Protein Structure

Proteins are long chains of amino acids that carry out a nearly innumerable number of different cellular functions from forming ion channels to catalyzing metabolic reactions they are critical for normal cellular functioning. To carry out this myriad of functions they each assume a different shape since form = function. This shape can be defined on four different structural levels primary structure (1°), secondary structure (2°), tertiary structure (3°), and quaternary structure (4°).

Primary Structure

Primary structure describes the chain of amino acids that make up individual proteins. Of all the different types of structure, it is the most stable due to the covalent peptide bonds that hold adjacent amino acids together.

Additionally, the primary structure defines what a protein can and can’t do. For example, a protein lacking cysteine would be unable to form disulfide bridges that help stabilize the tertiary and quaternary structure of a protein. Likewise, a large chain of hydrophobic amino acids in the primary structure would cause that portion to fold inwards on itself keeping the hydrophobic section of the amino acid away from the aqueous environment.

Secondary Structure

As our hydrophobic protein described above folds from its linear conformation into more complex structures and shapes it assumes one of two different secondary structures, the ⍺-helix or β-pleated sheet. Regardless of the specific shape encoded in the primary structure each is held together by intramolecular hydrogen bonds that form between the backbones of nearby amino acids.

This makes secondary structure highly dependent on the pH of their environment. Since protonation or deprotonation of the amino acid backbone can eliminate the stabilizing hydrogen bonds our bodies regulate pH within a strict range to ensure our proteins keep their shape and with it their function.


As mentioned above secondary structure comes in two major types ⍺-helices and β-pleated sheets. Alpha helices look like those old coiled telephone wires. Here the hydrogen bonds stabilize adjacent curls and the side chains of different amino acids stick outwards away from the helix.

β-Pleated Sheets

β-pleated sheets on the other hand are formed when multiple crinkled amino acid sheets are laid next to one another to form rows. Here the intramolecular hydrogen bonds span between rows holding each sheet next to its neighbor.

The rows are arranged either in parallel, where the adjacent rows all face the same direction, or antiparallel where the rows alternate the direction they face. (Note: In this context, direction refers to the arrangement of the N and C termini.


In the last few topics, we discussed the different amino acid classifications and some of the individual properties of each amino acid. Among those was proline a rigid and cyclic amino acid that acts as a secondary structure disrupter. As a result, proline is rarely if ever found in the middle of ⍺-helices or β-pleated sheets. Instead, it helps facilitate the turns between β-pleated sheets since it easily forms a rigid loop-like structure.

Prions and Alzheimer’s

Changes in secondary structure can have devastating consequences. For example, in both prion folding diseases, such as Creutzfeldt-Jakob disease (CJD) and Alzheimer’s disease ⍺-helical portions of proteins are misfolded as β-pleated sheets. This drastically alters their tertiary and quaternary structure. These misfolded proteins then accumulate in the brains of the affected and cause neuronal damage and dysfunction.

Tertiary Structure

Tertiary structure describes the overall shape of a single protein. A variety of different chemical interactions hold together tertiary structures including, London dispersion forces, dipole-dipole interactions, H-bonding, disulfide linkages, and ionic interactions.

Here different interactions will determine the overall stability of a protein for example a tertiary structure filled with disulfide bonds is likely to be stable to changes in pH while one dependent on H-bonds won’t. Disulfide bonds on the other hand are formed by the oxidizing environments and broken under reducing conditions.

Since the interior of the cell is highly reducing disulfide bonds aren’t formed within the cytoplasm of cells. However, the extracellular fluid is highly oxidizing leading to the formation of disulfide bonds outside of our cells.

Folding and the Hydrophobic Effect

Although tertiary structure incorporates a wide array of different types of interactions folding at this level is driven by the hydrophobic effect. The hydrophobic effect occurs when water-hating hydrophobic molecules in this case when nonpolar amino acid residues are exposed to a polar environment.

Here the blue dots represent hydrophilic amino acids and yellow hydrophobic ones.

