The sugar model: catalysis by amines and amino acid products

Gamma-Ray-Induced Amino Acid Formation during Aqueous Alteration in Small Bodies: The Effects of Compositions of Starting Solutions

Organic compounds, such as amino acids, are essential for the origin of life, and they may have been delivered to the prebiotic Earth from extra-terrestrial sources, such as carbonaceous chondrites. In the parent bodies of carbonaceous chondrites, the radioactive decays of short-lived radionuclides, such as 26Al, cause the melting of ice, and aqueous alteration occurs in the early stages of solar system formation. Many experimental studies have shown that complex organic matter, including amino acids and high-molecular-weight organic compounds, is produced by such hydrothermal processes. On the other hand, radiation, particularly gamma rays from radionuclides, can contribute to the formation of amino acids from simple molecules such as formaldehyde and ammonia. In this study, we investigated the details of gamma-ray-induced amino acid formation, focusing on the effects of different starting materials on aqueous solutions of formaldehyde, ammonia, methanol, and glycolaldehyde with various compositions, as well as hexamethylenetetramine. Alanine and glycine were the most abundantly formed amino acids after acid hydrolysis of gamma-ray-irradiated products. Amino acid formation increased with increasing gamma-ray irradiation doses. Lower amounts of ammonia relative to formaldehyde produced more amino acids. Glycolaldehyde significantly increased amino acid yields. Our results indicated that glycolaldehyde formation from formaldehyde enhanced by gamma rays is key for the subsequent production of amino acids.

Towards a prebiotic chemoton - nucleotide precursor synthesis driven by the autocatalytic formose reaction

The formose reaction is often cited as a prebiotic source of sugars and remains one of the most plausible forms of autocatalysis on the early Earth. Herein, we investigated how cyanamide and 2-aminooxazole, molecules proposed to be present on early Earth and precursors for nonenzymatic ribonucleotide synthesis, mediate the formose reaction using HPLC, LC-MS and 1H NMR spectroscopy. Cyanamide was shown to delay the exponential phase of the formose reaction by reacting with formose sugars to form 2-aminooxazole and 2-aminooxazolines thereby diverting some of these sugars from the autocatalytic cycle, which nonetheless remains intact. Masses for tetrose and pentose aminooxazolines, precursors for nucleotide synthesis including TNA and RNA, were also observed. The results of this work in the context of the chemoton model are further discussed. Additionally, we highlight other prebiotically plausible molecules that could have mediated the formose reaction and alternative prebiotic autocatalytic systems.

Stability of DL-Glyceraldehyde under Simulated Hydrothermal Conditions: Synthesis of Sugar-like Compounds in an Iron(III)-Oxide-Hydroxide-Rich Environment under Acidic Conditions

Researchers have suggested that the condensation of low-molecular-weight aldehydes under basic conditions (e.g., pH > 11) is the prebiotic reaction responsible for the abiotic formation of carbohydrates. It has also been suggested that surface hydrothermal systems were ubiquitous during the early Archean period. Therefore, the catalysis of prebiotic carbohydrate synthesis by metallic oxide minerals under acidic conditions in these environments seems considerably more probable than the more widely hypothesized reaction routes. This study investigates the stability of DL-glyceraldehyde and its reaction products under the simulated conditions of an Archean surface hydrothermal system. The Hveradalur geothermal area in Iceland was selected as an analog of such a system. HPLC-ESIMS, UV−Vis spectroscopy, Raman spectroscopy and XPS spectroscopy were used to analyze the reaction products. In hot (323 K) and acidic (pH 2) solutions under the presence of suspended iron(III) oxide hydroxide powder, DL-glyceraldehyde readily decomposes into low-molecular-weight compounds and transforms into sugar-like molecules via condensation reactions.

On the Evolutionary History of the Twenty Encoded Amino Acids

α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.

On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review

By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.

