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A point accepted mutation — also known as a PAM — is the replacement of a single amino acid in the primary structure of a protein with another single amino acid, which is accepted by the processes of natural selection. This definition does not include all point mutations in the DNA of an organism. In particular, silent mutations are not point accepted mutations, nor are mutations which are lethal or which are rejected by natural selection in other ways. A PAM matrix is a matrix where each column and row represents one of the twenty standard amino acids. In bioinformatics, PAM matrices are regularly used as substitution matrices to score sequence alignments for proteins. Each entry in a PAM matrix indicates the likelihood of the amino acid of that row being replaced with the amino acid of that column through a series of one or more point accepted mutations during a specified evolutionary interval, rather than these two amino acids being aligned due to chance. Different PAM matrices correspond to different lengths of time in the evolution of the protein sequence. ==Biological background== The genetic instructions of every replicating cell in a living organism are contained within its DNA.〔 Throughout the cell's lifetime, this information is transcribed and replicated by cellular mechanisms to produce proteins or to provide instructions for daughter cells during cell division, and the possibility exists that the DNA may be altered during these processes. This is known as a mutation. At the molecular level, there are regulatory systems that correct most — but not all — of these changes to the DNA before it is replicated.〔 One of the possible mutations that occurs is the replacement of a single nucleotide, known as a point mutation. If a point mutation occurs within an expressed region of a gene, an exon, then this will change the codon specifying a particular amino acid in the protein produced by that gene.〔 Despite the redundancy in the genetic code, there is a possibility that this mutation will then change the amino acid that is produced during translation, and as a consequence the structure of the protein will be changed. The functionality of a protein is highly dependent on its structure. Changing a single amino acid in a protein may reduce its ability to carry out this function, or the mutation may even change the function that the protein carries out.〔 Changes 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. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Point accepted mutation」の詳細全文を読む スポンサード リンク
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