Biochemistry Glutamine & Alanine: The Urea Cycle II

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

In the previous lesson, we started discussing the urea cycle with the formation of carbamoyl phosphate.0004

In this lesson, we are going to actually do the urea cycle, so let's just jump right on in.0011

OK, I am going to go ahead and diagram the urea cycle.0017

I am not going to go ahead and use the molecular structures.0021

I am just going to go ahead and use their names, and then, I am going to discuss each reaction individually; and there is where I am going to actually show the molecular structures of the individual molecules.0025

Let's start off with our central molecule, which is the carbamoyl phosphate.0035

That one I am going to draw out, though; yes, that is fine.0039

I guess I can go ahead and do it in black; it is not a problem.0043

We have got H₂N, C, carbonyl, and then, O, P, O, O^-, O^-.0046

This is the carbamoyl phosphate; OK, I am going to go ahead and write - yes, it is fine, I guess I can do it here - ornithine.0057

You know what, I think I am going to do this in a different color; I think I am going to go ahead and do that in blue.0070

We have ornithine over here, and we have citrulline over here.0079

OK, inorganic phosphate, let me go ahead and actually draw this out.0096

Ornithine is going to be reacting with this carbamoyl phosphate, and it is actually going to end up forming citrulline.0102

This happens in the mitochondrial matrix; the urea cycle, it starts in the mitochondrial matrix, then, this citrulline passes to the cytosol, and the other reactions actually take place in the cytosol, and then, the final reaction once the urea is actually formed - ornithine is actually formed in the cytosol - ornithine is transported back into the mitochondrial matrix to start the cycle again.0109

I am going to draw a little something here.0136

It is going to be that, then, I will just draw something that looks like mitochondrial matrix, something like this.0141

This is the intermembrane space that I am coloring right now.0150

This, right here, this is the mitochondrial matrix.0158

This reaction takes place in the mitochondrial matrix.0162

This, out here, down here, this is going to be the cytosol.0168

OK, now, let's go ahead like we said, the citrulline passes out to here.0174

Now, citrulline, it reacts to form an intermediate citrullyl adenosine monophosphate, and what we have here is an ATP comes in, and an inorganic pyrophosphate actually leaves.0180

Now, the citrullyl-AMP, it reacts with...aspartate comes in.0203

Aspartate comes in, and adenosine monophosphate actually leaves.0213

Actually I will number them later, and what you end up forming is argininosuccinate.0220

Now, the argininosuccinate ends up forming arginine with the release of fumarate, and arginine ends up turning into...let me go a little bit farther on this one.0231

Arginine becomes ornithine upon the release of - well, it is going to be a hydrolysis - urea.0254

Now, I will go ahead and draw the urea structure: NH₂, NH₂.0267

It is basically the same as acetone except the CH₃s are replaced by NH₂s.0273

You know what, I think I will do that in a different color, how is that?0282

Let's go ahead and use red for that; did we get red?0286

Yes, C, O, NH₂, NH₂, this is our urea, right here, and, of course, let me go back to blue- the ornithine.0292

What happens is the following; carbamoyl phosphate condenses with ornithine in the mitochondrial matrix to produce citrulline.0307

Citrulline passes to the cytosol; citrulline reacts with adenosine triphosphate to release an inorganic pyrophosphate, passes through an intermediate called citrullyl adenosine monophosphate, and this reacts with aspartate.0317

Remember aspartate that came from the condensation with oxaloacetate in the previous lesson?0330

It condenses with aspartate; the adenosine monophosphate leaves, and what you end up with is this molecule called argininosuccinate.0337

Argininosuccinate releases a molecule of fumarate.0345

OK, and it turns into arginine.0349

Arginine undergoes hydrolysis to release the urea.0353

Now, the urea is passed into the bloodstream, carried to the kidneys, where it is excreted in the urine.0358

Upon release of the urea, you have ornithine; ornithine is transported back into the mitochondrial matrix, where it can start the cycle again and keep it going.0363

