Related papers: Genetic code evolution as an initial driving force…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
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…
Programming languages are engineered languages that allow to instruct a machine and share algorithmic information; they have a great influence on the society since they underlie almost every information technology artefact, and they are at…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
What could cause the emergence of non-encoding codons in the course of evolution of the genetic code? Hypothesis of evolution of the genetic code from GC to the AGUC-alphabet account for existence of stop codons.
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
A molecular dynamics calculation of the amino acid polar requirement is presented and used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a…
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,…
The current theory of evolution is almost the one Darwin and Wallace proposed two centuries ago and the following discoveries e.g., Mendelian genetics and neutral mutation theory have not made significant modifications. The current…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
In a certain way, this paper presents the continuation of the previous one which discussed the harmonic structure of the genetic code (Rakocevic, 2004). Several new harmonic structures presented in this paper, through specific unity and…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The problem of the rate and mechanisms of biological evolution was considered. It was shown that species could not be formed due to undirected mutations in characteristic times of about one million years. A mechanism of deterministic…
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and…
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…