The monomer for a protein is an amino acid. All amino acids share the same backbone which consists of an amine group and carboxyl group both bound to what is known as the "alpha carbon." Also bound to that alpha carbon is the variable group, or R-group. This group is what varies (hence the name) between different types of amino acids. There are twenty different R groups, each that gives the amino acid its unique properties. There are non-polar, polar, and charged (both positive and negative) R groups, as well as R groups of varying sizes, some that branch, as well as some that have hydrocarbon rings.

Amino acids will form peptide bonds as they bind together, creating what is known as a "polypeptide." There is a distinct and consistent directionality in the formation of peptide bonds. Dehydration synthesis will occur between the carboxyl group of one amino acid with the amine group of the next.

Most proteins have somewhere between fifty and two thousand amino acids.

Proteins function based on their three-dimensional structure. Form fits function is a common phrase that represents this idea. In order to achieve this 3D structure, the string of amino acids must undergo a folding process.

The primary structure of a protein is the order of the amino acid sequence. In essence, it is the string of amino acids that have been bound together.

The secondary structure of a protein results in the beginning of folding of the primary sequence based on hydrogen bonds within the backbone. Because peptide bonds are planar, steric hindrance results in repulsion when two planes go into each other's space. This results in primarily two forms of secondary structure existing - alpha helices and beta sheets. Beta turns and omega loops also exist but are far less common.

Tertiary structure is where interactions between R groups, such as hydrogen bonds, the hydrophobic effect, and ionic interactions will result in further folding. The major driving force for this change, due to the strong increase of entropy for water (which will be discussed later when we talk about Gibbs Free Energy), is the hydrophobic effect. Hydrophobic side chains will cluster to avoid water. In addition, disulfide bridges form between the sulfur atoms of R groups and stabilize the protein's structure.

Quaternary structure does not exist in all proteins, only those proteins that consist of multiple polypeptide chains (such as hemoglobin). This structure results from linking multiple tertiary structures together.