This is the urea cycle.0373

This is the urea cycle, the formation of urea in the cytosol.0378

The first step takes place in the mitochondrial matrix.0383

It is a condensation of ornithine with a carbamoyl phosphate to form citrulline.0386

OK, now, we are going to go ahead and take a look at the individual reactions.0391

I am going to go ahead and label this reaction 1.0395

I am going to call this one reaction 2; I am going to call this one reaction 2 prime.0399

This is actually one reaction; this citrullyl adenosine monophosphate is an intermediate.0404

It is the same enzyme; in other words, the same enzyme actually catalyzes this reaction.0410

This just happens to be the intermediate; this is 2 and 2 prime.0415

This is 3, and this is 4- 4 reactions in the urea cycle.0419

If you want, you can consider them 5 reactions, but not really; it is actually just 4 primary ones because you have 4 enzymes, 1, 2, 3 and 4 enzymes.0426

It is the enzymes that specify the number of reactions.0435

Let's go ahead and actually break this down and see what is happening.0440

Let's take a look at reaction 1: the ornithine to the citrulline via carbamoyl phosphate.0444

Reaction 1, I think I am going to go ahead and leave this in red.0451

I kind of like red today, so reaction no. 1.0457

This one is going to be ornithine - I am going to write the words, and then, I will go ahead and do the molecular structures, let me write it, yes, that is fine - to citrulline via carbamoyl phosphate to release a PI.0461

OK, here is what we have got; we have got H₃N+, C, C, C.0500

We have another C, and we have another NH₃⁺; and we have a COO^-.0510

This is our ornithine; OK, and we have here our carbamoyl phosphate.0518

we have H₂N; we have C, O, O, P, O, O^- and O^-.0524

That is our carbamoyl phosphate; this particular reaction, it releases an inorganic phosphate.0532

What you end up with is the citrulline, which looks like this.0542

Basically, what happens is, this is just a nucleophilic substitution reaction here.0546

Well, it is a carbonyl reaction; this, one of the hydrogens goes away.0552

You are left with a pair of electrons on this nitrogen; it actually attacks here, kicks these electrons up.0556

They come back down, kicks off the phosphate; again, phosphate- good leaving group.0561

These are all phosphorylated to prepare them for something that is coming next.0566

OK, what you are left with is the following: H₂N, C, O.0572

This comes from that; OK, and then, you are left with NH, 1, 2, 3, 3, COO^-.0580

What you have here, this is your ornithine.0597

This is your carbamoyl phosphate, and what you are left with is your citrulline.0604

This is the first reaction that takes place in the mitochondrial matrix.0613

OK, this is catalyzed by ornithine transcarbamoylase.0618

The carbamoyl group is this group right here.0635

I have basically taken this group, and I have transferred it over to this molecule over on this side.0639

This, right here, that is this part.0645

This, right here, this carbamoyl group, that is this part; I have just attached it.0650

OK, that is all I have done here; OK, now, the next step, the citrulline that is formed, it passes to the cytosol.0656

Citrulline passes to the cytosol.0666

Now, we are ready for the next reaction.0672

Reaction no. 2: we are going to take this citrulline, and we are going to form the intermediate citrullyl adenosine monophosphate.0676

OK, reaction no. 2, what we have is citrulline to the intermediate citrullyl adenosine monophosphate.0684

What you end up with is, or what you start is ATP, and you kick off an inorganic phosphate.0703

OK, let's go ahead and take a look at what is happening here.0710

Now, we have got our citrulline, which is H₂N, C, O, and then, we have an NH.0713

We have C, C, C, C, NH₃⁺ and COO^-, and we have our adenosine triphosphate.0724

I am going to write this as adenosine, ribose, O, P, O, P, O, P, O, O, O, O.0737

We have that, right there, right?0752

OK, there is an...what you end up with is the following mechanisms.0756

This comes and kicks that, kicks that.0763

What you end up with is - right - what ends up leaving is this: PPI inorganic phosphate, 2 Ps, these Os.0768

