Protein Essentials: Structure, Properties, and Functions

Protein Definition

A protein consists of amino acids linked together. Each amino acid has a central carbon atom attached to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable radical group (side chain).

Protein Classification

Proteins can be classified based on their composition:

• Holoprotein: Composed solely of amino acids.
• Heteroprotein: Composed of amino acids along with other non-amino acid molecules (prosthetic groups).

Amino Acids

Amino acids are organic compounds characterized by having both a carboxyl group (-COOH) and an amino group (-NH2). They are typically solid, crystalline substances with high melting points, soluble in water, and possess optical activity. Their chemical behavior is amphoteric, meaning they can act as an acid, a base, or both simultaneously, depending on the pH of the surrounding medium, allowing them to ionize accordingly.

Peptide Bond Formation

Peptides and proteins are formed by joining amino acids via peptide bonds. This is a covalent bond formed between the carboxyl group of one amino acid and the amino group of the next, resulting in the release of a water molecule.

Protein Structure

The structure of a protein can be described at four levels:

Primary Structure

This refers to the linear sequence of amino acids in the polypeptide chain. It dictates which amino acids make up the protein and the order in which they are arranged.

Secondary Structure

This describes the local spatial arrangement of the polypeptide chain. As the chain is synthesized, it folds into stable arrangements due to hydrogen bonding between backbone atoms. Common types include:

• Alpha-helix (α-helix)
• Collagen helix
• (Note: Beta-sheets are also a common secondary structure, though not explicitly mentioned in the original text.)

Tertiary Structure

This refers to the overall three-dimensional shape of a single polypeptide chain, resulting from the folding of its secondary structures upon themselves. Interactions between amino acid side chains stabilize this globular conformation, which often facilitates solubility in water and salt solutions. Proteins that do not fold into compact tertiary structures remain elongated and are known as filamentous proteins.

Quaternary Structure

This level describes the assembly of multiple polypeptide chains (subunits) held together by non-covalent bonds (and sometimes disulfide bonds) to form a functional protein complex.

Active Site

The active site is a specific region within a protein, typically composed of a set of amino acid side chains, that has the ability to bind to other molecules (ligands or substrates) and potentially catalyze a reaction.

Properties of Proteins

Solubility

Due to their large size, globular proteins often form colloidal dispersions in water. They establish hydrogen bonds with surrounding water molecules, forming a hydration layer that helps prevent aggregation with other protein molecules.

Denaturation

Changes in environmental conditions such as pH, temperature, or high concentrations of certain solutes can disrupt the weak bonds maintaining the protein's secondary, tertiary, and quaternary structures. This loss of structure, called denaturation, results in the protein becoming non-functional. In some cases, if the denaturing conditions are removed, the protein can refold into its original, functional shape; this process is called renaturation.

Specificity

The specific sequence of amino acids determines a protein's unique structure and function. While some regions of the sequence are highly conserved (stable sectors), others (variable sectors) can tolerate amino acid substitutions without significantly altering the protein's overall function. This allows for species-specific proteins and even variations between individuals of the same species.

Buffering Capacity

Proteins can act as buffers because their amino acid side chains and terminal groups can accept or release protons (H+), helping to neutralize changes in the pH of the surrounding medium.

Examples of Fibrous Proteins

• Collagen: Found in connective tissues, cartilage, skin, and bone.
• Alpha-keratin (α-keratin): Found in nails, hair, feathers, and wool.
• Elastin: Found in tendons and blood vessel walls, providing elasticity.
• Beta-keratin (β-keratin): Found in silk threads (originally listed as A-keratin).

Functions of Proteins

Proteins perform a vast array of functions in living organisms:

• Structural: Form components like the cytoskeleton (microtubules), cilia, flagella, and associate with DNA (histones).
• Transport: Carry substances throughout the body (e.g., hemoglobin transports oxygen).
• Enzymatic: Catalyze biochemical reactions within cells.
• Hormonal: Act as chemical messengers (e.g., growth hormone, insulin).
• Defense: Act as antibodies, neutralizing foreign substances (antigens).
• Contractile: Enable movement, such as muscle contraction (e.g., actin and myosin).
• Reserve: Store amino acids for later use (e.g., ovalbumin in egg white).
• Homeostatic: Help maintain balance, such as regulating pH (buffering).