Are polyphosphates or phosphate esters prebiotic reagents?

It is widely held that there was a phosphate compound in prebiotic chemistry that played the role of adenosine triphosphate and that the first living organisms had ribose-phosphate in the backbone of their genetic material. However, there are no known efficient prebiotic synthesis of high-energy phosphates or phosphate esters. We review the occurrence of phosphates in Nature, the efficiency of the volcanic synthesis of P₄O₁₀, the efficiency of polyphosphate synthesis by heating phosphate minerals under geological conditions, and the use of high-energy organic compounds such as cyanamide or hydrogen cyanide. These are shown to be inefficient processes especially when the hydrolysis of the polyphosphates is taken into account. For example, if a whole atmosphere of methane or carbon monoxide were converted to cyanide which somehow synthesized polyphosphates quantitatively, the polyphosphate concentration in the ocean would still have been insignificant. We also attempted to find more efficient high-energy polymerizing agents by spark discharge syntheses, but without success. There may still be undiscovered robust prebiotic syntheses of polyphosphates, or mechanisms for concentrating them, but we conclude that phosphate esters may not have been constituents of the first genetic material. Phosphoanhydrides are also unlikely as prebiotic energy sources. Correspondence to: S.L. Miller     

Non-enzymatic synthesis of the coenzymes,uridine diphosphate glucose and cytidine diphosphate choline,and other phosphorylated metabolic intermediates

The synthesis of uridine diphosphate glucose (UDPG), cytidine diphosphate choline (CDP-choline), glucose-1-phosphate (G1P) and glucose-6-phosphate (G6P) has been accomplished under simulated prebiotic conditions using urea and cyanamide, two condensing agents considered to have been present on the primitive Earth. The synthesis of UDPG was carried out by reacting G1P and UTP at 70 °C for 24 hours in the presence of the condensing agents in an aqueous medium. CDP-choline was obtained under the same conditions by reacting choline phosphate and CTP. G1P and G6P were synthesized from glucose and inorganic phosphate at 70 °C for 16 hours. Separation and identification of the reaction products have been performed by paper chromatography, thin layer chromatography, enzymatic analysis and ion pair reverse phase high performance liquid chromatography. These results suggest that metabolic intermediates could have been synthesized on the primitive Earth from simple precursors by means of prebiotic condensing agents.     

The prebiotic synthesis and catalytic role of imidazoles and other condensing agents

In the past decade significant advances have been made in the synthesis of oligonucleotides and other polymers by means of imidazoles and other condensing agents. In spite of the current knowledge of the chemistry of imidazoles and their importance as prebiotic catalysts, their formation under primitive earth conditions has not been properly demonstrated. We have now been able to synthesize imidazole as well as its 2-methyl and 4-methyl derivatives under plausible prebiotic conditions. One method utilizes an aldehyde (formaldehyde or acetaldehyde), glyoxal and ammonia as the starting materials for the formation of imidazole and 2-methylimidazole. The other method uses a carbohydrate and ammonia as the key reagents for the synthesis of 4-methylimidazole. The importance of imidazole and related compounds (e.g., cyanamide) in the synthesis of oligonucleotides has been studied by us as well as others. Apparently the charge relay group (-N-C-N-) present in imidazoles, carbodiimides, cyanamide, or the histidine and arginine of enzyme active centers is essential for the synthesis of phosphodiester and pyrophosphate bonds.     

The prebiotic synthesis and catalytic role of imidazoles and other condensing agents

In the past decade significant advances have been made in the synthesis of oligonucleotides and other polymers by means of imidazoles and other condensing agents. In spite of the current knowledge of the chemistry of imidazoles and their importance as prebiotic catalysts, their formation under primitive earth conditions has not been properly demonstrated. We have now been able to synthesize imidazole as well as its 2-methyl and 4-methyl derivatives under plausible prebiotic conditions. One method utilizes an aldehyde (formaldehyde or acetaldehyde), glyoxal and ammonia as the starting materials for the formation of imidazole and 2-methylimidazole. The other method uses a carbohydrate and ammonia as the key reagents for the synthesis of 4-methylimidazole. The importance of imidazole and related compounds (e.g., cyanamide) in the synthesis of oligonucleotides has been studied by us as well as others. Apparently the charge relay group (–N–C–N–) present in imidazoles, carbodiimides, cyanamide, or the histidine and arginine of enzyme active centers is essential for the synthesis of phosphodiester and pyrophosphate bonds.     

Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH

The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0–100 °C) and acidity (pH 1–12), while open to the atmosphere. After 24 h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.     