A way to thioacetate esters compatible with non-oxidative prebiotic conditions

The centrality of pyruvate oxidative decarboxylation into acetyl-CoA in current biochemistry is a strong argument for proposing that a similar reaction have been necessary for the development of an effective protometabolism on the primitive Earth. However, such a decarboxylation requires the use of an oxidant and a catalyst, today enzymatic. Based on the mechanisms of the pyruvate dehydrogenase complex and pyruvate-ferredoxin oxidoreductase, we propose that the initial mechanism involved disulfides and occurred via radicals. A first disulfide is obtained by reacting glyoxylate with hydrogen sulfide. It is then possible to produce a wide variety of other disulfides by exchange reactions. When reacted with pyruvate under UV light they give thioesters. This process requires no oxidant and is therefore compatible with what is known of the redox conditions of the early Earth. Neither does it require any catalyst. It could be the first way to acetyl thioesters, a way that was later improved by the introduction of catalysts, first minerals, then enzymes.

Aerobic Glycolysis in the Retina: Functional Roles of Pyruvate Kinase Isoforms

One hundred years ago, Otto Heinrich Warburg observed that postmitotic retinal cells are the highest oxygen-consuming cells in the body. He compared these cells to actively growing mitotic tumor cells since both cells reprogram glucose for anabolic processes, which include lipid, protein, and RNA/DNA synthesis, and for antioxidant metabolism. To achieve this metabolic reprogramming, cancer cells preferentially express a less active dimeric form, the M2 isoform of pyruvate kinase (PKM2), which shuttles glucose toward the accumulation of glycolytic intermediates that redirect cell activities into anabolic processes. Similar to cancer cells, retinal photoreceptors predominantly express the M2 isoform of PKM2. This isoform performs both metabolic and non-metabolic functions in photoreceptor cells. This review focuses on the metabolic and non-metabolic roles of pyruvate kinases in photoreceptor cell functions.

The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.

Prebiotic synthesis of 2-deoxy-d-ribose from interstellar building blocks promoted by amino esters or amino nitriles

Amino esters and amino nitriles can promote the selective formation of 2-deoxy-d-ribose from materials present in interstellar ices. The use of amino nitriles suggests the possibility that carbohydrates may have existed before amino acids on the prebiotic Earth.

Prebiotic synthesis of phosphoenol pyruvate by α-phosphorylation-controlled triose glycolysis

Phosphoenol pyruvate is the highest-energy phosphate found in living organisms and is one of the most versatile molecules in metabolism. Consequently, it is an essential intermediate in a wide variety of biochemical pathways, including carbon fixation, the shikimate pathway, substrate-level phosphorylation, gluconeogenesis and glycolysis. Triose glycolysis (generation of ATP from glyceraldehyde 3-phosphate via phosphoenol pyruvate) is among the most central and highly conserved pathways in metabolism. Here, we demonstrate the efficient and robust synthesis of phosphoenol pyruvate from prebiotic nucleotide precursors, glycolaldehyde and glyceraldehyde. Furthermore, phosphoenol pyruvate is derived within an α-phosphorylation controlled reaction network that gives access to glyceric acid 2-phosphate, glyceric acid 3-phosphate, phosphoserine and pyruvate. Our results demonstrate that the key components of a core metabolic pathway central to energy transduction and amino acid, sugar, nucleotide and lipid biosyntheses can be reconstituted in high yield under mild, prebiotically plausible conditions.

Kinetics of the conversion of dihydroxyacetone to methylglyoxal in New Zealand mānuka honey: Part II--Model systems

The irreversible dehydration reaction of dihydroxyacetone (DHA) to methylglyoxal (MGO) in a honey model system has been examined to investigate the influence of added perturbant species on the reaction rate. The secondary amino acid proline, primary amino acids (alanine, lysine and serine), and iron, or combinations of these perturbants, were added to artificial honey with either DHA or MGO and stored at 20, 27 and 37°C. These systems were monitored over time. A 1:1 conversion of DHA to MGO was not observed in any system studied, including the control system with no added perturbants. Addition of proline to the matrix increased consumption of DHA but did not produce any more MGO than the control sample. Lysine and serine behaved similarly. Alanine enhanced the conversion of DHA to MGO and had the best efficiency of conversion of DHA to MGO for the amino acids studied. An iron II salt enhanced the conversion of DHA to MGO, even in the presence of proline.

