Question

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

Short answer

Ser-Ile-Arg-Val-Val-Pro-Tyr-Leu-Arg.

Step-by-step solution

Understand the Enzyme Specificity

First, we need to understand that trypsin cleaves at the carboxyl side of lysine (Lys, K) and arginine (Arg, R), while chymotrypsin cleaves at the carboxyl side of aromatic amino acids like phenylalanine (Phe, F), tryptophan (Trp, W), and tyrosine (Tyr, Y). This helps us establish potential cleavage points in the peptide sequence.

Analyze Trypsin Cleavage Results

According to the exercise, trypsin cleavage results in two fragments: Val-Val-Pro-Tyr-Leu-Arg and Ser-Ile-Arg. Since trypsin cleaves at the carboxyl side of Arg, the full peptide sequence must have Arg immediately following Tyr-Leu.

Analyze Chymotrypsin Cleavage Results

Chymotrypsin cleavage results in two fragments: Leu-Arg and Ser-Ile-Arg-Val-Val-Pro-Tyr. Since chymotrypsin cleaves after aromatic amino acids, and we see Tyr at the end of one fragment, the cleavage must have occurred after Tyr, matching one of the fragments derived from trypsin cleavage.

Align and Assemble Fragments

From Step 3, align the results of trypsin (Val-Val-Pro-Tyr-Leu-Arg and Ser-Ile-Arg) and chymotrypsin (Leu-Arg and Ser-Ile-Arg-Val-Val-Pro-Tyr) cleavages. This indicates the full structure: Ser-Ile-Arg-Val-Val-Pro-Tyr-Leu-Arg.

Verify the Complete Sequence

Verify by ensuring the sequence can produce the original cleavage patterns: trypsin's fragments (Val-Val-Pro-Tyr-Leu-Arg and Ser-Ile-Arg) and chymotrypsin’s fragments (Leu-Arg and Ser-Ile-Arg-Val-Val-Pro-Tyr). This confirms the assembled sequence is correct.

Key concepts

Nonapeptide

In the world of biochemistry, a nonapeptide is a peptide consisting of nine amino acid residues. Peptides are chains of amino acids linked by peptide bonds. The number of amino acids in a peptide is indicated by a prefix: "nona" in nonapeptide means nine.

Understanding the structure of a nonapeptide is essential for tasks such as predicting its behavior, interaction with enzymes, and its biological functions. The sequence and composition of amino acids in a nonapeptide determine its properties and how it folds into a specific 3D shape.

Nonapeptides can be found in nature as hormones, toxins, and other biologically active molecules. For instance, oxytocin and vasopressin are well-known nonapeptides. They play significant roles in the body's physiological processes.

Enzyme Specificity

Enzymes are biological catalysts that speed up biochemical reactions without being consumed in the process. Each enzyme is highly specific to its substrate, which means it only acts on specific molecules or bonds. This property is known as enzyme specificity.

There are different types of enzyme specificity:

• Absolute specificity: The enzyme acts on a single substrate.
• Group specificity: The enzyme targets substrates with a particular functional group.
• Bond specificity: The enzyme cleaves specific types of bonds.
• Stereospecificity: The enzyme acts on a particular stereoisomer of a substrate.

Trypsin and chymotrypsin are examples of enzymes with bond specificity because they cleave peptide bonds at specific amino acids. Understanding enzyme specificity is crucial when predicting how a protein will be degraded or modified by enzymes.

Trypsin Cleavage

Trypsin is a proteolytic enzyme, meaning it breaks down proteins into smaller peptides. The specificity of trypsin lies in its ability to cleave peptide bonds at the carboxyl side of the amino acids lysine (K) and arginine (R). This cleavage pattern is vital for analyzing protein sequences

Proteins often undergo tryptic digestion in both research and industry to determine their structure. When examining a nonapeptide, if trypsin treatment results in specific fragments, those fragments provide clues about the original sequence. For example, if the trypsin cleavage gives us fragments such as Val-Val-Pro-Tyr-Leu-Arg and Ser-Ile-Arg, we can deduce where arginine residues are located in the sequence, usually at the ends of these fragments.

Chymotrypsin Cleavage

Chymotrypsin is another proteolytic enzyme specific for cleaving at the carboxyl side of aromatic amino acids like phenylalanine (Phe), tryptophan (Trp), and tyrosine (Tyr). Its cleavage pattern is quite distinct and informative for protein sequence analysis.

When a peptide such as a nonapeptide undergoes chymotrypsin cleavage, the resulting fragments help identify positions of these aromatic residues. In this exercise, the chymotrypsin treatment provided certain peptide fragments, confirming the presence of a tyrosine residue at the end of one segment.

By piecing together the fragments from both trypsin and chymotrypsin cleavages, we develop a full understanding of the original peptide sequence. This combined approach is an excellent method to confirm peptide sequencing in biochemistry.