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PubMed1999

Toxins from sea cucumbers (holothuroids): chemical structures, properties, taxonomic distribution, biosynthesis and evolution.

Studies on structures, biological activities, chemical properties, taxonomic distribution, biosynthesis, and evolution of toxins from sea cucumbers (the phylum Echinodermata, the class Holothurioidea) were reviewed with special emphasis on recent results from our laboratory. These toxins are triterpene oligoglycosides having very often one or several sulfate groups in carbohydrate moieties. Their aglycones belong to lanostane derivatives and sometimes contain shortened side chains. Many aglycones are labile in the acid medium. There is a relationship between structures of the glycosides and taxonomic positions of corresponding animals, producers of these toxins. Toxins from sea cucumbers act on delta 5-sterol-containing biological membranes with the formation of glycoside-sterol complexes followed by the disturbance of membrane permeability and inhibition of activities of some membrane enzymes. The presence of the toxins causes the alterations in membrane sterol compositions of toxic sea cucumbers in comparison with non-toxic species. These alterations include the change of delta 5-sterols for those having 7(8)- and 9(11)-double bonds as well as biotransformation of a part of free sterol fractions into sterol sulfates and sterol xylosides.

Animals↗
PubMed1989

Mixed-valence hydroxides as bioorganic host minerals.

A range of naturally occurring divalent-trivalent metal cation hydroxides and modified artificial analogs have been synthesized and characterized. Structural and chemical properties of these minerals, determining their capability to selectively concentrate, order and alter molecules of prebiotic interest, include their anion exchange capacity and specificity, photochemical reactivity, production of nascent hydrogen, and catalytic efficiency. Properties relevant to these functions have been investigated and are discussed.

Aluminum↗
PubMed2003

A research proposal on the origin of life.

This paper describes some experiments the author would have liked to carry out if he had started earlier in the origin-of-life field. The proposal is preceded by a hypothetical outline of the main events in the origin of life. According to this outline, the emergence of life amounts to the transition between two kinds of chemistry: 1) cosmic chemistry, which is beginning to be understood and most likely provided the building blocks with which life was first constructed; and 2) biochemistry, the well-known set of enzyme-catalyzed metabolic reactions that support all living organisms today and must have supported the universal common ancestor, or LUCA, from which all known forms of life are derived. The pathway leading from one to the other of those two chemistries may be divided into three stages, defined as the pre-RNA, RNA, and protein-DNA stages. A brief summary of the events that may have occurred in these three stages and of the possible underlying mechanisms is given. It is emphasized that these events were chemical in nature and, especially, that they must have prefigured present-day biochemical processes. Protometabolism and metabolism, it is argued, must have been congruent. With congruence as the underlying working hypothesis, three problems open to experimental investigation are considered: 1) the involvement of peptides and other multimers as catalysts of early biogenic chemistry; 2) the participation of thioesters in primitive energy transactions; and 3) the influence of amino acids on the molecular selection of RNA molecules.

Amino Acids↗
PubMed1997

The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front.

Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150 degrees C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90 degrees C), iron-hearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS-, H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (delta Eh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural delta pH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism.

Bacteria↗
PubMed2002

Chemical and seismological constraints on mantle heterogeneity.

Recent seismological studies that use scattered waves to detect heterogeneities in the mantle reveal the presence of a small, distributed elastic heterogeneity in the lower mantle which does not appear to be thermal in nature. The characteristic size of these heterogeneities appears to be ca. 8 km, suggesting that they represent subducted recycled oceanic crust. With this stimulus, old ideas that the mantle is heterogeneous in structure, rather than stratified, are reinterpreted and a simple, end-member model for the heterogeneity structure is proposed. The volumetrically largest components in the model are recycled oceanic crust, which contains the heat-producing elements, and mantle depleted of these and other incompatible trace elements. About 10% of the mantle's mass is made up of recycled oceanic crust, which is associated with the observed small-scale seismic heterogeneity. The way this heterogeneity is distributed is in convectively stretched and thinned bodies ranging downwards in size from 8 km. With the present techniques to detect small bodies through scattering, only ca. 55% of the mantle's small-scale heterogeneities are detectable seismically.

Computer Simulation↗
PubMed1984

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine.

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

Amides↗
PubMedDate not supplied

Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.

Environmental conditions play an important role in conceptual studies of prebiotically relevant chemical reactions that could have led to functional biomolecules. The necessary source compounds are likely to have been present in dilute solution, raising the question of how to achieve selective concentration and to reach activation. With the assumption of an initial 'RNA World', the questions of production, concentration, and interaction of aldehydes and aldehyde phosphates, potential precursors of sugar phosphates, come into the foreground. As a possible concentration process for simple, uncharged aldehydes, we investigated their adduct formation with sulfite ion bound in the interlayer of positively charged expanding-sheet-structure double-layer hydroxide minerals. Minerals of this type, initially with chloride as interlayer counter anion, have previously been shown to induce concentration and subsequent aldolization of aldehyde phosphates to form tetrose, pentose, and hexose phosphates. The reversible uptake of the simple aldehydes formaldehyde, glycolaldehyde, and glyceraldehyde by adduct formation with the immobilized sulfite ions is characterized by equilibrium constants of K=1.5, 9, and 11, respectively. This translates into an observable uptake at concentrations exceeding 50 mM.

