Amino acids

Full Notes

Amino acids are molecules containing both an amine group (–NH₂) and a carboxylic acid group (–COOH).

Naturally occurring amino acids, known as alpha amino acids, share a common general structure but differ in their side chains (R groups). There are around 20 of these naturally occurring amino acids, and they are essential in biology as the building blocks of proteins.

(alpha) Amino acids have the general formula:
H₂N–CHR–COOH (where R is a side chain).

Acid–Base Properties and Zwitterions

Amino acids are amphoteric, meaning they can act as both acids and bases:

• The amine group (–NH₂) is basic and can accept a proton (H⁺ ion).
• The carboxylic acid group (–COOH) is acidic and can donate a proton (H⁺ ion).

At a specific pH, called the isoelectric point, an amino acid exists as a zwitterion:

• A zwitterion has no overall charge but has both a positive and a negative charge.
Example:H₃N⁺–CH(R)–COO⁻
• The isoelectric point depends on the R group (side chain) and varies for each amino acid.

Effect of pH

At low pH (acidic): the amine and carboxyl groups are both protonated giving an overall positive charge.

At high pH (alkaline): both groups are deprotonated giving an overall negative charge.

Formation of Amide (Peptide) Bonds

Amino acids can link together by condensation reactions to form peptides:

• The carboxylic acid group of one amino acid reacts with the amine group of another.

This forms a peptide bond (amide bond) and releases H₂O.
–CO–NH–

These bonds are covalent and strong, forming the primary structure of proteins.

Examples:

• Dipeptide: two amino acids linked by one peptide bond.
• Tripeptide: three amino acids linked in a chain.

Electrophoresis of Amino Acids and Peptides

Electrophoresis is a technique used to separate amino acids or peptides based on their overall charge in an electric field.

How it works:

• A mixture is placed on a gel or paper soaked in a buffer of known pH.
• An electric field is applied.
• Ions move toward the positive electrode (if negatively charged) or toward the negative electrode (if positively charged).
• Movement depends on their net charge, determined by the pH of the buffer relative to the amino acid’s isoelectric point.

Predicting Movement

If pH is low (below isoelectric point):

• amino acid is positively charged and moves to negative electrode.

If pH is high (above isoelectric point):

• amino acid is negatively charged and moves to positive electrode.

If pH = isoelectric point:

• no net charge and remains stationary (doesn’t move).

In mixtures, each amino acid behaves differently based on its unique isoelectric point and charge at a given pH, allowing separation. Ions with the same overall charge will be attracted to the same electrode, however lighter ions (with a lower relative molecular mass) will move faster than heavier ions with the same charge.

Summary

• Amino acids contain both –NH₂ and –COOH groups.
• They are amphoteric and can exist as zwitterions at their isoelectric point.
• They join by condensation to form peptide bonds, dipeptides, and tripeptides.
• Electrophoresis separates amino acids based on charge, which depends on pH relative to the isoelectric point.