Was photoresolution of amino acids the origin of optical activity in life?
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Amino Acids↗
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Evolution of early mechanisms of translation of genetic information into polypeptides.
In devising models of the origin of life it is necessary to tackle the problems that the processes of genetic information transfer that are central to life depend on molecules that are themselves the products of such processes--enzymes. A proposed model must eventually yield a detailed chain of processes that can be checked experimentally. We have developed a model in which interactions between the helices of hairpin-loop 'adaptor' RNA molecules (amino acid carrying), lined up side-by-side by sequence complementarity to another 'messenger' RNA, promotes polypeptide synthesis.
Base Composition↗
Chiral selection in poly(C)-directed synthesis of oligo(G).
Theories of the origin of optical asymmetry in living systems place fundamental importance on the amplification of optical asymmetry by an autocatalytic process. The replication of a polynucleotide is one obvious choice for such an autocatalytic growth mechanism. If an optically homogeneous polynucleotide could replicate by directing the polymerization of monomers of the same handedness, while excluding monomers of the opposite handedness, its chiral descendants would come to dominate what was once an achiral environment. Recently, two highly efficient template-directed reaction systems have been developed for the oligomerization of activated guanosine mononucleotides (Fig. 1) on a poly(C) template. The synthesis of L-guanosine 5'-mononucleotide makes it possible to study chiral selection in these systems. We report here that poly(C)-directed oligomerization of activated guanosine mononucleotides proceeds readily if the monomers are of the same optical handedness as the template, and is indeed far less efficient if the monomers are of the opposite handedness. However, in template-directed reactions with a racemic mixture, monomers of the opposite handedness to the template are incorporated as chain terminators at the 2'(3') end of the products. This inhibition raises an important problem for many theories of the origin of life.
Chromatography, High Pressure Liquid↗
Autocatalytic synthesis of a tetranucleotide analogue.
As an approach to the study of the kind of chemical process that might have contributed to the origin of life, attempts have been made to develop purely chemical systems in which oligonucleotides self-replicate. Although performed oligonucleotides have been shown to facilitate the formation of their complements from activated mononucleotides, only a restricted range of oligomers are efficient templates and it will clearly be difficult to find a pair of complementary oligomers each of which will facilitate the formation of the other. Many of the difficulties facing the development of a self-replicating system could be overcome by using a pair of complementary substrate molecules that condense together more easily than ribonucleotides. It would also be helpful if each substrate molecule contained equal numbers of purine and pyrimidine bases as, otherwise, there is a tendency for purines to be overrepresented in the products. We have therefore explored the chemistry of 3'-amino-3'-deoxynucleotides and their dimers. We report here that the tetranucleoside triphosphoramidate GNHpCNHpGNHpCN3 acts as a template to catalyse the condensation of GNHpCNH2 and pGNHpCN3, forming further molecules of the template. The system is therefore autocatalytic, and in accordance with elementary theory the amount of product made increases with the square root of the template concentration.
Catalysis↗
Synthesizing life.
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Cell Compartmentation↗
A self-replicating peptide.
The production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-foot of initial template concentration.
Amino Acid Sequence↗
Spectroscopic evidence for interstellar ices in comet Hyakutake.
Volatile compounds in comets are the most pristine materials surviving from the time of formation of the Solar System, and thus potentially provide information about conditions that prevailed in the primitive solar nebula. Moreover, comets may have supplied a substantial fraction of the volatiles on the terrestrial planets, perhaps including organic compounds that played a role in the origin of life on Earth. Here we report the detection of hydrogen isocyanide (HNC) in comet Hyakutake. The abundance of HNC relative to hydrogen cyanide (HCN) is very similar to that observed in quiescent interstellar molecular clouds, and quite different from the equilibrium ratio expected in the outermost solar nebula, where comets are thought to form. Such a departure from equilibrium has long been considered a hallmark of gas-phase chemical processing in the interstellar medium, suggesting that interstellar gases have been incorporated into the comet's nucleus, perhaps as ices frozen onto interstellar grains. If this interpretation is correct, our results should provide constraints on the temperature of the solar nebula, and the subsequent chemical processes that occurred in the region where comets formed.
Extraterrestrial Environment↗
RNA at santa cruz.
