Editing Silent mutation (section)

==Genetic code==
{{main|Genetic code}}{{see|Transfer RNA}}

The genetic code translates mRNA nucleotide sequences to amino acid sequences. Genetic information is coded using this process with groups of three nucleotides along the mRNA which are commonly known as codons.<ref name=":0" /> The set of three nucleotides almost always produce the same amino acid with a few exceptions like UGA which typically serves as the [[stop codon]] but can also encode [[tryptophan]] in mammalian [[Mitochondrion|mitochondria]].<ref name=":0">{{Cite book|title=Genetics: Analysis and Principles|last=Brooker|first=Robert| name-list-style = vanc |publisher=McGraw-Hill Higher Education|isbn=9781259616020|date=2017-02-01}}</ref> Most amino acids are specified by multiple codons demonstrating that the [[genetic code]] is [[Degeneracy (biology)|degenerate]]–different codons result in the same amino acid.<ref name=":0" /> Codons that code for the same amino acid are termed synonyms. Silent mutations are base substitutions that result in no change of the amino acid or amino acid functionality when the altered [[messenger RNA]] (mRNA) is translated. For example, if the codon AAA is altered to become AAG, the same amino acid – [[lysine]] – will be incorporated into the [[peptide]] chain. 

Mutations are often linked to diseases or negative impacts but silent mutations can be extremely beneficial in creating genetic diversity among species in a population. [[Germline mutation|Germ-line mutations]] are passed from the parent to the offspring.<ref name=":1">{{cite web |url=https://genetics.thetech.org/about-genetics/mutations-and-disease |title=Mutations and Disease |website=[[The Tech Interactive]] |archive-url=https://web.archive.org/web/20220118184448/https://genetics.thetech.org/about-genetics/mutations-and-disease |archive-date=2022-01-18}}</ref>{{Additional citation needed|date=November 2018}} Scientists have predicted that people have approximately 5 to 10 deadly mutations in their genomes but this is essentially harmless because there is usually only one copy of a particular bad gene so diseases are unlikely.<ref name=":1" /> Silent mutations can also be produced by [[Insertion (genetics)|insertions]] or [[Deletion (genetics)|deletions]], which cause a shift in the [[reading frame]].<ref>{{cite book |last=Watson |first=James D. | name-list-style = vanc |title=Molecular Biology of the Gene |publisher=Pearson/Benjamin Cummings |location=San Francisco |year=2008 |isbn=978-0805395921 |edition=6th}}</ref>

Because silent mutations do not alter protein function they are often treated as though they are [[Neutral theory of molecular evolution|evolutionarily neutral]]. Many organisms are known to exhibit [[codon usage bias]]es, suggesting that there is [[natural selection|selection]] for the use of particular codons due to the need for translational stability. [[Transfer RNA]] (tRNA) availability is one of the reasons that silent mutations might not be as silent as conventionally believed.<ref name="pmid21567958">{{cite journal | vauthors = Angov E | title = Codon usage: nature's roadmap to expression and folding of proteins | journal = Biotechnology Journal | volume = 6 | issue = 6 | pages = 650–9 | date = June 2011 | pmid = 21567958 | pmc = 3166658 | doi = 10.1002/biot.201000332 }}</ref>

There is a different tRNA molecule for each codon. For example, there is a specific tRNA molecule for the codon UCU and another specific for the codon UCC, both of which code for the amino acid [[serine]]. In this instance, if there was a thousand times less UCC tRNA than UCU tRNA, then the incorporation of [[serine]] into a polypeptide chain would happen a thousand times more slowly when a mutation causes the codon to change from UCU to UCC. If amino acid transport to the [[ribosome]] is delayed, [[Translation (biology)|translation]] will be carried out at a much slower rate. This can result in lower expression of a particular gene containing that silent mutation if the mutation occurs within an exon. Additionally, if the ribosome has to wait too long to receive the amino acid, the ribosome could terminate translation prematurely.<ref name="mboc"/>