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PubMedDate not supplied

Living nanovesicles--chemical and physical survival strategies of primordial biosystems.

Life on Earth and Mars could have started with self-assembled nanovesicles similar to the present nanobacteria (NB). To resist extreme environmental stress situations and periods of nutritional deprivation, nanovesicles would have had a chemical composition protected by a closed mineralized compartment, facilitating their development in a primordial soup, or other early wet environment. Their survivability would have been enhanced if they had mechanisms for metabolic communication, and an ability to collect primordially available energy forms. Here, we establish an irreducible model system for life formation starting with NB.

Apatites↗

PubMed1984

Radiation synthesis of polymers in aqueous cyanides.

Structures and properties of polymers isolated from the reaction mixtures obtained upon irradiation of dilute aqueous solutions of ammonium cyanide and HCN with gamma rays of 60Co were studied. On the basis of spectroscopic and chemical data it was concluded that two principal classes of polymers occur each of them having molecular weights that range from about 5000 to over 20000. In both types of polymers peptidic, urea-formaldehyde, and complex heterocyclic fragments are identified. In one type aliphatic fragments are more pronounced, while in the other heterocyclic structures predominate. The polymers interact with nucleic acid bases and some of them show catalytic properties as demonstrated by the hydrolysis of p-nitrophenylacetate.

Cobalt Radioisotopes↗

PubMed1995

Infrared spectroscopy of organics of planetological interest at low temperatures.

In the context of prebiotic chemistry in space, some of the outer planetary objects display H, C, N and O rich chemistry similar to the one in the biosphere of Earth. Of particular interest are Saturn's moon, Titan; Neptune's moon, Triton; and Pluto where extreme cold conditions prevail. Identifications of chemical species on these objects (surfaces and atmospheres) is essential to a better understanding of the radiation induced chemical reactions occurring thereon. There have been several ground based observations of these planetary objects in the infrared windows from 1 to 2.5 micrometers. Voyager also provided spectra in the thermal infrared (6 to 50 micrometers) region. Interpretation of these data require laboratory infrared spectra of relevant species under the temperature conditions appropriate to these objects. The results of some of these studies carried out in our laboratory and elsewhere and their impact on the analyses of the observed data will be summarized.

Cold Temperature↗

PubMed1975

Composition and structure of the pericellular environment. Physiological function and chemical composition of pericellular proteoglycan (an evolutionary view).

Connective tissue cells exist in a meshwork of insoluble fibres, the interstices of which are filled with soluble, high molecular mass, anionic material of a predominantly carbohydrate nature. The interactions of fibres with the interfibrillar material are central to the discussion of connective tissue physiology. As with all soluble polymers, the interfibrillar polyanion tends to "swell' and the tangled mass of chains offers considerable resistance to penetration by the large insoluble fibres. The consequent pressure to "inflate' the fibrous network is important in giving elasticity to cartilage, transparency to cornea, etc. Branched structures (of proteoglycans) and straight-chain forms (of hyaluronate) are compared for their ability to fulfil these functions. Apart from their physical ("non-specific') roles proteoglycans and glycosaminoglycans are able to interact physicochemically with, for example, collagen in ways which show considerable specificity, and which presumably are important in the laying down of the fibrous network as well as in maintaining its mechanical integrity. It is proposed that the role played by radiation, particularly as mediated via the hydrated electron (eaq) was dominant in the pre- and post-biotic evolution of pericellular environments.

Animals↗

PubMed2006

Phosphorus in prebiotic chemistry.

The prebiotic synthesis of phosphorus-containing compounds-such as nucleotides and polynucleotides-would require both a geologically plausible source of the element and pathways for its incorporation into chemical systems on the primitive Earth. The mineral apatite, which is the only significant source of phosphate on Earth, has long been thought to be problematical in this respect due to its low solubility and reactivity. However, in the last decade or so, at least two pathways have been demonstrated which would circumvent these perceived problems. In addition, recent results would seem to suggest an additional, extraterrestrial source of reactive phosphorus. It appears that the 'phosphorus problem' is no longer the stumbling block which it was once thought to be.

Evolution, Chemical↗

PubMed2000

Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system.

TNAs [(L)-alpha-threofuranosyl oligonucleotides] containing vicinally connected (3'-->2') phosphodiester bridges undergo informational base pairing in antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. Being derived from a sugar containing only four carbons, TNA is structurally the simplest of all potentially natural oligonucleotide-type nucleic acid alternatives studied thus far. This, along with the base-pairing properties of TNA, warrants close scrutiny of the system in the context of the problem of RNA's origin.

Base Pairing↗

PubMed1979

Arginyl residues and anion binding sites in proteins.