Nestled in an atmosphere that resembles a national park, the Center for Molecular Biology of RNA at the University of California, Santa Cruz is fulfilling Harry Noller's vision of bringing together multidisciplinary researchers to solve problems that range from finding obscure RNAs to understanding the origin of life.
Academic Medical Centers↗
Chiral selection on inorganic crystalline surfaces.
From synthetic drugs to biodegradable plastics to the origin of life, the chiral selection of molecules presents both daunting challenges and significant opportunities in materials science. Among the most promising, yet little explored, avenues for chiral molecular discrimination is adsorption on chiral crystalline surfaces - periodic environments that can select, concentrate and possibly even organize molecules into polymers and other macromolecular structures. Here we review experimental and theoretical approaches to chiral selection on inorganic crystalline surfaces - research that is poised to open this new frontier in understanding and exploiting surface-molecule interactions.
Adsorption↗
Organic compounds in carbonaceous meteorites.
The carbonaceous chondrite meteorites are fragments of asteroids that have remained relatively unprocessed since the formation of the solar system 4.6 billion years ago. These carbon-rich objects contain a variety of extraterrestrial organic molecules that constitute a record of chemical evolution prior to the origin of life. Compound classes include aliphatic hydrocarbons, aromatic hydrocarbons, amino acids, carboxylic acids, sulfonic acids, phosphonic acids, alcohols, aldehydes, ketones, sugars, amines, amides, nitrogen heterocycles, sulfur heterocycles and a relatively abundant high molecular weight macromolecular material. Structural and stable isotopic characteristics suggest that a number of environments may have contributed to the organic inventory, including interstellar space, the solar nebula and the asteroidal meteorite parent body. This review covers work published between 1950 and the present day and cites 193 references.
Algorithms↗
Asymmetric autocatalysis: product recruitment for the increase in the chiral environment (PRICE).
Asymmetric catalytic reactions are possible via efficient transfer of the chiral environment of a reaction to the transition state. In theory any asymmetric structure may contribute to this, including the product of the reaction itself. For product influence to be significant, a nonlinear effect needs to operate, whereby one diastereomer of the product/catalyst assists the reaction, and the other does not. When these conditions are satisfied, we obtain an asymmetric autocatalytic reaction in which the enantiomeric excess of a compound (that is both product and catalyst) actually increases as the reaction iterates. It is only recently that we have seen reports of such processes. Of particular interest are Soai's reports of the alkylation of aromatic heterocycles. Such reactions, aside from their inherent interest, may offer clues into the origins of asymmetric molecular replication that predated the origin of life.
Journal Article↗
Duodenocaval fistula: a life-threatening condition of various origins.
We report on two cases of duodenocaval fistula. The first patient, a 73-year-old man, had sepsis and occult digestive bleeding. We diagnosed a fistula that resulted from a right nephrectomy and subsequent radiotherapy for a urothelial tumor 20 months earlier. The second patient, a 60-year-old woman, complained of right abdominal pain. A duodenocaval fistula that was caused by duodenal perforation by a migrating caval filter placed 10 years earlier was revealed by means of endoscopy. Both patients had a successful operation to treat the condition. An extensive review of the literature disclosed 35 other cases and identified two factors of good prognosis: duodenocaval fistulas caused by migrating caval filters and early surgery.
Aged↗
Asymmetric autocatalysis and its implications for the origin of homochirality.
An autocatalytic reaction in which the reaction product serves as a catalyst to produce more of itself and to suppress production of its enantiomer serves as a mechanistic model for the evolution of homochirality. The Soai reaction provided experimental confirmation of this concept, nearly 50 years after it was first proposed. This Perspective offers a rationalization of the Soai autocatalytic reaction; accounting for enantiomeric excess and rate observations, that is both simple as well as gratifying in its implications for the chemical origin of life.
Journal Article↗
Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality.
