Enzymes - Video Tutorials & Practice Problems

Enzyme Basics

Hi in this video we're gonna be talking about enzymes. So enzymes are really crucial and cell biology um and a lot of biology and they have super important function. So we're gonna spend a lot of time talking about, you know, what enzymes are, what they do and how they work. So first what are enzymes, enzymes can be protein or RNA. Um That essentially their purpose is to reduce the energy necessary for a chemical reaction to occur. So enzymes act on what's known as the substrate, which is just the molecule that an enzyme acts on and it's highly specific. So enzymes don't just go around, you know, speeding up reactions of anything. They are really specific to a single molecule are really just a couple of molecules that are very similar. So they act very similar. And so they catalyze too. That's another term that you're gonna hear a lot with enzymes. And what that means is that they speed up the rate of or increase the re eight of a chemical reaction um that the sim straight needs to undergo. And so they can actually speed up reactions very, making them very fast. So the you know, the number that's mentioned in the text book is going to be 10 to the 8 to 10 to 13 times faster. So what does that actually mean? Well, for a reaction that would take 3 to 300,000 years to happen by itself, an enzyme can actually make happen in one single second. So they really speed up chemical reactions. Which you can imagine is very important because we can't wait around 300,000 years for a single chemical reaction to occur. We need to have we need them to happen now and usually we need them to happen repeatedly over the course of a lifetime. So we really need enzymes to speed up reactions. Now, they can work to speed up forward or reverse reactions. But essentially, and for an enzyme to be an enzyme, it has to meet three conditions. The first is that the enzyme cannot be consumed up in the reaction. So once the reaction takes place, the enzymes still needs to be present, they cannot be changed by the reaction, meaning that the enzyme stays the same before the reaction as it is after the reaction, so that it can be used again. So it can't be used up and it has to stay the same. Um and that the enzyme, this is really important. Let me back up. So you can see it is that the the enzymes only affect the rate of the reaction and do not affect the free energy. So the free energy of the reaction stays the same. All the enzyme does is come in and make it happen faster. So, so, if we're looking at an enzyme here, we can see this is this is the enzyme and these here are substrates and so the enzyme binds to the substrate and catalyze is some type of chemical reaction that the substrate needs to undergo. So it speeds up that chemical reaction. So now let's move on.

Activation Energy

So now let's talk a little bit about how enzymes speed up reactions. So they in order to do this, they must overcome what's known as the activation energy, which is the minimum amount of energy reactant must have before becoming products. So this um for this occurs this is needed in any type of reaction, including thermo dynamically favorable ones where the DELTA G is negative. So these don't necessarily need any help, but sometimes they just take a really long time. They can take years to occur without help. Um And so therefore in cells and in life enzymes come in and provide this energy boost to allow reactions to occur, even ones that would occur by themselves, but just are sort of slow about it. And so um there's another term that you're you may read about in your textbook and that's actually meta stable state. And what that means is that these are molecules or compounds that are thermo dynamically unstable. So meaning that their delta G. Is negative, DELTA G. Is negative and they will eventually occur by themselves, but they usually won't, they actually stay in this meta stable state for an extended period of time because they can't overcome this. Um this activation energy in order to produce the products. So, if we're looking at this on this graph. So this is a notice, we're looking at an X. Organic reaction, which if you remember what that means, that means that's energy releasing. So the delta G. Here is going to be negative. It's gonna be less than zero because the free energy of the reactant is higher than the free energy of the products. And so um we talked about activation energy. So what is that on this graph? Well, that's here, this one here activation energy. And so although this is an exotic reaction, it's going to release energy as it changes from reactions to products. We still need to get over this energy hump right here and this activation energy to occur. So enzymes come in here to really reduce the amount of activation energy necessary for reaction to occur. So how do enzymes do this? Well, there are two potential ways of overcoming the activation energy. The bad way is just increase the heat. So um this an increase in heat is going to increase kinetic energy and therefore the activation energy. Um and make everything move faster, reactions happen faster. But unfortunately, we'll all die because we'll all overheat. So obviously that's not a good way to do this. Now. The second way of overcoming activation energy is the good way. And that is using an enzyme that will lower the activation energy. So how do enzymes work? Well, they bind to what's known as the transition state form of the reactant. So here we have our reactant are two reactant. You have 12 here and you have our products which look different because some type of chemical reaction has occurred. Now the transition state is actually going to be this state here where um it's sort of in between the reactant and the product. And so the activation energy that is required to get to this point is fairly high. And so what happens and that this transition state is fairly unstable. So at any time it can go this way or it can go this way. So what an enzyme does. And an enzyme will just say that this here is an enzyme. It comes in right here and it binds to the transition state and it stabilizes it so that it can overcome the activation energy and proceed to the product. So that is how an enzyme works to reduce the activation energy and promote um the, you know, the formation of the products in a reaction. So now let's move on.