And what you are left with is the following.0782

No, wait a second; this is not right.0789

No, this is not the N that attaches; I am sorry.0794

This is the citrulline to citrullyl adenosine monophosphate.0797

OK, that is not the reaction that happens; what happens is the following.0801

What you end up with is...let me...yes, that is fine; I will go ahead and do this here, and here, it is going to be the actual carbon that is going to be attached to this thing.0807

OK, my apologies; now, what you end up is the fo...it is going to be the oxygen, itself.0820

This bond, these electrons are going to attack here, kick this off.0827

They are pushed by these electrons, a nitrogen coming down here.0833

What you are actually going to have is the oxygen attached to this phosphorus.0837

OK, what we have is the following; I am going to go ahead and keep this same arrangement here.0841

I have got H₂N, double bond C, and instead of the oxygen up, I am going to draw the oxygen down.0847

We have O, P, O^-.0858

This is going to be O, and this is going to be our ribose and adenine.0864

This part, right here, this is our adenosine monophosphate, and then, what we have is the N, the H.0870

We have the C, the C, the C, and then, we have the C, NH₃⁺; and we have COO^-.0882

OK, this is our citrullyl adenosine monophosphate.0894

OK, and again, we have a - 1, 2, 3, 4 - a positive charge there.0904

Note the double bond, its oxygen, so my apologies for earlier.0910

It is the oxygen that is actually connected to the phosphorus, so all is well.0915

Yes, that is reaction 2; now, let's go to reaction 2 prime.0922

Again, we are still in the same enzyme here; this is an intermediate.0926

Now, let's go ahead and take a look at reaction 2 prime; are we in black?0935

Yes, now, reaction 2 prime.0940

This is going to be our citrullyl-AMP, is going to be converted to the argininosuccinate.0945

It is usually 1 word; it is not capitalized.0965

I just like to separate them, and I would like to do capitalizations, but I like to write them as 1 word; it is a personal thing.0968

What comes in is the aspartate, and what leaves is the adenosine monophosphate.0976

OK, let's go ahead and draw out our molecule. our citrullyl adenosine monophosphate.0985

Slightly different way, I am just going to write AMP; I do not want to draw out the entire molecule.0993

I have got the H₂; I have the N⁺, carbon, O, and I am just going to write AMP here.0999

In the previous light it was below; now, I have just written it above.1009

Nothing is different, NH, C, C, C, C, NH₃⁺, C, O, and O^-.1013

Now, let's take a look at our aspartate molecule.1026

I am going to go ahead and do the aspartate in blue.1030

I have got C, COO^-.1034

That is H; I will go ahead and put NH₂, and this is going to be CH₂, COO^-.1039

This is the alpha-carbon; this is the amino group.1050

This is the aspartate, right here.1054

This is the aspartate, and this, right here, is our citrullyl adenosine monophosphate.1058

What we end up having is something like that.1063

Now, do the electrons actually move up to nitrogen and then, they kick back down here to kick that off like a tetrahedral intermediate that is characteristic of carbons double bonded to electronegative atoms most specifically carbonyl?1071

The only thing that is different here is that this is nitrogen instead of oxygen.1084

Maybe I have just represented it as one; you will see it both ways.1088

It is not really a problem; what you end up with is the following.1092

Adenosine monophosphate is what leaves, and what you will be left with is the following molecule: H₂N, C.1096

I will go ahead and draw out this part first: C, C, C, C, NH₃⁺, COO^-, and then, from here, we have NH.1109

Actually, I probably need a little more room here, but that is OK.1129

I have NH, and then, I have got C, COO^-.1134

I have the CH₂, and I will go ahead and put the C, other COO^- right there.1140

This is our argininosuccinate; this is argininosuccinate.1147

OK, this is what you want to pay attention to.1156

I will do this in red; you want to keep your eye on this group right here.1160

That is going to end up being the core of our urea; we are going to end up breaking this bond and replacing it with an oxygen.1167

