sabato 20 dicembre 2014

THE ORIGIN OF PROTEINS: The fundamental problems. Part One





Post n. 19 English

The water is made up of hydrogen and oxygen. We know the electronic structure of these two elements, their chemical-physical properties, but from this knowledge, we do not have information on the properties of water. The fact that water is liquid at room temperature is an emergent property that is not contained in the individual parts, which are hydrogen and oxygen. What is valid for the water is valid for all substances, whether they consist of a few atoms or from thousands of atoms. Ultimately with the term "emergence" we mean the appearance of a new property that is not contained in the individual parts. We also refer to an emergence when a number of complex substances, each with its own properties, are part of a complex interacting system. For many scientists life is an emergent property that is generated by a complex system of interactions of all the molecular species present in a cell. The emergence has to be understood as the way Ernst Mayr wrote in "The uniqueness of biology", 2005: «The appearance of unexpected characteristics in complex systems». «It does not enclose any kind of metaphysics implications». «Often in complex systems properties that are not obvious appear (nor can be predicted) even though we know the individual components of these systems».
The current organisms are very complex. Even the most simple uses thousands of species of organic macromolecules: nucleic acids, proteins, lipids, carbohydrates. It is always subject of debate, which ones and how many of these organic compounds were part of the primitive interacting complex system from which emerge we have homeostasis, ie a cytoplasm that gave birth to a proto body. Scientists, who deal with the problem of the origins of life, however all agree that two complex molecules couldn’t have been absent: the nucleic acids, probably the RNA, and proteins. These two macromolecules are interdependent in the sense that the nucleic acid contains the program to synthesize proteins. But the nucleic acid alone is unable to synthesize itself, it needs the proteins to do so. That is because they are interdependent: one always needs the other.
The origin of these fundamental macromolecules to this day is a mystery.
As Pier Luigi Luisi clarifies in "Sull’origine della vita e della biodiversità" in 2013, about the theories on the origin of life: «They all share a major problem: each of these theories must begin with a series of more or less arbitrary assumptions». Moreover, in reference to the fundamental macromolecules, he adds: «In fact, the vast majority of hypothesis ignores the main problem, that of the biogenesis of macromolecules with an ordered sequence in many identical copies».
But if the main problem is the genesis of the fundamental macromolecules, then the first objective of a theory for the origin of life must be to understand the origins of nucleic acids and proteins in the prebiotic era.
The RNA constituents are nucleotides. They are formed by a phosphate group, the ribose which belongs to the family of sugars and the nucleobases (adenine, cytosine, guanine and uracil). As we have already fully described in previous articles, sugars and nitrogenous bases in the prebiotic era did not exist. All research on these compounds are laboratory experiments without any connection to the prebiotic environment.
On the other hand, except for some astrophysicist, all those involved in the origin of life agree in considering plausible Miller's experiment. It is therefore to be considered that in the prebiotic era, starting from simple molecules such as methane, ammonia, water and other simple molecules thousands of organic compounds were formed and among them were amino acids too.
The presence of amino acids in the prebiotic era was confirmed by the analysis of meteorites dating back to the time of formation of the solar system. In particular, in the carbonaceous chondrites there was a presence of amino acids similar in quality and quantity, to that found by Miller in his experiment.
Since amino acids are the constituents of proteins, it is reasonable to conclude that in the first prebiotic era, the fundamental macromolecules to appear were just proteins. The formation of these complex molecules is therefore an important step towards the origin of a primitive cytoplasm and therefore towards the origin of life.
As we already discussed in other articles, protein synthesis however is problematic, but to be complete to those with less competences, it will be useful to repeat with some examples. 
it.wikipedia.org


1) Our hands are a mirror image of each other, right and left, and there is no visual correspondence if stacked. Forms, which are mirror images, not superposable, are called chiral. Alanine is an amino acid constituent of our proteins. If we want to prepare in laboratory 1g of alanine, we won’t get 1g of a single molecular, but 0.5 g of a right-handed (D) and 0.5g of its mirror image left-handed (L). The amino acids are therefore chiral and in fact, the amino acids obtained by Miller in his experiment are chiral. And chiral amino acids are also found in meteorites. Also amino acids formed in the prebiotic era, about 4 billion years ago, were surely chiral. There were two structures L (levo) and its mirror image D (destro).


