Amino Acids and Protein Structure: Classification and Biological Roles

Fundamentals of Amino Acids and Protein Structure

Defining Amino Acids (AA)

Amino acids (AA) are organic compounds characterized by the presence of both an amino group (-NH₂) and a carboxyl group (-COOH). There are 20 standard amino acids. We cannot metabolize the essential amino acids, meaning they must be obtained through the diet.

Classification of Amino Acid Side Chains

Amino acids are classified based on the properties of their side chain (R group):

• Nonpolar (Hydrophobic): R group is hydrophobic and typically located on the exterior in aqueous environments.
• Polar Ionizable: R group is polar and located internally.
• Polar Acids: R group contains an additional carboxyl group, located internally.
• Polar Basic: R group contains an additional amino group.

Key Characteristics of Amino Acids

Amino acids exist primarily in the L-form (where the NH₂ group is positioned on the left). They are solid, crystalline compounds with high melting points. They are also amphoteric, meaning they can behave as bases in acidic media and as acids in basic media.

When behaving simultaneously as both an acid and a base, they exist as a bipolar ion known as a zwitterion. The specific pH at which an amino acid takes on this bipolar form is called the isoelectric point.

The Peptide Bond and Polypeptides

The peptide bond is the union formed between the amino group of one amino acid and the carboxyl group of another, resulting in the formation of a dipeptide. This bond is a strong, tough covalent bond. It is planar, meaning rotation around the bond is restricted, maintaining characteristic distances and angles.

Polypeptides are formed by the joining of several amino acids. The resulting chain has an amino terminal end (H) and a carboxy terminal end (OH).

Examples of polypeptides include: insulin, enkephalin, vasopressin, and various antibiotics.

Levels of Protein Structure

Protein structure describes the complex three-dimensional arrangement of the polypeptide chain.

Primary Structure (1º)

The primary structure is defined by the specific sequence and union of more than 100 amino acids.

Secondary Structure (2º)

The secondary structure involves localized, repetitive folding patterns:

• Alpha Helix (α-helix): This is the most common arrangement, forming a helical structure. Approximately 3.6 amino acids exist per turn, with R groups oriented toward the exterior. The structure is maintained by hydrogen bonds between the first and fourth amino acid residues.
• Beta-Pleated Sheet (β-sheet): This structure has a zig-zag conformation, resulting in a folded-plate structure.

Secondary structures can consist of alpha and beta chains, often including undefined areas called irregular regions, which frequently contain the amino acid proline.

Tertiary Structure (3º)

The tertiary structure is the overall three-dimensional conformation of a single polypeptide chain. It is maintained by various interactions, including:

• Hydrogen bonds (H-bridges)
• Van der Waals forces
• Disulfide bonds
• Electrostatic forces

Fibrous vs. Globular Proteins

Tertiary structures result in two main protein forms:

• Fibrous Proteins: These are insoluble in water and salt solutions. Examples include collagen, elastin, and beta-keratin.
• Globular Proteins: These are soluble in water and aqueous solutions. They tend to have alpha conformations centrally and beta conformations externally. This type includes most enzymes and membrane proteins.

Quaternary Structure (4º)

Quaternary structure involves the association of multiple protein molecules (subunits) into higher-order complexes. The binding between these molecules is achieved through non-covalent interactions, such as:

• Hydrogen bonds
• Van der Waals forces
• Electrostatic interactions
• Disulfide bridges

Examples: Hemoglobin and immunoglobulins.

Essential Properties and Functions of Proteins

Proteins exhibit several key properties:

• They are generally soluble.
• They are function-specific and species-specific.
• They are amphoteric (behaving as a base or acid depending on the pH).
• They can be denatured (losing their structure and function) by heat or changes in pH, typically affecting structures from the primary level onward.

General functions of proteins include:

• Enzymatic catalysis
• Structural support
• Hormonal regulation
• Homeostatic maintenance
• Defense mechanisms (e.g., antibodies)
• Transportation
• Contractile movement
• Reserve storage