2. The Evolution of Molecules

2.2 Polymers

In the early phases of evolution, we can assume the presence of energy-rich molecules capable of polymerization. Also, we can assume strong fluctuations of the environment. These fluctuations were due to the presence of the moon, the fast spinning of the earth, solar winds and solar magnetic activity. These influences, also felt within the crust, may have been such that a solution of suitable substrates was alternately desiccated and dissolved, warmed and cooled. This may lead in certain places to extremely high concentrations of substances that may be diluted and even destroyed later on. It is not unreasonable to assume the possibility of an alternation between phases when polymers were formed and phases when they were gradually decomposed.

Few theories are as iconic as the prevailing explanation of how simple chemicals dissolved in a puddle of primordial soup assembled themselves into the precursors of the earliest forms of life. The primordial soup theory was advanced, among others, by the German biologist Haeckel in the late 19th century and was ignored until 1953, when Urey and Miller showed that a gas mixture of elementary compounds (methane, ammonia, water, etc.) produce amino-acids and nucleosides if sparked by electric discharges similar to bolts of lightning. These compounds would rain down into the primordial oceans until they self-assembled into polymers. However, methane and ammonia are too light sensitive to be stable under the conditions of the early earth. In addition, the dilution of the organic compounds in the early earth’s oceans make any chemical reaction between two molecules unlikely. Condensation of polymers cannot possibly occur in an aqueous environment, where the tendency is toward depolymerisation. Water must be excluded. This was advanced already in 1908 and ignored. But was water initially present?

In a series of articles appearing between 1969 and 1971, Neuman emphasized the role of crystals in the origin of life. G. Wächterhauser proposed in 1988 that the meeting place of molecules was provided by the surfaces of iron-sulfur minerals as pyrite, which abounds around underwater hydrothermal vents. Heckl, in Munich, is among the leaders in this field of research. In the view of his research team6, simple bases such as uracil or adenine, in solution in an evaporating salty broth at 80°C or more, concentrate and spontaneously purify themselves into monolayers on the surface of clay. In such a way, we have a creation of monolayers of pure polymers of cytosine, adenine, guanine, etc. Sometimes, a small contamination of one base with another is possible. Most engrossing is their observation that some amino acids, such as glycine, can thereafter add to the existing nucleic acid polymer, and they also polymerize.

From the concentrated broth of diverse molecules, more complex molecules were formed. This occurs simply with the condensation of similar components. High molecular weight substances such as proteins, lipids, carbohydrates and nucleic acids are created in this way. However, not all of them were ideally suited for further developments. Amino acids united into larger complexes. Yet, the inherent variability of the amino-acid building blocks available in at least 21 forms7 was too great to establish a meaningful regular pattern of repeating units: every protein chain made presents an individual character that must have set it apart from all the others (fig.2.3). In the case of the carbohydrates, the repeating unit8 ( glucose, galactose, etc.) was so regular that the pattern is monotonous in its uniformity (cellulose, glycogen, etc.). Sometimes the carbohydrate chains formed are branched. Lipid chains present for their part the rather forbidding characteristic that they become insoluble in water when the polymer reaches a certain length.

Bases such as adenine, guanine, cytosine, uracil, inosine etc., hooked to a ribose sugar, itself attached to a phosphate group, form a nucleotide (see fig.2.2). This nucleotide can rather easily attach itself to another nucleotide. This is done by nucleotides that have three phosphates. These trinucleotides are endowed with energy that can be used to establish sugar-phosphate linkages, just by relinquishing two of the three phosphates present (fig.2.4).

Figure 2.4. Energy-rich trinucleotides can link together by releasing 2 of the 3 phosphates. In this way, they form a polynucleotide chain such as AAACGU.

In this way a repeated pattern composed of nucleotides that form a long chain of nucleic acid is produced9. This filament is heat-resistant and resists boiling water. Each chain would be clearly distinguishable as being a nucleic acid chain made of building blocks similar to that of other nucleic acid chains, but also every single chain would have retained a certain amount of individuality because of the differences observable among the bases.

If we assume that the same probability exists for the condensation of a right-handed isomer of a nucleotide with another right-or-left-handed isomer, then one RNA molecule with 21 bases composed exclusively of right-or left-hand ribose will have one chance to appear among one million of such molecules formed. One can thus admit the chance formation of an RNA molecule with 21 bases containing exclusively the d-ribose isomer, as the sugar component. Note that the condensation of bases on the surface of some clay may favorably force the choice of a right- or left-handed isomer, so that the chance occurrence may in fact be much greater than assumed here. Our body, and that of all other organisms right down to nematodes, flies and of course other mammals, is flooded with these micro RNA’s that play an essential role in gene regulation and developmental control. They also regulate the stability of the larger RNA’s that have messenger duties.

Such a nucleic acid chain presents the peculiarity of being composed of a backbone that is bearing at repeated intervals a series of strong negative charges due to the phosphates. These charges work synergically and may bind very strongly to other positive charges. On the other side of the chain, protruding from the sugar, there are a series of weak positive charges due to the purine or pyrimidine bases (see fig.2.4). These charges also work in a synergetic manner and are able to attract, through peculiar weak forces called "hydrogen bonds", other positive charges. On both sides of the chain, thus, there are attracting forces that work like zippers: the more there are of them, the stronger the binding becomes established.

