Role of transition metal ferrocyanides (II) in chemical evolution

Due to ease of formation of cyanide under prebiotic conditions, cyanide ion might have formed stable complexes with transition metal ions on the primitive earth. In the course of chemical evolution insoluble metal cyano complexes, which settled at the bottom of primeval sea could have formed peptide and metal amino acid complexes through adsorption processes of amino acids onto these metal cyano complexes.Adsorption of amino acids such as glycine, aspartic acid, and histidine on copper ferrocyanide and zinc ferrocyanide have been studied over a wide pH range of 3.6 – 8.5. Amino acids were adsorbed on the metal ferrocyanide complexes for different time periods. The progress of the adsorption was followed spectro-photometrically using ninhydrin reagent. Histidine was found to show maximum adsorption on both the adsorbents at neutral pH. Zinc ferrocyanide exhibits good sorption behaviour for all the three amino acids used in these investigations.     

Cations as Mediators of the Adsorption of Nucleic Acids on Clay Surfaces in Prebiotic Environments

Monovalent ([Na⁺] > 10 mM) and divalent ([Ca²⁺], [Mg²⁺] > 1.0 mM) cations induced the precipitationof nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay. Divalent cations were more efficient than monovalent ones in mediating adsorption. Adsorption to the clay occurred only when both nucleic acids and cations were present. However, once the complexes were formed, the cations could not be removed from the system by washing, indicating that they are directly involved in the association between nucleic acids and mineral surfaces.These observations indicate that cations take part directly in the formation of nucleic acid-clay complexes, acting as a `bridge' between the negative charges on the mineral surface and those of the phosphate groups of the genetic polymer. The relatively low cation concentrations needed for adsorption and the ubiquitous presence of clay minerals in the environment suggest that the adsorption of nucleic acids on mineral surfaces could have taken place in prebiotic habitats. This may have played an important role in the formation and preservation of nucleic acids and/or their precursor polymers.     

Amino Acid Interaction with and Adsorption on Clays: FT-IR and Mössbauer Spectroscopy and X-ray Diffractometry Investigations

In the present paper, the adsorption of amino acids (Ala, Met, Gln, Cys, Asp, Lys, His) on clays (bentonite, kaolinite) was studied at different pH (3.00, 6.00, 8.00). The amino acids were dissolved in seawater, which contains the major elements. There were two main findings in this study. First, amino acids with a charged R group (Asp, Lys, His) and Cys were adsorbed on clays more than Ala, Met and Gln (uncharged R groups). However, 74% of the amino acids in the proteins of modern organisms have uncharged R groups. These results raise some questions about the role of minerals in providing a prebiotic concentration mechanism for amino acids. Several mechanisms are also discussed that could produce peptide with a greater proportion of amino acids with uncharged R groups. Second, Cys could play an important role in prebiotic chemistry besides participating in the structure of peptides/proteins. The FT-IR spectra showed that the adsorption of amino acids on the clays occurs through the amine group. However, the Cys/clay interaction occurs through the sulfhydryl and amine groups. X-ray diffractometry showed that pH affects the bentonite interlayer, and at pH 3.00 the expansion of Cys/bentonite was greater than that of the samples of ethylene glycol/bentonite saturated with Mg. The Mössbauer spectrum for the sample with absorbed Cys showed a large increase (～20%) in ferrous ions. This means that Cys was able to partially reduce iron present in bentonite. This result is similar to that which occurs with aconitase where the ferric ions are reduced to Fe 2.5.     

Role of Ferrocyanides in the Prebiotic Synthesis of α-Amino Acids

We investigated the synthesis of α-amino acids under possible prebiotic terrestrial conditions in the presence of dissolved iron (II) in a simulated prebiotic ocean. An aerosol-liquid cycle with a prebiotic atmosphere is shown to produce amino acids via Strecker synthesis with relatively high yields. However, in the presence of iron, the HCN was captured in the form of a ferrocyanide, partially inhibiting the formation of amino acids. We showed how HCN captured as Prussian Blue (or another complex compound) may, in turn, have served as the HCN source when exposed to UV radiation, allowing for the sustained production of amino acids in conjunction with the production of oxyhydroxides that precipitate as by-products. We conclude that ferrocyanides and related compounds may have played a significant role as intermediate products in the prebiotic formation of amino acids and oxyhydroxides, such as those that are found in iron-containing soils and that the aerosol cycle of the primitive ocean may have enhanced the yield of the amino acid production.     

