ENZYME EVOLUTION IS CLOCK WORK OUT OF CHOAS

There seems to be something fundamentally wrong with our approach to evolutionary theory. Theorists use a reductionist approach. Always looking for the simplest chemical compound or reduce from what we see today to the simplest mechanism followed by a build up in complexity from there. It is true that scientists are finding that modern or “evolved” mechanisms are turning out to be incredible complex. For example, it seems as if research laboratories are spawning new forms and functions of RNA everyday.

The concept of the “primordial pool” that has been with us since the study of biology began is becoming more, and more complex. For reductionists, even the most complex results seem understandable when thought about in their simplest form. The scientists can look at 3.3 billion base pairs in the DNA of the human 23 chromosome and reduce them to sequences of three letter codes, then to both instructions and transcriptional results, then to the inscriptional products. Therefore, they are making great strides in reading the result of Craig Venter’s unraveling of this magic memory macromolecule—the fruit of the multimillion dollar human genome project. Still, they cannot tell us how DNA and RNA codes originally formed.

While thinking about enzyme binding sites, I faced a similar challenge, as I did with trying to understand the formation of RNA/DNA code formation. I was unable to come up with any narrative in regard to their formation of either that seemed reasonable. There are 75,000 specific binding sites. In addition, non-enzymatic proteins, that are structural proteins including proteins such as hemoglobin, for example, have specific binding sites thus add tremendously to this number. Binding sites can be promiscuous, that is bind with many similar forms, or they can be so highly specific that they will identify and bind with only with one racemic form of a simple three-carbon molecule such as lactate.

In addition, enzymes posse a mechanism to bind substrates but also a mechanism to release product or products and do it thousand of times a second. I concluded that DNA and RNA codes and protein binding sites formation could not be products of the time honored mutations with subsequent natural selection through some laborious “one site at a time” process. While looking at a data bank of crystallography results of enzyme proteins it became obvious that enzyme-binding sites for substrates and cofactors involved different widely separated amino acids in the primary structure of the enzyme protein, yet the contributing amino acids were structurally close together as the result of protein folding. The answers seemed to be that it was not primary protein structure but secondary and tertiary structure, and in some cases quaternary structure that led to the formation of binding sites. I have not yet satisfied my self on the part protein domains play is binding site formation.

It became obvious it is not mutations in the originating DNA, or if you subscribe to the RNA worldview, to mutation in the originating RNA, but rather random chance, which is entirely consistent with the random formation of peptides and proteins in a primordial pool setting. Here is the narrative I developed. Somehow, somewhere long chains of amino acids formed in the primordial pool dependent on some kind of coding mechanism, not just peptide length but relatively large protein length macromolecules. A hint as to the originating protein size is found in the fact that 90% of protein domains have less than three hundred amino acids but range from 36 to 692 residues with less that 40 residues are stabilized by disulfide bonds  or metal ions.

Even the small proteins folded back on themselves and perhaps folded again forming globules. The primary amino acid structure controlled the nature of the folding.  Certain amino acids have positive charges others negative charges (polarity) and still others such as cystiene can form the disulfide bonds referred to above giving covalent bond stability to the folded structure. Relating binding sites to protein folding in this way provides molecular flexibility that would not exist in just linear primary structure. Some of the polarity if pH sensitive; pH in biological systems is essentially a function of CO₂. The point is that infinite numbers of stereochemically and electrostatically different sites can randomly form within the protein globule. The actual site location in the globule is somewhat limited by their physical position especially in the hydrophobic cores of larger proteins.

At this point in the narrative, I fall back on the Darwin inspired survival of the fittest concept. If a randomly formed binding site in a complex protein contributed to survival or did no harm to associated chemical equilibrium, the primary amino acid sequence would be conserved but if it did harm, it would not be conserved. The “associated chemical equilibrium” I have in mind are those reactions associated with capture and utilization of the suns energy. Of course, using the word ‘conserved’ implies a memory molecule and coding mechanism is involved in the formation of the random primary sequence, which in turn implies that the three-letter code sequence was random as well. The coding system would be necessary to preserve the precise sequencing of random amino acids to maintain the primary, secondary, and tertiary structure; thus, form the chemical nature of the binding site that are conserved to make the clock tick.

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