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PubMed1988

Condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solutions.

The dehydration condensation of glycine with trimetaphosphate in aqueous solution has been reinvestigated. Although it has been reported that the condensation of glycine under the alkaline conditions was brought about through the formation of cyclic acylphosphoramidate and hence the condensation of polyglycines could not occur, we found that the condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solution are possible through the formation of their acylphosphates under the neutral or weak acidic conditions. Aqueous solutions of 1.0 M glycylglycine and 1.0 M trimetaphosphate in the various pH from 4.0 to 9.0 were incubated at 38 degrees C. The solutions were analyzed by HPLC with ninhydrin reaction system. Tetraglycine and hexaglycine were detected and their maximum yields were given in the reaction carried out around pH 7. They are approximately 15% and 4% after 30 days, respectively. Analogous experiments were performed with tetrametaphosphate. The results showed a similar pH dependence for the condensation, but the yields were about one-tenth of those of corresponding experiments with trimetaphosphate. Relative rates of dimerization of glycine, diglycine and triglycine in the equimolar concentration were also investigated at pH 6.0 at 38 degrees C. The rates for diglycine and triglycine were approximately twice and four times as large as that for glycine. Relevance of the experiments to chemical evolution is discussed.

Chemical Phenomena↗
PubMedDate not supplied

[Critical phenomena, phase equilibria, and the temperature and structural optimum of homeostasis, as revealed by a model system water-biopolymer-electrolyte].

Equations of spinodal and two quasispinodals corresponding to critical and supercritical phase transitions leading to a rise of different dynamic structures of solution in the phase diagram of a model system water-biopolymer-electrolyte were obtained. The section of the phase diagram was considered where there exists the probability of quasi-equilibrium monomer-cluster and the principle of water-ion homeostasis is realized. Based on these results, a possible mechanism of origination of unspecific adaptation reactions of a biomolecular system at the stage of chemical evolution was suggested.

Biopolymers↗
PubMed2004

Theoretical model of interfacial polymerization.

We present a theoretical description for the creation of a thin polymeric layer through the interfacial polymerization of two immiscible, low molecular weight liquids. The theory specifically takes into account the effects of polydispersity on the formation of the polymer film at the liquid-liquid interface. Consequently, we can describe the structure of the growing film and the molecular weight distribution of the resultant polymer chains. We focus on a model system where alternating AB copolymers are formed at the interface between phase-separated, low molecular weight species A and B. It is assumed that any A(B) unit can reversibly attach to any available B(A) unit or B(A)-ended chain. The formation of the copolymer layer is described by a system of reaction-diffusion equations, which detail the chemical evolution and diffusive dynamics of the polydisperse mixture of AB copolymers around the interface, and the evolution of the interface itself. Using this model, we determine the effects of the chemical reaction rates and the initial conditions on the kinetics of forming the AB copolymer layer and the structure of this film.

Journal Article↗
PubMed1998

Biomimicry as a basis for drug discovery.

Selected works are discussed which clearly demonstrate that mimicking various aspects of the process by which natural products evolved is becoming a powerful tool in contemporary drug discovery. Natural products are an established and rich source of drugs. The term "natural product" is often used synonymously with "secondary metabolite." Knowledge of genetics and molecular evolution helps us understand how biosynthesis of many classes of secondary metabolites evolved. One proposed hypothesis is termed "inventive evolution." It invokes duplication of genes, and mutation of the gene copies, among other genetic events. The modified duplicate genes, per se or in conjunction with other genetic events, may give rise to new enzymes, which, in turn, may generate new products, some of which may be selected for. Steps of the inventive evolution can be mimicked in several ways for purpose of drug discovery. For example, libraries of chemical compounds of any imaginable structure may be produced by combinatorial synthesis. Out of these libraries new active compounds can be selected. In another example, genetic system can be manipulated to produce modified natural products ("unnatural natural products"), from which new drugs can be selected. In some instances, similar natural products turn up in species that are not direct descendants of each other. This is presumably due to a horizontal gene transfer. The mechanism of this inter-species gene transfer can be mimicked in therapeutic gene delivery. Mimicking specifics or principles of chemical evolution including experimental and test-tube evolution also provides leads for new drug discovery.

Algorithms↗
PubMed1999

Thermodynamics in the present progressive mode and its role in the context of the origin of life.

