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.     

16 Mechanical energy,protein motion,and the possible origin of life between mica sheets

The origins of life require reliable energy sources. One feasible energy source has not been considered until recently. This is mechanical energy-work (Hansma, 2010, 2012). The spaces between moving muscovite mica sheets are the environment in which mechanical energy is hypothesized to have been involved in the origins of life. Mechanical energy from moving mica sheets has two main sources: (1) The open-and-shut motions of mica sheets in response to water movements in and out between the sheets, and (2) Thermal cycles of day and night acting on bubble ‘defects’ between mica sheets. This mechanical energy is hypothesized to have been involved in the formation (and breaking) of covalent bonds, the rearrangement of polymers and molecular aggregates, and the budding-off of protocells, in the earliest form of cell division. Furthermore, it is hypothesized that the mechanical energy from mica sheets moving open-and-shut is the source of the common open-and-shut motions of enzymes, originating from a protobiotic era when mechanical energy was plentiful and chemical energy was not yet available.     

Domain protolife

We propose the Thermal Protein First Paradigm (protocell theory) that affirms that first life was cellular. The first cells emerged from molecular (chemical) evolution as protocells (heated amino acids self-order in copolymerization reactions to form thermal proteins which self-organize when in contact with water to form protocells). Metaprotocells are specialized protocells capable of synthesizing ATP (light energy conversion to chemical energy), polypeptides, and polynucleotides. Aggregations of protocells in thermal protein matrices form distinctive morphologies (protocellular networks). Prokaryotic cells emerged from metaprotocells. We classify protocells and metaprotocells as members of the Domain Protolife. We revised the cell theory to include protolife.     

Heteropolypeptides on Titan?

Since hydrogen cyanide is a component of Titan's hazy atmosphere, HCN polymers might also be present by way of a low energy pathway leading initially to the synthesis of polyaminomalonitrile. Subsequent reactions of HCN with the activated nitrile groups of this HCN homopolymer would then yield heteropolyamidines, readily converted to heteropolypeptides following contact with frozen water on the surface of Titan.Similar HCN polymers in the reducing atmospheres of Jupiter and Saturn could be major contributors to the yellow-brown-orange appearance of these giant planets.Any detection of such HCN chemistry by the Voyager missions or the pending Galileo probe would constitute evidence for the hypothesis that heteropolypeptides on the primitive Earth were synthesized directly from hydrogen cyanide and water without the intervening formation of -amino acids.Paper presented at the 6th College Park Colloquium, October 1981.     

Primeval cells: possible energy-generating and cell-division mechanisms

It is proposed that the first entity capable of adaptive Darwinian evolution consisted of a liposome vesicle formed of abiotically produced phospholipidlike molecules; a very few informational macromolecules; and some abiogenic, lipid-soluble, organic molecule serving as a symporter for phosphate and protons and as a means of high-energy-bond generation. The genetic material had functions that led to the production of phospholipidlike materials (leading to growth and division of the primitive cells) and of the carrier needed for energy transduction. It is suggested that the most primitive exploitable energy source was the donation of 2H+ + 2e- at the external face of the primitive cell. The electrons were transferred (by metal impurities) to internal sinks of organic material, thus creating, via a deficit, a protonmotive force that could drive both the active transport of phosphate and high-energy-bond formation. This model implies that proton translocation in a closed-membrane system preceded photochemical or electron transport mechanisms and that chemically transferable metabolic energy was needed at a much earlier stage in the development of life than has usually been assumed. It provides a plausible mechanism whereby cell division of the earliest protocells could have been a spontaneous process powered by the internal development of phospholipids. The stimulus for developing this evolutionary sequence was the realization that cellular life was essential if Darwinian "survival of the fittest" was to direct evolution toward adaptation to the external environment.     

