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Thread: One of the Greatest Mysteries: How did DNA develop the code for the 3-dimensional structure of proteins?!

  1. #1 One of the Greatest Mysteries: How did DNA develop the code for the 3-dimensional structure of proteins?! 
    Forum Sophomore Double Helix's Avatar
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    The central dogma of molecular biology (1), as defined by Francis Crick is :

    DNA codes for RNA, which codes for Proteins

    Clearly all forms of life on earth rely on proteins. These complex polymers are used for many functions, such as structural components, enzymes, various immunological activities, trans-membrane channels, and blood coagulation, to name just a few.

    Proteins are long polymers of 20 different amino acids, and their various sequences of these amino acids dictate how each will fold into their active, 3-dimensional shapes (2). This folding is largely driven by the impact of water dynamics on the various types of amino acids within a given protein's sequence. And protein variability is nearly infinite.

    Proteins are coded in DNA, a polymer with a linear sequence of four different nucleotides. In order to make proteins from a gene, the DNA code must be "transcribed" into RNA, a similar linear polymer. RNA is then "translated" by reading the code on a ribosome, which assembles the 20 various amino acids into the proteins coded by the DNA. This process is not reversible. It is strictly one-way.

    But DNA is a linear sequence, while proteins are 3-dimensional constructs. And neither of them are directly related chemically. How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?

    It is surely one of the greatest mysteries of science, and life itself.


    1. https://en.wikipedia.org/wiki/Centra...ecular_biology

    2. https://en.wikipedia.org/wiki/Protein_folding


    Last edited by Double Helix; March 18th, 2021 at 08:45 PM.
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    Quote Originally Posted by Double Helix View Post
    The central dogma of molecular biology (1), as defined by Francis Crick is :

    DNA codes for RNA, which codes for Proteins

    Clearly all forms of life on earth rely on proteins. These complex polymers are used for many functions, such as structural components, enzymes, various immunological activities, trans-membrane channels, and blood coagulation, to name just a few.

    Proteins are long polymers of 20 different amino acids, and their various sequences of these amino acids dictate how each will fold into their active, 3-dimensional shapes (2). This folding is largely driven by the impact of water dynamics on the various types of amino acids within a given protein's sequence. And protein variability is nearly infinite.

    Proteins are coded in DNA, a polymer with a linear sequence of four different nucleotides. In order to make proteins from a gene, the DNA code must be "transcribed" into RNA, a similar linear polymer. RNA is then "translated" by reading the code on a ribosome, which assembles the 20 various amino acids into the proteins coded by the DNA. This process is not reversible. It is strictly one-way.

    But DNA is a linear sequence, while proteins are 3-dimensional constructs. And neither of them are directly related chemically. How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?

    It is surely one of the greatest mysteries of science, and life itself.


    1. https://en.wikipedia.org/wiki/Centra...ecular_biology

    2. https://en.wikipedia.org/wiki/Protein_folding
    Crick knew as much about DNA as Columbus did about the Grand Canyon. So in all reality Crick is not even worth mentioning. The fallacy was and is that when DNA was discovered it was assumed that we now knew something when all the discovery of DNA did was create more questions that there are no answers too


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    Quote Originally Posted by Quantated View Post
    Quote Originally Posted by Double Helix View Post
    The central dogma of molecular biology (1), as defined by Francis Crick is :

    DNA codes for RNA, which codes for Proteins

    Clearly all forms of life on earth rely on proteins. These complex polymers are used for many functions, such as structural components, enzymes, various immunological activities, trans-membrane channels, and blood coagulation, to name just a few.

    Proteins are long polymers of 20 different amino acids, and their various sequences of these amino acids dictate how each will fold into their active, 3-dimensional shapes (2). This folding is largely driven by the impact of water dynamics on the various types of amino acids within a given protein's sequence. And protein variability is nearly infinite.

    Proteins are coded in DNA, a polymer with a linear sequence of four different nucleotides. In order to make proteins from a gene, the DNA code must be "transcribed" into RNA, a similar linear polymer. RNA is then "translated" by reading the code on a ribosome, which assembles the 20 various amino acids into the proteins coded by the DNA. This process is not reversible. It is strictly one-way.

    But DNA is a linear sequence, while proteins are 3-dimensional constructs. And neither of them are directly related chemically. How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?

    It is surely one of the greatest mysteries of science, and life itself.


