How to make a ribozyme (using abiotic starting compounds)

Ok,I'm really interested in organic chemistry, and so to brush up on my skills, I decided to see if I could find a way to build an RNA enzyme from prebiotic chemicals. Theoretically of course.So, the first step was to make some ribose. Now, I believe that using the Formose reaction using Pb (II) as the catalyst, one can make aldopentoses like ribose in high yield.However, that would require methanal (H₂CO). The only ways I know how to make that is as follows:Method 1
1. CO₂ + 3 H₂ ’ CH₃OH + H₂O2a. 2CH₃OH + O₂ ’ 2H₂CO + 2 H₂O2b. CH₃OH ’ H₂CO + H₂The problem is, this appear to require a heavy metal catalyst (like Ag or V). Also, one of the above pathways requires oxygen, which most assume didn't exist freely in prebiotic earth.Method 21. 3CO₂ + 12H₂ ’ 3CH₄ + 6H₂O2. 3CH₄ + 3O₂ ’ 3H₂CO + 3H₂OBut this method also uses oxygen, and exotic catalysts (like V and Se).So, does anyone know a way to make formaldehyde/methanal without requiring oxygen and catalysts? I think the best bet would be to look for alternative methods for the dehydrogenation of methanol, to see if we can get some room temperature reactions going (UV light or electric sparks?). Or do I have to 'appeal to space' to send me some on comets from oxygen-rich areas before I can make some ribose?Once we've done that, then we can start talking about getting some hydrogen cyanides to make nucleotides.As for forum section, methinks Origin of Life would be the best bet to get the organic chemists involved.Edited by Doddy, : mistake in stoichiometry

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Yes, I did originally notice that, but that just leads to questions about how much carbon monoxide would have been present in prebiotic earth (I know it is made in volcanoes and meteor impacts). In comparison to methanol or hydrogen, what composition would carbon monoxide be in the prebiotic atmosphere? I also have noticed that UV radiation can produce formaldehyde from CO₂ and H₂), via carbon monoxide (CO) and H₂ intermediates.(Pinto JP, 1980: Science 210, pp183-184).Ok, now we have some probable models of the formation of formaldehyde, we move onto the formose reaction. Interesting. I had found that going in the direction of phosphates made the coming chemistry (formation of nucleosides) a little harder though, so I'm not tempted to go that way yet.In my research, I noticed that a Pb⁺² could catalyze the formation of ribose quite readily in alkanine solutions, even at low temperatures (35^oC, though it is much faster around 60^oC) (Zubay, G.: 1998, Studies on the Lead-Catalyzed Synthesis of Aldopentoses, Origins Life Evol B 28, 13-26). This is useful because while lead isn't as common as iron, calcium or magnesium, it is still a very common ion in minerals.So, we now have ribose. I assume we can keep it stable while we set about the difficult task of making nucleosides.I say difficult because it appears we are going to require nitriles. Purines appear to be most likely a product of hydrogen cyanide (HCN) and pyramidines perhaps from hydrated cyanoacetylene C₃HN, both fairly common in space, but could they have been produced on Earth? Edited by Doddy, : formattingEdited by Doddy, : minor correctionEdited by Doddy, : correcting the correction

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I only said it was hard because that is one of the main fronts of abiogenesis where creationists like to attack - synthesis of nucleobases.Have a look at this page: No webpage found at provided URL: http://www.godandscience.org/evolution/rnamodel.php (never mind the fact that their references are almost all from the same person).Anyway, back on topic. I'll quote something from Leslie Orgel's 2004 paper "Prebiotic Chemistry and the Origin of the RNA World"

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The reactions of cyanoacetylene or cyanoacetaldehyde with urea or of cyanoacetylene with cyanate in eutectic solution seem the most plausible prebiotic routes to cytosine. Syntheses of this kind are particularly attractive because they could proceed in parallel with the synthesis of adenine from HCN

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So taking this route for now, we have the following reactions:Synthesis of Purines
Polymerisation of hydrogen cyanide to produce both adenine and guanine.Adenine - C₅H₅N₅5HCN + NH₃ ’ C₅H₅N₅ + ?Guanine - C₅H₅N₅O5HCN + NH₃ + H₂O ’ C₅H₅N₅O + ?Synthesis of Pyrimidines
Polymerisation of cyanoacetaldehyde in urea to produce cytosine, followed by hydrolysis of cytosine to uracil.Cytosine - C₄H₅N₃OC₃H₃NO + (NH₂)₂CO = C₄H₅N₃O + H₂OUracil - C₄H₄N₂O₂C₄H₅N₃O + H₂O ’ C₄H₄N₂O₂ + NH₃Next step, and also quite difficult (scientifically, not in terms of creationist attack this time) is the formation of nucleosides - we have to join that ribose to our freshly made nucleobases. You'd better be quick too - creationists have evidence that these bases will only last for a few decades!

