Unit 2: Amino Acids and Proteins

Amino acids are the building blocks of proteins. Each amino acid contains an amino group (-NH2), a carboxyl group (-COOH), and a unique side chain (R-group) attached to a central alpha-carbon.

Key Properties

• Zwitterionic Nature: In neutral pH, amino acids exist as dipolar ions where the amino group is protonated and the carboxyl group is deprotonated.
• Optical Activity: All amino acids except glycine are chiral and exist in L and D forms; proteins only incorporate L-amino acids.
• Amphoteric Behavior: They can act as both acids and bases due to their functional groups.

Proteins are large biomolecules consisting of one or more long chains of amino acid residues.

Physical Properties

• Solubility: Varies based on the R-groups and the surrounding pH.
• Isoelectric Point (pI): The pH at which a protein has no net electrical charge and is least soluble.
• Denaturation: Loss of tertiary/secondary structure due to heat, pH changes, or chemicals, leading to loss of biological activity.

Chemical Properties

• Biuret Reaction: A chemical test that identifies the presence of peptide bonds (turns violet).
• Hydrolysis: Breakdown of proteins into constituent amino acids using acids, bases, or proteolytic enzymes.

Proteins organize into four distinct levels of structure to achieve their functional shape.

The stability of a protein's 3D conformation depends on several intramolecular forces:

• Hydrogen Bonds: Formed between the backbone amides or polar R-groups.
• Hydrophobic Interactions: Non-polar side chains cluster together in the interior of the protein to avoid water.
• Ionic Bonds (Salt Bridges): Electrostatic attractions between oppositely charged R-groups.
• Disulfide Bridges: Covalent bonds between sulfur atoms of two Cysteine residues; provide high stability.
• Van der Waals Forces: Weak attractions between atoms in close proximity.

Proteins are classified into two broad categories based on their overall shape and solubility.

• Fibrous Proteins: Long, thread-like molecules. They are generally insoluble in water and serve structural roles (e.g., Collagen, Keratin).
• Globular Proteins: Spherical or oval-shaped. They are usually soluble in water and perform dynamic functions (e.g., Enzymes, Hemoglobin, Insulin).

Purification involves separating a target protein from a complex mixture based on differences in physical and chemical properties.

Common Methods

1. Protein Extraction: Cell disruption using mechanical (homogenization) or chemical (detergents) means to release proteins.
2. Fractionation (Salting Out): Using high salt concentrations (like Ammonium Sulfate) to selectively precipitate proteins based on their solubility.
3. Dialysis: Using a semi-permeable membrane to remove salts and small molecules.
4. Chromatography: Includes Ion-exchange (charge), Gel-filtration (size), and Affinity chromatography (specific binding).
5. Electrophoresis (SDS-PAGE): Separating proteins primarily by their molecular mass.

7. Exam Corner: Tips, Mnemonics & FAQs

Mnemonics for Non-Polar Amino Acids

GAVLI MP PT: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Proline, Tryptophan.

Frequently Asked Questions

Q: What is the difference between denaturation and hydrolysis?
A: Denaturation breaks non-covalent bonds (unfolding the 3D shape), while hydrolysis breaks covalent peptide bonds (breaking the chain into individual amino acids).

Q: Why is proline called an 'alpha-helix breaker'?
A: Proline has a rigid cyclic structure that creates a 'kink' in the polypeptide chain, preventing it from forming the regular hydrogen bonding required for an alpha-helix.