Unit 3: Proteins

1. Amino Acids: Structure and General Properties

Proteins are polymers of amino acids. Amino acids are organic compounds containing both an amino group and a carboxyl group.

General Structure of Alpha-Amino Acids

In an alpha-amino acid, the amino group (-NH2), carboxyl group (-COOH), a hydrogen atom, and a variable side chain (R group) are all attached to the same central carbon atom, called the alpha-carbon.

General Properties

• Zwitterion Formation: At physiological pH, amino acids exist as dipolar ions where the amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).
• Amphoteric Nature: They can act as both acids and bases depending on the pH of the medium.
• Optical Activity: All amino acids except glycine are optically active (chiral) because the alpha-carbon is attached to four different groups.

2. Essential and Non-essential Amino Acids

Amino acids are classified based on the body's ability to synthesize them.

3. Classification of Proteins

Proteins are classified based on their shape and solubility.

• Fibrous Proteins: Consist of polypeptide chains arranged in parallel rows; they are generally insoluble in water (e.g., Keratin, Collagen).
• Globular Proteins: Polypeptide chains are folded into spherical shapes; they are usually soluble in water (e.g., Enzymes, Hemoglobin).

4. Levels of Organization in Proteins

Protein structure is organized into four distinct levels to facilitate specific biological functions.

A. Primary Structure

The linear sequence of amino acids in a polypeptide chain, linked by peptide bonds.

B. Secondary Structure

Local folding of the polypeptide chain into regular patterns due to hydrogen bonding. Common types include the alpha-helix and beta-pleated sheet.

C. Tertiary Structure

The overall three-dimensional folding of a single polypeptide chain, giving the protein its specific functional shape.

D. Quaternary Structure

The arrangement and interaction of multiple polypeptide chains (subunits) in a multi-subunit protein (e.g., Hemoglobin).

5. Bonds Stabilizing Protein Structure

Various chemical bonds and interactions stabilize the complex 3D structures of proteins:

• Peptide Bonds: Covalent bonds between the carboxyl group of one amino acid and the amino group of another; primary stabilizer of the primary structure.
• Hydrogen Bonds: Formed between the N-H and C=O groups; essential for secondary structures like alpha-helices.
• Disulfide Bridges: Covalent bonds between the sulfur atoms of two cysteine residues; stabilizes tertiary and quaternary structures.
• Ionic Interactions: Between positively and negatively charged R-groups.
• Hydrophobic Interactions: Clustering of non-polar side chains away from water.

6. Exam Focus Enhancements