Nucleic Acid Structure and General Features

ID #1059

I understand how the phosphate groups in the middle have only one phosphate in them and the 5 prime end has 3 phosphates. However, I was wondering what happens with an entire string of nucleotides in that does the nucleotide at the 3 prime end also have a triphosphate group because it is at the end of the chain or does it only have one? If it has 3, how do you differentiate between the 5 prime and 3 prime end? I hope that makes sense.

Yes, your question makes sense, but let's take a closer look at the nucleotide at what we call the 3' end of the nucleic acid. How did it get added to the chain? It had its incoming triphosphate group hydrolyzed and the remaining phosphate linked to the 3' OH of the nucleotide that had been the last link in the chain, right? So is the phosphate group in the new end of the chain (the one we just added) free or occupied? It's occupied as the phosphodiester linkage, isn't it? Between the two groups that we've discussed, the 5' phosphate group and the 3' OH group, which one is "available" in this newly added nucleotide? The 3' OH group, right? Since that's the only "available" chemical group, we call it the 3' end of the molecule. Take a closer look at the figure from today's lecture, and verify that all the nucleotides in a given chain are oriented in the same direction, so you can't have two 5' ends!

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