Catalysis Considerations – Enzyme Classification

by Kevin Ahern, PhD

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    00:00 I have described so far how enzymes are flexible around the active site and how that flexibility at the active site facilitates the catalytic process that happens.

    00:09 But enzymes are flexible all over.

    00:11 And that flexibility all around the enzyme gives the enzyme some interesting properties as regards its activity.

    00:17 Now we can see here on the left an enzyme that is getting ready to bind a substrate, as we have seen before.

    00:22 And on the right we see the enzyme after having bound to substrate has adapted itself to the shape of the enzyme. This was the induced fit that I have been referring to.

    00:31 This induced fit makes a lot of sense for the active site, as I said.

    00:36 But the rest of the enzyme is also affected by these interactions.

    00:41 Now this has actually manifested itself in the plot that is shown on this figure right here.

    00:45 On this plot we can see the V versus S binding for an enzyme that's allosteric.

    00:51 Now I remind you that allosteric means that the enzyme is interacting with a small molecule and having its activity affected.

    00:58 In this case, the small molecule that's interacting with its affecting it, is actually its substrate.

    01:05 So this happens with multisubunit enzymes. Now what I am getting right to describe very much parallels what I talked about with hemoglobin's binding of oxygen in another of the presentations.

    01:16 When hemoglobin binds to oxygen, you may recall that the binding changed as the oxygen concentration increased.

    01:24 As the oxygen concentration increased, hemoglobin's affinity for oxygen went from low to high and that was important for the action of hemoglobin.

    01:33 The same thing can happen with an enzyme whose affinity can change depending in terms of binding of the substrate that affects it allosterically.

    01:44 Now multisubunit enzymes have this happen; because, one part of the enzymes binds its substrate and affects the binding of the substrate on other parts of the enzyme.

    01:54 Now this change that I have described to you results in a change in the overall physical shape of the enzyme, not just the catalytic site.

    02:02 Now this overall change of the enzyme is given a couple of names. First we talk about a state that's relaxed.

    02:08 It's called the R-state. The relaxed state of an enzyme is the state that really the enzyme is open to binding substrate and is very able to bind substrate.

    02:19 The relaxed state of an enzyme corresponds to a more active state of the enzyme.

    02:24 By contrast the T-state of an enzyme, where T stands for tight, is the enzyme is tensed; it is tight; it is not flexible, and it is not able to bind substrate as well.

    02:36 On this plot for example, we can see at the low substrate concentrations the enzyme is in the T-state.

    02:42 It's not binding substrate very well. But once the substrate concentration gets high enough the enzyme flips.

    02:49 And then it is able to bind substrate better. So its velocity change actually flips. We don't see the hyperbolic plot that we saw before.

    02:57 Well there is a couple of ways people have studied and tried to explain this phenomenon going on.

    03:02 So I wanna spend a little time going through and explaining ways that we interpret this change.

    03:08 They are called the concerted model and the sequential model.

    03:11 So the first of these, I will talk about here, is the concerted model.

    03:15 The concerted model is conceptually a little hard to get one's head around.

    03:19 We see the enzyme in this model, existing in two states, and for the purpose of this illustration we assume that this enzyme has 4 subunits.

    03:28 Enzymes can have many many subunits up to at least a dozen subunits in some cases. But for this illustration it has 4.

    03:36 In the T-state we have the enzyme shown in the squares on the top and the T-state where we call is the least favored of the states.

    03:45 The circles below refer to the enzyme in the R-state where the enzyme is relaxed and more able and more likely to bind substrate.

    03:52 What the concerted model says is that the flipping between the T-state and the R-state happens completely as shown.

    04:02 There is we go from top to the bottom, and there is no intermediate.

    04:06 And what this model says is something that seems counter-intuitive; because, this model says that the flipping from T to R is not caused by the binding of the substrate.

    04:19 But rather the R-state or the T-state is favored by whatever the state it happens to be it will not bind substrate.

    04:27 So if I have an enzyme that flips into the R-state and it binds substrate, the substrate will lock it in the R-state.

    04:35 So that it will tend to stay in the R-state and consequently be more reactive.

    04:41 If the enzyme binds it in the T-state, it's like to stay in the T-state.

