Another endoprotease is trypsin. Trypsin hydrolyzes peptide bonds on the carboxyl side of lysine and arginine. If the following peptide sequence is hydrolyzed by trypsin, how many fragments will there be? Use the three-letter amino acid abbreviations to write the fragments out.
 Ala-Phe-Lys-Cys-Gly-Asp-Arg-Leu-Leu-Phe-Gly-Ala

Verified step by step guidance

1. Identify the specific action of trypsin: Trypsin hydrolyzes peptide bonds on the carboxyl side of lysine (Lys) and arginine (Arg). This means it cleaves the peptide bond immediately after these amino acids in the sequence.
2. Examine the given peptide sequence: Ala-Phe-Lys-Cys-Gly-Asp-Arg-Leu-Leu-Phe-Gly-Ala. Locate all instances of lysine (Lys) and arginine (Arg) in the sequence.
3. Mark the cleavage points: After identifying Lys and Arg, mark the peptide bonds immediately following these residues as the cleavage points. In this sequence, Lys is the third residue, and Arg is the seventh residue.
4. Determine the resulting fragments: Break the peptide sequence at the marked cleavage points. Write out the fragments using the three-letter amino acid abbreviations. Ensure that each fragment ends at the cleavage point and the next fragment starts immediately after.
5. Count the number of fragments: After breaking the sequence at the cleavage points, count the total number of resulting fragments to determine how many pieces the peptide has been split into.

Key Concepts

Endoprotease Function

Endoproteases, like trypsin, are enzymes that cleave peptide bonds within protein chains, specifically targeting certain amino acids. Trypsin is known for hydrolyzing bonds on the carboxyl side of lysine (Lys) and arginine (Arg), which is crucial for understanding how proteins are broken down into smaller fragments during digestion.

Peptide Bond Hydrolysis

Peptide bond hydrolysis is the process by which water is used to break the bonds between amino acids in a peptide chain. This reaction results in the formation of smaller peptide fragments. In the context of the given peptide sequence, identifying where trypsin acts will determine the number of resulting fragments.

Amino Acid Abbreviations

Amino acids are often represented by three-letter abbreviations, which are standardized for ease of communication in biochemistry. For example, alanine is abbreviated as Ala, phenylalanine as Phe, lysine as Lys, and so on. Understanding these abbreviations is essential for accurately writing out the fragments produced after trypsin hydrolysis.