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Lecture Comments (10)

1 answer

Last reply by: Professor Hovasapian
Sat Aug 15, 2015 12:46 AM

Post by shashikanth sothuku on August 13, 2015

Hello professor
during peptide bond formation for the nitrogen to act as a nucleophile should it lose a hydrogen

1 answer

Last reply by: Professor Hovasapian
Wed Feb 5, 2014 12:22 AM

Post by Alan Delez on February 4, 2014

Hi Dr. Raffi,

You mentioned physiological conditions. What criteria does the environment have to be in order to be in those conditions?
Alan D.

1 answer

Last reply by: Professor Hovasapian
Tue Jan 28, 2014 2:49 AM

Post by crystal harnick on January 27, 2014

Hi Professor,
I believe that Tyrosine is drawn wrong in this example. One of the carbons has five bonds. I think it needs to be CH2 instead of CH3.

1 answer

Last reply by: Professor Hovasapian
Mon Sep 16, 2013 5:43 AM

Post by Yvonne Kum on September 15, 2013

Hi prof, could you please explain how many chiral centers each amino acid structure have, particularly when they form a peptide bond?

1 answer

Last reply by: Professor Hovasapian
Thu Sep 12, 2013 5:02 PM

Post by Vineet Kumar on September 10, 2013

please fix this video. I pay top dollar for this website and it doesn't work when I need it to

Peptides & Proteins

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
  • Peptides and Proteins 0:15
    • Introduction to Peptides and Proteins
    • Formation of a Peptide Bond: The Bond Between 2 Amino Acids
    • Equilibrium
    • Example 1: Build the Following Tripeptide Ala-Tyr-Ile
    • Example 1: Shape Structure
    • Example 1: Line Structure
    • Peptides Bonds
    • Terms We'll Be Using Interchangeably
    • Biological Activity & Size of a Peptide
    • Multi-Subunit Proteins
    • Proteins and Prosthetic Groups
    • Carbonic Anhydrase
    • Primary, Secondary, Tertiary, and Quaternary Structure of Proteins

Transcription: Peptides & Proteins

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

Today we are going to continue our discussion of amino acids by taking the next step.0004

We are going to put some amino acids together.0009

We are going to be talking about peptides and proteins.0011

Let's get started.0014


Peptides and proteins- it is just a string of different amino acids like beads on a string.0018

That's all it is- each one connected to the next.0025

Let's go; let's write that down.0029

Peptides and proteins are made up of amino acids - and again I'm just going to write AA like that - amino acids strung together- that's it.0035

Now, you’re probably wondering "Peptide, protein - what's the difference?".0053

The truth is there is no difference.0057

There are just a bunch of names that are used for proteins, amino acids that are strung together.0058

In general, if you want, you can think of a peptide as being anything less than about 10,000 atomic mass units, so molar mass of about 10,000 or less, we tend to call it a peptide.0064

A protein is 10,000 or more, and again it is not really this, you can call whatever you like.0080

We're actually going to be using several terms interchangeably.0086

So, just to sort of throw it out there, protein greater than about 10,000 atomic mass units or grams per mole, molar mass.0091


Now, let's go ahead and talk about the formation of a peptide bond- very, very important.0104

Bond is the bond that exists between two amino acids, and this is what holds the chain together.0114

OK....the bond between two amino acids.0124


Let’s go ahead and just take some generic amino acids, and see what we've got.0141

Again, when we write amino acids, I think it is the backbone that's important.0148

Yes, the R-groups are important, of course, when we're discussing them; but when we want to draw it out, it is the backbone that's connected- the peptide bond.0154

It is N, C, C, N, C, C repeating units, so if you’re going to write an amino acid, just start by writing N, C, C, and then fill in the rest.0162

We have N, C, C, I'll go ahead and put H3+ here, I'll go ahead and put the carbonyl there, and I'm going to write it in its fully protonated form just so you see that this is actually a condensation reaction.0171

The elements of water are going to be removed when we put these two amino acids together to form a dipeptide.0186

OK, so the carbonyl carbon is the second carbon.0194

The R-group goes here; the H is there, and then plus, and then, of course, we have, again, N, C, C.0197