Stereospecificity of peptide synthesis by means of phosphorus derivatives: a model of peptide synthesis in molecular evolution

A hypothesis is presented to explain the prebiotic formation of optically pure oligo- and polypeptides from racemic amino acids. Stereospecific condensation reactions favouring the formation of isotactic stereosequences (l-l and d-d blocks) are a basic requirement of this hypothesis. Since phosphorus derivatives such as polyphosphates or nucleic acid imidazolides were postulated to be prebiotic condensing reagents, a variety of peptide syntheses by means of phosphorus derivatives was investigated. Dipeptides and tripeptides were prepared from N-protected d,l-amino acids or d,l-amino acid esters, and d,l-leucine and d,l-valine were subjected to condensation polymerizations. The stereosequences were analysed by means of ¹³C n.m.r. spectroscopy. More than 80% of all condensations were more or less stereospecific and in all cases isotactic sequences were predominant. In the case of poly(d,l-leucines), ¹³C n.m.r. cross-polarization/magic angle spinning (CP/MAS) spectra revealed the formation of α-helical blocks.     

Prebiotic synthesis of histidyl-histidine

Summary Histidyl-histidine (His-His) has been synthesized in a yield of up to 14.4% under plausible prebiotic conditions using histidine (His), cyanamide, and 4-amino-5-imidazole carboxamide. A trace amount of His trimer was also detected. Because the imidazole group of His is involved in a number of important enzymatic reactions, and His-His has been shown to catalyze the prebiotic synthesis of glycyl-glycine, we expect this work will stimulate further studies on the catalytic activities of simple His-containing peptides in prebiotic reactions.     

Abiotic origin of biopolymers

A variety of methods have been investigated in different laboratories for the polymerization of amino acids and nucleotides under abiotic conditions. They include (1) thermal polymerization, (2), direct polymerization of certain amino acid nitriles, amides or esters, (3) polymerization using polyphosphate esters, (4) polymerization under aqueous or drying conditions at moderate temperatures using a variety of simple catalysts or condensing agents like cyanamide, dicyandiamide, imidazole, etc., and (5) polymerization under similar mild conditions but employing activated monomers or abiotically synthesized high energy compounds such as adenosine 5-triphosphate (ATP). The role and significance of these methods for the synthesis of oligopeptides and oligonucleotides under possible primitive Earth conditions is evaluated. It is concluded that the latter more recent approach involving chemical processes similar to those used by contemporary living organisms, appears to offer a reasonable solution to the prebiotic synthesis of these biopolymers.Given at the International Seminar Origin of Life, 2–7, August 1974, Moscow, U.S.S.R.     

Novel formation of alpha-amino acids from alpha-oxo acids and ammonia in an aqueous medium

In the course of a study of possible mechanisms for chemical evolution in the primeval sea, we found the novel formation of alpha-amino acids and N-acylamino acids from alpha-oxo acids and ammonia in an aqueous medium. Glyoxylic acid reacted with ammonia to form N-oxalylglycine, which gave glycine in a 5-39% yield after hydrolysis with 6N HC1. Pyruvic acid and ammonia reacted to give N-acetylalanine, which formed alanine in a 3-7% overall yield upon hydrolysis. The pH optima in these reactions were between pH 3 and 4. These reactions were further extended to the formation of other amino acids. Glutamic acid, phenylalanine and alanine were formed from alpha-ketoglutaric acid, phenylpyruvic acid and oxaloacetic acid, respectively, under similar conditions. N-Succinylglutamic acid was obtained as an intermediate in glutamic acid synthesis. Phenylacetylphenylalanineamide was also isolated as an intermediate in phenylalanine synthesis. Alanine, rather than aspartic acid, was produced from oxaloacetic acid. These reactions provide a novel route for the prebiotic synthesis of amino acids. A mechanism for the reactions will be proposed.     

Prebiotic Oligomerization on or Inside Lipid Vesicles in Hydrothermal Environments

Oligomerization of amino acids proceeded on or inside lipid vesicles as a model of prebiotic cells in a simulated hydrothermal environment. When the suspension of lipid vesiclestaking up monomeric glycine underwent a sudden temperature dropby traversing from a hot (180 °C) to a cold (0 °C) region repeatedly while circulating through a closedreaction circuit, oligopeptides up to heptaglycine were formed even in the absence of condensing agents.     

Conversion of Biosynthetic Precursors of RNA to Those of DNA by Photoredox Chemistry

Soon after the origin of RNA-based life, depletion of prebiotically synthesised ribonucleotides would have driven the evolution of a biosynthetic pathway to these key building blocks. Ribozyme-catalysed nucleosidation—the key biosynthetic step—requires that ribose and the nucleobases are produced by abiotic chemistry and are relatively stable to the conditions of their synthesis. The most plausible prebiotic synthesis of sugars involves photoreduction of cyanohydrins by hydrogen sulphide in the presence of copper(I) cyanide, and we therefore subjected ribose to these conditions whereupon it was partially converted to 2-deoxyribose. Furthermore, a derivative of uracil is reduced under similar conditions to thymine. Thus, DNA biosynthetic precursors can be formed abiotically from those of RNA allowing for an early evolutionary transition to life based on RNA and DNA.     

