Prebiotic RNA world

Scheme 2.2 Origin of life, in the popularized version of the prebiotic RNA world.

There is of course still the possibility that some brilliant chemist will soon discover a prebiotic scenario for making RNA sequences - in a way we all hope that this will be the case, it would indeed be a good day for those studying the origin of life. However, for the time being, the prebiotic RNA world is grounded on the above-mentioned dream, and not on solid science. 

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. 

Figure 2.3 The relation between the compartmentalistic approach and the prebiotic RNA world and the missing link (items 1 and 2).

It seems that there is a missing link between the scenarios of the prebiotic RNA-world and the compartmentalishc approach and the missing link is how to make RNA by a prebiotic sequence or network of internalized reactions. 

I have brought into this chapter another line of criticism against the naive version of the prebiotic RNA world, in particular about the assumption that selfreplication and the corresponding molecular evolution processes may be sustained by one single molecule. Clearly, self-replication in a prebiotic scenario, in order to be chemically important, has to respect realistic concentrations and rate constants. It may be different in a fully fledged cell, once specialized enzymes and biochemical matrices have evolved - but this is a point of arrival and not of origination. 

The RNA cells eventually have to evolve into protein/DNA cells. And this is a long and certainly not easy pathway. However, this is the beauty of the prebiotic RNA world that at least on paper, a possible pathway leading to DNA and proteins can be conceived. One ideal pathway showing the transition from the RNA to the DNA cell is illustrated in the Figure 11.4. 

I believe that the bottom-up approach to the origin of life will enjoy a considerable boost, when conditions are found for the prebiotic synthesis of many identical copies of long (>30) co-oligopeptide or co-oligonucleotide sequences. This would at least show that the prebiotic synthesis of enzymes and/or RNA is in principle possible. This remains the main problem with the prebiotic RNA world. 

Catalytic RNA ( Ribozymes ) and Conjectures about a Prebiotic RNA World ... 

The RNA World, Second Edition The Nature of Modern RNA Suggests a Prebiotic RNA World. Gesteland, R. Atkins, J. F., Eds. Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY, 1999 p 709. 

Gesteland RF, Cech TR, Atkins JF (1999) The RNA World The nature of modern RNA suggests a Prebiotic RNA, 2nd ed., Cold Spring Harbor Laboratory Press, New York. 

It remains an open question as to whether this newly identified species of amino acid was important in the construction of peptide nucleic acids (see Sect. 6.7) in the prebiotic chemistry of the RNA world phase of biogenesis (Meierheinrich et al 2004). 

Shapiro (1995) studied the prebiotic role of adenine, i.e., the question as to whether or not this nucleobase could have been involved in the hypothetical RNA world (see Chap. 6). He lists a series of problems ... 

The RNA world hypothesis caused prebiotic phosphate chemistry to become an attractive research area again unfortunately, no clear evidence for a realistic nucleotide synthesis under the simplified conditions of a primitive Earth has yet appeared. Important work on nucleoside phosphorylation has, however, been done. It is important to distinguish between ... 

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. 

The RNA world was the first biological world. If this is the case, we can learn or predict but little about the prebiotic chemistry of the RNA world from the biochemistry of today perhaps only the fact that the formation and polymerisation of nucleotides were once prebiotic processes. Thus Orgel is not of the... 

The RNA world was not the first biological world. In this case, the conclusions drawn above are not justified. We can then speculate that the monomers of an early genetic polymer can still be recognized today as important biochemical substances. Orgel considers it unlikely that RNA could have been formed prebiotically ribonucleotides are too complex to have evolved on the primeval Earth in sufficient amounts, and with sufficient purity. 

Lazcano, an evolutionary biologist, and Miller, an experienced prebiotic chemist, believe that the most important bottlenecks in the biogenesis process leading from the primeval soup to the RNA world, and thence to cyanobacteria, are the following ... 

In particular, the aminoacyl phosphate derivatives of 5 -AMP could condense to a polypeptide containing up to 56 residues. This is certainly a very elegant and impressive reaction, hut its relevance from the point of view of prebiotic chemistry is doubtful since, as already mentioned, it is not obvious whether and to what extent this reaction can be extended to co-oligopeptides. Also, of course, AMP cannot be considered (thus far) a prebiotic molecule. Here again we encounter the old problem of the RNA world, the fact that the prebiotic synthesis of mononucleotides is not understood. There is no doubt that if a robust and credible prebiotic route... 

Lazcano, A. MiUer, S.L. (1996) The origin and early evolution of life prebiotic chemistry, the pre-RNA world, and time. Cell 85, 793-798. 

A self-replicating polymer would quickly use up available supplies of precursors provided by the relatively slow processes of prebiotic chemistry. Thus, from an early stage in evolution, metabolic pathways would be required to generate precursors efficiently, with the synthesis of precursors presumably catalyzed by ri-bozymes. The extant ribozymes found in nature have a limited repertoire of catalytic functions, and of the ribozymes that may once have existed, no trace is left. To explore the RNA world hypothesis more deeply, we need to know whether RNA has the potential to catalyze the many different reactions needed in a primitive system of metabolic pathways. 

Probably because researchers involved in the study of amino acid and peptide prebiotic chemistry have seen their field of investigation challenged by the possible occurrence of an RNA world, much progress has been made in this field during the last decade. New directions have been explored, leading to prebiotically plausible pathways accounting for both amino acid and peptide production, and peptide chemo-metabolisms have been proposed. Since new... 

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