    1. https://en.wikipedia.org/wiki/Centra...ecular_biology

    2. https://en.wikipedia.org/wiki/Protein_folding
    Crick knew as much about DNA as Columbus did about the Grand Canyon. So in all reality Crick is not even worth mentioning. The fallacy was and is that when DNA was discovered it was assumed that we now knew something when all the discovery of DNA did was create more questions that there are no answers too
    Watson, Crick and Franklin discoverd the structure of DNA. Columbus never set foot in America, let alone mapped the Grand Canyon, which would be the equivalent feat.

    If you think we don't know anything as a result of this discovery you must be some kind of moron.
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    Quote Originally Posted by exchemist View Post
    you must be some kind of moron.
    This pretty much sums things up.
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    Trial and error would be how. Failures struggle to survive and reproduce and die out but successes survive and get reproduced in vast quantities.
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    Quote Originally Posted by Ken Fabos View Post
    Trial and error would be how. Failures struggle to survive and reproduce and die out but successes survive and get reproduced in vast quantities.

    The prevailing concept on the origin of life on earth is the initial use of RNA as both the mechanisms and code required for replicating cells to arise. This is based on the fact that there are numerous RNA forms that play a central role in modern life, and these roles are both enzymatic (ribozymes) and coding (mRNA). In reading the modern code, another RNA contribution is required - tRNAs - which reads the code and transfers amino acids to form the protein being constructed on a ribosome.

    This concept is known as The RNA World *. And trial and error likely played a critical role.

    So while The RNA World does not directly address the origin of information flow in modern life, i.e. from DNA to RNA to protein, there seems no other reasonable alternative from which to start.



    * https://en.wikipedia.org/wiki/RNA_world


    * https://en.wikipedia.org/wiki/Ribozyme
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    Quote Originally Posted by Double Helix View Post
    How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?
    It is surely one of the greatest mysteries of science, and life itself.
    Not sure if this is of use, but I remember reading On Being by Peter Atkins.
    I think the point he was trying to make was that entropy (the 2nd law of thermodynamics) is not only destructive but by sheer chance can be constructive.
    This law is always at work. The final chapter of this book is quite devastating.
    As energy and matter have a tendency to disperse it can spin out RNA and DNA molecules.
    I think this theory, though only a theory has been supported by Richard Dawkins.
    We are according to Atkins, the children of chaos.
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    Quote Originally Posted by ox View Post
    Quote Originally Posted by Double Helix View Post
    How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?
    It is surely one of the greatest mysteries of science, and life itself.
    Not sure if this is of use, but I remember reading On Being by Peter Atkins.
    I think the point he was trying to make was that entropy (the 2nd law of thermodynamics) is not only destructive but by sheer chance can be constructive.
    This law is always at work. The final chapter of this book is quite devastating.
    As energy and matter have a tendency to disperse it can spin out RNA and DNA molecules.
    I think this theory, though only a theory has been supported by Richard Dawkins.
    We are according to Atkins, the children of chaos.

    Most of the grand structures of biochemistry, such as proteins, membranes, and even the structure and folding of RNA and DNA polymers are largely driven by what Tanford called "The Hydrophobic Effect" (1). It is directly related to changes in entropy resulting from the activity of water in contact with non-polar (hydrophobic) surfaces.


    Quoting from (1):

    "In terms of thermodynamics, the hydrophobic effect is the free energy change of water surrounding a solute. A positive free energy change of the surrounding solvent indicates hydrophobicity, whereas a negative free energy change implies hydrophilicity."


    In the aqueous milieu of living cells, the dynamics of water force proteins and membranes to minimize their hydrophobic component's direct interaction with polar water molecules. All of the shapes and forms of macromolecular structures are largely based on this driving force (2). The end result is to minimize the free energy of water, which increases entropy.


    But none of this explains the origin of DNA's linear coding for the 3-dimensional structure of proteins. It simply provides the thermodynamic aspects by which such 3-D structures form.


    1. https://en.wikipedia.org/wiki/Hydrophobic_effect


    "Towards a structural biology of the hydrophobic effect in protein folding"

