Biochemistry Enzymes I

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

Today we are going to start our discussion of enzymes.0004

I cannot even begin to overemphasize the importance of enzymes.0009

I mean enzymes are biochemistry, so a really, really good understanding of enzymes, how they work, some of the quantitative aspects, things like that- absolutely essential to everything that goes on in biology.0016

Let's just jump right on in and spend a fair amount of time with enzymes.0032

OK, now, having said that, you see, what is going to happen is we are going to introduce enzymes, talk a little bit about the other general properties, a little bit about how they work.0037

We are going to get some examples of some enzyme reactions, and we are going to talk a little bit about the quantitative aspects, some of the kinetic aspects, things like that; but this whole idea...we are not going to get too much into it.0050

We do not want to say too much at this point.0064

This is one of those topics where you do run the risk of saying too much that is unnecessary.0068

We just want to give you a good, solid grounding in enzymes, and once we actually start to talk about the metabolic pathways - glycolysis, fatty acid breakdown, amino acid breakdown, citric acid cycle, things like that - we will be revisiting the enzymes.0075

A lot of what we ultimately want to learn about enzymes will come from all of the exposure that we get when we deal with the enzymes in the individual pathways.0091

Having said that, let's see what we can do.0103

Enzymes are, again, they are everything; enzymes are proteins- very, very large proteins.0107

Enzymes are proteins.0116

The only exception are the catalytic RNAs, which we will end up discussing in a subsequent class- molecular biology.0124

OK, now, some enzymes function as is.0148

That is without additional chemical groups to help them along, to make them work.0161

Others require something called a cofactor; excuse me.0186

Let's get comfortable here.0193

Others require something called a cofactor.0197

A cofactor can be one of several things; it can be an inorganic ion, maybe like iron(2+) or maybe magnesium(2+) or manganese(2+) etc., zinc, cobalt, something like that.0212

It can also be an organic molecule, an organic or occasionally a metallo-organic molecule called a - we usually call it a coenzyme because it is an actual molecule, it is not just 1 single metal ion - coenzyme.0233

Now, some enzymes require both ions and coenzymes.0263

OK, now, when an ion or coen...you know what, let's just call it a cofactor.0278

OK, all these names that we are throwing around, I know it can tend to be a little bit confusing.0294

The names, themselves, are not altogether that important except for the occasional quizzes that you take.0299

What is important, again, is the chemistry just understanding what the function of these things is.0305

When a cofactor, either ion or coenzyme, is tightly bound or covalently attached to the enzyme, we usually call it prosthetic group.0310

OK, now, I see.0350

The entire - let's try this again - enzyme plus cofactor is called a holoenzymes.0358

Again, just a bunch of nomenclature that is not altogether that important.0384

When you have the enzyme plus its cofactor, the thing that is all ready to go, it is called a holoenzyme.0388

The enzyme part alone without its cofactor, it is called an apoenzyme or sometimes an apoprotein.0395

OK, now, most coenzymes, they derive from vitamins.0423

Some examples would be...well, let's actually take a look at some.0444

We have this one right here; this, first one, this is riboflavin.0450

OK, this is one of the vitamins that we need to ingest in order for bodies to function properly, and the enzyme that is derived from riboflavin, this part right here, you notice, is right here.0454

OK, this looks like flavin adenine dinucleotide.0470

That is the coenzyme formed with the riboflavin.0480

We ingest the riboflavin; the body converts it to FAD.0484

This is the coenzyme; this is the active part that works in concert with the particular enzyme that it is attached to.0487

Another vitamin would be pyridoxine, and pyridoxine is the vitamin that we ingest.0495

The coenzyme, itself, is something called PLP.0502

It is called pyridoxal phosphate.0506

And again, we will be running into these; we will be getting into more details later on.0510

When we speak about specific enzymes, we are going to talk about these cofactors, what they do, how they do it.0515

We are going to get into detailed mechanisms and things like that.0520

Right now, I just wanted you to see some examples.0523

Let's see a couple of other examples; we have carbonic anhydrase.0528

I just wanted you to see actually, in this case, a ribbon diagram of the actual enzyme itself, and I do not know if you can see it here, that little zinc ion.0534

That is a prosthetic group; it is a cofactor for carbonic anhydrase, happens to just be a metallic ion, and this, of course, is a close up view.0546

This is zinc ion; you see it is coordinated to a histidine, to another histidine, to another histidine, and it is also coordinated to a hydroxide ion.0555

Within the enzyme, within the folds of the enzyme itself, there is this what you might call a partial active site.0565

This particular zinc ion is coordinated to 3 histidine residues and a hydroxide- that is it, nothing particularly strange going on here.0572

OK, now, I will just write "close up" here. "close up of the carbonic anhydrase".0582