Acetaldehyde↗
PubMed2004

Stepwise evolution of nonliving to living chemical systems.

Steps by which a nonliving chemical system could have transformed into a living system are described and discussed, assuming general features of Wächtershäuser's chemo-autotrophic surface theory of the origin of life. Environmental species such as CO2 and H2S are proposed to have reacted to form a quasi-steady state metal-bound intermediate (CH3-M) that slowly decayed into waste (CH4). Unpredictable dispersive reactions expanded the system to include surface-bound forms of the citric acid cycle intermediates (oxaloacetate-->citrate). Further reaction yielded an autocatalytic system in which raw materials are converted into the system at exponential rates. Combinatorial dispersive reactions that improved the performance of this system were automatically selected and incorporated into it. Systems evolved critical features of living systems (proteins, membranes, proteins, nucleic acids, etc.) using two related mechanisms called grafting and waste-conversion. Such living systems were transformed from less recognizable types (characterized by autocatalytic spreading, decentralization, poorly defined boundaries, etc.) into more recognizable ones (encapsulated by membranes, controlled by single-molecule genomes, etc.) that self-replicated by a cell division cycle and could evolve by the standard gene-based Darwinian mechanism. The resulting systems are viewed as having an autocatalytic network composed of three linked autocatalytic subreactions.

Cell Cycle↗
PubMed1994

Archean geochemistry of formaldehyde and cyanide and the oligomerization of cyanohydrin.

The sources and speciation of reduced carbon and nitrogen inferred for the early Archean are reviewed in terms of current observations and models, and known chemical reactions. Within this framework hydrogen cyanide and cyanide ion in significant concentration would have been eliminated by reaction with excess formaldehyde to form cyanohydrin (glycolonitrile), and with ferrous ion to form ferrocyanide. Natural reactions of these molecules would under such conditions deserve special consideration in modeling of primordial organochemical processes. As a step in this direction, transformation reactions have been investigated involving glycolonitrile in the presence of water. We find that glycolonitrile, formed from formaldehyde and hydrogen cyanide or cyanide ion, spontaneously cyclodimerizes to 4-amino-2-hydroxymethyloxazole. The crystalline dimer is the major product at low temperature (approximately 0 degrees C); the yield diminishes with increasing temperature at the expense of polymerization and hydrolysis products. Hydrolysis of glycolonitrile and of oxazole yields a number of simpler organic molecules, including ammonia and glycolamide. The spontaneous polymerization of glycolonitrile and its dimer gives rise to soluble, cationic oligomers of as yet unknown structure, and, unless arrested, to a viscous liquid, insoluble in water. A loss of cyanide by reaction with formaldehyde, inferred for the early terrestrial hydrosphere and cryosphere would present a dilemma for hypotheses invoking cyanide and related compounds as concentrated reactants capable of forming biomolecular precursor species. Attempts to escape from its horns may take advantage of the efficient concentration and separation of cyanide as solid ferriferrocyanide, and most directly of reactions of glycolonitrile and its derivatives.

Acetonitriles↗
PubMed1995

The prebiotic role of adenine: a critical analysis.

Adenine plays an essential role in replication in all known living systems today, and is prominent in many other aspects of biochemistry. It occurs among the products of oligomerization of HCN. These circumstances have stimulated the idea that adenine was a component in a replication system that was present at the start of life. Such replicators have included not only RNA, but also a number of simpler RNA-like alternatives which utilize a simpler backbone. Despite these encouraging indicators, a consideration of the chemical properties of adenine reveals reasons that disfavor its participation in such a role. These properties include the following: (1) Adenine synthesis requires HCN concentrations of at least 0.01 M. Such concentrations would be expected only in unique circumstances on the early Earth. Adenine yields are low in prebiotic simulations, and if a subsequent high-temperature hydrolysis step is omitted, the reported yield does not represent adenine itself, but 8-substituted adenines and other derivatives. (2) Adenine is susceptible to hydrolysis (the half life for deamination at 37 degrees C, pH 7, is about 80 years), and to reaction with a variety of simple electrophiles, forming a multiplicity of products. Its accumulation would not be expected over a geological time scale, and its regioselective incorporation into a replicator appears implausible. (3) The adenine-uracil interaction, which involves two hydrogen bonds (rather than three, as in guanine-cytosine pairing) is weak and nonspecific. Pairing of adenine with many other partners has been observed with monomers, synthetic oligonucleotides and in RNA. The hydrogen-bonding properties of adenine appear inadequate for it to function in any specific recognition scheme under the chaotic conditions of a prebiotic soup. New and fundamental discoveries in the chemistry of adenine would be needed to reverse this perception. An alternative and attractive possibility is that some other replicator preceeded RNA (or RNA-like substances) in the origin of life.

Adenine↗
PubMed2000

A thermodynamic assessment of the potential synthesis of condensed hydrocarbons during cooling and dilution of volcanic gases.