    2. https://www.nature.com/articles/srep28285
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    Quote Originally Posted by ox View Post
    Quote Originally Posted by Double Helix View Post
    How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?
    It is surely one of the greatest mysteries of science, and life itself.
    Not sure if this is of use, but I remember reading On Being by Peter Atkins.
    I think the point he was trying to make was that entropy (the 2nd law of thermodynamics) is not only destructive but by sheer chance can be constructive.
    This law is always at work. The final chapter of this book is quite devastating.
    As energy and matter have a tendency to disperse it can spin out RNA and DNA molecules.
    I think this theory, though only a theory has been supported by Richard Dawkins.
    We are according to Atkins, the children of chaos.
    This is clearly true, and not in the least contentious, in that thermodynamics dictates that any spontaneous process proceeds with increase in total entropy. The evolution of life has always proceeded with increase in entropy, just like any other spontaneous process. The ultimate driver has been low entropy (high temperature) energy, in the form of sunlight, being converted to low temperature (high entropy) heat radiated out into space.
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    Quote Originally Posted by exchemist View Post
    This is clearly true, and not in the least contentious, in that thermodynamics dictates that any spontaneous process proceeds with increase in total entropy. The evolution of life has always proceeded with increase in entropy, just like any other spontaneous process. The ultimate driver has been low entropy (high temperature) energy, in the form of sunlight, being converted to low temperature (high entropy) heat radiated out into space.
    Interesting way of describing how life first started.
    Evolution mainly by natural selection gets us to where we are today (robotic like machines still in conflict).
    If it is true then the dispersal of energy in a system like the earth describes why we live and die.
    Why our appearance changes as we get older and colder by the wasting away of mitochondria in our cells.
    Why we get cancer.
    Why we need to eat.
    But it seems unlikely we can prove how life first started, because it happened so long ago.
    Unfortunately this lets in supernatural explanations.
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    Quote Originally Posted by ox View Post
    Unfortunately this lets in supernatural explanations.

    The creationists already use the reverse argument - that life as defined by science violates the laws of thermodynamics because it is highly ordered. They do not want to understand that the order is obtained by converting higher energy forms (sunlight) to lower energy forms (heat) via the process of photosynthesis and its resulting cascade of decreasing biochemical "energy carriers". Primary among these are ATP and glucose.

    It is rather comical they even bother to employ science to support their anti-scientific beliefs.
    Last edited by Double Helix; April 7th, 2021 at 01:28 PM.
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    Quote Originally Posted by ox View Post
    Quote Originally Posted by exchemist View Post
    This is clearly true, and not in the least contentious, in that thermodynamics dictates that any spontaneous process proceeds with increase in total entropy. The evolution of life has always proceeded with increase in entropy, just like any other spontaneous process. The ultimate driver has been low entropy (high temperature) energy, in the form of sunlight, being converted to low temperature (high entropy) heat radiated out into space.
    Interesting way of describing how life first started.
    Evolution mainly by natural selection gets us to where we are today (robotic like machines still in conflict).
    If it is true then the dispersal of energy in a system like the earth describes why we live and die.
    Why our appearance changes as we get older and colder by the wasting away of mitochondria in our cells.
    Why we get cancer.
    Why we need to eat.
    But it seems unlikely we can prove how life first started, because it happened so long ago.
    Unfortunately this lets in supernatural explanations.
    We can't prove any scientific theory.
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    Quote Originally Posted by Double Helix View Post
    It is rather comical they even bother to employ science to support their anti-scientific beliefs.
    Naturally, if science contradicts the Bible then the Bible is correct and science is wrong.
    But they will use science if it suits them.
    Have you read the thermodynamic theories of Peter Atkins concerning life and the universe?
    If so, what do you think of his theories
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    Quote Originally Posted by ox View Post
    Quote Originally Posted by Double Helix View Post
    It is rather comical they even bother to employ science to support their anti-scientific beliefs.
    Naturally, if science contradicts the Bible then the Bible is correct and science is wrong.
    But they will use science if it suits them.
    Have you read the thermodynamic theories of Peter Atkins concerning life and the universe?
    If so, what do you think of his theories
    I was not familiar with Peter Atkins, but just read a brief on him in Wiki*, and quoting from that makes me a fan already:

    "In December 2006, Atkins was featured in a UK television documentary on atheism called The Trouble with Atheism, presented by Rod Liddle. In that documentary Liddle asked Atkins: "Give me your views on the existence, or otherwise, of god". Atkins replied: "Well it's fairly straightforward: there isn't one. And there's no evidence for one, no reason to believe that there is one, and so I don't believe that there is one. And I think that it is rather foolish that people do think that there is one". "

    end quote

    Will have to investigate his theories some more. He appears to be an expert on some pretty high-brow stuff, like "Molecular Quantum Mechanics"!

    He appears to be firmly grounded in reality, to say the least.


