Editing Stop codon (section)

== Nomenclature ==
Stop codons were historically given many different names, as they each corresponded to a distinct class of mutants that all behaved in a similar manner. These mutants were first isolated within [[bacteriophage]]s ([[Enterobacteria phage T4|T4]] and [[Lambda phage|lambda]]), [[virus]]es that infect the bacteria ''[[Escherichia coli]]''. Mutations in viral genes weakened their infectious ability, sometimes creating viruses that were able to infect and grow within only certain varieties of ''E. coli''.

=== ''amber'' mutations ({{mono|UAG}}) ===
{{anchor|Amber mutant}}
They were the first set of [[nonsense mutation]]s to be discovered, isolated by [[Richard H. Epstein]] and [[Charles M. Steinberg|Charles Steinberg]] and named after their friend and graduate Caltech student Harris Bernstein, whose last name means '''"[[amber]]"''' in German (''cf.'' [[:wikt:Bernstein#German|Bernstein]]).<ref>{{cite journal |author=Stahl FW |author-link=Franklin Stahl|year=1995 |title=The amber mutants of phage T4 |journal=Genetics |volume=141 |issue=2 |pages=439–442 |doi=10.1093/genetics/141.2.439 |pmid=8647382 |pmc=1206745}}</ref><ref name="Lewin2011">{{Cite book |last1=Lewin |first1=Benjamin |url=https://books.google.com/books?id=HZ34Ac2bS9sC&pg=PA204 |title=Lewin's Essential GENES |last2=Krebs |first2=Jocelyn E. |last3=Goldstein |first3=Elliott S. |last4=Kilpatrick |first4=Stephen T. |date=2011-04-18 |publisher=Jones & Bartlett |isbn=978-1-4496-4380-5 }}</ref><ref>{{cite journal |vauthors=Edgar B |title=The genome of bacteriophage T4: an archeological dig |journal=Genetics |volume=168 |issue=2 |pages=575–82 |date=October 2004 |pmid=15514035 |pmc=1448817 |doi=10.1093/genetics/168.2.575 }}</ref>

Viruses with amber mutations are characterized by their ability to infect only certain strains of bacteria, known as amber suppressors. These bacteria carry their own mutation that allows a recovery of function in the mutant viruses. For example, a mutation in the tRNA that recognizes the amber stop codon allows translation to "read through" the codon and produce a full-length protein, thereby recovering the normal form of the protein and "suppressing" the amber mutation.<ref>{{cite encyclopedia|url=http://www.bookrags.com/research/amber-ocher-and-opal-mutations-wog/|title=Amber, Ocher, and Opal Mutations Summary|encyclopedia=World of Genetics|author=Robin Cook|publisher=Gale}}</ref>
Thus, amber mutants are an entire class of virus mutants that can grow in bacteria that contain amber suppressor mutations. Similar suppressors are known for ochre and opal stop codons as well.

tRNA molecules carrying unnatural aminoacids have been designed to recognize the amber stop codon in bacterial RNA. This technology allows for incorporation of orthogonal aminoacids (such as p-azidophenylalanine) at specific locations of the target protein.

=== ''ochre'' mutations ({{mono|UAA}}) ===
It was the second stop codon mutation to be discovered. Reminiscent of the usual yellow-orange-brown color associated with amber, this second stop codon was given the name of '''"[[ochre]]"''', an orange-reddish-brown mineral pigment.<ref name="Lewin2011"/>

Ochre mutant viruses had a property similar to amber mutants in that they recovered infectious ability within certain suppressor strains of bacteria. The set of ochre suppressors was distinct from amber suppressors, so ochre mutants were inferred to correspond to a different nucleotide triplet. Through a series of mutation experiments comparing these mutants with each other and other known amino acid codons, [[Sydney Brenner]] concluded that the amber and ochre mutations corresponded to the nucleotide triplets "UAG" and "UAA".<ref name=brenner_1965>{{cite journal |pages=994–8 |doi=10.1038/206994a0 |pmid=5320272 |title=Genetic Code: The 'Nonsense' Triplets for Chain Termination and their Suppression |year=1965 |last1=Brenner |first1=S. |last2=Stretton |first2=A. O. W. |last3=Kaplan |first3=S. |journal=Nature |volume=206 |issue=4988|bibcode=1965Natur.206..994B |s2cid=28502898 }}</ref>

=== ''opal'' or ''umber'' mutations ({{mono|UGA}}) ===
The third and last stop codon in the standard genetic code was discovered soon after, and corresponds to the nucleotide triplet "UGA".<ref>{{cite journal |pages=449–50 |doi=10.1038/213449a0 |title=UGA: A Third Nonsense Triplet in the Genetic Code |year=1967 |last1=Brenner |first1=S. |last2=Barnett |first2=L. |last3=Katz |first3=E. R. |last4=Crick |first4=F. H. C. |journal=Nature |volume=213 |issue=5075 |pmid=6032223|bibcode=1967Natur.213..449B |s2cid=4211867 }}</ref>

To continue matching with the theme of colored minerals, the third nonsense codon came to be known as '''"[[opal]]"''', which is a type of silica showing a variety of colors.<ref name="Lewin2011"/> Nonsense mutations that created this premature stop codon were later called opal mutations or [[umber]] mutations.