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==Origin==
The genetic code is a key part of the [[origin of life|history of life]]. Under the [[RNA world hypothesis]], self-replicating RNA molecules preceded significant use of proteins. Under the nucleopeptide world hypothesis, significant use of peptides preceded the genetic code and was concurrent with early life's sophisticated use of RNA.<ref>{{cite journal |last1=Fried |first1=Stephen D. |last2=Fujishima |first2=Kosuke |last3=Makarov |first3=Mikhail |last4=Cherepashuk |first4=Ivan |last5=Hlouchova |first5=Klara |title=Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids |journal=Journal of the Royal Society Interface |date=February 2022 |volume=19 |issue=187 |doi=10.1098/rsif.2021.0641 |pmid=35135297 |pmc=8833103 }}</ref> Transfer RNA molecules appear to have evolved before modern [[aminoacyl-tRNA synthetase]]s<ref name=De1998>{{cite journal | vauthors = Ribas de Pouplana L, Turner RJ, Steer BA, Schimmel P | title = Genetic code origins: tRNAs older than their synthetases? | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 19 | pages = 11295–300 | date = Sep 1998 | pmid = 9736730 | pmc = 21636 | doi = 10.1073/pnas.95.19.11295 | bibcode = 1998PNAS...9511295D | doi-access = free }}</ref>. It is possible that synthetases replaced an earlier system of [[ribozyme]]s (RNA enzymes), or that amino acids were recognized by unique pockets in the tertiary structure of proto-tRNAs.<ref>{{cite journal |last1=Koonin |first1=Eugene |title=Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code |journal=Life |date=23 May 2017 |volume=7 |issue=2 |pages=22 |doi=10.3390/life7020022 |pmid=28545255 |bibcode=2017Life....7...22K |doi-access=free }}</ref> It is not known why the genetic code only uses L-amino acids and not D-amino acids.<ref name="pmid21779963">{{cite journal | vauthors = Erives A | title = A model of proto-anti-codon RNA enzymes requiring L-amino acid homochirality | journal = Journal of Molecular Evolution | volume = 73 | issue = 1–2 | pages = 10–22 | date = Aug 2011 | pmid = 21779963 | doi = 10.1007/s00239-011-9453-4 | pmc=3223571| bibcode = 2011JMolE..73...10E }}</ref>
Any evolutionary model for the code's origin must account for its [[Robustness (evolution)|robustness]] of encoded proteins to errors during DNA replication and during translation. Many single nucleotide errors are [[Synonymous substitution|synonymous]], and those that are not tend to cause the [[Conservative replacement|substitution of a biochemically similar amino acid]]. Even holding the structure of the code the same such that clusters of codons encode the same amino acid, which amino acids are encoded by which sets of codons is "one in a million" with respect to robustness.<ref name="pmid9732450">{{cite journal | vauthors = Freeland SJ, Hurst LD | s2cid = 20130470 | title = The genetic code is one in a million | journal = Journal of Molecular Evolution | volume = 47 | issue = 3 | pages = 238–48 | date = Sep 1998 | pmid = 9732450 | doi = 10.1007/PL00006381 | bibcode = 1998JMolE..47..238F }}</ref> Biochemically similar amino acids tend to share the same middle nucleotide, while synonymous changes generally happen at the third nucleotide.
Amino acids that share the same biosynthetic pathway tend to have the same first base in their codons. This could be an evolutionary relic of an early, simpler genetic code with fewer amino acids that later evolved to code a larger set of amino acids.<ref name="pmid2650752">{{cite journal | vauthors = Taylor FJ, Coates D | title = The code within the codons | journal = Bio Systems | volume = 22 | issue = 3 | pages = 177–87 | date = 1989 | pmid = 2650752 | doi = 10.1016/0303-2647(89)90059-2 | bibcode = 1989BiSys..22..177T }}</ref> It could also reflect steric and chemical properties that had another effect on the codon during its evolution. Amino acids with similar physical properties also tend to have similar codons,<ref name="pmid2514270">{{cite journal | vauthors = Di Giulio M | s2cid = 20803686 | title = The extension reached by the minimization of the polarity distances during the evolution of the genetic code | journal = Journal of Molecular Evolution | volume = 29 | issue = 4 | pages = 288–93 | date = Oct 1989 | pmid = 2514270 | doi = 10.1007/BF02103616 | bibcode = 1989JMolE..29..288D }}</ref><ref name="pmid6928661">{{cite journal | vauthors = Wong JT | title = Role of minimization of chemical distances between amino acids in the evolution of the genetic code | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 77 | issue = 2 | pages = 1083–6 | date = Feb 1980 | pmid = 6928661 | pmc = 348428 | doi = 10.1073/pnas.77.2.1083 | bibcode = 1980PNAS...77.1083W | doi-access = free }}</ref> reducing the problems caused by point mutations and mistranslations.<ref name="pmid9732450"/>
Three main hypotheses address the origin of the genetic code. Many models belong to one of them or to a hybrid:<ref name="pmid10742043">{{cite journal | vauthors = Freeland SJ, Knight RD, Landweber LF, Hurst LD | title = Early fixation of an optimal genetic code | journal = Molecular Biology and Evolution | volume = 17 | issue = 4 | pages = 511–18 | date = Apr 2000 | pmid = 10742043 | doi=10.1093/oxfordjournals.molbev.a026331| doi-access = free }}</ref>
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