Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction
How Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with respect to hydrolysis....
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-01-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/14/2/199 |
| _version_ | 1797297692283502592 |
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| author | Charles W. Carter |
| author_facet | Charles W. Carter |
| author_sort | Charles W. Carter |
| collection | DOAJ |
| description | How Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with respect to hydrolysis. So, it requires some form of chemical free energy to drive it. Amino acid activation and acyl transfer are also slow and must be catalyzed. All living things must thus also convert free energy and synchronize cellular chemistry. Most importantly, functional proteins occupy only small, isolated regions of sequence space. Nature evolved heritable symbolic data processing to seek out and use those sequences. That system has three parts: a memory of how amino acids behave in solution and inside proteins, a set of code keys to access that memory, and a scoring function. The code keys themselves are the genes for cognate pairs of tRNA and aminoacyl-tRNA synthetases, AARSs. The scoring function is the enzymatic specificity constant, k<sub>cat</sub>/k<sub>M</sub>, which measures both catalysis and specificity. The work described here deepens the evidence for and understanding of an unexpected consequence of ancestral bidirectional coding. Secondary structures occur in approximately the same places within antiparallel alignments of their gene products. However, the polar amino acids that define the molecular surface of one are reflected into core-defining non-polar side chains on the other. Proteins translated from base-paired coding strands fold up inside out. Bidirectional genes thus project an inverted structural duality into the proteome. I review how experimental data root the scoring functions responsible for the origins of coding and catalyzed activation of unfavorable chemical reactions in that duality. |
| first_indexed | 2024-03-07T22:25:02Z |
| format | Article |
| id | doaj.art-ad626091f2b748f3806ebdf0e0361258 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-07T22:25:02Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-ad626091f2b748f3806ebdf0e03612582024-02-23T15:24:36ZengMDPI AGLife2075-17292024-01-0114219910.3390/life14020199Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy TransductionCharles W. Carter0Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USAHow Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with respect to hydrolysis. So, it requires some form of chemical free energy to drive it. Amino acid activation and acyl transfer are also slow and must be catalyzed. All living things must thus also convert free energy and synchronize cellular chemistry. Most importantly, functional proteins occupy only small, isolated regions of sequence space. Nature evolved heritable symbolic data processing to seek out and use those sequences. That system has three parts: a memory of how amino acids behave in solution and inside proteins, a set of code keys to access that memory, and a scoring function. The code keys themselves are the genes for cognate pairs of tRNA and aminoacyl-tRNA synthetases, AARSs. The scoring function is the enzymatic specificity constant, k<sub>cat</sub>/k<sub>M</sub>, which measures both catalysis and specificity. The work described here deepens the evidence for and understanding of an unexpected consequence of ancestral bidirectional coding. Secondary structures occur in approximately the same places within antiparallel alignments of their gene products. However, the polar amino acids that define the molecular surface of one are reflected into core-defining non-polar side chains on the other. Proteins translated from base-paired coding strands fold up inside out. Bidirectional genes thus project an inverted structural duality into the proteome. I review how experimental data root the scoring functions responsible for the origins of coding and catalyzed activation of unfavorable chemical reactions in that duality.https://www.mdpi.com/2075-1729/14/2/199aminoacyl-tRNA synthetase•tRNA cognate pairsbidirectional genetic codingprotein foldingAND gatingorigin of catalysisorigin of free-energy transduction |
| spellingShingle | Charles W. Carter Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction Life aminoacyl-tRNA synthetase•tRNA cognate pairs bidirectional genetic coding protein folding AND gating origin of catalysis origin of free-energy transduction |
| title | Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction |
| title_full | Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction |
| title_fullStr | Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction |
| title_full_unstemmed | Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction |
| title_short | Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction |
| title_sort | base pairing promoted the self organization of genetic coding catalysis and free energy transduction |
| topic | aminoacyl-tRNA synthetase•tRNA cognate pairs bidirectional genetic coding protein folding AND gating origin of catalysis origin of free-energy transduction |
| url | https://www.mdpi.com/2075-1729/14/2/199 |
| work_keys_str_mv | AT charleswcarter basepairingpromotedtheselforganizationofgeneticcodingcatalysisandfreeenergytransduction |