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

NUCLEOSIDES AND NUCLEIC ACIDS

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Nucleosides

But starch has another property which might have been involved in the production of the D-forms of other natural molecules. The D-form of starch, which is shown below, exists as helical filaments which coil clockwise from back to front. The unnatural, L-form, coils in the mirror-image counter-clockwise direction. As mentioned above, the outer surfaces of D coils are highly hydrated but the cores are hollow with oxygen atoms strategically positioned on the inner walls.

Although water molecules prefer to hydrogen-bond outside, iodine molecules spontaneously move into the cores to form a blue complex and larger molecules, like the naphthol molecule shown above, bind to the ends, increase the circumference and move into the expanded cores in a spontaneous manner.39 Since the cores are anhydrous and molecular models indicate that D-ribose and adenine fit perfectly into the expanded coil as shown below, on heating, the molecules might well have dehydrated and bonded together.

Although the idea has not been tested, D-ribose and adenine have structures which fit into starch cores and might have combined within them to produce D-Adenosine.

The idea has not been tested experimentally, but it is distinctly possible that starch cores might have served a crude catalytic function. Ribose is one of the sugars which would have been produced spontaneously from formaldehyde in the same reaction as D-glucose22 and Dr. Sutherland and his group at the University of Cambridge in England recently reported that hydrogen cyanide, hydrogen sulfide and ultraviolet light, under a variety of conditions, produce nucleotide bases, like adenine, as well as amino-acids and lipids.40

However, the molecular mixtures produced by these types of reactions would have been so complex that it seems almost impossible that adenosine, uridine, guanosine and cytidine could have been produced in sufficient quantities to continue biomolecular development.

Since only D-forms of each of the four nucleosides are found in nature, they must have been produced in an asymmetric environment like the cores of starch.

Since only D-forms of each of these nucleosides are found in nature, they must have been produced in an asymmetric environment like right-hand core of D-starch. The fact that they form strong, selective hydrogen-bonded A/U and G/C pairs, as shown above, might have aided in their formation but experiments must be performed before any of the above hypotheses can be accepted as valid. However, there is little doubt that polysaccharides might have been involved because they and related sugars most likely were abundant molecular forms on the early earth. However, the next stage in biomolecular development was equally complex.

Adenosine Triphosphate, ATP

As illustrated below, this stage required the attachment of three anionic phosphates to the alcoholic group on the end of the nucleotide molecule to form ATP and the other three nucleoside triphosphates. In contrast to most of the reactions mentioned above, the attachment of a phosphate ion to the terminal alcohol to form a phosphate ester requires substantial energy. In living cells, the energy for this phosphate bond formation is provided by photosynthesis or the combustion of molecules like glucose in complex enzymatic systems.

If phosphoric acid is heated to high temperatures, the polyphosphate which forms, if heated with adenosine, would be expected to form adenosine  triphosphate.

However, once again, if an aqueous solution containing phosphate ions is evaporated to dryness and heated, the ions spontaneously dehydrate and attach together to form long chains of polyphosphates. Surprisingly, these polyphosphates, even though they store tremendous amounts of energy in their POP bonds, are relatively stable in water.41 If dissolved in water with a mixture of molecules like adenosine and glucose, evaporated to dryness and heated, one would expect a complex mixture of phosphorylated molecules to be produced. Since sulfides serve as catalysts in phosphate reactions, they might well have been intimately involved in the early formation of phosphorylated nucleosides.40 Since most phosphorylated molecules produced by this nonspecific solar-heated process would have been unstable in water, on dissolving in water and heating, they would have rapidly hydrolyzed back to original forms. However, the ATP molecule, as the sodium and calcium complex, is surprisingly stable in water.

Not only does the triphosphate chain wrap over the ribose ring to form an anhydrous hydrophobic core with all of the polar oxygen and nitrogen atoms directed outward to hydrogen-bond with surface water, it has hexagonal symmetry to conform with cubic hydration patterning around it.42 Thus, like the stable forms before it, ATP and the other nucleoside triphosphates might well have accumulated at the expense of less stable forms on repeated heating and cooling. Although no studies appear to have been performed to determine the types of molecules which might have been produced by this type of sequential dry-heating and dissolving, analytical tools are available to test the hypothesis. However, it is virtually impossible to know what kinds of conditions or catalysts might have been involved in the early phases of biomolecular development and, even if such experimental studies were successful, it would not prove that early formation occurred as speculated above.

However, there is little doubt that an entire world of complex polysaccharides would have been produced in the alkaline calcium/cyanide-catalyzed phase of molecule formation and that those molecules might well have been involved in the production of the nucleosides, their triphosphate esters and nucleic acids which were to follow.19 Today, polysaccharides of many types are attached to the outer surfaces of cells and serve as antigenic fingerprints. However, very few studies appear to have been performed to determine if they have “catalytic” properties.

