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Writing the DNA sequence is done with nuclosides that have three phosphates attached to them, and two of these phosphate are thrown away back into "phosphate pool" of cell. What are main reasons triphosphate structure is used? Conformational changes in the polymerase seems like it could be one of the primary ones.

rotaredom
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50cent
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    Welcome. Do you know where the 'A' in the 4-letter DNA code stands for, and what function it has in the cell? That may give you a clue. – AliceD Feb 09 '21 at 12:08
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    We expect questions to be accompanied by evidence of prior research. This requirement is especially important for homework questions. Is this a homework question? – AliceD Feb 09 '21 at 12:10
  • unrelated to 4 bases, question is on why chain grows from nucleoside triphosphates – 50cent Feb 09 '21 at 12:22
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    It seems I'm missing what your question is. Are you asking why phosphate links are used in DNA, or why a diphosphate is released (the latter seems to be the question)? – AliceD Feb 09 '21 at 12:25
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    Please finish the [Tour]. Before posting read the Help on how to ask a good question. Then search for similar previous questions, which I know exist. But from your strange statement about conformation changes I wonder whether you might benefit from reading a chapter on basic chemical thermodynamics. – David Feb 09 '21 at 20:08
  • @AliceD it's very clear, "why does DNA synthesis require nucleside triphosphates". if your answer to why is so self-evident and obvious that the mere question is absurd, then I apologize. if not, then nothing wrong with the question. – 50cent Feb 09 '21 at 21:23
  • @David whoever you are, nothing wrong with the question. there's nothing strange about nucleoside triphosphates alosterically regulating protein conformation, very basic. that the same principles is at work when it comes to nucleoside triphosphates in DNA synthesis, seems likely to me, you can Google "polymerase conformation change nucleoside triphosphates" and read around for yourself – 50cent Feb 09 '21 at 21:31
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    You still have not clarified your question. Do you understand that it takes chemical energy to make a phosphodiester bond, that the free energy change of hydrolysis of the phosphodiester bond in dNTP is coupled to making the phosophodiester bond in DNA? Or are you asking why pyrophosphate rather than orthophosphate is released? The answer to that is discussed in an answer of mine here which also touches on biochemical energetics. Or what? – David Feb 10 '21 at 17:42

2 Answers2

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Questions of "why" in biology are not completely proper - evolution simply happened that way, and the reasons we suggest are rationalizations that may not encompass the "real" reason. Still...

Enzymatic reactions are inherently reversible. If you make an enzyme that converts XMPs (nucleoside monophosphates) into DNA, then the same enzyme can convert DNA to XMPs also. Plus, there's "entropy" to consider, which is to say, if you pop off an XMP it goes flying off into the solution, it's a lot harder to round it back up again. Last but not least -- we're talking about DNA here. Every time DNA is degraded, even if the other strand is still intact, there is some chance that some mutation will occur with harmful effect.

All this can be set right by wasting a lot of energy every time DNA is extended. We snip off two phosphates - a pyrophosphate which is rapidly broken down by pyrophosphatase. The way equilibrium works, that second step pulls the reaction forward because it makes sure there is no pyrophosphate left lying around. Even if a freak surge of thermal energy at the level of molecular vibration would allow the enzyme to reattach it, the pyrophosphate no longer exists.

Mike Serfas
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  • "f you make an enzyme that converts XMPs (nucleoside monophosphates) into DNA, then the same enzyme can convert DNA to XMPs" good point, had not thought of that. In ribosomes transfer RNA would also fill same role I guess. – 50cent Feb 11 '21 at 11:59
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As OP suggested, was correct. From Stryer Biochemistry, https://www.ncbi.nlm.nih.gov/books/NBK22374/

"the binding of a nucleoside triphosphate (NTP) to DNA polymerase induces a conformational change, generating a tight pocket for the base pair consisting of the NTP and its partner on the template strand. "

Further, as Mike Serfas answer states, "Enzymatic reactions are inherently reversible. If you make an enzyme that converts XMPs (nucleoside monophosphates) into DNA, then the same enzyme can convert DNA to XMPs also. " This was also a good anwer to the question, since the OP had not considered that. The OP associates is with how the substrate for translation from RNA to proteins in ribosome is not amino acids but tRNA + amino acids.

Then, as some angry comments from some random person mentioned, and the good answer from Mike Serfas also mentioned, and, the standard explanation (but, not what OP was fishing for, OP was looking more in-depth) always focuses around, entropy etc.

There was nothing wrong with the question, no formally legitimate reason to close it. It helped the learning process of the OP, and potentially others that acesss this collaboratively generated content on this public Q&A site.

50cent
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    So what question does this statement answer? A change in conformation of the enzyme may be involved in binding dNTP, but the question was "What are main reasons triphosphate structure is used?". Enzymes adapt to substrates, the structure of which are determined by chemical and evolutionary factors, not the other way round. – David Feb 10 '21 at 17:52