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Lecture Comments (5)

2 answers

Last reply by: Sally Reina
Tue Sep 5, 2017 9:57 PM

Post by Sally Reina on September 5, 2017

The previous lecture "Overview & The Aminotransferase Reaction" lesson is not working. It reads:

404 Not Found

The requested URL /learn/chemistry/biochemistry/hovasapian/overview-%20-the-aminotransferase-reaction.php does not exist.

1 answer

Last reply by: Professor Hovasapian
Sun Apr 27, 2014 4:06 PM

Post by Torrey Poon on April 17, 2014

Prof. Hovasapian,
For Rxn 2 you said we are still in the same enzyme.  Are you referring to ornithine transcarbamoylase?

Glutamine & Alanine: The Urea Cycle I

Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  • Intro 0:00
  • Glutamine & Alanine: The Urea Cycle I 0:45
    • Excess Ammonia, Glutamate, and Glutamine
    • Glucose-Alanine Cycle
    • Introduction to the Urea Cycle
    • The Urea Cycle: Production of the Carbamoyl Phosphate
    • The Urea Cycle: Reaction & Mechanism Involving the Carbamoyl Phosphate Synthetase

Transcription: Glutamine & Alanine: The Urea Cycle I

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

In the previous lesson, we started talking about amino acid degradation, amino acid catabolism, did a quick little overview about what is actually happening in the liver cell, and today, we are going to start a detailed discussion.0004

I am going to be talking about glutamine and alanine and the role that they play in holding the amino groups from amino acids that are broken down outside of the liver cell like the amino acids that are broken down in muscle tissue or the amino acids that are actually not in the liver but brought to the liver.0020

And then, we will start the discussion of the urea cycle.0039

Let's get started.0043

OK, now, the excess ammonia that is produced in tissues other than the liver is combined with glutamate to form glutamine.0047

Excess ammonia - oops, let's make sure we spell this correctly - produced in tissues other than the liver - the formal term would be extra hepatic tissues - is combined with glutamate to form glutamine.0060

OK, now, this glutamine is transported to the liver.0104

You remember from the overview in the last lesson that was one of the sources of amino groups was the amino groups from outside of the liver, that was brought into the liver via glutamine.0112

This glutamine is transported to the liver where it gives up its ammonia and becomes glutamate again.0128

Again, this glutamate is the central molecule for this whole amino acid metabolism.0160

OK, let's go ahead and do this here.0169

Let me go ahead and do this in blue; oops, excuse me.0174

I will go ahead and readjust that; OK, what have we got here?0178

We have got our 1, 2, 3, 4 and 5.0182

OK, let's go ahead and draw it this way, and again, I tend to not draw in my hydrogens simply because they just take up space.0193

Any carbon that you see that does not have 4 bonds, the other bonds are hydrogens.0202

OK, 1, 2, 3, 4, 5, 1, 2, 3, 4, yes, that is good.0209

We have that, and, of course, we have our NH3+ group.0215

Yes, actually, I will put this H in there to let you know that this is the alpha-carbon of the amino acid.0223

OK, the first transformation is going to be ATP releasing ADP and this is the glutamate; and the enzyme is glutamine synthetase.0229

It is an enzyme that catalyzes the actual synthesis of glutamine from glutamate.0260

OK, now, let's go back to blue, and what you end up with is the following.0266

You end up with 1, 2, 3, 4 and 5.0272

We have that there; we have our NH3 group there, our alpha-carbon, and then, over here, we have this, and we have O, and we have a phosphate group.0280

Basically, we have just phosphorylated this because we want to create a good leaving group on this end because that is the end that we are going to attach this ammonia, this excess ammonia.0293

This glutamate first is converted to this phosphate.0304

It is called gamma-glutamyl phosphate; I will go ahead and write the name.0309

The name does not really matter all that much but just in case.0311

Everything has a name in biochemistry; I am not sure if that is a good thing or a bad thing, so gamma-glutamyl phosphate.0318

Again, we are just putting this phosphate here to create a good leaving group here because now, the ammonia is actually going to come in and attack this, and this is going to be the leaving group.0323

OK, now, what we have is the next step.0335

What comes in is NH4+ or NH3, and what is going to leave is the phosphate.0339

This NH4 group is going to replace this, so we are going to have an amide right there.0350

That is what makes it the glutamine instead of the glutamate.0355

The glutamine has this NH3, and it also has an NH2 over here, so what you get is the following.0359

And again, this is the same enzyme, so I have written it in 2 steps.0365

This is glutamine synthetase.0369

OK, and the molecule that we end up with is the following.0378

We get C, C, C, C and C.0383

This is 1 carboxyl end; we have an NH3+ here.0387

I will put this H to let you know that that is the alpha-carbon of the amino acid, and then, we have this; and now, we have the NH2.0393