Obviously, at this point in the story, creationists have an advantage - they simply can say: “All natural molecules and mechanisms were produced at time X” without worrying about how they might have been formed originally. For creationists, the chicken and the egg were produced together, but, for evolutionists, the study of how natural molecules originally formed, how they function today and how changes occur in living systems are extremely important to understand how they can be altered to address physical and health problems, whether inherited or acquired. For example, in living cells today, it is important to know that adenosine triphosphate, ATP, is a pivotal molecule.44 By binding to specific enzymes, ATP molecules transfer the energy-rich terminal phosphates or diphosphates to oxygen and nitrogen atoms on other molecules - it “activates” those molecules to form new bonds and gives them a negative charge.

Since adenosine triphosphate, in the presence of sodium or calcium ions, exists in a cyclic structure, it is relatively stable in water and stores energy in the phosphate bonds.

In fact, all mechanical motion and all chemical syntheses, in both the plant and animal worlds, depend on ATP and GTP for energy. Proper levels of these two triphosphates are critical for cellular function and studies have begun, using phosphorous magnetic resonance, to monitor health in tissues.

Once again, before proteins were available to catalyze the synthesis of ATP, UTP, GTP and CTP, their syntheses had to be catalyzed by some other molecules, perhaps polysaccharides or sulfur-containing complexes.40 But, no matter what synthetic systems were involved, the interfacial and patterning properties of linear elements of water were involved, defining the spatial properties for functionality and dramatically limiting the options of molecular forms which would be stable and form cooperatively-functioning units. However, once mechanisms were available to produce nucleoside triphosphates, progress toward more catalytic, spontaneously-functioning, reproductive systems most likely proceeded at a much more rapid rate. By “rapid,” we do not mean years – it may have required millions of years.

Nucleic Acids

When enzymes hold oxygen atoms of alcohols or nitrogen atoms of amines in proper positions relative to ATP molecules, terminal phosphates are transferred to those atoms.

Based on available evidence, the next stage in cellular development was the coupling of nucleoside phosphates together to form nucleic acids. Today this coupling is carried out by enzymes which align the nucleoside triphosphates next to strands of DNA so that specific sequences of A, U, G and C are produced in the RNA strands, but original strands most likely were produced simply by heating the triphosphates on some ordering mineral or polysaccharide surface. Preliminary studies suggest that this is a reasonable possibility.44

As strands of nucleic acids formed with random sequences of nucleosides, they immediately would have begun searching in the aqueous environment for complimentary sequences with which they could couple to form preferred A/U and G/C attachments - like a zipper with a programmed sequence of attaching units.

Nucleic acids are formed by reacting the 2’ oxygen of the ribose ring of one nucleotide triphosphate with the triphosphate of another to produce long chains.

As shown above, the strongest attachments are achieved when the strands are oriented in opposite directions. If nucleotides in the sequence do not form a paired linkage, like the U/U pair at the top, a water molecule would bridge the gap, break the coupling and permit the strands to turn away from each other.

When complimentary regions of a single strand combine together they form a coil with a turn at nucleotides which are not complimentary and hydrogen bond with surface water.

But coupled strands were not straight - bonding within the chains caused them to coil around each other to form a helix. If a sequence of uncoupled nucleosides was present in a strand, they would bend back on themselves in search of complementary sequences. If a sequence was found which could form A/U and G/C couplings, it formed a helical loop as illustrated above. However, if a complementary sequence was not found, it would search strands in other nucleic acids for a match. The spatial structure of the transfer RNA molecule, which was shown before and is shown below, illustrates the unique way the chains bend back on themselves to form new couplings and produce stable forms. Once again, the finished molecule has a geometry which uniquely fits into cubic hydration patterning.

Living cells contain about twenty t-RNA molecules with the same spatial structure but a specific sequence of three nucleotides at the loop end.

If transfer RNA molecules of the type shown above are heated in saline water, they unwrap to form a single strand which waves around in the linear-element disordering medium. However, on cooling, the strand spontaneously wraps to form the same original structure. Nucleic acids, which were produced at random in prebiotic times, that could wrap spontaneously to form stable assemblies, such as the t-RNA molecule shown above, would have accumulated at the expense of those which remained as linear segments - they would have been hydrolyzed back to the nucleotides from which they were formed. Like polysaccharides before them, millions of years of synthetic cycling would have accumulated sets of stable spatial forms, all compatible with the stabilizing properties of standard transient dielectric linear elements of water molecules which spanned between phosphates on the outside and base-pairs within.

Fifty years ago, only proteins were considered to have unique catalytic properties - today, even short segments of nucleic acids have been shown to be able to hold other nucleic acid strands together, attach new strands to the ends, remove sections and perform almost all of the functions which, at one time, only proteins were considered to be capable of performing.43 In fact, a natural nucleic acid has been discovered which catalyzes the attachment of amino acids to tRNA’s.46 Thus, it is likely that the “Age of Polysaccharides,” was followed by an “Age of Nucleic Acids,” all driven by energy of the sun and directed by the linearizing property of environmental water to yield stable cooperatively-functioning spatial forms.

In fact, as will be illustrated shortly, the central catalytic regions of huge ribosomal particles which exist today and produce all proteins, are not protein, they are composed of nucleic acids - possibly with the same sequences as those which assembled spontaneously in a polysaccharide-nucleic acid age before proteins existed at all.43,44, 45

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