This is going to end up being the urea.1175

I will say keep your eyes on this group right here.1180

OK, let me see; have we forgotten anything?1190

We have our citrullyl adenosine monophosphate; we have our aspartate, and then, we have our argininosuccinate.1193

This is reaction 2 prime; again, 2 and 2 prime- single reaction.1200

OK, let's see what we have got.1208

OK, catalyzed by...let me go ahead and write the enzyme.1212

This reaction is catalyzed by argininosuccinate - well - synthetase.1218

Again, you are just synthesizing that molecule.1235

OK, now, let's go ahead and go to reaction no. 3.1241

Let me go back to black here.1246

Our third reaction of the urea cycle is the following.1250

We have argininosuccinate releasing fumarate to become arginine.1255

OK, let's go H₂N, double bond, C.1272

Let's put a little plus sign here; let's go NH.1280

Let's just put the H there, C, C, C, C, the NH₃⁺, COO^-.1284

I hope I have not put an extra carbon here, 1, 2, 3, and it happens when you do these things by hand.1292

We have got our...nope, it is going to be a nitrogen because it is the amino group that attached.1300

OK, N, C, COO^-, CH₂, COO^-, let me write this one a little bit differently.1308

I am going to write this one down here.1323

OK, what ends up happening is the following; this thing, right here, gets released.1327

That ends up getting released, so what you end up with is fumarate; and the fumarate is...let me go ahead and write a COO^- here, COO^- here.1337

Remember this from the citric acid cycle?1350

This is your fumarate; this is what actually is lost.1354

This is lost, and what you are left with is arginine.1357

It is going to look like this; it is going to look like H₂N, double bonded C⁺, and we have NH₂.1362

We have N and we an H; we have C, C, C, C.1375

We have NH₃⁺, and we have COO^-- pretty extraordinary here.1383

You have a carbon surrounded by 3 nitrogens and a double bond here- very, very unusual molecule, actually.1390

This is going to be our arginine.1399

This fumarate, we will talk about it in a minute; it actually goes back and enters the citric acid cycle as metabolized malate to enter the citric acid cycle.1405

Now, we have our arginine; now, we are ready for our fourth reaction.1415

Actually, let me go ahead and let me just say that this is catalyzed by argininosuccinase.1420

You are just breaking it up.1438

OK, now, we are ready for our final reaction.1442

It is reaction no. 4; let me go back to black.1448

OK, reaction no. 4, this is going to be arginine.1451

Excuse me.1461

Under hydrolysis, we are going to release urea, and we are going to form ornithine, which is transported back into the mitochondrial matrix to start the cycle all over again.1465

Let's go ahead and write out arginine again.1478

Again, there is no harm in writing these out as many times as possible.1482

We have NH₂; we have NH, C, C, C, C, NH₃⁺, COO^-, and, of course, we have our H₂O with its lone pair of electrons, hydrolysis.1487

This is the bond that is going to break.1508

OK, the H₂O is going to come in, and it is going to hydrolyze that bond.1512

What you are left with, well, arginase is the enzyme that catalyzes this, and what you end up with is the following products.1520

Let me go back to black; you end up with, of course, urea.1530

That comes from here with just this O, which comes from the water, and then, you are left with ornithine again, so H₃N⁺, and then you have got C, C, C, C, NH₃⁺, COO^-.1541

That is this, right here.1567

There you go; that is it.1571

The urea, this is exported to the kidneys, where it is excreted, and this ornithine, well, it returns to the matrix for another turn of the urea cycle; and that is it.1574

The urea cycle, that is all that happens.1623

You have your ornithine in the mitochondrial matrix that condenses with the carbamoyl phosphate that was formed in the matrix to form citrulline.1627

Citrulline passes out of the matrix into the cytosol, passes through the intermediate citrullyl adenosine monophosphate to become argininosuccinate.1636

