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PubMed2006

The chemistry of life's origin: a carbonaceous meteorite perspective.

Carbonaceous chondrite meteorites are primitive asteroidal fragments that contain organic carbon and offer a glimpse of the abiotic chemical processes that preceded the onset of life. Their organic material displays structures as diverse as kerogen-like macromolecules and simpler soluble compounds that range from polar amino acids and polyols to nonpolar hydrocarbons. Several of these compounds have identical counterparts in terrestrial biomolecules and some of the amino acids show a unique l-asymmetry, suggesting their possible contribution to terrestrial molecular evolution and the origin of biological homochirality.

Amino Acids↗
PubMed1980

Bile salts of frogs: a new higher bile acid, 3 alpha, 7 alpha, 12 alpha, 26-tetrahydroxy-5 beta-cholestanoic acid from the bile Rana plancyi.

Bile salts of ten species of frogs of the family Ranidae were examined by means of thin-layer chromatography, gas-liquid chromatography, and gas-liquid chromatography-mass spectrometry. Their major bile alcohols were ranol, cyprinol, or bufol. Four species of frogs contained lesser amounts of higher bile acids, and in two species C24 bile acids were present. A higher bile acid that has not been previously described was detected in Rana plancyi. On the basis of the spectral data and the direct comparison with a synthetic sample, the chemical structure of the new bile acid was established to be 3 alpha, 7 alpha, 12 alpha, 26-tetrahydroxy-5 beta-cholestanoic acid.

Animals↗
PubMed1985

Double nondisjunction during karyotypic progression of chemically induced Syrian hamster cell lines.

The karyotypic evolution of three chemically induced cell lines of Syrian hamster embryo in culture are described. The only karyotypic alteration of one clone was a trisomy of chromosome #11, which presumably arose by nondisjunction after carcinogen treatment. A pure population of cells with the trisomy was observed repeatedly upon karyotyping of cells at the first three passages after cloning. However, at a late passage, apparently normal diploid cells appeared in the culture, which we propose resulted from a second nondisjunction of one chromosome #11, reverting the cells from trisomy 11 to disomy 11. The karyotypic evolution of two other cell lines also involved double nondisjunction, which resulted in duplication of a translocated chromosome and concurrent loss of the normal nonrearranged chromosome. Taken together with the reported findings of others, the results indicate that double nondisjunction is a mechanism in karyotypic progression during neoplastic development.

Animals↗
PubMed2005

Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assemblies.

The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly's composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a 'monomer world' towards polymer-based living entities. We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a 'scaffold' for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer 'take-over' - the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.

Computer Simulation↗
PubMed1995

A study of chemical systems using signal flow graph theory.

Photochemistry of giant planets and their satellites is characterized by numerous reactions involving a lot of chemical species. In the present paper, chemical systems are modeled by signal flow graphs. Such a technique evaluates the transmission of any input into the system (solar flux, electrons ... ) and gives access to the identification of the most important mechanisms in the chemical system. This method is applied to the production of hydrocarbons in the atmospheres of giant planets. In particular, the production of C2H6 in the atmosphere of Neptune from the photodissociation of CH4 is investigated. Different pathways of dissociation of CH4 are possible from L alpha radiation. A chemical system containing 14 species and 30 reactions including these different pathways of dissociation is integrated. The main mechanism of production of C2H6 is identified and evaluated for each model of dissociation. The importance of various reaction pathways as a function of time is presented.

Ethane↗
PubMed2005

A model for the role of short self-assembled peptides in the very early stages of the origin of life.

The molecular basis of the origin of life is one of the most fundamental questions in modern biology. While the "RNA world" hypothesis offers a very sensible model for the evolvement of the current biochemical networks, there is a lack of knowledge about the early steps that led to the formation of the first RNA molecules. This issue is essential as it is practically impossible that complex molecules as functional RNA oligonucleotides had evolved spontaneously. It was recently demonstrated that peptide molecules as simple as dipeptides can self-assemble into well-ordered tubular, fibrilar, and closed-cage structures. Other studies have confirmed the ability of dipeptides to act as catalysts and the capability of other peptides, as short as tripeptides, to serve as a template for nucleotide binding and orientation. Unlike complex RNA molecules, the spontaneous formation of functional short peptides in the primordial earth conditions is very likely. We suggest a novel mechanism for the origin of life that is based on the ability of short peptides to form encapsulated structures, catalyst chemical reaction, and serve as highly ordered template for the assembly of nucleotides. This model may explain the early events that led to the formation of the current biochemical machinery that combines the elaborated and coordinated interaction between nucleic acids and proteins to allow the function of living systems.

