arpi 1

MODULE 2: AMINO ACID AND PROTEINS

Introduction

This module focuses on the fundamental aspects of amino acids and proteins, their structures, classifications, and properties that facilitate their roles in biochemistry.

Primary Structure of Proteins

• Primary Structure: The sequence of amino acids in a peptide chain.

  • Classification and Acid-Base Properties: Involves understanding the properties of amino acids, peptide bonds, and peptide synthesis methods such as the Merrifield synthesis.

  • Determination Techniques: Interpretation of the primary structure involves amino acid composition analysis, determination of N and C terminals, cleavage of disulfide bonds, and methods for fragmentation and sequencing (e.g., Edman’s degradation).

Secondary Structure of Proteins

• Characteristics of Secondary Structure: Includes various forms such as:

  • α-Helix

  • β-Pleated Sheets (along with β and π bends)

  • Peptide Bond Geometry and Conformational Maps: Understanding how the geometry of the peptide bond influences protein folding.

  • Chou and Fasman Algorithm: A systematic approach to predicting secondary structure based on empirical observations.

  • Super Secondary Structures: Discussion of motifs and domains that arise from the arrangement of secondary structures of proteins.

Overview of Amino Acids

• Basic Composition: Each amino acid has a basic structure that includes:

  • Amine Group (-NH2)

  • Carboxyl Group (-COOH)

  • Distinctive Side Chain (R Group)

• Key Elements: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O) are fundamental elements in amino acid structure.

Structural Representation of Amino Acids

• Ionization: At physiological pH, amino acids exist predominantly in their ionized forms.

  • The carboxyl group is deprotonated (-COO-) and the amine group is protonated (NH3+).

• L and D Amino Acids: The chirality is indicated with L-amino acids being predominant in biological systems, whereas D-amino acids are less common.

Classification of Amino Acids

Based on Structure & Chemical Nature

1. Aliphatic Side Chains: Glycine, Alanine, Valine, Leucine, Isoleucine.

2. Side Chains with Hydroxyl Groups: Serine, Threonine, Tyrosine.

3. Side Chains with Sulfur Atoms: Cysteine, Methionine.

4. Acidic Amino Acids: Aspartic Acid, Glutamic Acid, and their amides (Asparagine, Glutamine).

5. Basic Amino Acids: Arginine, Lysine, Histidine.

6. Aromatic Amino Acids: Phenylalanine, Tyrosine, Tryptophan.

7. Imino Acid: Proline.

Based on Polarity

• Hydrophilic (Polar) and Hydrophobic (Non-polar) classifications based on their side chain properties.

Based on Nutritional Requirements

• Essential Amino Acids: Required from diet, including Phenylalanine, Valine, Threonine, etc.

• Non-Essential Amino Acids: Can be synthesized by the body, e.g., Glycine, Glutamine.

• Semi-Essential: Include certain amino acids like Histidine that may be conditionally essential.

Significance of Amino Acids

• Amino acids are precursors for several biological compounds such as:

  • Neurotransmitters: Glycine, Glutamic Acid, Tyrosine.

  • Hormones and Metabolites: Thyroxine, Melanin.

  • Creatine and Coenzymes: Essential in various metabolic processes.

Acid-Base Properties of Amino Acids

• Dual Nature: Amino acids exhibit both acidic and basic properties due to their functional groups: the amino group can accept protons, while the carboxyl group can donate protons.

• Influence of pH:

  • At low pH (acidic): Positively charged.

  • At high pH (basic): Negatively charged.

  • At neutral pH: Exist as zwitterions, contributing to buffering capacity in biological systems.

Titration of Amino Acids

• Monitoring pH Changes: The process of titration helps determine the pKa values and isoelectric points (pI) crucial for understanding stability and reactivity in proteins.

• Titration Curves: Depict how the charge states of amino acids change with pH, illustrating their interaction with buffers and their role in protein folding.

  • Example: Glycine has pKa values of approximately 2.3 for the carboxyl group and 9.6 for the amino group.

Conclusion

Understanding the properties and classifications of amino acids is critical for grasping the biochemical foundations of protein structure and function, influencing numerous biological processes.