Origin of organic compounds on the primitive earth and in meteorites

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

The chemical logic of a minimum protocell

Traditional schemes for the origin of cellular life on earth generally suppose that the chance assembly of polymer synthesis systems was the initial event, followed by incorporation into a membrane-enclosed volume to form the earliest cells. Here we discuss an alternative system consisting of replicating membrane vesicles, which we define as minimum protocells. These consist of vesicular bilayer membranes that self-assemble from relatively rare organic amphiphiles present in the prebiotic environment. If some of the amphiphiles are primitive pigment molecules asymmetrically oriented in the bilayer, light energy can be captured in the form of electrochemical ion gradients. This energy could then be used to convert relatively common precursor molecules into membrane amphiphiles, thereby providing an initial photosynthetic growth process, as well as an appropriate microenvironment for incorporation and evolution of polymer synthesis systems.     

Amino Acid Formation in Gas Mixtures by High Energy Particle Irradiation

Amino acids were formed from carbon monoxide, nitrogen and water, which are possible constituents of the primitive earth's atmosphere, by irradiation with high energy particles (components of cosmic rays). Glycine yield was proportional to the total energy deposited to the gas mixture, and its G-value was as high as 0.02 when the carbon monoxide/nitrogen ratio was 1. Based on an estimate of the effective energies of various types of energy sources available in the primitive earth's atmosphere for amino acid synthesis, it is suggested that cosmic rays were one of the most important energy sources for the synthesis of amino acids on the primitive earth.     

15 Combinatorial chemistry in the prebiotic environment

The pathway leading to the origin of life presumably included a process by which polymers were synthesized abiotically from simpler compounds on the early Earth, then encapsulated to form protocells. Previous studies have reported that mineral surfaces can concentrate and organize activated mononucleotides, thereby promoting their polymerization into RNA-like molecules. However, a plausible prebiotic activation mechanism has not been established, and minerals cannot form cellular compartments. We are exploring ways in which nonactivated mononucleotides can undergo polymerization and encapsulation. We found that small yields of RNA-like molecules are synthesized by a condensation reaction when mixtures of amphiphilic lipids and mononucleotides are exposed to cycles of dehydration and rehydration. The lipids concentrate and organize the monomers within multilamellar liquid-crystalline matrices that self-assemble in the dry state. The chemical potential driving the polymerization reaction is supplied by the anhydrous conditions in which water becomes a leaving group, with heat providing activation energy. Significantly, the polymeric products are encapsulated in trillions of microscopic compartments upon rehydration. Each compartment is unique in its composition and contents, and can be considered to be an experiment in a natural version of combinatorial chemistry that would be ubiquitous in the prebiotic environment. A successful experiment would be a compartment that captured polymers capable of catalyzing their own replication. If this can be reproduced in the laboratory, it would represent a significant step toward understanding the origin of cellular life.     

A System of Two Polymerases – A Model for the Origin of Life

What was the first living molecule – RNA or protein?This question embodies the major disagreement instudies on the origin of life. The fact that incontemporary cells RNA polymerase is a protein andpeptidyl transferase consists of RNA suggests theexistence of a mutual catalytic dependence betweenthese two kinds of biopolymers. I suggest that thisdependence is a `frozen accident', a remnant from thefirst living system. This system is proposed to be acombination of an RNA molecule capable of catalyzingamino acid polymerization and the resulting proteinfunctioning as an RNA-dependent RNA polymerase. Thespecificity of the protein synthesis is thought to beachieved by the composition of the surrounding mediumand the specificity of the RNA synthesis – by Watson– Crick base pairing. Despite its apparent simplicity,the system possesses a great potential to evolve intoa primitive ribosome and further to life, as it isseen today. This model provides a possible explanationfor the origin of the interaction between nucleicacids and protein. Based on the suggested system, Ipropose a new definition of life as a system ofnucleic acid and protein polymerases with a constantsupply of monomers, energy and protection.     

