Question

Activity of the bacterial enzyme acetoacetate decarboxylase sharply declines below pH 6, suggesting there is an ionizable catalytic residue with pKa ~ 6. Using mutagenesis, this critical catalytic residue was determined to be Lys-115. a) What is the typical pKa of a lysine side chain and what ratio of deprotonated to protonated lysine would be expected at pH 7.5 (standard pH inside a bacterium)

Answer 1

• The typical pka of a lysine side chain is 10.5
• At pH=7-5 the ratio of deprotonated to protonated lysine is 0.001

Step-by-step explanation:

From literature, we know that the typical pka of a lysine side is 10.3.

Then we use the Henderson-Hasselbalch equation:

`pH=pka+log([A^(-) ])/([HA])`

In this case, [A⁻] is the concentration of deprotonated lysine, and [HA] is the concentration of protonated lysine.

We put the data from the problem in the equation and calculate the ratio of deprotonated to protonated lysine:

`7.5=10.5+log([A^(-) ])/([HA])\\-3.0=log([A^(-) ])/([HA])\\10^(-3.0)=([A^(-) ])/([HA])\\0.001=([A^(-) ])/([HA])`