The origin of RNA and "my grandfather's axe"

The origin of RNA is one of the most formidable problems facing prebiotic chemists. We consider RNA as a product of evolution, as opposed to the more conventional view of RNA as originally being the product of abiotic processes. We have come to accept that life's informational polymers have changed in chemical structure since their emergence, which presents a quandary similar to the paradox of "My Grandfather's Axe". Here, we discuss reasons why all contemporary components of RNA--the nucleobases, ribose, and phosphate--are not likely the original components of the first informational polymer(s) of life. We also evaluate three distinct models put forth as pathways for how the earliest informational polymers might have assembled. We see the quest to uncover the ancestors of RNA as an exciting scientific journey, one that is already providing additional chemical constraints on the origin of life and one that has the potential to produce self-assembling materials, novel catalysis, and bioactive compounds.

Catalysis of glyceraldehyde synthesis by primary or secondary amino acids under prebiotic conditions as a function of pH

The synthesis of an excess of D-glyceraldehyde by coupling glycolaldehyde with formaldehyde under prebiotic conditions is catalyzed by L amino acids having primary amino groups at acidic pH's, but at neutral or higher pH's they preferentially form L-glyceraldehyde. L Amino acids having secondary amino groups, such as proline, have the reverse preferences, affording excess L-glyceraldehyde at low pH but excess D-glyceraldehyde at higher pHs. Detailed mechanistic proposals make these preferences understandable. The relevance of these findings to the origin of D sugars on prebiotic Earth is described.

The role of carbohydrates at the origin of homochirality in biosystems

Pasteur has demonstrated that the chiral components in a racemic mixture can separate in homochiral crystals. But with a strong chiral discrimination the chiral components in a concentrated mixture can also phase separate into homochiral fluid domains, and the isomerization kinetics can then perform a symmetry breaking into one thermodynamical stable homochiral system. Glyceraldehyde has a sufficient chiral discrimination to perform such a symmetry breaking. The requirement of a high concentration of the chiral reactant(s) in an aqueous solution in order to perform and maintain homochirality; the appearance of phosphorylation of almost all carbohydrates in the central machinery of life; the basic ideas that the biochemistry and the glycolysis and gluconeogenesis contain the trace of the biochemical evolution, all point in the direction of that homochirality was obtained just after- or at a phosphorylation of the very first products of the formose reaction, at high concentrations of the reactants in phosphate rich compartments in submarine hydrothermal vents. A racemic solution of D,L-glyceraldehyde-3-phosphate could be the template for obtaining homochiral D-glyceraldehyde-3-phosphate(aq) as well as L-amino acids.

Production of tartrates by cyanide-mediated dimerization of glyoxylate: a potential abiotic pathway to the citric acid cycle

An abiotic formation of meso- and DL-tartrates in 80% yield via the cyanide-catalyzed dimerization of glyoxylate under alkaline conditions is demonstrated. A detailed mechanism for this conversion is proposed, supported by NMR evidence and (13)C-labeled reactions. Simple dehydration of tartrates to oxaloacetate and an ensuing decarboxylation to form pyruvate are known processes that provide a ready feedstock for entry into the citric acid cycle. While glyoxylate and high hydroxide concentration are atypical in the prebiotic literature, there is evidence for natural, abiotic availability of each. It is proposed that this availability, coupled with the remarkable efficiency of tartrate production from glyoxylate, merits consideration of an alternative prebiotic pathway for providing constituents of the citric acid cycle.

The "strong" RNA world hypothesis: fifty years old

This year marks the 50(th) anniversary of a proposal by Alex Rich that RNA, as a single biopolymer acting in two capacities, might have supported both genetics and catalysis at the origin of life. We review here both published and previously unreported experimental data that provide new perspectives on this old proposal. The new data include evidence that, in the presence of borate, small amounts of carbohydrates can fix large amounts of formaldehyde that are expected in an environment rich in carbon dioxide. Further, we consider other species, including arsenate, arsenite, phosphite, and germanate, that might replace phosphate as linkers in genetic biopolymers. While linkages involving these oxyanions are judged to be too unstable to support genetics on Earth, we consider the possibility that they might do so in colder semi-aqueous environments more exotic than those found on Earth, where cosolvents such as ammonia might prevent freezing at temperatures well below 273 K. These include the ammonia-water environments that are possibly present at low temperatures beneath the surface of Titan, Saturn's largest moon.