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Interesting. I have also noticed that one could use 90%N₂-10%CO-H₂O gas mixture in , producing guanine, uracil and cytosine (Miyakawa et al, 2000; "Abiotic synthesis of guanine with high-temperature plasma." Orig Life Evol Biosph 30:557-566.) Ok, well adenosine (thus probably guanosine too) can be formed by the simple heating and dehydrating reaction, but what about the others?Adenosine - C₁₀H₁₃N₅O₄C₅H₅N₅ + C₅H₁₀O₅ ’ C₁₀H₁₃N₅O₄ + H₂OSeeing as many researchers haven't found a simple method for prebiotic synthesis of pyrimidine nucleosides, and have even proposed that perhaps the modern pyrimidine nucleosides are not the same as those of ancient life, then perhaps we shall have to skip over this problem. Next step is phosphorylation (although it may have occured before the formation of nucleosides) of the 5' carbon on the ribose. If that's something you know a lot about Matt, then I'll hand over to you.Edited by Doddy, : minor correction of htmlEdited by Doddy, : spelling

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Ok, that will be enough to create nucleotide triphosphates, I take it?I'll just provide one reaction, as most will be much the same. This is a phosphorylation using an orthophosphate, such as calcium phosphates (found in minerals like hydroxylapatite), under acidic conditions. According to Lohrmann and Orgel (Science, 1971), this reaction is catalysed by urea at 100^oC, especially in the presence of ammonium chloride.Adenosine Triphosphate (ATP): C₁₀H₁₆N₅O₁₃P₃C₁₀H₁₃N₅O₄ + 3PO₄^3’ +9H⁺ ’ C₁₀H₁₆N₅O₁₃P₃ + 3H₂OLet us not forget also that this may not have been the way it happened, and ribose may have been phosphorylated before being incorporated into the nucleobase.Next step: polymerisation

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You do have a point Rob - the conditions that chemists can create are likely to be far more favourable to the creation of life than was present primordially. I once read that it was like a golfer putting a golfball into the hole, then surmising that wind, rain, tornadoes and earthquakes could have done the same, given enough time.However, it isn't especially likely that life originated in this manner. Not only are these steps quite probably not the ones that occurred, but a ribozyme might not even be the first sort of life (if the RNA world isn't true).But then, a few humans have only looked at this problem for a few dozen years, whereas there were billions of years and billions of planets for this to occur randomly. I don't care how smart you think humans are, or how dumb you think chemical reactions are - I have no problem believing that this would have happened.

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The very definition of life, as proposed by Schrdinger, is something that organised itself - negative entropy. However, negative entropy is not restricted to life. Snowflakes are an example, but I think a better one is galaxies - the force of gravity caused them to organise, forming a lower entropy state. It isn't to hard to imagine, at least for myself, that such a low entropy state would happen upon a formation that could indeed become reproducible (in that life must grow). As Dr Jones* tried to point out, albeit slight erroneously, life itself isn't prohibited by the second law. DrJones* was right in that the particular interpretation of the second law stating "everything tends to a higher entropy state" only applies to closed systems, although the law has no problem dealing with open systems - you just need to factor in the enthalpy change too. To discuss this in depth would drag the thread off topic, but suffice it to say that supernatural things are not only beyond the scope of science, but indeed one must presuppose their non-existence if one intends to investigate the natural world. Else, one can never be sure if one is observing the natural or the supernatural world, thus making all experiments meaningless. The fact that certain conformations of RNA are able to reproduce others is precisely what drives the RNA world hypothesis. That is why I asked to make a ribozyme, as it is an RNA molecule that can make another RNA molecule. It is DNA that is dependant on RNA, not the other way around, as a strand of DNA cannot, IIRC, be created by itself, but must extend from an RNA molecule (which is then degraded to be replaced with DNA). It is unlikely that current life-forms are the simplest form of replication that can exist. Just as I would say that current media players (eg an iPod) are unlikely to be the simplest that exist (a record player? a phonograph?). It is only those lifeforms that are complicated enough to survive for billions of years that will be seen today, not the simplest ones. But we do have evidence for one - we see a self-replicating cycle, and it is only extrapolation backwards that leads to the assumption of one existing. It's an entirely different thing with supernatural beings, but I fear dragging this thread off the rails if I elaborate. Oh yeah, that is the case. It's not extremely unlikely, but I wouldn't have money on it, personally. After all, the areas where one RNA molecule would exist are likely to be friendly to others. It is also likely that this didn't occur in a vast ocean, but a small pond or something. But yeah, it's not likely, but it's possible. Bold words coming from a self-organizing system such as yourself! As I said above, a self-perpetuating low entropy anomaly violates no known law of physics, whereas a perpetual motion machine does. Why not? Knowledge is good.