Urea-acetylene dicarboxylic acid reaction: A likely pathway for prebiotic uracil formation

A number of routes have been suggested for the prebiotic synthesis of uracil involving the reaction of urea with malic acid, propiolic acid, cyanoacetylene and others. Cyanoacetylene has been detected in the interstellar medium as well as simulated prebiotic experiments. It is therefore plausible that dicyanoacetylene and its hydrolytic product acetylene dicarboxylic acid, (ADCA) may have played a role in chemical evolution. This aspect has been examined in the present work for the synthesis of uracil from ADCA and urea reaction.It was found that when ADCA reacted with urea, uracil was formed only in the presence of phosphoric acid and phosphates. Ammonium phosphates gave higher yields of uracil than other phosphates. In the absence of phosphoric acid or phosphates no uracil formation took place. This type of synthesis could have taken place in prebiotic oceans which contained ammonium phosphates and other salts.     

Sugar-Driven Prebiotic Synthesis of 3,5(6)-Dimethylpyrazin-2-one: A Possible Nucleobase of a Primitive Replication Process

Reaction of glyceraldehyde with alanine amide (or ammonia) under anaerobic aqueous conditions yielded 3,5(6)-dimethylpyrazin-2-one that is considered a possible complementary residue of a primitive replicating molecule that preceded RNA. Synthesis of the dimethylpyrazin-2-one isomers under mild aqueous conditions (65 degrees C, pH 5.5) from 100 mM glyceraldehyde and alanine amide (or ammonia) was complete in about 5 days. This synthesis using 25 mM glyceraldehyde and alanine amide gave a total pyrazinone yield of 9.3% consisting of 42% of the 3,5-dimethylprazin-2-one isomer and 58% of the 3,6-dimethylpyrazin-2-one isomer. The related synthesis of the dimethylpyrazin-2-one isomers from glyceraldehyde and ammonia was about 200-fold less efficient than the alanine amide reaction. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of small organic molecules. Possible sugar-driven pathways for the prebiotic synthesis of polymerizable 2-pyrazinone monomers are discussed.     

Catalysis by a prebiotic nucleotide analog of histidine

A ribosylated derivative of adenine, N6 ribosyl adenine, likely to have formed under prebiotic synthesis conditions, is shown to be as active as histidine in the model reaction of p-nitrophenyl acetate hydrolysis. This property widens the range of reactions accessible to RNA catalysis.     

Model for prebiotic pyrophosphate formation: Condensation of precipitated orthophosphate at low temperature in the absence of condensing or phosphorylating agents

Summary The formation of pyrophosphate (PPi) by condensation of orthophosphate (Pi) at low temperature (37°C) in the absence of condensing or phosphorylating agents could have been an ancient process in chemical evolution. In the present investigation the synthesis of³²PPi from³²Pi was carried out at pH 8.0 and PPi was found in larger amounts in the presence of insoluble Pi (with calcium or manganese ions) than in its absence (with magnesium ions, or with no divalent cations present). After 10 days of incubation in the presence of precipitated calcium phosphate, about 1.6 nmol/ml of PPi was formed (0.057% yield relative to insoluble Pi). The hypothesis that the reaction is dependent on precipitated Pi was reinforced by the effect of adding dimethyl sulfoxide (2.1–9.9 M) in the presence of magnesium ions: the amount of magnesium phosphate precipitated in the presence of the organic solvent was proportional to the amount of PPi formed. The large and negative activation entropies found in aqueous media with calcium ions and in a medium containing 11.3 M dimethyl sulfoxide with magnesium ions suggest that the reaction was favored by a hydrophobic phenomenon at the surface of solid Pi. This reaction could serve as a model for prebiotic formation of PPi.     

Synthesis of β-Peptide Standards for Use in Model Prebiotic Reactions

A one-pot method was developed for the preparation of a series of β-alanine standards of moderate size (2 to ≥12 residues) for studies concerning the prebiotic origins of peptides. The one-pot synthesis involved two sequential reactions: (1) dry-down self-condensation of β-alanine methyl ester, yielding β-alanine peptide methyl ester oligomers, and (2) subsequent hydrolysis of β-alanine peptide methyl ester oligomers, producing a series of β-alanine peptide standards. These standards were then spiked into a model prebiotic product mixture to confirm by HPLC the formation of β-alanine peptides under plausible reaction conditions. The simplicity of this approach suggests it can be used to prepare a variety of β-peptide standards for investigating differences between α- and β-peptides in the context of prebiotic chemistry.     