Homochirality in bio-organic systems and glyceraldehyde in the formose reaction

The article explores the possibility that the ordering of bio-organic molecules into a homochiral assembly at the origin of life was performed not in aqueous solutions of amino acids or related materials but in racemic glyceraldehyde in the "formose" reaction at high concentration and temperature. Based on physical chemical evidence and computer simulations of condensed fluids, it is argued that the isomerization kinetics of glyceraldehyde is responszible of the symmetry break and the ordering of molecules into homochiral domains.

Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA

RNA has been called a "prebiotic chemist's nightmare" because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. However, a discontinuous synthesis model is well-supported by experimental work that might produce RNA from atmospheric CO(2), H(2)O, and N(2). For example, electrical discharge in such atmospheres gives formaldehyde (HCHO) in large amounts and glycolaldehyde (HOCH(2)CHO) in small amounts. When rained into alkaline aquifers generated by serpentinizing rocks, these substances were undoubtedly converted to carbohydrates including ribose. Likewise, atmospherically generated HCN was undoubtedly converted in these aquifers to formamide and ammonium formate, precursors for RNA nucleobases. Finally, high reduction potentials maintained by mantle-derived rocks and minerals would allow phosphite to be present in equilibrium with phosphate, mobilizing otherwise insoluble phosphorus for the prebiotic synthesis of phosphite and phosphate esters after oxidation. So why does the community not view this discontinuous synthesis model as compelling evidence for the RNA-first hypothesis for the origin of life? In part, the model is deficient because no experiments have joined together those steps without human intervention. Further, many steps in the model have problems. Some are successful only if reactive compounds are presented in a specific order in large amounts. Failing controlled addition, the result produces complex mixtures that are inauspicious precursors for biology, a situation described as the "asphalt problem". Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a "water problem". Finally, some bonds in RNA appear to be "impossible" to form under any conditions considered plausible for early Earth. To get a community-acceptable "RNA first" model for the origin of life, the discontinuous synthesis model must be developed. In particular, the model must be refined so that it yields oligomeric RNA from CO(2), H(2)O, and N(2) without human intervention. This Account describes our efforts in this direction. Our hypothesis centers on a geological model that synthesizes RNA in a prebiotic intermountain dry valley (not in a marine environment). This valley receives high pH run-off from a watershed rich in serpentinizing olivines and eroding borate minerals. The runoff contains borate-stabilized carbohydrates, formamide, and ammonium formate. As atmospheric CO(2) dissolves in the subaerial aquifer, the pH of the aquifer is lowered. In the desert valley, evaporation of water, a solvent with a nucleophilic "background reactivity", leaves behind formamide, a solvent with an electrophilic "background reactivity". As a result, nucleobases, formylated nucleobases, and formylated carbohydrates, including formylated ribose, can form. Well-known chemistry transforms these structures into nucleosides, nucleotides, and partially formylated oligomeric RNA.

Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective

"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.

Primitive genetic polymers

Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?

Extended high circular polarization in the Orion massive star forming region: implications for the origin of homochirality in the solar system

We present a wide-field (approximately 6' x 6') and deep near-infrared (K(s) band: 2.14 mum) circular polarization image in the Orion nebula, where massive stars and many low-mass stars are forming. Our results reveal that a high circular polarization region is spatially extended (approximately 0.4 pc) around the massive star-forming region, the BN/KL nebula. However, other regions, including the linearly polarized Orion bar, show no significant circular polarization. Most of the low-mass young stars do not show detectable extended structure in either linear or circular polarization, in contrast to the BN/KL nebula. If our solar system formed in a massive star-forming region and was irradiated by net circularly polarized radiation, then enantiomeric excesses could have been induced, through asymmetric photochemistry, in the parent bodies of the meteorites and subsequently delivered to Earth. These could then have played a role in the development of biological homochirality on Earth.

