domenica 5 maggio 2013



Post n.11 (English)

Hence the biogenic elements (C, N, O, H) are the only ones which, through their compounds, are adapted to carry out, in living organisms, the numerous biological functions. We know that between these compounds the most important  are the Nucleic acid, DNA and RNA, and the proteins.
The proteins constitute tissues and organs, they permit the cells to communicate, they control that which must enter and exit from the cell, they act as antibodies.
All living organisms have a complexity of independent functions which permit them: nourishment, growth, reproduction, evolution, reaction to stimuli, death. All these vital functions have in common the metabolism; that is that process of chemical reactions which co-operate with proteins (enzymes) which permit the living organisms to function. Inside the cell thousands of enzymes can be found which rule and program thousands of chemical reactions. No biological reaction and none of the functions mentioned above can happen without their intervention, not even the synthesis of the nucleic acids.
The proteins are macromolecules whose constituents are the amino acids.
But the amino acids, in the prebiotic era, were present in our planet?
In 1953 S. L. Miller, made the hypothesis of a primordial atmosphere made up CH4, NH3, H2O, H2, succeeded, applying electrical energy, in obtaining various organic substances and, among these, many amino acids of which components of our proteins. This experiment, carried out in plausible prebiotic conditions, marked the date of the birth of prebiotic chemistry.
In the years which followed various researchers have performed experiments both by varying the composition of the gas mixture and the sources of energy. All these studies have confirmed that in the prebiotic era, on our planet, the synthesis of a large number of organic substances was possible, and among these, amino acids were often present. Through those experiments was demonstrated the presence, in the prebiotic era, of about 60 different amino acids. Moreover also the presence of cyan hydric acid (HCN) precedent of purine, of formic aldehyde  (HCHO) precedent of ribose and of other important organic substances among which urea have been demonstrated.
It is remarkable that the same substances, in particular the amino acids, were found in the meteorites going back to the era of the formation of our solar system. The discovery of the amino acids in Miller’s experiments and their presence in the meteorites demonstrates, according to scientists, the ease of synthesis of these compounds. Even the sustainers of the “RNA World” have no doubts on the presence of amino acids in the prebiotic era. Manfred Eigen, referring to experiments like Miller’s, in “Gradini verso la vita” 1992, affirms: «That which renders significant these experiments is not so much the fact that in general amino acids form, but their relative frequency corresponds to those that one meets in nature, and in particular in organic compounds discovered in the meteorites».
At the beginning of the 90’s, some research workers expressed doubt about the presence of a primordial atmosphere made up of CH4, NH3, H2O, H2. These research workers have supposed a primordial atmosphere made up of CO2, N2 and H2O, and in such conditions the formation of the amino acids with application of energy does not take place. Miller has defined these studies hypotheses without sustaining data.
No serious research has doubted of the presence of amino acids in the prebiotic era.
We can conclude that numerous and strong indications demonstrate the presence of amino acids in the prebiotic era. From the synthesis of these molecules the proteins have their origin.
But why the amino acids? And again, are other solutions possible?
According to my knowledge, in 60 years of prebiotic chemistry, the only scientist who tried to give an answer to these questions was Mario Ageno in “Lezioni di biofisica 3” 1984.
Prof. Mario Ageno starts with the ascertainment  that the cells of living organisms do not contain molecules of intermediate dimensions, but they are made up of:
a) Little molecules as much possible simple, which can be found already in the ambiance, or are easy to synthesize.
b) Linear polymers (macromolecules) realized by repetitive operation as a limited number of small molecules (monomers).
As it is known the linear polymers can be obtained both by polyaddition  and by polycondensation. The polyaddition is obtained by the union
of thousands but also millions of molecules of the same type. It is the repetition of the same motive without any content of information, it causes polymers usually of the linear type, for example polyethylene, and it takes place through a chemical process fairly complex.
The polycondensation can happen between different molecules, through the elimination of water molecules. This type of polymerization cannot take place in the presence of water; however the chemical process is much more simple than the polyaddition. It can lead to plastic material, but it is used by living organisms for the construction of the macromolecules necessary to life. In fact, as they are not the monotonous repetition of the same motive, the polymers which result can contain information.
According to Ageno the choice of the linear polymers has a constructive logic of its own. Starting with a limited number of pieces, always with the same constructive operation, molecular structures different but all connected between them are realized. Probably there exists other solutions to accumulate informations and functions but they are all very complicated. The most convenient solution from an evolution point of view seems to be really that of the linear polymers. In the end chemical evolution has chosen the polymeric process the most simple, the polycondensation, and the simplest polymers that is linear polymers and Ageno adds: «Hence it seems very probable that, wherever they appear under the impulse of natural causes systems, in a way similar for their general characteristics to living organisms which we know, these systems are based for their reproduction, on some species of linear polymers. At the end, this solution can be attained more easily and before any other in the course of a chemical evolution which begins (this is inevitable) with small molecules made up of very few atoms. And hence, what monomers once accepted the solution of linear polymers?».
 Ageno examining the constituents of the proteins asks himself the question: «What can be imagined more simple than an amino acid, as structural  element of a linear polymer?». It is essentially a Carbon atom which establishes a bond with the most simple of elements, the H.
 A second bond takes place with the most simple of the basic function, -NH2. A third link takes place with the simplest acid function, -COOH. In the end, the fourth link takes place with a side chain (R) of a  hydrocarbon simple  or with one of its derivates. Ageno concludes, that the ease with which they are found in nature, for example in meteorites, demonstrates that it is a question of simple molecules and which are easy to synthesize, and they suggest the conclusion that polypeptide chains represent the simplest solution.
Hence, to the question: why the amino acid? The answer: because they are simple and easy to synthesize.
Now the question is that the amino acids are yes simple and easy to synthesize, but they present a complex of properties without which life could not exist. Such complexity confronts us with, as we shall see, a difficult question on the problem of the origin of life, which normally does not fall in the ambiance of physical science.
When Ageno speaks of linear polymers, he refers to the primary structure that is to the disposition and to the structure of the amino acids in the polymer chain. The fact is that if the primary structure remained such, that is in all simplicity a long polymer, it would not perform any vital function. In reality the single proteins, over and above the primary structure, present a secondary structure and a tertiary structure. The proteins perform their vital functions only by having recourse to the secondary and tertiary structures.
To understand how such new structures are possible, it is necessary to examine the properties of amino acids.
1) The first characteristic of amino acids is exactly that of being simple molecules and easy to synthesize in a prebiotic ambiance.
2) A second property is that amino acids are soluble in water and stable. If they were not soluble in water, life would not exist, because they would have grouped together like piece of tar or like large oily stains at the surface of the water basins.
3) Miller’s experiments have shown the presence, in the prebiotic era, of about 60 different amino acids, but life uses only 20. If these could have reacted in water they would have given origin to an enormous number of polypeptides, of casual composition and length, but of no interest for the origin of life. Hence the amino acids must be soluble in water but they must not react in water. And in fact they form polymers through the polycondensation which in water is not permitted.
4) The peptide bond is a link which is realized between the group –COOH of an
 amino acid and the group –NH2 of another amino acid with the elimination of a molecule of H2O. The characteristic of this link is that it is a link in resonance. That is the  double link between the Carbon atom and Oxygen is not situated between the two atoms but it is distributed also on the link C-N. The consequence of this delocalization is that every zone on the peptide 
bond of the protein lies on a plane and the molecule of the protein cannot rotate around the peptide bonds. As we have said,
the proteins are not 
only long linear chains of amino acids.
This is only what is called a primary structure.