Hardware and software in biology: Simultaneous origin of proteins and nucleic acids via hydrogen cyanide polymers

Hydrogen cyanide polymers—heterogeneous solids varying in color from yellow to orange to red to black—may be among the organic macromolecules most readily formed within the solar system. Current studies of these ubiquitous compounds point to the presence of polyamidine structures readily converted by water to polypeptides. Implications for prebiotic chemistry are profound. Primitive Earth may have been covered by HCN polymers as well as other organic compounds, either through bolide bombardment or by photochemical reactions in a reducing atmosphere. Membrane material—carboxylic acids, carbohydrates, polypeptides—accumulated in lakes and oceans, while in the absence of water, on land, polyamidines could have been the original dehydrating agents directing the synthesis of nucleosides and nucleotides from available sugars, phosphates and nitrogen bases. Most significant would have been the parallel synthesis of polypeptides and polynucleotides ariaing from the dehydrating action of polyamidines on nucleotides. Metabolic material—hardware—thus arose separately from genetic components—software—with subsequent interfacting producing the first replicating protocells.On our dynamic planet this polypeptide-polynucleotide symbiosis mediated by polyamidines may have set the pattern for the evolution of protein-nucleic acid systems controlled by enzymes, the mode characteristic of life today.     

Conformational studies on nucleotide-amino acid interactions leading to origin of life

Living processes may be defined as the self-sustained chemical reactions based on the special chemical machinery of nucleic acid-directed protein synthesis. Its genesis may be traced to the molecular interaction between nucleotides and amino acids leading to a primitive adaptor-mediated ordered synthesis of polypeptides. A primitive decoding system is described and its characteristics are shown to imitate, in a primitive manner, the present-day elaborate machinery of protein synthesis. This molecular interaction theory may be rightly considered as the missing link between the Protochemical and biological Evolution. The origin of chiral specificity observed in living organisms is also traced to this specific molecular interaction in the protobiological milieu.     

Early steps of metabolism evolution inferred by cladistic analysis of amino acid catabolic pathways

Among abiotic molecules available in primitive environments, free amino acids are good candidates as the first source of energy and molecules for early protocells. Amino acid catabolic pathways are likely to be one of the very first metabolic pathways of life. Among them, which ones were the first to emerge? A cladistic analysis of catabolic pathways of the sixteen aliphatic amino acids and two portions of the Krebs cycle is performed using four criteria of homology. The cladogram shows that the earliest pathways to emerge are not portions of the Krebs cycle but catabolisms of aspartate, asparagine, glutamate, glutamine, proline, arginine. Earliest enzymatic catabolic functions were deaminations and transaminations. Later on appeared enzymatic decarboxylations. The consensus tree allows to propose four time spans for catabolism development and corroborates the views of Cordón in 1990 about the evolution of catabolism.     

Origins of life: conformational energy calculations on primitive tRNA nestling an amino acid

We report conformational energy calculations on our proposal of a molecular interaction theory for the origin of the nucleic acid-directed, adaptor-mediated synthesis of proteins that links the phenomena of chemical and biological evolution. A particular conformation of a pentanucleotide turns out to be a double-sided template for a primitive decoding system. It is able to neatly nestle an amino acid via hydrogen bonds, and this complex is found to be an energetically favourable conformation. The total potential energy of the complex is calculated using semi-empirical potential energy functions. A local-minimum conformation is obtained and its features are reported. The template conformation of the pentanucleotide is found to have an energy value far lower than a regular helical conformation. When the amino acid is nestled in the cleft of the template-conformation through specific hydrogen bonds, the energy is further lowered. A D-amino acid nestled into the PIT (Primitive tRNA) is found to be less stable than its L counterpart, as revealed by energy calculations.     

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

Summary 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.     