This time I'm just going to put H there.0208

Actually, you know what, let me do it this way.0212

Let me put an H here, and let me put an H here.0215

I decided this one, I’m going to not protonate.0220

Don't worry about why, as far as where the Hs go, whether it is 3 Hs, 2 Hs, things like that, that's not what’s important right now.0221

Right now, we just want to be able to get a global sense of how these bonds form.0230

We have an H here.0237

This is the second R-group, and we have the carbonyl, and this one, I'm just going to go ahead and leave as an O-; if you want you can put an OH again.0238

Now, what happens is this.0247

I'll go ahead and do an equilibrium arrow this way and this way, so when water leaves this, the elements of water are right here.0251

Let me do this in red.0262

OK, the elements of water.0268

Basically, it is going to be, this carbon is the electrophile, and this nitrogen is going to be the nucleophile.0272

Remember the nucleophile is the one that actually has the electrons; it has the negative charge.0289

Electrophile is the one that carries the positive charge, so this thing is actually is going to attack this thing.0294

We’re not going to worry about mechanism right now, but that’s what happens.0299

What you’re going to connect is - and I’ll to do this one in blue - you’re connecting those two.0302

You’re connecting this carbon of 1 amino acid to the nitrogen of the amino group of the other amino acid.0310


And in this direction, it is condensation, because again, the elements of water are removed, and we're going to go ahead and write out our dipeptide; and again, we're going to go N, C, C - oops, straight lines, we definitely don't need those - N, C, C, N, C, C.0322

Now, let's go ahead and put the H3, let's leave that as plus.0348

Let's go ahead and put an R-group there; let's put the H here.0352

Here's our carbonyl, the N; let's go ahead and leave that one H that was there.0357

This is our R2 group - right? - of the other amino acid.0364

Now, we have this, and we have that.0368

The peptide bond is this thing right here; that is your peptide bond.0370

It is the carbonyl carbon attached to the nitrogen of the amino group of the amino acid to its right.0377

This is your peptide bond.0389


And just to let you know, in this direction, it is hydrolysis, so when we actually add water to a peptide, it actually splits this bond right here, the peptide bond; and it releases 2 free amino acids.0396

So, in this direction, two amino acids’ condensation, in this direction, it is called - got a little too much floating around here so when H2O comes in, OK, when this H2O leaves, this, well, here I will just do this - in this direction, it is called hydrolysis.0415

That's it- simple peptide formation.0440

The elements of water leave, the carbonyl carbon attaches to the nitrogen of the other amino acid, and you get your peptide bond; and it goes on like this, so N, C, C, N, C, C- it is the second carbon.0443

If this were going to attach to another amino acid, it would be this carbon that’s going to be attached.0459

If this one were going to be attached to something to its left, that would be attached.0464

That is all that’s going on here.0469


Under physiological conditions, under physio conditions, interestingly enough, the equilibrium of the previous reaction of peptide bond formation, the equilibrium lies to the left.0476

In other words, it lies to the formation of free amino acids, not the peptide, the left, and the reason that is so is because the hydroxy group is not a good leaving group; and you remember that from organic chemistry, just a straight hydroxy is not exactly a good leaving group.0499

It doesn't just go away to make the reaction move forward and form the peptide bond.0521

The hydroxy must be activated, and if you remember from your first year biology course or those of you who had already perhaps taken molecular biology, the amino ace will transfer RNA, ribosomes, protein synthesis, that is what is active.0537

That is activated with adenosine triphosphate and all that other stuff, so you’re welcome to look that up.0561

I'm not going to go through it here0565

It has to be activated to induce it to leave.0567

We just wanted you to know that in general, under normal physiological conditions, as is, the equilibrium tends to lie to the left, which is why you need it to be catalyzed.0577

OK. Let's do an example here.0588

Example 1: let's build the following tripeptide, so 3 amino acids, let's do Ala, Tyr and Ile, so alanine, tyrosine, isoleucine.0595


Let's go ahead and draw these out.0621

Again, we have N, C, C, we have N, C, C, we have N, C, C.0624

OK. I'm going to go ahead and draw them out individually so that we see- again, this is all great practice.0636

