like these may severely impact a crucial function in a cell, potentially causing the cell — and in extreme cases, the organism — to die. Conversely, the change may allow the cell to continue functioning albeit differently, and the mutation can be passed on to the organism's offspring. If this change does not result in any significant physical disadvantage to the offspring, the possibility exists that this mutation will persist within the population. The possibility also exists that the change in function becomes advantageous. In either case, while being subjected to the processes of natural selection, the point mutation has been accepted into the genetic pool. The 20 amino acids translated by the genetic code vary greatly by the physical and chemical properties of their side chains. However, these amino acids can be categorised into groups with similar physicochemical properties. Substituting an amino acid with another from the same category is more likely to have a smaller impact on the structure and function of a protein than replacement with an amino acid from a different category. Consequently, acceptance of point mutations depends heavily on the amino acid being replaced in the mutation, and the replacement amino acid. The PAM matrices are a mathematical tool that account for these varying rates of acceptance when evaluating the similarity of proteins during alignment. Terminology The term accepted point mutation was initially used to describe the mutation phenomenon. However, the acronym PAM was preferred over APM due to readability, and so the term point accepted mutation is used more regularly. Because the value in the PAMn matrix represents the number of mutations per 100 amino acids, which can be likened to a percentage of mutations, the term percentage accepted mutation is sometimes used. It is important to distinguish between point accepted mutations (PAMs), point accepted mutation matrices (PAM matrices) and the PAMn matrix. The term 'point accepted mutation' refers to the mutation event itself. However, 'PAM matrix' refers to one of a family of matrices which contain scores representing the likelihood of two amino acids being aligned due to a series of mutation events, rather than due to random chance. The 'PAMn matrix' is the PAM matrix corresponding to a time frame long enough for mutation events to occur per 100 amino acids. Construction of PAM matrices PAM matrices were introduced by Margaret Dayhoff in 1978. The calculation of these matrices were based on