Comparative biochemistry is the study of different kinds of proteins (including enzymes), their fundamental base units (called amino acids) and their cell machinery. Organisms consist predominantly of organic compounds, including proteins. They rely on enzymes to carry out chemical reactions efficiently and share similarities in the structure of their cell membrane. The amino acid sequence of particular proteins found in a number of organisms, such as haemoglobin and cytochrome-C, has been analysed and the similarities provide evidence for evolution.

Proteins consist of long chains of amino acids, and each protein differs in the number, type and sequence. The number of differences of amino acids in the same protein in different species is used to determine the relationship between species.

• A small number of differences indicated a recent divergence from a common ancestor

• A large number of differences indicated a more distant evolutionary relationship

Proteins are subject to the same mechanisms of evolution as the larger traits in which individuals possess. They undergo natural selection; a protein that is well suited to its function will be preserved/conserved, while other traits around it may evolve.

Cumulative mutations have the chance of altering a protein's function, making it less suited to its original function. If a point mutation results in the loss of an amino acid which is essential for its function, the mutation may not be preserved. Sometimes, mutations may arise that change an encoded amino acid to one with a very similar charge and shape, hence essentially conserving the protein as the substituted amino acid still allows for normal functioning.