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Current time:0:00Total duration:8:26

Video transcript

so I've got two arbitrary amino acids here we recognize the tell-tale 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 we call that the Alpha carbon and that alpha carbon is going to be bonded to a hydrogen and some type of a sidechain and we're just going to call this sidechain r1 and we're going to call this sidechain r2 and what we're going to 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 a peptide is nothing more than a chain of amino acids so chain chain of amino chain of amino acids and so how do you take these two peptides I start how to 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 is that this nitrogen uses its lone pair to form a bond with this carbon II 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 this oxygen could be used net-net to form a water molecule to form a water molecule that's let go from both of these from both of these amino acids so this reaction you end up with the nitrogen being attached to this carbon and a release a release of a water molecule and because you have the release of this water molecule this type of reaction we've seen that many other times and other types of for with other types of molecules we call this a condensation reaction or dehydration synthesis so cohn condensation condensation reaction or or dehydration synthesis dehydration we saw this type of reaction we're putting glucoses together when reforming when we were forming carbohydrates dehydration dehydration synthesis but whenever I see a reaction like this it's it's somewhat satisfying to just be able to do the accounting and saying alright this is going to bombed with that we see the bond right over there I have and I'm going to let go of an oxygen and two hydrogen's which net-net equals h2o equals a water molecule but how could 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 want to do here I'm not going to do a kind of 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 in it 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 want to do what we call an organic chemistry and nucleophilic attack on this carbon right over here and when it does that if you were doing a more formal reaction mechanism we could say hey well maybe these one of the double one of the double bonds goes back the electrons in it go back to this oxygen and then that would have a negative and then that oxygen would have a negative charge but then that lone pair from that double bond could then reform it could reform and as that happens as that happens this this oxygen that's in the hydroxyl group will take back both of these electrons would take back would take back both of those electrons and now it's going to have an extra lone pair now it's going to have an extra lone pair and let me do that by erasing this bond and then giving it giving it an electric extra lone pair it already had two lone pairs it already had two lone pairs and then when it took that bond it's going to have a third lone pair and then it's going to have it's going to have a negative charge and now you could imagine it's going to grab a hydrogen proton someplace now I could just grab any hydrogen proton but the probably the most convenient one would be this one because if this nitrogen is giving it's going to use its this lone pair to form a bond with carbon it's going to have a positive charge and it might want to take these electrons back so you could imagine where this 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 well what could actually happen here and so you see the this lone pair of electrons from the nitrogen forms this orange bond with the carbon it forms this orange this let me do it in orange color if I'm going to call it an orange bond it forms this orange bond this is what we call this orange bond we could call this a peptide bond so or peptide linkage peptide peptide bond sometimes called a peptide peptide peptide linkage and we have and then we have the release of a water molecule so you have this oxygen is this oxygen and you could imagine this hydrogen is this hydrogen and this hydrogen is this hydrogen right over here and so now that it all works out now when I first saw this reaction it's like okay that kind of makes sense except for the fact that in at physiological pH is amino acids don't tend to be in this form in physiological PHS you're more likely you're more likely to find this form of the amino acids to find them as whitter ions or zwitterions Swit or ions let me write down that word it's a fun word to say is whitter and it's one word but I'm going to write the two parts of the words in different colors so you can see it's saying it's a zwitterion so what does that mean wells whitter in German means hybrid it's a hybrid ion it's an ion it has charge on on different ends of it has parts of parts of the parts of the molecule have charge but when you net them out you have it is neutral so they have parts are charged but it is neutral overall and so at physiological pH is the the amino the 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 so this is your and this is actually going to be in equilibrium with the forms that we just saw before but at physiological pH is it will actually tend to the Ritter Souter Eon or the zwitterion form and so how do you get from this form to what to form a peptide well you could imagine you could imagine this character over here after giving its hydrogen protons has an extra lone pair so it's got the it's got one lone pair two lone pairs and then it's got this I'll do the extra lone pair in I'll do the extra lone pair in purple it's got an extra lone pair well maybe it could use it could use an extra lone pair to either grab a proton from from the solution or maybe just for for accounting convenience to exhale maybe just bumps in the right way to grab this proton and then allows and then allows the nitrogen and then allows the nitrogen to take back these electrons and if it did that 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 going to become a hydroxyl and if this if this nitrogen takes back these two electrons from this pair then it's just going to be NH 2 so it's going to be it's going to be at least this part of the molecules are going to be just what we started with up here and so you could imagine how you get back to the peptide linkage the peptide linkage which we have right over here this is the peptide linkage and then the only difference between the resulting the resulting peptide that I have and this in this reaction I guess you could say in the previous one is this is Ritter jewellery on this whitter ion form where this carboxyl group I still have it 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 hopefully you found that fun
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