Peptide bonds: Formation and cleavage

Let's talk about the peptide bond. Now, proteins are formed from the folding of polypeptide chains. And polypeptide chains are formed by linking amino acids together. And these links are called peptide bonds. So before we can work our way up to the fully-formed and functional protein, we have to start at the very beginning by forming a peptide bond between the first two amino acids. So let's review the structure of an amino acid really quickly. Here we have our backbone. We have our amino group, our carboxylic acid group. Here is our alpha carbon. And then, the r represents our side chain. Now, peptide bonds are formed by the nucleophilic addition-elimination reaction between the carboxyl group of one amino acid and the amino group of another amino acid. So let me show you what that looks like here. Let's have another amino acid drawn right here. So the electron pair on the amino group of the second amino acid comes over to form a bond with the carbonyl carbon of the first amino acid. You give off a water molecule in the process, and then you get your newly-formed dipeptide. And here is our newly-formed peptide bond. Now, remember that a peptide bond is just an amide bond that is formed between two amino acids. And you should also make note of the fact that this bond is a rigid and planar bond that is stabilized by resonance delocalization of this nitrogen's electrons to this carbonyl oxygen. So we can draw that out here. Remember that there is a lone pair of electrons on this nitrogen that can move here. And then, these electrons will move to this oxygen atom, which also has its own two lone pairs of electrons. So it can also be represented like this. And we'll have the formation of a double bond here and then an extra lone pair on the oxygen atom. So as you can see, the peptide bond with this resonance delocalization of electrons has a lot of double bond character. And because of this double-bond-like character, the peptide bond is a very rigid and planar one. But don't confuse this with thinking that an entire polypeptide chain would be a rigid-like structure because-- even though there isn't much rotation about the peptide bond-- you do still have for free rotation about these alpha carbon atoms here. So now, here we can see we have a dipeptide. And if we kept adding amino acids along in a chain here, we would have a polypeptide. Now, if we take a closer look at the backbone of this chain, we can see that there is a pattern formed by the atoms that form this backbone. And here, you have a nitrogen atom, the alpha carbon, and a carbonyl carbon. And then, it repeats with the nitrogen atom, the alpha carbon, and a carbonyl carbon. And you get a pattern that looks like this. And each time you add a new amino acid, the pattern just repeats. So that, whatever length of your polypeptide chain, you always start out with a nitrogen atom and you always end with the carbonyl carbon. And so this end of the backbone of the polypeptide chain is called the amino or N terminal. And then, this end of a polypeptide chain is called the C terminal. And then once, within a polypeptide chain, each amino acid is called a residue. So that's the formation of a peptide bond and a polypeptide chain. So now how do we go about breaking this peptide bond to get two amino acids again? Let's give ourselves just a little bit more room here to work, and we'll redraw a bond between two amino acids as a peptide bond here. And remember that here is our peptide bond-- just to highlight it for you. And we can break this peptide bond in a process called hydrolysis. So if we have hydrolysis of this peptide bond, then we go back to forming two free amino acids. The hydrolysis of a peptide bond is helped along by two common means, and those two means are with the help of strong acids or with proteolytic enzymes. So when we use strong acids, we call this acid hydrolysis. And acid hydrolysis, when combined with heat, is a nonspecific way of cleaving peptide bonds. So say you have a long polypeptide chain. And then, you throw this polypeptide into a pot with some strong acid, and then turn up the stove to add a little heat. Then, you would just end up with a jumbled up mix of amino acids as each of the peptide bonds gets cleaved. So the other way of cleaving a peptide bond is with proteolysis. And proteolysis is a specific cleavage of the peptide bond with the help of a special protein, an enzyme called a protease. So unlike acid hydrolysis, proteolytic cleavage is a specific process. And you can choose which peptide bonds you cleave because proteases are pretty picky about where they will cut, and many of them will only cleave peptide bonds between certain specific amino acids. One example of this is with the protease trypsin. Trypsin only cleaves on the carboxyl side of basic amino acids, like arginine and lysine. And interestingly, this is the same enzyme that is produced by our pancreas to help us digest food. So now say we have the following polypeptide chain-- and it can be any old, arbitrary polypeptide chain-- and say we add trypsin to the environment that this polypeptide chain is in. And here I'm just representing the amino acids as their abbreviated form. Now with the addition of trypsin, where would this polypeptide chain be cleaved? Well, remember that trypsin cleaves on the C terminus of arginine and lysine. Here we have an arginine, and this would be considered the C terminal of arginine, since it's closest to the C terminal of the polypeptide chain. So we would get cleavage here. And then, likewise, we would have cleavage on the C terminal of this lysine residue here. And so with this particular polypeptide chain, you would end up with three different fragments after the addition of trypsin since it cleaves in these very specific places. And there are many other examples of specific proteases that cleave in at certain parts of polypeptide chains. And you probably don't really need to memorize which proteases cleave after which amino acids, but you should probably remember that they are just specific means of breaking a peptide bond-- unlike acid hydrolysis over here, which is a very nonspecific way of cleaving a peptide bond.