Amino Acid study

AMINO ACIDS STUDY NOTES

INTRODUCTION

• Definition of Amino Acids: Amino acids are organic compounds containing two functional groups:

  • Amino group (-NH₂): Basic in nature.

  • Carboxyl group (-COOH): Acidic in nature.

• General structure of amino acids:

  • α-amino acids: Both carboxyl and amino groups are attached to the same carbon atom, α-carbon.

  • Structure representation:
    $ext{H}_2N- ext{C}( ext{R})- ext{COOH}$ where R represents the side chain variant.

• Mostly exist in an ionized form in biological systems.

HISTORY

• Discovery Timeline:

  • First amino acid discovered: Asparagine in 1806.

  • Last amino acid discovered: Threonine in 1938.

• Origins of names:

  • Asparagine: Found in asparagus.

  • Glutamine: Found in wheat gluten.

  • Tyrosine: Isolated from cheese.

  • Glycine: Named from Greek "glykos" meaning sweet, due to its taste.

CLASSIFICATION OF AMINO ACIDS

A) BASED ON NUTRITION (DIET)

1. Essential (Indispensable) Amino Acids: Must be obtained from diet as they cannot be synthesized by the body.

   • Essential amino acids list:

     • Arginine

     • Valine

     • Histidine

     • Isoleucine

     • Leucine

     • Lysine

     • Methionine

     • Phenylalanine

     • Threonine

     • Tryptophan

2. Non-Essential (Dispensable) Amino Acids: Can be synthesized by the body.

   • Non-essential amino acids list:

     • Glycine

     • Alanine

     • Serine

     • Cysteine

     • Aspartate

     • Asparagine

     • Glutamate

     • Glutamine

     • Tyrosine

     • Proline

B) BASED ON POLARITY

1. Non-polar Amino Acids with Aliphatic ‘R’ Group: Hydrophobic, no charge on R-group.

   • Includes: Glycine, Alanine, Leucine, Isoleucine, Valine, Methionine.

2. Non-polar Amino Acids with Aromatic ‘R’ Group: Aromatic side chains are hydrophobic.

   • Includes: Phenylalanine, Tryptophan, Tyrosine.

3. Polar Amino Acids with No Charge on ‘R’ Group: Hydrophilic, possess hydroxyl, sulfhydryl, and amide groups.

   • Includes: Serine, Threonine, Cysteine, Glutamine, Asparagine.

4. Polar Amino Acids with Negative ‘R’ Group: Includes dicarboxylic amino acids.

   • Includes: Aspartic acid, Glutamic acid.

5. Polar Amino Acids with Positive ‘R’ Group: Carry positive charge, dibasic monocarboxylic amino acids.

   • Includes: Lysine, Arginine, Histidine.

C) BASED ON METABOLIC FATE

1. Glycogenic Amino Acids: Serve as precursors for glucose formation.

   • Includes: Alanine, Aspartate, Glycine, Methionine.

2. Ketogenic Amino Acids: Amino acids from which fat can be synthesized.

   • Exclusively ketogenic: Leucine, Lysine.

3. Glycogenic and Ketogenic Amino Acids: Precursors for both glucose and fat synthesis.

   • Includes: Isoleucine, Phenylalanine, Tryptophan, Tyrosine.

D) BASED ON STRUCTURE

1. Amino Acids with Aliphatic Side Chains

2. Hydroxyl Group Containing Amino Acids

3. Sulfur Containing Amino Acids

4. Acidic Amino Acids and their Amides

5. Basic Amino Acids

6. Aromatic Amino Acids

7. Imino Acids

E) BASED ON TWO (2) MAIN GROUPS

1. Standard Amino Acids: The 20 standard amino acids that participate in protein structure.

   • List includes: Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Glycine, Alanine, Serine, Cysteine, Aspartate, Asparagine, Glutamate, Glutamine, Tyrosine, Proline.

2. Non-Standard Amino Acids: Modified residues based on standard amino acids.

   • Examples include: 4-Hydroxyproline, 5-Hydroxylysine, N-Methyllysine, γ-Carboxyglutamate, Desmosine, Selenocysteine.

STRUCTURES OF NON-STANDARD AMINO ACIDS

• 4-Hydroxyproline: $ext{HO-CH}_2- ext{CH}- ext{COOH}$

• 5-Hydroxylysine: $ext{HOOC-CH}- ext{CH}_2- ext{COOH}$

• γ-Carboxyglutamate: $ext{HOOC-CH} ext{-CH}_2- ext{NH}_2$

• Selenocysteine: $ext{HSe}- ext{CH}_2- ext{COOH}$

• 6-N-Methyllysine: $ext{CH}_3- ext{NH}- ext{CH}_2- ext{COOH}$

• Desmosine: Complex structure derived from lysine.

PROPERTIES OF AMINO ACIDS

A. PHYSICAL PROPERTIES

1. Solubility: Most amino acids are soluble in water, insoluble in organic solvents.

2. Melting Point: Generally above 200°C.

3. Taste: Varies: Sweet (e.g., Glycine, Alanine), Tasteless (e.g., Leucine), Bitter (e.g., Arginine, Isoleucine).

   • Monosodium glutamate (MSG) is a flavoring agent.

4. Optical Properties: All amino acids except Glycine have optical isomers due to chiral centers.

5. Amphoteric Nature: Contains both acidic and basic groups, allowing for proton donation or acceptance.

6. Zwitterionic Form: At physiological pH, amino acids exist in dipolar form.

7. Isoelectric pH (pI): pH where the amino acid carries no net charge.

   • pI calculation: Averaging pKa values of ionizable groups.

B. CHEMICAL PROPERTIES

1. Reaction with Ammonia: Carboxyl group reacts with ammonia to form amides.

   • Example: Aspartic acid + NH₃ → Asparagine.

2. Formation of Salts: Amino acids can react with acids to form salts.

3. Ninhydrin Reaction: Reaction with ninhydrin yields a blue/purple color.

4. Color Reactions: Identifying Specific Amino Acids:

   • Xanthoproteic reaction: Aromatic amino acids → Yellow.

   • Millons reaction: Tyrosine → Red.

   • Hopkins-Cole reaction: Tryptophan → Purple.

   • Sakaguchi reaction: Arginine → Red.

   • Nitroprusside reaction: Cysteine → Bright red.

   • Pauly’s test: Histidine → Red.

CONCLUSION

• Amino acids are fundamental to all life processes, essential for metabolic processes, nutrient transport, and storage.

• Implicated in the pathogenesis of various diseases, including obesity, diabetes, and arthritis.

• Positive effects on health, including arthritis, osteoporosis, cholesterol levels, and overall metabolism.

REFERENCES

• David L. Nelson and Michael M. Cox, Third Edition, Lehninger Principles of Biochemistry.

• U. Satyanarayana and U. Chakrapani, Third Edition, Biochemistry.

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