Biochemistry Citric Acid Cycle II

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

In the last lesson, we talked about how the pyruvate that was formed in glycolysis is converted to acetyl-CoA in this amazing enzyme called the pyruvate dehydrogenase complex.0004

Today, we are actually going to start with the reactions of the citric acid cycle, how this acetyl-CoA enters the cycle and runs through it.0016

Let’s just jump right on in.0025

This first thing that I have here is the cycle itself but just the names of the molecules that take place.0029

In the next page, I am actually going to draw out - or it is is already drawn out - the structures themselves.0037

I wanted us to get, sort of, a big picture view of this, talk about what happens, talk about the number of reactions, what goes in, what goes out, just to get a big picture idea of what the citric acid cycle is.0044

And then, we will take a look at the structures, correlate them with the individual reactions- the 1 through 8.0055

And then, we will look at the individual reactions and their mechanisms.0061

A lot of information, so we will try to cover as much as possible.0065

And again, I encourage you to look at your books.0069

One of the things that I really, really want to stress in this particular course is that the biochemistry books are really fantastic.0073

They are an incredible resource with lots of information and lots of beautiful illustrations, and I think it is nice to be able to see it like this and then, look at the illustrations in the book and to see the correlation.0080

It, sort of, locks it in your mind; now, again, there is a difference between looking at something passively and being able to write it out actively.0090

This is something that you want to be able to write out yourself, starting with the oxaloacetate going to the citrate going to the isocitrate and so on all the way around the cycle.0099

It is very, very important to be able to produce this actively instead of just looking at it passively.0110

OK, so let’s see what is going on here.0115

Acetyl-CoA, that is the molecule that we actually formed from the pyruvate.0119

That actually enters the cycle, and what it does is it condenses with oxaloacetate.0125

In some sense, oxaloacetate, you could say, is the beginning and the end of the cycle.0131

That is where things, sort of, start; these 2 condense.0135

Water comes in; coenzyme A leaves, and you end up forming this molecule called citrate, thus, the name citric acid cycle.0139

This reaction - notice - is an arrow in one direction.0150

This particular reaction is irreversible under physiological conditions; notice, these other ones are reversible.0154

Most of these reactions are reversible.0160

Reaction 1, reaction 3 and reaction 4, under physiological conditions, are irreversible; and we will talk about that a little bit later also.0164

The first step is the conversion of oxaloacetate to citrate; that is the first reaction.0171

Now, citrate loses water, and it becomes something called cis-aconitate.0177

Now, notice, I have reaction 2 and reaction 2.0183

The conversion is actually from citrate to isocitrate.0186

That is actually reaction 2, but it takes place through an intermediate called cis-aconitate.0190

In some illustrations for the citric acid cycle, you may not see this.0195

In the individual reaction, they will show you what the intermediate passes through.0199

In this particular case, I thought it would be nice to actually include it in the citric acid cycle.0203

The conversion is citrate to isocitrate, but it passes through this thing called cis-aconitate.0208

Water leaves; water comes in again, and you get the isocitrate.0214

OK, now, here is your first oxidative step and decarboxylation step.0219

In this case, NAD⁺ oxidizes the isocitrate to alpha-ketoglutarate, and not only does it oxidize it, it also decarboxylates it.0224

It takes away one of the carbon dioxides; that is why you have a CO₂ leaving and you have an NADH leaving.0234

The things that I have put squares around, the CO₂ here, the NADH, CO₂, FADH₂, here and here, these are the important things that you want to concentrate on in the citric acid cycle.0239

These are the things that end up leaving and these are for example...well, we will talk about what they do in just a second.0250

Reaction number 3: isocitrate to alpha-ketoglutarate.0257

Reaction number 4: it is another decarboxylation, and it is another oxidation, and again, irreversible under physiological conditions.0260

We have alpha-ketoglutarate, which is converted to succinyl-CoA.0268

Now, the succinyl-CoA is transformed into succinate, and in this particular case, notice that GDP plus an inorganic phosphate is used to actually produce a GTP.0273

In this particular case, GDP produces the GTP, and the coenzyme A leaves.0286

ATP is also possible to produce here directly, depending on the particular isozyme that is used in this reaction.0293

It will either produce GTP directly or ATP directly.0300

But ultimately, the GTP is converted to ATP in subsequent reactions in the body.0304

OK, so now, the next reaction, the no. 6 reaction, again, we have an oxidation this time by FAD, is reduced to FADH 2, and that ends up leaving.0309

It is succinate to fumarate; water comes in, fumarate to malate, and then, the final oxidation, malate to oxaloacetate, NAD⁺ releasing NADH.0320

The NADH is here, these 3, and the FADH₂s, those are, of course, carrying the high energy electrons from the oxidation.0331

Those ends up being funneled into the electron transport chain for oxidative phosphorylation, for complete oxidation to water.0339

OK, and there you have it, oxaloacetate, and then the cycle starts all over again.0349

Acetyl-S-CoA comes in; it condenses with the oxaloacetate, and it runs through this process.0353

What you want to learn is the sequence.0359

Acetyl-CoA + oxaloacetate or you want to start...I usually start with citrate, myself: citrate, cis-aconitate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate to start the cycle all over again.0364

This is the big picture of what is happening; again, concentrate on the things that are leaving.0378

Reaction 1, reaction 3, reaction 4, irreversible under physiological conditions; the rest of them are reversible.0384

