Amino Acids

Amino Acids

• Proteins and essential biomolecules comprise amino acids.
• Alpha-amino acids are the most abundant in nature.

Chirality of Amino Acids

• Glycine stands out as the sole achiral amino acid among the twenty common ones.
• The remaining amino acids exist in the L-optical form.

Acid-Base Properties

• Amino acids possess both acidic and basic properties.

20 Amino Acids

• There are 20 amino acids
• Amino acids are classified based on their R groups:
  • Nonpolar, aliphatic R groups
  • Polar, uncharged R groups
  • Aromatic R groups
  • Positively charged R groups
  • Negatively charged R groups
• Aromatic amino acids facilitate protein visualization.

Isoelectric Point

• Every amino acid has a characteristic isoelectric point.
• For neutral amino acid side chains the isoelectric point (pI) is calculated as: pI = 1/2 (pKaCOOH + pKaNH3+).
• For acidic amino acid side chains the isoelectric point (pI) is calculated as: pI = 1/2 (pKaCOOH + pKaR).
• For basic amino acid side chains the isoelectric point (pI) is calculated as: pI = 1/2 (pKaR + pKaNH3+).

Oligopeptides, Polypeptides, and Proteins

• Aspartame, a dipeptide, contains two amino acids.
• Oligopeptides are composed of 2-10 amino acid residues, utilizing suffixes such as di, tri, tetra, penta, hexa, hepta, octa, nona, and deca.
• Polypeptides consist of 10-50 residues and have a molecular weight (Mw) less than 5,000.
• Proteins typically contain 50-400 residues with a molecular weight ranging from 5,000 to 400,000.

Amide Formation

• Amides form through the condensation of carboxylic acids and amines.

Peptide Bond Characteristics

• Peptide bonds exhibit considerable resonance.
• A delocalization energy of 75-90 kJ/mol stabilizes most peptides.
• Peptides tend to adopt a planar, trans (anti / Z) conformation.

Tetrapeptide Example

• An example of a tetrapeptide is alanylglutamylglycyllysine.
• The naming convention for peptides initiates at the N-terminal amino acid.
• At pH 7, the red coloring indicates charged groups.

Pentapeptide Example

• An example pentapeptide is Serylglycyltyrosylalanylleucine.

Cysteine and Disulphide Bonds

• Cysteines have the ability to link with disulphide bonds.

Glutathione

• Glutathione serves as a natural antioxidant.
• It is composed of Glu-Cys-Gly.
• It links via the sidechain of glutamic acid.
• It forms a disulphide in the presence of oxidizing agents.
• Glutathione is known to combat aging and cancer.

Medically Important Small Peptides

• Leucine enkephalin (Tyr-Gly-Gly-Phe-Leu) and Methionine enkephalin (Tyr-Gly-Gly-Phe-Met) are responsible for pain control.
• Bradykinin (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg) is anti-inflammatory.
• Vasopressin (Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH2) controls blood pressure.
• Oxytocin (Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2) induces labour and milk production.

Insulin Structure

• Insulin comprises of two amino acid chains.
• It is linked through disulphide bonds.

Purification of Peptides and Proteins

• Polyacrylamide gel electrophoresis (PAGE) is used in purification.
• Agarose is used for DNA, large proteins, and enzyme complexes due to larger pore size.
• Movement is determined by mass, shape, and charge.
• Sodium dodecyl sulphate (SDS) denatures proteins into uniform rods.

pH Electrophoresis

• pH electrophoresis profiles enable identification of a protein's isoelectric points.

Summary of Key Points

• Twenty commonly occurring amino acids (AA) exist.
• Amide formation is achieved through linking amino acids via peptide bonds.
• Oligopeptides include short AA chains.
• Polypeptides are larger and proteins are the largest of all.
• The amino terminus is the starting point for naming AA sequences.
• Disulphide bonds and peptide linkages can connect AA.
• Isoelectric points enable the characterisation and separation of amino acids, peptides, and proteins.