Challenge: why ribose? A theory, and a prediction.
Two posts ago, I issued two challenges for readers to try their hand at developing theory, and so far I have received a disappointing response. Does nobody care about theory? Anyway, my second question was, why did nature choose ribose? Recall that ribose is not the easiest sugar to make, and in the Butlerov synthesis, under normal conditions essentially no ribose is made. However, that may be misleading, as there are other options. One that appeals is, providing pH 9 or more is reached, silicates dissolve slightly, and catalyse the condensation of glyceraldehyde and glycolaldehyde to form pentoses, and the furanose form is favoured (Lambert et al. 2010. Science 327: 984-986). This strongly favours ribose.
However, even if we can find a way to make ribose, it is inconceivable that we can do that without making other sugars, so why did nature choose ribose? One answer is, it is the most suitable, but that begs the question, why? It is certainly not that it alone can lead to duplexes once the strand is made, because it has been shown that duplexes based on xylopyranoside or arabinopyranoside, or even ribopyranoside have better duplex binding, and xylose and arabinose are easier to make.
I think the answer lies in part in what is an essentially forgotten paper by Ponnamperuma et al. 1963 (Nature 199: 222-226.) What Ponnamperuma et al. did was to take adenine, ribose and phosphate in aqueous solution, then they shined hard UV light (wavelength about 250 nm) on it. Products included adenosine and adenosine phosphates, including adenosine tripolyphosphate. This was quite a stunning achievement, but it leaves open the question, why did it work? Before addressing that, however, we might see why this has been forgotten, apart from the issue of who reads the literature before computer searching? There is a serious flaw in this being the cause of life, and that is that it is almost impossible to conceive of an atmosphere that will remain transparent to such short wavelength UV. For example, water gets photolysed to oxygen, thence to ozone, which screens out the hard UV. If there are reducing materials there, you get a haze like that on Titan, and again, the hard UV gets screened out.
My recommended way of forming a theory is to ask questions, and in this case, the question is, why does light make the phosphate ester? The adenine is clearly absorbing the photon, and one can see that the link between adenine and ribose may be photocatalysed, but what happens next? All bonds in the ribose are σ bonds, so there should be no extension to the excited electronic state. The next question is, how can one make phosphate esters? This is slightly easier: if you heat a hydroxyl and a phosphate with a hydroxyl to about 200 degrees C, water is eliminated and we get the phosphate ester.
This suggests the answer to the problem should lie in radiationless decay of the excited state, where the energy is dissipated in a sequence of vibrational energy levels decaying to the ground state. We now see that a vibrationally excited hydroxyl could form an ester if it had the same kinetic energy as a hydroxyl at 200 degrees C. If that is the case, we now see why nature chose ribose: the furanose is more flexible, and the 5-hydroxyl on a furanose will behave a little like the end of a whip. Ribose is the only sugar that forms a reasonable fraction of itself in the furanose form in aqueous solution. Now, adenine cannot be the primary absorber originally, but there is another option, and that is, given the appropriate reduced rocks, if the cell wall hydrocarbons contain dissolved porphyrans, or some similar material, the absorption could be through them.
Which brings us to an experiment that could be carried out. Make micelles or vesicles from hydrocarbon alcohols with phosphate esters as the surfactant, and have them with dissolved porphyran, and ensure the water within contains phosphate, adenine, and a mixture of ribose, xylose and arabinose. The prediction is that adenosine phosphates will be formed, but the xylose and arabinose will not participate in forming phosphate esters. If that is true, it is fairly clear why nature chose ribose: it is the only sugar that works
Thus we have a clear possible explanation, and an experiment that would confirm of falsify it. The question now is, will anyone carry it out?
Posted by
Ian Miller on Mar 23, 2015 12:17 AM Europe/London
