Protein and Amino Acid Chemistry

Protein and Amino Acid Chemistry

• Proteins are nitrogenous compounds made of amino acids linked by peptide bonds.
• There are twenty amino acids that commonly occur in proteins, and a twenty-first, selenocysteine, is also found in some proteins.

General Formula of Amino Acid

• Amino acids have a general formula of R-CH(NH2)-COOH, where 'R' represents a side chain unique to each amino acid.

Peptide Bond Formation

• A peptide bond is formed between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another amino acid, releasing a water molecule.

Classification of Amino Acids

• Amino acids can be classified based on chemical structure, polarity, nutritional essentiality, and metabolic role.

Chemical Classification of Amino Acids

• Amino acids are classified into aliphatic, aromatic, heterocyclic, and imino acids:

Aliphatic

• Uncharged, Nonpolar: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline
• Charged:
  • With OH: Serine, Threonine, Homoserine, Homocysteine
  • With Sulfur: Cysteine, Cystine
  • With COOH: Aspartic acid, Glutamic acid
  • With NH2: Lysine, Arginine, Histidine

Aromatic

• Phenylalanine, Tyrosine, Tryptophan

Heterocyclic

• Tryptophan, Histidine

Imino acids

• Proline, Hydroxyproline

Notes on Chemical Classification

• Glycine and alanine are considered short-chain amino acids.
• Homoserine and homocysteine do not typically occur in proteins.
• Selenocysteine is the 21st amino acid, similar to cysteine but with selenium replacing sulfur.
• Hydroxyproline and hydroxylysine are formed by hydroxylation of proline and lysine after protein synthesis.
• Tryptophan is both aromatic and heterocyclic.
• Histidine is a basic heterocyclic amino acid.
• Tyrosine is an aromatic amino acid containing a hydroxyl group.

Classification According to Polarity

• Uncharged Non-Polar (hydrophobic) Amino Acids: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
• Uncharged Polar Amino Acids: Serine, Threonine, Tyrosine, Hydroxyproline, Cysteine, Asparagine, Glutamine
• Charged Amino Acids:
  • Basic (Diamino Monocarboxylic): Arginine, Lysine, Hydroxylysine, Histidine
  • Acidic (Monoamino Dicarboxylic): Aspartic acid (Aspartate), Glutamic acid (Glutamate)

Nutritional Classification

• Essential Amino Acids: Not synthesized by the body and must be obtained from the diet. These are often grouped as "Vital Lymph". Includes Valine, Isoleucine, Threonine, Arginine, Leucine, Lysine, Tryptophan, Methionine, Phenylalanine, and Histidine.
• Semi-Essential Amino Acids: Can be synthesized by the body but are not readily produced in amounts sufficient for growth. Arginine is an example of a semi-essential amino acid.
• Non-Essential Amino Acids: Synthesized by the body in sufficient amounts for both adult and growing individuals.

Protein Quality

• High Biological Value Proteins: Contain all essential amino acids and are easily digested.
• Low Biological Value Proteins: Deficient in at least one of the nine essential amino acids and may be difficult to digest.

Metabolic Classification

• Ketogenic Amino Acids: Produce Acetyl-CoA and ketone bodies. Include Leucine and Lysine.
• Mixed Glucogenic and Ketogenic Amino Acids: Produce both glucose and ketone bodies. Include Phenylalanine, Tyrosine, Tryptophan, and Isoleucine.
• Glucogenic Amino Acids: Produce glucose. Includes the rest of the amino acids.

Properties of Amino Acids

• Amphoteric Properties: Amino acids can act as both acids and bases, depending on the pH of the environment.
• Isoelectric Point (IEP): The pH at which an amino acid exists as a zwitterion (carrying both positive and negative charges). The IEP for most amino acids is around 6.02.
• At IEP: The amino acid will not migrate in an electric field because it has a neutral overall charge.