The functions of a number of amino acid residues in proteins have been studied by chemical modification techniques and much useful information has been obtained. Methods using dicarbonyl compounds for the modification of arginine residues are the most recent to have been developed. Since their introduction about 10 years ago, they have led to the identification of a large number of enzymes and other proteins that contain arginine residues critical to biological function. These reagents are discussed in terms of their chemical reactivity and mechanisms of action and in relation to the unique chemical properties of the guanidinium group. Butanedione, phenylglyoxal and cyclohexanedione are the most commonly employed arginyl reagents, and their relative advantages are examined. A survey of the functional role of arginine residues in enzymes and other proteins is presented in which nearly 100 examples are cited. The prediction that arginine residues would be found to serve a general role as anionic binding sites in protein has obviously been validated. The genetic and physiological implications of the selection of arginine for this important function are discussed.

Anions↗

PubMed2006

The origin of replicators and reproducers.

Replicators are fundamental to the origin of life and evolvability. Their survival depends on the accuracy of replication and the efficiency of growth relative to spontaneous decay. Infrabiological systems are built of two coupled autocatalytic systems, in contrast to minimal living systems that must comprise at least a metabolic subsystem, a hereditary subsystem and a boundary, serving respective functions. Some scenarios prefer to unite all these functions into one primordial system, as illustrated in the lipid world scenario, which is considered as a didactic example in detail. Experimentally produced chemical replicators grow parabolically owing to product inhibition. A selection consequence is survival of everybody. The chromatographized replicator model predicts that such replicators spreading on surfaces can be selected for higher replication rate because double strands are washed away slower than single strands from the surface. Analysis of real ribozymes suggests that the error threshold of replication is less severe by about one order of magnitude than thought previously. Surface-bound dynamics is predicted to play a crucial role also for exponential replicators: unlinked genes belonging to the same genome do not displace each other by competition, and efficient and accurate replicases can spread. The most efficient form of such useful population structure is encapsulation by reproducing vesicles. The stochastic corrector model shows how such a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be. Prebiotic and early evolution cannot be understood without the models of dynamics.

Biological Evolution↗

PubMed1997

The primitive matrix components of the unique carbonaceous chondrite Acfer 094: a TEM study.

The mineralogical and chemical characteristics of the fine-grained matrix (< or = 3 micrometers) of the unique primitive carbonaceous chondrite Acfer 094 have been investigated in detail by scanning electron microscopy (SEM) and analytical transmission electron microscopy (ATEM). Generally, the fine-grained matrix represents a highly unequilibrated assemblage of an amorphous material, small forsteritic olivines (200-300 nm), low Ca-pyroxenes (300-400 nm), and Fe,Ni-sulfides (100-300 nm). The matrix is basically unaffected by secondary processes. Only minor amounts of serpentine and ferrihydrite, as products of hydrous alteration, are present. Texturally, the amorphous material acts as a groundmass to olivines, pyroxenes, and sulfides, mostly exhibiting rounded or elongated morphologies. Only very few clastic mineral grains have been found. The texture and chemical composition of the amorphous material are consistent with an origin by disequilibrium condensation in either the cooling solar nebula or a circumstellar environment. As such, the amorphous material may be considered as a possible precursor of matrix materials in other types of chondrites. The non-clastic matrix olivines (Fo98-99) and pyroxenes (En97-100) are suggested to have formed either by condensation in the solar nebula under highly oxidizing conditions or by recrystallization from the amorphous material. The formation of these grains by fragmentation of chondrule components is unlikely due to chemical and microstructural reasons. Rapid cooling caused the observed intergrowths of clino/orthoenstatite in the Mg-rich matrix pyroxenes. Although some similarities exist comparing the fine-grained matrix of Acfer 094 with the matrices of the unequilibrated CO3 chondrite ALHA77307 and the unique type 3 chondrite Kakangari, Acfer 094 remains unique. Since it contains the highest measured concentrations of circumstellar SiC and the second highest of diamond (highest is Orgueil), it seems reasonable to suggested that at least parts of the amorphous material in the fine-grained matrix may be of circumstellar origin.

Carbon↗

PubMed2000

The origin of intermediary metabolism.

The core of intermediary metabolism in autotrophs is the citric acid cycle. In a certain group of chemoautotrophs, the reductive citric acid cycle is an engine of synthesis, taking in CO(2) and synthesizing the molecules of the cycle. We have examined the chemistry of a model system of C, H, and O that starts with carbon dioxide and reductants and uses redox couples as the energy source. To inquire into the reaction networks that might emerge, we start with the largest available database of organic molecules, Beilstein on-line, and prune by a set of physical and chemical constraints applicable to the model system. From the 3.5 million entries in Beilstein we emerge with 153 molecules that contain all 11 members of the reductive citric acid cycle. A small number of selection rules generates a very constrained subset, suggesting that this is the type of reaction model that will prove useful in the study of biogenesis. The model indicates that the metabolism shown in the universal chart of pathways may be central to the origin of life, is emergent from organic chemistry, and may be unique.

