Fit model

Transcription

So today, I'm going to talk to you about the induced fit model of enzyme catalysis and how this concept can tell us a lot about how enzymes work. But before we do that, let's review the idea that enzymes make reactions go faster. And when you look at a reaction on a reaction coordinate diagram, you'd see that the catalyzed reaction would have a much smaller activation energy than the uncatalyzed one. Also remember that because of this, the energy of the catalyzed reaction's transition state is far lower than the energy of the uncatalyzed reaction's transition state. So what do enzymes look like? Well, most enzymes are proteins, or at least partially made up of protein. And substrates are any molecule that an enzyme will act on. And often, these substrates are the reactants that the enzyme will ultimately help turn into products through a reaction. Now enzymes also have what is called the active site, which is the location on the enzyme where substrates bind. And that's where the reaction ultimately happens. And it's important to recognize that every enzyme has a unique active site that will only bind to certain substrates. And just to clarify, I've referred to the active site here as both of the notches found on the enzyme, and not the space in between them. So here, of the two substrates I've drawn, the enzyme will only be able to bind to substrate 1, since they fit together like puzzle pieces. Whereas the shape of substrate 2 isn't going to fit nicely in the enzyme's active site. Now since enzymes have unique active sites, we say that enzymes are specific to certain substrates, and by extension certain reactions. But let's dive a little deeper into what happens when enzymes and substrates bind to each other and how that binding pattern changes as a reaction progresses. So first you'll have your enzyme here and your substrate over here. And I'm just going to label this with the number 1, since it'll be the first thing that happens in the sequence of events to come. And at this stage, nothing has happened yet. And the enzyme and the substrate have yet to come in contact. So next what will happen is the enzyme will bind to the substrate. But this binding won't be perfect. So we'll call this initial binding, which is stage 2 of the process. And what that means is that the forces holding these two together are strong, but they're not at their maximum strength just yet. And enzymes and substrates don't actually fit together quite like puzzle pieces. And they actually work a little bit more like two pieces of clay that will both mold together so that the fit is much tighter. So in our next step, this is exactly what happens. The enzyme and the substrate will both change shape a little bit and bind to each other really strongly. And we call this the induced fit because both the enzyme and the substrate have changed their shape a little bit so that they bind together really tightly. And it's at this point where the reaction that the enzyme is catalyzing is at full force. And this would be stage 3. So our next stage occurs after the reaction is completed and the binding becomes similar to what it was in stage 2. But the difference here is that there was something different about the substrate. So in this reaction, the enzyme is cutting our substrate into two parts. So now, the two parts have become separated. And this would occur after the reaction is finished. And we'll call this stage 4. Now in our next and last stage, the products of the reaction have been released from the enzyme. And our enzyme is back in the same state that it was in stage 1. And we'll call this stage 5. Now, let's look at this from a slightly different angle. I'm going to label the enzyme as E, the substrate as S, and our two products as P1 and P2. And they're going to represent this series of events, these different steps in the sequence of reactions. So first we'll have E and S separate. And this is stage 1. And next, E and S will bind to each other to form an enzyme substrate complex, which I have called ES. And it corresponds to stage 2 from before. Now what's really interesting is that in the next step, where we had the induced fit of stage 3, we're actually at the transition state of the entire reaction. And this is the same as that really high energy point that we saw at the beginning of this video. And it's at the point of the transition state where our enzyme is most tightly bound to its substrate. Now, I've written the substrate out here with the letter X. Because of the reaction's transition state our substrate isn't quite a reactant and it isn't quite our product either. It's somewhere in between. So that's why I've written it out as X instead of S. And I've also written this double dagger symbol, which is just a universal symbol for transition states. Now in our next stage, which is after the reaction has occurred, since it exists after the transition stage, we have the enzyme bound to the two products P1 and P2. And this was stage 4 from before. And then finally in our last stage, stage 5, we have our enzyme, which is now separated from our two products, P1 and P2. Now the big M away from this is that binding between enzyme and substrate is strongest at the reaction's transition state. And this is because the enzyme and the substrate have molded together. And that's why we call it the induced fit. Now, some enzymes will actually bind to more than one substrate. And if we look at a reaction that might be familiar, which is lactic acid fermentation, we can see that our enzyme, lactase dehydrogenase, will have space to bind to two different substrates in this reaction, one space being for NADH and the other being for pyruvate. So enzymes don't necessarily bind just to one substrate. Now, sometimes things will bind to enzymes at places other than their active sites. And we call this allosteric binding. So if we have an enzyme here with it's active site, a regulating molecule like an inhibitor made by the enzyme at a different location than the enzyme's active site. Now when something binds to an enzyme like this, it usually has the effect of changing the shape of an enzyme in some way to affect its ability to catalyze reactions. So in this case, when an inhibitor binds top the enzyme, it might change the shape of the active site, thereby inhibiting the enzyme, as it's no longer able to bind to its intended substrate. They don't quite fit together anymore. So while enzymes bind to reactive groups at their active sites, they can also bind to regulators at their allosteric sites. And allosteric sites just refer to any binding site outside of the active site. And remember allosterically binding molecules can either be activators or inhibitors, any regulating molecule. So what did we learn? Well, first we learned that enzymes are specific and that they can each bind to only specific substrates to catalyze specific reactions. Next, we learned about the induced fit model and how enzymes bind their substrates most tightly in the middle of a reaction at the reaction's transition state. And finally, we learned that enzymes have both active sites and allosteric sites, with active sites being where the reaction takes place and allosteric sites being where regulation takes place.