Amino Acids, pKa, and Charge States (Glycine & Lysine)

Vocabulary-style flashcards covering key concepts from the lecture about ionizable groups, pKa values, protonation/deprotonation, isoelectric point, zwitterions, and amino acid examples (glycine, lysine), plus related phenomena.

Ionizable functional group

A functional group that can gain or lose a proton, giving rise to different charged forms and a pKa.

pKa

The pH at which half of a given acidic or basic group is protonated and half is deprotonated; indicates acid strength.

Protonation

The process of gaining a proton (H+) by a functional group.

Deprotonation

The removal of a proton (H+) from a functional group.

Dissociation reaction

An acid–base reaction showing a species losing or gaining a proton (e.g., HA ⇌ H+ + A−).

Conjugate base

The species formed when an acid donates a proton.

Conjugate acid

The species formed when a base accepts a proton.

Isoelectric point (pI)

The pH at which a molecule has zero net charge.

Zwitterion

A neutral molecule carrying both positive and negative charges, common for amino acids at certain pH.

Net charge

The total charge of a molecule calculated by summing all charges of ionizable groups at a given pH.

Glycine

The simplest amino acid with a hydrogen side chain; at physiological pH it is a zwitterion with net zero charge.

Lysine

An amino acid with a basic side chain that is positively charged at physiological pH; has multiple ionizable groups.

Amino group

The -NH2 / -NH3+ group in amino acids; can be protonated to -NH3+ (pKa ~9–10).

Carboxyl group

The -COOH / -COO− group; deprotonates around pKa ~2, becoming negatively charged.

Thiol

The -SH group (as in cysteine); can be deprotonated to -S− (pKa ~8–9).

Thiolate

The deprotonated form of a thiol (-S−) carrying a negative charge.

Nonpolar aliphatic amino acids

Amino acids with nonpolar, aliphatic side chains contributing to hydrophobic interactions.

Aromatic amino acids

Amino acids with aromatic side chains (phenylalanine, tyrosine, tryptophan) that absorb UV light.

Conjugation

Delocalization of electrons across adjacent bonds, contributing to UV absorption in aromatic amino acids.

Zwitterion formation at pH

State where an amino acid carries both positive and negative charges, yielding overall zero net charge.

Protonation state transitions

Charge changes on ionizable groups as pH crosses their pKa values, creating different net charges.

Net charge at pH 7

Sum of all group charges at pH 7; often zero for many amino acids but not universally.