OK, now, enzymes are classified according to the reactions they catalyze.0595

That makes sense.0612

Excuse me; OK, an international system has been agreed upon, but beware that many - if not most - common names are still in regular use.0620

Most of the time, we will be referring to things with their common names.0671

We will be calling them, for example, alcohol dehydrogenase.0675

We will not be calling it alcohol:NAD oxidoreductase.0679

That is going to be the formal name; for the most part, we are going to be using common names.0683

Now, clearly, a lot of the enzymes that were discovered early on before the international agreement of systematization, those common names, I mean they are just so entrenched in the literature.0688

They are just so entrenched in our daily use that they are never going to go anywhere.0700

So, they have formal names, but it is the common names that you are going to see them as.0705

The more recently discovered enzymes, those are the ones where you are going to actually use the systematic name instead of the common name because no common name exists for them.0709

OK, common names are still in regular use.0719

Let's see here; let's go ahead and move on to this.0724

Each new enzyme or each enzyme is given a number.0729

It is called the enzyme commission number and a systematic name.0741

It is given both a number and a name.0759

Now, the easy number has 4 digits.0763

The first number specifies the class of the enzyme/enzyme classes.0774

There are 6 classes; an example would be...and then, of course, you have your subclasses underneath that.0783

Example would be, let's just take the most basic one, EC 1.1.1.1.0792

Class 1: these are enzymes, and they are called oxidoreductases.0800

They are involved in electron transfer, oxidation-reduction.0810

They are involved in electron transfer facilitating the transfer of electrons from 1 molecule to another molecule, from 1 substrate to another substrate- that is it.0815

That first number, that is what that specifies.0834

Let's go ahead and look at a systematic name, in this particular case the EC 1111.0838

Its systematic name is going to be, as we said, alcohol:NAD⁺ oxidoreductase.0844

Oxidoreductase tells me there is a transfer of electrons.0865

The electrons are transferred from the alcohol.0869

There is a colon; they are transferred to NAD⁺.0873

That is what this means, from here to here- oxidoreductase.0877

The common name is alcohol dehydrogenase.0881

This is the enzyme that is responsible for metabolizing the alcohol that you drink, so it does not poison you.0895

OK, now, we have the 1111.0903

This tells me its class, an oxidoreductase.0909

OK, this one right here, it tells me that it is acting on an alcohol group, a COH group.0916

This one right here, the third number, it tells me that the electron acceptor is either NAD⁺ or NADP⁺, and this one right here, it is specifically NAD⁺.0932

If you had 1.1.1.2, that would be alcohol dehydrogenase NADP⁺-that is it.0950

Ultimately, what is important...I mean there are all the numbers; I mean you can look all of these up.0960

It is not a problem; you do not have to know any of these.0964

It is really important to know that the first one is what specifies the class, and your teacher will probably ask you to know at least that, the 6 classes of say, you have oxidoreductase.0966

You have liaise; you have ligase- things like that.0978

That is all that is going on here; the particular reaction that this enzyme catalyzes is the following.0982

Let's see; it takes a primary alcohol.0991

The enzyme binds 2 things; it binds the alcohol, and it binds the NAD⁺.0999

It brings them in close proximity, and it allows the transfer of electrons and hydrogen from the alcohol to the NADH - I am sorry - to the NAD⁺ to produce the following.1004

What the enzyme ends up releasing...you end up turning the alcohol into an aldehyde, and then, you have also created this thing- that is it.1017

Basically, all you have done is...what this enzyme has done is it rips away that hydrogen.1031

That hydrogen, it turns this single--bonded oxygen into a carbonyl, and then, it releases something called NADH and H⁺ into solution.1035

OK, alcohol dehydrogenase, now, of course, you probably already know this.1045

If not, ACE is the standard ending for an enzyme.1050

Alcohol dehydrogenase, pyruvate dehydrogenase, something isomerase, hexokinase, ACE, ACE, ACE, ACE, that is the enzyme.1066

In this particular case, the cofactor, this enzyme does have a cofactor.1078

The cofactor happens to be that molecule, and in this particular case, it is a cofactor that is not tightly bound to the alcohol dehydrogenase.1082

It is actually free to float around, so we do not call it a prosthetic group; but we do call it coenzyme.1094

OK, now enzymes are catalysts.1102

OK, let's go to blue here.1107

Enzymes are catalysts- that is it.1111

They are just catalysts; all they do is they speed up a reaction.1119

They speed up a reaction, but they do not affect the equilibrium position of a reaction.1127

That is very important; they allow a system to come to equilibrium faster.1141

They just do not change the equilibrium position.1148

Again, there are many reactions that cannot take place.1153

For example, if I put oxygen and hydrogen in a container, well, thermodynamically, that reaction want to happen.1156

It is very thermodynamically favorable; the problem is kinetically, it is not, because it has a very high activation energy.1169

It takes a lot for it to go over that initial hump in order to become water.1175