Under the right circumstances, when there are salts present in the water and the temperature not too high, such a nucleic acid chain would attract and bind another nucleic acid chain that is provided with the adequate bases: an adenine (A) in one chain should oppose uracil (U) in the other chain and also a guanine (G) should be located opposite a cytosine (C). In this manner, a double-chain is formed (fig. 2.5).

Figure 2.5. An adenine in one polynucleotide chain should oppose a uracil in the other chain, and a guanine should oppose a cytosine. With 21 bases involved, the double chain so formed becomes difficult but by no means impossible to separate.

An RNA molecule composed of about 21 bases hooked onto identical isomeric ribose sugars linked together through phosphates, presents three properties that all other nucleic acid chains of the same length lack10. Firstly, such a nucleic acid chain attracts and binds another nucleic acid, provided complementary bases are present on the other chain: an adenine in one chain should oppose an uracil in the other and a cytosine should oppose an inosine or a guanine. Even if no other chain is present in the environment, a second chain can be created: the first RNA molecule will serve as a template and collect energy-rich triphosphates that can thereafter link with one another into a complementary chain. The double helix so formed is tightly packed. This tight packing is destroyed if one single sugar of the wrong isomeric type is included within the nucleic acid chain. Secondly, the tight packing protects such a double helix from destruction, allowing it to survive decay phases that eliminate all other chains formed. The third property is that, upon entering a new constructive phase, these double helixes may unwind. Each of the two may then form new double helixes.

These processes displaced the polymers containing the left- and right-hand ribose types simultaneously. Since only the d-ribose type is now present in nucleic acids, one should assume that this species was able to displace all the species containing the l-ribose. The initial phase of polymerization was thus a phase of divergence: a large number of RNA molecules were formed having all possible sequences of d- and l-ribose. This divergent phase was followed by a convergent phase. The spontaneous polymerization was suppressed in this phase, in favor of selective formation of double helixes. Given the sufficient number of RNA molecules synthesized, the probability that the convergent phase would not occur is extremely small. Thus, with this system of complexification, we switch from the addition of building blocks at the end of the chain, so as to form an ever longer chain, to a complexification similar to that occurring in a crystal: it goes into another dimension. What is happening is no longer an increase in length but in thickness. This increase is no longer accomplished with ionic bonds but with weak hydrogen bonds that can be easily formed and broken. A series of succeeding weak hydrogen bonds act in a synergetic manner to form a solid bond. This phenomenon is not frequently found among carbohydrates, lipids and proteins.

The following evolutive step is again a divergent phase. During this phase, complementary double helixes will sometimes undergo condensation by hooking to each other at the end of the chain. In this way, the chain doubles in length. Also, the longer species exhibits a series of bases that are complementary to each other. Intrapairing of bases can occur and the longer RNA species folds in order to permit this. The new molecule exhibits thus a tertiary structure that protects it almost fully against degrading influences (fig.2.6).

Figure 2.6. With chains composed of 50 bases or more, intra-pairing between various bases may occur, thus provoking the formation of a tertiary structure that renders the chain resistant to degradative processes. Such a chain, composed of 112 bases, is used currently in our bodies as transfer RNA.

A replication of RNA molecules of that length, without the intervention of an enzyme, is bound to result in some errors of copying. Sometimes, the correct complementary base will be missed. Such a copying error occurs for one base out of one hundred. Since we are now dealing with RNA molecules composed of about 50 nucleotides, errors result in the formation of various new molecules. A great diversification of such RNA molecules occurs. Whenever an optimal resistance to destructive agents is reached, stabilization takes place and the molecule survives, while the less resistant molecules are destroyed and eliminated.

Some RNA molecules show catalytic activity: these RNA’s capable of promoting chemical reactions are the ribozymes. It is now well established that these ribozymes, which may be composed of as much as 247 nucleotides, are able to pack into the regular arrays of well diffracting crystals. Still more remarkable is that the ribozyme crystals maintain their catalytic activity: they are pre-organized for substrate recognition. The discovery in 1981 that some RNA’s, the ribozymes, could catalyze reactions just as proteins do, while other RNA’s have the information storage of DNA, the realization that RNA combines features of proteins and DNA, led to the "RNA world" hypothesis for the origin of life.

It is possible that some plant diseases and also scrapie are pathogens relying on such RNA. RNA molecules of twice this size have been retained for higher evolutive purposes and, in our cells, serve for the transfer of information stored away in the genetic material and expressed in proteins.

References

6. The role of self-assembled monolayers of the purine and pyrimidine bases in the emergence of life, O.L.E.B. 28: 283-310, 1998

7. times two if one takes also into account the "right hand" form; archaea have command over an additional amino-acid, pyrolysine

8. ibid.: each sugar type consists of two isomers

9. Inorganic polyphosphate, i.e. a linear chain of hundreds of phosphate residues made from ATP are also found, in all cells. Their role has remained elusive. In some bacteria (e.g. Pseudomonas aeruginosa) the polyphosphate is a factor of virulence.

10. Kuhn: Ang. Chem. Intern. Edit. 11: 798-820, 1972

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