The triose model: glyceraldehyde as a source of energy and monomers for prebiotic condensation reactions

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 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.

Possible chemical and physical scenarios towards biological homochirality

The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.

The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life

The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life.

Chiral encoding may provide a simple solution to the origin of life

The route by which the complex and specific molecules of life arose from the 'prebiotic soup' remains an unsolved problem. Evolution provides a large part of the answer, but this requires molecules that can carry information (that is, exist in many variants) and can replicate themselves. The process is commonplace in living organisms, but not so easy to achieve with simple chemical systems. It is especially difficult to contemplate in the chemical chaos of the prebiotic world. Although popular in many quarters, the notion that RNA was the first self-replicator carries many difficulties. Here, we present an alternative view, suggesting that there may be undiscovered self-replication mechanisms possible in much simpler systems. In particular, we highlight the possibility of information coding through stereochemical configurations of substituents in organic polymers. We also show that this coding system leads naturally to enantiopurity, solving the apparent problem of biological homochirality.

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.

Metabolism of biodiesel-derived glycerol in probiotic Lactobacillus strains

Three probiotic Lactobacillus strains, Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus delbrueckii, were tested for their ability to assimilate and metabolize glycerol. Biodiesel-derived glycerol was used as the main carbon and energy source in batch microaerobic growth. Here, we show that the tested strains were able to assimilate glycerol, consuming between 38 and 48 % in approximately 24 h. L. acidophilus and L. delbrueckii showed a similar growth, higher than L. plantarum. The highest biomass reached was 2.11 g L⁻¹ for L. acidophilus, with a cell mass yield (Y (X/S)) of 0.37 g g⁻¹. L. delbrueckii and L. plantarum reached a biomass of 2.06 and 1.36 g L⁻¹. All strains catabolize glycerol mainly through glycerol kinase (EC 2.7.1.30). For these lactobacillus species, kinetic parameters for glycerol kinase showed Michaelis-Menten constant (K(m)) ranging from 1.2 to 3.8 mM. The specific activities for glycerol kinase in these strains were in the range of 0.18 to 0.58 U mg protein⁻¹, with L. acidophilus ATCC 4356 showing the maximum specific activity after 24 h of cultivation. Glycerol dehydrogenase activity was also detected in all strains studied but only for the reduction of glyceraldehyde with NADPH (K(m) for DL-glyceraldehyde ranging from 12.8 to 32.3 mM). This enzyme shows a very low oxidative activity with glycerol and NADP+ and, most likely, under physiological conditions, the oxidative reaction does not occur, supporting the assumption that the main metabolic flux concerning glycerol metabolism is through the glycerol kinase pathway.

The origins of the RNA world

The general notion of an "RNA World" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this "RNA-first" view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA.

RNA in evolution

RNA has played a variety of roles in the evolutionary history of life on the Earth. While this molecule was once considered a poor cousin of the more influential polymers in the cell, namely DNA and proteins, a string of important discoveries over the last 50 years has revealed that RNA may in fact be the cornerstone of biological function. In particular, the finding that RNA can be catalytic, and thus possess both a genotype and a phenotype, has forced us to consider the possibility that life's origins began with RNA, and that the subsequent diversification of life is aptly described as a string of innovations by RNA to adapt to a changing environment. Some of these adaptations include riboswitches, ribonucleoproteins (RNPs), RNA editing, and RNA interference (RNAi). Although many of these functions may seem at first glance to be recent evolutionary developments, it may be the case that all of their catalytic activities trace their roots back to a primordial 'RNA World' some four billion years ago, and that RNA's diversity has a continuous thread that pervades life from its very origins.

On the free energy that drove primordial anabolism

A key problem in understanding the origin of life is to explain the mechanism(s) that led to the spontaneous assembly of molecular building blocks that ultimately resulted in the appearance of macromolecular structures as they are known in modern biochemistry today. An indispensable thermodynamic prerequisite for such a primordial anabolism is the mechanistic coupling to processes that supplied the free energy required. Here I review different sources of free energy and discuss the potential of each form having been involved in the very first anabolic reactions that were fundamental to increase molecular complexity and thus were essential for life.

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.

The influence of environmental conditions, lipid composition, and phase behavior on the origin of cell membranes

At some point in life's development, membranes formed, providing barriers between the environment and the interior of the 'cell.' This paper evaluates the research to date on the prebiotic origin of cell membranes and highlights possible areas of continuing study. A careful review of the literature uncovered unexpected factors that influence membrane evolution. The major stages in primitive membrane formation and the transition to contemporary cell membranes appear to require an exacting relationship between environmental conditions and amphiphile composition and phase behavior. Also, environmental and compositional requirements for individual stages are in some instances incompatible with one another, potentially stultifying the pathway to contemporary membranes. Previous studies in membrane evolution have noted the effects composition and environment have on membrane formation but the crucial dependence and interdependence on these two factors has not been emphasized. This review makes clear the need to focus future investigations away from proof-of-principle studies towards developing a better understanding of the roles that environmental factors and lipid composition and polymorphic phase behavior played in the origin and evolution of cell membranes.

Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism

The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates.

Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily

A comprehensive, structural and functional, in silico analysis of the medium-chain dehydrogenase/reductase (MDR) superfamily, including 583 proteins, was carried out by use of extensive database mining and the blastp program in an iterative manner to identify all known members of the superfamily. Based on phylogenetic, sequence, and functional similarities, the protein members of the MDR superfamily were classified into three different taxonomic categories: (a) subfamilies, consisting of a closed group containing a set of ideally orthologous proteins that perform the same function; (b) families, each comprising a cluster of monophyletic subfamilies that possess significant sequence identity among them and might share or not common substrates or mechanisms of reaction; and (c) macrofamilies, each comprising a cluster of monophyletic protein families with protein members from the three domains of life, which includes at least one subfamily member that displays activity related to a very ancient metabolic pathway. In this context, a superfamily is a group of homologous protein families (and/or macrofamilies) with monophyletic origin that shares at least a barely detectable sequence similarity, but showing the same 3D fold. The MDR superfamily encloses three macrofamilies, with eight families and 49 subfamilies. These subfamilies exhibit great functional diversity including noncatalytic members with different subcellular, phylogenetic, and species distributions. This results from constant enzymogenesis and proteinogenesis within each kingdom, and highlights the huge plasticity that MDR superfamily members possess. Thus, through evolution a great number of taxa-specific new functions were acquired by MDRs. The generation of new functions fulfilled by proteins, can be considered as the essence of protein evolution. The mechanisms of protein evolution inside MDR are not constrained to conserve substrate specificity and/or chemistry of catalysis. In consequence, MDR functional diversity is more complex than sequence diversity. MDR is a very ancient protein superfamily that existed in the last universal common ancestor. It had at least two (and probably three) different ancestral activities related to formaldehyde metabolism and alcoholic fermentation. Eukaryotic members of this superfamily are more related to bacterial than to archaeal members; horizontal gene transfer among the domains of life appears to be a rare event in modern organisms.

Oligoglyceric acid synthesis by autocondensation of glyceroyl thioester

The autocondensation of the glyceroyl thioester S-glyceroyl-ethanethiol yielded oligoglyceric acid. The rates of autocondensation and hydrolysis of the thioester increased from pH 6.5 to pH 7.5 in 2,6-lutidine and imidazole buffers. Autocondensation and hydrolysis were much more rapid to imidazole buffers than in 2,6-lutidine buffers of the same pH. The efficiency of ester bond synthesis was about 20% for 40 mM S-glyceroyl-ethanethiol in 2,6-lutidine and imidazole buffers near neutral pH. The size and yield of the oligoglyceric acid products increased when the concentration of the thioester was increased. The relationship of these results to prebiotic polymer synthesis is discussed.

Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

Thermal synthesis and hydrolysis of polyglyceric acid

Polyglyceric acid was synthesized by thermal condensation of glyceric acid at 80 degrees in the presence and absence of two mole percent of sulfuric acid catalyst. The acid catalyst accelerated the polymerization over 100-fold and made possible the synthesis of insoluble polymers of both L- and DL-glyceric acid by heating for less than 1 day. Racemization of L-glyceric acid yielded less than 1% D-glyceric acid in condensations carried out at 80 degrees C with catalyst for 1 day and without catalyst for 12 days. The condensation of L-glyceric acid yielded an insoluble polymer much more readily than condensation of DL-glyceric acid. Studies of the hydrolysis of poly-DL-glyceric acid revealed that it was considerably more stable under mild acidic conditions compared to neutral pH. The relationship of this study to the origin of life is discussed.

Origin of fatty acid synthesis: thermodynamics and kinetics of reaction pathways

The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, we here propose an alternative pathway of primitive fatty acid synthesis that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy (ATP). Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

Glycerol: a neglected variable in metabolic processes?