Prebiotic ribose synthesis: A critical analysis

The discovery of catalytic ability in RNA has given fresh impetus to speculations that RNA played a critical role in the origin of life. This question must rest on the plausibility of prebiotic oligonucleotide synthesis, rather than on the properties of the final product. Many cliams have been published to support the idea that the components of RNA were readily available on the prebiotic earth. In this article, the literature cited in support of the prebiotic availability of one subunit, D-ribose, is reviewed to determine whether it justifies the claim.Polymerization of formaldehyde (the formose reaction) has been the single reaction cited for prebiotic ribose synthesis. It has been conducted with different catalysts: numerous basic substances, neutral clays and heat, and various types of radiation. Ribose has been identified (yields are uncertain, but unlikely to be greater than 1%) in reactions run with concentrated (0.15 M or greater) formaldehyde. It has been claimed in reactions run at lower concentration, but characterization has been inadequate, and experimental details have not been provided.The complex sugar mixture produced in the formose reaction is rapidly destroyed under the reaction conditions. Nitrogenous substances (needed for prebiotic base synthesis) would interfere with the formose reaction by reacting with formaldehyde, the intermediates, and sugar products in undesirable ways.The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.     

The prospect of life on Jupiter

Recent research into the possibility of there being life in the Solar System other than on the Earth has suggested that Jupiter may be a good candidate. The reactions within its atmosphere, both photolytic and electrical, lead to the formation of many nitrile and amino compounds. We have simulated electrical discharges in the Jovian atmosphere, using anhydrous methane-ammonia mixtures, and shown the formation of simple aliphatic nitriles, amino-nitriles, and their oligomers. Including hydrogen sulfide in the gas mixture, it appears that sulfur-containing amino-nitriles are not formed, since the hydrolysate of the products did not contain the corresponding amino-acids. There is a strong analogy between these reactions and the classical spark reactions simulating the primitive Earth's atmosphere. We are attempting a closer simulation of Jupiter's atmosphere by using appropriate temperature and pressure conditions. It seems that prebiotic synthesis on Jupiter may have reached an advanced state. As an alternative approach we have tested the survival ability of common terrestrial microorganisms in aqueous media at 102 atmospheres pressure and at 20°C. in a simulated Jovian atmosphere.E. coli, S. marcescens, A. aerogenes andB. subtilis will all tolerate 24 h. under these conditions with conditions with little death. The ability of terrestrial organisms to survive Jovian atmospheric conditions, coupled with the likelihood of advanced prebiotic synthesis, suggests that a parallel evolution of life may have occurred on Jupiter and Earth, and that the two forms need not be so different as has been supposed. Lunar Science Institute Contribution.     

Imidazolium-Catalyzed Synthesis of an Imidazolium Catalyst

Origins of Life and Evolution of Biospheres - The chemistry of imidazolium-catalyzed imidazolium synthesis was studied as part of an effort to develop a plausible prebiotic synthesis of a small...     

Bioenergetics and Life's Origins

Bioenergetics is central to our understanding of living systems, yet has attracted relatively little attention in origins of life research. This article focuses on energy resources available to drive primitive metabolism and the synthesis of polymers that could be incorporated into molecular systems having properties associated with the living state. The compartmented systems are referred to as protocells, each different from all the rest and representing a kind of natural experiment. The origin of life was marked when a rare few protocells happened to have the ability to capture energy from the environment to initiate catalyzed heterotrophic growth directed by heritable genetic information in the polymers. This article examines potential sources of energy available to protocells, and mechanisms by which the energy could be used to drive polymer synthesis.Previous research on life''s origins has for the most part focused on the chemistry and energy sources required to produce the small molecules of life—amino acids, nucleobases, and amphiphiles—and to a lesser extent on condensation reactions by which the monomers can be linked into biologically relevant polymers. In modern living cells, polymers are synthesized from activated monomers such as the nucleoside triphosphates used by DNA and RNA polymerases, and the tRNA-amino acyl conjugates that supply ribosomes with activated amino acids. Activated monomers are essential because polymerization reactions occur in an aqueous medium and are therefore energetically uphill in the absence of activation.A central problem therefore concerns mechanisms by which prebiotic monomers could have been activated to assemble into polymers. Most biopolymers of life are synthesized when the equivalent of a water molecule is removed to form the ester bonds of nucleic acids, glycoside bonds of polysaccharides, and peptide bonds in proteins. In life today, the removal of water is performed upstream of the actual bond formation. This process involves the energetically downhill transfer of electrons, which is coupled to either substrate-level oxidation or generation of a proton gradient that in turn is the energy source for the synthesis of anhydride pyrophosphate bonds in ATP. The energy stored in the pyrophosphate bond is then distributed throughout the cell to drive most other energy‐dependent reactions. This is a complex and highly evolved process, so here we consider simpler ways in which energy could have been captured from the environment and made available for primitive versions of metabolism and polymer synthesis. Because the atmosphere of the primitive Earth did not contain appreciable oxygen, this review of primitive bioenergetics is limited to anaerobic sources of energy.