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arpi 1

Module Overview

Amino Acids and Proteins

  • Module 2 focuses on the structure and function of amino acids and proteins.

Primary Structure of Proteins

Key Topics

  • Structure: Classification and acid-base properties of amino acids.

  • Peptide Bonds: Formation and properties of peptides, including Merrifield synthesis.

  • Determination Techniques:

    • Analysis of amino acid composition.

    • N and C terminal analysis.

    • Cleavage of disulfide bonds.

    • Chemical and enzymatic fragmentation.

    • Sequencing using Edman’s reagent.

Secondary Structure of Proteins

Types of Structures

  • Helices: α-, PP-, 310-, and π-helices.

  • Sheets: β-pleated sheets, β and ℽ bends.

  • Peptide Bond Geometry: Understanding of conformational maps.

  • Super Secondary Structures: This includes motifs and domains.

Amino Acids

Basic Structure

  • Amino acids are organic compounds made up of:

    • Amine group [-NH2]

    • Carboxyl group [-COOH]

    • Distinctive side chain [R group]

  • Major elements include carbon, hydrogen, nitrogen, and oxygen.

Classification of Amino Acids

Standard and Non-Standard Amino Acids

  • 20 standard amino acids plus:

    • Selenocysteine (21)

    • Pyrrolysine (22)

  • Non-standard amino acids include D-amino acids and amino acid derivatives.

Structural Classification

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

  2. Hydroxyl Groups: Serine, Threonine, Tyrosine.

  3. Sulphur Atoms: Cysteine and Methionine.

  4. Acidic Groups: Aspartic acid, Asparagine, Glutamic acid, Glutamine.

  5. Basic Groups: Arginine, Lysine, Histidine.

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

  7. Imino Acid: Proline.

Functional Properties of Amino Acids

  • Hydrophobicity and Stability: Hydrophobic R-groups cluster within proteins, stabilizing their structures through interactions.

  • Glucogenic vs. Ketogenic: Glucogenic amino acids produce pyruvate or Krebs Cycle intermediates, while ketogenic amino acids yield acetyl CoA.

Nutritional Classification

Essential vs. Nonessential Amino Acids

  • Essential Amino Acids: Include phenylalanine, valine, tryptophan, threonine, isoleucine, methionine, histidine, arginine, leucine, and lysine (PVT. TIM HALL).

  • Semi-Essential Amino Acids: Histidine and Arginine.

  • Non-Essential Amino Acids: Glycine, alanine, serine, cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine, proline.

Biochemical Significance

Biologically Important Compounds

  • Amino acids serve as precursors for various biologically significant compounds:

    • Thyroxine and melanin from Tyrosine.

    • Neurotransmitters like GABA from Glutamic acid.

    • Creatine from Arginine and Methionine.

    • Bile salts from Glycine.

Acid-Base Properties of Amino Acids

Functional Groups

  • Amino Group (-NH2): Can accept a proton, thus basic.

  • Carboxyl Group (-COOH): Can donate a proton, thus acidic.

Behavior in Solution

  • Acidic Conditions: Amino acids become positively charged as the amine group gets protonated.

  • Basic Conditions: Amino acids become negatively charged after carboxyl deprotonation.

  • Zwitterion Form: At the isoelectric point (pI), the amino acid exhibits no net charge.

Influence of Side Chains

Ionizable Side Chains

  • Acidic amino acids such as Aspartic acid and Glutamic acid contribute additional acidic properties.

  • Basic amino acids like Lysine and Arginine can accept protons, displaying basic characteristics.

Titration of Amino Acids

Importance of Titration

  • Titration helps determine pKa values and the isoelectric point, crucial for understanding amino acid behavior in different pH environments.

Glycine Titration Example

  • pKa Values: Glycine has distinct pKa values around 2.3 (carboxyl) and 9.6 (amino).

  • Isoelectric Point: Average of pKa values, around 5.95.

Conclusion

Understanding Amino Acids

  • Mastery of the amino acid properties and behaviors in solutions is critical for biochemistry, protein folding, enzyme activity, and their roles as buffers.