The Structures of Proteins

Proteins are large, globular macromolecules that perform a variety of functions in the body. They are made up of chains of amino acids linked together by peptide bonds. There are 21 different amino acids, each with a specific structure and a unique set of properties.


A protein’s shape depends on its primary, secondary and tertiary structures. These are influenced by the interactions of side chains from the polypeptide chain.

Primary Structure

A protein is a large polymer of amino acid residues joined together by peptide bonds. The central part of the protein is its primary structure, which consists of a particular linear sequence of amino acid residues in one of the polypeptide chains. This is the part of a protein that determines its function and it is encoded in its gene (DNA).

The first level of protein structure, termed secondary structure, is what local folded structures form when amino acid residues in a region of the polypeptide chain interact. These interactions form hydrogen bonds between the -CO and -NH groups of adjacent amino acids, stabilizing the polypeptide backbone in its new shape. This folding results in the formation of alpha helix and beta-pleated sheets, which are characteristic of many proteins.

These structures are held in place by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide nitrogen of another, in addition to electrostatic or ionic interactions, covalent disulphide bonds or hydrophobic interactions between non-polar amino acid side chains. A combination of these structural elements gives each protein its unique three-dimensional shape, known as tertiary structure.

Tertiary structure is important because it influences a protein’s ability to interact with other molecules, including other proteins and other cells. When a protein’s tertiary structure is disrupted, the protein loses its functionality and turns into an unstructured string of amino acid residues. This is called denaturation and can be reversed by changing the temperature or chemical environment in which the protein is exposed, such as frying an egg.

Secondary Structure

The specific geometric shape of a protein is caused by intramolecular and intermolecular hydrogen bonding between the amide groups of the amino acids. The amide group consists of the carboxyl group of one amino acid and the amine group of another amino acid attached by a strong bond, called the peptide linkage. This group flexes by rotation about the single bond between two carbons in the backbone of the polypeptide chain, forming two types of structures called alpha helix and beta-pleated sheets.

Each type of protein structure occurs in short sections of the chain and is dependent on the local amino acid sequence. Amino acids with bulky side chains tend to form b-sheet, while those with smaller side chains form a-helix. The occurrence of these regular, repeating patterns gives the protein its unique three-dimensional shape.

In addition to helix and sheet formations, proteins also contain less common regions of unstructured sequence. Loops are areas of the sequence that are found between the regular secondary structure elements and typically have polar or charged side-chains. These regions can be connected by hydrogen bonds to other proteins, forming chemical bridges, which give the protein its overall shape and function.

Linus Pauling worked out the molecular geometry of a protein’s secondary structure by studying distances between the atoms in the chain. He used exact scale models to determine the atomic radii, bond lengths and angles of a protein. These data allowed him to predict the structure of a protein by analyzing the position of the atoms in the helices and sheets formed by the polypeptide chain.

Tertiary Structure

The tertiary structure is the final stage of protein formation. This is when a protein adopts its three-dimensional shape, which determines the way it will interact with other molecules. The tertiary structure of a protein is determined by the interaction of amino acid side chains. Often these side chains are far apart from each other along the chain, but are brought together in a very complex way by interactions that stabilize the structure. These include hydrogen bonds, electrostatic interactions (attraction between opposite charges of polar residues), Van der Waals forces and disulfide bridges (covalent bonds formed between cysteine residues).

Hydrogen bonds form between the carbonyl oxygen of one amino acid and the amino hydrogen of another, forming the backbone of the polypeptide chain. Hydrogen bonds also form between the polar amino acids on the surface of the protein. These bonds can be very stable and help to keep the protein folded into alpha helices and beta pleated sheets.

Moreover, ionic bonds can form between amino acid side chains with differing charges. These bonds help stabilize the structure of the protein at physiological pH. Disulfide bridges are covalent bonds between the sulfur atoms of adjacent cysteine amino acid residues, which can be very strong and help stabilize tertiary structures. Some proteins may also contain disulfide bridges between different regions of the protein, which can give it more stability and a wider range of functions.

Quaternary Structure

The quaternary structure of proteins is the final stage in protein folding. It describes how individual polypeptide chains assemble and interact with each other to form a functional protein complex. It is only found in proteins that consist of multiple polypeptide subunits, such as enzymes, antibodies and hemoglobin. The quaternary structure is stabilized by nonlocal interactions, such as hydrogen bonds and Van der Waals forces. It can also be stabilized by covalent or noncovalent mechanisms such as salt bridges and disulfide bonds.

The number and arrangement of protein subunits in a quaternary structure is crucial to its function. For example, the quaternary structure of hemoglobin, a four-subunit protein, is critical for its oxygen-binding and transport functions. Proteins with different quaternary structures can also form protein complexes with the same quaternary structure, such as enzyme-substrate complexes.

Another important characteristic of a quaternary structure is the formation of protein domains, which are distinct structural units that function as binding modules for other protein molecules. For example, the SH3 domain in the protein adenylate kinase is an enzymatic domain that binds to proline-rich sequences in other proteins.

It is believed that protein quaternary structures are formed by direct interaction between nascent chains emerging from the ribosome. This is supported by the fact that dozens of proteins have been found to assemble into large oligomers without using dedicated assembly machines.