Draw out the following polypeptides and calculate their char

Draw out the following polypeptides and calculate their charge at the given pH. You do not need to include the amine and carboxyl termini. For amino acids that will have a partial charge at that pH, you do not need to calculate the exact percentage of the charge, but you do need to know and state if more or less than 50% will be charged.

a) GLEFIN - pH 5

b) WHATS - pH 7.5

c) KRDVIQ - pH 11

d) YESCRIMP - pH 9

Solution

amino acid residues loose or gain a proton at particular ph depending upon their pKa values. A higher basic pH than the pka of the basic aa residues, deprotonates the aa residue. For a basic amino acid, acid pH doesnt change the residues charge. For negatively chraged acidic amino acid residues, more acidic pH deprotonates them to neutral. In short the one that is higher gains a proton.

a) GLEFIN Glycine-leucine-glutamic acid-phenylalanine-isoleucine-asparagine

Pka Values of side chain in order of the amino acid residues- X-X-4.25-X-X-X (X =No charge)

glutamic acid is negatively charged with a pka of 4.25. At a ph more than the pka charge is unchanged. Therefore, the total charge on the polypeptide comes out to be -1 at ph5 where 1 of the 6 amino acid residues are charged- glutamic acid.

b) WHATS- ph7.5

Tryptohan-histidine-alanine-threonine-serine

pka-X-6.04-X-X-X

at ph 7.5, a basic amino acid with 6.04 will loose its proton and become neutral. The overal charge on the polypeptide is 0 and 0% of amino acids are charged.

c) KRDVIQ- Lysine-arginine-aspartate-valine-glutamine at ph 11

pka values- 10.79-12.48-3.86--X-X

At a basic pH lysin will become deprotonated and loose the charge to become neutral; arginine being very basic keeps the proton with +1 charge; aspartate at a basic pH gains a proton and becomes -1. The overall charge on the polypeptide comes out to be 0. 2 of the six amino residues are charged at ph11.

d) YESCRIMP ph9

Tyrosine-glutamic acid-serine-cystein-arginine-isoleucine-methionine-proline

10.07-4.25-X-8.33-12.48-X-X-X

Tyrosine is protonated +1; glutamic acid is deprotonated -1; cystein is also deprotonated -1 and arginine is basic and retains the proton +1

overall charge 0. 4 of the 6 residues are charged