In: Chemistry
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 α-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
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