Glycerol is a small and simple molecule produced in the breakdown of glucose, proteins, pyruvate, triacylglycerols and other glycerolipid, as well as release from dietary fats. An increasing number of observations show that glycerol is probably involved in a surprising variety of physiopathologic mechanisms. Glycerol has long been known to play fundamental roles in several vital physiological processes, in prokaryotes and eukaryotes, and is an important intermediate of energy metabolism. Despite some differences in the details of their operation, many of these mechanisms have been preserved throughout evolution, demonstrating their fundamental importance. In particular, glycerol can control osmotic activity and crystal formation and then act as a cryoprotective agent. Furthermore, its properties make it useful in numerous industrial, therapeutic and diagnostic applications. Few studies have focussed directly on glycerol, however, and while its metabolism is increasingly well documented, much of the details remain unknown. Considering the importance of glycerol in multiple vital physiological processes, its study could help unlock important physiopathological mechanisms.

The sugar model: catalysis by amines and amino acid products

Ammonia and amines (including amino acids) were shown to catalyze the formation of sugars from formaldehyde and glycolaldehyde, and the subsequent conversion of sugars to carbonylcontaining products under the conditions studied (pH 5.5 and 50 degrees C). Sterically unhindered primary amines were better catalysts than ammonia, secondary amines, and sterically hindered primary amines (i.e. alpha-aminoisobutyric acid). Reactions catalyzed by primary amines initially consumed formaldehyde and glycolaldehyde about 15-20 times faster than an uncatalyzed control reaction. The amine-catalyzed reactions yielded aldotriose (glyceraldehyde), ketotriose (dihydroxyacetone), aldotetroses (erythrose and threose), ketotetrose (erythrulose), pyruvaldehyde, acetaldehyde, glyoxal, pyruvate, glyoxylate, and several unindentified carbonyl products. The concentrations of the carbonyl products, except pyruvate and ketotetrose, initially increased and then declined during the reaction, indicating their ultimate conversion to other products (like larger sugars or pyruvate). The uncatalyzed control reaction yielded no pyruvate or glyoxylate, and only trace amounts of pyruvaldehyde, acetaldehyde and glyoxal. In the presence of 15 mM catalytic primary amine, such as alanine, the rates of triose and pyruvaldehyde of synthesis were about 15-times and 1200-times faster, respectively, than the uncatalyzed reaction. Since previous studies established that alanine is synthesized from glycolaldehyde and formaldehyde via pyruvaldehyde as its direct precursor, the demonstration that the alanine catalyzes the conversion of glycolaldehyde and formaldehyde to pyruvaldehyde indicates that this synthetic pathway is capable of autocatalysis. The relevance of this synthetic process, named the Sugar Model, to the origin of life is discussed.

Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe

Our previous analysis of the energetics of metabolism showed that both the biosynthesis of amino acids and lipids from sugars, and the fermentation of organic substrates, were energetically driven by electron transfer reactions resulting in carbon redox disproportionation (Weber, 1997). Redox disproportionation--the spontaneous (energetically favorable) direction of carbon group transformation in biosynthesis--is brought about and driven by the energetically downhill transfer of electron pairs from more oxidized carbon groups (with lower half-cell reduction potentials) to more reduced carbon groups (with higher half-cell reduction potentials). In this report, we compare the redox and kinetic properties of carbon groups in order to evaluate the relative biosynthetic capability of organic substrates, and to identify the optimal biosubstrate. This analysis revealed that sugars (monocarbonyl alditols) are the optimal biosynthetic substrate because they contain the maximum number of biosynthetically useful high energy electrons/carbon atom while still containing a single carbonyl group needed to kinetically facilitate their conversion to useful biosynthetic intermediates. This conclusion applies to aqueous life throughout the Universe because it is based on invariant aqueous carbon chemistry--primarily, the universal reduction potentials of carbon groups.

Prebiotic synthesis of vitamin B6-type compounds

Heating a dilute solution of NH3 and glycoaldehyde gives a large family of pyridines substituted with the same functional groups as occur in the forms of vitamin B6. Thus, vitamin B6-like molecules could have been present on the early Earth and could have been available for catalysis of primitive transamination reactions. Ethanolamine and N-methylethanolamine are also formed as major products. These are choline-like molecules, the latter of which is apparently formed by a prebiotic methylation process.

Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded alpha-hydroxy acid thioesters (Weber, 1984a, b), the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters--intermediates capable of forming peptides (Weber and Orgel 1979). A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40 degrees C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.

The first living systems: a bioenergetic perspective

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.

Mirror symmetry breaking at the molecular level

Reasoning from two basic principles of molecular physics, P invariance of electromagnetic interaction and the second law of thermodynamics, one would conclude that mirror symmetry retained in the world of chiral molecules. This inference is fully consistent with what is observed in inorganic nature. However, in the bioorganic world, the reverse is true. Mirror symmetry there is definitely broken. Is it possible to account for this phenomenon without going beyond conventional concepts of the kinetics of enantioselective processes? This study is an attempt to survey all existing hypotheses containing this phenomenon.