The possibility for abiotic synthesis of condensed hydrocarbons in cooling/diluting terrestrial volcanic gases has been evaluated on the basis of the consideration of metastable chemical equilibria involving gaseous CO, CO2, H2 and H2O. The stabilities of n-alkanes and polycyclic aromatic hydrocarbons (PAHS) have been evaluated for several typical volcanic gas compositions under various conditions for cooling/diluting of quenched volcanic gas. The modeling shows that n-alkanes and PAHs have a thermodynamic potential to form metastably from H2 and CO below approximately 250 degrees C within the stability field of graphite. Despite the predominance of CO2 in volcanic gases, synthesis of hydrocarbons from CO2 and H2 is less favored energetically than from CO and H2. Both low temperature and a high H/C atomic ratio in volcanic gas generally favor stability of hydrocarbons with higher H/C ratios. PAHs are thermodynamically stable at temperatures approximately 10 degrees -50 degrees C higher than large n-alkanes; however, at lower temperatures, PAHs and n-alkanes have similar stabilities and are likely to form metastable mixtures. Both the energetic drive to form hydrocarbons and possible temperatures of formation increase as the oxidation state (fO2) of the volcanic gases decreases and as the cooling/dilution ratios of volcanic gases increase. Synthesis of hydrocarbons is energetically more likely in cooling trapped gases than in ashcloud eruptive columns. Mechanisms for hydrocarbon formation may include Fischer-Tropsch-type synthesis catalyzed by magnetite from solid volcanic products. On the early Earth, Mars, and Jupiter's satellite Europa, several factors would have provided more favorable conditions for hydrocarbon synthesis in volcanic gases than under current terrestrial conditions and might have contributed to the production of organic compounds required for the emergence of life.

Alkanes↗
PubMed1989

The chemical kinetics of molecular evolution.

This article describes a current view of the events that initiated the transition from the rich organic and inorganic chemistry of the primitive Earth to the earliest forms of life. It is a personal condensation of the basic ideas developed in the so-called Göttingen school. Most of these will be found in the seminal paper of Eigen and the other sources cited. A detailed exposition is given by Küppers.

Biological Evolution↗
PubMed2005

Evolution of temperature and chemical parameters during composting of the pig slurry solid fraction amended with natural zeolite.

A 3-month experiment was conducted at a 300 kg scale to observe decomposition processes in pig slurry solids amended with two different doses of natural Slovak zeolite-clinoptilolite (substrates S1 and S2, 1% and 2% of zeolite by weight, respectively) in comparison with the control (unamended solids). The experimental and control substrates were stored outdoors in sheltered static piles at ambient temperatures ranging from 8.0 to 34.7 degrees C. The solid fraction (SF) of pig slurry was obtained by separation on vibration sieves prior to slurry treatment with activated sludge. The initial water content of the SF was 77.1% and no water was added to the piles during the storage. The temperature in the core of the piles was recorded throughout the experiment. By day 3 and 5 of storage (1% and 2% zeolite, resp.), the temperature in the substrates S1 and S2 exceeded 55 degrees C and remained above this level for 15 days while the highest temperature recorded in the control during the experiment was 29.8 degrees C. Samples from the core of the piles were taken periodically to determine pH, dry matter at 105 degrees C (DM), ash (550 degrees C/4 h), ammonia nitrogen (N-NH(4)(+)), nitrate nitrogen (N-NO(3)(-)), total nitrogen (N(t)), total phosphorus (P(t)); total organic carbon (TOC) was computed. The results showed that pH levels in S1 and S2 remained below that in the control for most of the thermophilic stage. This may be related to water-soluble ammonia and the affinity of zeolites to ammonium ions. A significant decrease in the level of ammonia nitrogen in water extracts from S1 and S2 was observed between days 5 and 35 in comparison with the control. The values of ash also differed and corresponded to the intensity of the decomposition processes in the respective substrates.

Ammonia↗
PubMed1999

Interruption of chemical mosquito control and evolution of insecticide resistance genes in Culex pipiens (Diptera: Culicidae).

Within the Llobregat Delta (Barcelona, Spain), Culex pipiens L. has been the target of organophosphate insecticide (OP) control for 10 yr (1982-1992). Between 1991 and 1992, OPs were replaced by Bacillus-based toxins in all the mosquito control programs within > 150 km of this area. The distribution of several OP-resistance genes was surveyed within the Llobregat Delta and neighboring populations (< 25 km) during the 2 yr following this regional pesticide change to investigate how the change in selection pressure affected the dynamics of OP-resistance genes. The immigration failure of the A2-B2 resistant esterases and the observed difference in OP-resistance dynamics between isolated and nonisolated populations may indicate fitness disadvantages associated with OP-resistance genes, hence a tendency for a decrease in OP-resistance. In contrast, one OP-resistance gene further increased in frequency, whereas the frequencies of some others were maintained. These unexpected results question the importance of pesticides from sources other than mosquito control, and the variability of pleiotropic fitness costs among pesticide resistance genes.

Animals↗