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I'm sorry, but that is the entirety of it. Speaking for myself, however. I'm just curious about this stuff. I'm sure much the same reason applies to other scientists. Plus, it helps me learn about organic chemistry.What answer did you expect? "We want to learn about this so that we can better support our materialistic worldview by explaining how life doesn't need a creator."

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Extrapolation is scientific. It is assuming something without any evidence from which to extrapolate or interpolate that isn't. What is the difference? In order for something to replicate, it must go from one organised entity to two organised entities. Thus, it must have a mechanism of organisation - anabolism ('organising' reactions). Replication is just one major form of this type of metabolism. So replication is self-organization.It is possible that anabolism precedes replication, but this thread shall assume otherwise for the reason that most research has been done on the replicator-first hypothesis.

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Excellent question! I'm sure you know that biological information is not the only order in the universe. Look at the orderly rotation of the heavenly bodies, for instance. Why shouldn't biology ultimately be driven by physical laws? Thus, the origin of order is not a topic for this forum, but for the Big Bang forum section, where you can discuss the origin of the laws of the universe to your hearts content.Right, let's get back on to the current topic in this organic synthesis. This is probably the one that creationists go on and on about, so be warned.In my last post (way back in post 12), I had accepted the explanations of Matt P and my own research into the field of synthesis to the extent that I showed it wasn't impossible that the bases of RNA could have formed. We might not have pursued the correct biochemical pathway, but at least it's not inconceivable.Now, the next step is to join the RNA bases together. I'm sure everyone knows that RNA is joined together by phosphodiester bonds between the 3' carbon atom of one ribose and the 5' carbon of the other? That's two carbons joined together by not one oxygen (an ester) not two (a diester) by two oxygens and a phosphorus, as part of a phosphate (a phosphodiester). See this image if unsure on that: No webpage found at provided URL: http://www.ktf-split.hr/glossary/image/rna_en.gifNote also that unlike in DNA, the 2' carbon atom of RNA also has an -OH group, allowing it to form 2'-5' linkages as well as 3'-5' linkages.Now this is what a normal RNA nucleotide trisphosphate looks like - this is Adenosine Triphosphate (ATP): C₁₀H₁₆N₅O₁₃P₃: When two nucleotide trisphosphates polymerise, the excess phosphates (and the hydrogen of the hydroxyl group of the ribose) are released. In aqueous solution, this polymerisation reaction is not thermodynamically favoured, however, so there must be a source of energy. It doesn't take much, even moderate temperatures can enable a net polymerisation reaction to proceed, although this is a very slow process. As such, it isn't really known how far this polymerisation can go (who wants to wait for decades to get a paper out of this?).Regardless, this reaction doesn't need to synthesise a large molecule - a ribozyme may only be a few hundred nucleotides in length.Single stranded molecules will influence the synthesis of their complement, as the hydrogen bonding between complementary nucleotides will increase the probability of their ligation (in the same way that your friend's partner and your partner are more likely to meet than if they were just loners). dsRNA naturally forms helical structures.The problem that creationists bring up, however, is the likelihood of a given ribozyme occurring by random polymerisations reactions. I think that will be a good next topic, given that that is the last step for this discussion.Edited by Doddy, : clarify

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You're confused. ATP is an energy medium. ATP is no more a source of energy than a battery is a source of energy. That is, in local systems, you can consider a battery to be a source of energy, but ultimately the energy came from somewhere else. The only ways that an organism can gain energy from the environment are listed there. Because it doesn't make sense. Given that we know that animals alive today aren't the same as they were 300,000,000 years ago, why shouldn't we assume the same is true of metabolic processes? Anyway, this is digressing. I wish we knew. It's a mystery. But we can make intelligent hypotheses about what could have gone on, try to replicate it or compare it to known reaction parameters to corroborate the hypotheses, and use those to make some more hypotheses. That's science.

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You can have devices that run directly off the mains. So, likewise you could have primitive organisms that don't store energy. And the current batteries aren't like they used to be, and indeed soon may be replaced by fuel cells or similar. Likewise, it is unlikely that living creatures always used exactly what is present today. That is perhaps a flaw in my aralogy, but the main point of it rests untouched. ATP, and other nucleotide triphosphates too, do indeed 'just happen' to provide energy to the cell. Or rather, energy to the cell 'just happens' to use nucleotide triphosphates. It's quite possible to have another form of energy.

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