Prebiotic polymerization: oxidative polymerization of 2,3-dimercapto-1-propanol on the surface of iron(III) hydroxide oxide

The oxidation of 2,3-dimercapto-1-propanol by ferric ions on the surface of iron(III) hydroxide oxide (Fe(OH)O) yielded polydisulfide oligomers. This polymerization occurred readily at low dithiol concentration under mild aqueous conditions. Polydisulfide polymers up to the 15-mer were synthesized from 1 mM dithiol in 5 ml water reacted with iron(III) hydroxide oxide (20 mg, 160 micromoles Fe) for 3 days under anaerobic conditions at 40 degrees C and pH 4. About 91% of the dithiol was converted to short soluble oligomers and 9% to insoluble larger oligomers that were isolated with the Fe(OH)O phase. Reactions carried out at the same ratio of dithiol to Fe(OH)O but at higher dithiol concentrations gave higher yields of the larger insoluble oligomers. The relationship of these results to prebiotic polymer synthesis is discussed.

Evolution of metabolic pathways by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes

In order to get an insight into the evolutionary aspect of metabolic pathways, especially of the ubiquitous glycolytic pathway, we have carried out an extensive search of sense-sense and sense-antisense similarities for enzyme proteins in the glycolytic pathway, the pentose phosphate cycle, alcohol and lactate fermentation pathways and the TCA cycle. This investigation of amino acid sequences reveals a curious pattern of similarity relations; no similarity can be found between the enzyme proteins in a section of the glycolytic pathway where the glyceraldehyde-3-phosphate or even glycerol-3-phosphate is converted into the pyruvate while many examples of sense-sense and sense-antisense similarities are found even between enzyme proteins in distant blocks, e.g. between the proteins in the TCA cycle and those in the pentose phosphate cycle, as well as between the functionally associated proteins in each of these blocks. Complementary to this characteristic pattern of amino acid sequence similarity, the search for similarities of nucleotide sequences also finds that the similarities of glycolytic enzyme genes, some sense-sense and others sense-antisense similarities, are concentrated on the nucleotide sequences of prokaryotic 16S or eukaryotic 18S ribosomal RNA gene with its flanks, although some of the copy sequences are also found in transfer RNA genes as well as in 23S or 26S ribosomal RNA gene. These results strongly suggest that the metabolic pathways have been developed by the chance assembly of enzyme proteins generated from the sense and antisense strands of pre-existing genes, e.g. the fermentation pathways and pentose phosphate cycle by the proteins from the genes of enzymes in the glycolytic pathway and the TCA cycle from all these successively increased genes, ascribing the origin of metabolic enzyme genes to the close relation between the glycolytic enzyme protein genes and the RNA gene cluster.

Molecular replication

Simple replicating molecules are likely to have played a critical role in the origin of life. Recent experiments show that non-enzymatic replication is conceivable in a wide range of synthetic chemical systems. The challenge now facing these studies is how to develop information-coding systems from simple prebiotic precursors.

Prebiotic sugar synthesis: hexose and hydroxy acid synthesis from glyceraldehyde catalyzed by iron(III) hydroxide oxide

Iron(III) hydroxide oxide [Fe(OH)O] efficiently catalyzed the condensation of 25 mM DL-glyceraldehyde to ketohexoses at 25 degrees C (pH 5-6). At 16 days the yields were sorbose (15.2%), fructose (12.9%), psicose (6.1%), tagatose (5.6%), and dendroketose (2.5%) with 19.6% of triose unreacted. Analysis at 96 days showed no decomposition of hexoses. Under these conditions Fe(OH)O also catalyzed the isomerization and rearrangement of glyceraldehyde to dihydroxyacetone and lactic acid, respectively. In these reactions, about 10% of the glyceraldehyde was oxidized to glyceric acid with concurrent reduction of the iron(III) to iron(II). The partial reduction of Fe(OH)O did not noticeably reduce its ability to catalyze hexose synthesis. The relationship of these results to prebiotic sugar synthesis is discussed.

Energy-rich glyceric acid oxygen esters: implications for the origin of glycolysis

The apparent Gibbs free energy change of hydrolysis (delta G degrees', pH 7) of the 2- and 3-O-glyceroyl esters of 2- and 3-O-L-glyceroyl-L-glyceric acid methyl ester were measured at 25 degrees C. The 2- and 3-glyceroyl esters were found to be 'energy-rich' with delta G degrees' values of -9.1 kcal mol-1 and -7.8 kcal mol, respectively. This result indicates that the analogous 2- and 3-glyceroyl esters of polyglyceric acid are also 'energy-rich' and, therefore, could have acted as an energy source for primitive phosphoanhydride synthesis.