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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)

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Answer:

  • 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

Explanation:

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

Then we use the Henderson-Hasselbalch equation:

[tex]pH=pka+log\frac{[A^{-} ]}{[HA]}[/tex]

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:

[tex]7.5=10.5+log\frac{[A^{-} ]}{[HA]}\\-3.0=log\frac{[A^{-} ]}{[HA]}\\10^{-3.0}=\frac{[A^{-} ]}{[HA]}\\0.001=\frac{[A^{-} ]}{[HA]}[/tex]

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