Self-replication mechanism

So far, only the self-replication mechanisms of linear molecules have been described it is now time to consider closed spherical structures, such as micelles and vesicles. Here, the term self-reproduction will be used rather than self-replication, because, as it will be seen, the population increase is generally based on statistical processes. The subject of micelles and vesicles self-reproduction is dealt with in other chapters in this book a certain degree of repetition and/or mis-match is unavoidable. 

There are still several uncertainties, even from the conceptual point of view, about the notion of self-replication. However the advantages of one such autocatalytic scheme for producing a significant concentration of active macromolecular species are commonly accepted. It is easy, at least on paper, to see how a self-replicative mechanism can give rise to the next important steps for the origin of life suppose in fact that during the self-replication cycles the compound undergoes some... 

The self-reproduction mechanism illustrated here for vesicles is of course extremely primitive with respect to the self-replication mechanisms of RNA. However, one should recognize that the first prebiotic self-replicators cannot have been chemically well-developed and sophisticated macromolecules. Most likely, the first replicators were primitive structures. In this sense, the self-reproducing supra-molecular structures have a distinct relevance, since the reproduction mechanism happens almost spontaneously. 

In accordance with the autocatalytic process, matrices are again formed. It is surprising that the autocatalysis decreases when only 1 of the 15 building blocks of the peptide has the opposite handedness, e.g., when the N-peptide fragment contains one D-amino acid as well as the 14 L-amino acids. These experimental results show that such a system is able to form homochiral products via self-replication. It can be assumed that similar mechanisms influenced the origin of homochirality on Earth (Saghatelian et al., 2001 Siegel, 2001). 

More information on the square root law and on kinetic and thermodynamic aspects of the minimal replicator theory can be found in the literature (von Kiedrowski, 1999 and 1993). The square root law has its origin in the product inhibition involved in the mechanism of self-replication. The more C units are formed, the greater is the tendency of the molecules of C to dimerize to give C2 this species, however, cannot function as a catalyst. 

These experimental results are astounding a few years ago, the reaction mechanisms for the self-replication of oligonucleotides which have been discovered and established would have been considered impossible ... 

Clearly what we need are verifying experimental demonstrations to help us select among the various mechanisms outlined above for the appearance of a small enantiomeric excess (e.e.) within a mixture of two enantiomers. Only after such an initiating event can an e.e. be amplified into the state of homochirality and enantiomeric purity necessary to permit the emergence of self-replicating biopolymers. In what... 

FRACTAL REACTION KINETICS Self-phosphorylation process, AUTOPHOSPHORYLATION SELF-PROTECTION MECHANISM SELF-QUENCHING Self-replicating elements,... 

Also, if the self-replicating structure were to possess chemical information, and in addition the capability to mutate, then self-reproduction, information and evolution would occur all at the same time something already very close to life (see Figure 7.1). It is then clear why the search for self-reproduction mechanisms is the holy grail of the research on the origin of life. 

Obviously, with one single molecule no successful chemistry can be achieved (although it may he different with one DNA molecule in a living cell). In normal wet chemistry, in order to self-replicate, the replicator A must bind to another molecule A. It takes at least two molecules to make an active complex A-A, capable of starting a replication mechanism. In addition, in the case of nucleic acids one needs the four nucleotides (or whatever monomers are implied as substrates). 

Are there other types of self-replication in nature, possibly based on a quite different mechanism There are not many, but there is a famous case the formose reaction, described in 1861, and based on a reaction cycle of formaldehyde. This reaction has already been mentioned in Chapter 3, on the subject of prebiotic... 

No longer than twenty years ago, self-replication was one of those mysterious processes considered the monopoly of living matter. The fact that we are now able to achieve it in the laboratory means that we understand self-replication and selfreproduction in terms of simple rules of chemistry. In turn, this means that we have proceeded a step further in the understanding of the mechanisms of life. Of course, this is just one step, but it shows that conceptual and experimental progress in the ladder of the transition to life is advancing. 

This is illustrated in Figure 11.3. It consists of a vesicle containing two ribozymes, one (Rib-2) capable of catalyzing the synthesis of the membrane component the other (Ribl) being an RNA replicase that is capable of repUcating itself, and reproducing the Rib-2 as well. In this way, there is a concerted shell-and-core replication, and there is therefore a basic metabolism, self-reproduction, and - since the replication mechanism is based on RNA replication - also evolvability. 

Thanks to the outside supply of substrates, such a cell should be capable of selfmaintenance and of self-reproduction, including replication of the membrane s components. However it would not make low-molecular-weight compounds and would not have redundancies for its own defense and security - all self-repair mechanisms are missing. Also, there is the problem of leakage and lack of concentration gradients and cell division would be simply due to a physically based statistical process. 

Frank proposed a mechanism for the autocatalytic self-replicating process in which a chemical substance catalyzes its own production and acts as an anticatalyst for the production of the enantiomer without mentioning any actual compound or actual reaction [17]. hi this kinetic model, it is possible to obtain an enantiomerically enriched compound from an ex-... 

What matters is that the genotype - the biological software - is a deposit of instructions and therefore is potentially capable of carrying the project of embryonic development. This was the long-awaited answer to vitalism, and the computer became therefore the new model of mechanism. In reality, the new model of a living machine is not the computer that we encounter in our daily life, but an ideal machine known as von Neumann s self-replicating automaton. 

The process of evolution demonstrated in these studies depended on the existence of machinery for the replication of RNA fragments in the form of the Q p replicase. As noted in Chapter 1. one of the most elegant characteristics of nucleic acids is that the mechanism for their replication follows naturally from their molecular structure. This observation suggests that nucleic acids, perhaps RNA, could have become self-replicating. Indeed, the results of studies have revealed that single-stranded nucleic acids can serve as templates for the synthesis of their complementary strands and that this synthesis can occur spontaneously—that is, without biologically derived replication machinery. However, investigators have not yet found conditions in which an RNA molecule is fully capable of independent selfreplication... 

There is an important connection. Life developed under non-equilibrium conditions. Consider first an example. Far from equilibrium, you have chemical oscillations in which millions of millions of molecules change their color simultaneously. This type of coherence is possible only if there are long-range correlations. They occur only far from equilibrium. Similarly, biomolecules, with their complex structures, would be impossible to build in equilibrium conditions. They would have a negligible probability. This is no more so in far-from-equilibrium conditions. However, the detailed mechanism by which biomolecules appeared is still a controversial problem. But surely, biomolecules are non-equilibrium structures maintained from one generation to the next by self-replication. 

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