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At least 631 records · Page 35Linked to original sources
PubMed2001

Why genetic information processing could have a quantum basis.

Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimization criteria in this information processing can be searched for using the laws of physics. Quantum dynamics can explain why living organisms have 4 nucleotide bases and 20 amino acids, as optimal solutions of the molecular assembly process. Experiments should be able to tell whether evolution indeed took advantage of quantum dynamics or not.

Animals↗
PubMed1998

Biased usages of arginines and lysines in proteins are correlated with local-scale fluctuations of the G + C content of DNA sequences.

Amino acid residues arginine (R) and lysine (K) have similar physicochemical characteristics and are often mutually substituted during evolution without affecting protein function. Statistical examinations on human proteins show that more R than K residues are used in the proximity of R residues, whereas more K than R are used near K residues. This biased use occurs on both a global and a local scale (shorter than approximately 100 residues). Even within a given exon, G + C-rich and A + T-rich short DNA segments preferentially encode R and K, respectively. The biased use of R and K on a local scale is also seen in Saccharomyces cerevisiae and Caenorhabdidtis elegans, which lack global-scale mosaic structures with varying GC%, or isochores. Besides R and K, several amino acids are also used with a positive or negative correlation with the local GC% of third codon bases. The local-, or "within-gene"-, scale heterogeneity of the DNA sequence may influence the sequence of the encoded protein segment.

Amino Acid Substitution↗
PubMed2006

What is a gene? From molecules to metaphysics.

Mendelian genes have become molecular genes, with increasing puzzlement about locating them, due to increasing complexity in genomic webworks. Genome science finds modular and conserved units of inheritance, identified as homologous genes. Such genes are cybernetic, transmitting information over generations; this too requires multi-leveled analysis, from DNA transcription to development and reproduction of the whole organism. Genes are conserved; genes are also dynamic and creative in evolutionary speciation-most remarkably producing humans capable of wondering about what genes are.

Adaptation, Biological↗
PubMed1990

Development of a spin-glass model of prebiotic evolution: environmental effects on ensembles of genetic polymers.

We develop in two ways an existing spin-glass model of prebiotic polymer evolution. First, by choosing the environment J in a prescribed manner, similar to neural network presciptions, we may create an environment which favors a linearly independent set of evolutionary niches (Ea). That is, we may control which polymer "species" will evolve in our system. Computer simulations confirm this result. We obtain a quantitative value for the sharpness of a niche. Second, we extend the model by allowing a surviving polymer to act upon--to "remold"--its environment; the nature of the environmental action is governed by the "molding" matrix M. When the mold M is the identity matrix, the feedback algorithm reduces to a Hebb learning algorithm form, and a surviving polymer acts to enhance its own survival prospects. Molds having a structure analogous to (temporal) associative memories in neural networks can generate autocatalytic species or can exhibit symbiotic interspecies relationships.

Biological Evolution↗
PubMed1997

Zinc-dependent tRNA binding by a peptide element within a tRNA synthetase.

The class I aminoacyl-tRNA synthetases are defined by an N-terminal nucleotide binding fold that contains the active site for adenylate synthesis. Insertions and additions of idiosyncratic RNA binding elements that facilitate docking of the L-shaped tRNA structure are superimposed onto this basic fold. These RNA binding elements are imagined to have been acquired during the evolution and development of the modern genetic code. The monomeric Escherichia coli isoleucyl-tRNA synthetase has a zinc-containing peptide at its C terminus. Removal of the zinc-containing peptide was shown previously to create a shortened enzyme with activity for adenylate synthesis but no detectable binding to tRNA(Ile). We show here that the isolated zinc-containing peptide binds to tRNA with relatively low affinity. This binding is not tRNA-specific but shows a strict requirement for zinc. In contrast, the zinc-containing peptide conferred specific and high-affinity binding when combined with the shortened enzyme. Thus, when combined with another protein, a nonspecific tRNA binding peptide is essential for formation of a high-affinity and specific tRNA binding site. These results demonstrate the feasibility of the idea that noncovalent complexes of general RNA-binding peptides with a domain for adenylate synthesis were precursors to modern tRNA synthetases. In addition, the results offer the first direct evidence of a role for zinc in the tRNA-binding activity of one of these peptide elements.

Amino Acid Sequence↗