Prebiotic conditions

Very few chemical experiments resulted in as much publicity as the first synthesis of biomolecules under prebiotic conditions carried out by the doctoral candidate... 

The synthesis of pyrimidines under specific prebiotic conditions, at low temperature, has apparently been carried out successfully (Fig. 4.8). The formation of the DNA building blocks was carried out by freezing out a dilute solution of cyanoacetaldehyde (CAA) and urea or guanidine. The concentration of CAA was only 1(T3 M, that of guanidine 1M. The reaction took 2 months at 273 K and a pH of 8.1. Yields were as follows ... 

The above-mentioned facts require that ribose must have undergone further reactions immediately after its formation under prebiotic conditions. More than 20 years ago R. Shapiro (1984) pointed out the immense problems which would have needed to be solved in prebiotic nucleic acid formation. 

Two points thus argue against the participation of ribose in nucleic acid formation the lability of the molecule and the problems with its synthesis (the concentrations of the starting materials are too high). Other, newer and more effective syntheses seem necessary, whereby prebiotic conditions (although these are not known precisely) strongly limit the possibilities. 

Since no efficient reactions for the synthesis of high-energy phosphates under prebiotic conditions had been found, Keefe and Miller (1995) came to a negative, pessimistic conclusion with respect to previous results in this sector of prebiotic chemistry. Some studies on the problem have in fact shown positive results. 

In all simulation experiments carried out under assumed prebiotic conditions, the question of possible concentrations in a primeval ocean arises 0.1 M solutions appear unrealistic, as this would correspond to about 12 g of amino acid per litre of seawater Miller s lagoons and Darwin s ponds then come to mind, i.e., the concentration of dilute solutions in small localized areas due to evaporation of water. Recently, the attention of scientists has shifted towards concentration processes occurring at the surface of minerals however, many of the problems involved remain unsolved. 

A combination of SIPS with the stabilising and synthesis-favouring properties of clay minerals was studied by Rode et al. (1999) in experiments involving dry/wet cycles. The simultaneous use of both SIPS and clay minerals as catalytically active surfaces led to peptides up to and including the hexamer (Gly)6. The question as to whether this technique fulfils prebiotic conditions can (within certain limitations) be answered positively, since periodic evaporation phases in limited areas (lagoons, ponds) are conceivable. The container material could have consisted of clay minerals. Further progress in the area of peptide synthesis under conditions which could have been present on the primeval Earth can be expected. 

Although the results of all experiments so far carried out on nucleoside synthesis under prebiotic conditions have been disappointing, the next step, to give the nucleotides, has been carried out using nucleosides synthesized in today s laboratories. There are two preconditions for nucleotide syntheses ... 

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). 

The term peptide nucleic acids was chosen because of the peptide bond in the polymer (see Sect. 5.2). The bond between the polyamide strand and the organic bases involves an acetyl group. The formation of DNA-like double helix structures by PNAs was described by Pernilla Wittung et al. (1994). The question arises as to whether peptide nucleic acids can in fact be synthesized under prebiotic conditions. 

Keefe et al. (1995) from Stanley Miller s laboratory reported a possible prebiotic synthesis of pantetheine, the part of the CoA molecule without its ADP moiety. They were able to synthesize the CoA precursor from P-alanine, pantoyllactone and cysteamine. This condensation requires concentration of the reaction mixture the warm lagoon theory is required here in order to achieve prebiotic conditions ... 

The manufacture of liposomes (which is, for example, carried out by the cosmetics industry) is a complex technical process. Thus, the question arises as to whether a simple mechanism for liposome formation exists which could have functioned under plausible prebiotic conditions. More than 20 years ago, Deamer and co-workers... 

A mixture of Gly, c-Ala, L-Val, c-Lys, c-Asp, and l-G1u was heated without a solvent at 160-200°C, thereby simulating prebiotic conditions. Several tricyclic heterocycles and a pteridine derivative were isolated from the reaction mixture (79AG510). 

In other words, since we do not know, each of us is free to choose. Do as you wish so long as you show that it is possible, respecting the prebiotic conditions, to create life from inanimate matter. This is the challenge and the method is open-ended. The ambition of scientists working in the field would be simply to arrive at minimal life a system containing the minimal and sufficient molecular ingredients to be called alive (this notion will be discussed in detail later on in this book). Of course this also calls into question the definition of hfe, a difficult issue but not an unsolvable one, as we will also see in the next chapter. 

Following Miller s experiment, many chemists successfully synthesized other compounds of biochemical relevance under prebiotic conditions - thereby demonstrating convincingly that several molecular bricks of life might have been present on prebiotic Earth. 

In the case of proteins or nucleic acids we do not have two, but several comonomers furthermore we are not dealing with the simple case of radical polymerization, but with the more complex polycondensation. Very little is known about the kinetics of the copolymerization of polycondensates - for example analysis of ta and re has not been done systematically for amino acids. However, a few general points can still be made on the basis of the general principles of copolymerization. One has been already mentioned that the initial composition of amino acids in the prebiotic soup may not correspond to the amino-acid composition in the chain. Thus, the fact that one given amino acid has a very small frequency of occurrence in protein chains may not necessarily mean that this amino acid was not present under prebiotic conditions the low frequency in the chains can simply be the result of the kinetics of polycondensation. Conversely, the presence of preferred residues or short sequences in protein chains might be due to the interplay of kinetic parameters, and have little to do with the initial biological constraints. 

Chemical activation is indeed the weak point of the prebiotic chemistry of polycondensation. In principle, this should be a prebiotic activation, namely a kind of spontaneous reaction under prebiotic conditions. Several more or less friendly activation methods have been used in the field, and most of them cannot, reasonably, be called prebiotic. On the other hand, the chemist must start working with some tool at hand. Let us now take a few examples from the literature on the prebiotic synthesis of biopolymers. 

Let us go back to the problem of the formation of specific macromolecular sequences. The core of the problem lies in the fact that the synthesis of such copoly-meric sequences, like lysozyme or t-RNAP, is not under thermodynamic control. How can we then conceive their formation under prebiotic conditions, i.e., in a time where only spontaneous reactions were possible ... 

The precision of enantiomeric purity determinations by gas chromatography is high123 124-1 >s. This statement holds not only for small enantiomeric purities ( 0% ee), e.g., in the differentiation of a true racemate from enantiomerically slightly enriched mixtures (in reactions devoted to the amplification of optical activity under prebiotic conditions), but also for very high enantiomeric purities (— 100% ee), with detection of 1.0 to 0.1% (and less) of enantiomeric impurities (see Section 3.1.5.8). It is always advantageous if the enantiomer present as an impurity is eluted as the first peak from the gas chromatographic column (Section 3.1.5.3.). This is achieved by the proper selection of the chirality of the nonracemic stationary phase147-188 which, unfortunately, is not possible for the cyclodextrin phases. 

The next feature that I would like to discuss is the notion of selection that is central to the concept of evolution. That selection occurs even at the level of prebiotic conditions has been well demonstrated by Eigen and his group. In these experiments it was shown that several RNA sequences compete and of the many possibilities only a small fraction of... 

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