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Encyclopedia > Synonymous substitution

A synonymous substitution (also called a silent substitution) is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the amino acid sequence produced is not modified. Base pairs, of a DNA molecule. ... For other meanings of this term, see gene (disambiguation). ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ...

Redundancy in DNA

Proteins translation involves a set of twenty amino acids. Each of these amino acids is coded for by a sequence of three DNA base pairs called a codon. Because there are 64 possible codons, but only 20 amino acids (as well as a stop signal, indicating that translation should stop), some amino acids are coded for by 2, 3, 4, or 6 different codons. For example, the codons TTT and TTC both code for the amino acid phenylalanine. This is often referred to as redundancy of the genetic code. There are two mechanisms for redudancy: several different transfer RNAs can deliver the same amino acid, or one tRNA can have a non-standard "wobbly" base in position three of the anti-codon, which recognises more than one base in the codon. Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ... Phenylalanine is one of the standard amino acids. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... RNA codons. ... Phe redirects here. ... Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ...

In the above phenylalanine example, suppose that the base in position 3 of a TTT codon got substituted to a C, leaving the codon TTC. The amino acid at that position in the protein will remain a phenylalanine. Hence, the substitution is a synonymous one.

Substitution versus mutation

Although mutation and substitution are often used interchangeably, there is a subtle but important difference. A nucleotide mutation is a base change (whether synonymous or non-synonymous) such that the mutant and wild-type forms coexist in a population. A nucleotide substitution is a base change between two related species. Thus, a mutation only becomes a substitution after it has increased to 100% frequency, or fixed, in the species.

Synonymous substitutions and evolution

When a synonymous or silent mutation occurs, the change is generally neutral, meaning that it does not affect the fitness of the individual carrying the new gene to survive and reproduce. Redundancy of the genetic code provides some protection against the effect of mutations. Silent mutations or synonymous mutations are DNA mutations that, although they alter a particular codon, they do not alter the final amino acid, and hence do not affect the final protein. ... The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. ... It has been suggested that mutant be merged into this article or section. ...

Substitutions that are not synonymous are often detrimental to the host cell. For instance, a mammalian cell might have a gene coding for a protein that regulates cell division. A mutation that results in a change to the methionine codon that marks the beginning of the gene's open reading frame may cause the gene to become inactivated. The protein that regulates cell division would not be produced, and the cell would grow unchecked, resulting in a tumor cell. Drawing of the structure of cork as it appeared under the microscope to Robert Hook from Micrographia which is the origin of the word cell. Cells in culture, stained for keratin (red) and DNA (green). ... This does not adequately cite its references or sources. ... Methionine (Met, M. C5H11NO2S) is an essential nonpolar amino acid, and a lipotropic. ... An open reading frame or ORF is any sequence of DNA or RNA that can be translated into a protein. ... Tumor or tumour literally means swelling, and is sometimes still used with that meaning. ...

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