Biochemistry Amino Acid Sequencing of a Peptide Chain

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

At the close of the last lesson, we talked about the levels of protein structure; we had primary, secondary, tertiary and quaternary.0004

Today, we're going to talk about the primary structure- the amino acid sequence.0012

We want to know what is the sequence of amino acids- which is next to which, which amino acid is next to which, and how are they arranged in a linear fashion.0017

That is what we're going to be working on.0028

Let's get started.0029

OK.0032

The amino acid sequence determines how the peptide is going to actually fold, how the peptide will fold, and thus, ultimately determines its structure.0034

As you can see, the primary sequence of a protein, of a peptide, is very, very important because depending on what amino acids are aware, it's going to basically guide how the protein is going to assume its 3-dimensional shape; and it is that 3-dimensional shape which is going to determine its structure and function.0080

Let me write these words a little bit better.0109

The amino acid sequence determines how the peptide will fold and thus ultimately determines its structure and function.0113

Amino acid sequence implies the function, and that's what is important in a protein, what does it do.0126

OK.0135

Well, there are many techniques for elucidating amino acid sequence.0137

We will discuss a chemical method.0160

We will discuss a chemical method still used in laboratories.0165

It is called the Edman degradation.0174

Excuse me.0186

Basically, what the Edman degradation does is it labels and removes the N-terminal amino acid for identification.0187

It labels it for identification.0210

It removes it so that it can be separated, and that way you can identify it.0211

The remaining peptide, now, has a new N-terminal amino acid; and now, what we do is we just repeat the process.0218

That's it.0243

Excuse me.0245

We're basically taking an amino acid and we're labeling the end, cutting it off, identifying it.0247

Next one, labeling the end, cutting it off, identifying it, and we just go down the list.0250

We are just chopping it up until we finally get to the last amino acid.0254

That's all the Edman degradation does, and, of course, this is an automated procedure because we have really, really good chemical control; so we can just put our sample into a machine, and it will do everything for us, and it will give us a read out at the end.0259

It is really quite wonderful.0271

OK.0275

I'm going to do a schematic representation of the Edman degradation describing each step, and then we’ll go ahead and do an example of an Edman degradation with a specific amino acid.0276

OK.0289

I wonder if I should start on a new - yes - let me go ahead and start on a new page here.0291

Yes, that's fine.0296

This is going to be the Edman degradation; let me go ahead and do this in blue.0299

OK.0306

I have to warn you there is going to be a lot of chemical names being thrown around, and there is going to be a lot of chemical structures being thrown around.0307

This is where you have to be really, really, really careful, and that includes me.0315

So, please, by all means, you definitely want to confirm that I'm actually drawing the right structures.0320

I would definitely encourage you to take a look at the Edman degradation procedure in your book to see what they have to say about the particular mechanism and how they draw it- really, really important.0330

But again, ultimately, it is just not about passive learning.0340

You don't just want to look at a diagram and say I understand it; you need to be able to reproduce it.0344

That's when you actually understand it.0350

OK, so, the Edman degradation.0352

Let's start off with just a generic peptide.0354

We have H₃, N, C, C, and I'm just going to go ahead and write peptide for the other because again, we're just going to be concerned with the N-terminal, the one on the left.0360

We have the carbonyl carbon there, and we have our R-group attached to the alpha-carbon, and this is A⁺.0372

The first step is...where should I write this, I'll go ahead and write it here, wonder if I should do it in, this one I'm going to do in black, I think.0379

OK.0402

I'm going to be drawing this thing, N, double bond C, double bond S.0403

OK.0410

What we do is we take this peptide and we react it with something called phenyl isothiocyanate under mildly alkaline conditions.0411

OK.0418

That's the first step0419

Let me go ahead and write this as one.0421

I'm going to write the products below instead of to the right.0425

I'm going to write the steps over here; I just wanted to do it in a schematic way.0427

You know what I need a little bit more room to write this out.0438

One, phenyl isothiocyanate- that is this molecule right here.0443

OK.0454

It is abbreviated PITC, phenyl isothiocyanate, under mild basic conditions, alkaline conditions - there we go - under mild OH.0455