Argininosuccinate becomes arginine, and arginine releases urea; and it releases ornithine.1647

Ornithine goes back into the mitochondrial matrix for another turn of the cycle- that is it.1653

That is the urea cycle- pretty basic, pretty straightforward, nothing really strange happening.1657

It is just keeping track of what is going on; that is the only thing that is going to seem a little odd here.1660

OK, let's close this off with the discussion of some of the connections between the urea cycle and the citric acid cycle.1668

These happen to be the 2 cyclic pathways that we have discussed so far, and there is a connection between them.1675

It is actually connections between all the pathways, but this one is important.1682

Let's talk about some links between the citric acid cycle and the urea cycle.1688

OK, now, several of the citric cycle enzymes - and you remember the citric acid cycle actually takes place in the mitochondrial matrix - they have cytosolic versions.1705

They have cytosolic isozymes, the same enzyme; it just happens to do what it does in the cytosol instead of the mitochondrial matrix.1730

They have cytosolic isozymes.1737

The fumarate that is formed in the urea cycle - and remember, this happens in the cytosol - can be converted to malate - remember from the citric acid cycle, fumarate to malate - which can be further metabolized in the cytosol, or it can re-enter the mitochondrial matrix and enter the citric acid cycle.1745

OK, now, the aspartate that was formed by the transamination of the glutamate oxaloacetate.1830

Remember that one in the mitochondrial matrix?1838

Glutamate can do 1 of 2 things; glutamate can either just directly release its amine group and turn into alpha-ketoglutarate, or it can react with oxaloacetate to form aspartate and alpha-ketoglutarate.1842

The aspartate formed by the transamination of glutamate oxaloacetate - that pair - it can leave the mitochondrial matrix, and it can enter the urea cycle in the cytosol.1863

Let's go ahead and draw this out.1920

This process, right here, it is called the aspartate argininosuccinate shunt.1925

This is called the aspartate argininosuccinate - at this point I am not going to worry too much about spelling because these words are just getting very, very long - shunt.1932

Let's finish off by drawing what this looks like.1954

OK, let's see here.1959

I am going to go ahead, and I think I will do it over on this side.1963

We have oxaloacetate.1968

Let's go ahead and go to our cycle.1973

We have fumarate.1977

This is going to be the citric acid cycle.1981

Fumarate goes to malate, and if you remember, malate goes back to oxaloacetate.1985

Now, oxaloacetate can go to aspartate, right?1991

Oxaloacetate can condense with glutamate to form aspartate.2003

This aspartate can enter the citric acid cycle - remember the aspartate and the citrulline, that particular reaction - passes through the argininosuccinate, and one of the things that is released is fumarate.2010

Well, fumarate can be converted to malate, and malate can re-enter the mitochondrial matrix to enter the citric acid cycle.2039

This is the dividing line, right here.2053

What happens here is the mitochondrial matrix.2057

What happens here is in the cytosol.2062

Let's go ahead and finish this off; over here, we have citrulline, and, of course, we have the ornithine.2066

In the mitochondrial matrix is where the first step of the urea cycle actually takes place.2081

So, what comes in here, that is the carbamoyl phosphate, right?2087

That is the beginning; this citrulline passes to the cytosol, goes to argininosuccinate.2094

Argininosuccinate goes to arginine, and arginine releases urea to become ornithine; and ornithine passes back into the mitochondrial matrix in order to start the cycle again.2100

This, right here, this is called the aspartate argininosuccinate shunt.2126

These are the connections between the citric cycle, which is this one right here, and the urea cycle, which is this one right here.2142

Aspartate from oxaloacetate can go and enter the urea cycle releasing fumarate.2153

Fumarate to malate, malate can come back into the mitochondrial matrix and enter the citric acid cycle.2162

These cycles are connected by various intermediates, and there you have it.2169

That is the urea cycle; thank you so much for joining us here at Educator.com.2176

We will see you next time, bye-bye.2180