Genetic code: Difference between revisions

Revision as of 23:38, 18 July 2025

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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 might 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>

AAny hypotheticalevolutionary randomlymodel evolvedfor geneticthe code's furtherorigin motivatesmust a biochemical or evolutionary modelaccount for its origin.[[Robustness If(evolution)|robustness]] aminoof acidsencoded wereproteins randomlyto assignederrors toduring tripletDNA codons,replication thereand wouldduring be 1translation.5&nbsp;×&nbsp;10⁸⁴ possibleMany geneticsingle codes.<refnucleotide name="isbn0-674-05075-4">{{citeerrors book|first=Michaelare |last=Yarus|author-link=Michael[[Synonymous Yarussubstitution|title=Lifesynonymous]], fromand anthose RNAthat World:are Thenot Ancestortend Within|url={{googleto bookscause |plainurl=ythe |id=-YLBMmJE1WwC}}|year=2010|publisher=Harvard University Press|isbn=978-0-674-05075-4}}</ref>{{rp|[{{google books[Conservative replacement|plainurl=ysubstitution |id=-YLBMmJE1WwC|page=163}}of 163]}}a Thisbiochemically numbersimilar isamino foundacid]]. byEven calculatingholding the numberstructure of waysthe thatcode the 21same itemssuch (20that aminoclusters acidsof pluscodons oneencode stop)the cansame beamino placed in 64 binsacid, whereinwhich eachamino itemacids isare usedencoded atby leastwhich once.<ref>{{Citesets web|url=http://community.wolfram.com/groups/-/m/t/319970|title=Mathematicaof functioncodons foris # possible arrangements of items"one in bins?a –million" Onlinewith Technicalrespect Discussionto Groups—Wolfram Community|website=community.wolfram.com|language=en-US|access-date=2017-02-03}}</ref> However, the distribution of codon assignments in the genetic code is nonrandomrobustness.<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> In particular, the genetic code clusters certain amino acid assignments.

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"/>