Protein and Protein Structure

Proteins are polymers of amino acids linked together through peptide bonds. Most proteins fold into specific three-dimensional structures to perform their function.

Protein structure is classified into four categories: primary, secondary, tertiary, and quaternary.

The linear sequence of amino acids in the protein is its primary structure. These sequences are read in the polymer synthesis order, from the N-terminal the free amino end, to the C-terminal, the free carboxyl end.

Secondary structures form through hydrogen bonding between the oxygen from the carbonyl group of one amino acid and the hydrogen from the amide group of another. Common secondary structures include α-helices and β-pleated sheets. 

In an α-helix, hydrogen bonds form within a single polypeptide chain, giving it a coiled structure. In β-pleated sheets, hydrogen bonds form between adjacent strands, creating a sheet-like arrangement.

These and other connecting structures, such as β-turns, further interact to form the protein’s three-dimensional structure, known as the tertiary structure.

The formation of the tertiary structure occurs due to interactions between the R-groups of the amino acids.

R-groups with opposite charges can form ionic bonds, and sulfur in two cysteines can form a covalent disulfide bridge. Other contributors include hydrophobic interactions between nonpolar side chains and hydrogen bonds between polar side chains.

Additionally, some proteins form quaternary structures, assemblies of two or more polypeptide chains. For example, hemoglobin is a protein made up of four subunits, two α and two β.

Scientists often use the structure of a protein to predict its function and location in the cell. For example, proteins in the cell cytoplasm have hydrophilic amino acids on their surfaces that interact with the surrounding water, while hydrophobic amino acids are typically buried in the protein’s core.

In contrast, proteins that form pores have hydrophobic amino acids on their surface that interact with membrane lipids and have hydrophilic cores.