Substrate Interactions

So now let's talk about enzyme and substrate interactions. So enzyme and substrate interactions actually are responsible for regulating the actual reaction that's occurring. So one way to promote enzyme substrate interaction is through diffusion, which is the passive movement of substrates throughout the cytoplasm. So in order for an enzyme and substrate to work, they have to interact with each other. They have to be close together in the cell. So for instance, I am here and you are there. So if I'm the enzyme and you're the substrate, we're not going to interact. But if we were in a cell I could diffuse so I can move over to where you were. We can interact and the chemical reaction could move forward. So diffusion is a major way that enzyme and substrates come in contact with each other. And so for instance, um molecule in a cell we sort of don't think about things moving a lot in cells. They really are dynamic. So a molecule in a cell takes 1/15 of a second to travel 10 micrometers. So what does that mean? Well, the average cell diameter is 15 micrometers. So in 1/15 of a second, a single molecule can move, I mean very close, almost two thirds the distance of the diameter of the cell. So that means that enzymes get hit by about 500,000 random collisions each second of things just sort of snacking into it. And so that means that enzymes can actually catalyze thousands of substrate reactions every second just because they run into each other, they diffuse together in the cytoplasm and can interact now the other way. Um so once an enzyme and substrate have found each other, they actually have to interact. And they interact in what is known as the active site, which is a groove in the enzyme through which the substrate binds and the reaction takes place. So um what we can see here in this image, we have the enzyme here and you can see there's this blue region and that is going to be the active site and that's where the molecule comes in and binds in this case which is the substrate. Now, usually the shape or the bonds that it can make are pretty complimentary between the substrate and the enzyme and typically also usually the binding site isn't, you know, right here on the surface instead, it's sort of buried inside the enzyme and that's in order to separate the substrate from other chemical reactions that are occurring in the side. It's all or whatever environment that the enzyme is in. And so um very complimentary and usually they they are sort of internalized into the enzyme structure in order to separate from the outside environment. Now, the enzymes combined in enzymes combine substrates into ways. The first is the lock and key model. And the second is the induced fit model. So for the lock and key model, what we see is that we have an enzyme and a substrate that shapes just go together and so when they bind to each other, you can see that these fit together perfectly are almost perfectly their bonds, their shape, everything fits in the lock and key. Just as if you are unlocking a door, your keys gonna fit now with the induced fit model. This is a little different in the fact that the enzyme and the substrate have shapes that don't fit. So when they come together they actually don't fit perfectly. But what happens is that usually there's some type of confirmation all change in the enzyme that makes them fit together in the chemical reaction to occur. So these are two models of how enzymes and substrates interact. Now. A third thing that you need to know about enzymes and how they interact with things like substrate is that they can also interact with other molecules called co factors or co enzymes dependent on whether they are inorganic or organic. And when they bind these um sort of co facilitators, they help facilitate the reaction. And so what you can see here is um here in yellow there's this nice co factor that can come in and bind the enzyme and somehow this helps the reaction take place now sometimes. And you may see this in your textbook um co factors can also be referred to as prosthetic groups. Um so just know if you see prosthetic groups, it's referring to the same things, these co factors or um co enzymes that are facilitating the enzyme substrate reaction. So now let's move on.

Enzyme Regulation

Okay, so now we're going to talk about enzyme regulation. And so enzyme catalysis is highly regulated, which makes sense because enzymes speed up chemical reactions. So we don't want enzyme speeding up reactions that we don't want to take place. And so they have to be regulated. So there are many different ways that enzymes are regulated. I'm only going to mention a few here and we'll talk about more later in the course. But these are just sort of three that are mentioned in your textbook and are just good to know conceptually about how enzymes are regulated. So the first is feedback inhibition and that's when a product of one pathway inhibits the enzyme involved in its synthesis. So if you have an enzyme here acting on this to produce some other type of product here and that product can come back up here and inhibit the enzyme. And so this feedback inhibition can stop enzyme catalysis when enough of the product has been made. That's one way of regulation. Another way of regulation is a lost erIC regulation. And that's when some type of small molecule actually binds to a regulatory site on the enzyme. And so when it does that it binds to the enzyme, it can change, it can change the shape or structure and that can affect binding of the substrate or its ability to speed up reactions. And so generally it usually inhibits the reaction moving forward. Um and so that's one way enzymes are regulated and then a final way is actually threw phosphor relation. And so phosphor relation occurs when there's an addition of a phosphate group. And this actually has the ability to inhibit or activate enzyme activity. So if we're going to look at just an example of regulation, we see here that there is an enzyme here and a substrate here and you can see that the activated the active site is right here. And so normally the enzyme is going to bind the substrate and then release products. But there can be all of this um regulation that occurs um in this process. So for instance this product here, this red one can come back and bind to the enzyme and block substrate binding. So that would be feedback inhibition. There can be some type of binding side of something else. Some co factor here which block substrate binding. So that would be Alice Terek regulation. And then you can have phosphor relation which is gonna be a little difficult to draw. So I'll just put here false phosphate group, there's a S A. P. Because you didn't see but and that foss relation can actually stimulate or inhibit the enzyme substrate binding and reaction that occurs. So now let's move on

Which of the following is not one of the three major conditions of enzymes?

• A. Enzymes cannot be consumed by a reaction
• B. Enzymes cannot be changed by a reaction
• C. Enzymes do not effect the rate of the reaction, only the free energy
• D. Enzymes do not effect the free energy of the reaction, only the reaction rate