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Thread: Replicating molecule..

  1. #1
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    Replicating molecule..

    What is the difference between a normal molecule and a replicating molecule like RNA or DNA ?

    What mechanism triggers a non replicating molecule to suddenly start replicating itself ?

    Also, when RNA starting replicating, did it already have the instructions to build a cell around itself to keep it safe or was it floating around on its own without any protection ?




    Just musing really, but cheers for any answers
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    Quote Originally Posted by kevin1981 View Post
    What is the difference between a normal molecule and a replicating molecule like RNA or DNA ?
    In organic chemistry, molecular size and complexity.
    Very large and complex molecules such as RNA/DNA are self-replicators.

    Quote Originally Posted by kevin1981
    What mechanism triggers a non replicating molecule to suddenly start replicating itself ?
    Autocatalysis is hypothesized as possibly being a possible phase in the lead-up to organic molecular self replication:
    Quote Originally Posted by Wiki
    A single chemical reaction is said to be autocatalytic if one of the reaction products is also a catalyst for the same or a coupled reaction.[1] Such a reaction is called an autocatalytic reaction.
    So-called 'clock reactions' such as the Belousov–Zhabotinsky reaction are one such example of autocatalysis. (Others are also known as existing).
    Quote Originally Posted by kevin1981
    Also, when RNA starting replicating, did it already have the instructions to build a cell around itself to keep it safe or was it floating around on its own without any protection ?
    The evolution of cell membranes is the subject of yet other hypotheses. In general lipid formation has been demonstrated (in lab environments) as leading towards fundamental membrane-like functionality.

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    There are much simpler replicators.
    They're not really useful as a base for transcription, since they're super simple.
    It's not a self-replicating molecule, it's a cycle of molecules whose outcome is a second copy of the first molecule.

    I wish I could remember what it's called.

    It's got something to do with Chlorine and occurs near hydrothermal vents, where the right elements are available.

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    Quote Originally Posted by DaveC426913 View Post
    There are much simpler replicators.
    They're not really useful as a base for transcription, since they're super simple.
    It's not a self-replicating molecule, it's a cycle of molecules whose outcome is a second copy of the first molecule.
    In the context of discussions about modern biological mechanisms and processes, 'self-replication' is fairly well explained.

    In the context of so-called 'pre-biotic' chemistries however, I think the terms 'replication' and more specifically, 'self-replication', really take on a different meaning.

    Quote Originally Posted by DaveC426913
    I wish I could remember what it's called.

    It's got something to do with Chlorine and occurs near hydrothermal vents, where the right elements are available.
    I'd be interested to see references/papers on this(?)

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    Quote Originally Posted by kevin1981 View Post
    What is the difference between a normal molecule and a replicating molecule like RNA or DNA ?
    I'm not exactly sure what you mean by a "replicating molecule." A molecule that is created by some program? In that case, I think that all proteins are replicating molecules. Or do you mean one that has a code in it that is used to make other molecules?
    As above, so below

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    Quote Originally Posted by Jens View Post
    I'm not exactly sure what you mean by a "replicating molecule." A molecule that is created by some program? In that case, I think that all proteins are replicating molecules. Or do you mean one that has a code in it that is used to make other molecules?
    He mentioned RNA and DNA. Surely he literally means self-replicating.

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    Quote Originally Posted by DaveC426913 View Post
    He mentioned RNA and DNA. Surely he literally means self-replicating.
    But they're not self-replicating as far as I know. A molecule of RNA or DNA left in a solution will not replicate.
    As above, so below

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    Quote Originally Posted by Selfsim View Post
    In organic chemistry, molecular size and complexity.....
    Autocatalysis is hypothesized as possibly being a possible phase in the lead-up to organic molecular self replication....
    Yes, and a good introduction to something like 20 years of study on the question is At Home in the Universe by Stuart Kauffman.
    Everyone is entitled to his own opinion, but not his own facts.

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    Quote Originally Posted by Jens View Post
    But they're not self-replicating as far as I know. A molecule of RNA or DNA left in a solution will not replicate.
    The so-called 'translational apparatus', (ribosomes and other proteins), are themselves derived from subunits of the RNA molecule (rRNA).
    In this sense, RNA is still referred to as self-replicating (tis 'the origin').

