Amino acid analysis of an octapeptide revealed the following composition: \(\begin{array}{llllll}\text { 2 Arg } & \text { 1 Gly } & \text { 1 Met } & \text { 1 Trp } & \text { 1 Tyr } & \text { 1 Phe } & \text { 1 Lys }\end{array}\) The following facts were observed: a. Edman degradation gave b. CNBr treatment yielded a pentapeptide and a tripeptide containing phenylalanine. c. Chymotrypsin treatment yielded a tetrapeptide containing a C-terminal indole amino acid and two dipeptides. d. Trypsin treatment yielded a tetrapeptide, a dipeptide, and free Lys and Phe. e. Clostripain yielded a pentapeptide, a dipeptide, and free Phe. What is the amino acid sequence of this octapeptide?

Understanding the Edman Degradation process is essential when trying to determine the sequence of amino acids in a peptide. This method, developed by Pehr Edman, is used to sequentially remove one residue at a time from the amino (N-) terminus of a peptide chain. Through a chemical reaction, the N-terminal amino acid is converted to a phenylthiohydantoin (PTH) derivative, which can then be identified by chromatographic techniques.

Each cycle of Edman degradation provides the identity of the next amino acid, which allows us to sequentially build the amino acid sequence of the peptide. This is particularly useful for relatively short peptides and requires only a very small amount of the peptide to determine its sequence. However, it becomes less efficient for peptides longer than about 30 amino acids. Additionally, the information from Edman degradation often complements other peptide fragmentation methods to obtain a complete sequence.

Peptide fragmentation is a cornerstone of protein sequencing. When an entire polypeptide sequence cannot be determined through direct methods, it is often necessary to break the peptide into smaller fragments. These fragments can be produced using various chemical and enzymatic treatments, each targeting specific amino acid residues.

For instance, in the given problem, Cyanogen bromide (CNBr) is used to cleave the peptide at methionine (Met) residues. Similarly, the enzymes trypsin and chymotrypsin specifically cleave at the C-terminal side of certain amino acids: trypsin targets arginine (Arg) and lysine (Lys), while chymotrypsin cleaves at tryptophan (Trp), tyrosine (Tyr), and phenylalanine (Phe). Knowing where these enzymes cut allows researchers to deduce the order of amino acids in a protein sequence.

These facts can help to locate different amino acids within a peptide sequence. Such enzymatic and chemical cleavage techniques are vital because they help to simplify the complex problem of amino acid sequencing into smaller, more manageable pieces, paving the way for a full reconstruction of the sequence.

Enzyme specificity is a fundamental concept in biochemistry, referring to the ability of an enzyme to choose its substrate from a pool of similar molecules. In the context of peptide sequencing, this specificity is invaluable as it dictates which bonds within a protein will be cut by an enzyme.

As demonstrated by the problem, trypsin and chymotrypsin have specific cleavage patterns. Trypsin cuts next to the C-terminal side of lysine and arginine residues, except when followed by proline. Chymotrypsin prefers to cleave next to the aromatic residues like tryptophan, tyrosine, and phenylalanine. Clostripain, another enzyme used in the exercise, behaves similarly to trypsin but is more restrictive and cleaves primarily at the C-terminal side of arginines.

Each enzyme's specificity can be exploited to create a 'map' of the protein's structure. By understanding which amino acids are released and which remain bonded after treatment with specific enzymes, a scientist can infer sequences and positions of amino acids, progressively piecing together the complete structure of the peptide.