This is the Edman reagent, so you'll often hear it.0471

They might say PITC, or they will just say “use Edman reagent”.0475

This is our Edman reagent; let me go ahead and put that there.0480

This is called the Edman reagent; let me go back to black.0485

OK.0490

When this reaction actually takes place, what you end up with is this product.0491

Let me see.0499

It is going to be this here; let's go ahead and put the H on there.0500

It is going to be C, double bonded S, and it is going to be attached to the N, C, C.0510

This is carbonyl, and this is our peptide.0518

This is our R-group, and we have our H.0523

OK.0527

The bond is formed between this carbon and that nitrogen.0531

This is the bond that is formed- right there.0539

OK.0542

Now, again, let's keep track of our peptide.0544

Our peptide is right here- N, C, C.0548

That is what you want to look for.0550

When you're doing these yourself, again, keep track of your peptide; and you can keep track of it by looking for that N, C, C motif.0551

N to the left, C to the right, C to the right, carbonyl on the second C, R-group on the first C, counting from left to right- here is our peptide, I'm sorry, here is our amino acid.0559

This is the one that we're actually pulling off.0574

This is the isothiocyanate part here.0576

So, what I've actually ended up forming here is something called phenylthiocarbamoyl that refers to this particular arrangement of atoms.0580

Phenyl is this, thio is the sulfur, carbamoyl is this carbon attached to a nitrogen and a nitrogen here.0599

What I've done is I've taken this peptide that I have, and I've created a phenylthiocarbamoyl derivative of it, by reacting it with the phenyl isothiocyanate, the PITC.0606

This phenylthiocarbamoyl derivative, they call it PTC.0620

OK.0626

Now, we'll go to our second step.0627

Now, we'll go ahead and do another black here.0628

OK.0633

This one, we are going to react it with C, COOH; and this is going to be anhydrous.0634

What we're going to do is, we're going to react this PTC with anhydrous trifluoroacetic acid.0644

It is just a weak acid that happens to be a little bit stronger than acidic acid.0663

Actually, any acid will do; it's fine.0667

It just needs to be anhydrous.0669

Now, what happens when this reaction takes place is the following.0672

What you end up with is the following 2 molecules; this is the one that actually breaks the bond that we are trying to break.0675

OK.0683

And, I'll tell you which bond in just a minute once I draw it out.0685

Let' me see.0688

That's fine; I guess I can fit it in here.0689

Let me go back to blue.0691

We have our C, we have our NH, and we have our phenyl group, C, then we have our...here's our N, here is our C, and here's our C, that is our that, and then we have our S, and C, and we have our 1.0693

Let me make sure I have everything on here, N, trivalent, S.0728

OK.0733

Everything is good.0734

Yes, and, of course, we have that plus our new peptide, 3 peptide- the new amino-terminus.0735

The bond that we have actually broken is the following.0750

We've broken this bond; let me do this in black.0754

We have broken this bond, and again I'm going to go through the mechanism in just a little bit, but I just wanted you to see chemically what happens.0765

This thing, when we form this species or again, let me see, N, C, C, keep track of the N, C, C.0771

This is our amino acid.0781

OK.0784

This is our that; this is our that.0785

That is what this is.0787

We want to keep track of our amino acids.0788

This is called, in case you want to know, it's called an anilinothiazolinone.0790

Anilino refers to the phenyl group attached to nitrogen; thiozolinone happens to be this thing, the C, the N, the S, arranged in a ring.0803

OK.0813

Now, we take the third step - oops this is not...this is 2, not number 1, number 1 was that, sorry about that - this is step 2 of the Edman degradation.0816

Now, we're going to go to step 3 of the Edman degradation.0829

Let me move on to the next page, and let me write the molecule in blue.0832

Now, we've pulled off that other peptide.0837

We have that one N-terminus that we've actually broken off; that's the thing that we're going to react.0842

Let me redraw that one; let me draw it here.0847

C, we have NH, we have that, we have N, we have C, we have C, we have S, this is our R group, this is our carbonyl.0852

Let me see; am I missing anything here?0871

No, I don't think so; everything looks good.0874

OK.0877

Now, again, let me, N, C, C, just to keep track of our amino acid or N-terminal.0878

Now, the third step here, what we do is we're just going to react this particular molecule with aqueous acid.0888

So, step 3 is aqueous acid, and what you end up with is the following molecule.0901

