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posted by martyb on Sunday November 05 2017, @12:31AM   Printer-friendly
from the primordial-soup dept.

From Quanta Magazine: Life's First Molecule Was Protein, Not RNA, New Model Suggests

Proteins have generally taken a back seat to RNA molecules in scientists' speculations about how life on Earth started. Yet a new computational model that describes how early biopolymers could have grown long enough to fold into useful shapes may change that. If it holds up, the model, which is now guiding laboratory experiments for confirmation, could re-establish the reputation of proteins as the original self-replicating biomolecule.

For scientists studying the origin of life, one of the greatest chicken-or-the-egg questions is: Which came first — proteins or nucleic acids like DNA and RNA? Four billion years ago or so, basic chemical building blocks gave rise to longer polymers that had a capacity to self-replicate and to perform functions essential to life: namely, storing information and catalyzing chemical reactions. For most of life's history, nucleic acids have handled the former job and proteins the latter one. Yet DNA and RNA carry the instructions for making proteins, and proteins extract and copy those instructions as DNA or RNA. Which one could have originally handled both jobs on its own?

For decades, the favored candidate has been RNA — particularly since the discovery in the 1980s that RNA can also fold up and catalyze reactions, much as proteins do. Later theoretical and experimental evidence further bolstered the "RNA world" hypothesis that life emerged out of RNA that could catalyze the formation of more RNA.

But RNA is also incredibly complex and sensitive, and some experts are skeptical that it could have arisen spontaneously under the harsh conditions of the prebiotic world. Moreover, both RNA molecules and proteins must take the form of long, folded chains to do their catalytic work, and the early environment would seemingly have prevented strings of either nucleic acids or amino acids from getting long enough.

Ken Dill, a biophysicist at Stony Brook University, has been studying protein folding for decades. He's now using that work to examine the chemistry-to-biology transition that took place four billion years ago.

Ken Dill and Elizaveta Guseva of Stony Brook University in New York, together with Ronald Zuckermann of the Lawrence Berkeley National Laboratory in California, presented a possible solution to the conundrum in the Proceedings of the National Academy of Sciences (PNAS) this summer. As models go, theirs is very simple. Dill developed it in 1985 to help tackle the "protein-folding problem," which concerns how the sequence of amino acids in a protein dictates its folded structure. His hydrophobic-polar (HP) protein-folding model treats the 20 amino acids as just two types of subunit, which he likened to different colored beads on a necklace: blue, water-loving beads (polar monomers) and red, water-hating ones (nonpolar monomers). The model can fold a chain of these beads in sequential order along the vertices of a two-dimensional lattice, much like placing them on contiguous squares of a checkerboard. Which square a given bead ends up occupying depends on the tendency for the red, hydrophobic beads to clump together so that they can better avoid water.

Is this a real world example of Auto-catalytic Sets?
I've always thought the proteins evolved first.


Original Submission

Related Stories

Diamidophosphate (DAP): "Missing Link" for Abiogenesis? 7 comments

Scientists Just Found a Vital Missing Link in The Origins of Life on Earth

Researchers from The Scripps Research Institute in California have identified a molecule capable of performing phosphorylation in water, making it a solid candidate for what has until now been a missing link in the chain from lifeless soup to evolving cells. In the classic chicken and egg conundrum of biology's origins, debate continues to rage over which process kicked off others in order to get to life. Was RNA was[sic] followed by protein structures? Did metabolism spark the whole shebang? And what about the lipids?

No matter what school of abiogenesis you hail from, the production of these various classes of organic molecules requires a process called phosphorylation – getting a group of three oxygens and a phosphorus to attach to other molecules.

Nobody has provided strong evidence in support of any particular agent that might have been responsible for making this happen to prebiotic compounds. Until now. "We suggest a phosphorylation chemistry that could have given rise, all in the same place, to oligonucleotides, oligopeptides, and the cell-like structures to enclose them," says researcher Ramanarayanan Krishnamurthy.

Enter diamidophosphate (DAP). Combined with imidazole acting as a catalyst, DAP could have bridged the critical gap from early compounds such as uridine and cytidine. That might not seem overly exciting, but phosphorylating nucleosides like these is a crucial step on the road to building the chains of RNA that could serve as the first primitive genes.

Also at Newsweek. Diamidophosphate.

Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions (DOI: 10.1038/nchem.2878) (DX)

Related: Life's First Molecule Was Protein, Not RNA, New Model Suggests


Original Submission

Chemists Outline How the Citric Acid Cycle Could Have Developed Before Life on Earth 5 comments

Chemists have found a series of chemical reactions that could have led to the first life on Earth:

Chemists at The Scripps Research Institute (TSRI) have developed a fascinating new theory for how life on Earth may have begun. Their experiments, described today in the journal Nature Communications, demonstrate that key chemical reactions that support life today could have been carried out with ingredients likely present on the planet four billion years ago.

[...] For the new study, Krishnamurthy and his coauthors, who are all members of the National Science Foundation/National Aeronautics and Space Administration Center for Chemical Evolution, focused on a series of chemical reactions that make up what researchers refer to as the citric acid cycle.

[...] Leaders of the new study started with the chemical reactions first. They wrote the recipe and then determined which molecules present on early Earth could have worked as ingredients. The new study outlines how two non-biological cycles—called the HKG cycle and the malonate cycle—could have come together to kick-start a crude version of the citric acid cycle. The two cycles use reactions that perform the same fundamental chemistry of a-ketoacids and b-ketoacids as in the citric acid cycle. These shared reactions include aldol additions, which bring new source molecules into the cycles, as well as beta and oxidative decarboxylations, which release the molecules as carbon dioxide (CO2).