 The single proteins present a secondary structure and a tertiary structure through which they perform their vital functions. In the secondary structure they realize helical structures and pleated sheet structures, α-helix and β-pleated sheet. Well, so that these structures ca be realized, one necessary condition is that one prevents the rotation of the molecule around the peptide bond.
The delocalization  of the peptide bond prevents exactly such a rotation.
5) A second condition so that these secondary structures can realize themselves is that the constituent molecules be asymmetrical. We know that the amino acids, except for Glycine, are chiral symmetry, that is they exist in two forms asymmetrical one the mirror image of the other, called D and L.
Symmetrical molecules cannot realize either  α helix or β pleated sheet. The secondary structures of the proteins can be realized by choosing  one of the two asymmetrical forms. In the livings organisms the form L was chosen.
6) Another important characteristic of the peptide link is the presence of an atom of Hydrogen linked to azote. The link between these two
elements  gives origin to -Hδ+. As we can see in the image of the α helix, broken line, -Hδ+ links to the -CO δ- of another amino acid and  it is these links which stabilize  α helix. Without these links the secondary structure of the proteins could not exist.
7 ) To conclude, we have seen that in the amino acids Carbon is linked to a R side-chain.
These side-chains are not chosen by chance. Some of these are hydrophilic, mixable with water, others are hydrophobic not mixable with water. In the tertiary structure of the protein, that is the globular structure the R hydrophobic concentrates inside and the R hydrophilic in the external part. The final result is that the protein results very stable and it is defended from the
degradation of water.
It is known that the compounds in organic chemistry are about 1,5 million and grouped in families. There does not exist another family of organic compounds which presents likewise characteristics: the amino acids are unique, the passage was obliged.
One could conclude that the amino acids are versatile. But we have before us life and, if we wish to try to understand its origin, to the initial question: why the amino acids?
The answer that they are simple and easy to synthesize is not enough; because in reality they must possess the following characteristics:
1) Simple and easy to synthesize
2) Soluble and stable in water
3) They must not react in water
4) They must link between each other giving origin to a peptide bond in resonance.
5) They must be chiral
6) They must contain a -Hδ+ residue on the atom of azote
7) The R side-chain is not casual
If only one of these properties were missing, we do not know how life would have been or perhaps it would not exist. Amino acids are unique compounds.
And so the question is: but how is it possible for the amino acids to have all these properties, just there in these compounds unique, simple and easy to synthesize, exactly those properties necessary to life, when life is still becoming?
Seven strokes of luck?   

Giovanni Occhipinti

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