Let me do this in...yes, that's fine; I'll go ahead and do it in blue.0913

We have C, we have S, we have N, we have C, we have C, and we have N, and we have phenyl, and we have an H, we have our R group, and we have that.0917

OK.0943

The reason we actually do this step is this thing is more stable than this thing, so it allows us to deal with it better.0946

This is more stable, and it is called phenylthiohydantoin; and this is PTH- that's the acronym.0952

Now, it's ready for identification.0972

There you go.0983

And now, let's go ahead and red N, C, C.0985

That is our motif; that’s what we want to keep track of.0990

All that has happened here is that this thing under acidic conditions, aqueous acidic conditions, has actually rearranged, and has formed something more stable.0993

You want to take a look what has happened form here to here.1004

The only thing that has happened is this carbon right here that is attached to nitrogen, this S, went up to where the nitrogen was, double bond; this nitrogen with the phenyl group came down to where the S was.1006

This S and this thing switched places; that's all that happened- the rearrangement.1019

OK.1026

And, of course, the last part, since now you have the H₃N - oops - you have the peptide left over, the fourth step.1028

Let me do this in blue.1038

H₃, N⁺, now, you have the rest of the peptide with a new N-terminal amino acid group.1040

So, step 4, just repeat the process.1047

That is the Edman degradation.1052

The first step is phenyl isothiocyanate, and then after that, you're going to treat it with trifluoroacetic acid; third step, you're going to treat it with aqueous acid, and you're going to form this molecule right here- this phenylthiohydantoin.1054

You've basically taken this N-amino acid, and you've labeled it with this thing.1075

You've made a derivative of this thing for that thing, and now, you can identify it; and you just repeat the process, go down the chain.1080

OK.1087

Now, let's take a look at some mechanisms.1088

It's important to talk about mechanisms, how electrons move, arrow pushing.1090

You remember from organic chemistry, electrons go this way, nucleophile, electrophile.1095

If it is something that's strange to you or perhaps you’re not too familiar with it, it intimidates you a little bit, don't worry about it.1101

I think it will just be reasonably clear what are these that's going on.1108

Don't attach any more deeper meaning than what it actually is.1111

It is just electrons moving around forming bonds.1116

You remember in general chemistry, we just sort of do this chemistry, and we wouldn’t talk about how it happened.1119

When you got to organic chemistry, that's when you started talking about "OK, this carbon is moving in here, these electrons are forming this bond, this bond is breaking"- that's all a mechanism is.1124

It is a molecular level, single step, what's happening.1134

OK.1140

Let's see if we can do - let's do this in blue - mechanism for PTC formation.1141

That is the phenylthiocarbamoyl formation.1156

This is step one.1167

OK.1175

Here we go.1176

Let's go ahead and draw out the phenyl isothiocyanate first.1177

So, I’m going to draw this vertically.1182

Actually, let me do this in black.1185

OK.1188

And, we've got N, we have C and S, so this is our PITC- phenyl isothiocyanate.1191

Now, let's go ahead and write our H₂; this is N.1200

I’ll go ahead and put the electrons on the nitrogen; I’ve got N, C, C, and then I've got...I'm going to actually write out the second, N, C, C, N, C, C.1204

Carbonyl goes here; carbonyl goes here.1220

I'm just going to do it for a dipeptide.1222

This is going to be the R₁ group; this is going to be the R₂ group, and let's go ahead and put an H on that nitrogen.1225

OK.1232

Here is what happens.1233

These electrons, it is a nucleophile; this nitrogen is a nucleophile.1236

This carbon here that is attached to nitrogen and sulfur, it's the electrophile.1242

It is a little bit positively charged.1248

Nitrogen is an electronegative element.1249

It's going to pull electrons away from that.1252

This is negatively charged.1253

So, these electrons are going to attack here, and when these electrons come in, electrons that are there have to make room for these that come in, so they have to go away.1256

These electrons move away and they grab an H from the solution; and what you end up getting is the following.1269

Should I draw it?1280

Yes, that is fine; I'll go ahead and draw it horizontally.1284

N, H, C, double bond S, this is N, H.1292

It is going to be C, C, and then N, C, C.1302

OK.1311

Well, that's fine; I'll do this in just a minute.1312

N, C, C, this is the carbonyl, this is our R₁ group, there is an H here, this is our R₂ group.1315

