Where did the right amino acids come from?

All those spectacular molecular machines, which confer precision and efficiency on the living cell, are made up of proteins. The precise shapes of proteins come from their component amino acids. These latter small molecules vary greatly in their chemical characteristics. Moreover, the order in which the amino acids are attached together determines how the proteins fold into the correct shapes.

It turns out that the amino acids themselves are hard to synthesize and that only a very particular twenty, of hundreds of possible candidates, are suitable as a component of proteins. Could the correct amino acids have appeared in the environment before the living cell existed? Origin of life specialists like to think so. A recent paper out of Europe discussed this very issue. [Andreas Kirschning. 2022. On the evolutionary history of the twenty encoded amino acids. Chemistry Europe Journal. E202201419  ]

Amino acids are the building blocks of proteins and without proteins there are no living cells and no life. Naturally for scientists seeking to explain the origin of life, it is very important to know where the amino acids came from. We know that some amino acids can be synthesized through purely chemical processes. Analysis of meteorites has revealed more than 80 amino acids, but only 12 of these are actually found in proteins from living cells. [Kirschning p. 2] Also various versions of the Miller-Urey experiment have yielded 10 proteinaceous amino acids. Two questions arise from these results.

Can non-living chemical processes produce all 20 amino acids needed for proteins and life, and what processes selected the 20 favoured ones from all the possible choices. Why only 20 and why these particular ones? One expert, Prof. Dr. Kirschning. discusses this topic and declares that what we see today is the best possible choice of amino acid. And the reason this is so, is the unexpected chemical versatility of the amino acids involved. [“With respect to proteins, there is a growing body of evidence that the modern genetically encoded amino acid alphabet is evolutionarily highly optimized. These include the structural chemical diversity of the side chains and the number twenty.”  p. 1 emphasis mine ]

The foundation upon which the experts build their origin of life studies, is the assumption that chemical reactions, in advance, were able to produce the molecules, like amino acids, which were needed for life.  [“In principle, it is accepted that a prebiotic chemistry for the formation of peptides {proteins} must have existed on planet Earth.” p. 4] One problem with this assumption however is that nobody has figured out how synthetic chemistry could manage to produce certain amino acids. [“For some amino acids, no convincing synthetic routes under prebiotic conditions have been found so far.” p. 4 ]

The problems scientists have encountered in a search for chemistry-only synthesis of amino acids is that all these processes require coenzymes and cofactors. These latter are small organic non-protein compounds that specifically bind to enzymes and actively participate in the reactions. [p. 5] Also the string of reactions required to generate a desired product may be long (up to 13 reactions, one after the other) and may require up to 5 different coenzymes/cofactors. Also, if suitable intervention by a chemist is not involved, the amount of product may become catastrophically so low that the reaction stops altogether. {“The idea of primordial metabolic cycles has generated controversial debates. Orgel pointed out that abiotic reactions proceed at low yields, i.e., the more reaction steps that occur in linear succession, the more catastrophically the overall yield decreases. This is a particularly fatal problem in metabolic cycles…” p. 13 emphasis mine]

The whole idea that there ever were prebiotic chemical cycles not connected to living cells, turns out to be a chicken and the egg problem. The successful production of coenzymes and cofactors requires protein enzymes made of the very amino acids we are trying to synthesize in the first place. [“Three ‘chicken and egg’ problems need to be resolved. Considerations on the biosynthesis of amino acids, their possible timing in evolution, and the special role of coenzymes have obscured some fundamental dilemmas. The generation of the 20 encoded amino acids are catalyzed by enzymes, supported by the presence of coenzymes. Enzymes themselves consist of alpha-amino acids whose formation they catalyze, so we are facing a case of causal circularity or, in more general parlance, a ‘chicken and egg’ problem.” p. 10 capitals the author’s]

The author plaintively then asks some hard questions. [“Why and in which way could finally a metabolism evolve?” p. 10   and “Why then did life stop exploring chemical space further with the 20 encoded amino acids?” p. 13]

In answer to all these issues, the author confesses that any answers appear shrouded in fog. [“The two transitional phases from the prebiotic world to the first premetabolic systems and proto cells as well as the transition to LUCA [last universal common ancestor] appear shrouded in fog.” P. 17]

The take-home message the author provides is that we need to bear in mind that nucleotides (components of DNA and RNA) coenzymes, and cofactors were all required to be present in the prebiotic world when amino acids were first being synthesized and recruited to form proteins. [p. 18] 

What the take-home message actually boils down to is that a prebiotic precursor of the cell is assumed to have existed but nobody has any idea how it could possibly work.

The amazing complexity of even the most basic building blocks of the living cell, clearly demonstrates the choices and wisdom of God who does know how to create life and the living cell. He did not need precursors and a long evolutionary process. “How manifold are your works. In wisdom you have made them all!” [Psalm 104:24]

Related Resources:

• On the Evolutionary History of the Twenty Encoded Amino Acids