The origin and evolution of biological organizations proceeding on Earth are put in a nonequilibrium thermodynamic framework within a cosmological context. The dynamic process responsible for chemical evolution leading to the origin of biological being depends upon consumer-dominating thermodynamics, in which the heat sink is taken to be active in extracting heat energy from a body at a higher temperature. Consumer-dominating thermodynamics follows from the fact that when a small hot body contacts a cold heat sink, it decreases the temperature at the possible fastest rate. The fastest temperature drop, when applied to chemical products being synthesized through the energy supplied from an external heat source, is selective in keeping only those products that can decrease the temperature at the fastest rate among the available alternatives. Synthesis of small organic molecules in the small ice grains in interstellar diffuse clouds irradiated by ultraviolet radiation is a representative case of consumer-dominating thermodynamics, in which diffuse clouds serve as cold heat sinks in the cosmological context. Another case of consumer-dominating thermodynamics predominant on Earth especially in the perspective of the origin and evolution of life is with submarine hydrothermal vents, in which the surrounding cold seawater constantly serves as the cold heat sink.

Biological Evolution↗
PubMed1963

On biochemical variability and innovation.

Examples of variability and apparent innovation presented in this paper are but a portion of the many examples in the literature. Thus, the notion of the "unity of biochemistry" has been advanced in an overly simplified form and reflects a primitive stage in the development of the discipline. Cells contain many more compounds and biosynthetic mechanisms than we had suspected or list in our texts. Accordingly, either early chemical evolution was far more extensive than we have postulated or an evolution of biochemical synthesis and function took place which was more extensive than has been postulated; perhaps both have occurred. The chemical choices available from the environment have been considerable rather than limited and the cells have chosen, adapted, improved upon a limited number of these, and in turn have themselves been selected. In the case of the naturally occurring antibiotic substances, biosynthetic mechanisms for compounds which do not fit within the cells' own nucleic acids and proteins to advantage have nevertheless been preserved since they contribute to survival. On the other hand, some of these compounds such as alpha-ribazole, are fitted to other metabolic uses. The existence of the large number of uncommon relatives of the common components of the nucleic acids and proteins in turn implies an enormous untapped area of potential knowledge concerning their paths of biosyntheses and the genetic and physiological controls for these same paths. That these compounds exist perhaps also indicates an expanded material basis for a continuing biochemical evolution.

Biochemical Phenomena↗
PubMed2006

The stepwise evolution of early life driven by energy conservation.

Two main theories have emerged for the origin and early evolution of life based on heterotrophic versus chemoautotrophic metabolisms. With the exception of a role for CO, the theories have little common ground. Here we propose an alternative theory for the early evolution of the cell which combines principal features of the widely disparate theories. The theory is based on the extant pathway for conversion of CO to methane and acetate, largely deduced from the genomic analysis of the archaeon Methanosarcina acetivorans. In contrast to current paradigms, we propose that an energy-conservation pathway was the major force which powered and directed the early evolution of the cell. We envision the proposed primitive energy-conservation pathway to have developed sometime after a period of chemical evolution but prior to the establishment of diverse protein-based anaerobic metabolisms. We further propose that energy conservation played the predominant role in the later evolution of anaerobic metabolisms which explains the origin and evolution of extant methanogenic pathways.

Acetates↗
PubMed2000

Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies.

Mutually catalytic sets of simple organic molecules have been suggested to be capable of self-replication and rudimentary chemical evolution. Previous models for the behavior of such sets have analyzed the global properties of short biopolymer ensembles by using graph theory and a mean field approach. In parallel, experimental studies with the autocatalytic formation of amphiphilic assemblies (e.g., lipid vesicles or micelles) demonstrated self-replication properties resembling those of living cells. Combining these approaches, we analyze here the kinetic behavior of small heterogeneous assemblies of spontaneously aggregating molecules, of the type that could form readily under prebiotic conditions. A statistical formalism for mutual rate enhancement is used to numerically simulate the detailed chemical kinetics within such assemblies. We demonstrate that a straightforward set of assumptions about kinetically enhanced recruitment of simple amphiphilic molecules, as well as about the spontaneous growth and splitting of assemblies, results in a complex population behavior. The assemblies manifest a significant degree of homeostasis, resembling the previously predicted quasi-stationary states of biopolymer ensembles (Dyson, F. J. (1982) J. Mol. Evol. 18, 344-350). Such emergent catalysis-driven, compositionally biased entities may be viewed as having rudimentary "compositional genomes." Our analysis addresses the question of how mutually catalytic metabolic networks, devoid of sequence-based biopolymers, could exhibit transfer of chemical information and might undergo selection and evolution. This computed behavior may constitute a demonstration of natural selection in populations of molecules without genetic apparatus, suggesting a pathway from random molecular assemblies to a minimal protocell.

