1) Predict (write the sequences of) the fragments that would be generated from t

Question

1)         Predict (write the sequences of) the fragments that would be generated from the treatment of

            the following peptide

Gly-Ala-Trp-Asp-Arg-Lys-Ala-Glu- Gly-Phe-Gln

            with:

            a) trypsin (4 pnts)

            b) chymotrypsin

            c) pepsin

2)         A certain protein has an -helix which is 18 residues long with the sequence shown below.

            It is known that hydrogen bonding through the backbone H-bond donor/acceptor groups

            stabilizes most of the structure. Show what other interactions would help stabilize the helix

            by drawing lines (or brackets) between the interacting amino acid residues and naming the

            type of interaction involved.

Q         L          A         N         R         Y         R         T         D         L          E          Q         K         W        Q         N         E          P

Explanation / Answer

Trypsin: cleaves peptide chains mainly at the carboxyl side of the amino acids lysine (Lys) or arginine (Arg), except when either is followed by proline

Chymotrypsin: acts on carboxyl side of large hydrophobic amino acid such as tryptophan (Trp), tyrosine (Tyr) and phenylalanine (Phe), Isoleusine, (Ile), Valine (Val), Leusine (Leu)

Pepsin: cleaves on the carboxyl side of phenylalanine, (Phe), Leusine (Leu), tryptophan (Trp), or tyrosine (Tyr)

Step:1 Find out the N and C terminal (amino and carboxy terminal in peptide chain)

Usually we will write peptide chain which starts from N-termianl left to write

N-terminal-----Gly-Ala-Trp-Asp-Arg-Lys-Ala-Glu- Gly-Phe-Gln----C-terminal

Step:2 Now find out the above mentioned amino acid moieties listed for each protease enzyme (trypsin, chymotrypsin and pepsin)

For trypsin: Lys and Arg

So it cleaves the positions marked as X in the peptide series

N-terminal-----Gly-Ala-Trp-Asp-Arg-X-Lys-X-Ala-Glu- Gly-Phe-Gln----C-terminal

After cleavage we resulted in two small chain peptide and one amino acid, those are

Gly-Ala-Trp-Asp-Arg, Lys and Ala-Glu- Gly-Phe-Gln

Apply same concept to other protease also

For Chymotrypsin: Phe, Trp, Tyr, Ile, Val, Leu

N-terminal-----Gly-Ala-Trp-X-Asp-Arg-Lys-Ala-Glu- Gly-Phe-X-Gln----C-terminal

We get Gly-Ala-Trp, Asp-Arg-Lys-Ala-Glu- Gly-Phe and Gln

For Pepsin: Phe, Leu, Trp, Tyr

N-terminal-----Gly-Ala-Trp-X-Asp-Arg-Lys-Ala-Glu- Gly-Phe-X-Gln----C-terminal

We get Gly-Ala-Trp, Asp-Arg-Lys-Ala-Glu- Gly-Phe and Gln

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