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PubMed1985

pH profile of the adsorption of nucleotides onto montmorillonite. II. Adsorption and desorption of 5'-AMP in iron-calcium montmorillonite systems.

The interaction of 5'-AMP with montmorillonite saturated with various ratios of two metals found ubiquitously on the surface of Earth, that is, iron and calcium, is investigated. Adsorption and desorption of the nucleotide were studied in the pH range of 2-12 at three levels of addition: 0.080, 0.268 and 0.803 mmole 5'-AMP per gram of clay. Two desorption stages were employed--H2O wash and NaOH extraction (pH = 12.0). 5'-AMP was preferentially adsorbed on the Fe-containing clays relative to the Ca clay. The nucleotide was fully recovered by the two desorption stages, mostly by the NaOH extraction. The evidence at hand indicates that 5'-AMP reaction with clay is affected by electrostatic interactions involving both attraction and repulsion forces. Some specific adsorption, possibly the result of covalent bonding and complex formation with the adsorbed ion, cannot be ruled out for iron but does not appear to operate for calcium. Changes in pH cause varying degrees of attraction and repulsion of 5'-AMP and may have been operating on the primitive Earth, leading to sequences of adsorption and release of this biomolecule.

Adenosine Monophosphate↗
PubMed1986

Role of amphiphilic compounds in the evolution of membrane structure on the early earth.

A variety of amphiphilic compounds have the capacity to self-assemble into membranous structures in the form of bilayers. The earliest cellular organisms must have incorporated such compounds into boundary membranes, and this review discusses amphiphilic components of the prebiotic environment which would be candidates. One possible source is organic material carried to the earth's surface by meteoritic infall. To test this, we have extracted and analysed non-polar substances from the Murchison carbonaceous chondrite, and found that at least some of the components can produce boundary structures which resemble membranes. This observation suggests that membranous boundary structures were present on the early earth, and available to participate in the origin and evolution of the first cellular forms of life.

Biological Evolution↗
PubMed1996

A search for interstellar oxiranecarbonitrile (C3H3NO).

We report a search in cold, quiescent and in 'hot core' type interstellar molecular clouds for the small cyclic molecule oxiranecarbonitrile (C3H3NO), which has been suggested as a precursor of important prebiotic molecules. We have determined upper limits to the column density and fractional abundance for the observed sources and find that, typically, the fractional abundance by number relative to molecular hydrogen of C3H3NO is less than a few times 10(-10). This limit is one to two orders of magnitude less than the measured abundance of such similarly complex species as CH3CH2CN and HCOOCH3 in well-studied hot cores. A number of astrochemical discoveries were made, including the first detection of the species CH3CH2CN in the massive star-forming clouds G34.3+0.2 and W51M and the first astronomical detections of some eight rotational transitions of CH3CH2CN, CH3CCH, and HCOOCH3. In addition, we found 8 emission lines in the 89 GHz region and 18 in the 102 GHz region which we were unable to assign.

Astronomy↗
PubMed1996

Was ferrocyanide a prebiotic reagent?

Hydrogen cyanide is the starting material for a diverse array of prebiotic syntheses, including those of amino acids and purines. Hydrogen cyanide also reacts with ferrous ions to give ferrocyanide, and so it is possible that ferrocyanide was common in the early ocean. This can only be true if the hydrogen cyanide concentration was high enough and the rate of reaction of cyanide with ferrous ions was fast enough. We show experimentally that the rate of formation of ferrocyanide is rapid even at low concentrations of hydrogen cyanide in the pH range 6-8, and therefore an equilibrium calculation is valid. The equilibrium concentrations of ferrocyanide are calculated as a function of hydrogen cyanide concentration, pH and temperature. The steady state concentration of hydrogen cyanide depends on the rate of synthesis by electric discharges and ultraviolet light and the rate of hydrolysis, which depends on pH and temperature. Our conclusions show that ferrocyanide was a major species in the prebiotic ocean only at the highest production rates of hydrogen cyanide in a strongly reducing atmosphere and at temperatures of 0 degrees C or less, although small amounts would have been present at lower hydrogen cyanide production rates. The prebiotic application of ferrocyanide as a source of hydrated electrons, as a photochemical replication process, and in semi-permeable membranes is discussed.

Earth, Planet↗
PubMed1996

Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment.