Catalysis↗
PubMed1988

Historical perspective: the problem of the origin of life in the context of developments in biology.

The structure of the history of scientific ideas on the origin of life, after Darwin's theory of evolution brought the problem into focus, is discussed. 19th-century theories in the mainstream of historical development already included some notion of chemical evolution. These theories were limited, however, by their reliance on a protoplasmic view of life, according to which the protoplasmic substance combines all vital properties. It was only when this holistic concept of protoplasm was abandoned that a clear distinction between different vital functions such as metabolism and replication was made. This led to two schools of thought in the origin of life field, one inspired by biochemistry and one by genetics. Oparin's theory, which was rooted in the metabolic traditions of biochemistry, provided a model which has had a lasting impact in methodological terms and which helped to transform the field from a largely theoretical one to an area of active research. Genetically based theories, on the other hand, had a delayed impact in this respect, because of long-lasting uncertainty regarding the structural basis of gene function.

Genes↗
PubMed2002

Glycine and diglycine as possible catalytic factors in the prebiotic evolution of peptides.

Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.

Catalysis↗
PubMed1979

The effect of clays on the oligomerization of HCN.

The reaction of 0.1 M HCN and dilute solutions of diaminomaleonitrile (DAMN) at pH 8--9 and 25 degrees C in the presence of suspensions of montmorillonite (bentonite) clays were investigated. Montmorillonite clays inhibit the oligomerization of aqueous solutions of HCN. Yields of colored oligomers, ura, and DAMN, are all diminished by clays, but the rate of loss of cyanide is not significantly decreased. The inhibition of oligomer formation is due to the clay-catalyzed decomposition of DAMN. The absence of strong binding of DAMN to clays was suggested by our failure to detect DAMN when a clay that had been incubated with DAMN was washed with spermidine (6 x 10(-3) g/liter). It was established that DAMN does not simply bind to the clays by the observation that the bulk of the radioactivity was recovered from the supernatant in the reaction of 14C-DAMN with montmorillonite. The clay-catalyzed decomposition of DAMN was observed when montmorillonite from two different sources was used and with a variety of homoinic montmorillonites and bentonites. A modification of the established procedure for using the cyanide electrode for cyanide analyses was used to follow the release of HCN from DAMN. This new method can be used in both the acidic and basic pH range and it does not result in the destruction of DAMN by the reagents used for the analysis. Quantitative analyses of the reaction solution from the clay-catalyzed decomposition of DAMN revealed the formation of 1--2 equivalents of HCN per mole of DAMN. The possible significance of these clay-catalyzed reactions in chemical evolution is discussed.

Bentonite↗
PubMed1993

What can meteorites tell us about nebular conditions and processes during planetesimal accretion?

Analysis of the most primitive meteorites can yield detailed information about environmental conditions and physical/chemical processes in the earliest Solar System, including the nebular stage during which planetesimals were accreted. Such information pertains to time scales, thermal and chemical evolution, inhomogeneity and mixing, magnetic fields, and grain growth in the solar nebula. Nebular processes identified include evaporation, condensation, localized melting, and fractionation both of solids from gas and among different solids. Little direct evidence remains even in primitive meteorites of the actual accretion process. The absence of intrinsic factors capable of enhancing accretion among meteoritic constituents suggests that gravitational instabilities might have been important in promoting planetesimal accretion.

Chemical Phenomena↗
PubMed1978

Current status of space medicine and exobiology.

An overview of the present state of aerospace medicine and planetary biology is given with emphasis on the ongoing search for extraterrestrial life and life science studies being made both by independent and cooperative investigations of the United States, the Soviet Union, the European Space Agency, and countries with an interest in gravitational physiology, radiation, planetary quarantine, exobiology, and general space biology. A suitable animal model for outer space medical research, in-orbit vestibular function investigations, biomedical problems in the Earth's normal 1-G gravitational intensity, and biological satellite experiments are discussed. The scope of exobiology, life detection programs, solar system organic chemistry, and attempted elucidation of the question of the origin and early evolution of life are also discussed. Evaluation of data acquired from a variety of sources indicates that all phases of exobiology lead to biopoesis and chemical evolution, with allied aviation, space, and environmental medicine being the major part of the search for extraterrestrial life.

Arrhythmias, Cardiac↗
PubMed2002

The evolution of multicomponent systems at high pressures: VI. The thermodynamic stability of the hydrogen-carbon system: the genesis of hydrocarbons and the origin of petroleum.