DNA and the origins of life in micaceous clay

Reproducible imaging of DNA by atomic force microscopy was a useful predecessor to Ned Seeman’s DNA nanotechnology. Many of the products of DNA nanotechnology were imaged in the atomic force microscope. The mica substrate used in this atomic force microscopy research formed the inspiration for the hypothesis that micaceous clay was a likely habitat for the origins of life. Montmorillonite clay has been a successful substrate for the polymerization of amino acids and nucleotides into peptides and DNA oligomers in research on life’s origins. Mica and montmorillonite have the same anionic lattice, with a hexagonal spacing of 0.5 nm. Micas are nonswelling clays, with potassium ions (K⁺) holding the crystal sheets together, providing a stable environment for the processes and molecular complexes needed for the emergence of living cells. Montmorillonite crystal sheets are held together by smaller sodium ions (Na⁺), which results in swelling and shrinking during wet-dry cycles, providing a less stable environment. Also, the cells in all types of living systems have high intracellular K⁺ concentrations, which makes mica a more likely habitat for the origins of life than montmorillonite. Finally, moving mica sheets provides mechanical energy at the split edges of the sheets in mica “books.” This mechanical energy of mica sheets, moving open and shut, in response to fluid flow, may have preceded chemical energy at life’s origins, powering early prebiotic processes, such as the formation of covalent bonds, the interactions of molecular complexes, and the budding off of protocells before the molecular mechanism of cell division had developed.     

Clays and other minerals in prebiotic processes

Clays and other minerals have been investigated in context with prebiotic processes, mainly in polymerization of amino acids. It was found that peptides adsorbed on the clay, prior to polymerization, influence the reaction. The ratio between the amount of the peptides adsorbed and that of the clay is important for the yield as well as for the degrees of polymerization obtained. Adsorption prior to reaction produces a certain order in the aggregates of the clay particles which might induce better reaction results. Excess of added peptides disturbs this order and causes lesser degrees of polymerization. In addition to adsorption, clays are also able to occlude between their layers substances out of the environment, up to very high concentrations.     

Clays and other minerals in prebiotic processes

Clays and other minerals have been investigated in context with prebiotic processes, mainly in polymerization of amino acids. It was found that peptides adsorbed on the clay, prior to polymerization, influence the reaction. The ratio between the amount of peptides adsorbed and that of the clay is important for the yield as well as for the degrees of polymerization obtained. Adsorption prior to reaction produces a certain order in the aggregates of the clay particles which might induce better reaction results. Excess of added peptides disturbs this order and causes lesser degrees of polymerization. In addition to adsorption, clays are also able to occlude between their layers substances out of the environment, up to very high concentrations.     

Clay-Nucleic Acid Complexes: Characteristics and Implications for the Preservation of Genetic Material in Primeval Habitats

The equilibrium adsorption of three nucleic acids: chromosomal DNA, supercoiled plasmid DNA, and 25S rRNA, on the clay minerals, montmorillonite (M) and kaolinite (K), were studied. Adsorption of the nucleic acid on the clays was rapid and maximal after 90 min of contact time. Chromosomal DNA was adsorbed to a greater extent than plasmid DNA and RNA, and the adsorption was also greater on M than on K. Adsorption isotherms were of the L type, and a plateau was reached with all the complexes, with the exception of chromosomal DNA adsorbed on M. To determine where nucleic acids are adsorbed on clay minerals and the nature of the interaction, complexes were studied by X-ray diffraction (X-RD), electron microscopy, and Fourier transform infrared (FT-IR) spectroscopy. X-RD showed that nucleic acids did not penetrate the clay, indicating that the adsorption occurred primarily on the external surfaces of clay particles, as also suggested by electron microscopy observations. FT-IR spectra of clay-tightly bound nucleic acid complexes showed absorption bands that indicate a variation of the nucleic acids status as a consequence of their adsorption on clay. Data obtained suggested that the formation of clay-nucleic acid complex could have an important role in the preservation of genetic material in primeval habitats.     

