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PubMed2005

Catalysis and selectivity in prebiotic synthesis: initiation of the formation of oligo(U)s on montmorillonite clay by adenosine-5'-methylphosphate.

Adenosine-5'-methylphosphate (MepA) initiates the oligomerization of the 5'-phosphorimidazolide of uridine (ImpU) in the presence of montmorillonite clay. Longer oligomers form because the 5'-phosphate is blocked with a methyl group that prevents the formation of cyclic- and pyrophosphate-containing compounds. The MepA initiates 69-84% of the 5-9 charge oligomers, respectively. The montmorillonite catalyst also provides selectivity in the oligomerization reactions so that the main reaction pathway is MepA --> MepA3'pU --> MepA3'pU2'pU --> MepA3'pU2'pU3'pU. MepA did not enhance the oligomerization of ImpA. The relative rates of the reactions were determined from an investigation of the products in competitive reactions. Selectivity was observed in the reaction of ImpU with equimolar amounts of MepA3'pU and MepA2'pU where the relative reaction rates are 10.3:1, respectively. In the reaction of ImpA with MepA3'pA and MepA2'pA the ImpA reacts 5.2 times faster with MepA3'pA. In the competitive reaction of ImpU and ImpA with MepA3'pA and MepA3'pU the elongation proceeds on MepA3'pA 5.6 times more rapidly than with MepA3'pU. There is no correlation between the extent of binding to the montmorillonite and reaction rates in the formation of longer oligomers. The formation of more than two sequential 2',5'-linkages in the oligomer chain proceeds more slowly than the addition to a single 2',5'-link or a 3',5'-link and either chain termination or elongation by a 3',5'-linage occurs. The central role that catalysis may have had in the prebiotic formation of biopolymers is discussed.

Adenosine Monophosphate↗

PubMed2005

Nitrogen fixation by corona discharge on the early precambrian Earth.

We report the first experimental study of nitrogen fixation by corona discharge on the anoxic primitive Earth. The energy yields of nitric oxide (NO) and nitrous oxide (N(2)O) were experimentally determined over a wide range of CO(2)-N(2) mixtures simulating the evolution of the Earth's atmosphere during the Hadean and Archean eras (from 4.5 ba to 2.5 ba). NO, the principal form of fixed nitrogen in lightning and coronal discharge in early Earth, is produced ten times less efficiently in the latter type of electrical discharge with an estimated maximum annual production rate of the order of 10(10) g yr(-1). For N(2)O the maximum production rate was estimated to be approximately 10(9) g yr(-1). These low rates of syntheses indicate that corona discharges as point discharges on the clouds and ground did not play a significant role in the overall pool of reactive nitrogen needed for the emergence and sustainability of life.

Atmosphere↗

PubMed2005

Ammonia formation by the reduction of nitrite/nitrate by FeS: ammonia formation under acidic conditions.

One issue for the origin of life under a non-reducing atmosphere is the availability of the reduced nitrogen necessary for amino acids, nucleic acids, etc. One possible source of this nitrogen is the formation of ammonia from the reduction of nitrates and nitrites produced by the shock heating of the atmosphere and subsequent chemistry. Ferrous ions will reduce these species to ammonium, but not under acidic conditions. We wish to report results on the reduction of nitrite and nitrate by another source of iron (II), ferrous sulfide, FeS. FeS reduces nitrite to ammonia at lower pHs than the corresponding reduction by aqueous Fe+ 2. The reduction follows a first order decay, in nitrite concentration, with a half-life of about 150 min (room temperature, CO2, pH 6.25). The highest product yield of ammonia measured was 53%. Under CO2, the product yield decreases from pH 5.0 to pH 6.9. The increasing concentration of bicarbonate, at higher pH, interferes with the reaction. Comparing experiments under N2 CO2 shows the interference of bicarbonate. The reaction proceeds well in the presence of such species as chloride, sulfate, and phosphate, though the yield drops significantly with phosphate. FeS also reduces nitrate and, unlike with Fe+ 2, the reduction shows more reproducibility. Again, the product yield decreases with increasing pH, from 7% at pH 4.7 to 0% at pH 6.9. It appears that nitrate is much more sensitive to the presence of added species, perhaps not competing as well for binding sites on the FeS surface. This may be the cause of the lack of reproducibility of nitrate reduction by Fe+ 2 (which also can be sensitive to binding by certain species).

