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We all know deoxyribonucleotides form DNA while ribonucleotides form RNA, DNA is double stranded while RNA is single stranded, and RNA can transcribe from DNA. We also know that DNA use A, G, C, T, while RNA use A, G, C, U and that it's the DNA that stores genetics information, not RNA.

My question is: how does the lost oxygen atom on deoxyribonucleotides 2' site of the sugar (turning it into a ribonucleotide), make such a large difference in function? It just an oxygen atom. Why don't they just all use U or all use T?

Why deoxyribose for DNA and ribose for RNA? This answer may solve the question why is DNA double strand, RNA single strand, but it doesnt explain why does RNA uses U instead of T.

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    $\begingroup$ The question isn't really the same, but the (excellent) answer to the linked question probably answers this one. $\endgroup$
    – Luigi
    Sep 5, 2015 at 23:35
  • $\begingroup$ RNA can and does form double helices, either through intrastrand base pairs or between strands. biology.stackexchange.com/questions/19115/… $\endgroup$
    – canadianer
    Sep 6, 2015 at 2:37
  • $\begingroup$ "My question is, all the different is due to the deoxyribonucleotides lose an oxygen atom on the 2' site of the sugar, how could be so much different? It just an oxygen atom." Hydroxyl groups are more reactive than a hydride group. The 2' -OH can be deprotonated and react with the Phosphate in the backbone of the RNA molecule and break the phosphodiester bond and cyclize with the phosphate attached to the 3' carbon. The 2' -H cannot react with the phosphate group, so the phosphate backbone of DNA is more stable than an equivalent RNA molecule in that regard $\endgroup$
    – AMR
    Sep 6, 2015 at 4:56
  • $\begingroup$ The difference between the T and the U likely has more to do with the enzyme catalyzing the synthesis reaction en.wikipedia.org/wiki/Nucleotide#Synthesis and is not directly related to the 2' - hydroxyl. $\endgroup$
    – AMR
    Sep 6, 2015 at 5:02
  • $\begingroup$ "It just an oxygen atom". Umm... If you remove an oxygen atom from water, you get a highly flammable gas and not something you would drink to quench your thirst. There's no such thing as "it's just a single atom". Changing an atom is a huge difference. $\endgroup$
    – terdon
    Sep 6, 2015 at 13:04

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For the switch from thymine (T) to uracil (U), it actually doesn't have anything to do with the sugar backbone of the nucleotides. This article on Science Daily explains that U is more cost efficient to produce than T because it can be easily gotten from a chemical degradation of cytosine (C). Since RNA has a short life span and because the cell needs a lot of RNA it uses U. DNA, on the other hand, undergoes a lot of checks and repairs. If it were to use U, it wouldn't know if the U was really a U or if it was a C that got damaged. Since it is important to keep the number of mutations to a minimum, DNA uses the more costly T to ensure fidelity.

I would also like to point out @AMR's comment. It isn't just an oxygen atom. An oxygen atom is the difference between the air we breath and ozone that can kill you. It's the difference between water and highly flammable hydrogen gas.

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  • $\begingroup$ RNA forms double stranded structures! $\endgroup$
    – canadianer
    Sep 6, 2015 at 6:13
  • $\begingroup$ dsRNA is thermodynamically more stable than dsDNA, actually. $\endgroup$
    – canadianer
    Sep 6, 2015 at 8:20
  • $\begingroup$ @canadianer The A, B, and Z forms of ds helicies is an artifact of in vitro preparation of the molecule related to the the salt content and consistency of the humidity during the crystallization process. This does not mean that we actually see these structures in vivo, though for DNA, our best model if B. And as I asked on a different thread, is the thermodynamic stability related to the hybridization and thus melt temps needed to open dsRNA or is the relationship actually referring to the stability of the molecules sugar-phosphate backbone. $\endgroup$
    – AMR
    Sep 6, 2015 at 13:35
  • $\begingroup$ 2'-OH can and does get deprotonated and can then attack the phosphate, breaking its bond with the 5' carbon of the next nucleotide it the chain. The phosphate and 2'-OH cyclize and the backbone is broken and broken chromosomes lead to apoptosis and cell death, so using an RNA double helix for chromatin would be riskier. Also, it may not be an advantage in larger genomes to have a molecule that is thermodynamically more stable, as this would likely slow and/or increase the energy required to replicate that genome. $\endgroup$
    – AMR
    Sep 6, 2015 at 13:41
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    $\begingroup$ @canadianer Thank you for the link. It might be a bit difficult to draw genome wide conclusions from 24bp strands, but I am sure that the results are accurate. Adding to my comment above, I also wonder how ribonucleotides interact with histones or if they can, as packing becomes a very important and highly conserved chromosomal element as genome size increases. $\endgroup$
    – AMR
    Sep 6, 2015 at 19:16

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