Prebiotic molecular evolution

These schemes have been frequently suggested [105-107] as possible mechanisms to achieve the chirally pure starting point for prebiotic molecular evolution toward our present homochiral biopolymers. Demonstrably successftd amplification mechanisms are the spontaneous resolution of enantiomeric mixtures under race-mizing conditions, [509 lattice-controlled solid-state asymmetric reactions, [108] and other autocatalytic processes. [103, 104] Other experimentally successful mechanisms that have been proposed for chirality amplification are those involving kinetic resolutions [109] enantioselective occlusions of enantiomers on opposite crystal faces, [110] and lyotropic liquid crystals. [Ill] These systems are interesting in themselves but are not of direct prebiotic relevance because of their limited scope and the specialized experimental conditions needed for their implementation. 

There is another point about the thermodynamic stability of prebiotic compounds. This is the fact that a series of thermodynamically very stable molecules seem to have been ignored in the course of prebiotic molecular evolution as building blocks of living structures. Take sugars, for example six-membered rings have not been used for the construction of nucleic acids, where only o-ribose takes the stage. Furthermore, only two types of purine and only two of the pyrimidine bases have been utilized among the many possible nucleic acids. Actually one could make a... 

Figure 20.5. Transmission electron microscopic (TEM) images of hpid-Uke glycine peptide enclosures. Glycine tail and aspartic acid head peptides formed tube and vesicle structures. Note the growth of the tube opening (A, B, C) and the presumed vesicle division (D). If these dynamic enclosures can encapsulate other biomolecules, this may be one step closer for prebiotic molecular evolution.

Figure 20.10. Amphiphilic ionic self-complementary peptides. This class of peptides has 16 amino acids, c. 5 nm in size, with an alternating polar and non-polar pattern. They form stable (3-strand and 3-sheet structures thus, the side chains partition into two sides, one polar and the other non-polar. They undergo self-assembly to form nanofibers with the non-polar residues inside positively and negatively charged residues form complementary ionic interactions, like a checkerboard. These nanofibers form interwoven matrices that further form a scaffold hydrogel with a very high water content ( 99.5%). The simplest peptide scaffold may form compartments to separate molecules into localized places where they can not only have high concentration, but also form a molecular gradient, one of the key prerequisites for prebiotic molecular evolution.

Zhang, S. and Egli, M. (1994). A hypothesis reciprocal information transfer between oligoribonucleotides and oligopeptides in prebiotic molecular evolution. Origins of Life and Evolution of Biospheres, 24, 495-505. 

In fact, the main assumption in the field is still the one proposed by Alexander Oparin in the late 1920s that life originated on this planet from a prebiotic molecular evolution, namely a series of successive spontaneous chemical steps that brought about a gradual increase of size and specificity (complexity) up to the staggering level of the living cell. 

In addition to inducing a process of ordering and compartimentation, can supra-molecular surfactant aggregation induce other phenomena which are relevant for the prebiotic molecular evolution The answer is affirmative, as will be seen in the following sections. 

Until the 1980s, yields of nucleobases obtained in prebiotic syntheses were very small. Thus, some scientists assumed that in earlier phases of molecular evolution, the nucleic acids used other bases in their information-transmitting substances. Piccirilli et al. (1990) suggested isocytosine and diaminopyridine, while Wachtershauser (1988) suggested that the first genetic material possibly consisted only of purines. However, pyrimidine (about a fifth of the total amount of purines present) had been detected in the Murchison meteorite, so that an effective pyrimidine synthesis should have been possible. 

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. 

A collection of almost 100 articles on all aspects of prebiotic and early biological evolution probably the single best source on molecular evolution. 

M. Levy and S. L. Miller. The prebiotic synthesis of modified purines and their potential role in the RNA world. Journal of Molecular Evolution, 48 (1999), 631-7. 

Deamer, D. W. and Barchfeld, G. L. (1982). Encapsulation of maeromolecules by lipid vesicles under simulated prebiotic conditions. Journal of Molecular Evolution, 18, 203-6. 

It is unlikely that under prebiotic conditions the complex and sophisticated biomacromolecules commonplace in modem biochemistry would have existed. Thus, research into the origin of life is intimately associated with the search for plausible systems that are much simpler than those we see today. However, it is also plausible that these simple building blocks of life might have been amphiphilic molecules in which water could have had an enormous influence on their prebiotic molecular selection and evolution, because water can either form clathrate stmctures or drive these simplest molecules together (Ball, 2001). 

