Related papers: Evolution of the genetic code. Emergence of stop c…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…
A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early…
Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
To synthesize peptides alongside the RNAs making the so-called RNA world, some genetic coding involving RNA had to develop. Herein, it is proposed that the first real-coding setup was a direct one, made up of continuous poly-tRNA-like…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the…
The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…
A simple explanation for the symmetry and degeneracy of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. This hypothesis offers explanations for: i) the difference between thymine and uracil,…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…