Prebiotic experiment

Prebiotic chemistry must cope with many problems a particularly difficult one is contamination. Prebiotic experiments often lead to the formation of important molecular species in extremely low concentrations. The successes of the synthesis may sometimes appear sensational, but there is always the danger that artefacts may be involved. Control experiments carried out with ultrapure deionised water showed that, at higher temperatures (>373 K), synthetic polymers in components of the apparatus could provide a source of organic contaminants such as formate, acetate or propionate ions. Stainless steel had a catalytic effect on the decomposition of formate, so that the use of titanium alloys in the apparatus is recommended. 

Ward, Peter. Ufe As We Do Not Know It. New York Viking Penguin, 2005. This book describes the NASA search for extraterrestrial life and related prebiotic experiments. 

These tautomerization experiments have also been performed with uroporphyrinogens,25e 24 which are important intermediates in the biosynthesis of natural porphinoids and corrinoids. This has led to a deeper insight into biosynthetic pathways and a possible prebiotic origin of... 

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

Several institutes throughout the world immediately began to carry out experiments on prebiotic chemistry. At this point, we need to realize that the prebiotic synthesis of protein building blocks is only a first step towards solving the biogenesis problem. Put simply, it is a method for making bricks which will later be used in building a multi-storey office block ... 

Although the Miller-Urey experiments of 1953 are of only historic interest today, they do mark the beginning of prebiotic chemistry and modern biogenesis research. 

New experiments using weakly reducing or neutral gas atmospheres were conceived and carried out more than 20 years after Miller s first successes (Schlesinger and Miller, 1983). Comparisons of a series of simulated prebiotic atmospheres containing CH4, CO and CO2 as carbon sources, using electrical discharges at 298 K, led to the following results ... 

However, the amino acids were not necessarily formed in the gas phase. John Oro, one of the pioneers in prebiotic chemistry, carried out syntheses in the liquid phase by reacting HCN, NH3 and H2O at 353 K. The results were confirmed by Lowe et al. (1963) and developed further ten years later, Jim Ferris took them up and did considerable further work (Ferris et al., 1973, 1974). In all these simulation experiments, the simplest amino acids (glycine, alanine and in small amounts aspartic acid and a-aminobutyric acid) are, as expected, the main products the yields of glycine are around 1%, those of the other amino acids much lower. 

Sidney Fox and Kaoru Harada, in particular, used simulation experiments to show how volcanism may have been involved in the synthesis of prebiotic molecules. They heated a stream of gas (CH4, NH3 and H2O) to about 1,123 K (using a silicate contact) after cooling, they could detect glycine, alanine, p-alanine and aspartic acid (among others). This experiment was intended to simulate exhalation from the earth s crust, as in volcanoes (Fox and Harada, 1961 Harada and Fox, 1964). 

The many successful simulation experiments indicate that electrical discharges on prebiotic Earth may have been involved in the synthesis of biomolecules. However, we simply do not know how important they actually were Studies of energy... 

Critics of such experiments may And the concentration of reducing gases too high. It is, however, possible that there were localized areas on Earth where conditions were more strongly reducing for short periods (e.g., after volcanic eruptions). In the search for potential prebiotic syntheses of condensed phosphates, Keefe and Miller (1996) allowed a series of condensation agents to act on o-phosphate or tripolyphosphate, and determined the yields of diphosphate and trimetaphosphate obtained. 

In all the experiments, the main decomposition products were phosphonates, which are also stable in concentrated solutions of Mg and Ca chlorides. In some experiments, pyrophosphate, and in smaller amounts triphosphate, could also be detected. The authors thus assume that the primeval ocean contained phosphonates as a source of phosphorus for reactions leading to biochemically relevant molecules. Iron meteorites could have delivered sufficient reduced phosphorus (Fe3P) to the primeval Earth, so the question of prebiotic phosphorus chemistry should be looked at in more detail in the future (Pasek and Lauretta, 2005). 

The simplest amino acid, glycine, is almost always the one formed in highest yield in prebiotic syntheses. Thus, the first polycondensation experiments were carried out with glycine. Akabori (1955) and Hanabusa and Akabori (1959) reacted aminoace-tonitrile with kaolin at 403 108 K. The starting material is readily formed as follows ... 

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. 

There is no doubt that volcanic activity had various effects on the chemical processes occurring on the young Earth. Two articles deal with simulation experiments intended to study how volcanic exhalations may have affected prebiotic chemistry. 

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. 

The importance of this sensational discovery for biogenesis research only became apparent in the next few years (Lahav, 1999). It is clear that prebiotic chemistry is much more complex and versatile than was thought about 50 years ago, when Stanley Miller carried out his first successful amino acid syntheses. Experiments similar to the ones described above, as well as new ones which must first be devised, could help to slowly close the wide gap which still exists between the prebiotic and the living worlds (Wills and Bada, 2000). 

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). 

In prebiotic simulation experiments, the problems referred to were avoided by keeping competing substances out of the polymerisation mixtures, i.e., the conditions were idealized. The formation of an information-transmitting homopolymer from a complex mixture of substances cannot be excluded, but it is extremely unlikely ... 