The formation of NADH, NADH, NADH, 3 times, the formation of FADH₂ once, and the release of 2 carbon dioxides, and the formation of 1 guanosine triphosphate or adenosine triphosphate.0391

OK, now, I am going to reproduce this picture on the next page, but now, I am going to deal just with the structures.0404

I would like you to see what the structures of these molecules look like.0410

I do not have all the other information, the H₂O, the CO₂.0414

I just wanted you to see what the structures look like just to get a global view, and then, of course, we will deal with the individual reactions themselves- not a problem.0417

OK, here we go, oxaloacetate, again, citrate, cis-aconitate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate and back to oxaloacetate.0424

Alright, oxaloacetate is this molecule right here, and it is going to condense with the acetyl-CoA; and what I have done is, I have written the acetyl-CoA in red.0438

OK, this is the group that is actually going to attach because coenzyme A is going to leave.0449

I have written that group in blue; now, notice, blue, blue, blue, blue, blue.0456

At this point, I did not forget to put this into blue.0460

At this point, what you end up having is a symmetrical molecule.0464

Once we get to the succinate, we are not going to be able to tell anymore which acetyl group, CH₂, COO^-, whether it is this one or whether it is this one because, now, the molecule becomes symmetric.0468

And now, you cannot tell which of these acetyl groups actually comes from the original acetyl-CoA.0480

Up to here, you can; that is another important point for this.0487

Again, we go to reaction no. 1; we form citrate, and again, this is the acetyl group that comes from the acetyl-CoA.0492

We have got this; a water leaves to form a double bond, the cis-aconitate intermediate, and we end up forming the isocitrate.0499

Really, all we have done is we have taken this OH group from this carbon, and we have moved it to this carbon.0505

We have switched the OH and the H.0511

Let me actually make one little change here.0515

Let me go ahead and write the H that way because that way, the OH and the OH switched0520

That is why it is citrate and isocitrate; OK, reaction no. 3.0525

This is one of the decarboxylations; I did write the CO₂ leaving this one because these are important.0530

These are the 2 decarboxylation steps, 2 of the oxidation steps.0534

Isocitrate becomes alpha-ketoglutarate; notice, what has happened here.0538

A CO₂ is gone, right?0541

We have taken this CO₂ away, and we have taken this OH, and we have oxidized it with the dehydrogenase.0545

We have turned it into a ketone, a carbonyl, so we have oxidized that carbon.0551

OK, we lose another CO₂; we lose this one.0555

The carbonyl stays, but we oxidized that carbon with an acetyl, I am sorry, with a coenzyme A group- the S, a further oxidation.0562

OK, now, you have the succinyl-CoA, and at this point, it is converted to succinate, which is your symmetrical molecule.0572

And from here, it goes to fumarate, double bond, and then here, OH is attached, malate; and then, of course, oxidized to oxaloacetate, and then, it starts again.0579

These are the structures; again, this is citrate.0590

This is the cis-aconitate; here is the isocitrate.0594

This is the alpha-ketoglutarate; this is the succinyl-CoA.0598

This is the succinate, fumarate, malate and oxaloacetate, and here is your acetyl-CoA.0603

Just, sort of, take a look at this, whether you want to use this particular diagram.0612

Again, I encourage you to take a look at the diagrams in your book.0617

I think it is always great to see multiple diagrams, not just one, because each one brings just something a little subtly different.0621

And there might be something in there that strikes you, that speaks to you, that maybe is more comfortable for you, that makes more sense to you.0626

Maybe there is more room, and maybe it is clearer; maybe the structures, somehow, make more sense to your particular eye.0634

It is not a problem; what is important is, again, the cycle, the sequence and what is going on where.0640

OK, let’s go ahead and say a couple of things about this - a couple of things to note - and then, we will start with the reactions themselves.0649

OK, things to note, let’s go ahead and do this in black.0658

Well, the first thing you want to note is that steps 1, 3 and 4 are irreversible under physiological conditions.0667

That is why they have those single arrows.0677

And again, when we see reactions that are irreversible, that should be a clue that these reactions tend to be points of regulation for the particular cycle.0688

It is difficult to regulate a reversible reaction because, again, it goes back and forth.0702

It is not difficult to regulate an irreversible reaction because we can control the extent to which it moves forward or does not move forward.0706

Irreversible reactions in biochemistry are points of regulation for that particular metabolic pathway.0715

OK, now, steps 3, 4 and 8 are oxidations that yield NADH, are oxidations yielding NADH, the high energy electrons that pass to the electron transport chain.0725

Now, step 6 is also an oxidation, but it yields FADH₂ - remember that flavin adenine dinucleotide - oxidation yielding FADH₂.0750

Now, step 5, can produce, as we said, ATP or GTP directly depending on the isozyme that is used.0771

You Remember isozymes, they actually catalyze the same reaction, but they do it under different circumstances, maybe a slightly different substrate, things like that; but it is the same enzyme.0792

I am sorry, it is not the same enzyme; it catalyzes the same reaction.0801

The enzymes themselves are close to being identical, but they are not quite identical.0805

They have a different primary structure, a different amino acid sequence, but they do the same thing depending on the isozyme, yes.0810

OK, and finally 2 CO₂ molecules are released.0818

We have 2 decarboxylations, and they take place in steps 3 and 4.0828