Ammonia↗

PubMed2005

Sodium chloride enhanced oligomerization of L-glutamic acid in aqueous solution.

The presence of NaCl was found to significantly enhance the formation of longer peptides in N,N'-carbonyldiimidazole induced oligomerization of L-glutamic acid in homogeneous aqueous solution. The enhancement was detected in the presence of as low as 0.01-M NaCl and the highest yield of longer oligomers was achieved in the presence of 1-M NaCl. The possible prebiotic relevance is discussed.

Chromatography, High Pressure Liquid↗

PubMed2005

Parity violation energy of biomolecules--I: polypeptides.

A computational algorithm is developed to compute the energy of parity-violation (E(pv)) due to weak-nuclear forces acting within chain polymers. The method is applied to estimate the magnitude of E(pv) associated with the folding of alpha-helices in polypeptide chains and, in turn, of typical proteins. Implications to the development of biological homochirality in nature are discussed in terms of a simple evolutionary model to assess the likelihood for energies of the order of the computed E(pv) to have determined the direction of natural homochirality.

Algorithms↗

PubMed2005

Aqueous synthesis of peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole.

A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1'-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol.

Amino Acids↗

PubMed2005

The structure and synthetic capabilities of a catalytic peptide formed by substrate-directed mechanism--implications to prebiotic catalysis.

Previously, we have shown that a small substrate may serve as a template in the formation of a specific catalytic peptide, a phenomenon which might have had a major role in prebiotic synthesis of peptide catalysts. This was demonstrated experimentally by the formation of a catalytic metallo-dipeptide, Cys2-Fe2+, around o-nitrophenyl beta-D-galactopyranoside (ONPG), by dicyandiamide (DCDA)-assisted condensation under aqueous conditions. This dipeptide was capable of hydrolyzing ONPG at a specific activity lower only 1000 fold than that of beta galactosidase. In the present paper we use molecular modeling techniques to elucidate the structure of this catalyst and its complex with the substrate and propose a putative mechanism for the catalyst formation and its mode of action as a "mini enzyme". This model suggests that interaction of Fe2+ ion with ONPG oxygens and with two cysteine SH groups promotes the specific formation of the Cys2-Fe2+ catalyst. Similarly, the interaction of the catalyst with ONPG is mediated by its Fe2+ with the substrate oxygens, leading to its hydrolysis. In addition, immobilized forms of the catalyst were synthesized on two carriers--Eupergit C and amino glass beads. These preparations were capable of catalyzing the formation of ONPG from beta-D-galactose and o-nitrophenol (ONP) under anhydrous conditions. The ability of the catalyst to synthesize the substrate that mediates its own formation creates an autocatalytic cycle where ONPG catalyzes the formation of a catalyst which, in turn, catalyzes ONPG formation. Such autocatalytic cycle can only operate by switching between high and low water activity conditions, such as in tidal pools cycling between wet and dry environments. Implications of the substrate-dependent formation of catalytically active peptides to prebiotic processes are discussed.

Catalysis↗

PubMed2005

An investigation of prebiotic purine synthesis from the hydrolysis of HCN polymers.

The polymerization of concentrated NH4CN solutions has been studied at various temperatures and ammonia concentrations. The products of the oligomerization of ammonium cyanide include adenine and guanine, as well as trace amounts of 2,6-diaminopurine. Our results indicate that the adenine yield is not strongly dependent on temperature. Guanine is produced in lower yield. The original studies by Oró and Kimball (1961) showed that the 6 N HCl hydrolysis of the NH4CN polymerization supernatant greatly increased the adenine yield. However, this hydrolysis also decomposes adenine and other purines. Therefore, we have measured the yields from an NH4CN polymerization as a function of hydrolysis time, and found that shorter hydrolytic periods give higher yields of adenine. We have also investigated the hydrolysis of the supernatant at pH 8, which is a more reasonable model of primitive oceanic conditions, and found that the adenine yield is comparable to that obtained with acid hydrolysis (approximately 0.1%). The yield of adenine does not decline at longer hydrolysis times because of the greater stability of adenine at pH 8. The insoluble black polymer formed from NH4CN has been analyzed by both acid and neutral hydrolysis. In both cases adenine yields of approximately 0.05% were obtained. This suggests that the polymer may have been as important a prebiotic source of purines as the usually analyzed supernatant.