So, the bond that we formed is this bond right here.1325

That is the bond that we formed.1329

These electrons formed this bond.1330

Now, notice, it has 2 hydrogens on it, but this nitrogen now, has 1 hydrogen on it.1333

So, I'm going to go ahead and write this minus H plus.1339

That means that it has given up that hydrogen.1342

Once this bond forms, now, nitrogen has 1, 2, 3, 4 things attached to it.1343

It is going to be positively charged.1351

It is going to release that hydrogen in the solution.1352

This is the mechanism.1357

Nitrogen is the nucleophile; this carbon of the PITC is the electrophile- standard, basic mechanism, single step.1359

OK.1369

This is our PTC, phenylthiocarbamoyl.1370

OK.1377

Now, let's go ahead and do the mechanism for the second step.1380

This is very important.1384

This one we'll do in blue again.1386

This is going to be the mechanism for ring formation and peptide bond cleavage.1389

This is the big one.1408

This is step 2.1414

This is where we add the trifluoroacetic acid.1416

OK, step 2.1419

So, we've added the trifluoroacetic acid, this is what happens.1421

Let's draw our molecule again, and we'll make sure to draw it very, very carefully.1424

And again, you need to be able to reproduce this.1429

OK.1433

It's the only way you'll have a full grasp of what it is that is going on.1434

We have N, C, C, N, C, C.1437

There is an H here, our carbonyl goes there, carbonyl goes there.1445

This is our R₁ group; this is our R₂ group, and let me go ahead and put the electrons on the nitrogen on that one.1450

OK.1462

Now, here is what happens.1463

Alright.1466

We are just going to be pushing arrows; electrons are going to be moving around.1467

Here is what happens.1471

Actually, you know what, I'm going to make this arrow a little bit smaller here because I want to do 3 structures on this page.1473

OK.1481

These arrows right here on the nitrogen, that is N, C, C, our N-terminal, OK, this nitrogen.1482

Again, look for the N, C, C.1489

This is N, C, N; that's not it- N, C, C.1491

This is your terminal amino acid.1493

These electrons, they go that way.1498

These electrons, they push, these electrons they attack that.1501

You know what, I'm going to do this in a different color.1509

Sorry about that.1513

Let me do this in red.1516

These electrons go down here to form a double bond.1520

They push these electrons; they attack the carbonyl right here, and these actually end up going up onto oxygen.1522

So, what you end up getting is this tetrahedral intermediate, which is very typical of carbonyl reactivity.1533

What you end up with is the following.1540

Now, I'm going to retain certain structural features.1542

I'm going to keep this C, this arrangement, while I draw a structure.1545

It's going to be...let me do this in blue.1551

I'll try to do it underneath.1554

C, C, O^-, N, C, C, let me fill these up, R₂.1557

Now, the S, these electrons have moved and formed a bond here, so what I have is, I have formed a bond with this sulfur.1568

Now, this sulfur is attached to this carbon.1576

It is attached to that carbon.1581

Well, that carbon is now attached to this nitrogen with a double bond, and that nitrogen is attached to this carbon.1583

That is what's happening.1595

Also attached to this carbon is the...that's it.1597

Just keep track of your carbons.1608

That is all that's happening here.1611

Again, and this is N, C, C, so the R₁ group is right here.1613

Again, let's keep track of our...OK.1620

We formed this as an intermediate species.1632

Now, the next step of the reaction is the following.1635

Let me do this in red again.1642

OK.1644

This bond is the bond that we are going to break right here- right between the C and the N.1645

This is one amino acid; this is the other amino acid residue- N, C, C, N, C, C.1652

So, what happens is these electrons right here, they go back down to form the carbonyl because the carbonyl is very stable, and they kick off these bonds, and they go on to grab an H⁺.1659

There is an H right here, by the way.1673

And therefore, this bond is actually broken.1676

What you end up with is the following.1680

I'm going to draw this out.1690

This is going to be in blue.1692

Actually, you know what, let me draw...that's fine.1695

I'll just go ahead and do that, that's fine, but I'm going to draw this molecule over here.1702

