Biochemistry Protonation States: pH, pKa, and Functional Groups

Vocabulary flashcards covering Henderson-Hasselbalch, pH, pKa, and the protonation states of carboxyl and amino groups in biochemistry.

Henderson-Hasselbalch equation

Relates pH to the ratio of conjugate base [A−] to acid [HA] for an acid–base pair; pH = pKa + log([A−]/[HA]).

pH

A measure of how acidic or basic a solution is; higher pH means fewer free protons.

pKa

The pH at which half of the acid is protonated and half is deprotonated; threshold for protonation state.

Protonated

The state of a functional group that has gained a proton (H+); e.g., amines become positively charged when protonated.

Unprotonated (deprotonated)

The state of a functional group that has lost a proton; often carries a negative charge for acids like carboxylates.

Conjugate base

The base form of an acid after donating a proton (e.g., formate from formic acid).

Conjugate acid

The acid form of a base after accepting a proton.

Formic acid (HCOOH)

Weak acid with pKa ≈ 3.75; predominates as HCOOH below pH 3.75 and as HCOO− above.

Formate ion (HCOO−)

Conjugate base of formic acid; negatively charged and predominant above pH 3.75.

Carboxyl group (–COOH/–COO−)

Functional group with typical pKa ~2–4; protonated form (–COOH) is neutral; unprotonated form (–COO−) is charged.

Amino group

Functional group that can be protonated or unprotonated; protonated form carries a +1 charge; typical pKa ~9–10.

Primary amine

Amines with one carbon substituent; protonated form is NH3+; pKa ~9–10.

Secondary amine

Amines with two carbon substituents; protonated form is R2NH2+; pKa ~9–10.

Rule: pH > pKa

Majority of ionizable groups are unprotonated (deprotonated) at pH higher than the pKa.

Rule: pH < pKa

Majority of ionizable groups are protonated at pH lower than the pKa.

Rule: pH = pKa

There is an equal, 1:1 ratio of protonated to unprotonated forms.