Question

Any Parts answered are greatly appreciated

1. *A PKA value was not provided*

Consider the following peptide, with the sequence in 1-letter code:

CHART. (amino acids: Cytesine, Histidine, Alanine, Arginine, and Theorine, respectively.)

How many chiral atoms (in total) does this peptide contain?

b) If you have a solution containing 1.2 mmol CHART, how many mmol of NaOH will you need to completely titrate this peptide?

c) What is the pI of the peptide CHART?

d) At which pH will CHART have an average net charge of +1.5?

e) Which amino acid side chains in CHART will be H-bond acceptors at pH 8?

f ) Which amino acid side chains in CHART will be H-bond donors at pH 10?

Answer 1

Ans. 1) CHART have total 6 chiral carbon. All the amino acids have only one chiral carbon, i.e., their alpha Carbon, but threonine have two chiral carbon, one aplha carbon and second R chain carbon. As their are 5 amino acids which means 5 aplha chiral carbon and one R chain chiral carbon of threonine, so there are total 6 chiral carbon.

Below in the peptide sequence chiral carbons are circled.

Ans. 3) to calcutate pI it is important to find the ionisable group present apart from amino and carboxyl group. Out of 20 amino acids there are 7 ionisable amino acids, cystein, tyrosine, aspartic acid, glutamic acid, lysine, arginine and histadine. In the CHART we have 3 ionisable amino acids, Cysteine, Histidine and Arginine. pKa amino, carboxyl group and side chaine of these ionisable amino acid is known.

pKa for carboxyl group is approximately 2.3

pKa of amino group is approximately 9.5

pKa of side chain of cysteine is 8.3

pKa of side chain of histidine is 6.0

pKa of side chain of arginine is 12.4

So, to find the pI of CHART, we have to calculate the net charge of these amino acid at different pI. So to find that we can start with the lowest pH where peptide will be protonated. Important point to remember is that, at pH lower than the pKa value the amino acids are protonated as protons concentration is higher in solution so the amino acids will accept the proton easily, and when pH is higher than the pKa, amino acids will be deprotonated as the protons concentration in solution is very less so, amino acids will easily donate their protons. So, at pH 2, there will be net +3 charge, at amino group, side chain of histidine and side chain of arginine, and cystein and carboxyl group will have zero charge. As we increase the pH, suppose at 2.3, net charge on peptide will be +2, one positive charge on each arginine, histidine and amino group and one negative charge in carboxyl group and cystein will be neutral. At pH 6, net charge will be +1 as histidine will be deprotonated. At pH 8.3, net charge will be zero, as cysteine will be negatively charged, so, two positive charge (amino group and R) and two negative charge ( C and carboxyl group) and histidine is neutral. When we increase pH to 9.5, net charge will be -1, as amino group will become deprotonated, so two neutral group ( amino and H), two negative group ( carboxyl and C) and one positive group R. At pH 12.4, net charge will be -2, three neutral group ( H, R and amino) two negative group (C, and carboxyl). Now we will take average of two pH where peptides have net zero charge, so thag two pH is 8.3 and 9.5. So, pI = 1/2(pKa1 + pKa2)

1/2(8.3 + 9.5) = 8.9.

Ans. 4) net charge 0.5 means where the ionisable group will be half positive and half negative. This normally happer at the very near value, suppose, the pKa of histidine is 6 so at pH 5.9 it will have +1/2 charge because it is about to donate it's proton but not completely donated, that mean, it will be half protonated and half deprotonated. So to find the pH where the he net charge is +1.5, we know that at pH 6 net charge is +1, to have net charge +1.5 the pH should be lower than this as at lower pH protonated form are more. 1/2 charge on any group is considered when pH is near lower than it's pKa, so, if we take the average of 2.3 and 6 we will get the mid value where both group will have complete charge, so the value should be near to 6 to have half charge at histidine. So, if the pH is 5.9 we can say that histidine have +1/2 charge, arginine and amino have +1 charge each. Cystein is neutral and carboxyl group have negative charge. So we can say that net charge at CHART is +1.5.

Ans. 5) in amino acid, protonated amino acid behave as hydrogen bond doner, i.e., acid, as they have hydrogen to donate, whereas deprotonated amino acid behave as hydrogen bond acceptor, i.e. base. So at pH 8, arginine and cysteine is fully protonated, so it will be hydrogen bond donor and histidine is deprotonated, so it will be hydrogen bond acceptor.

Ans. 6) at pH 10, arginine will be fully protonated so it will act as hydrogen bond donor. Whereas, cystein and histidine are deprotonated, so it will act as hydrogen bond acceptor.