Primeval cells: Possible energy-generating and cell-division mechanisms

Summary It is proposed that the first entity capable of adaptive Darwinian evolution consisted of a liposome vesicle formed of (1) abiotically produced phospholipidlike molecules; (2) a very few informational macromolecules; and (3) some abiogenic, lipid-soluble, organic molecule serving as a symporter for phosphate and protons and as a means of high-energy-bond generation. The genetic material had functions that led to the production of phospholipidlike materials (leading to growth and division of the primitive cells) and of the carrier needed for energy transduction. It is suggested that the most primitive exploitable energy source was the donation of 2H⁺+2e^– at the external face of the primitive cell. The electrons were transferred (by metal impurities) to internal sinks of organic material, thus creating, via a deficit, a protonmotive force that could drive both the active transport of phosphate and high-energy-bond formation.This model implies that proton translocation in a closed-membrane system preceded photochemical or electron transport mechanisms and that chemically transferable metabolic energy was needed at a much earlier stage in the development of life than has usually been assumed. It provides a plausible mechanism whereby cell division of the earliest protocells could have been a spontaneous process powered by the internal development of phospholipids. The stimulus for developing this evolutionary sequence was the realization that cellular life was essential if Darwinian survival of the fittest was to direct evolution toward adaptation to the external environment.     

Lipase/esterase-catalyzed synthesis of aliphatic polyesters via polycondensation: A review

Over the last decade, there has been an increasing interest in lipase/esterase-catalyzed polycondensation as an alternative to metal-based catalytic process, because the former can proceed under mild reaction conditions and does not cause undesirable side reactions or produce trace metallic residues. In this review, the in vitro synthesis of aliphatic polyesters by polycondensation using lipases or esterases is systematically summarized, especially for the synthesis of complex and well-defined polyesters. The polycondensation of diols with diacids or their activated esters, including alkyl, haloalkyl and vinyl esters, through esterification and transesterification polycondensation reactions is discussed. In addition, three or more monomers can also be polymerized simultaneously, which provides a new route for preparing functional polymers. Self-polycondensation with respect to hydroxyl and mercapto acids or their esters is another reaction mode discussed in the review. Finally, concurrent enzymatic ring-opening polymerization and polycondensation has been developed to construct novel polyesters with tailor-made structures and properties. Overall, the review demonstrates that lipase/esterase-catalyzed synthesis of polyesters via polycondensation provides an effective platform for conducting “eco-friendly polymer chemistry”.     

Enzymatic reactions in biotechnology (48th Bach lecture)]

The paper is the 48th Bach Lecture presented under the same title. It covers the biochemical mechanisms of the biogenesis of microbial biosynthetic products, role of acetyl-CoA, function of the succinate-glycine cycle, reactions of the hexose-monophosphate pathway of carbon metabolism. The reversible action of hydrolases in enzymatic catalysis and degradation of xenobiotics are discussed. The data on redox reactions are pooled. Such modern biotechnological processes as epoxidation, synthesis of acrylamide and some monomers involved in chemical syntheses of polymers, synthesis of oligosaccharide and fluorine-containing amino acids are considered. Promising commercial applications of biocatalysis are discussed.     

How did bacterial ancestors reproduce? Lessons from L‐form cells and giant lipid vesicles

In possible scenarios on the origin of life, protocells represent the precursors of the first living cells. To study such hypothetical protocells, giant vesicles are being widely used as a simple model. Lipid vesicles can undergo complex morphological changes enabling self‐reproduction such as growth, fission, and extra‐ and intravesicular budding. These properties of vesicular systems may in some way reflect the mechanism of reproduction used by protocells. Moreover, remarkable similarities exist between the morphological changes observed in giant vesicles and bacterial L‐form cells, which represent bacteria that have lost their rigid cell wall, but retain the ability to reproduce. L‐forms feature a dismantled cellular structure and are unable to carry out classical binary fission. We propose that the striking similarities in morphological transitions of L‐forms and giant lipid vesicles may provide insights into primitive reproductive mechanisms and contribute to a better understanding of the origin and evolution of mechanisms of cell reproduction. Editor's suggested further reading in BioEssays Synthesizing artificial cells from giant unilamellar vesicles: State‐of‐the art in the development of microfluidic technology Abstract     

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.