    04:45 Once the enzyme is in the R-state it's gonna stay there and keep producing and since the R-state is producing more and more of the product, anything that favors or locks in the R-state is going to favor the reaction more.

    04:58 So the concerted model is an all or none. But the locking into one state or another is central to what it does.

    05:08 You can see here that there is equilibrium between the two, and the equilibrium shifts as we get more of the substrate binding or locking it into a given state.

    05:18 As we go further to the right, the R-state is favored; because, there is more enzymes now in that R-state, and more enzymes means more product.

    05:28 The R-state can flip, as I said, independently of each other but the bound state is favoring in this case the R-state.

    05:38 Now the other model that we called the sequential model is very much like what we saw when I described the flipping or the changing of hemoglobin.

    05:47 We also refer the states, R-state and T-state, in hemoglobin but we more commonly used this as regards enzymes.

    05:55 Now in this model what happen is we have an enzyme that starts out in the T-state is shown in the 4 squares on the left.

    06:04 The binding of the first substrate causes one of the subunits of the enzyme to flip.

    06:09 And that's shown in blue in the second model from the left.

    06:13 When that flipping occurs, the blue interacts with the other two units of the enzyme and we can see that there is sort of a purple that happens and a rounding of those two.

    06:23 That's indicating that the blue circle which is in the R-state, is affecting the two units around it and causing them to start to flip into the R-state.

    06:35 Well the starting to flip favors the binding in more substrate and so we can see sequentially then that the blues are becoming more dominant as we get further to the right.

    06:45 The binding of the substrate is a critical thing for this enzyme; because, the binding of the substrate in this model says it's the cause of the flip.

    06:55 Now casually when we talk about it, we frequently say "Well this causes the enzyme to do this or that", and when we say that, we sort of loosen the language that we use.

    07:03 In this case the cause is physically causing the flipping to occur.

    07:08 In the concerted model the cause is not a direct but it's an indirect as a result of the locking that I described.

    07:14 So the distinguishing difference between the concerted model and the sequential model is that cause that I mentioned.

    07:21 Causing the flipping is a physical causing.

    07:25 The two models that I have just described, the concerted model and the sequential model are just that. They are just models in terms of explaining how the T-state and the R-state come to be within enzymes.

    07:36 It's very likely that no enzyme actually uses exclusively one of the other and there is a lot of evidence that enzymes may use a sort of a hybrid of these two models.

    About the Lecture

    The lecture Catalysis Considerations – Enzyme Classification by Kevin Ahern, PhD is from the course Enzymes and Enzyme Kinetics.

    Included Quiz Questions

    1. R/T flipping occurs independently of binding of substrate
    2. The binding of the substrate causes the enzyme to flip T/R state
    3. The R-state is favored
    4. The binding of allosteric effector(s) cause the enzyme to flip states
    1. The binding of substrate molecules causes the enzyme to flip T/R states
    2. The flipping occurs independently of binding of substrate
    3. The R-state is favored
    4. The binding of product(s) cause the enzyme to flip states
    1. Conformational changes in the enzyme by the binding of effector molecules
    2. Amino acid sequence changes in the enzyme by the binding of effector molecules
    3. Formation of new phosphodiester bonds in the enzyme by the binding of effector molecules
    4. Formation of new peptide bonds in the enzyme by the binding of effector molecules
    5. Peptide bond breakage in the enzyme by the binding of effector molecules
    1. According to the concerted model, the binding of substrates favors the equilibrium towards the T state of the enzyme
    2. According to concerted model, an enzyme exists in two states: R-state and T-state
    3. The concerted model and sequential model explain the allosteric regulation of enzymes
    4. The sequential model states that binding of the substrate to the enzyme subunit facilitates the change of T form to R form
    5. In the concerted model, the conformations of all the subunits change simultaneously

    Author of lecture Catalysis Considerations – Enzyme Classification

     Kevin Ahern, PhD

    Kevin Ahern, PhD

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    Clear, concise enough and interestingly explained
    By Benjamin K. on 25. October 2017 for Catalysis Considerations – Enzyme Classification

    It is very clearly and enthusiastically explained. You make Biochem easy to understand.