• Common origins of RNA, protein, and lipid precursors

    The origin of life on Earth is a fascinating topic. But to be truly informed, you really have to get into chemistry… and not the bits you learned in high school or intro classes in college. We’re talking about some really exotic chemistry.

    Technically, organic chemistry is chemistry using of carbon. Much of organic chemistry involves compounds made by life. But in origins of life research, the idea is that the molecules used by life came from non-living sources. Those compounds were able to form into simple molecules that, while we wouldn’t call them “living”, they would be capable of simple reproduction and once a molecule can reproduce imperfectly, then evolution can occur.

    One of the problems with the various models of pre-biotic (before life) chemistry is that many of them require slightly different conditions and/or reactants (those compounds that chemically react to form the products). Then all those different compounds have to come together in sort of the right order and sort of the right concentrations. I say sort of because the tolerances are generally very loose.

    The Miller-Urey experiment is a classic. In a single-pot, they mixed in some basic chemicals that they thought would be available on pre-biotic Earth, put them into a flask with a reducing atmosphere, hit it with lightening and examined the results. They got most of the amino acids, or their precursors, used by life. But that’s for proteins.

    Other experiments show how sugars form from formaldehyde reactions on minerals. Still other show how some of the bases in DNA and RNA can form from reactions of ammonium cyanide.

    These types of reactions also run into problems with some products interfering with other reactions. Maybe reacting before the useful compounds can form or, at the least, slowing reactions down.

    Most of the recent research suggests that RNA probably came first. While proteins can act as a catalyst for other chemical reactions, so can RNA and RNA can act as the information storage mechanism for life.

    Some think that these problems are insurmountable, but the evidence is against them.

    The research paper I want to discuss today was written by Bhavesh H. Patel, Claudia Percivalle, Dougal J. Ritson, Colm D. Duffy and John D. Sutherland. It is called Common origins of RNA, protein and lipid
    precursors in a cyanosulfidic protometabolism (Nature Chemistry, 16 March 2015 | DOI: 10.1038/NCHEM.2202).

    All that fancy text of the title basically means that all of the chemical precursors of RNA (information and enzyme activity), protein (energy, enzyme activity) and lipids (energy and cells) can all come from a common set of reactions. Further, they suggest a mechanism by which the various reactions can proceed singly and then be combined in such a way as to provide concentrated compounds that can react relatively quickly.

    The first bit is fairly chemically complex, but I’ll be gentle.

    The starting reactant is hydrogen cyanide (HCN). This compound can be formed in a variety of ways, not the least of which is the high temperature reaction of atmospheric nitrogen and a carbonaceous meteorite. The evidence supports the idea that life on Earth began during or immediately after the Late Heavy Bombardment. So that’s a possible source. Another source is the corrosion of some minerals in low oxygen conditions, which is reasonable because the early Earth was low to zero oxygen in the atmosphere.

    This starting reactant is the key that results in all the products that are used by life now, which suggests that life on Earth is the way it is, not by design, but because the chemistry just works out that way.

    Some important drivers for the chemical reactions are ultraviolet light and hydrogen sulfide, which would be fairly common on the prebiotic Earth. Copper is used as a catalyst in these reactions.

    The chemistry is a large series of reactions, which we can skip, because the details are very interesting only to chemists and geeks like me. But the results are very interesting.

    First, the hydrogen cyanide forms the sugars glycolaldehyde and glyceraldehyde. These are needed for ribonucleotide assembly which eventually forms RNA and DNA. These also lead to the precursors for the amino acids glycine, alanine, serine, and threonine. So, this reaction series produces precursors for both nucleic acids and proteins.

    Next, a glyceraldehyde isomer (an alternate chemical shape) reacts to form acetone and glycerol. The acetone reacts to form the precursors of the amino acids valine and leucine. The glycerol leads to the precursor of a lipid.

    Then, copper catalyses the hydrogen cyanide and acetylene to lead to the amino acids proline and arginine. It also leads, through a different series of reactions to the amino acids aspartic acid, glutamine, and glutamic acid.

    This series of reactions results in the precursors for 11 of the 22 used amino acids used in life. It also results in the precursors for lipids (energy storage and cell walls) and nucleic acids. Most of these reactions require 2 or fewer steps and have yields on the order from 30% to almost 100%. Only two reactions require 3 steps or 5 steps.

    The authors have constructed a very plausible geochemical scenario that gathers the feedstock, the reactions, and products at the needed times and the needed environments.