This is now an amide.0402

I will go ahead and do this in black; that is this.0407

OK, it came in, attacked this, kicked off the phosphate.0411

That is why you have this inorganic phosphate leaving; it replaced it.0415

OK, now, this is our glutamine.0420

Excess ammonia is tied up as glutamine by converting glutamate to glutamine.0428

OK, now, we have that.0434

When glutamine enters the liver and when it releases that ammonia that it brought from other parts of the body for it to be processed, this particular one is the one that it releases.0439

Glutamine releases the one on the end, not this one.0451

It is true that glutamate, itself, is the central molecule; glutamate in the liver releases this one, but glutamine, when it comes in, release this one, so there are 2 that glutamine has.0455

The first one is released that way, and then, glutamate releases that one; but we will talk about that in just a little bit.0467

OK, the final conversion that takes place, that converts glutamine back to glutamate, is the following.0475

Let me go ahead and go back to...actually, you know what, let me stick with black on this one, so we can do that.0482

This is going to be just a basic hydrolysis reaction.0488

What comes in is water, and what ends up leaving is NH4+ - this thing right here - and what you get is your glutamate back, so 1, 2, 3, 4, 5.0493

Let me see; this is our carboxyl.0509

This is our amino; let's go ahead and put the H there to let us know, and then, of course, we have this other carboxylate.0513

Now, we are back at glutamate - that is it - and this conversion, glutamine, to release the ammonia group at the end of as tied up as an amide group, right here, to become glutamate - let's draw a little arrow here - the enzyme for that is glutaminase or glutaminase.0522

Wherever you want to put the accent, however you want to pronounce it, it does not really matter.0550

That is what happens with glutamine.0555

The excess ammonia from other tissues in the body, the excess ammonia that is produced, is tied up as glutamine by using glutamate.0560

Glutamate to glutamine, glutamine to the liver, glutamine gives up this ammonia, and that gets processed.0572

That is going to actually enter the urea cycle and turns into glutamate.0583

Glutamate is the central molecule of amino acid metabolism.0590

OK, now, let's talk about something called the glucose alanine cycle.0594

Let's talk about alanine and what it does; OK, let me go to black here.0600

Now, the amino groups from the amino acids that are metabolized in muscle tissue from amino acids metabolized, catabolized actually, degraded...let me go ahead and say...yes, let me go ahead and say degraded or broken down.0606

The amino groups from the amino acids broken down in muscle tissue, they are collected as glutamate.0640

OK, let's be very clear about this.0660

There are going to be amino acids in the liver.0668

Well, we talked a little bit about that- the overview.0672

Here, in this lesson, we are talking about the role of glutamine and the role of alanine.0676

In muscle tissue, the excess ammonia, the ammonia groups that are produced from the breakdown of amino acids in muscle tissue, it is collected as glutamate, not glutamine.0681

In other tissues, glutamate is there already.0693

The excess ammonia is tied up as glutamine, so basically, glutamate already has an NH3 group.0699

It is an amino acid; the glutamine has that extra amino group, which is at the end as an NH2- that amide bond, that carbonyl connected to a nitrogen.0704

OK, in this particular case, from the muscle tissue, it is tied up as glutamate, just the 1 ammonia group.0715

Now, here is what is interesting; glutamate can do 1 of 2 things.0723

Now, glutamate can either be converted to glutamine and transported to the liver to do what we just discussed, or it can do the following, which is absolutely extraordinary.0728

This one, I love it; it is absolutely beautiful.0774

OK, I wanted to go ahead and draw this out as we discuss it, so let's go ahead.0776

I am not going to do the molecular structures; I am just going to write the names.0782

I will let you deal with the molecular structures.0786

I do not think that your teacher is going to be too concerned about the molecular structures for many of these molecules, but you will have to know, of course, what these molecules are, for example, glutamate becomes alpha-ketoglutarate.0790

You may not necessarily have to know what alpha-ketoglutarate looks like.0800

OK, here is what happens; let's go ahead and do this in blue.0804

I have got glutamate, alpha-ketoglutarate, pyruvate to alanine.0810

OK, now, the glutamate can either be converted to glutamine and transported to the liver, and then when there, it is going to release one of its amino groups; and then, at that point, once it becomes glutamate, again, from the glutamine, that glutamate, itself, will release its second amino group, or the glutamate can do the following.0836

The glutamate can actually react with pyruvate to transfer its amino group from itself to pyruvate to become alanine, and, itself, turns into alpha-ketoglutarate, which is just the glutamate without the amino group.0856

