Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.

Peter R Wills,Charles W Carter

doi:10.3390/ijms21197392

Abstract

We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, Iσ; an impedance parameter, Z; and an effective alphabet size, neff; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small.

Highlights

One of the impenetrable questions about biological evolution is how and why it is “open ended”
We show that three types of dissipative losses in information have a similar formal structure to dissipative energy losses in engineering, and that in the course of building the standard genetic code, information dissipation was converted, via evolutionary changes, into dissipative losses in chemical free energy, leading to enhanced fidelity
The energy directly expended attaching an amino acid to a growing peptide chain is, to a first approximation and in the absence of specific editing, independent of whether it is correctly or erroneously matched to the mRNA codon coupled to the tRNA occupying the A site of the ribosome. Hydrolytic expenditure of both phosphates of ATP is required to attach an amino acid directly to a tRNA and expenditure of a further two high energy phosphates is required to transfer the amino acid to the nascent peptide at the ribosomal peptidyl transfer center, i.e., hydrolysis of a total of 4 ATP molecules [34]. (We introduce the additional cost of editing steps in Figure 1 and discuss it further below in Section 3.4.) any difference between the Shannon information content of genes and proteins arises from the differences in the relative frequencies of monomers, nucleotides in genes and amino acids in proteins

Summary

Introduction

One of the impenetrable questions about biological evolution is how and why it is “open ended”. Systems of ever-increasing complexity appear and open up completely new possibilities of function, interaction and organized system structure. Nowhere is this more evident than at the origin of life, when functional molecular inheritance and translation systems, whose symbolic relationships could be used to write and read their own self-description, emerged from initial, high-temperature chemical disorder, presumably rather rapidly. Functionally organized arrangement, typical of the nanoscale dynamic structure of living cells, first maintain itself and stave off the disrupting effects of thermal molecular activity?. Recent results facilitate serious investigation of these issues [2,3,4,5]

Results

Discussion

Conclusion