Biological Evolution↗

PubMed2004

Chemistry and biodiversity.

Complex structures produced by noncatalyzed multi-step chemical processes must have highly probable origins and assembly routes. Within any frame of reference, life is easily the most-complex self-assembled structure known to man. It is not possible to calculate a finite time for biogenesis by statistical mechanics, but the abundance of life makes it reasonable to propose an accelerating principle of nature that naturally shortened the time for cell formation to a billion years or less. This hypothetical principle, which I have called valence-orbital bias, is thought to be responsible for the discrepancy between statistics and observation, and carries with it, as a conditio sine qua non, multiple origins of life.The new concept resolves the differences between the predictions based on statistical mechanics and the relatively rapid appearance of life during the post-accretion period. It suggests as well that species and variants, the units of propagation, may also have been the units of evolution. Produced in profusion by chemistry, the origins are culled by natural selection, whereby failure means extinction, not adaptation. Biodiversity, thus, becomes a direct consequence of chemistry without positive feedback from the environment and without a constructive role for mutation.

Animals↗

PubMed2005

On the chemical nature and origin of teleonomy.

The physico-chemical characterization of a teleonomic event and the nature of the physico-chemical process by which teleonomic systems could emerge from non-teleonomic systems are addressed in this paper. It is proposed that teleonomic events are those whose primary directive is discerned to be non-thermodynamic, while regular (non-teleonomic) events are those whose primary directive is the traditional thermodynamic one. For the archetypal teleonomic event, cell multiplication, the non-thermodynamic directive can be identified as being a kinetic directive. It is concluded, therefore, that the process of emergence, whereby non-teleonomic replicating chemical systems were transformed into teleonomic ones, involved a switch in the primacy of thermodynamic and kinetic directives. It is proposed that the step where that transformation took place was the one in which some pre-metabolic replicating system acquired an energy-gathering capability, thereby becoming metabolic. Such a transformation was itself kinetically directed given that metabolic replicators tend to be kinetically more stable than non-metabolic ones. The analysis builds on our previous work that considers living systems to be a kinetic state of matter as opposed to the traditional thermodynamic states that dominate the inanimate world.

Evolution, Chemical↗

PubMed2001

Solid organic matter in the atmosphere and on the surface of outer Solar System bodies.

Many bodies in the outer Solar System display the presence of low albedo materials. These materials, evident on the surface of asteroids, comets, Kuiper Belt objects and their intermediate evolutionary step, Centaurs, are related to macromolecular carbon bearing materials such as polycyclic aromatic hydrocarbons and organic materials such as methanol and related light hydrocarbons, embedded in a dark, refractory, photoprocessed matrix. Many planetary rings and satellites around the outer gaseous planets display such component materials. One example, Saturn's largest satellite, Titan, whose atmosphere is comprised of around 90% molecular nitrogen N2 and less than 10% methane CH4, displays this kind of low reflectivity material in its atmospheric haze. These materials were first recorded during the Voyager 1 and 2 flybys of Titan and showed up as an optically thick pinkish orange haze layer. These materials are broadly classified into a chemical group whose laboratory analogs are termed "tholins", after the Greek word for "muddy". Their analogs are produced in the laboratory via the irradiation of gas mixtures and ice mixtures by radiation simulating Solar ultraviolet (UV) photons or keV charged particles simulating particles trapped in Saturn's magnetosphere. Fair analogs of Titan tholin are produced by bombarding a 9:1 mixture of N2:CH4 with charged particles and its match to observations of both the spectrum and scattering properties of the Titan haze is very good over a wide range of wavelengths. In this paper, we describe the historical background of laboratory research on this kind of organic matter and how our laboratory investigations of Titan tholin compare. We comment on the probable existence of polycyclic aromatic hydrocarbons in the Titan Haze and how biological and nonbiological racemic amino acids produced from the acid hydrolysis of Titan tholins make these complex organic compounds prime candidates in the evolution of terrestrial life and extraterrestrial life in our own Solar System and beyond. Finally, we also compare the spectrum and scattering properties of our resulting tholin mixtures with those observed on Centaur 5145 Pholus and the dark hemisphere of Saturn's satellite Iapetus in order to demonstrate the widespread distribution of similar organics throughout the Solar System.

Ammonia↗

PubMed2005

On the emergence of biological complexity: life as a kinetic state of matter.

