Amino Acids

In the solid state and in aqueous solution near neutral pH, amino acids exist as zwitterions, which are internal salts formed by the transfer of a proton from the carboxyl group to the amine group.

This results in a molecule with a localized positive charge on the nitrogen ($\text{-NH}_3^+$) and a localized negative charge on the oxygen ($\text{-COO}^-$), while the overall net charge remains zero.

The ionic nature of zwitterions leads to strong intermolecular electrostatic attractions, explaining why amino acids are typically high-melting, soluble crystalline solids.

In acidic conditions (low pH), the carboxylate group ($\text{-COO}^-$) accepts a proton to form $\text{-COOH}$, resulting in a net positively charged cation.

In alkaline conditions (high pH), the ammonium group ($\text{-NH}_3^+$) donates a proton to form $\text{-NH}_2$, resulting in a net negatively charged anion.

This transition allows amino acids to participate in different chemical environments and influences their behavior during separation techniques like electrophoresis.

Amino acids link together via a condensation reaction between the amine group of one molecule and the carboxylic acid group of another.

This process eliminates a water molecule ($H_2O$) and creates a covalent amide bond, specifically referred to in biochemistry as a peptide link.

The resulting chain has a distinct directionality, with an unreacted amine group at one end (N-terminus) and an unreacted carboxyl group at the other (C-terminus).

Mixtures of amino acids can be separated and identified using Thin Layer Chromatography (TLC), where the stationary phase is a thin layer of silica and the mobile phase is a solvent.

Separation is based on the relative affinity of different R groups for the solvent versus the silica; more polar amino acids generally move slower.

Because amino acids are colorless, they are visualized using ninhydrin (which turns them purple/blue) or by viewing the plate under UV light.

• Drawing Structures: Always ensure the nitrogen in a zwitterion has four bonds and a positive charge, while the carboxylate oxygen has a negative charge.

• pH Transitions: When asked for the structure at a specific pH, first compare it to the isoelectric point. If $pH < pI$, protonate the groups; if $pH > pI$, deprotonate them.

• TLC Calculations: Remember that the $R_f$ value is always $\le 1$. If your calculation yields a number greater than 1, you have likely swapped the distance of the component and the solvent front.

• 2D Chromatography: If two amino acids have similar $R_f$ values in one solvent, a second run in a different solvent (rotated 90 degrees) is required to resolve the spots.