Unit 2: Amino Acids, Peptides, and Proteins: Structure and Function

Amino Acids, Peptides and their Classification

Amino acids are the fundamental building blocks of proteins. Each amino acid contains at least one amino group (-NH₂) and one carboxyl group (-COOH), both attached to a central carbon atom known as the α-carbon. The α-carbon also has a hydrogen atom and a unique side chain (R-group) attached to it, which determines the specific properties of each amino acid.

Definition: Amino Acid

An amino acid is an organic compound containing both a carboxyl (-COOH) and an amino (-NH₂) group, typically with the amino group being on the α-carbon. They are the monomers that polymerize to form peptides and proteins.

Peptides are short chains of amino acids linked together by peptide bonds. When two amino acids link, they form a dipeptide; three form a tripeptide, and so on. Longer chains are called polypeptides.

Definition: Peptide Bond

A peptide bond is an amide bond formed between the carboxyl group of one amino acid and the amino group of another amino acid, with the elimination of a water molecule.

Classification of Amino Acids

Amino acids are commonly classified based on the characteristics of their R-groups, which influence their polarity, charge, and overall behavior in proteins.

• Nonpolar, Aliphatic R-groups: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline. These R-groups are hydrophobic.
• Aromatic R-groups: Phenylalanine, Tyrosine, Tryptophan. These are relatively nonpolar and can absorb UV light.
• Polar, Uncharged R-groups: Serine, Threonine, Cysteine, Asparagine, Glutamine. These R-groups contain functional groups that can form hydrogen bonds.
• Positively Charged R-groups (Basic): Lysine, Arginine, Histidine. These R-groups are protonated at neutral pH.
• Negatively Charged R-groups (Acidic): Aspartate, Glutamate. These R-groups are deprotonated at neutral pH.

Classification of Peptides

• Dipeptide: Two amino acids linked by one peptide bond.
• Tripeptide: Three amino acids linked by two peptide bonds.
• Oligopeptide: A peptide chain containing a small number of amino acids (typically 2-20).
• Polypeptide: A longer chain of amino acids (typically more than 20-50). Proteins are often composed of one or more polypeptide chains.

α-Amino Acids - Synthesis, Ionic Properties and Reactions

Synthesis of α-Amino Acids

Various methods exist for the laboratory synthesis of α-amino acids. One common method is the Strecker synthesis.

Strecker Synthesis

1. Formation of Iminium Ion: An aldehyde reacts with ammonia (or ammonium chloride) and cyanide to form an imine.
2. Nucleophilic Attack: The cyanide ion (CN⁻) attacks the iminium carbon to form an α-aminonitrile.
3. Hydrolysis: The α-aminonitrile is then hydrolyzed under acidic or basic conditions to yield the α-amino acid.

Example (Strecker Synthesis for Alanine):

CH₃CHO (acetaldehyde) + NH₃ + HCN → CH₃CH(NH₂)CN (α-aminopropionitrile)

CH₃CH(NH₂)CN + 2H₂O + H⁺ → CH₃CH(NH₂)COOH (Alanine) + NH₄⁺

Ionic Properties of α-Amino Acids

Zwitterions

Amino acids exist predominantly as zwitterions (German for