This is going to be C…nope, do it in blue.1710

We have C, we have C, we have the carbonyl is formed again.1713

We have S, we have C, we have double...oops...we have double bonded N, single bonded C.1720

We have our R₁ group, and, of course, here, we have our NH and our benzene ring, plus we have N, NH.1736

It grabbed an H, so we have NH₂, C, C, O^-, R₂, and again, keep track, N, C, C.1750

There we go.1769

We have our amino acid; we have our derivative part, and this is the one that undergoes that rearrangement to form the final PTH; but I wanted you to see this mechanism.1771

It is the nitrogen electrons that move here to form the double bonded carbon.1788

They push the double bond on the sulfur, and attacks the carbonyl.1792

The electrons move up onto the oxygen to carry a negative charge.1795

The electrons come back down to form the carbonyl, and they kick off these electrons to have it to do whatever it does; and that actually breaks this bond right there.1798

Let me go ahead and do this in black after the fact- this bond is broken.1809

There you go.1823

That is the mechanism.1824

OK.1827

Let's go on here, see what we can do.1828

Let's go ahead and do an example.1830

OK, an example.1833

OK.1840

Write out the Edman degradation for the tripeptide Ala, Tyr, Ser- alanine, tyrosyl, serine.1843

We have this tripeptide.1873

We want you to write out structurally the Edman Degradation using arrows, not mechanism arrows.1874

We just want you to show what reagents you are using, what the products are going to be for the entire Edman degradation for this thing.1880

OK.1887

Let's just jump in, and you need to be able to do this.1888

You have to be able to reproduce this - very, very important.1889

You get practice with amino acid structures; you get practice with writing out the PITC, PTC, PTH- all of that stuff.1892

Again, you do enough of this, 3 or 4, 5 of these, you'll be perfect; but you have to do them.1900

OK.1907

Let's draw it out.1910

Let's see; let's go.1913

Shall we do it in blue or black?1915

It doesn't really matter; let's do it in blue.1917

Again, do the backbone first, N, C, C...oops...N, C, C, N, C, C.1919

And again, you can use the shape structure; you can use line structure- whatever works best for you.1931

I just love seeing everything.1935

We've got H₂ or H₃- it doesn't really matter.1937

We have carbonyl on the second carbon, carbonyl on the second carbon, carbonyl on the second carbon.1944

Let's go ahead and put an O^- there.1948

We have alanine, which is CH₃.1950

Notice, I'm not putting the H on the alpha-carbon anymore.1953

We have tyrosine.1957

I probably should have picked something a lot easier, but OK, and a little less tedious to draw out, but that's OK; it's good practice.1959

I like tyrosine and serine, which is CH₂OH, if I'm not mistaken.1971

OK.1978

The first step is, you are going to use PITC, phenyl isothiocyanate, under mildly basic conditions, and you are going to form the following.1979

You are going to form N, C, S, N, H, C, C.1996

Here, this is going to be CH₃, and this is going to be N, C, C, N, C, C.2014

We've got N, H, C.2022

This is going to be CH₂.2026

We have OH, we have our carbonyl, and we have NH, we have CH₂OH, we have that, and we have that.2031

That is our first step.2040

We have formed this thing.2041

OK.2044

This is our phenylthiohydantoin.2045

So, we've formed this PTC thing.2052

Let me just go ahead and write that in red.2053

Where do I put it?2058

That is fine; I'll just put it here.2059

We have formed PTC.2060

OK.2062

Our next step, let's go ahead and actually...that's fine; I'll just do it on the next page.2063

Let's go back to blue.2069

Now, we're going to use trifluoroacetic acid.2071

Let's just write TFA- trifluoroacetic acid.2078

When I do that, I'm going to actually form a ring, and I'm going to break a bond.2082

So, let's see which bond am I going to break.2087

Well, I have that.2091

I'm looking for N, C, C, N, C, C, N - my first peptide bond.2092

That is the bond that is going to break.2096

The ring that I'm going to form is going to be made up of sulfur, 1, 2, 3, 4, 5, 5-membered rings starting with sulfur - sulfur, carbon, nitrogen, carbon, carbon.2099