Sugar-driven prebiotic synthesis of ammonia from nitrite

Reaction of 3-5 carbon sugars, glycolaldehyde, and alpha-ketoaldehydes with nitrite under mild anaerobic aqueous conditions yielded ammonia, an essential substrate for the synthesis of nitrogen-containing molecules during abiogenesis. Under the same conditions, ammonia synthesis was not driven by formaldehyde, glyoxylate, 2-deoxyribose, and glucose, a result indicating that the reduction process requires an organic reductant containing either an accessible alpha-hydroxycarbonyl group or an alpha-dicarbonyl group. Small amounts of aqueous Fe(+3) catalyzed the sugar-driven synthesis of ammonia. The glyceraldehyde concentration dependence of ammonia synthesis, and control studies of ammonia's reaction with glyceraldehyde, indicated that ammonia formation is accompanied by incorporation of part of the synthesized ammonia into sugar-derived organic products. The ability of sugars to drive the synthesis of ammonia is considered important to abiogenesis because it provides a way to generate photochemically unstable ammonia at sites of sugar-based origin-of-life processes from nitrite, a plausible prebiotic nitrogen species.

Planetary organic chemistry and the origins of biomolecules

Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as "tar" or "tholin." These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive "dead ends" under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a "carbohydrate world," but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.

Imitating prebiotic homochirality on Earth

We show how the amino acids needed on prebiotic earth in their homochiral L form can be produced by a reaction of L-alpha-methyl amino acids-that have been identified in the Murchison meteorite-with alpha-keto acids under credible prebiotic conditions. When they are simply heated together they perform a process of decarboxylative transamination but with almost no chiral transfer, and that in the wrong direction, producing D-amino acids from the L-alpha-methyl amino acids. With copper ion a square planar complex with two of the reaction intermediates is formed, and now there is the desired L to L transformation, producing small enantioexcesses of the normal L-amino acids. We also show how these can be amplified, not by making more of the L form but by increasing its concentration in water solution. The process can start with a miniscule excess and in one step generate water solutions with L/D ratios in the over 90% region. Kinetic processes can exceed the results from equilibria. We have also examined such amplifications with ribonucleosides, and have shown that initial modest excesses of the D-nucleosides can be amplified to afford water solutions with D to L ratios in the high 90's. We have shown that the homochiral compound has two effects on the solubility of the racemate. On one hand it decreases the solubility of the racemate by its role in the solubility product, as a theoretical equation predicts. On the other hand, it increases the solubility of the racemate by changing the nature of the solvent, acting as a cosolvent with the water. This explains why the amplification, while large, is not as large as the simple theoretical equation predicts. Thus when credible examples are produced where small enantioexcesses of D-ribose are created under credible prebiotic conditions, the prerequisites for the RNA world will have been exemplified.

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.

On the origin of terrestrial homochirality for nucleosides and amino acids

Before life could start on earth, it was important that the amino acid building blocks be present in a predominant handedness called the L configuration and that the ribose of RNA be predominantly in the D configuration. Because ordinary chemical processes would produce them in equal L and D amounts, it has long been a puzzle how the needed selectivities could have arisen. Carbonaceous chondrites such as the Murchison meteorite, which landed in Australia in 1969, brought some unusual amino acids with a methyl group replacing their alpha hydrogen. They cannot racemize and have a small but real excess of those with the L configuration. We have shown that they can partake in a synthesis of normal L amino acids under credible prebiotic conditions. We and others showed that small preferences can be amplified into solutions with very high dominance of the L amino acids because of the higher solubility of the pure L form than of the more stable DL racemic compound crystal. Here, we show that such solubility-based amplification of small excesses of three D nucleosides, uridine, adenosine, and cytidine, can also occur to form solutions with very high D dominance under credible prebiotic conditions. Guanosine crystallizes as a conglomerate and does not amplify in this way. However, under prebiotic conditions it could have been formed from homochiral D ribose from the hydrolysis of amplified adenosine or cytidine.

Origin of homochirality in biosystems

Experimental data for a series of central and simple molecules in biosystems show that some amino acids and a simple sugar molecule have a chiral discrimination in favor of homochirality. Models for segregation of racemic mixtures of chiral amphiphiles and lipophiles in aqueous solutions show that the amphiphiles with an active isomerization kinetics can perform a spontaneous break of symmetry during the segregation and self-assembly to homochiral matter. Based on this observation it is argued that biomolecules with a sufficiently strong chiral discrimination could be the origin of homochirality in biological systems.

