In the previous video, we introduced one enzyme catalyzed mechanism that can facilitate the hydrolysis of a peptide backbone. In this video, we're going to see another way that a different class of enzymes can do this. And this class of enzymes are known as serine proteases.
They're known as serine proteases because there's a really important serine in the active site that plays an absolutely essential role. in the catalytic mechanism. So I'm using the same color scheme here as I used in the previous video, where everything in white represents the enzyme active site. Green here represents the peptide backbone that ends up getting lysed.
We'll see our water molecules in red, and electron flow is gonna be in yellow. Okay, so what we see in the enzyme active site are three important amino acids. an aspartic acid, a histidine, and a serine.
And these three amino acids are positioned such that they're next to each other. Now this doesn't necessarily mean that they have to be right next to each other in the peptide backbone, it just means that in the overall tertiary structure of the enzyme, they are positioned such that they can interact with each other. Alright? So the So one last really important thing that I want to point out that we observe in the enzyme active site. And that's a hydrogen bond is present between the aspartic acid and this nitrogen on our histidine.
As it turns out, this is really important because it influences the overall electron density in our catalytic or in our enzyme active site. OK, so ultimately what it does is it makes. this lone pair on nitrogen a lot more reactive than normally it would be. The reason that's really important is because the way this enzyme functions is by creating a nucleophile out of this serine that's present in the active site. So this serine becomes a nucleophile.
And in fact it becomes the nucleophile that initiates or starts our mechanism. Okay, so let's go ahead and see how that works. Okay, so in the very first step, we have this really reactive lone pair on this nitrogen.
It's so reactive that it's able to reach over here and deprotonate the serine. This is pretty surprising because this alcohol group has a really, really, really high pKa, meaning it's really hard to deprotonate. But the chemical environment that this...
active site generates allows it to do so. Upon deprotonation, we now have a negatively charged oxyanion on our serine. And as I mentioned, this is the nucleophile that actually initiates our chemical reaction.
So this lone pair attacks the carbonyl, which as we've seen in the past, this forces electrons from the double bond to go up onto the oxygen in that carbonyl. This creates our tetrahedral intermediate that we've seen several times in the past on our oxygen. So we have an oxyanion.
And we now have a lone pair here on the nitrogen that's able to reach over and deprotonate that histidine. So this is our proton shuffling step where we end up with a nitrogen on our peptide backbone that has a positive charge. This newly formed positive charge on the nitrogen has now set us up so that when our oxyanion or our tetrahedral intermediate collapses, the electrons flow over to the nitrogen and break that covalent bond that we know we want to break in this mechanism.
Okay, we've now broken this covalent bond. So I've redrawn... the N-terminus or this amine off to the side because it's no longer important. And in the active site it gets replaced with a water molecule.
This is the water that we knew had to come in at some point because it's a hydrolysis reaction which relies on water as part of the reaction. Okay, as we saw in the previous video we need to create a better nucleophile out of water and we do so by deprotonating it with the lone pair on that nitrogen. We've now generated a hydroxide anion, which is a really good nucleophile, and this can go ahead and initiate the attack onto our electrophilic carbon. which triggers the oxyanine to be formed in our tetrahedral intermediate. The next step in our mechanism is to create a positive charge on this oxygen so that the CO bond between the serine and our substrate is the one that breaks in the next step.
So we do this by reacting this lone pair, reaching over, deprotonating that nitrogen, on our histidine. The resulting structure now has a positive charge on that oxygen atom, which allows us to collapse our tetrahedral intermediate, reforming the double bond, making the electrons in this covalent bond break and move towards the positive charge. So we now have regenerated our active site in our enzyme, and we've broken this covalent bond, the peptide bond, using water. But the very, very last thing that we want to do is go ahead and adjust the position of our protons because we know that under biological conditions, we have protonated amines and deprotonated carboxylic acids.
At this point, As we saw in the previous video, we've completely regenerated the active site and we have successfully created our two products. So at this point, the products can diffuse out of the active site, creating space for another substrate, another peptide bond, to interact with our active site and we can start this process over. So this mechanism has a lot of the same themes as we saw in the previous video, as well as what we understand for hydrolysis reactions. The key difference is that this mechanism is really two complete steps built into one. The very first step includes using the serine as the nucleophile to initiate the reaction.
Once you've gone through a full process, Now you bring in water to go through another full process and regenerate the active site.