Animals↗
PubMedDate not supplied

[Physico-chemical basis of the genetic code origin: stereochemical analysis of interactions of amino acids and nucleotides based on the progene hypothesis].

A progene hypothesis has been proposed earlier to explain the mechanism of origin of the self-reproducing genetic system. Progenes (precursors of the genetic system) are mixed anhydrides of an amino acid and deoxyribotrinucleotide at the 3'-gamma-terminal phosphate (NpNpNppp-AA); they are produced from dinucleotides (NpNp) and 3'-gamma-aminoacylnucleotidylates (Nppp-AA) as a result of specific interaction between amino acid and dinucleotide. The postulated mechanism of progene formation accounts for the selection of substances, including chirality, the origin of the genetic code as well as for the mechanisms of formation, self-reproduction and evolution of the simpliest genetic system ("gene--polypeptide"). A stereochemical analysis of the progene formation mechanism has allowed us to support the main statements of the hypothesis that relate to the origin of the genetic code and to selection of substances. Atomic groups that could be responsible for the specificity of interaction between dinucleotides and amino acids in progene formation have been revealed. Stereochemical evidence for the physicochemical basis of the origin of the existing genetic code have been produced: 1) a special role of the second nucleotide in the codon is demonstrated in amino acid coding by the progene hypothesis principle; 2) an advantage of T against U in such coding is demonstrated; 3) for 16 amino acids out of 20 an agreement has been obtained between the optimal dinucleotide as revealed by the stereochemical analysis and the codon dinucleotides; 4) an explanation for the third nucleotide selection mechanism is offered. A restoration of the prebiotic code, based on these results, has indicated that the code contains 32 codons, is statistical and group-wise. It encodes 7 groups of isofunctional amino acids: 3 overlapping groups of non-polar amino acids 1) medium-size hydrophobic amino acids (chiefly Val, n-Val and a-But), 2) small and medium-size non-polar amino acids (chiefly Ala Val, n-Val a-But and Gly), 3) small non-polar amino acids (Gly, Ala, a-But) and 4 groups of polar amino acids--1) hydroxy--+dicarbonic (Asp, Glu, Ser and Thr), 2) dicarbonic (Asp and Glu), 3) hydroxy (Ser and Thr) and 4) basic (Arg and Lys). The code includes about 20 amino acids among which are 15-17 canonical and a few common non-canonical. The prebiotic code explains many properties of the existing genetic code and is capable of evolving into the latter by way of a gradual replacement of the physicochemical coding mechanism by the enzymatic coding mechanism.

Amino Acids↗
PubMedDate not supplied

[Change in the chemical sensitivity of the visual cortical synapses in rabbit ontogeny].

In experiments on newborn rabbits under nembutal (pentobarbital) anaesthesia, studies have been made on changes of visual evoked potential in the visual cortex during application of 1% solutions of GABA and nembutal. At the age of 7--9 days, these drugs decreased the evoked response, which may be associated with their hyperpolarizing effect on cortical synapses. Between the 11th and the 13th days, no effect of GABA and nembutal upon the evoked potential was noted. Definitive reaction to application of these pharmacological drugs typical for adult animals is formed not earlier than to the 15th--17th day. Beginning from this time, application of GABA and nembutal significantly increases visual evoked potential. The postnatal evolution of chemical sensitivity of postsynaptic membrane of neurons of the visual cortex in rabbits is discussed.

Animals↗
PubMed1987

Isotopic characterisation of kerogen-like material in the Murchison carbonaceous chondrite.

Isotopic data for C, H and N in acid-resistant residues from carbonaceous chondrites show substantial variability during stepwise pyrolysis and/or combustion. After subtraction of contributions due apparently to inorganic C grains, of probably circumstellar origin, considerable isotopic variability remains, attributable to the kerogen-like organic fraction. That variability may be interpreted in terms of three or four distinct components, based on C, H and N isotopes. The relative proportions of those components vary significantly from sample to sample. The different isotopic components are tentatively identified in terms of specific chemical/structural moieties within the kerogen-like material. This combination of chemical, structural and isotopic information suggests a complex for meteoritic organic matter. At least three components within the organic populations as a whole still carry a signature of apparently interstellar D-enrichment. Part, at least, of the interstellar carrier consisted of reactive entities, not solely polymers.

Carbon↗
PubMed1992

Heteronuclear X-Y double quantum MAS NMR in crystalline inorganic solids. Applications for indirect detection and spectral editing of rare-spin resonances.