Adenine↗

PubMed2005

Production of low molecular weight hydrocarbons by volcanic eruptions on early Mars.

Methane and other larger hydrocarbons have been proposed as possible greenhouse gases on early Mars. In this work we explore if volcanic processes may have been a source for such molecules based on theoretical and experimental considerations. Geologic evidence and numerical simulations indicate that explosive volcanism was widely distributed throughout Mars. Volcanic lightning is typically produced in such explosive volcanism. Therefore this geologic setting was studied to determine if lightning could be a source for hydrocarbons in volcanic plumes. Volcanic lightning was simulated by focusing a high-energy infrared laser beam inside of a Pyrex reactor that contained the proposed volcanic gas mixture composed of 64% CH(4), 24% H(2), 10% H(2)O and 2% N(2), according to an accretion model and the nitrogen content measured in Martian meteorites. The analysis of products was performed by gas chromatography coupled to infrared and mass spectroscopy. Eleven hydrocarbons were identified among the products, of which acetylene (C(2)H(2)) was the most abundant. A thermochemical model was used to determine which hydrocarbons could arise only from volcanic heat. In this case, acetylene and ethylene are formed at magmatic temperatures. Our results indicate that explosive volcanism may have injected into the atmosphere of early Mars approximately 6 x 10(12) g yr(-1) of acetylene, and approximately 2 x 10(12) g yr(-1) of 1,3-butadiyne, both produced by volcanic lightning, approximately 5 x 10(11) g yr(-1) of ethylene produced by volcanic heat, and 10(13) g yr(-1) of methane.

Evolution, Chemical↗

PubMed2005

How was membrane permeability produced in an RNA world?

Darwinian evolution in an RNA World required that catalysts be encapsulated in membranes since this would allow superior catalysts to benefit from the products of their own reactions. However, typical membranes are relatively impermeable to polar and complex molecules and, thus, even primitive cells had to have RNA-based mechanisms for the uptake of external nutrients and the excretion of waste products. Nucleic acids form weak non-specific contacts with the surface of the lipid membrane in the presence of divalent cations, and strongly binding species can be obtained in the course of SELEX experiments. The only currently suggested mechanism for the production of permeability is through formation of supramolecular RNA complexes capable of destabilizing and transiently opening lipid membranes by action from one side, but neither natural nor selected examples of RNA channels or transmembrane shuttles are known so far. The necessity to evolve proteins could be strongly driven by the need to build defined hydrophobic structures that when integrated into membranes could provide selective permeability.

Evolution, Chemical↗

PubMed2006

Effect of cosmological neutrinos on discrimination between the two enantiomers of a chiral molecule.

In the framework of an extraterrestrial origin of biological homochirality, universal mechanisms are of particular interest. In this sense we consider the weak parity-violating neutrino-electron interaction through weak charged currents W (+/-) between the relic flux of cosmological neutrinos and the electrons of a chiral molecule. We use the known theoretical result of the split in energy of the two helicity sates of an electron in the cosmic neutrino bath, due to weak charged currents. In the case that electrons of a chiral molecule are submitted to a helicoidal potential due to the nuclear conformation, these electrons have opposite helicities for the two enantiomers of the molecule and consequently the mentioned neutrino-electron interaction would produce a splitting in energy between the two enantiomers. An estimation of this energy for the case of a single electron yields a small value of the order of 10(-26) eV. This value results amplified by the contribution of all the molecular electrons having helicity and other possible mechanisms.

Electrons↗

PubMed2006

Evolution of homochirality by epimerization of random peptide chains. A stochastic model.

A cyclic process is described which is constituted of polymerization, epimerization, and hydrolysis steps. During the first cycle peptides with random sequences are formed from racemic amino acids. A small portion of these peptides have substructures with a terminal residue linked to a homochiral sequence of optical antipodes. In such a substructure the terminal residue is assumed to invert into its mirror image so that a thermodynamically favourable epimeric stucture with continuous homochirality is formed. In the hydrolysis step the peptides are split back to monomeric units with retention of configuration. Due to stochastic differences between L- and D-substructures a net excess of one of the enantiomers results. This excess enhances the probability of the formation of substructures having the dominant configuration in the next cycle. It is shown by probabilistic considerations and computer simulations that this mechanism generates an autocatalytic growth of one of the enantiomers which finally results in homochiral populations of amino acids. The number of cycles necessary to attain homochirality depends on the number of residues of the substructure, on the chain length distribution of the polymers and on the total number of amino acid units.