It is the carbon skeleton; it is the alpha-ketoacid that happens when you remove the amino group and replace it with a carbonyl on amino acids.0872

The glutamate can react with pyruvate to produce alanine.0881

Now, this alanine travels in the blood, and I will go ahead and write alanine here.0884

Now, alanine reacts with alpha-ketoglutarate - I will go ahead and draw this - to become pyruvate again, and we have alpha-keto - I will write it down here - alpha-ketoglutarate and what it turns into is glutamate.0894

OK, glutamate gives up its amino group to pyruvate to become alanine.0925

Alanine travels in the blood; OK, it goes to the liver.0930

I will write this as blood alanine; now, it goes to the liver, and the liver, the alanine, gives up its amino group to alpha-ketoglutarate to become glutamate again.0936

Now, here is where it becomes interesting.0948

This pyruvate - OK - undergoes gluconeogenesis to become...pyruvate goes through gluconeogenesis in the liver to become glucose.0952

Now, this glucose travels through the blood stream, so we will call it blood glucose; and it goes to muscle tissue to be used as energy.0977

It undergoes glycolysis to use up its energy.1009

Now, let's go ahead and finish this off; this glutamate here in the mitochondrion...OK, well, you know what, let me go ahead and do this here.1017

This glutamate here - I will go ahead and just let you know...OK - enters the mitochondrion and releases its NH3 group, or it transaminates with oxaloacetate to form aspartate.1029

And again, this right here, we will talk about a little bit later and in a subsequent lesson.1078

This part that I am writing in red is not altogether important for what I have written.1088

What is important is what alanine does, but oxaloacetate...I will go ahead and write what it form aspartate.1092

OK, now, let's see what we have got going on here.1106

The glutamate, we said it can be converted to glutamine and transported to the liver, or it can do the following.1110

It can react with pyruvate to form alanine; the alanine is carried.1115

OK, this is muscle tissue; let me go ahead and make sure we know what is happening where.1120

This is muscle tissue, and this part right here, this is happening in the liver.1130

In muscle tissue, the glutamate reacts with the pyruvate, transaminates to form alanine.1146

Alanine is carried in the blood to the liver; alanine transaminates again with alpha-ketoglutarate to form glutamate.1152

Now, this glutamate goes and does what it does; we will talk about that later.1160

The pyruvate that is formed once alanine has given up its amino group - now, you have an alpha-keto acid, the carbon skeleton - this pyruvate undergoes gluconeogenesis to form glucose.1165

This glucose is transported back to muscle tissue to be used as energy.1177

This glucose undergoes glycolysis, and, of course, the final result of glycolysis is pyruvate to close out this cycle.1183

This is the glucose alanine cycle.1192

This is the glucose alanine cycle.1198

We can start here if you want.1205

Glutamate to alanine, blood alanine to the liver, the liver, glutamate, pyruvate to glucose, glucose carried back to muscle tissue, where it can be used as energy to produce the final product is pyruvate to start the cycle all over again- that is how alanine is actually brought the excess ammonia that is produced in muscle tissue is carried as alanine to the liver to be processed in the liver, so this glutamate can actually release its ammonia and have it processed in the urea cycle.1209

OK, that takes care of glutamine, and that takes care of alanine.1251

Now, let's go ahead and see if we can actually start talking about the urea cycle.1257

Alright, OK, now, the NH4+ that is released by the glutamate and/or the glutamine in the liver is converted to urea in human beings.1263

In other species, it might be excreted as ammonia, and in some other species, it is excreted as uric acid.1310

For most terrestrial animals, for human beings, it is converted to urea.1320

OK, and now, let's see what is going on.1327

Now, the urea cycle, it begins in the mitochondrial matrix, and it continues in the cytosol.1331

Urea itself is actually formed in the cytosol.1342

The cycle begins in the mitochondrial matrix.1350

When we say mitochondrion, we mean the mitochondrial matrix.1357

It, then, continues in the cytosol.1363

OK, now, let's talk about what it is that is actually going to be going on.1374

Let's see if we can actually do this in this page, or should I use a whole separate page for this otherwise?1379

You know what, that is fine; I will go ahead and keep it on here.1388

It should not be too much of a problem; let me see.1390

Let me go ahead and write glutamate, and let me go ahead and do a little arrow and rewrite glutamate.1393

OK, now, let me go ahead and draw.1405

What I am drawing here is a mitochondrion, a mitochondrial matrix- not exactly the best picture, but I just want you to know that this is the mitochondrial matrix.1415

Oops, no, wait a minute.1426

I already have a second glutamate there; I need one of those glutamates to be outside.1430