    * https://en.wikipedia.org/wiki/Peter_Atkins
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    Quote Originally Posted by Double Helix View Post
    Quote Originally Posted by ox View Post
    Quote Originally Posted by Double Helix View Post
    It is rather comical they even bother to employ science to support their anti-scientific beliefs.
    Naturally, if science contradicts the Bible then the Bible is correct and science is wrong.
    But they will use science if it suits them.
    Have you read the thermodynamic theories of Peter Atkins concerning life and the universe?
    If so, what do you think of his theories
    I was not familiar with Peter Atkins, but just read a brief on him in Wiki*, and quoting from that makes me a fan already:

    "In December 2006, Atkins was featured in a UK television documentary on atheism called The Trouble with Atheism, presented by Rod Liddle. In that documentary Liddle asked Atkins: "Give me your views on the existence, or otherwise, of god". Atkins replied: "Well it's fairly straightforward: there isn't one. And there's no evidence for one, no reason to believe that there is one, and so I don't believe that there is one. And I think that it is rather foolish that people do think that there is one". "

    end quote

    Will have to investigate his theories some more. He appears to be an expert on some pretty high-brow stuff, like "Molecular Quantum Mechanics"!

    He appears to be firmly grounded in reality, to say the least.


    * https://en.wikipedia.org/wiki/Peter_Atkins
    Atkins lectures on molecular QM were a highlight of my time at university. I have a well-annotated copy of "Molecular Quantum Mechanics" on my bookshelf still. He was PhDemon's tutor, by the way.
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    Quote Originally Posted by Double Helix View Post
    The central dogma of molecular biology (1), as defined by Francis Crick is :

    DNA codes for RNA, which codes for Proteins

    Clearly all forms of life on earth rely on proteins. These complex polymers are used for many functions, such as structural components, enzymes, various immunological activities, trans-membrane channels, and blood coagulation, to name just a few.

    Proteins are long polymers of 20 different amino acids, and their various sequences of these amino acids dictate how each will fold into their active, 3-dimensional shapes (2). This folding is largely driven by the impact of water dynamics on the various types of amino acids within a given protein's sequence. And protein variability is nearly infinite.

    Proteins are coded in DNA, a polymer with a linear sequence of four different nucleotides. In order to make proteins from a gene, the DNA code must be "transcribed" into RNA, a similar linear polymer. RNA is then "translated" by reading the code on a ribosome, which assembles the 20 various amino acids into the proteins coded by the DNA. This process is not reversible. It is strictly one-way.

    But DNA is a linear sequence, while proteins are 3-dimensional constructs. And neither of them are directly related chemically. How could such an astonishing chemical evolution occur to ultimately give rise to the life forms which exist today?

    It is surely one of the greatest mysteries of science, and life itself.


    1. https://en.wikipedia.org/wiki/Centra...ecular_biology

    2. https://en.wikipedia.org/wiki/Protein_folding
    Crick had no idea what DNA was when he discovered it
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    Quote Originally Posted by Quantated View Post
    Crick had no idea what DNA was when he discovered it
    Stop posting crap.
    Crick didn't discover DNA.
    "[Dywyddyr] makes a grumpy bastard like me seem like a happy go lucky scamp" - PhDemon
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    Quote Originally Posted by Quantated View Post

    Crick had no idea what DNA was when he discovered it
    Idiot. Crick didn't discover DNA. Everyone knows that he discovered a way to store moonlight. Get your history right.
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    If only the "Like" button still worked...
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    Quote Originally Posted by Double Helix View Post
    I was not familiar with Peter Atkins, but just read a brief on him in Wiki*, and quoting from that makes me a fan already:

    Will have to investigate his theories some more. He appears to be an expert on some pretty high-brow stuff, like "Molecular Quantum Mechanics"!

    He appears to be firmly grounded in reality, to say the least.
    Atkins and Dawkins. A firm of real estate solicitors from Oxford (the murder capital of the UK).
    What will people say in 100 years? Things do change (the 2nd Law again).
    Like, do you remember when people believed there was no God!
    And a guy called Peter Atkins was saying there is no such thing as good and junk DNA. All DNA according to Atkins is junk. Life on earth is nothing but a DNA junkyard.
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    Quote Originally Posted by tk421 View Post
    Quote Originally Posted by Quantated View Post

    Crick had no idea what DNA was when he discovered it
    Idiot. Crick didn't discover DNA. Everyone knows that he discovered a way to store moonlight. Get your history right.
    Discovering that DNA is there in no way implies understanding of what is there. Columbus discovered America but did he ever see the rockies? Answer no, but then Eric the Red was here first so Columbus discovered nothing
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    Quote Originally Posted by Quantated View Post
    Discovering that DNA is there in no way implies understanding of what is there.
    And your point?
    "[Dywyddyr] makes a grumpy bastard like me seem like a happy go lucky scamp" - PhDemon
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