Computer Simulation↗

PubMed2006

Prebiotic microreactors: a synthesis of purines and dihydroxy compounds in aqueous aerosol.

We report the synthesis of purine bases and other heterocycles and the formation of amino acids, hydroxy acids and dihydroxy compounds by the spark activation of an atmosphere of methane, nitrogen and hydrogen, in the presence of an aqueous aerosol. With the aid of the interface air-water, the organic material obtained shows greater amounts and diversity of molecules with biological interest than the products obtained in the absence of an aerosol. Our results support the suggestion that aerosols may have played a significant role in the prebiotic origin of molecular diversity and evolution.

Aerosols↗

PubMed2006

From Never Born Proteins to Minimal Living Cells: two projects in synthetic biology.

The Never Born Proteins (NBPs) and the Minimal Cell projects are two currently developed research lines belonging to the field of synthetic biology. The first deals with the investigation of structural and functional properties of de novo proteins with random sequences, selected and isolated using phage display methods. The minimal cell is the simplest cellular construct which displays living properties, such as self-maintenance, self-reproduction and evolvability. The semi-synthetic approach to minimal cells involves the use of extant genes and proteins in order to build a supramolecular construct based on lipid vesicles. Results and outlooks on these two research lines are shortly discussed, mainly focusing on their relevance to the origin of life studies.

Cell Membrane↗

PubMed2006

Cryogenic synthesis of molecules of astrobiological interest: catalytic role of cosmic dust analogues.

We have studied the effects of the substrate, namely amorphous olivine (MgFeSiO(4)) cosmic dust analogues (CDAs), in synthesis of molecules obtained after 200 keV proton irradiation of formamide (NH(2)COH). Formamide has been deposited on the olivine substrate at 20 K. The abundances of new molecular species formed after an irradiation dose of 12 eV/16 amu in formamide pure (i.e. deposited on an inert silicon substrate) and deposited on CDAs have been compared. Specifically, MgFeSiO(4) amorphous olivine is a selective catalyst preventing formation of NH(3) and CN(-) molecules and changing the relative abundances of NH4(+)OCN(-), CO(2), HNCO, CO. We have shown that the role of CDAs has to be taken into account in experiments simulating processes occurring in astronomical environments.

Ammonia↗

PubMed2006

About a formamide-based origin of informational polymers: syntheses of nucleobases and favourable thermodynamic niches for early polymers.

Formamide NH(2)CHO chemistry provides a unitary frame into which several pieces of the origin-of-life puzzle may be adjusted. Synthetic processes were uncovered which, starting from formamide and prebiotically easily available common catalysts, yield all the necessary nucleic bases precursors, including acyclonucleosides. Formamide allows phosphorylations and trans-phosphorylations, favours the micellar aggregation of surfactants and, most importantly, determines conditions in which the formation of nucleic polymers is thermodynamically favoured. In the detected conditions, the phosphoester bonds are more stable in the polymeric than in the monomeric form, thus allowing formation and survival of informational nucleic polymers.

Evolution, Chemical↗

PubMed2006

Asymmetric spatiotemporal evolution of prebiotic homochirality.

The role of asymmetry on the evolution of prebiotic homochirality is investigated in the context of autocatalytic polymerization reaction networks. A model featuring enantiometric cross-inhibition and chiral bias is used to study the diffusion equations controlling the spatiotemporal development of left and right-handed domains. Bounds on the chiral bias are obtained based on present-day constraints on the emergence of life on early Earth. The viability of biasing mechanisms such as weak neutral currents and circularly polarized UV light is discussed. The results can be applied to any hypothetical planetary platform.

Catalysis↗

PubMed2007

The role of supernova neutrinos on molecular homochirality.

Electroweak parity violating interaction between supernova (SN) neutrinos and electrons of a simple chiral molecule is studied related to the origin of molecular homochirality. Appearance of supernova remnants inside molecular clouds favours the interaction of SN-neutrinos with interstellar molecules, leading to a energetic difference between the two enantiomers of the order of 10(-5) eV. This energetic difference is closer to the thermic energy of the interstellar medium, so molecular homochirality could be enhanced in molecular clouds containing supernova remnants inside it due to neutrino interaction.

Elementary Particles↗