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.