Question

9. Peptides: (20 pts.). A polypeptide (X) gives 7 fragments when treated with chymotrypsin (A-G). The same peptide also gives 9 fragments when treated with trypsin (I- IX). After Chymotrypsin A) Thr-Thr-Tyr-Ala-Gly-Phe-Phe-Ile-Asp- Lys B) Ala-Cys-Pro-Leu-Tyr-Gin-lle-Arg C) Met-Ser-Thr-Tyr-Pro-Gly-Arg D) Cys-Leu-Val-Phe-Ile-Lys E) Leu-Ala-Trp-Gly-Val F) Ser-Phe-Ala-Pro-Lys G) Met-Asp-Lys Afier Trypsin I) Ala-Pro-Lys-Met-Asp-Lys-Thr-Thr-Tyr II) Pro-Gly-Arg-Cys-Leu-Val-Phe III) Ile-Lys-Ala-Cys-Pro-Leu-Tyr IV) Ile-Asp-Lys-Met-Ser-Thr-Tyr V) Gin-Ile-Arg-Leu-Ala-Trp VIAla-Gly-Phe VII) Gly-Val VIII) Ser-Phe LX) Phe A) What is the primary sequence of peptide X? List the picces in order by the chymotrypsin letter code. G- B-ヒ-COOH B) Edman degradation of the peptide X will yield a Ser amino acid.

please explain how to solve this problem, the answer is provided

Answer 1

A) First let me explain how trypsin and chymotrypsin are used. These two are endopeptidases which means that they break internal peptide bonds and initially praduce peptide fragments. Particularly, these two endopeptidases have a strong or absolute preferetial ability to hydrolyse amide bond between certain amino acids in a peptide Basically i) Trypsin only cleaves the peptide bonds after the C-terminal side of the basic amino acids such as lysine and arginine. i) Chymotrypsin prefers cleaving after large hydrophobic amino acids such as phenylalanine, tyrosine, tryptophan. The following figure shows where chymotrypsing and trypsin can cleave in a peptide, in order to get an idea. Chymotrypsin H2N-ser-ala-phe-gly-lys-pro-gly-arg-cys-trp-glu-arg-asp-gly-COOH Trypsin Now, let us focus on the prohlem at hand. Fisrt thing, I natice is, there is a problem in the question. I think the result of fragmentation is switched between chymotrypsin and trypsin. Please, check the example that I have given above to see which peptidase cleaves which arrnino acid's carboxylic acid end. The answer given is correct. But you need to follow what I have explaind and assume the fragrents they have given for trypsin is for chymotrypsin and vice versa. B) Edman degradation: Edman degradation is the process of purifying protein by scquentially removing one residuc at a time from the amino end of a pepticde with out damaging the overall sequence of the peptide. The reagent used is phenyl isothiocyanate. It reacts with the N-terminal of the peptide to produce phenylthio carbamoyl derivative. The N- terminal is then cleaved under less harsh acidic conditions, creating a cyclic compound of phenylthiohydantoin PTH amino acid H2N Peplice HNN Peptide heat Peptide NH H NH Peptide NHa phenylthiohycantoin (PTH) As our peptide X's N-terminal is serine. Edman reagent first react with it and forms phenylthiohydantoin with serine which can then be converted to serine. This proves that the peptide X's N-terminal is serine