    Imagine an impact on Earth. The carbonaceous meteor creates various compounds, including hydrogen cyanide as described above. The crater fills with water, allowing various chemical reactions to take place. Over time, the water evaporates. As it does, compounds that are not as soluble in water will collect in layers above the water line, on the crater rim. Compounds that are more soluble in water will become more and more concentrated in smaller areas as the water evaporates.

    The layers of compounds left behind will be further reacted by heat into some of the precursor compounds. Rainfall on higher ground then, dissolves the salts, concentrated them and flowing them over other compound deposits. These are further reacted by ultraviolet light and copper salts (as catalysts).

    Finally, different streams, with different compounds (and concentrations of compounds) merge together in a single basin where they mix. Subsequent evaporation, further concentrate these compounds.

    Additionally, research has previously shown that RNAs can form in little more than warm water.

    I’ll let the authors describe the conclusions of their work.

    Although it necessarily has to be painted with broad brushstrokes, the picture that emerges is of an overall reaction network developing over time in separate streams and pools, according to a dynamic flow chemistry scheme. The various products would be synthesized by subtle variations in the flow-chemistry history of the streams and the order in which they merged or ran into pools. Although the overall scheme would not involve all the steps of the reaction
    network taking place simultaneously in ‘one pot’, the various products would end up mixed together in pools. Rather than invoking fundamentally different scenarios and chemistries for the syntheses of the molecular components of informational, compartment forming and metabolic subsystems, and then concluding that one or other subsystem must have come first, we describe a scenario in which variations on a chemical homologation theme result in the components of all three subsystems being produced and then blended together. The reliance of the homologation chemistry on hydrogen cyanide (11) (all the carbon and nitrogen atoms in the compounds of the reaction network derive from this single source) and hydrogen sulfide (12) prompts us to use the term ‘cyanosulfidic’ to describe this protometabolic38 systems chemistry.

    So, that’s the idea. Now, let’s be clear, this isn’t a hypothesis. The authors have done the chemistry and gotten the results we’ve talked about. This isn’t hypothetical. It can happen this way.

    Did life on Earth form in this fashion… maybe, maybe not. We will not know until humans invent a time machine. We’re talking about trying to figure out what happened on a chemical level well over three and half billion years ago.

    However, and this is the critical point, this is all possible. It works chemically. What’s really elegant about the solution in this paper is that the entire sequence comes from just two basic compound, hydrogen cyanide and hydrogen sulfide. The end result will be at least 11 of the 20 common amino acids, nucleic acid precursors and lipid precursors. That is, the three building blocks of life. All from the same set of chemical reactions.

    The plausible scenario of a meteor impact is just a bonus on top of that. It is very reasonable considering the conditions of the early Earth and solar system.

    Category: ChemistryfeaturedOrigins of LifeResearchScience

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    Article by: Smilodon's Retreat

    • Peter White

      Amazing; some knowledge, some evidence, some intelligence, a lot of hard work, and we have an answer to yet another piece of the puzzle.

      Thank you for another excellent article.

    • Andrew Howard

      Excellent work. If they can extend it all the way to energy extracting loops then it’s Nobel Prize time.

    • RexTugwell

      Oh look! Another OOL theory.

      • Eddie Janssen

        Rex, two questions:
        1. Any idea how OOL scientific research will look in 200 years?
        2. Any idea how theological OOL explanations will look in 200 years?

        My guesses:
        Question 1: No idea
        Question 2: God did it.

        • RexTugwell

          Oh look! Another Darwinist bringing theology and God into the discussion.

          • Eddie Janssen

            I suppose you are not going to answer the questions?

            • RexTugwell

              Question 1: Judging from the progress of the last 100 years, my outlook is bleak.
              Question 2: Ask me in 200 years.

            • Doc Bill

              Rex doesn’t even have an understanding of high school chemistry. He’s totally out of this conversation.

      • Doc Bill

        Nope, Rexy, wrong again as usual. Same theory: chemistry.

        • RexTugwell

          Chemistry is not a theory. That’s like saying the theory of aging is biology. Nope.

          • Doc Bill

            Seriously, Rexy, you are one dumb shit. Theory of chemistry? I have a PhD in the subject and you are a fucking ignorant idiot. Don’t try to lecture me until you’ve spent a decade in the lab.

            Fucking moron.

    • Christine Janis

      I just posted a link to this paper at an Amazon discussion forum, and the resident clown called it “religious propaganda”

      • SmilodonsRetreat

        Pot callin the kettle black I suspect.