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment

Any proposed model of Earth’s primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5’AMP onto Na⁺montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5’AMP?>?adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH₂ group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.     

The possible role of clays in prebiotic peptide synthesis

Hypotheses of macromolecule formations during the prebiotic era are described. The presumed role of minerals and clays in these reactions are: concentration of monomers, proton release by ion exchange whenever the reaction demands it, scattering of the charges of the interacting substances, thus allowing such substances to interact, which in the absence of clays repel each other due to their charges. Because of these reasons the polymerization mechanism in the presence of clays is different from that in their absence. While in the absence of clays only free amino acids or peptides can interact with active amino acid anhydrides, giving thus peptides increased by only one unit, in the presence of clays two molecules of amino acid anhydrides can interact, giving a still active peptide anhydride which can interact with another active peptide. Clays catalyze polymerization only in these cases where the amino acid is small enough to enter between the sheets of the clay. Apparently most of the reactions also occur there and not on the surface of the clay. Copolymerization of different pairs of amino acids proceeds selectively in the presence of clay. The relationship between this selecitvity and prebiotic parent proteins is discussed.     

Clays in prebiological chemistry

Summary In this review an attempt is made to highlight the structures and properties of clay that may contribute to a better understanding of the role of clays in chemical evolution. The adsorption of organic molecules on clays has been demonstrated, as has the synthesis of bioorganic monomers in the presence of clays. For instance, amino acids (glycine, aspartic acid, threonine, alanine and others) as well as purines and pyrimidines, have been obtained from CO and NH₃ in the presence of clays at relatively high temperatures (250-325°C). Carbohydrates are also easily derived from formaldehyde at relatively low temperatures (80°C). The oligomerization of biochemical monomers, mediated by clays has also been shown to result in the formation of polymer molecules basic to life. For instance the condensation of amino acyl adenylates at room temperature in the presence of montmorillonite is known to yield polypeptides in discrete ranges of molecular weights with degrees of polymerization up to 56. Clays have also been found to affect the condensation of mononucleotides to oligonucleotides. Although the role of clays in the origin of metabolic pathways has not been demonstrated, it is possible that clays may have played a cooperative role with catalytic peptides in an intermediate stage of prebiological chemistry preceding the emergence of life on this planet.     

Prebiotic nucleotide oligomerization in a fluctuating environment: Effects of kaolinite and cyanamide

Summary The clay kaolinite was tested for its ability to promote nucleotide oligomerization in model prebiotic systems. Heterogeneous mixtures of clay, water and nucleotide were repeatedly evaporated to dryness at 60°C and redissolved in water in cyclic fashion in the presence or absence of cyanamide and/ or ammonium chloride. With or without cycling, kaolinite alone did not promote the oligomerization of nucleotides at detectable levels. Cycling of clay in combination with cyanamide, however, promoted high levels of condensation to a mixture of oligonucleotides and dinucleotide pyrophosphate without requiring ammonium chloride. Although cycling with clay favored synthesis of dinucleotide pyrophosphate, cycling without clay enhanced formation of oligonucleotides. These results support the hypothesis that the presence of clays in fluctuating environments would have influenced the course of prebiotic condensation reactions.     

On the Origin of Metabolic Pathways

The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO₂ to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking from preexisting pathways as well as prebiotic compounds from the environment.     