That is the whole idea.1437

OK, there we go.1442

This is the mitochondrial matrix, and here is what is going to happen.1448

Glutamate, it is going to release NH4+, so the glutamate in the liver cells travels to the mitochondrial matrix in the liver cells.1456

The glutamate releases its amino group, the NH4+, as ammonium ion - OK - this ammonium ion now.1471

Now, let's go ahead and see what it is that we are going to be doing with this.1482

Well, this ammonium ion is actually converted to something called carbamoyl phosphate.1490

That is going to be the first molecule that is going to begin the urea cycle.1496

Let me go ahead and...that is the structure I am going to draw.1501

This is going to be H2, N, C, O, O, P, OO-.1505

This is the carbamoyl phosphate, and this is the molecule.1516

This NH4, the NH4 that is released, the processing of ammonia in order to turn it into urea starts by converting this into this molecule called carbamoyl phosphate, which begins the urea cycle.1520

We are just looking at the first phase before something actually begins.1534

OK, what comes in here is HCO3-, and we also end up having 2 ATPs; and we are going to release 2 ADPs and an inorganic phosphate.1539

You notice, we have 2 ATPs and 2 ADPs, but we have only released 1 inorganic phosphate.1557

That is because the other inorganic phosphate is tied up as the carbamoyl phosphate.1562

OK, now, let's go ahead and finish this picture up, and then, we will discuss what it is that is actually going on.1567

We have, right there, this is going to be alpha-ketoglutarate, and then, we can go this way; and we can go oxaloacetate to aspartate.1574

I always think it is a great idea not necessarily to...I mean, I love illustrations, but I think it is great to use illustration to actually draw these things out, yourself.1601

That is why I do them by hand; I love doing them by hand.1612

OK, now, let me go ahead and put a little box around glutamate to let us know that it is central.1616

Now, we have got glutamine.1624

This was that extra-hepatic glutamine.1631

Remember the amino-groups in extra-hepatic tissues that are tied up as glutamine?1635

OK, we have that and that, this glutaminase or the glutaminase that we mentioned earlier.1640

Now, let me go ahead and write glutamate.1660

This is going to be alanine.1670

This is from the muscle that we just discussed.1674

Alpha-ketoglutarate to pyruvate- we just talked about these, and then, we have another source.1689

We have - we will just say, I will say - amino acids, and then, I will tell you where they come from.1695

They are either dietary or intra-cellular - alpha-ketoglutarate - and they become random alpha-keto acids.1706

OK, let's talk about what is going on here.1730

This part right here, at least this, sort of, this part right above, this was in the overview.1734

We are talking about these sources of the amino groups and where they come from.1742

OK, we just talked about the amino groups that come from the degradation of amino acids in muscle tissue.1747

They are carried as alanine from muscle tissue.1752

Alanine reacts with alpha-ketoglutarate to release pyruvate; it is converted to glutamate.1757

Glutamate is transported from the cytosol in liver cells to the mitochondrial matrix of liver cells, where it gives up its amino group as NH4+, and it is converted to alpha-ketoglutarate to go and do what alpha-ketoglutarate does.1762

Now, there are amino acids from the diet, from the proteins that we eat, that are broken down into amino acids that are carried to the liver, or the proteins, the amino acids, that already happen to be in the liver cells.1779

That is another source of amino acids; it is another source of amines.1792

Remember we mentioned earlier, these react with alpha-ketoglutarate in a transamination reaction.1797

They give up their amino groups to alpha-ketoglutarate.1803

OK, and the alpha-ketoglutarate ends up becoming glutamate, and the amino acid becomes the alpha-ketoacid.1807

The alpha-ketoglutarate takes the amino group from the amino acids.1820

These amino acids are either from dietary sources, or they are already there in the liver cell; and it becomes glutamate.1827

Glutamate does what it does; it enters the mitochondrial matrix.1834

It releases its ammonia, and ammonia goes on to do what it does.1838

The third source of ammonia or of amino acids are the amino acids that are being degraded in extra-hepatic tissues that are not necessarily muscle tissues.1842

They are tied up as glutamine; glutamine is transported to the liver.1855

OK, again, all of this is cytosolic; this is the mitochondrial matrix of a liver cell.1859

This happens in the cytosol of the liver cell; the glutamine travels into the mitochondrial matrix.1866

It gives up its NH2 group to become glutamate, right?1872

That is this one, and glutamate, then, gives up its NH3 or its ammonia group, its amine group, to that.1878

Glutamine, you end up actually releasing 2 equivalents of ammonia- that is it.1888

