Prebiotic Models

If thymidylic acid is heated with cyanamide at pH 3, oligomers, for the most part cyclic, are formed, presumably via activated phosphate intermediates such as (68).107 On addition of acid salts, the same reactions can be realized at neutral pH.108 

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Various comprehensive studies on the polymerization of enantiopure and racemic esters of a-amino acids performed at the air/water interface to yield peptides have been reported over the years [189,190]. Recent reinvestigations of the products of these reactions by MALDI-TOF MS have demonstrated, however, that they are not longer than dipeptides [191]. For this reason, such esters cannot be regarded as realistic prebiotic model systems for the formation of long oligopeptides. On the other hand, amphiphilic Na-carboxyanhydrides [192] and thio-esters [193] of a-amino acids yield longer oligopeptides. 

In 2004, Pizzarello and Weber studied a water-based prebiotic model of sugar syntheses from glycoaldehyde and formaldehyde in the presence of nonracemic alanine or isovaline. They demonstrated that the configuration of tetroses is affected by the chirality of the amino acid catalyst. 

Any discussion of the prebiotic phosphorylation of nucleosides must take into account the probably neutral or alkaline conditions in a prebiotic environment. Some model phosphorylating systems have been studied, for example, the synthesis of /S-o-ribofuranose 1-phosphate from ribose and inorganic phosphate in the presence of cyanogen. Sodium trimetaphosphate will phosphorylate cw-glycols in good yield under alkaline... 

From the viewpoint of a model of prebiotic chemical evolution and of the primitive atmosphere of the Earth,174175 photosynthetic reactions of C02 were also examined, and formaldehyde with various nitrogen-containing products was obtained. 

Thus it was necessary to develop models which would make self-replication of nucleic acids possible. Such models would need to be simple, since they should simulate prebiotic processes (von Kiedrowski, 1999). The realisation of such a scheme would require the fulfilment of several conditions ... 

However, the question must always be asked as to whether these processes could have taken place on the primordial Earth in its archaic state. The answer requires considerable fundamental consideration. Strictly speaking, most of the experiments carried out on prebiotic chemistry cannot be carried out under prebiotic conditions , since we do not know exactly what these were. In spite of the large amount of work done, physical parameters such as temperature, composition and pressure of the primeval atmosphere, extent and results of asteroid impacts, the nature of the Earth s surface, the state of the primeval ocean etc. have not so far been established or even extrapolated. It is not even sure that this will be possible in the future. In spite of these difficulties, attempts are being made to define and study the synthetic possibilities, on the basis of the assumed scenario on the primeval Earth. Thus, for example, in the case of the SPREAD process, we can assume that the surface at which the reactions occur could not have been an SH-containing thiosepharose, but a mineral structure of similar activity which could have carried out the necessary functions just as well. The separation of the copy of the matrix could have been driven by a periodic temperature change (e.g., diurnal variation). For his models, H. Kuhn has assumed that similar periodic processes are the driving force for some prebiotic reactions (see Sect. 8.3). 

An information science research group devised a new model which could explain information storage in the prebiotic phase of the biogenesis process. They assume that layered double hydroxide (LDH) minerals acted as proto-RNA molecules on the young Earth about 4 billion years ago. This hypothesis relates to Cairns-Smith s genetic takeover thesis, which thus again became the subject of discussion. 

The authors chose pyruvic acid as their model compound this C3 molecule plays a central role in the metabolism of living cells. It was recently synthesized for the first time under hydrothermal conditions (Cody et al., 2000). Hazen and Deamer carried out their experiments at pressures and temperatures similar to those in hydrothermal systems (but not chosen to simulate such systems). The non-enzymatic reactions, which took place in relatively concentrated aqueous solutions, were intended to identify the subsequent self-selection and self-organisation potential of prebiotic molecular species. A considerable series of complex organic molecules was tentatively identified, such as methoxy- or methyl-substituted methyl benzoates or 2, 3, 4-trimethyl-2-cyclopenten-l-one, to name only a few. In particular, polymerisation products of pyruvic acid, and products of consecutive reactions such as decarboxylation and cycloaddition, were observed the expected tar fraction was not found, but water-soluble components were found as well as a chloroform-soluble fraction. The latter showed similarities to chloroform-soluble compounds from the Murchison carbonaceous chondrite (Hazen and Deamer, 2007). 

The importance, and the performance, of the FeS/FeS2 system were studied by Kaschke et al. (1994) in Glasgow. They were able to show that the system is capable of reducing carbonyl groups their model substance was cyclohexanone. Although the reactions cannot be regarded as prebiotic, the results agree with thermodynamic calculations on the reductive power of the Fe/S system. 

The formation of relatively stable vesicles did not require the presence of pure compounds mixtures of components could also have done the job. However, whether the concentrations of the compounds isolated from the Murchison meteorite would have been sufficient for the formation of prebiotic protocells or vesicles is unclear, even if concentration effects are assumed. Sequences in which the technical Fischer-Tropsch synthesis is the role model have been proposed as possible sources of amphiphilic building blocks. 

D. W. Deamer and J. P. Dworkin have reported in detail on the contribution of chemistry and physics to the formation of the first primitive membranes during the emergence of precursors to life the authors discussion ranges from sources of amphiphilic compounds, growth processes in protocells, self-organisation mechanisms in mixtures of prebiotic organic compounds (e.g., from extracts of the Murchison meteorite) all the way to model systems for primitive cells (Deamer and Dworkin, 2005). 