    How functional ribsosomes came about in the first place, is one of the big questions, though.
    They have been artificially synthesised (by Ventner etc) but this was done based on the known structures of modern fully functional ribosomes.

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    Quote Originally Posted by Cougar View Post
    Yes, and a good introduction to something like 20 years of study on the question is At Home in the Universe by Stuart Kauffman.
    Yep .. even though he cast a big opinion in his conclusions about the 'inevitability' of it all.

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    Quote Originally Posted by Selfsim View Post
    The so-called 'translational apparatus', (ribosomes and other proteins), are themselves derived from subunits of the RNA molecule (rRNA).
    In this sense, RNA is still referred to as self-replicating (tis 'the origin').

    How functional ribsosomes came about in the first place, is one of the big questions, though.
    They have been artificially synthesised (by Ventner etc) but this was done based on the known structures of modern fully functional ribosomes.
    Interestingly, it seems that researchers have only just recently succceded in engineering a ribosome to replicate itself for the very first time:
    Normally when copying RNA, an enzyme would add single bases (C, G, A or U) one at a time, but the new ribozyme uses three bases joined together, as a 'triplet' (e.g. GAU). These triplet building blocks enable the ribozyme to copy folded RNA, because the triplets bind to the RNA much more strongly and cause it to unravel—so the new ribozyme can copy its own folded RNA strands.
    Previously, they've only been able to get ribosomes to replicate straight strands of RNA, thus blocking its ability to copy its (very) folded self.

    Also interesting, (from the same article), is that triplet binding seems to also be a 'sweet spot' for opening up the folds, whilst maintaining a high replication accuracy.

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    Quote Originally Posted by Jens View Post
    But they're not self-replicating as far as I know. A molecule of RNA or DNA left in a solution will not replicate.
    I would argue they are self-replicating in that they are able to replicate themselves.

    What you're describing sounds to me more like spontaneous replication. i.e. that they would replicate if simply left to their own devices. They won't of course, but I don't think that's what the OP is looking for anyway.

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    Quote Originally Posted by DaveC426913 View Post
    I would argue they are self-replicating in that they are able to replicate themselves.
    I know itís a subtle point, but I was thinking that it is the cell that is self-replicating, and that the genome provides the code that guides the process.


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    As above, so below

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    Quote Originally Posted by Selfsim View Post
    In the context of discussions about modern biological mechanisms and processes, 'self-replication' is fairly well explained.

    In the context of so-called 'pre-biotic' chemistries however, I think the terms 'replication' and more specifically, 'self-replication', really take on a different meaning.

    I'd be interested to see references/papers on this(?)
    Ah! Found it again! Not chlorine - citric acid!!

    https://en.wikipedia.org/wiki/Citric_acid_cycle

    It's a cyclic reaction that, provided the right elements, produces more citric acid, which can then be used to start another cycle.

    Again, it's too simple a molecule to encode anything useful, but it's a start. Give it a billion years or so...

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    Amyloid 'self-replication'

    There are other so-called 'self-replicators' also.

    It has been demonstrated that amyloid structures (in a 'soup') can spontaneously form from simple amino acids which settle at just the right sites, and then chemically combine with eachother. Amyloids are composed of short peptides and form fibres which are also able to accelerate chemical reactions (same as enzymes). This peptide synthesis mechanism, when applied to the amyloids themselves, gives rise to the 'self-replication' argument.

    The researchers campaigning for this one, argue that the formation and replication mechanism is more 'plausible' (to them) than the 'RNA-first' hypothesis of abiogenesis.

    Paper here.

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    Quote Originally Posted by DaveC426913 View Post
    Ah! Found it again! Not chlorine - citric acid!!

    https://en.wikipedia.org/wiki/Citric_acid_cycle

    It's a cyclic reaction that, provided the right elements, produces more citric acid, which can then be used to start another cycle.

    Again, it's too simple a molecule to encode anything useful, but it's a start. Give it a billion years or so...
    Yep .. thanks.
    A key part of metabolism .. which makes available the energy for cellular processes, (including self-replication).

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