                                             L(levo)                                   D (destro)


These two molecular forms have the same chemical-physical properties and always travel together. Since both the D-form and the L-form were dissolved in water in the prebiotic era, the molecular disorder would produce cross-reactions between L and D amino acids and given birth to proteins containing the two forms, but of no biological interest.
The issue is that in all living organisms, proteins are made up of only L-form amino acids. 

                                                                         L(levo)


Since the existing living organisms descended by evolution from primitive organisms, also the proteins of primitive organisms had to be constituted by L amino acids. But then, if the two molecular forms having the same chemical-physical properties and were inseparable, how come the choice fell on L amino acids and what happened to the Destro?

2) In the prebiotic era a large number of different amino acids were surely available. In Miller’s experiment, for example, about 60 different amino acids were found as many as in meteorites.
But in the current living organisms, only 20 amino acids are necessary for the formation of proteins.
How did the choice of the 20 amino acids occur?

3) The reaction between amino acids for the formation of proteins takes place with the elimination of H2O.

 In prebiotic conditions, in an aqueous environment, this reaction is not spontaneous because it goes against the second law of thermodynamics. It would like seeing a rock spontaneously rolling up a hill.
These problems are interconnected and it makes no sense to imagine to solve three different models. You cannot think that for the first problem it was just by chance, for the second based on an evolutionary process and the third due to a puddle in evaporation.
On these issues Giuseppe Galletti and Valentina Sorgi in "Astrobiologia: le frontiere della vita" in 2009, identified the centrality of the problem when they say: «These features should be explained, possibly with a single initial model».
In addition to these three specific points, there are other general questions that need be answered.
A) As Miller's experiment showed, in the prebiotic era there were many other organic substances. Most of these substances were definitely useless, if not harmful and would jeopardize the formation of polymers.
B) The concentration of amino acids, dissolved in water, was certainly very low and, in such conditions, the synthesis of the polymers would have been impossible.
It is therefore logical to conclude that in the prebiotic era, chemical and physical constraints of the prebiotic environment worked as an organized principle for selection and concentration of substances essential for the origin of life and subsequently catalyse the formation of the macromolecules necessary for life.
It is also not possible that these processes took place in the North Pole, on the equator and another on the South Pole. These processes must be located in the same spot.
But the location alone is not enough. As suggested by Paul Davies in relation to these issues, selection, concentration and catalysis must take place simultaneously. You can not think that amino acids at a given moment are selected, then the Levo are selected after a month and after one year the catalysis occurs.
Ultimately, the unique initiation pattern must contain: selection, concentration and catalysis, and all must have be a simultaneous and localized processes.
Science has long highlighted that the planets, the stars and the entire universe are the product of chance and natural laws: chance and necessity. And no doubt that the evolution of living organisms is the result of chance and necessity too.
Did chance and necessity govern the first steps of the origin of life, specifically, the synthesis of biopolymers? If the steps listed above are part of a single coherent model, there are two possibilities: either the events were all random or were all deterministic. Introducing here and there, with discretion, some random event, or to use the new terminology some "frozen accident", it is just an expedient ad hoc to support theories which lack credibility. But the probability that all the steps listed above were random events and coincidence is like screaming out a miracle. Therefore, the events that led to the origin of the proteins must have all been deterministic.
Well, is there a theory that gives us an organizing principle and allows us to build a coherent model exclusively through deterministic processes?
In a century of research on the origin of life, the only scientist who suggested a solution was J. D. Bernal in 1951. As known clays are formed of various stacked crystalline layers. Each layer consists of two sub layers, one of silica tetrahedrons (Si2O52-) the other of octahedrons of hydrated alumina   
Al2(OH)42+]n. Without going into details, due the presence of electric charges the various layers or under layers are neutralized at a distance. Between one layer and the other or between an under layer and another there are empty spaces whereby water molecules or molecules that exhibit electric dipoles like the fundamental constituents of the macromolecules, can settle it. It is calculated that in a cm3 of clay the surface of these empty spaces is equivalent to almost the area of ​​a football field. Bernal suggested that the clays could select and concentrate the essential ingredients for the origin of life and subsequently catalyze the formation of the macromolecules necessary for life. He also suggested the importance of quartz in the formation of primitive molecules. Quartz in fact is found together with clay and presents, just like amino acids, a D and L form, and could have caused a prefered adsorption, separating the Destro from Levo. Since inside the clay there would be simultaneity and location, the hypothesis of Bernal gives us, in fact, a consistent model.                                                                                                              

Giovanni Occhipinti

Translated by: Sydney Isae Lukee

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