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In dehydration synthesis of nucleotides, the hydrogen atom from the 3' carbon on the deoxyribose sugar of one nucleotide reacts with the hydroxyl group on the phosphate group of another nucleotide to form water. As the water molecule forms, a new covalent bond comes into existence between the two nucleotides.

Hydroxyl group can be in different positions within the phosphate group, for example:

Hydroxyl group on the left Hydroxyl group on the top Hydroxyl group at the bottom

I'm wondering if different positions of the hydroxyl group have an impact on the dehydration synthesis between nucleotide monomers. For example, when the hydroxyl group is at the bottom, will the dehydration synthesis occur at all? Also, when the hydroxyl group is on the left, does the spatial structure of the sugar-phosphate backbone have a spatial shape different from when the OH group is on the top?

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    $\begingroup$ You need to keep in mind that simple chemical structure drawings like these do not at all reflect reality on the atomic scale. The 2D electron from the "double bond" is shared among the 3 O atoms (except the one on the right, AFAIK), as is the proton from the hydroxyl group. Everything is floating around in quantum probability clouds, not permanently fixed in one specific position in rigid bonds. The other thing to keep in mind is that a phosphate is a tetrahedron in 3D space and can rotate pretty freely, allowing the dehydration reaction to occur in any conformation. $\endgroup$
    – MattDMo
    Commented Sep 9, 2020 at 17:26

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Wherever the hydroxyl group is; the result is the same I think. The phosphate has oxygen arranged in a tetrahedron around it.

In cells the hydrogen is not attached most of the time. For example the triphosphate on ATP is a weak base with a pKa of about 6.6. Cytoplasm usually has a pH of about 7.2, so an ATP molecule is only protonated (very approximately) 15% of the time.

https://en.wikipedia.org/wiki/Polyphosphate#Acid-base_and_complexation_properties

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