That is my 5-membered ring.2114

OK.2116

Let's go ahead and form that then.2117

Let me see; do I actually do a...yes, that's not a problem.2122

Let's go ahead and form that.2127

Let me write it out over here.2129

Let me go back to blue.2134

It is going to be C, C, carbonyl, CH₃; it's going to be N, C, S, and on this C is going to be the NH, and it's going to be that thing, and what we are left with is...where am I? yes... I'm left with tyrosine and serine.2136

I'm left with H₃, N⁺, N, C, C, N, C, C.2176

I've got a carbonyl there; I’ve got a carbonyl there.2184

This is CH₂, and yes it is CH₂, and this is going to be my tyrosine.2190

As you can see, keeping track of all these gets really kind of confusing.2207

So, don't feel bad if you have difficulty with this because we all do.2211

OK.2216

So, I formed this thing right here, my anilinothiazolinone; and this is what I'm going to subject to H⁺, under aqueous conditions.2217

And again, what we want to reverse is, this and this are going to switch places.2235

I'm going to leave everything the same; I'm just going to switch that and that.2245

I'm going to write this one in back to blue.2249

I'm going to go C, C; I'm going to go N.2252

I'm going to go C; I'm going to go N that way.2259

This one is the carbonyl; this is the alanine.2264

This C has now an S, and this actually has that phenyl group attached to it.2270

So, this is my final product; this is my PTH, my phenylthiohydantoin.2279

This is the one that I'm going to identify.2285

And again, my amino acid, N, C, C, is right here.2287

That's it.2295

Now, we go ahead and we take the next step.2297

Now, we take in this molecule, so we've gone ahead and identified one, now, we are going to subject this molecule - I hope you don't mind if I change colors here - I'm going to react now, this one for the second cycle.2299

I'm going to react it with PITC under mildly alkaline conditions, and I'm going to end up forming the following molecule.2314

Yes, that's very, very important that you write all of these out, at least a couple of times.2325

C, S, N, C, C, N, C, C, N, C, C, that carbonyl goes there, that carbonyl goes there, and here we have the tyrosine R-group, and here we have the serine R-group.2330

OK.2357

We have actually formed this bond right here with the phenyl isothiocyanate.2358

Now, this is the one that we are going to subject to trifluoroacetic acid in order to form the ring and break this bond.2365

Now, we are going to break that bond, and we are going to form a ring from this molecule.2376

Let's go ahead and form that; let's see what that looks like.2382

That is going to end up looking like this.2386

It is going to be C, C, O, we have an S, we have a C, we have double bonded N, we have that.2389

On this C, we have NH, and we have that.2402

And on this C, we have our tyrosine, CH₂, and OH.2408

Now, we have plus our CH₂, N, C, C.2417

We have our final serine residue which is going to be CH₂OH.2425

Oops, let me do it the way that I usually do which is vertically.2430

OK.2436

That one is taken cared of, and this one is going to go on into a third cycle, which I will have you do.2437

And, let me see, this is going to be our anilinothiazolinone, which we are going to subject to aqueous acid; and when we subject it to aqueous acid, we are going to rearrange.2444

And again, what we are going to rearrange is, this thing and this thing are going to switch places.2457

Everything stays the same except those that switch places.2463

So, what I end up with is C, C, N goes there, C stays, N goes here.2466

And again, this double bond changes; it becomes a single bond that goes there.2478

That is a carbonyl; this is going to be our tyrosine group.2482

OK.2489

And this is going to happen...no, sorry about that, this and this switched, so we actually have that there.2493

This one has an H, and, of course, we have an S; but we don't want these stray lines, otherwise you are going to think that they are double bonds.2502

We don't want that.2509

So, we have that.2510

That is our final PTH, and in this particular case, our amino acid residue is right there.2513

Again, N, C, C, just follow the N, C, C, and attach the rest.2523

We can identify this, and then we just subject this to the next cycle.2530

That is it; that' all you are doing.2535

Again, it is very, very important that you do at least a couple of these by writing out the reactants, the reagents, and the product.2537

That is the only way to get a full sense of what's going on, to have full command of what's going on; and I promise you, after doing a couple of these, you'll really, really feel like you understand the material, drawing it out actively.2546

That is the only way to learn this.2561

OK.2563

Thank you for joining us here at Educator.com and Biochemistry.2564

We'll see you next time, bye-bye.2566