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.

The origin of the RNA world: Co-evolution of genes and metabolism

Discoveries demonstrating that RNA can serve genetic, catalytic, structural, and regulatory roles have provided strong support for the existence of an RNA World that preceded the origin of life as we know it. Despite the appeal of this idea, it has been difficult to explain how macromolecular RNAs emerged from small molecules available on the early Earth. We propose here a mechanism by which mutual catalysis in a pre-biotic network initiated a progression of stages characterized by ever larger and more effective catalysts supporting a proto-metabolic network, and the emergence of RNA as the dominant macromolecule due to its ability to both catalyze chemical reactions and to be copied in a template-directed manner. This model suggests that many features of modern life, including the biosynthetic pathways leading to simple metabolites, the structures of organic and metal ion cofactors, homochirality, and template-directed replication of nucleic acids, arose long before the RNA World and were retained as pre-biotic systems became more sophisticated.

The sugar model: autocatalytic activity of the triose-ammonia reaction

Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose-ammonia reaction product on the kinetics of a second identical triose-ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate of formation of pyruvaldehyde, the product of triose dehydration. 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 autocatalytic molecules.

On a Hypothetical Generational Relationship between HCN and Constituents of the Reductive Citric Acid Cycle

Encouraged by observations made on the course of reactions the HCN-tetramer can undergo with acetaldehyde, I delineate a constitutional and potentially generational relationship between HCN and those constituents of the reductive citric acid cycle that are direct precursors of amino acids in contemporary metabolism. In this context, the robustness postulate of classical prebiotic chemistry is questioned, and, by an analysis of the (hypothetical) reaction-tree of a stepwise hydrolysis of the HCN-tetramer, it is shown how such a non-robust chemical reaction platform could harbor the potential for the emergence of autocatalytic cycles. It is concluded that the chemistry of HCN should be revisited by focussing on its non-robust parts in order to demonstrate its full potential as one of the possible roots of prebiotic self-organizing chemical processes.

The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution

Using a water-based prebiotic model of sugar synthesis involving glycolaldehyde self-condensation, we demonstrate that homochiral L-dipeptide catalysts lead to the stereospecific syntheses of tetroses. The asymmetric effect is largest for erythrose, which may reach a D-enantiomeric excess of >80% with L-Val-L-Val catalyst. Based on results obtained with various peptides, we propose a possible catalytic-reaction intermediate, consisting of an imidazolidinone ring formed between the two nitrogen atoms of the peptide catalyst and the C1 of one glycolaldehyde molecule. The study was motivated by the premise that exogenous material, such as the nonracemic amino acids found in meteorites, could have participated in the terrestrial evolution of molecular asymmetry by stereospecific catalysis. Because peptides might have formed readily on the early Earth, it is possible that their catalytic contribution was relevant in the prebiotic processes that preceded the onset of life.

5-(Pyrrolidin-2-yl)-1H-tetrazole and 5-[(Pyrrolidin-2-yl)methyl]-1H-tetrazole: Proline Surrogates with Increased Potential in Asymmetric Catalysis

Catalytic enantioselective methodology has dramatically been enriched by the re-discovery of the simple amino acid proline as a chiral catalyst in the year 2000. Although no catalyst offers such a simple and broad access to quite complex reaction products, as does proline, its synthetic potential is not unrestricted, what is especially connected to its poor solubility in organic media. Exchange of the carboxylic moiety by a tetrazole unit leads to proline surrogates, that by far outperform proline with respect to yield, enantioselectivity, reaction time, substrate and solvent scope, catalyst loading, and stoichiometry of the compounds used in excess. These factors are discussed and critically compared with selected representative proline-catalyzed reactions.

Glyoxylate as a backbone linkage for a prebiotic ancestor of RNA

The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate (the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group in modern RNA. Although in low yields ( approximately 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions, provided that metal ions are present (e.g., Mg2+), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 degrees C), i.e. under "drying conditions". Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge. Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate.