Molecular Creation (logo) A Story of Natural Molecular Evolution from Atoms and Water to the living Cell

DEOXYNUCLEOSIDES AND DNA

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Deoxynucleosides

Prior to the formation of proteins, reactions were catalyzed primarily by nucleic acids which had no extended hydrophobic surfaces and cations like calcium, magnesium and sodium were around them to neutralize their surface charge.43 Proteins with enzymatic activity dramatically increased reaction rates and metabolic efficiencies.44 In fact, the increased efficiency in digesting nucleic acids, particularly single-stranded messenger RNAs, threatened to destroy the entire polypeptide coding system. However, reducing enzymes appeared which could remove the oxygen from the 2-position of the ribose ring of nucleosides and transcribe m-RNAs into strands of deoxyribonucleic acid, DNA.54

By removing the 2’ hydroxyl of nucleotides and adding a methyl group to the ring of the uridine molecule, four deoxynucleotides were produced.

One difference in these new nucleic acids was that they contained thymidines with a methyl group on the uridine ring. With two less polar oxygen atoms per base pair and an additional methyl on the uridines, strands of DNA could bind much more tightly together and exclude most of the water within the double helices - so tightly, in fact, that it took enzymatic proteins to separate them.

DNA

This dramatic increase in conformational stability was not only due to tighter binding and exclusion of internal water, but to the extremely regular arrangement of negatively-charged phosphate groups around the perimeter which, based on the TLH hypothesis, permitted uniform linear dielectric hydration bridging between the strands. In spite of the fact that the double helix structure of B-DNA is never displayed as hydrated, 13 water molecules per base pair are required to maintain it in its orderly helical form.55 When Watson and Crick, Linus Pauling and a number of other investigators were attempting to obtain an interpretable X-ray diffraction pattern of DNA, it was Rosalind Franklin at Kings College in London, who sprayed a sample of sodium DNA with water and obtained the pattern which was used by Watson and Crick to complete their model and publish their classical paper.55 It is unfortunate that they did not emphasize the importance of water in maintaining the spatial structure of DNA and give credit to Rosalind for her critical contribution to the program .

In spite of the fact that water is never shown around double helix DNA, 13 water molecules per base pair are required for stabilization; probably by bridging between ions.

In fact, infrared and NMR analyses reveal that the water around the double helix is not liquid, it is “ice-like.” 9, 55 Based on the TLH hypothesis, linear segments of DNA in the living cell are always in motion with dynamic transient linear elements of 5 to 7 water molecules bridging between anionic phosphates across the wide groove and 3 to 4 across the narrow groove to permit delocalization of the high negative surface charge. Transient linear elements also form in the large groove and between the base pairs and they continually form kinetically in multiple layers around the helix in covalent ice-like forms to transfer charge outward to sodium ions which, by being spherically hydrated, are held out away from the helix the same as they are when water forms covalent cubic structuring as it begins to freeze.26, 56

Since the hydrating elements last for less than a billionth of a second, helical segments have the freedom to bend and twist and move as bridging elements change quantized length. In fact, quantized entanglement coupling of protons in water around the helix may provide additional stabilization.7 By being held out away from the helix by the linearization of surface water, sodium ions retain rotational freedom as hydrated spheres while neutralizing the high surface negative charge. For a more detailed view of Quantized Hydration Model, check out www.linearwater.com.

DNA Storage and Reading

Soon after double helices began to form, small spherical Histone proteins with positively-charged surfaces most likely began to form and wrap the negatively-charged helices around them. These proteins not only provided compact storage for DNA, they are so similar among species, that they may be the same today as the original ones which formed.57

DNA is stored in the nucleus of cells as coils around histone proteins.

By bonding to enzymes, DNA filaments dehydrate, unwind and are transcribed into specific sequences of m-RNAs, t-RNAs and new filaments of DNA.56, 57 Multiple enzymes are involved in each stage of reading. However, other proteins, like the one shown below, bind to specific sequences of base-pairs in the wide groove to prevent unwinding and reading.57

Proteins with specifically sequenced coils bind to surfaces of DNA coils to prevent unwinding and code reading.

Still other enzymes attach methyl groups to nucleoside bases to prevent unwinding. If you can think of a way that DNA filaments can be selectively read, nature thought of it first because only those segments which were required to be read, are read.56 Of course, the fundamental importance of double helix DNA was that it permitted permanent storage of the polypeptide codes.Truly, when the first DNA code was transcribed into the first m-RNA and then into a specific polypeptide, we can say that the first phase of reproductive life had begun.

However, life at that stage was not the same as it is today. Undoubtedly, there were no cells as we know them. Most likely, there were gelatinous masses of starches and polypeptides floating in the seas and in shoreline tidal pools with compartments of reproductive nucleic acid molecules. Only as proteins developed which could efficiently electrolyze water into hydrogen and oxygen, could the production of fatty acids begin and biomolecular evolution continue.

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