The spontaneous genesis of hydrocarbons that comprise natural petroleum have been analyzed by chemical thermodynamic-stability theory. The constraints imposed on chemical evolution by the second law of thermodynamics are briefly reviewed, and the effective prohibition of transformation, in the regime of temperatures and pressures characteristic of the near-surface crust of the Earth, of biological molecules into hydrocarbon molecules heavier than methane is recognized. For the theoretical analysis of this phenomenon, a general, first-principles equation of state has been developed by extending scaled particle theory and by using the technique of the factored partition function of the simplified perturbed hard-chain theory. The chemical potentials and the respective thermodynamic Affinity have been calculated for typical components of the H-C system over a range of pressures between 1 and 100 kbar (1 kbar = 100 MPa) and at temperatures consistent with those of the depths of the Earth at such pressures. The theoretical analyses establish that the normal alkanes, the homologous hydrocarbon group of lowest chemical potential, evolve only at pressures greater than approximately 30 kbar, excepting only the lightest, methane. The pressure of 30 kbar corresponds to depths of approximately 100 km. For experimental verification of the predictions of the theoretical analysis, a special high-pressure apparatus has been designed that permits investigations at pressures to 50 kbar and temperatures to 1,500 degrees C and also allows rapid cooling while maintaining high pressures. The high-pressure genesis of petroleum hydrocarbons has been demonstrated using only the reagents solid iron oxide, FeO, and marble, CaCO3, 99.9% pure and wet with triple-distilled water.

Carbon↗
PubMed1999

Evolution of Dust Extinction and Supernova Cosmology.

We have made a quantitative calculation for the systematic evolution of the average extinction by interstellar dust in host galaxies of high-redshift Type Ia supernovae by using a realistic model of photometric and chemical evolution of galaxies and supernova rate histories in various galaxy types. We find that the average B-band extinction at z approximately 0.5 is typically 0.1-0.2 mag larger than the present value, under a natural assumption that dust optical depth is proportional to gas column density and gas metallicity. This systematic evolution causes average reddening with E(B-V&parr0; approximately 0.025-0.05 mag with the standard extinction curve, and this is comparable with the observational uncertainty of the reddening of high-redshift supernovae. Therefore, our result does not contradict the observations that show no significant reddening in high-z supernovae. However, the difference in apparent magnitude between an open universe and a Lambda-dominated flat universe is only approximately 0.2 mag at z approximately 0.5, and hence this systematic evolution of extinction should be taken into account in a reliable measurement of cosmological parameters. Considering this uncertainty, we show that it is difficult to discriminate between open and Lambda-dominated flat cosmologies from the current data.

Journal Article↗
PubMed1995

[The origin and early development of biological catalysts].

Biochemical processes are based on the catalytic activity of enzymes. Highly ordered stereometry of protein macromolecules perfectly adapted to fyziological function of enzymes is the result of a long evolution. Catalytic processes, e.g. inorganic catalysis on the surface of cosmic dust grains, or on the surface of clay particles on the Earth, occurred as early as during chemical evolution. Enzyme predecessors in prebiotic systems-probably, thermal polymers of amino acids (proteinoids)-were polyfunctional catalysts. Low-effective proteinoids have been replaced by the highly efficient and specific enzymes in the course of evolution; spatial and temporal co-ordination of the individual enzymes has developed instead of the proteinoid polyfunctionality. The comprehensive effect of the mixtures of hydrolytic enzymes in systemic enzyme therapy can be regarded as a as a sort of reflection of these evolutionary trends.

Catalysis↗
PubMed1975

Origin and early evolution of transition element enzymes.

In this paper we speculate on the origin and early evolution of transition element enzymes. Iron, molybdenum, and zinc, the most abundant transition elements in seawater, presumably complexed with compounds accumulated in the primeval sea in the course of chemical evolution forming compounds with subsequently evolved to form proenzymes or early enzymes with low activity and broad specificity. Iron complexes may be regarded as precursors of electron transfer enzymes, molybdenum complexes as precursors of enzymes involved in the metabolism of small molecules, and zinc complexes as precursors of hydrolytic and transferring enzymes, including enzymes participating in the metabolism of macromolecules and information transfer. The different iron, molybdenum, and zinc enzymes found in bacteria including Clostridium may then have arisen through specialization by increases in the enzyme specificity of these proenzymes. Copper would have been incorporated as an enzyme constituent after the elevation of environmental redox potential, probably due to the accumulation of atmospheric oxygen.

Aerobiosis↗