To Understand Nature - Computer Modelling between Genetics and Evolution

TL;DR

This paper explores the molecular mechanisms of genetic information transfer, DNA replication asymmetry, and the role of the genetic code in evolution, supported by Monte Carlo simulations and genomic data analysis.

Contribution

It introduces a novel simulation approach linking DNA replication asymmetry to genome structure and evolution, bridging molecular biology and computational modeling.

Findings

Asymmetric DNA replication influences genome organization and gene function.

Genetic code minimizes amino acid changes despite nucleotide substitutions.

Simulation results align with genomic and proteomic data analyses.

Abstract

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have described the differences of mutational pressure connected with replication of the leading and lagging DNA strands. We have shown how the asymmetric replication of DNA affects the structure of genomes, positions of genes, their function and amino acid composition. Results of Monte Carlo simulations of evolution of protein coding sequences have shown a specific role of genetic code in minimizing the effect of nucleotide substitutions on the amino acid composition of proteins. The results of simulations were compared with the results of analyses of genomic and proteomic data bases. This chapter is considered as an introduction to further chapters where chromosomes with genes represented by nucleotide sequences were replaced by bitstrings with single bits representing genes.