Mineral interface in extreme habitats: a niche for primitive molecular evolution for the appearance of different forms of life on earth

Innumerable primitive membrane and protocell models in latter stages of chemical evolution are based on the properties of minerals' interfaces with primitive seawater. The ordering mechanism induced by mineral interfaces has been the basis of several prebiotic models of molecular complexification and compartmentalization towards the appearance and evolution of different forms of life. Since mineral-aqueous media interfaces have been considered as initial stages of prebiotic models dealing with the formation of energy-transducing systems, the interface formed by pyrite in the presence of artificial primitive seawater was chosen to show the functional richness of this special niche. Interfaces--especially sulphide interfaces--were proposed as suitable niches for a two-carbon extant metabolism, synthesis and polymerization of nucleotides--to form ancient RNA strands--and assembly of amino acids synthesized in its vicinity. Accumulation of precursors at sulphide interfaces could have avoided their dilution into the Hadean seas and provided a suitable geochemical environment for a variety of molecular interactions. In this essay, we present a short review of the proposed roles of mineral interfaces in chemical evolution towards the appearance of primitive membranes, which might have been relevant for the advent of cellular life before its divergent evolution and differentiation. This survey covers several previous studies on the early cycles of energy conservation and of the formation of molecules carrying genetic information.     

The possible role of solid surface area in condensation reactions during chemical evolution: Reevaluation

Summary Published data on adsorption and condensation of amino acids, purine and pyrimidine bases, sugars, nucleosides, and nucleotides are analyzed in connection with Bernal's hypothesis that clays and other minerals may have provided the most likely surface for adsorption and condensation of these molecules in prebiotic times. Using surface concentration and reaction rate as the main criteria for the feasibility of condensation reactions, four types of prebiotic environments were analyzed: (1) an ocean-sediment system, (2) a dehydrated lagoon bed produced by evaporation, (3) the surface of a frozen sediment, and (4) a fluctuating system where hydration (rainstorms, tidal variations, flooding) and dehydration (evaporation) take place in a cyclic manner. With the possible exception of nucleotides, low adsorption of organomonomers on sediment surfaces of a prebiotic ocean (pH 8) is expected, and significant condensation is considered unlikely. In dehydrated and frozen systems, high surface concentrations are probable and condensation is more likely. In fluctuating environments, condensation rates will be enhanced and the size distribution of the oligomers formed during dehydration may be influenced by a redistribution mechanism in which adsorbed oligomers and monomers are desorbed and redistributed on the solid surface during the next hydration-dehydration cycle.On leave from the Faculty of Agriculture, Rehovot, The Hebrew University of Jerusalem, Israel.     

Clays as possible catalysts for peptide formation in the prebiotic era

From the point of view of prebiotic synthesis, clays might have performed functions of concentration, catalysis, and protection of molecules.The degrees of polymerization obtained, when amino acid adenylates are added to montmorillonite suspensions in water, are much higher than those obtained by polymerization in the absence of such a clay. In addition, they are of a discrete spectrum, usually multiplies of 6 or 7, and reach values of up to 40 mers. In the absence of clay a continuous spectrum of degrees of polymerization is obtained, and usually up to 4–6 mers only. Copolymerization in the absence of clays yields mostly random copolymers, in their presence mostly block copolymers are obtained.Optical density measurements show that after adsorption has taken place on the clay, stacking of its layers occurs. Polymerization starts only after these stacked layers have been formed. The distances between the layers — as measured by X-rays — increase during polymerization, probably because the resulting polymers settle in their interspace, while the adsorption site of the active monomers is at the edges of the clay.     

Origin of organic compounds on the primitive earth and in meteorites

The role and relative contributions of different forms of energy to the synthesis of amino acids and other organic compounds on the primitive earth, in the parent bodies or carbonaceous chondrites, and in the solar nebula are examined. A single source of energy or a single process would not account for all the organic compounds synthesized in the solar system. Electric discharges appear to produce amino acids more efficiently than other sources of energy and the composition of the synthesized amino acids is qualitatively similar to those found in the Murchison meteorite. Ultraviolet light is also likely to have played a major role in prebiotic synthesis. Although the energy in the sun's spectrum that can be absorbed by the major constituents of the primitive atmosphere is not large, reactive trace components such as H2S and formaldehyde absorb at longer wavelengths where greater amounts of energy are available and produce amino acids by reactions involving hot hydrogen atoms. The thermal reaction of CO + H2 + NH3 on Fischer-Tropsch catalysts generates intermediates that lead to amino acids and other organic compounds that have been found in meteorites. However, this synthesis appears to be less efficient than electric discharges and to require a special set of reaction conditions. It should be emphasized that after the reactive organic intermediates are generated by the above processes, the subsequent reactions which produce the more complete biochemical compounds are low temperature homogenous reactions occurring in an aqueous environment.     

