Part II: https://systemity.livejournal.com/4661607.html
Original paper "View on Lipids of Microorganisms from the Standpoint of Prebiotic and Biological Evolution" published in: Voprosy Evolutsii Bakterij (Evolution of Bacteria), USSR Academy of Sciences, Center for Biological Research, Institute of Biochemistry and Physiology of Microorganisms, Pushchino, 1984, pp. 93-119 (https://www.dropbox.com/s/
It would seem that this logical deadlock could be resolved by comprehensive investigation of regularities in the evolution of those macromolecules which perform same functions in evolutionarily distant contemporary organisms. With the fundamental capabilities created by molecular biology methods, it is possible now not only to investigate evolutionary relations between various organisms but also to estimate a relative time point of their divergence, i.e. evolutionary distances. The idea of the “molecular evolutionary clock” was first proposed by Zuckerkandl and Pauling  in 1965. It is based on the fact of existence of a great variety of macromolecules that, having different sequences of monomers, are capable of performing same functions. Consequently, mutational changes in proteins and nucleic acids can provide a measure of the evolution time. Woese  recently made a detailed analysis of the results obtained with the use of the molecular chronometry method and discussed the ways for further improvement of the method and overcoming its limitations.
For instance, one of the major limitations of the method is caused by the fact that the relative speed of homologous macromolecular clocks can be different in different organisms. Also, in bacteria, an intensive interspecies transfer of genes with totally different evolutionary backgrounds may contribute into different genealogy of macromolecules of one and the same organism. Both of those limitations can be resolved in one or another way. For instance, it was shown that the use of two independent molecular clocks – cytochrome c and ribosomal RNA – provided consistent data on purple synthesizing bacteria . Phylogenetic structures based on molecular chronometry studies [25, 29] attract a lot of interest in biologists of various areas of specialization, and there is a hope that this method can help to develop objective criteria for evaluation of evolutionary relations between various groups of organisms. Nonetheless, the areas in which molecular chronometry is either ineffective or insufficiently effective include, first and foremost, the issues of prebiotic evolution, emergence of life and the functioning of early life forms. It is also important to realize that the discovery of the paths of evolution of life on Earth is not an answer to the question about the reasons for the choice of those paths.
Interpolation of the regularities of evolutionary changes in the structure of most conservative macromolecules to the possibly distant past has resulted in a seemingly substantiated concept of progenote, the last common ancestor of urkaryotes, eubacteria, and archaebacteria – the “forefathers” of the three contemporary kingdoms of life forms [29, 31]. However, the question of where that proto-ancestor came from will send us back to the idea of spontaneously emerging biologically purposeful macromolecules.Comprehensive studies of the fine structure of biological macromolecules have not added anything new into the understanding of how such molecules could have emerged in the ancient Earth atmosphere, and, if that did occur, then how exactly it could have led to formation of systems with some signs of life and sufficient for the start of evolution towards living organisms.
Molecular model of a protobiont
Previously, we proposed a molecular model of a hypothetical structure capable to accumulate energy in certain conditions as the earliest structure that has the properties of a biologically purposeful organization, or – more precisely – as a structure that could have evolved into something very similar to the biological cell . To a certain extent, this hypothetical model represents a molecular model of a protobiont, although it does not touch upon the reproduction issues. In the proposed model, the role of a
phase-separated system evolving into a protobiont is played by coacervate formations, built by the principle of the polylipid membrane. Supposedly, in the process of evolution, most of the mechanisms underlying the self-development of phase-separated polylipid formations had been replaced by significantly more efficient mechanisms, and therefore it is practically impossible to locate them in the contemporary forms of life. Particularly, most of the processes that were dependent on physical environment had acquired a highly efficient regulation factor, such as a large assortment of structural and catalytic proteins. Other mechanisms, in particular, membrane oxidative phosphorylation and photosynthesis, which had achieved the highest level of evolutionary improvement as far as their respective underlying principles are concerned, have been kept unchanged by most of the contemporary forms of life.
Phase-separated systems organized by the above-described principle of the polylipid membrane could spontaneously emerge at the very early stages of chemical evolution as a result of physical factors – for instance, high compression as a result of impact of ultrasound waves that cause conformational changes in the polylipid structure. Lipids that were required for their emergence were available from fatty acids, glycerin and phosphoric acid which were present in the primordial soup. Formation of the polylipid membrane involved ions of Mg, Ca, K and Na, most widely distributed in the Universe.
Under the influence of mechanical or thermal energy from external sources, the polylipid membrane could provide for formation of primary macroergic compounds – oxides of bivalent metals (Mg, Ca) which are known to release considerable amounts of energy (more than 12 Kcal/mol) when interacting with water. Formation of metal oxides involves the dissociation of the bidentate complex produced by substitution of protons of enolyzed phospholipids by a metal ion. This whole hypothetical process includes several tages:
where L is an abstract phospholipid.
