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Peptide bond formation

Video transcript

- [Voiceover] So I've got two arbitrary amino acids here. We recognize the telltale signs of an amino acid. We have an amino group right over here that gives us the amino and amino acid. We have a carboxyl group right over here. This is the acid part of an amino acid. And in between we have a carbon, and we call that the alpha carbon. And that alpha carbon is gonna be bonded to a hydrogen and some type of a side chain, and we're just gonna call this side chain R1, and then we're gonna call this side chain R2. And what we're gonna concern ourselves with in this video is, how do you take two amino acids and form a peptide out of them? And just as a reminder, a peptide is nothing more... than a chain of amino acids. And so, how do you take these two amino acids and form a dipeptide like this? A dipeptide would have two amino acids. That would be the smallest possible peptide, but then you could keep adding amino acids and form polypeptides. And a very high-level overview of this reaction is that this nitrogen uses its lone pair to form a bond with this carbonyl carbon right over here. So this lone pair goes to this carbonyl carbon, forms a bond, and then this hydrogen, this hydrogen, and this oxygen could be used net net to form a water molecule... that's let go from both of these amino acids. So this reaction, you end up with the nitrogen being attached to this carbon, and a release of a water molecule. And because you have the release of this water molecule, this type of reaction, and we've seen it many other times with other types of molecules, we call this a condensation reaction, or a dehydration synthesis. So condensation... condensation reaction or dehydration synthesis. We saw this type of reaction when we were putting glucoses together, when we were forming carbohydrates. Dehydration synthesis. But whenever I see a reaction like this, it's somewhat satisfying to just be able to do the counting and say, "All right, this is gonna bond "with that, we see the bond right over there, "and I'm gonna let go of an oxygen and two hydrogens, "which net net equals H2O, equals a water molecule." But how can we actually imagine this happening? Can we push the electrons around? Can we do a little bit of high-level organic chemistry to think about how this happens? And that's what I wanna do here. I'm not gonna do a formal reaction mechanism, but really get a sense of what's going on. Well, nitrogen, as we said, has got this lone pair, it's electronegative. And this carbon right over here, it's attached to two oxygens, oxygens are more electronegative. The oxygens might hog those electrons. And so this nitrogen might wanna do what we call in organic chemistry a nucleophilic attack on this carbon right over here. And when it does that, if we were doing a more formal reaction mechanism, we could say, "Hey, well, maybe one "of the double bonds goes back, "the electrons in it go back to this oxygen, "and then that oxygen would have a negative charge." But then that lone pair from that double bond could then reform, and as that happens, this oxygen that's in the hydroxyl group will take back both of these electrons. Would take back both of those electrons, and now it's going to have an extra lone pair. Let me do that by erasing this bond and then giving it an extra lone pair. It already had two lone pairs, and then when it took that bond, it's gonna have a third lone pair. And then it's going to have a negative charge. And now you could imagine it's going to grab a hydrogen proton someplace. And now it could just grab any hydrogen proton, but probably the most convenient one would be this one, because if this nitrogen is going to use this lone pair to form a bond with carbon, it's going to have a positive charge, and it might wanna take these electrons back. So you could imagine where one of these lone pairs is used to grab this hydrogen proton, and then the nitrogen can take these electrons, can take these electrons back. So hopefully you didn't find this too convoluted, but I always like to think, what could actually happen here? And so you see, this lone pair of electrons from the nitrogen forms this orange bond with the carbon. Let me do that in orange color if I'm going to call it an orange bond. It forms this orange bond. What we call this orange bond, we could call this a peptide bond, or a peptide linkage. Peptide bond, sometimes called a peptide... peptide linkage. And then we have the release of a water molecule. And so you have this oxygen is this oxygen, and you could imagine that this hydrogen is this hydrogen, and this hydrogen is this hydrogen right over here, and so net net it all works out. Now when I first saw this reaction, I was like, "OK, that kind of makes sense." Except for the fact that in physiological pHs, amino acids don't tend to be in this form. In physiological pHs, you are more likely to find this form of the amino acids, to find them as zwitterions. Zwitterions. Let me write down that word. It's a fun word to say. And it's one word, but I'm gonna write the two parts of the word in different colors so you can see. It's a zwitterion. So what does that mean? Well, zwitter in German means hybrid. It's a hybrid ion. It's an ion, it has charge on different ends of it, parts of the molecule have charge, but when you net 'em out, it is neutral. Parts are charged, but is neutral overall. And so at physiological pHs, the amino, the nitrogen end of the amino acid, tends to grab an extra proton, becomes a positive charge, and the carboxyl group tends to let go of a proton and has a negative charge. And this is actually going to be in equilibrium with the forms that we just saw before, but at physiological pHs, it will actually tend to the zwitterion form. And so how do you get from this form to form a peptide bond? Well, you could imagine this character over here, after giving its hydrogen protons, has an extra lone pair. So it's got one lone pair, two lone pairs, and then it's got, I'll do the extra lone pair in, I'll do the extra loan pair in purple. It's got an extra lone pair. Well, maybe it could use an extra lone pair to either grab a proton from the solution or maybe just for accounting convenience we could say, "Well, maybe just bumps in the right way "to grab this proton and then allows the nitrogen... "to take back these electrons." And if it did that, well, then you're getting, at least when you're looking at this carboxyl group and this amino group, you're going to get to the form that we just saw. If this gets a hydrogen here, this is gonna become a hydroxyl, and if this nitrogen takes back these two electrons from this pair, then it's just going to be NH2. So it's going to be, at least this part of the molecules, are gonna be just what we started with up here, and so you could imagine how you get back to the peptide linkage which we have right over here. This is the peptide linkage. And then the only difference between the resulting peptide that I have in this reaction, I guess you could say, in the previous one, is this is a zwitterion. The zwitterion form, where this carboxyl group... having donated its proton to the solution, and over here the nitrogen, this nitrogen, has taken a proton from the solution, so it has a net neutral charge, even though you do have a charge at either end. So hopefully you found that fun.