has a preference for recognizing these positively charged side chains. When trypsin finds a Lys or Arg in a protein sequence, it cleaves the peptide bond on the carboxyl side of these amino acids.

In the sequence Phe-Leu-Met-Lys-Tyr-Asp-Gly-Gly-Arg-Val-Ile-Pro-Tyr, trypsin will target the amide bonds after Lys at position 4 and Arg at position 9. So, it cleaves the bonds between Lys-Tyr and Arg-Val. It's this precise cutting action that makes trypsin a crucial tool for protein digestion in various biological processes.

Chymotrypsin Specificity

Chymotrypsin is another enzyme that plays a unique role in cleaving polypeptides. However, its specificity differs from trypsin. Instead of lysine and arginine, chymotrypsin prefers aromatic amino acids like phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp).

These amino acids have bulky and aromatic side chains, making them excellent targets for chymotrypsin's enzymatic action. Occasionally, it may also cleave at methionine (Met).

• It cleaves peptide bonds just after these amino acids on the carboxyl side.
• In the given sequence, aromatic residues such as Phe, Tyr, and another Tyr are pivotal cleavage points.

Chymotrypsin will act on the sequence to cleave after Phe (Phe-Leu), Tyr at position 5 (Tyr-Asp), and the final Tyr (Tyr), efficiently breaking down the protein.

Polypeptide Cleavage

Polypeptide cleavage is a crucial process in biochemistry where enzymes break down proteins into smaller peptides or amino acids. This process is vital for many biological functions, including digestion and protein recycling.

Enzymes like trypsin and chymotrypsin play significant roles due to their ability to recognize specific amino acid sequences. By cleaving these sequences at precise points, they make the polypeptide chains more manageable and allow for the correct protein expression or degradation.

• Trypsin targets lysine and arginine residues.
• Chymotrypsin targets aromatic residues like phenylalanine, tryptophan, and tyrosine.

These enzymes thus help in intricate biological pathways by regulating protein breakdown precisely.

Amide Bonds

Amide bonds, also known as peptide bonds, are the key links in proteins that hold amino acids together. These bonds form between the amino group of one amino acid and the carboxyl group of another, releasing a molecule of water in the process.

In proteins, amide bonds form robust chains that provide stability and structure to the polypeptides. Enzymes like trypsin and chymotrypsin precisely break these amide bonds at selective sites, facilitating the controlled breakdown and digestion of proteins.

• These bonds ensure the correct folding and functionality of proteins.
• Enzyme specificity determines the precise sites where these bonds are cleaved.

Understanding amide bonds is crucial for comprehending how enzymes function and manipulate proteins in biological systems.

Enzymatic Cleavage Sites

Enzymatic cleavage sites are specific locations in a polypeptide chain where enzymes break peptide bonds. These sites are determined by the enzyme's preference for certain amino acid sequences.

For example, trypsin and chymotrypsin have unique recognition patterns in polypeptides, which dictate where they cut:

• Trypsin cleaves after lysine (Lys) and arginine (Arg).
• Chymotrypsin cleaves after aromatic amino acids like phenylalanine (Phe) and tyrosine (Tyr).

These specific cleavage points are essential for protein research and applications in biotechnology, as they allow researchers to predict and manipulate protein structures and functions precisely. By understanding these enzymatic preferences, scientists can better study protein interactions and functions in living organisms.