As they ran these reactions, the researchers found they could produce amino acids in addition to CO2, which are also the end products of the citric acid cycle. The researchers think that as biological molecules like enzymes became available, they could have led to the replacement of non-biological molecules in these fundamental reactions to make them more elaborate and efficient.

Citric acid cycle.

Linked cycles of oxidative decarboxylation of glyoxylate as protometabolic analogs of the citric acid cycle (open, DOI: 10.1038/s41467-017-02591-0) (DX)

Previously: Diamidophosphate (DAP): "Missing Link" for Abiogenesis? (also by The Scripps Research Institute)

Related: Did Life on Earth Start Due to Meteorites Splashing Into Warm Little Ponds?
Life's First Molecule Was Protein, Not RNA, New Model Suggests
Analysis of Microfossils Finds that Microbial Life Existed at Least 3.5 Billion Years Ago


Original Submission

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  • (Score: 0) by Anonymous Coward on Sunday November 05 2017, @01:08AM (4 children)

    by Anonymous Coward on Sunday November 05 2017, @01:08AM (#592327)

    I've always thought the proteins evolved first.

    rylyeh -- why? Care to elaborate?

    • (Score: 2) by FatPhil on Sunday November 05 2017, @01:35AM (2 children)

      by FatPhil (863) <{pc-soylent} {at} {asdf.fi}> on Sunday November 05 2017, @01:35AM (#592335) Homepage
      Erm, one of them is more complicated than the other. The simpler one is more likely, surely. The simpler one is a protein.

      Story sounds a bit "water is wet" to me.
      --
      Life is a precious commodity. A wise investor would get rid of it when it has the highest value.
      • (Score: 0) by Anonymous Coward on Sunday November 05 2017, @01:59AM

        by Anonymous Coward on Sunday November 05 2017, @01:59AM (#592348)

        Proteins aren't self-replicating... DNA/RNA form basepairs.

      • (Score: 0) by Anonymous Coward on Sunday November 05 2017, @02:38AM

        by Anonymous Coward on Sunday November 05 2017, @02:38AM (#592356)

        Erm, one of them is more complicated than the other. The simpler one is more likely, surely.

        Define "complicated". Define "simpler". (In molecular (protein/nucleic) terms.)

        The simpler one is a protein.

        Care to elaborate?

        (Different AC here)

    • (Score: 1) by rylyeh on Sunday November 05 2017, @01:41AM

      by rylyeh (6726) Subscriber Badge <{kadath} {at} {gmail.com}> on Sunday November 05 2017, @01:41AM (#592339)

      FatPhil beat me to this one.

      --
      don’t tell nobody, but I swar ter Gawd thet picter begun ta make me hungry fer victuals I couldn’t raise nor buy—
  • (Score: 2) by Bot on Sunday November 05 2017, @08:41AM

    by Bot (3902) on Sunday November 05 2017, @08:41AM (#592425)

    Looking for a different way of reconstructing things is necessary, I always write that I consider life as "matter x time". But I have trouble when people speak about irreducible complexity or probabilities. First, because we would not be here to witness failed attempts, so if the universe is virtually infinite and life is virtually impossible there are no problems, on average. Second, on the other side, I consider a problem the underlying assumption that particles interact in a completely impersonal, mechanical, random way. "Ineffable" way, thanks to the quantum field, yes they do. Ineffable is not random. And even if it were still random, probabilities go out of the window when you introduce a quantum field which seems unbound by spacetime, because probability is based on time to define what a result is.

    Basically it seems people are bent on analysis so much that they are gonna discard good results or stick to bad ones, because they do not consider the context they operate in, the "how deep the rabbit hole goes".

  • (Score: 3, Interesting) by gringer on Sunday November 05 2017, @10:06AM (1 child)

    by gringer (962) on Sunday November 05 2017, @10:06AM (#592449)

    If this is the case, then there must have been some mechanism for converting protein into RNA and/or DNA, otherwise whether or not protein came first is irrelevant.

    As far as I'm aware, we don't yet have an example of reverse translation in the natural world. Discovering such a mechanism would be a huge achievement, as it would open up the possibility of protein sequencing that's as easy as DNA sequencing, and also a method for making genes that make a protein.

    • (Score: 0) by Anonymous Coward on Sunday November 05 2017, @03:02PM

      by Anonymous Coward on Sunday November 05 2017, @03:02PM (#592521)

      Why wouldn't reverse translation happen? Im sure it does but just isnt very useful since info is lost each time. Also the myriad of post translation modifications, disulfide bonds, etc may cause problems.

  • (Score: 0) by Anonymous Coward on Sunday November 05 2017, @12:58PM

    by Anonymous Coward on Sunday November 05 2017, @12:58PM (#592492)

    If some specific protein had a survival advantage, it could not be passed down unless it could replicate.

    One solution is to have one molecule that both helps for survival and can replicate.
    Perhaps later, these two functions were separated into protein for doing and RNA for remembering.

    So what neat molecule can both harvest energy and use the energy to make more of itself?
    Seems like something to go look for near a place with chemical energy in abundance.
    Perhaps a thermal vent.

  • (Score: 3, Informative) by Immerman on Sunday November 05 2017, @02:49PM

    by Immerman (3985) on Sunday November 05 2017, @02:49PM (#592517)

    I wonder if anyone has seriously considered the possibility that both "species" of protolife coexisted, and some of them developed a symbiotic relationship that gave them a dramatic evolutionary advantage.

  • (Score: 0) by Anonymous Coward on Sunday November 05 2017, @07:13PM

    by Anonymous Coward on Sunday November 05 2017, @07:13PM (#592609)

    Stop reporting this crap. This is suggestion, not hard science that can be proved.

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