Question

What is the structure of a nonapeptide that gives the following fragments when cleaved? Trypsin cleavage: Val-Val-Pro-Tyr-Leu-Arg, Ser-Ile-Arg Chymotrypsin cleavage: Leu-Arg, Ser-Ile-Arg-Val-Val-Pro-Tyr

Short answer

Nonapeptide sequence: Ser-Ile-Arg-Val-Val-Pro-Tyr-Leu-Arg.

Step-by-step solution

Understand the Enzymes' Specificities

Trypsin cleaves at the carboxyl side of the amino acids Lysine (K) and Arginine (R), whereas chymotrypsin cleaves at the carboxyl side of aromatic amino acids like Tryptophan (W), Phenylalanine (F), and Tyrosine (Y). Knowing this helps us deduce the sequence.

Analyze Trypsin Cleavage Fragments

Trypsin produced two fragments: Val-Val-Pro-Tyr-Leu-Arg and Ser-Ile-Arg. This indicates that in the original nonapeptide sequence, an arginine (R) must be present at the cleavage sites, coming after the residues Val-Val-Pro-Tyr-Leu and Ser-Ile respectively.

Analyze Chymotrypsin Cleavage Fragments

Chymotrypsin produced two fragments: Leu-Arg and Ser-Ile-Arg-Val-Val-Pro-Tyr. Since chymotrypsin cleaves after tyrosine, the presence of Tyr and the resulting fragments suggest that Tyr-Leu-Arg is one part of the peptide, which aligns with one of the trypsin fragments.

Assemble the Nonapeptide Sequence

By integrating the information from both cleavages, the nonapeptide sequence starts with Ser-Ile-Arg, followed by Val-Val-Pro-Tyr (the connection point due to Tyr cleavage in chymotrypsin), and finally ends with Leu-Arg, matching the trypsin cleavage.

Key concepts

Peptide Cleavage

Peptide cleavage refers to the breaking down of a peptide chain into smaller fragments by cutting the peptide bonds. This process is crucial for protein analysis and is typically facilitated by proteolytic enzymes like trypsin and chymotrypsin. These enzymes help researchers understand protein sequences by cutting the peptide chains at specific sites.

• Trypsin cleaves at the carboxyl side of the basic amino acids lysine and arginine.
• Chymotrypsin targets aromatic amino acids like tryptophan, phenylalanine, and tyrosine.

Understanding where these cuts occur helps predict the possibilities for the original sequence, especially when examining peptide mixtures gained from experimental techniques. Improved knowledge of peptide cleavage can aid in better constructing or deducing the sequence of peptides derived from complex biological samples.

Enzyme Specificity

Enzyme specificity refers to the ability of an enzyme to choose exact substrates out of a pool of similar molecules. For proteolytic enzymes, specificity is about selecting certain peptide bonds to cleave. This selective activity is due to the chemical environment within the enzyme's active site, which complements the specific side chains of the amino acids.
Trypsin, for example, specifically cleaves bonds after lysine or arginine because of the arrangement of charged regions in its active site. Chymotrypsin, on the other hand, is tuned to cleave after amino acids with bulky aromatic side chains. This specificity is crucial for the accurate breakdown of peptides into predictable fragments, enabling researchers to reconstruct the potential original sequence of the peptide from its fragments.

Amino Acid Sequence Analysis

Amino acid sequence analysis involves determining the order of amino acids in a peptide or protein. In practice, this involves interpreting data from peptide cleavage experiments to deduce the original sequence. The fragment patterns provided by specific enzymes like trypsin and chymotrypsin give insight into the arrangement of amino acids within a peptide.

• Fragments created by enzyme cleavage help identify where specific residues occur.
• These residues indicate cleavage points, which are essential for deducing the complete sequence.
• Combining information from different enzymes, as with trypsin and chymotrypsin, provides a comprehensive view of the peptide.

The accurate interpretation of these fragments relies on understanding enzyme specificity and cleavage patterns, guiding researchers in sequence reconstruction efforts. In the case of the given exercise, combining the cleavage results leads us to reconstruct the sequence as Ser-Ile-Arg-Val-Val-Pro-Tyr-Leu-Arg, illustrating how different enzyme actions can be pieced together to form a whole.