Thus, the overall effect of the above-shown hypothetical process is dissociation of water. However, if during this process, the metal oxide was transferred to the opposite part of the phospholipid membrane, it would cause the separation of charges, placing the protons on the membrane outer side, and hydroxyls on the inner side. Hydroxyls could recombine into hydrogen peroxide whose decomposition (for instance, under the influence of iron salts) was releasing atomic hydrogen. The latter could interact with the gradient-driven protons from across the membrane, as well as participate in oxidation of the dissolved organic substances. Already in this version, the proposed hypothetical process of energy concentration, which – as is seen from the above formulae – does not require free oxygen, has all the necessary prerequisites to allow the primitive phase-separated systems, within which it could supposedly develop even at a negligibly small scale, to evolve into systems with the signs of biological purposefulness. This is an example of a quite concrete model of the emergence of life, which excludes a “voodoo” element that is present in all of the heretofore proposed hypotheses on the origin of life.
Within the context of this model, photosynthesis, for instance, can be viewed upon as an improved variant of the primitive energy production process in prebiotic systems. As is seen from the formulae of the known chlorophylls, all of them contain enolized carbonyl at the 9-position of the porphyrin ring. Substitution of protons of enolic hydroxyl groups in chlorophyll molecules by a Mg atom from the porphyrin ring of other chlorophyll molecules could result in formation of aggregates, which is a known  but unexplained fact.
The influence of light could cause the decomposition of such aggregates by the same mechanism that, according to the model of primitive energy production, provided the metal oxide formation. That means the formation of chlorophyll molecules containing highly active magnesium oxide, coordinated in the porphyrin ring, which in that form can participate in various syntheses and, in particular, interact with carbon dioxide. Thus, from the standpoint of the proposed model, photosynthesis as a method for transformation of the energy of light into the chemical energy could in general be implemented in primitive systems that did not yet know the synthesis of bio-purposefully organized proteins and nucleic acids.
As was earlier noted, formation of MO (metal oxide) – the earliest macroergic compounds – was occurring when the rigid, asymmetrical structure of the polylipid membrane was exposed to a mechanical impact. In the course of time, the response to occasional environmental impacts developed into efficient and organized conformational changes in the membrane-embedded proteins. Thus, polylipid membrane was serving as a sort of template for the purposeful selection of proteins whose spontaneous synthesis was occurring under direct energetic control. Evolution of proteins was developing in two directions. One group of proteins, by building-in to the polylipid membrane, was improving the membrane structure to facilitate energy concentration from external sources. Another group of proteins which were capable to change their conformation due to certain factors – for instance, interaction with protons – was used to increase the efficiency of the mechanism of MO production based on utilization of the energy of chemical transformations.
The application of MO as a macroergic compound was restricted to polylipid-protein membranes of the earliest phase-separated systems, as metal oxides could not survive in water systems. Therefore, there had been developed and maintained a primitive mechanism for transformation of the primary macroergic compounds – metal oxides – into secondary macroergic compounds, which are supposed to have been polyphosphates, as well as the third generation macroergic compounds – nucleoside phosphates – which became possible as the metabolism system was developed. This should explain the macroergic properties of these compounds: it is apparently due to their history of being the mediators of that critically important role that metal oxides played in the emerging metabolism.
As was previously proposed [5, 8, 12, 25], the transition from primary to secondary and tertiary macroergic compounds involved cardiolipin, one of the most easily synthesized phospholipids, which consists of two residua of phosphoric acid, bonded with three molecules of glycerin, two of which are esterified with fatty acids. The role of the phosphate group donor was played by a cardiolipin salt produced at cardiolipin interaction with MO. After elimination of the phosphate group, cardiolipin was turning into phosphatidyl glycerin, no longer capable of linking the polylipid chains, which made that area of the polylipid membrane incapable of producing MO until the cardiolipin
re-synthesis from phosphatidyl glycerin by connecting it with the phosphate group and diglyceride.
To produce macroergic oxides, the early polylipid membrane needed high energy, which, in its turn, demanded that the system had a highly cooperative structural-functional organization – one of the main properties of the live matter. Had the protobiont an easier way for accumulating the energy from outside, it would probably never had a chance to evolve into a live biological cell. It is also possible to visualize a model of the early primitive mechanism that could further provide for information accumulation and reproduction in the form of nucleic acids. It could consist in condensation of phosphoric acid residues in those areas of the polylipid membrane where MO was produced. In the same areas, under the influence of MgO, the synthesis of carbohydrates from formaldehyde could occur. Thus produced oligomers were able to carry the information about the optimal topography of monomer phospholipids most helpful in MO production and, therefore, to become a template of the optimal structure of the polylipid membrane.
We have presented the outlines of a few hypotheses concerning the biological role of lipids. Some of positions of these hypotheses are extremely hard for experimental proof or disproof, at least at present time. By presenting those hypothetical mechanisms, we mostly wanted to draw the attention of researchers in the origin of life to the fact that here are other logical roads that can take to solving the problem of the emergence and evolution of the Earth-based life on the molecular level, than those where every significant event starts with the miraculous appearance of “live” macromolecules. In the proposed model, both the “enlivening” and evolution of functionally active macromolecules occur in the course of the protocell “enlivening” and the cell evolution. This principle – of the primary unity and inseparability of the molecular and cellular levels of life processes – is obviously an advantage in designing a model of the origin of life.
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