Biochemistry Enzymes II

Hello and welcome back to Educator.com; welcome back to Biochemistry.0000

Today, we are going to continue our discussion of enzymes, and we are going to start off by talking a little bit more about the enzyme substrate complex and how it actually facilitates, how it does what it does, how it contributes to an enzyme doing what it does.0004

Let's just go ahead and get started; we mentioned that you have an enzyme that comes in contact with its particular substrate, and it forms something called the enzyme substrate complex.0018

OK, this enzyme substrate complex is absolutely key to understanding why an enzyme does what it does and how it does what it does.0032

Now, catalysts, we know, they bring about their effects by binding well...catalysts, let's not use the word catalyst.0042

Let's go ahead and just call them enzymes.0066

OK, enzymes bring about their effects - let's start again, shall we, alright - by binding well not to the substrate as is but fitting well or binding well with the transition state.0072

In other words, let me talk about this a little bit.0116

When an enzyme...yes, I mean an enzyme is going to recognize its particular substrate.0120

That is part of the specificity of an enzyme; an enzyme is not just random.0125

It has a particular substrate that it works with and only that substrate, maybe another one, but it is very, very specific for the molecule that it wants to bind.0129

When it binds that molecule, it is not just going to bind the substrate as is.0138

It recognizes the substrate, and then, what happens is, it plays around.0145

It moves a little bit; it twists the substrate around a little bit.0152

The best binding interactions, the optimal binding that takes place between a substrate and an enzyme, in other words, when it is at its most optimal enzyme substrate complex state, it is when the enzyme has actually bound well to the transition state of the substrate.0158

In other words, the substrate, in order for it to actually go through and go from substrate to product, it has to pass through some transition state.0178

Well, the enzyme does what it does not by binding well to the substrate, but the best binding happens because it binds well to the transition state; and we will show what happens energetically in just a minute.0186

Enzymes bring about their effects by binding well not to the substrate as is, but by fitting well, binding well, with the transition state.0199

That is what is important; now, this is actually best explained diagrammatically.0207

I am going to put up an image in just a moment, and then, we will go through that.0215

Let's say that the particular reaction we want to talk about, let's say that our particular reaction is the breaking of a stick.0221

OK, I have this stick, no catalyst, no anything.0247

In order for me to break it, I have to take that stick, and I have to invest a little bit of energy and actually bend that stick.0253

I have to take it to this point, right?0259

I have to take it to a point where it is just about to break and at that point, a little extra push, and you end up getting 2 pieces, right?0261

It breaks right there; now, what a catalyst does is the following.0270

I have to invest a certain amount of energy before boom.0276

That is this; here is the stick.0280

Here is the broken stick; this point right here, the transition state, that is this point right here.0285

I have to put in a bunch of energy in order to get it to that point, and then, after that, boom.0290

I go over, and I end up with my 2 pieces.0296

Now, let's take a look at a diagram what a catalyst actually does.0300

What a catalyst does is it recognizes that stick, and then, what it does is it fiddles with that stick.0306

It twists it; it changes it.0312

What the catalyst does, it actually bends it; the catalyst, the interactions that the stick has with the amino acid residues in the active site of the enzyme, every time it does that, it actually takes it to the transition state for me.0315

That is what a catalyst does.0330

Here is the substrate energy; here is the product energy.0334

Without a catalyst, I have to go up to here, but because the catalyst, what it does, the enzyme, it takes it to the transition state for me.0337

It takes it to the bent position; it is in this position that all of the interactions are really, really tight and strong between the enzyme and the substrate.0348

At that point, it has already raised the energy level up to here, here, here, here, here.0358

Now, the only thing that the reaction has to do is just go over that hump.0365

Now, it has less energy that the actual reaction has to invest in order to go over that hump.0369

That is how an enzyme, a catalyst lowers the activation energy.0375

It is not so much of lowering of the activation energy; that is true.0381

I mean the transition state is a transition state; in order for the stick to go from single stick to a broken stick to pieces, it has to pass through this transition state.0384

Instead of us putting in the energy to actually bend it, the interactions between the amino acids, the weak interactions, the hydrogen bonding, the hydrophobic interactions, the ionic dipole interactions, all of those things, they end up stabilizing the transition state enzyme complex.0395

And now, it is already at its transition state.0416

Now, because it is here, all it has to do is - poop - go over and form product.0420

That is what is happening; the energy that comes from all of the small interactions of binding, those actually lower the activation energy.0425

Really, what you are doing is you are taking this, and you are bringing it closer to this and that.0435

A substrate energy level is not going to change; a substrate is at a certain energy level.0443

The products are at a certain energy level; that does not change.0447

What does change is the amount of energy that we have to invest to make it go over that transition state.0450

The enzyme is there to do most of the work for us; that is why reaction rates proceed faster.0458

In the process of forming this enzyme substrate complex, which is really an enzyme transition state complex because the optimal binding between the 2 happens when the substrate is in its transition from here.0464

