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Thread: DNA structure

  1. #1 DNA structure 
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    May 2013
    I knew that Phosphate groups bound to 5' and 3' carbon of ribose and deoxy ribose sugar ..My doubt is why phosphate group need to bind only to 3' and 5' carbon of sugar.. ? and specific bonds are formed in each specific carbon with phosphate , nitrogenous base?

    Pls clear this doubt...Why it is specific bonding in each carbon?

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  3. #2  
    Forum Professor Zwirko's Avatar
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    Sep 2008
    55 N, 3 W
    Not 100% sure what you're asking. If you're asking why the phosphodiester bonds in nucleic acids are 5'-3', and not some other arrangement, then I'd assume it's because the enzymes involved in the synthesis of DNA and its immediate precursors don't act upon subunits that are phosphorylated at other positions or are incapable of forming a bond that is not 5'-3'.

    So, something like ribose-4-phosphate can't be incorporated into a DNA molecule and one nucleotide can't be joined to another via a 2'-4' linkage.

    That's my hypothesis anyway; you might want to check with a more reliable source.

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  4. #3  
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    Oct 2013
    The truth is that if all of the bonds made in your cells were random, you would have phosphates bonded all over the ribose, and you would see any combination you could imagine. But our cells are not random in this way. If you think of the ribose as a physical object (let's imagine a chair, a really teeny tiny chair), then it has a different shape depending on which side you approach it from. You can think of enzymes sort of like people when it comes to interacting with ribose (or with a chair). We humans have a preference to sit on the top of the chair in the groove between the seat and the back much like a specific nucleotide-producing enzyme or DNA synthesis enzyme prefers to sit on a ribose in a specific way (you wouldn't turn the chair upside down before you sat on it, would you?).

    Consequently, when the cell is attempting to create these bonds, it just so happens that they have evolved enzymes that really like sitting on ribose in such a way that favors 3' 5' ester formation (and we really like this because it just so happens that this specific conformation, or organization, of the bonds in nucleotides is perfect for creation of the DNA helical structure that is so important). You might imagine that if an organism evolved a different way to link phosphates to the ribose, that its genetic material might have a different structure. This idea of imagining the molecules as a chair, or something, is called CHIRALITY. If you are interested in this topic, you can look up the "chirality" of enzyme active sites or the "chirality" of biomolecules.
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  5. #4  
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    Oct 2013
    Indeed as explained in a nica analogous way by iRNAblogger, the DNA polymerase enzyme that assembles new DNA strands only attaches new nucleotides to the 3′-hydroxyl (-OH) group, via a phosphodiester bond. So the orientation is actually enforced by the enzymes.
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