Since water also dislikes interacting with these residues it forms a rigid and highly ordered solvation shell adjacent to the hydrophobic portion of a protein. The universe with its order-despising attitude forces the hydrophobic residues to the interior of a protein and hydrophilic residues to the outside of a protein.

I like to imagine water molecules are playing a game of twister when forced to interact with hydrophobic residues. Since it is uncomfortable they “force” the protein to fold.

This whole process occurs because the entropy of the water molecules increases when the protein folds. Since the universe tends towards disorder proteins spontaneously fold due to this effect. Hold up a moment! Isn’t the protein becoming more ordered though? Sure is, but the entropy increase experienced by the water is much greater than the entropy decrease experienced by the protein. Therefore protein folding leads to a favorable net increase in entropy and the universe is quite pleased with that!


While most proteins fold just fine on their own some proteins require the help of chaperones, other proteins that provide additional folding assistance. Although only a small number of proteins require chaperones many more exist and play another vital role in our cells, the refolding of misfolded proteins.

Under cellular stress, proteins assume dysfunctional tertiary structures. Unfortunately, these dysfunctional proteins can wreak havoc on our cells. So chaperones such as heat shock proteins will unfold them and then refold them back into their normal and functional state. During this process, the “broken” protein is restored to its original and functional tertiary structure.

Quaternary Structure

Quaternary structure is composed of multiple fully folded proteins that form subunits of a larger protein. Not every protein has a quaternary structure, but those that do are held together by the same interactions that stabilize tertiary structure.

For example, two protein subunits could be held together by hydrophobic interactions, ionic interactions, hydrogen-bonds, or disulfide bonds.


When describing the quaternary structure of proteins we refer to them as _____mers. Here the blank is filled in with two different pieces of information that tell us how many subunits are present and whether those subunits are different or identical.

When discussing the number of subunits present we use the common numbering prefixes such as mono, di, tri, tetra, penta, hexa, etc. If the subunits present are the same we use the prefix homo meaning the same and if they are different we use the prefix hetero meaning different. So a protein lacking quaternary structure is referred to as a monomer while a protein with two identical proteins attached to one another is called a homodimer.


Throughout this article, we have discussed the various bonds and interactions that hold different levels of structure together. These bonds can be disrupted and result in denaturation. When a protein undergoes denaturation it loses its 3-D conformation and reverts back to its linear protein structure. While a protein can lose its primary structure peptide bonds are quite stable and often require enzymes to break therefore denaturation only affects quaternary, tertiary, and secondary protein structure. When this process occurs proteins lose their function too since structure equals function!


Temperature is one of the most common ways denaturation occurs and literally shakes apart a protein’s 3-D structure. Since temperature is a measure of the average kinetic energy of a substance increases in temperature results in increased velocity of the bonded molecules. Thus they shake themselves apart breaking the bond that holds 2°, 3°, and 4° structure together.


The acidity and basicity of the surrounding environment also affects the stability of protein structure and disrupts H-bond dependent interactions within proteins. For example, if two asparagine residues were deprotonated they would lose the ability to H-bond and become negatively charged. In this case, the residues would now repel one another and the interaction between the two would be lost. If the environment was extremely acidic protonation would occur and the positive charges created by this would also repel. Since 2° is composed entirely of H-bonding, it is susceptible to changes in pH.

Salts and Solvents

Lastly, the concentration of salts and certain solvents can cause protein denaturation. Salts such as NaCl interrupt the ionic interactions that hold different structural elements together. This occurs as negatively charged residues such as D and E are bound by Na+ ions rendering them neutral. Since they no longer carry a net negative charge they can’t bind to positive residues elsewhere on the protein. Additionally, those positive residues have also been neutralized by the negatively charged chloride ions in solution.

Other solvents such 2-Mercaptoethanol are reducing agents and effectively undo disulfide bonds destroying any covalently linked disulfide bridges between cysteine. While others are detergents interrupt the hydrophobic interactions that help stabilize protein structure.

Concept Check: Protein Structure