Although the pre-RNA world is now much more the centre of scientific attention in prebiotic chemistry, there have been several attempts in recent years to understand the synthesis of oligonucleotides from the normal nucleotides by using simulation experiments (Ferris, 1998). In condensation reactions in aqueous media, there is always competition between synthesis and hydrolysis synthesis is generally only successful when supported by catalysts. 

Four billion years ago, the Earth s thin crust consisted of geochemicals (i.e., compounds containing the elements Si, O, Al, Fe, Mg, Ca, K and Na, as well as traces of other elements). Thus, some biogenesis researchers believed that the first replicating material consisted of geochemical material rather than substances containing carbon and other bioelements. Clay minerals in particular were included in experimental and theoretical studies. The most important are kaolinite and montmorillonite the latter was, and still is, used in many experiments carried out to simulate prebiotic reactions. 

Hazen and Deamer looked at the chemical and physical properties of the end products of hypothetical prebiotic reactions carried out under extreme conditions of pressure and temperature, for example in CCh-rich regions of hydrothermal vents. The results of laboratory experiments indicate that prebiotic syntheses leading to a variety of products could have occurred in hydrothermal systems some of these have amphiphilic properties, and would have been capable of self-organisation processes. 

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 question of the elimination of water in polycondensation reactions still provides an unsolved problem. Solutions are being searched for in many laboratories, for example in Italy Paly6 and Zucchi from the University of Modena consider it possible that limited regions where liquid or supercritical CO2 phases were present could have existed on the young Earth. Such regions, with non-aqueous media, could have been particularly favourable for some prebiotic reactions, such as those involving the elimination of water. Experiments to study this hypothesis are planned (Paly6 and Zucchi, 2002 Holm and Andersson, 1998). 

These experiments were, however, not completely accepted by some chemists working in the area of prebiotic chemistry these critics were unhappy with some synthetic conditions used, such as the KCN concentrations (0.1-0.2 M at 373 K). They felt that cyanide in such concentrations would have been relatively rapidly hydrolysed at 373 K in addition, CO pressures of 75 atm were considered incommensurate with real conditions in hydrothermal systems. 

Pyrite is not only one of the key compounds in Wachtershauser s theory, but could also have fulfilled an important function for phosphate chemistry in prebiotic syntheses. A group in Rio de Janeiro studied the conditions for phosphate sorption and desorption under conditions which may have been present in the primeval ocean. In particular, the question arises as to the enrichment of free, soluble inorganic phosphate (Pi), which was probably present in low concentrations similar to those of today (10 7-10 8M) (Miller and Keffe, 1995). Experiments show that acid conditions favour sorption at FeS2, while a weakly alkaline milieu works in an opposite manner. Sorption of Pi can be favoured by various factors, such as hydrophobic coating of pyrite with molecules such as acetate, which could have been formed in the vicinity of hydrothermal systems, or the neutralisation of mineral surface charges by Na+ and K+. 

The clay mineral montmorillonite, which is often used in different prebiotic syntheses, is probably now the most important mineral for experiments on prebiotic chemistry. It has shown its abilities in the area of simulation experiments on the formation of primitive cellular compartments montmorillonite accelerates the spontaneous conversion of fatty acid micelles to vesicles. Clay particles are often incorporated into the vesicle, just as is RNA, which is adsorbed at such clay particles. If the vesicles have been formed, they can continue to grow if fatty acids are fed to them via micelles. If the vesicles are pressed through 100 nm pore filters, they divide without dilution of their contents. 

These successful experiments suggest possible prebiotic reaction pathways for the formation, growth and multiplication of the first cells (Hanczyc et al., 2003). 

Amino acid formation in the Urey-Miller experiment and almost certainly in the prebiotic environment is via the Stecker synthesis shown in Figure 8.3. This reaction mechanism shows that the amino acids were not formed in the discharge itself but by reactions in the condensed water reservoir. Both HCN and HCO are formed from the bond-breaking reactions of N2 and H2O in a plasma, which then react with NH3 in solution. The C=0 group in formaldehyde or other aldehydes is replaced by to form NH and this undergoes a reaction with HCN to form the cyano amino compound that hydrates to the acid. The Strecker synthesis does not provide stereo-control over the carbon centre and must result in racemic mixtures of amino acids. There is no room for homochirality in this pathway. 

Changing the initial conditions in the Urey-Miller experiment to favour a primordial atmosphere with CO2 as the primary carbon source does not produce such a rich mixture of prebiotic molecules and there is a significantly lower yield of amino acids an argument against an endogenous source of organic molecules. 

Endogenous organic synthesis Urey-Miller experiments as a source of prebiotic molecules via the Strecker synthesis for amino acids, HCN polymerisation for purines and pyrimidines and the formose reaction for sugars... 

Several factors indicate that the amino acids detected in all of these carbonaceous chondrites are indigenous and that they must have originated abiotically. First, the presence of protein and non-protein amino acids, with approximately equal quantities of D and L enantiomers points to a nonbiological origin and precludes terrestrial contamination. In addition, the non-extractable fraction of the Murchison is significantly heavier in 13C than terrestrial samples. Finally, the relative abundances of some compounds detected resemble those of products formed in prebiotic synthesis experiments. The aliphatic hydrocarbons are randomly distributed in chain length, and the C2, C3, and C4 amino acids have the highest concentrations (i.e., the most easily synthesized amino acids with the least number of possible structures are most abundant) [4]. 

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