Background of Enzymatic Reactions – Enzyme Catalysis

by Kevin Ahern, PhD

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    00:02 The ability of enzymes to speed up reaction is actually mind-boggling.

    00:06 The subject of this presentation is to talk about the ways in which we study the kinetics or the ways that enzymes speed up reactions.

    00:12 In this presentation, I will give a little bit of background about the process of catalysis, talk about the flexibility of enzymes and how that enables them to do what they do.

    00:21 Talk about activation energy which is another consideration for enzymatic catalysis.

    00:26 I will talk about the mechanism of a specific reaction for an enzyme called a serine protease.

    00:30 And then I will give the kinetic considerations that we have during that analytical process.

    00:34 And finally talk about the overall overview, of using what are called Michaelis Menten Kinetics.

    00:41 Now, when we think about enzymatic reactions there is actually a series of different ways that molecules can react in interacting with an enzyme.

    00:49 We can have for example a reaction that is a single substrate reaction and a single product, A is converted into B.

    00:56 We can have a reaction in which a single substrate is converted into multiple products so for example if I took A and I split it into two molecules I would make B and C.

    01:06 I could take multiple substrates and make single products which is the opposite which would mean I will be putting two things together to make a third.

    01:12 That third being C, as shown here.

    01:15 And last I could have multiple substrates and multiple products in which A and B are converted into two different things, C and D.

    01:24 Now enzymes are, as I said, magical in their ability to catalyze reactions and they are so much faster than a chemical catalyst that it's important to think about the ways in which they are able to accomplish what they accomplish. And so this illustration of an enzymatic reaction goes step by step into some of the considerations for the ways that enzymes accomplish what they do.

    01:46 Chemical catalysts, I want you to remember, are things that are very fixed.

    01:50 A platinum catalyst for example, has no breathing. It has no movement to it, it simply is a surface on which something can happen.

    01:58 And enzymes are fundamentally different from that.

    02:01 In this illustration we see an enzyme shown in green and we see the active site of the enzyme, that is the place where the reaction is catalyzed, shown in light green.

    02:11 Now the enzyme in this reaction I am showing you is a reaction of multiple substrates, multiple products. So we will have A and B, as you can see here, that will be converted into two other molecules.

    02:22 We start with the enzyme unloaded.

    02:24 No products on the enzyme and of course no substrates.

    02:29 The substrates are the molecules that bind to the enzyme and they will bind so as to position be positioned at the place where the reaction occurs, the active side.

    02:41 We can see here there are substrates have started to bind to the enzyme.

    02:43 We see the enzyme again in green. We see substrate A that has bound at the top portion of the enzyme and substrate B that has bound the bottom.

    02:52 Now the interaction of the substrates with the enzymes will actually cause the enzyme to start to change.

    02:58 This is the Koshland Induced Fit model of the enzymes.

    03:01 And the Koshland Induced Fit it says that not only does the enzyme change the substrates into products, but transiently during the catalytic process, the substrates change the enzyme. And as we will see that's essential for this reaction to occur.

    03:19 So the substrate binding has happened.

    03:21 We have formed at this point what we call the ES Complex, enzyme substrate complex.

    03:28 Now in the next step you see right here, what has happened is we see the reaction going on.

    03:32 And the enzyme has actually changed its shape slightly from the initial binding to bring A and B into closer proximity.

    03:42 Well, of course, for a chemical reaction closeness is an absolutely essential requirement for the reaction to occur. So the slight change in the shape of the enzyme has converted A and B from being apart to being slightly closer together.

    03:56 These changes of shape can be very large on enzyme terms, or it can be very very startle, but nonetheless the change happens with every reaction.

    04:06 Now the reaction is occurring again, as we can see, because they have been brought into close proximity.

    04:11 At this point as the reaction is going on we have something called the ES* complex.

    04:18 And we can just simply think about this as the place where the reaction is now able to occur.

    04:23 As we look at this reaction closer, we see during the reaction a part of A, has moved from A to B.

    04:29 And this has been a transfer of a part of one substrate to another.

    04:33 A is no longer A and B is no longer B, at this point.

    04:38 We have made what we call the EP complex.

    04:42 We have made the products but we haven't released the products yet.

    04:44 So A has become C and B has become D.

    04:49 Now the products are still contained within the enzyme.

    04:53 But the products are different than A and B were.

    04:56 So just as A and B cause the enzyme to change shape so too will C and D cause the enzyme to change shape.

    05:05 And you can probably see where this is headed.

    05:08 The enzyme is going to back to where it was.

    05:10 And that's what happens right here.

    05:12 We see in this reaction now that the enzyme has been changed and it's changed back to its initial state.

    05:18 In the initial state, we can think of its finger being open like my hand is open and C and D are ready to go flying away.

    05:26 The enzyme now being back in its original state is able to go and bind more substrate.

    05:32 It's ready for the next process. Now if we think about this, our definition of a catalyst that everybody learns in freshmen chemistry, is a molecule or an entity that catalyzes a reaction but it's unchanged in the process.

    05:45 That's a principle that is hammered into every freshmen chemistry student.

    05:50 Now we see that enzymes are actually slightly violating that principle.

    05:55 They are being changed transiently during the process but they ended up in the end in the same way they started.

    06:00 So overall they are not violating it but they cheat a bit.

    06:03 We see in this slide then a summary of all the reactions or the steps and the process that you have seen before.

    06:08 And I don't wanna go through those again but I do wanna make the point that you notice that the arrows are going both ways.

    06:15 And that means that this reaction and every step in this reaction is reversible.

    06:20 Now reversibility of a reaction is a very important thing to keep in mind when we are talking about metabolic processes. For that matter even non-metabolic processes. But especially for metabolic processes; because, we have to think that is "What are the conditions that would make something go backwards?" We have seen how enzymes flexibility enables enzymes to accomplish what they accomplish.

    About the Lecture

    The lecture Background of Enzymatic Reactions – Enzyme Catalysis by Kevin Ahern, PhD is from the course Enzymes and Enzyme Kinetics.

    Included Quiz Questions

    1. The active site of an enzyme
    2. The allosteric site of an enzyme
    3. The site near the hydrophobic regions
    4. The site near the hydrophilic regions
    5. The location rich in sulfur-containing amino acids
    1. During an enzymatic reaction, the enzyme's shape gets changed permanently, hence the cell needs to produce an enzyme at faster speeds to keep it alive
    2. During an enzymatic reaction, the enzyme brings changes in the substrate molecule or molecules to form product or products
    3. An enzyme speeds up a biochemical reaction by lowering the activation energy
    4. At the end of the enzymatic reaction, the enzyme regains its original shape by releasing the product/products from its surface
    5. According to the induced fit model of enzyme action, the binding of substrate(s) also causes transient changes in the shape of the enzyme

    Author of lecture Background of Enzymatic Reactions – Enzyme Catalysis

     Kevin Ahern, PhD

    Kevin Ahern, PhD

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