Heteronuclear double quantum MAS NMR experiments in the solid state, involving pairs of highly abundant 31P spins and the rare spins 113Cd, 77Se, and 29Si, are described for the three crystalline compounds CdSiP2, CdGeP2, and Ag7PSe6. These experiments offer the opportunity of indirectly detecting the rare-spin resonance via chemical shift evolution of heteronuclear double quantum coherence. For suitable cases, this method results in significantly enhanced detection sensitivities. Criteria for favorable indirect detection experiments are established. Besides offering high sensitivity, the pulse sequence also acts as a heteronuclear double quantum filter, hence providing heteronuclear correlation and useful spectral editing for peak assignments.

Cadmium↗
PubMed1987

Chemistry and biochemistry of metallothionein.

A wealth of chemical, spectroscopic and structural data attest to the uniqueness of the metallothioneins as a group of novel bioinorganic structures. Their earmarking feature is the arrangement of "soft" metal ions in complexes with cysteine side chains to form discrete metal-thiolate clusters. In this review an account is given of the chemical characteristics of the 52 metallothioneins whose primary structures are now known completely or in part. Also included is an up-to-date summary of the spectroscopic properties and of the spatial structure models derived from X-ray diffraction crystallographic analysis and from two-dimensional nuclear magnetic resonance spectroscopy.

Amino Acid Sequence↗
PubMed2006

A plausible prebiotic synthesis of pyridoxal phosphate: vitamin B6 - a computational study.

A set of chemical reactions is proposed to account for the formation of pyridoxal phosphate, Vitamin B6, from a primeval atmosphere composed of cyanoacetylene, diacetylene, carbon monoxide, hydrogen, water, and a phosphoric acid. The reactions have been shown to be feasible from the overall enthalpy changes in the ZKE approximation at the HF and MP2/6-31G* level.

Acetylene↗
PubMed1980

The contribution of cometary volatiles to the primitive Earth.

It has been estimated that during its early history the Earth captured a mass of cometary material of the order of 10(23) grams. Since carbon is supposed to be at least three times more abundant in comets than in carbonaceous chondrites (3.5% C in C 1 chondrites), it can be deduced that about 1 x 10(22) grams of carbon (as carbon compounds), was added by comets to the surface of the prebiotic Earth. This carbon value is of the same order of magnitude as the value of the organic carbon buried in the Earth's sedimentary shell, but approximately one order of magnitude lower than the Earth's surface total carbon (7 x 10(22) gm). The capture of comets by the Earth would also have contributed to generating the appropriate aqueous and reducing environmental conditions necessary for organic synthesis. Although it is possible that some of the cometary carbon compounds falling on the Earth survived, most of them were probably decomposed by the heat and shock waves of the cometary collision. Upon quenching to low temperatures, however, the reactive chemical species produced by the impact would have recombined, leading to the synthesis of a great variety of organic molecules. Laboratory experiments with radiation, heat and shock waves have demonstrated that some of the synthesized compounds are biochemical molecules: amino acids, sugars, purines, and pyrimidines. These are essential to all living systems.

Carbon↗
PubMed1995

Dust in the Universe: implications for terrestrial prebiotic chemistry.

In the present review we analyze the available literature on the distribution of dust in the Universe, methods of its observation and determination of the chemical composition, and the roles for terrestrial prebiotic chemistry. The most plausible natural sources of dust on the Earth in the prebiotic era are sedimentation of interplanetary dust, meteoritic and cometary impacts, volcanic eruptions, and soil microparticulates; the interplanetary medium being among the most powerful supplier of the dust matter. Two fundamental roles of dust particles for the origins of life are considered: (1) catalytic formation of prebiotic compounds; and (2) delivery of organic matter to the Earth by space dust particles. Due to the fact that there is only approximate information on the chemical composition and properties of interstellar, circumstellar, and major part of interplanetary dust, even the simulating experiments are difficult to perform. Until these gaps are filled, it seems reasonable to focus efforts of the scientists dealing with dust-driven catalytic formation of prebiotically important compounds on the volcanic and meteoritic/cometary impact environments.

Cosmic Dust↗
PubMed2004

Evolution of dietary specialization and chemical defense in poison frogs (Dendrobatidae): a comparative analysis.

