2. The Evolution of Molecules

2.1 Chemical Complexification

The earliest stage of Earth’s history from 4.56 to 4.45 billion years ago was hot and has been referred to as “Hadean”. The first solid mantle covering the earth was formed about 4.5 to 4.3 billion years ago, i.e. 9 billion years after the creation of the Universe. The oldest known rocks date from 4 billion years ago and the oldest known water-derived sedimentary rocks date from 3.8 billion years ago. This is consistent with a cooled earth made of a stable crust and liquid water oceans. The intervening stage from 4.4 to 4.0 billion years was a period of rapid cooling that was heated up again between 4.0 and 3.8 billion years ago by a heavy bombardment of solid impacts that probably was brief and unable to destroy the nascent hydrosphere and the first inklings of life.

Within 500 million years, the iron and other heavy elements were drawn into the core of the spinning earth while the lighter ones such as silicon, carbon, oxygen etc., remained on the surface. The primary hydrogen atmosphere was in the mean time blown off into space. Thereafter, an intense de-gassing expelled the entrapped nitrogen, hydrogen, water, and carbon dioxide. The very hot secondary atmosphere gave the light elements of the slowly cooling earth the opportunity to unite into various combinations. With hydrogen still abundantly present, molecules of H2O, H3N, H4C, H4Si appeared and remained. With time, the atmosphere and the crust of the juvenile earth was enriched with water (H2O), ammonia (H3N) and methane (H4C) (fig. 2.1). These three molecules, under the further influence of heat, light, cosmic rays and thunderbolts, formed two compounds: formaldehyde (CH2O) and prussic acid (HCN) which are very reactive but could have stabilized and accumulated for a long time under the primitive atmospheric conditions or hyper baric conditions within the crust.

Figure 2.1. Simple molecules (water, methane and ammonia) form formaldehyde and prussic acid. A concentration of these reactive substances leads to the formation of a sugar (ribose) and a purine base (adenine). These can then condense together to form adenosine.

Formaldehyde and prussic acid contain carbon. Carbon is found only at a concentration of 0.2% on surface solid ground and 0.0014 % in oceans. Yet, this element was chosen preferentially for the building of living matter. Carbon can form long stable molecules and ring structures, which are solid, yet not permanent: they can be decomposed.

Under the appropriate stimulus, when the concentration of formaldehyde and prussic acid is high, 5 molecules of formaldehyde interact and form a molecule of ribose (C5H5O5) while 6 molecules of formaldehyde form glucose. On the other hand, 5 molecules of prussic acid can form a molecule of adenine (C5H5N5). With adenine and ribose jointly available, there exists the possibility of synthesis, always in prebiological conditions, of a molecule of adenosine; it is very easily synthesized in an aqueous environment with the stimulus of ultra-violet light. The reader will remember that a strong UV-radiation is postulated at the beginning of the earth’s existence, which disappeared once an ozone layer was built. Also, the sun’s radiations were at least 25% less intense initially than they are today. In other words, the newly formed molecules would not be destroyed later when engaged in more complex structures. As already mentioned, synthesis may have taken place within the earth’s crust itself.

If phosphate is added to the mixture of adenine and ribose – and this presupposes the availability of phosphate in primeval times – then the ultra-violet light can induce the formation of adenine-ribose-phosphate, also called adenosine monophosphate or AMP (fig.2.2). More phosphates can be added to the adenosine monophosphate, so as to form adenosine diphosphate (ADP), adenosine triphosphate (ATP) and adenosine tetraphosphate (A4P). This tetraphosphate has been retained in biological systems only in very rare cases.

Figure 2.2. The riboside adenosine condenses with one, two, three or four phosphates. The formation of these phosphoric acid compounds involves large amounts of energy. These compounds, especially the adenosine triphosphate (ATP), store energy that can be released and reused during a subsequent controlled removal of these phosphates.

Triphosphate is our prime storage of the energy made available by the burning of glucose. Indeed, the phosphoric link in these phosphates yields large amounts of energy when broken down, its energy of formation being considerable.

Other complex molecules were also formed. A combination of formaldehyde, prussic acid and water can form a molecule of glycine. Glycine is the simplest of the amino acids that are the building blocks of proteins. Under appropriate conditions, amino acids spontaneously form long molecules of proteinoids (fig. 2.3). Lipids are formed by the polymerization of glycerol, which is itself formed by the condensation of three molecules of methanol (CH3OH). Starch, cellulose, glycogen and other polymers are formed by the polymerization of glucose or other simple sugars. More new compounds are thereafter synthesized from those already present.

Figure 2.3. A polysaccharide chain of glycogen composed of β-glucose subunits is shown in the upper part.

Proteinoids are formed by the linkage of various amino acids. At least 21 different amino acids can be incorporated in such a fashion to form a long chain. Some of these amino-acids, as threonine (not shown) and tyrosine, are easily amenable to phosphorylation, just as are the nucleic acids. The modification of proteins by phosphorylation is observable in all animal organisms, starting with bacteria. This phosphorylation of proteins allows all living systems to respond to environmental variations and adapt.

Since no oxygen was present as its free molecular form, no oxidation of the newly synthesized compounds took place. These compounds slowly accumulated either in the atmosphere and the shallow seas or at depths within the crust and formed a rich broth of nutrients estimated at about 100 grams per liter of water. This was such a high concentration that the next evolutive step could proceed. It is possible that the high concentrations were reached within clay particles.

The choice material for the generation of life turned out to be the nucleotides. These molecules are extremely rich in energy as a result of the inclusion of phosphates in the form of ADP and ATP. Other bases than adenine can undergo such a condensation pattern. Many such bases were initially used for further evolutive probes. Yet, only five of them acquired predominance in the genetic material of higher organisms. These are adenine, guanine, cytosine, thymine and uracil. Uracil is not included in the genetic material, sensu stricto: it is not a constituent of DNA.

It seems that the 21 amino-acids (with the exception of cysteine and tryptophan) can be categorized into 4 groups whose synthesis runs parallel with the mode of synthesis applied to the 4 main nucleotides: amino-acids and nucleic acids seem to have been synthesized together and the correlation Amino-Acid with Nucleic-Acid existed before the development of a genetic code.

One should note at this point that, even with simple molecules, life is not evenhanded. Molecules that are essential to life exist in two forms, just like human hands are left or right which cannot be superimposed: they are mirror-images of each other. Life on earth has been built exclusively using the "left" form of these molecules. Chemists characterize these left isomers with the prefix l-(levo-rotatory).

Researchers have been struggling since the 1950s to explain how life acquired this bias, looking for an astronomical, electromagnetic or nuclear phenomenon that could have imprinted this left-handedness on nature. The question is, is it due to a local phenomenon and is it possible that forms of life eclosing elsewhere in the Universe may be based on right-handedness or is the phenomenon a universal character? It seems that local phenomena such as polarized light from supernovae, which gyrate in a corkscrew fashion, have not much to do with it. The source of nature’s chiral bias is not light from the depths of space but subtle forces in the heart of matter, namely the weak force that governs the radioactive decay of a neutron into a proton and an electron. This force has an inherent asymmetry. The decay always produces an electron with a left-handed spin. Electrons produced by radioactive decay are ubiquitous in the natural world. This could have set the ball of prebiotic chemistry, anywhere in the Universe, rolling toward a left bias5.

References

5. R. Service. Does Life’s handedness come from within? Science 286, 1999, 1282-1283

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