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Hi, Are you basically asking why DNA has thymine, and why RNA has uracil?
Yes, that`s it! I think it`s something related to the chemistry reaction between these bases and the sugars. But I couldn`t figure out why the thymine doesn`t react to the ribose... Why does this reaction doesn`t fit??
This was a question that bugged me for a long time! I'll do my best to share what I've learned. So the difference between the two bases is simply an extra methyl group on thymine, which presumably is necessary for DNA's stability. So how exactly does that small change stabilize DNA? For one, it prevents DNA from being recognized and chopped up by nucleases - the methyl group thus helps to protect DNA against invaders. The hydrophobic effect of the methyl group also helps to ensure proper base pairing (uracil can occasionally pair with other bases). Thymine’s methyl group also provides a point of interaction for amino acids in proteins (possibly resulting in better recognition by polymerases, transcription factors, etc). If you consider uracil to originally have been the "base of choice" to pair with adenine, all of the above factors pushed towards a switch to thymine. Perhaps the strongest impetus, though, for the incorporation of thymine into DNA comes from the spontaneous deamination of cytosine. This undesirable chemical reaction results in a uracil base, and occurs, on average, 100 times per day in a mammalian cell. The buildup of these “illegitimate” uracils could be catastrophic for the organism - at the very least, copying fidelity of DNA would be detrimentally affected (and your proteins get messed up as well!). Thus, cells have repair systems in place to remove these “illegitimate” uracils. But if uracil were already present in DNA, paired to adenine, the repair system would be forced to somehow differentiate between “illegitimate” and “legitimate” uracils (kinda tough!). An easy solution to this problem? Add a methyl group to all of the “legitimate” uracils, allowing the repair system to easily tell between the two. This usage of methylated uracil, (or thymine!), in DNA allowed for the long-term storage of crucial genetic information - the cell could now get rid of the "broken" cytosines while leaving the correct uracils unharmed. I can't comment on why the reaction doesn't occur - sorry! But if you look at things from the natural selection viewpoint presented above, the energetics of the reaction doesn't matter. What I mean is - energetically speaking, a thymine/ribose reaction and a uracil/deoxyribose reaction could indeed be favorable. However, natural selection has selected for thymine/deoxyribose and uracil/ribose simply because it ensures copying fidelity, regardless of the details of energy loss and energy spent. This is only one, I'm sure, of numerous possible answers - I apologize since I was unable to answer your original question, but I hope this helped! If you do find out a thermodynamic approach, I'd love to hear! :)
Wow. You didn't answer the original question, but still gave me o lot of important info... Thanks! I will keep looking for it, once I figure it out I come back... =D
Principle of complementarity (of basis): A large base can't attach to another large base, a small base can't attach to a small base. Two large basis together provoque a protrusion, two small basis together provoque an entrance, leading to instability in the DNA.
In this Lecture Prof. Eric Lander says to the class he has know idea either... "whereas I have a good explanation for this I don't have a good explanation for that, although maybe some of my Origin of Life colleagues have an explanation. But I've always been a little puzzled. Why does it use U instead of T?" http://ocw.mit.edu/courses/biology/7-012-introduction-to-biology-fall-2004/video-lectures/lecture-11-molecular-biology-2/ But still, there are some theories about it! I guess it has something to do with energy. it`s always about it anyway...
kindly share the answer when you find out. I am intrigued with what thermodynamics explanation has to offer. I hope to find the answer when I gain more knowledge in biochemistry.