Proteins: Structure, Function, and Biological Importance

Proteins

Introduction to Proteins

Proteins are essential macromolecules in all living organisms, responsible for a vast array of biological functions. Unlike other organic molecules, the term protein is applied based on function rather than structure. Proteins are composed of one or more polypeptides that perform specific functions. Different molecular shapes or structures that perform the same function are considered the same protein.

• Protein: A molecule composed of one or more polypeptides, performing a specific biological function.

• Polypeptide: A single polymer of amino acids. It may be functional on its own, part of a functional protein, or non-functional.

Functions of Proteins

Major Biological Roles

Proteins carry out a wide range of functions in cells and organisms. The following are eight major functions commonly described in introductory biology textbooks:

• Enzymatic: Catalyze biochemical reactions (e.g., amylase in saliva).

• Structural: Provide support and shape to cells and tissues (e.g., collagen in connective tissue).

• Storage: Store amino acids or other substances (e.g., ovalbumin in egg whites).

• Transport: Move substances across membranes or within the body (e.g., hemoglobin transports oxygen).

• Hormonal: Act as chemical messengers (e.g., insulin regulates blood sugar).

• Receptor: Receive and transmit signals (e.g., neurotransmitter receptors).

• Contractile and Motor: Enable movement (e.g., actin and myosin in muscles).

• Defensive: Protect against disease (e.g., antibodies in the immune system).

Polypeptides and Peptide Linkages

Definition and Formation

A polypeptide is a polymer consisting of many amino acids linked by peptide bonds. Peptide bonds are covalent linkages formed between the carboxyl group of one amino acid and the amino group of another via a dehydration reaction.

• Peptide linkage (peptide bond): The covalent bond joining two amino acids in a polypeptide chain.

• Equation for peptide bond formation:

$ext{Amino acid}_1 + ext{Amino acid}_2 ightarrow ext{Dipeptide} + H_2O$

Amino Acid Structure

Components and Variability

Amino acids are the monomers of polypeptides and proteins. Each amino acid consists of five components:

• A central carbon atom (α carbon)

• A hydrogen atom

• An amino group ($-NH_2$)

• A carboxyl group ($-COOH$)

• A variable R group (side chain)

The R group determines the identity and properties of each amino acid. All other components are identical among amino acids.

Amino Acid Structure: Non-Ionized and Ionized Forms

• Non-ionized form: The amino and carboxyl groups are not charged.

• Ionized form: At physiological pH, the amino group is positively charged ($-NH_3^+$) and the carboxyl group is negatively charged ($-COO^-$).

The Importance of Structure and Folding to Function

Protein Folding and Functionality

Most proteins fold into complex, three-dimensional shapes, which are critical for their function. Many proteins are polymeric, composed of more than one polypeptide. The sequence and order of amino acid R groups strongly influence folding and shape, and thus function.

• Proteins fold spontaneously due to hydrophobic interactions and van der Waals forces.

• Some require helper molecules called chaperonins for proper folding.

• Loss of structure or improper folding results in loss of function (denaturation).

Folded/Functional Proteins and Denatured/Non-Functional Proteins

Structural Changes and Consequences

Functional proteins have a specific folded structure. Denatured proteins lose this structure and, consequently, their biological activity.

• Denaturation: The process by which a protein loses its native structure due to environmental changes (e.g., pH, temperature).

• Denatured proteins are typically non-functional.

Levels of Protein Structure

Hierarchical Organization

Proteins have four levels of structural organization:

• Primary structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding patterns such as α-helix and β-pleated sheet, stabilized by hydrogen bonds.

• Tertiary structure: The overall three-dimensional shape of a single polypeptide, stabilized by interactions among R groups (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).

• Quaternary structure: The arrangement of multiple polypeptide chains into a functional protein complex (e.g., hemoglobin).

Protein Denaturation

Causes and Effects

Proteins can be denatured by environmental conditions that disrupt hydrogen bonding, ionic bonding, hydrophobic interactions, and disulfide bridges.

• Common denaturing conditions: Extreme pH, heat, heavy metals, non-polar solvents.

• Denatured proteins may sometimes refold spontaneously or require chaperonins.

Summary Table: Levels of Protein Structure

Level	Description	Stabilizing Forces
Primary	Sequence of amino acids	Peptide bonds
Secondary	α-helix, β-sheet	Hydrogen bonds (backbone)
Tertiary	3D folding of polypeptide	R-group interactions: hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions
Quaternary	Assembly of multiple polypeptides	Same as tertiary, between polypeptides

Additional info:

• Examples of protein types: Globular proteins (e.g., albumin) are generally soluble and functional, while fibrous proteins (e.g., tropomyosin) provide structural support.

• Proteins such as antibodies (e.g., human IgG) are composed of multiple polypeptides and play key roles in immune defense.