Question

a. The glutamate side chain has a pKa of 4.4. Calculate the percentage of glu that is unprotonated at a pH of 4.7.

Answer 1

1. The glutamate side chain has a pKa of 4.4. Calculate the percentage of glu that is unprotonated at a pH of 4.7.

pH is the negative log of the hydrogen ion concentration in a solution. Similarly pK_A is the negative log of the acid dissociation constant for an amino acid side chain.

pH = -Log [H⁺]

pKa = - Log Ka

In solution, if pH < pK_A, then the protonated form of an amino acid side chain predominates according to the Henderson-Hasselbalch equation . If pH > pK_A, then the deprotonated form of the amino acid side chain predominates. The charge on an acidic side chain can therefore vary between -1 (when pH << pK_A) and 0 ( when pH >> pK_A).

In case of glutamate, with a side chain pK_A = 4.4.

When the pH = pK_A, the concentration of the protonated and deprotonated forms is equal and the charge is -0.5.

When pH = 6.4, the glutamate is about 99% deprotonated, leading to a charge of -0.99. When pH = 2.4, the glutamate is about 99% protonated, leading to a charge of -0.01.

If we consider at pH= 4.7 concentration of protonated form reduce by 5% then we can use Henderson-Hasselbalch equation as follows,

pH = pKa + log [Deprotonated form]/[Protonated form]

4.7 = 4.4 + log (X/45)

X = 89.78% approximately

Concentration of deprotonated form at pH 4.7 will be 89.78% approximately