It is just ready to go over; now, all the molecules have more than enough energy to go over.0478

All of them will; 100% of them will, not just 3% or 5% or 10%.0483

That is where this comes from; OK, this difference in energy...let me see.0487

Actually, let's do another diagram here; I am going to do another energy diagram.0499

We have something like this; we have our substrate and our product.0508

This is the uncatalyzed reaction- something like that.0514

Here, this is the enzyme substrate complex.0518

This is substrate; this is enzyme substrate.0524

This other one does not matter; because it is in this form, because the substrate is already in its transition state when it is bound to the enzyme, now, this transition state is here.0527

Now, instead of all of this energy, all I have to do is go - poop - a little bit that way, just a little bit of energy in order to get from here all that way to product.0539

That is what is happening; the transition state is easier to reach.0549

The energy for that instead of us putting it in to make it go over this hump, the enzyme with its weak interactions - hydrogen bonding, hydrophobic interactions, ionic interactions - that it has with the substrate, bending it and twisting it and already taking it into the transition state, now, we do not have to work as hard to get over that transition state.0554

All it does is it brings the transition state within reach of us.0581

That is all that is doing; that is how enzyme works.0585

This difference in energy, in other words, the difference in energy from here, now, here, this difference comes from weak interactions between substrate and functional groups on the amino acid residues of the active site.0592

This is called binding energy.0651

OK, now, these weak interactions, I can do a little bit better than that.0662

Actually, it is hydrogen bonding, bonding hydrophobic interactions, ionic interactions, account for an enzyme's specificity.0687

When an enzyme binds to its substrate, every time some weak interaction takes place, it actually acts as a support for the substrate.0734

Every time there is some hydrogen bonding interaction, every time there is some ionic interaction, some hydrophobic interaction, that energy is released as free energy, and what that does is that brings the transition state, the amount of energy that we need to invest.0745

In order to get to the transitions state, it makes it a lot smaller.0759

That is what it is doing.0763

The best way to think about it is let's say you are standing on a stair step or something.0767

You know that if you lean over too far, you are just going to fall over.0773

Gravity is going to pull you; it is just going to pull you down.0777

Well, if you were to lean over a little bit, let's say one of your friends grabs your hand, now, you can, sort of, release yourself.0781

Your friend is supporting you; he has you.0786

Let's say you lean over a little further; now, another friend comes and basically, let's say, grabs your other hand and maybe another friend is holding you from the back.0788

At this point, you can, sort of, let your entire weight fall on your friends.0796

Those friends are the weak interactions; they are supporting the substrate.0801

You are the substrate; they are supporting you.0805

You do not have to expend any energy in order not to fall over; now, they are the ones that are actually taking the energy and supporting you.0809

That is what an enzyme does; an enzyme supports a substrate so that the substrate does not have to support itself, and it takes it to the transitions state.0816

Now, it is very, very simple; now, your friends can just, sort of, take you, lean you down and put you down on the ground, if that is the reaction that needs to take place, and it happens in a very controlled manner as opposed to just - boom - falling over.0825

That is what an enzyme does; well, these interactions, they not only account for the lowering of the transitions state energy, the activation energy.0839

They also account for the specificity of an enzyme.0847

In other words, an enzyme is going to reach out for the substrate that has the most affinity for its particular active site, and the more tightly the substrate binds, the more weak interactions, the more tightly it binds, now, it is more specific.0851

It is not just any random molecule that can wander into the active site of an enzyme, but they do.0870

I mean, molecules wander into active site of enzymes all the time, but the enzyme is not going to interact with them because there is no way that the enzyme is going to twist and turn to make that particular substrate, whatever it happens to be, bound tightly; but there is usually 1 substrate, the substrate for that enzyme that binds beautifully, that binds tightly.0876

It is the substrate that the enzyme is designed for, that it evolved for.0896

That is what makes enzymes so amazing.0900

The evolved for specific substrates; it is absolutely fantastic.0904

These weak interactions, they also account for an enzyme's specificity.0909

OK, the key point, the point that we actually want to makes is the following.0914

I will do this in red- the key point.0923

Optimal interactions between substrate and enzyme happen when the substrate is in its transition state.0929

The closer the substrate gets to its normal transition state, it is at that point that it binds very, very, very tightly with the enzyme, and it is at that point that the reaction actually takes place because it is already at the transition state.0969

There is no actual energy; it says "boom"- that is it.0983

It happens; OK, now, let's go back to black.0985

An enzyme is much, much larger than its substrate.0997

OK, now, although substrate molecules tend to be flexible, although substrates can be flexible because of the sheer size of enzymes and the fact that they are made up of amino acids, enzymes enjoy greater flexibility.1010

This is very convenient.1045

Now, since optimal enzyme substrate interactions occur not between enzyme and substrate as is, but between enzyme and transition state for the substrate, the enzyme will often - always actually - undergo changes in conformation to accommodate this.1050

An enzyme is very flexible; it has a certain active site.1137

It recognizes the substrate, starts to bind with it.1142