This up here, it is just a description of the different sources of the amino groups- amino groups from muscle tissue, amino groups from dietary protein or intracellular protein and amino groups from extrahepatic tissue.1895

Now, of course, what is central is what happens in the mitochondrial matrix.1909

The glutamate can do 1 of 2 things.1913

Glutamate can go ahead and just give up its ammonia group; this ammonia reacts as it does to from this carbamoyl phosphate, which is the first molecule that actually begins and enters the urea cycle, which we will discuss in a subsequent lesson.1917

This is carbamoyl phosphate, or we said that it can actually react with oxaloacetate to form aspartate.1935

It has 2 possibilities; it can either give up its ammonia group to become alpha-ketoglutarate, or it can react with oxaloacetate, again, to become alpha-ketoglutarate but to also produce aspartate.1950

This aspartate actually ends up leaving the mitochondrial matrix and entering the urea cycle a little further down the line, again, which we will discuss in a subsequent lesson.1965

What is important here is the sources, the central glutamate and in this particular case, this reaction right here, the formation of the carbamoyl phosphate.1975

That is the reaction that I am going to discuss next in detail.1986

This is catalyzed by exactly what you think.1990

Carbamoyl phosphate synthetase is an enzyme that catalyzes the synthesis of a particular molecule that we are talking about.1997

Now, let's take a look at this particular reaction in detail including mechanism.2010

OK, let's go here; let me go ahead and do this in...I think I am going to do this in blue.2017

Let's go ahead and draw out our first ATP.2025

I am going to draw all of this out: O, P, O, P, O, P, O.2029

And then, we have our ribose, and we have our adenine.2036

This is our first ATP; remember, we need 2 ATPs here.2040

Let me go ahead and finish this off: double bond, double bond, double bond.2045

This is minus; that is minus.2050

That is minus, and that is minus; now, we also said that we have this HCO3.2052

Well, you know what, I am going to draw this out.2064

This is going to be COO-, and this is OH.2069

OK, this is bicarbonate; here is what happens.2077

This attacks a gamma-phosphorus, kicks those off.2082

What you end up producing is the following.2090

You release an adenosine diphosphate; that is the first ADP that is released.2096

That is this thing right here, and what you end up with is this.2100

You end up with H, O, C and then, O, then P, O, O.2105

That is what you end up with there; OK, now, let's go ahead and do this in red.2117

The ammonium that has been ready to be processed, this pool of the amino groups that have been released by glutamate inside the mitochondrial matrix, are now, ready for processing.2126

As ammonia, what happens, what you kick off is...this is your inorganic phosphate.2140

This inorganic phosphate goes away, and what you are left with is the following molecule.2156

I am going to go ahead and also take off this H.2161

So, you are going to be left with O, C, O and NH2, after some proton exchange and things like that.2165

What you are left with is that; now, the second adenosine triphosphate is going to be used, and I am going to go ahead and do that in black.2180

I am just going to write it as ADP, and then, I am going to go O, P, O, O, O2190

I did not want to write out the whole thing; this is just adenosine triphosphate, adenosine diphosphate.2198

I have actually written out the third phosphate.2204

This is our second ATP that was required, and what happens is exactly what you think.2209

This attacks here to kick that off.2220

What ends up going away is ADP, adenosine diphosphate, and what you are left with is your carbamoyl phosphate.2227

What you are left with is the following molecule; you are left with C, NH2, O, O, P, O, O-, O- - that, right here.2235

OK, and we said that this is catalyzed by carbamoyl phosphate synthetase.2255

There you go; in the previous picture, the formation of carbamoyl phosphate is the first step to processing this ammonia- this ammonia, which is toxic.2273

So, it has to be taken cared of; it has to be excreted.2290

This is the first step to form carbamoyl phosphate, and now, from carbamoyl phosphate, we are going to enter the urea cycle to produce urea, which the body actually excretes.2293

One ATP, this bicarbonate attacks here, kicks this off.2304

What you are left is this molecule right here.2308

Now, this ammonia group, this is the ammonia that we need to take care of.2312

That nucleophile, carbonyl reaction, kicks off this phosphate.2317

That is why we reacted it with ATP to produce a good leaving group.2321

That is what we need; we need a good leaving group, which is a phosphate.2325

We end up producing this, and now, this, again, is involved in a nucleophilic substitution on a second molecule of adenosine triphosphate.2330

This combined with a phosphate gives you your carbamoyl phosphate.2339

Carbamoyl just means a carbonyl with an NH2 attached.2346

That is what carbamoyl means; in the next lesson, we are going to actually start the urea cycle.2350

Thank you so much for joining us here at; we will see you next time, bye-bye.2355