Put more simply, when considering prebiotic selection and evolution in the context of the origin of life, the enormously powerful force of water must never be underestimated. As all life is based on water, all molecules in living systems interact with it, and water likely has driven molecular evolution from the very beginning, here on earth or plausibly elsewhere in the universe - or multiverse. 

Wong, J. T.-F. and Bronskill, P. M. (1979). Inadequacy of prebiotic synthesis as origin of proteinous amino acids. Journal of Molecular Evolution, 13, 115-25. 

The influence of plant sterols on the phase properties of phospholipid bilayers has been studied by differential scanning calorimetry and X-ray diffraction [206]. It is interesting that the phase transition of dipalmitoylglycerophosphocholine was eliminated by plant sterols at a concentration of about 33 mole%, as found for cholesterol in animal cell membranes. However, less effective modulation of lipid bilayer permeability by plant sterols as compared with cholesterol has been reported. The molecular evolution of biomembranes has received some consideration [207-209]. In his speculation on the evolution of sterols, Bloch [207] has suggested that in the prebiotic atmosphere chemical evolution of the sterol pathway if it did indeed occur, must have stopped at the stage of squalene because of lack of molecular oxygen, an obligatory electron acceptor in the biosynthetic pathway of sterols . Thus, cholesterol is absent from anaerobic bacteria (procaryotes). 

The physiologist de Duve concentrated his efforts on a material link between the prebiotic phase of the primeval Earth and the state of development at which RNA (or a similar type of molecule) determined the further progress of the evolution process. In particular, this connecting link needed to have been able to transfer chemical energy, since without such a procedure, the RNA synthesis appears impossible. The molecular species which Christian de Duve favours for this important function is that of the thioesters. The exact reasoning as to why this is the case is discussed in detail in his book Vital Dust Life As a Cosmic Imperative (de Duve, 1996). 

The conventional hypothesis in prebiotic times, both forms were present in equal amounts. A still unknown event caused only one of the two (enantiomeric) molecular species to be built into the corresponding macromolecules. Thus, a non-linear evolution process determined the direction (d- or L-form). 

Buick R, Thornett JR, McNaughton NJ, Smith JB, Barley ME, Savage M (1995) Nature 375 574 Bungenberg de Jong H, Decker WA, Swan OS (1930) Biochem Z 221 392 Deamer DW (1998) Membrane Compartments in Prebiotic Evolution. In Brack A (Ed.) The Molecular Origins of Life. Cambridge University Press, p 189 Deamer DW, Dworkin JP (2005) Chemistry and Physics of Primitive Membranes. In Walde P (Ed.)... 

Boiteau, L., Rlasson, R., Collet, H., etal. (2002). Molecular origin of life when chemistry became cyclic. The primary pump, a model for prebiotic emergence and evolution of petides. In Fundamentals of Life, eds. G. Ralyi, C. Zucchi, and L. Caglioti. Elsevier, pp. 211-18. 

Figure 3. Some facts and open questions about the origin of life. The concept of an RN A world preceding present-day genetics based on DNA, RNAand protein, has been conceived by chemists and molecular biologists interested in problems of prebiotic chemistry and early biological evolution. Several pathways which are plausible under...

Allamandola and Hudgins have considered the formation of complex organic species in ice matrices and provided a summary of the photochemical evolution on those ices found in the densest regions of molecular clouds, the regions where stars and planetary systems are formed 42 Ultraviolet photolysis of these ices produces many new compounds, some of which have prebiotic possibilities. These compounds might have played a part in organic chemistry on early Earth. 

At this point, however, we cannot ignore the fact that the evolution of protein synthesis started before the origin of the first cells, in systems which could not have cell walls, cytoskeleton filaments or sodium pumps, for the very good reason that all these structures require well-developed proteins. How could precellular systems have high potassium concentrations, and low sodium levels, without any of the molecular mechanisms that cells employ to this end The most plausible answer is that those concentrations did not have to be produced in prebiotic systems because they already existed in the environment of the primitive seas. The ribotype world, in short, was also a potassium world. 

---