The reaction of iron sulfide (FeS) with H2S in water, in presence of CO2 under anaerobic conditions was found to yield H2 and a variety of organic sulfur compounds, mainly thiols and small amounts of CS2 and dimethyldisulfide. The same compounds were produced when H2S was replaced by HCl, in the H2S-generating system FeS/HCl/CO2. The identification of the products was confirmed by GC-MS analyses and the incorporation of H2 in the organic sulfur compounds was demonstrated by experiments in which all hydrogen compounds were replaced by deuterium compounds. Generation of H2 and the synthesis of thiols were both dependent upon the relative abundance of FeS and HCl or H2S, i.e. the FeS/HCl- or FeS/H2S-proportions. Whether thiols or CS2 were formed as the main products depended also on the FeS/HCl-ratio: All conditions which create a H2 deficiency were found to initiate a proportional increase in the amount of CS2. The quantities of H2 and thiols generated depended on temperature: the production of H2 was significantly accelerated from 50 degrees C onward and thiol synthesis above 75 degrees C. The yield of thiols increased with the amount of FeS and HCl (H2S), given a certain FeS/HCl-ratio and a surplus of CO2. A deficiency of CO2 results in lower thiol synthesis. The end product, pyrite (FeS2), was found to appear as a silvery granular layer floating on the aqueous surface. The identity of the thiols was confirmed by mass spectrometry, and the reduction of CO2 demonstrated by the determination of deuterium incorporation with DCl and D2O. The described reactions can principally proceed under the conditions comparable to those obtaining around submarine hydrothermal vents, or the global situation about 4 billion years ago, before the dawn of life, and could replace the need for a reducing atmosphere on the primitive earth.

Anaerobiosis↗
PubMed1990

Nonrandomness in prebiotic peptide synthesis.

We have synthesized and studied the properties of phosphoanhydrides of alanine with guanosine monophosphate, uridine monophosphate, and adenosine monophosphate. This series of compounds allowed us to investigate the specificity of peptide bound formation in a reaction that could have taken place on the prebiotic earth. We asked whether the intrinsic reactivity of the amino acids, the nature of the nucleotide in the anhydride, or the complementary polynucleotide template influences the specificity of the peptide synthesis reaction. We observed that the differential reactivity of the amino acids results in nearest-neighbor preferences during the peptide synthesis, whereas the nature of the nucleotides and the presence of complementary polynucleotides had no influence on the specificity. These results suggest that some peptides would have been more abundant than others on the prebiotic earth and have implications for the study of the origins of the genetic code and protein synthesis.

Amino Acid Sequence↗
PubMed1989

The extension reached by the minimization of the polarity distances during the evolution of the genetic code.

The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary minimum, with respect to the optimization of the polarity distances, by the genetic code during its formation.

Amino Acids↗
PubMed1996

The origin of kinetic cooperativity in prebiotic catalysts.

A polyallylamine carrying long hydrophobic dodecyl groups and adenine residues as side chains (PALAD C12) may be able to catalyze the hydrolysis of N-carbobenzoxy-l-alanine p-nitrophenyl ester (N-Cbz-Ala) as well as p-nitrophenyl acetate (pNPA). The progress curve of hydrolysis of the former displays a long lag and apparently no steady state. After this transient the rate falls off due to the accumulation of the products. Conversely, the hydrolysis of p-nitrophenyl acetate displays classical burst kinetics followed by a slow decline of the reaction rate.Theoretical considerations show that a steady state may be expected to occur only if the concentration of the free catalyst is very small during the reaction. This condition is sufficient to allow the rate of disappearance of the substrate to be equal to the rate of appearance of the products, which is precisely a condition for the existence of a steady state. If the catalyst is poorly active and has a loose affinity for its substrate and product, the measurement of a significant reaction rate will require a much larger concentration of the catalyst. Therefore, under these conditions, one cannot expect a steady state to occur. The mathematical expression of the error made in the steady-state assumption has been derived. This error increases with the catalyst concentration and decreases if the affinity of the substrate for the catalyst is high. Therefore the lack of steady state is associated with the affinity (or the dissociation) of the substrate and the product for the catalyst. When this affinity is low, the free concentration of the catalyst during the reaction is high and one cannot expect a steady state to occur. This is precisely what takes place with N-Cbz-Ala.A mathematical expression of the rate of hydrolysis of N-Cbz-Ala and of any reactant that displays this type of kinetics may be derived at the end of the transient when the rate is close to its maximum value. Under these conditions the rate cannot follow classical Michaelis-Menten kinetics and displays positive cooperativity. It may therefore be speculated that primordial template-like catalysts that were displaying a poor affinity for their substrates and products were already exhibiting apparent positive cooperativity in the kinetic reactions they were able to catalyze.

Alanine↗
PubMed1996

The effect of smectite composition on the catalysis of peptide bond formation.

