Consider the peptide: NH 2 -GAPAGPAGTGKTETTKDLAKSMALLCWFNCS-COOH Table I. pK val

Question

Consider the peptide:
NH2-GAPAGPAGTGKTETTKDLAKSMALLCWFNCS-COOH

Table I. pK values of some amino acids

Using Table I above, determine the net charge of the peptide at pH9.

(the answer is not -1 or 1)

amino acid pK of side chain or terminal group Alanine (Ala or A) uncharged Arginine (Arg or R) 12.5 Asparagine (Asn or N) uncharged Aspartic acid (Asp or D) 3.9 Cysteine (Cys or C) 8.3 Glutamic acid (Glu or E) 4.3 Glycine (Gly or G) uncharged Histidine (His or H) 6.0 Leucine (Leu or L) uncharged Lysine (Lys or K) 10.8 Phenylalanine (Phe or F) uncharged Serine (Ser or S) uncharged Tryptophan (Trp or W) uncharged Tyrosine (Tyr or Y) 10.9 Valine (Val or V) uncharged peptide N terminus 7.8 peptide C terminus 3.6

Explanation / Answer

The ionizable side chain amino acids in this peptide are : 3 Lysine (K), 1 Glutamic acid (E) , 1 aspartic acid (D), 2 cysteine (C).

pKa is the tendency to give proton. It is a measure of acidity.When pka = pH, ionizable group is deprotonated and concentration of protonated and deprotonated forms are equal. When pH is above pka deprotonation of the ionizable group is complete and deprotonated form dominantes.

Lysine with a pka of 10.8 will not deprotonate at ph9. There are 3 lysine residues. Therefore total charge contribute will be +3 as each residue has a side chain with NH3+ group.

glutamic acid with a pka of 4.3 will be deprotonated at ph9. It will contribute a charge of -1 due to side chain carboxyl group.

aspartic acid with a pka 3.9 will also be deprotonated at ph9. It will contribute a charge of -1 due to side chain carboxyl group.

cysteine with a pka 8.3 will also be deprotonated at ph9. It will contribute a charge of -1 due to side chain sulfur atom which becomes negatively charged on deprotonation. 2 cysteine residue will give -2 charge.

The terminal amino group is NH3+ and has a pka of 7.8 .It will also deprotonate at ph9 and become NH2 having neutral charge.

The terminal COOH and has a pka of 3.6 .It will also deprotonate at ph9 and become COO- having negative charge.

Therefore at ph9 , total negative charge is -5 and total positive charge is +3. The net charge on the peptide is -5 + 3 = - 2

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