pH profile of the adsorption of nucleotides onto montmorillonite

The effect of adsorbed ions and pH on the adsorption of several purine and pyrimidine nucleotides on montmorillonite was studied. The cations used to prepare homoionic montmorillonite were Na⁺, Mn²⁺, Fe³⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. The nucleotides studied were 5-, 3-, and 2-AMP, and 5-CMP in the pH range 2 through 12. The results show that preferential adsorption amongst nucleotides and similar molecules is dependent upon pH and the nature of the substituted metal cation in the clay. At neutral pH, it was observed that 5-AMP was more strongly adsorbed than 2-AMP, 3-AMP, and 5-CMP. Cu²⁺ and Zn²⁺ clays showed enhanced adsorption of 5-AMP compared to the other cation clays studied in the pH range 4–8. Below pH 4, the adsorption is attributed to cation and anion exchange adsorption mechanisms; above pH 4, anion exchange may also occur, but the adsorption (when it occurs) likely depends on a complexation mechanism occurring between metal cation in the clay exchange site and the biomolecule. It is thus proposed that homoionic clays may have played a significant role in the concentration mechanism of biomonomers in the prebiotic environment, a prerequisite step necessary for the formation of biopolymers in the remaining steps leading to the origin of life.On leave from Saegram Centre for Soil and Water Sciences, Hebrew University, Rehovot, 76100, Israel.     

Interaction between bacteriophage PBS1 and clay minerals and transduction of Bacillus subtilis by clay-phage complexes

Bacteriophage PBS1 of Bacillus subtilis was rapidly adsorbed on montmorillonite (M) and kaolinite (K), and adsorption was maximal after 30 min on both clays. There was no correlation between adsorption and the cation exchange capacity of the clays. Studies with sodium metaphosphate (a polyanion that interacts with positively charged sites on clay) indicated that positively charged sites on K were primarily responsible for the adsorption of the phage, whereas other mechanisms appeared to be involved in adsorption of the phage on M. X-ray diffraction and electron microscopic analyses showed that the phage partially intercalated M. Survival of the phage was increased by adsorption on the clays, and adsorbed phage maintained its ability to transduce bacterial cells for at least 30 days (the longest time studied) after the preparation of the clay–phage complexes. Electron microscopic observations indicated that transduction by the clay–phage complexes was primarily the result of the phage detaching from the clays in the presence of host cells.     

Photosynthesis and the Origin of Life

The origin and evolution of photosynthesis is considered to be the key to the origin of life. This eliminates the need for a soup as the synthesis of the bioorganics are to come from the fixation of carbon dioxide and nitrogen. No soup then no RNA world or Protein world. Cyanobacteria have been formed by the horizontal transfer of green sulfur bacterial photoreaction center genes by means of a plasmid into a purple photosynthetic bacterium. The fixation of carbon dioxide is considered to have evolved from a reductive dicarboxylic acid cycle (Chloroflexus) which was then followed by a reductive tricarboxylic acid cycle (Chlorobium) and finally by the reductive pentose phosphate cycle (Calvin cycle). The origin of life is considered to have occurred in a hot spring on the outgassing early earth. The first organisms were self-replicating iron-rich clays which fixed carbon dioxide into oxalic and other dicarboxylic acids. This system of replicating clays and their metabolic phenotype then evolved into the sulfide rich region of the hotspring acquiring the ability to fix nitrogen. Finally phosphate was incorporated into the evolving system which allowed the synthesis of nucleotides and phospholipids. If biosynthesis recapitulates biopoesis, then the synthesis of amino acids preceded the synthesis of the purine and pyrimidine bases. Furthermore the polymerization of the amino acid thioesters into polypeptides preceded the directed polymerization of amino acid esters by polynucleotides. Thus the origin and evolution of the genetic code is a late development and records the takeover of the clay by RNA.