What are Proteins?

An amino acid contains four key components: a carboxyl group (–COOH), an amino group (–NH2), a side chain called the R-group, and a hydrogen atom, all attached to a central alpha carbon. The R-group determines each amino acid's unique chemical properties and identity. There are 20 different amino acids used in protein synthesis, each with a distinct R-group ranging from simple hydrogen atoms to complex structures.

Amino acids are linked through covalent peptide bonds formed during a dehydration reaction. The amino group of one amino acid bonds with the carboxyl group of an adjacent amino acid, releasing water. This creates a polypeptide backbone with a free amino group at the N-terminus and a free carboxyl group at the C-terminus, with the sequence always read from N-terminus to C-terminus.

Amino acids are classified into four groups based on their side chains. Acidic amino acids contain carboxyl groups and act like acids at physiological pH. Basic amino acids have amino groups in their side chains and act like bases. Polar uncharged amino acids are hydrophilic and typically locate on protein surfaces. Nonpolar amino acids have hydrophobic side chains ranging from simple glycine to complex structures like proline and tryptophan.

At low pH, both carboxyl and amino groups are protonated, making amino acids act as bases. At alkaline pH, both groups are deprotonated, causing amino acids to act as acids. At physiological pH (~7.4), amino acids form zwitterions with a protonated amino group (–NH3+) and deprotonated carboxyl group (–COO–), enabling hydrogen bonding with the aqueous environment and supporting complex protein structures.

The chemical properties of the R-group determine hydrophilicity or hydrophobicity. Polar and charged R-groups are hydrophilic and interact favorably with water, typically positioning on protein surfaces. Nonpolar R-groups are hydrophobic and repel water, generally burying inside folded proteins. These interactions among amino acid side chains help proteins fold into stable three-dimensional native structures essential for biological function.

Polypeptides and proteins are both chains of amino acids linked by peptide bonds, but they differ in molecular weight. Polypeptides have fewer than 10,000 daltons, while proteins exceed this threshold. Polypeptides with fewer than 20 amino acids are called oligopeptides or peptides. Proteins fold into native three-dimensional structures that are functionally active, enabling diverse cellular roles including structural support, catalysis, and transport.

Proteins perform diverse cellular functions determined by their native structure. They provide structural support as collagen, facilitate movement through actin and myosin in muscles, catalyze reactions as enzymes, transport molecules across membranes as channels, and defend vertebrates against pathogens as antibodies. The enormous diversity in protein structure and composition enables this wide range of biological functions essential for cell survival and organism health.