Clay-catalyzed glycine and diglycine oligomerizations were performed as drying/wetting cycles at 80 degrees C. Two trioctahedral smectites (hectorite and saponite), three pure montmorillonites, a ferruginous smectite, an Fe(II)-rich smectite, and three smectites containing goethite admixture were used as catalysts. Highest peptide bond formation was found with trioctahedral smectites. About 7% of glycine was converted to diglycine and diketopiperazine on hectorite after 7 days. In the case of dioctahedral smectites, highest yields were achieved using clays with a negative-layer charge localized in the octahedral sheets (up to 2% of converted glycine after 7 days). The presence of Fe(II) in clay is reflected in a higher efficiency in catalyzing amino acid dimerization (about 3.5% of converted glycine after 7 days). The possible significance of the results for prebiotic chemistry is discussed.

Aluminum Silicates↗
PubMed1998

Comments on the role of H2S in the chemistry of Earth's early atmosphere and in prebiotic synthesis.

: Free energy calculations and experimental measurements have been used to show that H2S/CO2 mixtures outgassing from a prebiotic Earth's crust would have produced a reducing gas mixture containing CO, H2, H2O, and Sx as principal components. Due to rapid recombination of H2, CO, and Sx to H2S and CO2 on cooling from a high temperature to ambient conditions, reducing components would have been retained only if efficient quenching of the reduced gas mixture had been possible. Consequently, subsea vents or vents with efficient infusion of water would have been ideal sites for retention of reduced species and for prebiotic organic synthesis. It is suggested that C/H/O/S ratios are important factors in controlling the degree of prebiotic organic synthesis and, hence, the emergence of life, since if oxygen is abundant, CO2 and SO2 would have been dominant species.

Ammonia↗
PubMed1998

Site-specific prebiotic oligomerization reactions of glycine on the surface of hectorite.

Condensation reactions of the amino acid glycine on the surface of Cu(II)-exchanged hectorite are investigated using the technique of scanning force microscopy. Prebiotic conditions are simulated using alternate wetting and heating cycles. Concentration, immobilization, and subsequent polymerization resulting in glycine oligomers are seen to occur primarily at step edges or faults in the topmost layer. Condensation reactions also occur within tiny micropores or defects in the topmost layer. These reactions are facilitated by the availability of intergallery metal cations at the step edges or pores in the surface region.

Copper↗
PubMed1999

Production of guanine from NH(4)CN polymerizations.

The synthesis of adenine from the polymerization of concentrated ammonium cyanide solutions is well known. We show here that guanine is also produced by this reaction but at yields ranging from 10 to 40 times less than that of adenine. This synthesis is effective at both +80 and -20 degrees C. Since high concentrations of NH(4)CN are obtainable only by freezing, this prebiotic synthesis would be applicable to frozen regions of the primitive Earth, the Jovian satellite Europa and other icy satellites, and the parent body of the Murchison meteorite.

Cyanides↗
PubMed2006

The prebiotic synthesis of pyrimidines in frozen solution.

Most prebiotic syntheses depend on the reaction of concentrated precursor compounds to produce bio-organic molecules. It is now believed that the early Earth's atmosphere was not reducing enough to have permitted copious synthesis of precursor molecules. Freezing allows reaction to occur even from dilute solution. This reaction has been demonstrated for the purines but not for the pyrimidines. It is shown here that dilute solutions of simple prebiotic molecules produce the biological pyrimidines cytosine and uracil upon freezing. Cold environments may have allowed synthesis of all of the RNA bases even from low organic yielding atmospheres, such as those of the early Earth, Mars, Titan and Europa.

Earth, Planet↗
PubMed2002

The evolution of the ribonucleotide reductases: much ado about oxygen.

Ribonucleotide reduction is the only known biological means for de novo production of deoxyribonucleotides, the building blocks of DNA. These are produced from ribonucleotides, the building blocks of RNA, and the direction of this reaction has been taken to support the idea that, in evolution, RNA preceded DNA as genetic material. However, an understanding of the evolutionary relationships among the three modern-day classes of ribonucleotide reductase and how the first reductase arose early in evolution is still far off. We propose that the diversification of this class of enzymes is inherently tied to microbial colonization of aerobic and anaerobic niches. The work is of broader interest, as it also sheds light on the process of adaptation to oxygenic environments consequent to the evolution of atmospheric oxygen.

Allosteric Regulation↗
PubMed2005

Enantiomeric excess of amino acids in hydrothermal environments.

In a simulated hydrothermal environment allowing fluid circulation between hot and cold regions repeatedly, D- and L-alanine molecules were racemized differently depending upon the concentration of alanine, whether D or L, present in the solution. In particular, the relative population of L-alanine was slightly more enhanced compared to that of D-alanine when the concentration of alanine increased. Enantiomeric excess of L-alanine was also observed when metallic ions such as zinc were sufficiently present in the environments. Hydrothermal environments in the primitive ocean could have maintained the capacity of selectively retaining enantiomeric excess in favor of L-amino acids once the concentration of amino acids could reach a sufficiently high level.

Alanine↗