A kinetic model that attempts to further clarify the nature of biological complexification is presented. Its essence: reactions of replicating systems and those of regular chemical systems follow different selection rules leading to different patterns of chemical behavior. For regular chemical systems selection is fundamentally thermodynamic, whereas for replicating chemical systems selection is effectively kinetic. Building on an extension of the kinetic stability, concept it is shown that complex replicators tend to be kinetically more stable than simple ones, leading to an on-going process of kinetically-directed complexification. The high kinetic stability of simple replicating assemblies such as phages, compared to the low kinetic stability of the assembly components, illustrates the complexification principle. The analysis suggests that living systems constitute a kinetic state of matter, as opposed to the traditional thermodynamic states that dominate the inanimate world, and reaffirms our view that life is a particular manifestation of replicative chemistry.

Evolution, Chemical↗

PubMedDate not supplied

The lipid world.

The continuity of abiotically formed bilayer membranes with similar structures in contemporary cellular life, and the requirement for microenvironments in which large and small molecules could be compartmentalized, support the idea that amphiphilic boundary structures contributed to the emergence of life. As an extension of this notion, we propose here a 'Lipid World' scenario as an early evolutionary step in the emergence of cellular life on Earth. This concept combines the potential chemical activities of lipids and other amphiphiles, with their capacity to undergo spontaneous self-organization into supramolecular structures such as micelles and bilayers. In particular, the documented chemical rate enhancements within lipid assemblies suggest that energy-dependent synthetic reactions could lead to the growth and increased abundance of certain amphiphilic assemblies. We further propose that selective processes might act on such assemblies, as suggested by our computer simulations of mutual catalysis among amphiphiles. As demonstrated also by other researchers, such mutual catalysis within random molecular assemblies could have led to a primordial homeostatic system displaying rudimentary life-like properties. Taken together, these concepts provide a theoretical framework, and suggest experimental tests for a Lipid World model for the origin of life.

Catalysis↗

PubMed2005

Possible origin for porphin derivatives in prebiotic chemistry--a computational study.

A set of chemical reactions is postulated to account for the formation of the macrocyclic porphin structure, basic to the pyrrole derivatives chlorophyll, protoporphyrin, heme and bilirubin, important in photosynthesis, respiration and digestion. A set of equations is given for the prebiotic synthesis of porphin derivatives from the simple molecules; cyanoacetylene, diacetylene, carbon monoxide and ammonia that have been detected in space. A number of isomers of hydrogenated porphin arise which may lose hydrogen to give ultimately porphin and its dehydrogenated derivative. The reactions, while not unique, provide a pathway which has been shown to be feasible from the overall enthalpy changes in the ZKE approximation at the HF and MP2/6-31G* level.

Evolution, Chemical↗

PubMed2004

Does she smell like a queen? Chemoreception of a cuticular hydrocarbon signal in the ant Pachycondyla inversa.

Primitive ant societies, with their relatively simple social structure, provide an opportunity to explore the evolution of chemical communication, in particular of mechanisms underlying within-colony discrimination. In the same colony, slight differences in individual odours can be the basis for discrimination between different castes, classes of age and social status. There is some evidence from correlative studies that such inter-individual variation is associated with differences in reproductive status, but direct proof that certain chemical compounds are detected and recognized by ants is still lacking. In the ponerine ant Pachycondyla inversa, fertile queens and, in orphaned colonies, dominant egg-laying workers are characterized by the predominance of a branched hydrocarbon, 3,11-dimethylheptacosane (3,11-diMeC(27)) on the cuticle. Using electroanntennography and gas chromatography with electroantennographic detection, we show that the antennae of P. inversa workers react to this key compound. 3,11-diMeC(27) is correlated with ovarian activity and, because it is detected, is likely to assume the role of a fertility signal reflecting the quality of the sender.

Alkanes↗

PubMed1992

Radiolysis of aqueous formaldehyde relevant to cometary environments.

The radiation chemistry of aqueous solutions of formaldehyde was studied in order to obtain an insight into the possible role of ionizing radiation on cometary environments. Aqueous solutions of 1.0 mol dm-3 formaldehyde were exposed to gamma-radiation in the dose range from 0.01 to 1200 kGy at 298 K. The radiation chemical yield of decomposition of formaldehyde was determined to be: G(-CH2(OH)2)-26.3 +/- 1.2. The high radiation chemical yield of decomposition was explained by a chain reaction initiated by the radical CH(OH)2 with formaldehyde. Computer fitting of the experimental data gives k(CH(OH)2 + CH2(OH)2)- 8.0xl0(1) dm3 mol-1 s-1. In the computer treatment of experimental findings we used 54 equations to consider the radiolysis of water and 11 reactions for the radiolysis of aqueous formaldehyde. Based on previous estimates of the total dose of ionizing radiation that comets have accumulated over 4.6 billion years, we predict a radiation damage-depth curve of formaldehyde in comet nuclei.

Cobalt Radioisotopes↗