Defensive mechanisms, including noxious or toxic substances, are favored by predation-driven natural selection. The acquisition of noxious/toxic substances can be either endogenous, in which the substances are produced by the organism, or exogenous, in which the substances are produced by another organism and are sequestered. Evidence indicates that the defensive skin alkaloids of Neotropical poison frogs (Dendrobatidae) have an exogenous source: a diet of ants and other small alkaloid-containing arthropods, which we term the diet-toxicity hypothesis. A critical prediction of the diet-toxicity hypothesis is that independent origins of dietary specialization will be found to be correlated with independent origins of skin alkaloids. We tested this prediction in an integrated framework using comparative methods with new and published data on feeding ecology and chemical defense for 15 species of dendrobatids in five genera. We found a significant correlation between alkaloid profiles and degree of dietary specialization. This reveals a recurring association of dietary specialization and alkaloid sequestration in dendrobatids, which suggests parallel evolutionary trends in the origins of defensive mechanisms.

Alkaloids↗
PubMed2002

The subsurface origin of microbial life on the Earth.

Life on Earth can be divided into life on the surface made possible by photosynthesis and subsurface life with chemical energy as the driving force. An understanding of both environments is central to our understanding of the origin of life, the search for novel microbial species in the subsurface and for extraterrestrial life or life signatures. In this manuscript, the surface and subsurface worlds are examined with a focus on the origin or assembly of bacterial life.

Bacteria↗
PubMed1979

The origin of life. A cybernetic and informational process.

According to the model presented in this paper, the beginning of life was marked by the coupling of two complementary nucleotide bases: adenine and thymine. The adenine-thymine system received photons from the sun and stored their energy in the form of a chemical high-energy bond between two phosphoric acid molecules, which were before-hand fixed by adenine from the aqueous environment. The energy of the high-energy bond was then delivered in the form of two waves of electronic excitation. These were utilized to synthesize new molecules, starting from the carbonic acid and ammonia molecules, fixed from the aqueous environment by the polar groups of the nucleotide bases. In this way, a nucleotides-histone protosystem (NHPS) was self-synthesized, evolving step by step towards complexity, by means of some internal cybernetic and informational mechanisms. During its evolution, the NHPS synthesized a limiting membrane, produced the organizing elements of the cellular organelles (chloroplastes, mitochondria, ribosomes etc) and constructed microtubules and microfilaments. Subsequently, the NHPS evolved to the building of DNA-histone system and formed the cellular nucleus.

Adenine↗
PubMed1990

Early expression of type I K13 keratin in the progression of mouse skin papillomas.

The premalignant evolution of chemically induced mouse skin papillomas is characterized by dysplastic changes, aneuploidy, induction of gamma-glutamyl transpeptidase (GGT), and changes in the expression of keratins, especially differentiation-associated K1. This keratin, which is expressed in normal epidermis and early papillomas, is no longer present in more advanced dysplastic and aneuploid papillomas and in fully invasive carcinomas. More recently, it has been shown that K13, a keratin normally present in internal epithelia but not in epidermis, is aberrantly expressed in epidermal tumors. In the present study, the timing of expression of K13 and its correlation with other markers of premalignant evolution were investigated. Papillomas were induced by SENCAR mice by a single initiating dose of 20 nmol of 7,12-dimethylbenz[a]-anthracene (DMBA) and promotion with 12-O-tetradecanoylphorbol-13-acetate (TPA) (2 micrograms twice a week). Tumors were randomly harvested at 10, 20 and 35 weeks of promotion. K13 and K1 expression in papillomas was studied using immunoblotting and immunostaining of consecutive sections, as previously described. As expected from previous studies, the distribution of K1 in papillomas collected at 10 weeks of promotion was restricted to differentiated cells and was uniform throughout the section of the papilloma. Conversely, K13 was expressed only as small foci in 10 out of 21 papillomas (48%). Papillomas of 20 weeks were also positive for K1. Staining for K13 was positive in these papillomas with the exception of only one that was essentially negative, presenting only one small positive focus. Some of the papillomas collected at week 35 were negative for K1, but immunostaining with K13 showed uniform staining of suprabasal cells in all the papillomas studied. In all cases, immunohistochemical results were confirmed by immunoblotting with proteins extracted from 7 microns sections from each paraffin block. These results indicate that keratins K1 and K13 are coexpressed in most papillomas from 10 to 35 weeks of promotion. However, analysis of adjacent sections showed that K13 positive areas are topographically located in the K1 negative areas of the papillomas, suggesting a shift in the differentiation program from epidermal to mucosal types of keratinization. Based on these and previous studies from our laboratory, we conclude that K13 is an early marker of papillomas progression, which occurs before gross chromosomal abnormalities are present in the stem line of the tumors, and precedes dysplastic changes and the onset of GGT expression, and is probably concomitant at the individual cell level with loss of K1.

9,10-Dimethyl-1,2-benzanthracene↗