Abstract
We address the question of why the translation from nucleic acids to protein forming amino acids is carried out by triplets known as codons. We approach this problem from a dynamical point of view by considering the translocation properties of primitive molecular machines operating under prebiotic conditions [1 2 3 4]. Our model captures some basic ribosome-mRNA interaction features. We consider short chains of charged particles interacting with polymers via electrostatic forces, constrained to move in quasi one dimensional geometries, subject to external forcing. 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, traversing swiftly two monomers and lingering on the third one as in a waltz. This behavior is enhanced when we consider present day protein coding sequences. We also comment on noncoding sequences. We argue that this property could be one of the underlying causes for the three base codon structure of the genetic code.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
G. Martínez-Mekler, M. Aldana, F. Cázarez-Bush, R. Garcia-Pelayo, G. Cocho, Primitive molecular machine scenario for the origin of the three base codon compositionOrg Life Evol Bios29, 203–214 (1999).
M. Aldana, F. Cázarez-Bush, G. Cocho, G. Martínez-Mekler, Primordial synthesis machines and the origin of the genetic codePhysica A257, 119–127 (1998).
G. Martínez-Mekler, M. Aldana, G. Cocho, On the role of molecular machines in the origin of the genetic code, in “Statistical mechanics of biocomplexity: proceedings of the XV Sitges Conference, held at Sitges, Barcelona, Spain 812 June 1998”, editors D. Reguera, J.M.G. Vilar, J.M. Rubi, Springer VerlagLecture Notes in Physics527, 112–123 (1999).
M. Aldana-González, G. Cocho, H. Larralde and G. Martínez-Mekler, Translocation properties of primitive molecular machines and their relevance to the structure of the genetic codeJ. Theor. Biol.220, 27–45 (2003).
A.J. Doig, Inproving the efficiency of the genetic code by varying the codon length: the perfect genetic codeJ. Theor. Biol.188, 355–360 (1997).
P. Ehrenfreund et al., Astrophysical and astrochemical insights into the origin of lifeRep. Prog. Phys.65, 1427–1487 (2002).
Jr A.D. MacKerell, J. Wiórkiewicz-Kuczera, M. Karplus, An all-atom empirical energy function for the simulation of nucleic acidsJ. Am. Chem. Soc.117, 11946–11975 (1995).
B. Lewin, Genes VII, Oxford University Press (1999).
J. Frank, R.K. Agrawal, A ratchet-like inter-subunit reorganization of the ribosome during translocationNature405, 318–322 (2000).
M. Bier, Brownian ratchets in physics and biologyCont. Phys. 38(6)371379 (1997); F. Jülicher, A. Ajdari, J. Prost, Modeling molecular motorsRev. Mod. Phys.69(4), 1269–1281 (1997).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer Basel AG
About this paper
Cite this paper
Aldana-González, M., Cocho, G., Larralde, H., Martínez-Mekler, G. (2003). Polymer Transport in Random Potentials and the Genetic Code: The Waltz of Life. In: Iagolnitzer, D., Rivasseau, V., Zinn-Justin, J. (eds) International Conference on Theoretical Physics. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-7907-1_36
Download citation
DOI: https://doi.org/10.1007/978-3-0348-7907-1_36
Publisher Name: Birkhäuser, Basel
Print ISBN: 978-3-0348-9618-4
Online ISBN: 978-3-0348-7907-1
eBook Packages: Springer Book Archive