The emergence of biochemical homochirality was a key step in the origin of life, yet prebiotic mechanisms for chiral separation are not well constrained. Here we demonstrate a geochemically plausible scenario for chiral separation of amino acids by adsorption on mineral surfaces. Crystals of the common rock-forming mineral calcite (CaCO(3)), when immersed in a racemic aspartic acid solution, display significant adsorption and chiral selectivity of d- and l-enantiomers on pairs of mirror-related crystal-growth surfaces. This selective adsorption is greater on crystals with terraced surface textures, which indicates that d- and l-aspartic acid concentrate along step-like linear growth features. Thus, selective adsorption of linear arrays of d- and l-amino acids on calcite, with subsequent condensation polymerization, represents a plausible geochemical mechanism for the production of homochiral polypeptides on the prebiotic Earth.
Adsorption↗
The origin of intermediary metabolism.
The core of intermediary metabolism in autotrophs is the citric acid cycle. In a certain group of chemoautotrophs, the reductive citric acid cycle is an engine of synthesis, taking in CO(2) and synthesizing the molecules of the cycle. We have examined the chemistry of a model system of C, H, and O that starts with carbon dioxide and reductants and uses redox couples as the energy source. To inquire into the reaction networks that might emerge, we start with the largest available database of organic molecules, Beilstein on-line, and prune by a set of physical and chemical constraints applicable to the model system. From the 3.5 million entries in Beilstein we emerge with 153 molecules that contain all 11 members of the reductive citric acid cycle. A small number of selection rules generates a very constrained subset, suggesting that this is the type of reaction model that will prove useful in the study of biogenesis. The model indicates that the metabolism shown in the universal chart of pathways may be central to the origin of life, is emergent from organic chemistry, and may be unique.
Biological Evolution↗
A simple energy-conserving system: proton reduction coupled to proton translocation.
Oxidative phosphorylation involves the coupling of ATP synthesis to the proton-motive force that is generated typically by a series of membrane-bound electron transfer complexes, which ultimately reduce an exogenous terminal electron acceptor. This is not the case with Pyrococcus furiosus, an archaeon that grows optimally near 100 degrees C. It has an anaerobic respiratory system that consists of a single enzyme, a membrane-bound hydrogenase. Moreover, it does not require an added electron acceptor as the enzyme reduces protons, the simplest of acceptors, to hydrogen gas by using electrons from the cytoplasmic redox protein ferredoxin. It is demonstrated that the production of hydrogen gas by membrane vesicles of P. furiosus is directly coupled to the synthesis of ATP by means of a proton-motive force that has both electrochemical and pH components. Such a respiratory system enables rationalization in this organism of an unusual glycolytic pathway that was previously thought not to conserve energy. It is now clear that the use of ferredoxin in place of the expected NAD as the electron acceptor for glyceraldehyde 3-phosphate oxidation enables energy to be conserved by hydrogen production. In addition, this simple respiratory mechanism readily explains why the growth yields of P. furiosus are much higher than could be accounted for if ATP synthesis occurred only by substrate-level phosphorylation. The ability of microorganisms such as P. furiosus to couple hydrogen production to energy conservation has important ramifications not only in the evolution of respiratory systems but also in the origin of life itself.
Biochemical Phenomena↗
Computer-modeling origin of a simple genetic apparatus.
This computer simulation is based on a model of the origin of life proposed by H. Kuhn and J. Waser, where the evolution of short molecular strands is assumed to take place in a distinct spatiotemporal structured environment. In their model, the prebiotic situation is strongly simplified to grasp essential features of the evolution of the genetic apparatus without attempts to trace the historic path. With the tool of computer implementation confining to principle aspects and focused on critical features of the model, a deeper understanding of the model's premises is achieved. Each generation consists of three steps: (i) construction of devices (entities exposed to selection) presently available; (ii) selection; and (iii) multiplication of the isolated strands (R oligomers) by complementary copying with occasional variation by copying mismatch. In the beginning, the devices are single strands with random sequences; later, increasingly complex aggregates of strands form devices such as a hairpin-assembler device which develop in favorable cases. A monomers interlink by binding to the hairpin-assembler device, and a translation machinery, called the hairpin-assembler-enzyme device, emerges, which translates the sequence of R(1) and R(2) monomers in the assembler strand to the sequence of A(1) and A(2) monomers in the A oligomer, working as an enzyme.
Computer Simulation↗
Expanding protein universe and its origin from the biological Big Bang.
The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. By understanding the cause of these patterns, we attempt to glance at the very origin of life.
Computer Simulation↗