Propose an acid-catalyzed mechanism by which cytosine can form...

Question

Propose an acid-catalyzed mechanism by which cytosine can form a β-1 N-linkage with 2-deoxy-β-Dribofuranose to produce a deoxynucleoside (DNA) called deoxycytidine.

Chemical reaction showing 2-deoxy-β-D-ribofuranose and cytosine forming deoxycytidine with acid.

Accepted Answer

Propose an acid catalyzed mechanism by which cytosine can form a beta 1 N linkage with 2 deoxy beta D riboferenose to produce a deoxynucleoside or DNA called deoxycytidine. Guys, this sounds so hard, but it's actually not that hard, okay? We're just gonna go step by step, okay? First of all, we have to proposed an acid catalyzed mechanism. We're already given what the product looks like. So we know at some point this nitrogen that's in the one position on my cytosine has to come in and be attached to the top of the anomeric position there, and then it makes this. So really like this isn't this isn't that bad, we just need to draw out what the mechanism would look like, okay? Now I do want to find some stuff really quick, some terminology before we get started. First of all, I called the linkage a beta 1N linkage. Why is it called that? Well, let's look at the final product. We're talking about a beta anomer. So that's a beta linkage. It's an n linkage because it's an n glycosidic bond. And specifically the reason it's called beta1 is because it's attached to the one position of my cytosine. So it's a beta 1 n linkage because the nitrogen, that is attached to the carbon happens to be in the first position of that base. You don't know you don't know how to you don't need to know how to number bases ever. Okay? I mean not in this course, maybe in biochemistry later. But right now I will always or you will always get the numbering for the bases, okay? They don't always attach in the one position. For cytosine it does, but for other bases it will be another position, okay? Cool. Second piece of terminology, 2 deoxy. The actual sugar, ribosugar that we're using is not a regular ribofernose, it's 2 deoxyribofernose. So why did I include that? Well guys it turns out that this is a modified monosaccharide. Remember that to be a monosaccharide you need to have oxygens at every carbon. This carbon is missing an oxygen, so is it a mono saccharide? It's not it's not like a true unmodified monosaccharide. So it turns out that in, in biochemistry, DNA is missing the Oh at the two position. So that's why it's called DNA. DNA is deoxyribonucleo nucleic acid. Deoxyribonucleic acid. It's missing the Oh in that 2 position. So the reason that I put it there is because I want you guys to see what DNA would look like. DNA is always missing that Oh, it makes it much more stable if it doesn't have that Oh there, which is why. But just you know it's like a modification of a monosaccharide, but it reacts exactly the same. Obviously you can't epimerize this one, right? You wouldn't be able to like switch the 2 positions, that's a that's a difference, okay? But in terms of this mechanism it's going to work exactly the same as regular glycosidation. So let's go ahead and actually get started. So let's go ahead and redraw this structure. Oh. Oh. And the first step guys would be to use acid. I'm just going to use H3O plus because it's my favorite. And I'm going to protonate the Oh that I want to leave which is this one. I'm going to protonate the oxygen that I want to leave. Cool. So what that's going to make is a protonated sugar that looks like this. And remember guys that the next step is that my o can eliminate the water. So now what I'm gonna get is that this Oh is still here, this Oh is still here, but now I have a double bond here, right, with a positive charge. And that double bond can resonate, right? So let's draw the resonance structure. That resonance structure would push the electrons up to form the carbenium ion that looks like, oops, that looks like this. Cool? Awesome. So this is actually I'm gonna bring that structure down so we're gonna have more room to work with it. So let's bring that structure down. So Oh, Oh, positive charge. And this is where my nitrogenous base comes in. So let's bring down cytosine. So it looks like this. And that's an amine. And all I'm going to do, guys, is I'm going to draw this n with the h, it has an h, right? This n attacks that positive charge. So now what I'm going to get is what's called a nucleoside because it's an N glycoside that specifically has a nucleobase or a heterocyclic base attached to it. So it's gonna be N, just draw the whole thing with a positive h and that just has to get deprotonated. So we'll deprotonate that using water and that is gonna give us our final answer. Which is this sugar, which actually doesn't really have, oops. It doesn't have a super complicated name. You would think that this would have like a super complicated name that you would need to that you would need to name or whatever, but this is just known as deoxycytidine. So deoxy because we're missing the oxygen at the two position. Citidine. And later on when we get to DNA and or maybe in in biochemistry, you're going to realize that all you need to turn this into actual DNA is just 3 phosphate groups, or actually just a single phosphate group on that O that's linked to other DNAs or other base pairs, other bases is gonna make DNA. Isn't that so cool? Awesome guys. So we just made our first molecule of genetic code by using the reaction of N glycosidation. I hope this was interesting to you guys, and I hope that you're that you were able to follow the whole process. And just remember that even though you could get 2 different animers, the one that we specifically wanted to draw here was the beta anomer. The alpha anomer probably wouldn't form in very high yield because it's not his favored. Okay? Awesome guys. So we're done with this question, let's move on.

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Propose an acid-catalyzed mechanism by which cytosine can form a β-1 N-linkage with 2-deoxy-β-Dribofuranose to produce a deoxynucleoside (DNA) called deoxycytidine.

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