dorsal/arxiv
View SchemaTranslocation Properties of Primitive Molecular Machines and Their Relevance to the Structure of the Genetic Code
| Authors | Maximino Aldana, Germinal Cocho, Hernan Larralde, Gustavo Martinez-Mekler |
|---|---|
| Categories | |
| ArXiv ID | physics/0202056 |
| URL | https://arxiv.org/abs/physics/0202056 |
Abstract
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the translocation properties of primitive molecular machines, which capture basic features of ribosomal/messenger RNA interactions, while operating under prebiotic conditions. Our model consists of a short one-dimensional chain of charged particles(rRNA antecedent) interacting with a polymer (mRNA antecedent) via electrostatic forces. The chain is subject to external forcing that causes it to move along the polymer which is fixed in a quasi one dimensional geometry. Our numerical and analytic studies of statistical properties of random chain/polymer potentials suggest that, under very general conditions, a dynamics is attained in which the chain moves along the polymer in steps of three monomers. By adjusting the model in order to consider present day genetic sequences, we show that the above property is enhanced for coding regions. Intergenic sequences display a behavior closer to the random situation. We argue that this dynamical property could be one of the underlying causes for the three base codon structure of the genetic code.
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"abstract": "We address the question, related with the origin of the genetic code, of why\nare there three bases per codon in the translation to protein process. As a\nfollowup to our previous work, we approach this problem by considering the\ntranslocation properties of primitive molecular machines, which capture basic\nfeatures of ribosomal/messenger RNA interactions, while operating under\nprebiotic conditions. Our model consists of a short one-dimensional chain of\ncharged particles(rRNA antecedent) interacting with a polymer (mRNA antecedent)\nvia electrostatic forces. The chain is subject to external forcing that causes\nit to move along the polymer which is fixed in a quasi one dimensional\ngeometry. Our numerical and analytic studies of statistical properties of\nrandom chain/polymer potentials suggest that, under very general conditions, a\ndynamics is attained in which the chain moves along the polymer in steps of\nthree monomers. By adjusting the model in order to consider present day genetic\nsequences, we show that the above property is enhanced for coding regions.\nIntergenic sequences display a behavior closer to the random situation. We\nargue that this dynamical property could be one of the underlying causes for\nthe three base codon structure of the genetic code.",
"arxiv_id": "physics/0202056",
"authors": [
"Maximino Aldana",
"Germinal Cocho",
"Hernan Larralde",
"Gustavo Martinez-Mekler"
],
"categories": [
"physics.bio-ph",
"q-bio"
],
"title": "Translocation Properties of Primitive Molecular Machines and Their Relevance to the Structure of the Genetic Code",
"url": "https://arxiv.org/abs/physics/0202056"
},
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