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Ends and Means: More on Meyer and Nelson in BIO-Complexity

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Stephen Meyer and Paul Nelson recently published a paper in the journal BIO-Complexity addressing the findings of Yarus et al. that there may be a chemical connection between nucleotides and amino acids after all.
ENV has already noted and commented on Nelson and Meyer’s article, providing background on the DRT model that the Yarus group proposes. (See Ann Gauger’s article and Jonathan M‘s article.) There is more to say, however, about this important paper.
Meyer and Nelson assess origin-of-life experiments performed by Yarus’s group on the stereochemical affinities of transfer RNA (tRNA) amino acid binding sites and the messenger RNA (mRNA) codon that codes for the amino acid. Seeking to explain the origin of DNA-to-protein translation, the Yarus group looked for some kind of chemical attraction between the nucleotides (DNA is made of nucleotides) that specify a particular amino acid (proteins are made of amino acids).
A particularly difficult hurdle for origin-of-life chemists is not just the synthesis of nucleotides, but how a sequence of nucleotides translates into a particular amino acid. Let’s consider some of the chemical issues involved in Yarus et al.‘s DRT model as a supplement to points brought up in the Meyer and Nelson paper.
Within an organism there are several tRNAs ready to be called into action. They are called into action with messenger RNA (mRNA). Remember that RNA comes from DNA. The mRNA has a codon (three nucleotides) that matches the particular tRNA’s anticodon (three other nucleotides). There are different tRNAs for different codons. A particular tRNA is assigned a particular amino acid. There are twenty amino acids. So mRNA calls a particular tRNA and that tRNA is going to bind to a specific amino acid.
An amino acid is called “amino acid” because it has a carboxylic acid group (-COOH) and an amine group (-NH) bound to a carbon. This carbon also has the backbone that is particular to every amino acid. For example, glycine, the simplest amino acid, has a hydrogen attached to this carbon; while alanine, another simple amino acid, has a methyl group (-CH3) attached to the carbon. These backbones grow increasingly complicated. Yet all amino acids are arranged in such a way that when the protein forms, the carboxylic acid group of one amino acid reacts with the amine group of another amino acid. However when this peptide bond forms, the respective backbones do not interact with each other. This fact makes the code arbitrary.
When a tRNA is called into action, a chemical reaction takes place where the amino acid attaches to the 3′ end of the tRNA. This covalent organic reaction is catalyzed with a specific enzyme.
In this reaction the carboxyl group of the amino acid reacts with the -OH group on the 3′ end of tRNA to form an ester. This is catalyzed by an enzyme called aminoacyl tRNA synthetase. Not only is there a specific tRNA for each amino acid, there is also a specific aminoacyl tRNA synthetase enzyme for each tRNA.
According to Garrett and Grisham’s Biochemistry, the aminoacyl tRNA snythetase is a “second genetic code” because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: “Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer.”
This enzyme “activates” the amino acid to prepare it to form a peptide bond. The aminoacyl tRNA synthetase enzyme operates at two levels. The first level finds an amino acid. Some amino acids are very similar, so sometimes the aminoacyl tRNA synthetase will activate the wrong one, except the second level kicks in to “edit” this mistake and activate the right amino acid. There are more technicalities to the reaction that we’ll omit here.
Why does all of this matter? Because Yarus et al.‘s DRT model does not account for this catalyzed reaction or for these levels of specificity. Furthermore, once the Yarus group had amino acids in place, they positioned their amino acids to ease the stress of steric hindrance for the peptide formation. This is “chemist intervention,” not an origin-of-life scenario. Nelson and Meyer outline several problems with the group’s studies. However, from a chemistry perspective, Yarus is dealing with a completely different system from what is actually going on in real life.
Consider an analogy: a chemical laboratory, where there are several chemicals on the shelf, including the amino acids and their respective tRNAs. The chemists use the same chemicals as nature does, but the reaction that results is totally different. What they’ve done does not prove anything other than they can elicit a chemical reaction with these compounds. It does not demonstrate what actually goes on in the cell.

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