The complexity of life in two dozen amino acids

Everything we recognize as living, at least for the time being, shares the same chemical nature, being formed by a few classes of molecules – Dna, Rna, sugars, fats, proteins and some other chemical species depending on the case, such as the mineral salts that form our skeleton or the vitamins that are used in various biological processes. Among these compounds, proteins are the tiny machines that perform most of the functions that keep us alive: they catalyze all sorts of chemical reactions, they recognize other molecules, they translate the external and internal environmental signals into stimuli of the appropriate nature, and in a word they move the whole factory of the body of living organisms, from unicellular ones to whales.

Like all machines, proteins are also made up of smaller partsthe equivalents of gears, screws, bolts, springs, circuitry and so on: in particular, all proteins, of any living organism, are composed of about twenty different types of amino acids, linked together to build the protein nanomachine with the right shape to perform one or more specific functions. As far as the human being alone is concerned, it is estimated that there are approx 70,000 different proteins, all always made up of the usual two dozen types of amino acids, taken in different quantities and linked in different sequences: it is as if every single tool or machine we use, from a fork to the shuttle, was built using only twenty different types of gears and components. For all living things, and not only for humans, the same is always observed: life is moved and maintained by the work of hordes of protein machines of very different kindsless than a millionth of a meter in size, all always built using those few different types of amino acids.

Now, we need to know that there are many, many more known amino acids than the twenty that are found in our proteins; moreover, it is known that amino acids very different from the biogenic ones are formed in every corner of the cosmos, and were certainly present even in the primordial Earth. Why then, since 3.8 billion years ago, have living organisms used such a limited number of “building blocks”? Or, in other words: what specific property did certain amino acids have, such as to favor their selective use to form the proteins that became typical of every living organism?

With a new research work, just published, the answer has apparently been found, filling an important gap in the explanation of why life on our planet, from a biochemical point of view, is what it appears to us today. First, we must know that numerous tests indicate how the first proteins should have been formed from only a part of the types of amino acids that are observed today, or about a dozen different types; the other 10 other types of amino acids are products of biosynthetic pathways that emerged after the birth of the first living organisms, for the good reason that these amino acids either cannot form spontaneously in prebiotic conditions or because they can be accommodated within proteins as components, only provided that the proteins are in environments other than the aqueous one, environments that are found only in living beings. So the question becomes: Why, out of hundreds of alternatives available on the primitive Earth, the first proteins, as far as we know today, were formed based on only ten different types of “gears”, i.e. amino acids? And why, among these 10, are there not those that were certainly the most abundant on our planet billions of years ago?

The answer came from studying the properties of small proteins in the laboratory (peptides) that can be formed using the different types of ancient amino acids. First, it was found that the most abundant types of amino acid, bound to any other in sufficient quantity, prevent the folding of the resulting macromolecule into complex shapes. Basically, with those amino acids it is impossible to obtain the great variety of shapes of the protein machines, necessary to perform their functions: long filaments are obtained which remain flexible and extended in solution, without folding to form a specific three-dimensional shape, a necessary precondition for exercising any nanoscale-specific function at which the protein machinery operates. Other primitive amino acids, such as those capable of conferring a positive electrical charge – or rather basic – to proteins, if linked with those available before the beginning of life, caused a decrease in solubility, and the precipitation of the obtained macromolecules; for this reason, if new facts do not emerge with respect to those discussed by the authors of the cited work, all the first existing proteins must have been acidic (i.e. with negative electric charge) or without electric charge, and only after the evolution of life new amino acids, not available in primitive conditions and formed directly by biological organisms, were incorporated into proteins to obtain “machines” with positive electric charge .

Precisely those ten types of modern amino acids which are hypothesized to be the basis of primitive proteins have instead a fundamental property: that of promote the folding of amino acid chains into complex and stable structures in aqueous solution, capable, if necessary, of performing functions of a different type. Among the functions that these primitive proteins with a very specific shape can assume, it has long been proven that there was the ability to form complexes with molecules of different types, i.e. RNA capable of replicating, stabilizing and protecting its structure from environmental insults and, in some case, promoting its replicative function; and so, the first Darwinian RNA replicators recruited proteins, taking an important step towards the complexity of subsequent living organisms, even before a functioning genetic code emerged and therefore the synthesis of the most useful proteins was guided by the RNAs themselves.

The new work, as well as filling an important gap in our knowledge of the chemical world that preceded life and from which life was able to emerge, also shows us an important aspect: natural selection, in this case of proteins composed of certain types of specific amino acids, can act well before and separately from the existence of Darwinian replicators, if there is enough variety that it produces spontaneously, as in the chemical soup of the primordial oceans. When the first replicators emerged, they too, like the rest of the entities around them, were subjected to natural selection; but if it is replicator selection that triggered the Darwinian process that led to life as we know it, it is simple environmental selection that led to those replicators using a certain biochemical machine instead of whatever it could theory be produced starting from the chemistry present in every corner of our universe.