The current models of the Sun suggest that its luminosity would have been some 20-30 per cent lower than its present value during the early part of the formation of the Earth. After the enormous temperatures of the Hadean period, the early precambrian may have been cooler, requiring prebiotic chemistry to occur below a layer of ice, perhaps heated by volcanic activity such as that found in geothermal vents. A layer of ice several hundreds of kilometres thick may have formed over the entire surface of the early Earth, providing protection from UV radiation and some global warming - conditions such as these may exist on the Jovian moon Europa. 

The conditions on Titan, both in the atmosphere and in the oceans, can be investigated using the kinetics and thermodynamics introduced in the modelling of the ISM and the prebiotic Earth, now tuned to the surface temperature and atmospheric temperature conditions on Titan. We have seen previously what happens to reaction rates in the ISM and the atmosphere using the Arrhenius equation but we have not yet extended the concepts of AG and thermodynamics to low temperatures. 

Yi-Jehng Kuan el al. (2004). Searches for interstellar molecules of potential prebiotic importance. Advances in Space Research 33 31-39 Yung Y., Allen M. and Pinto J. (1984). Photochemistry of the atmosphere of Titan comparison between model and observations. Astronomy Astrophysics Supplement... 

These model experiments involving e.e. amplification of amino adds during polymerization admittedly need prebiotically unrealistic substrates as well as carefully contrived experimental conditions. Nevertheless, it is noteworthy that both secondary structures of proteins, a-helices, and P-sheets have been found capable of acting stereoselectively to provide e.e. enhancements during these model polymerizations. 

A critical property of minimum protocells in the prebiotic environment would be their ability to sequester other molecules, including macromolecules. [142] In 1982, Deamer and Barchfeld [143] subjected phospholipid vesides to dehydration-rehydration cycles in the presence of either monomeric 6-carboxyfluorescein molecules or polymeric salmon sperm DNA molecules as extraneous solutes. The experiment modeled a prebiotic tidal pool containing dilute dispersions of phospholipids in the presence of external solutes, with the dehydration-rehydration cydes representing episodic dry and wet eras. They found that the vesides formed after rehydration... 

The metal-catalyzed amplification of e.e. in small molecules, demonstrated by Soai and coworkers, along with the chiral enrichment of amino arid polymers by sequential polymerization/depolymerization steps, have shown that small enantiomeric excesses in nearly racemic mixtures can be reactively amplified to produce chiral dominance. These real chemical systems, which include plausible prebiotic reactions, experimentally demonstrate the principle of the chiral amplification of a spontaneously broken chiral symmetry in a dynamic and authentic chemical milieu. Therefore amplification to dominance of a small chiral excess of both small and polymeric molecules can be credibly incorporated into an origin-of-life model. 

Prior sequestration of the prebiotic reactions within the micropores of weathered feldspars or other porous rock matrices also avoids many of the other problems of catalysis and dilution encountered by models of chemical biogenesis. That is, this mechanism attains viable evolutionary chemical selection among spatially discrete systems without the need to assume an unlikely capture-and-enclosure event involving a pre-existing lipid membrane. [192] Thus autocatalysis of chiral molecules could evolve before the actual appearance of free-floating lipid vesicles. 

The synthesis in many extant organisms of these two amide residues from their respective precursors glutamate and aspartate esterified to tRNA (the indirect aminoacylation pathways described in Sections 5.14.3 and 5.14.4) and that of other amino acid residues, such as selenocysteine (which is also synthesized from a precursor esterified on a tRNA °) support the model of prebiotic metabolism taking place at the surface of solid particles, " analogous to ancestral RNAs. 

Why then is there this popularity of the prebiotic RNA world There are three reasons that come to mind. One is the already mentioned great success of the RNA world at large, which, by inference, gives confidence in the power of RNA. Another reason is that from self-rephcating and mutating ribozymes, one can conceive in paper a route to DNA and proteins - and then one has the whole story. A third reason is the lack of a good competitive model - namely the fact that there is no alternative mechanism that is supported experimentally. 

In the following I will present a model to tackle this question. We are at the level of speculations, but we will use some known facts. For example, let s start from the condensation of NCA-anhydrides, a reaction which, as we have seen in the previous chapter, is considered prebiotic. In this way, oligopeptides up to (say) a length of ten can be built, possibly under thermodynamic control, but starting from a definite set of conditions (amino-acid composition in the starting mixture, pH, salinity, etc.). We can assume, and this is actually quite reasonable, that in this way copious libraries of different decapeptides have been formed, each in a significant concentration. 

Bachmann, P. A., Luisi, P. L., and Lang, J. (1992). Autocatalytic self-replication of micelles as models for prebiotic structures. Nature, 357, 57-9. 

Boiteau, L., Rlasson, R., Collet, H., etal. (2002). Molecular origin of life when chemistry became cyclic. The primary pump, a model for prebiotic emergence and evolution of petides. In Fundamentals of Life, eds. G. Ralyi, C. Zucchi, and L. Caglioti. Elsevier, pp. 211-18. 

Montmorillonite catalysis of RNA oligomer formation in aqueous solution a model for the prebiotic formation of RNA. J. Am. Chem. Soc., 115, 12270-5. 

Our ideas on the prebiotic synthesis of organic compounds are based largely on the results of experiments in model systems. So it is extremely gratifying to see that such synthesis really did take place on the parent body of the meteorite, and so it becomes quite plausible that they took place on the primitive earth. 

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