Let's see, alanine was CH3; and please, by all means, confirm that I'm actually writing the correct structures.0644

We all human; we have a bunch of carbons, nitrogens, hydrogens floating around.0652

We're going to be doing lots of structures.0657

The molecules are going to go get bigger and bigger and bigger, so, by all means, please make sure that I'm actually writing the correct structures because I get things wrong.0658

Let's see, we have that carbonyl; I'm going to go ahead and do an OH.0668

I'm going to go ahead and write an NH3+, because I'm writing them as individuals, and we said that tyrosine is the next one; so, tyrosine, CH3, I believe we have this one, the phenyl group with a hydroxy attached, and then we have the carbonyl carbon, and then, of course, we have the isoleucine, this is a plus charge, this is that, here's our carbonyl.0675

I'm going to go ahead and put an OH there, and our R-group, isoleucine - I never remember our isoleucine - this one is H, this is CH2, and I think this is CH3, yes, that is correct.0702

OK. Again, the carbonyl carbon attaches to the nitrogen.0715

The two things that we are going to connect are this and this, and we're going to connect this and this.0720

This is going to go away; this is going to go away.0730

Now, let's go ahead and draw our structure; and again, this time we go N, C, C bond, N – oops, we don't want extra straight lines because we're dealing with lines - N, C, C bond, N, C, C, OK, H3+.0734

I'm going to go ahead and put the carbonyls on first.0759

The carbonyl is on the second carbon, N, C, C.0762

The carbonyl goes on the second carbon, N, C, C, carbonyl on the second carbon, carbonyl on the second carbon.0763

This is the free end, so I'll go ahead and put that one there.0769

This is going to be alanine, so I'll do that here.0774

It is going to be tyrosine, so I'll put the OH there.0778

This one is going to be isoleucine: CH3, H, CH2, CH3.0785

I'm going to go ahead - well, you know what, that's fine - I'll go ahead and put the hydrogens.0796

In a little bit, I am probably going to start leaving off the hydrogen that's on the alpha carbon; it is there.0799

Again, from the organic chemistry, we don't always write all of the hydrogens.0809

That's it.0812

Our peptide bonds are that one - oh, you know what I should do, yes, I'm going to go ahead and put the hydrogens on the nitrogens - that's important, those are important.0813


Let me go back to blue.0831

That's one peptide bond right there; here is another peptide bond right here.0833

Actually, you know what, why don't we consider this whole thing a peptide bond, but that's the actual bond.0839


That's it.0846

This is called, if you want the name of it, basically, you just take the name of the individual acids starting from the left, you drop off the INE, and you add YL to have the "eel" sound like, remember, carbonyl, alkyl.0848

This is actually alanyl, tyrosyl, isoleucine as one word; but it is not the end of the world if you want to separate them.0866


This is the structure of this tripeptide, and notice, I actually use all my carbons.0887

When I do my structures, I personally like to write out every single atom; I like to write out my carbons.0893

I've never really cared for line structures myself; obviously, you want to be able to understand them, but I like to see every single carbon that I'm dealing with.0899

That is just a personal taste.0907

You have your personal taste, and by all means, don't feel compelled just because everybody else is, let's say, using line structures, that you have to use line structures, unless you have a professor that's going to take points off.0908

Understanding is more important than aesthetics at this point.0920

Later on, maybe, you can get into, maybe you’re starting to draw your line structures; but again, we want to be able to understand.0924

To this day, I actually prefer to write everything out as a straight line like this, but I'm going to go ahead and show you a couple of the other representations here, just so you know.0933

I'm going to give you the shape structure, and the shape structure is the same except it actually takes into account the angles, so it is going to look like this.0944

If you do a shape structure, it is going to be N, C, C, alternating N, C, C just like when you did alkyl change, C ,C, C, C, that little zigzag pattern, N, C, C, N, C, C, and then N, C, C.0956

Again, you just sort of fill everything in.0974

This is a plus; the carbonyl goes on the second carbon, N, C, C.0976

The carbonyl goes on the second carbonyl, N, C, C.0980

Carbonyl goes on the second carbon, something like that; and, of course, you can put your R-groups.0982

So, alanine is going to be CH3; tyrosine, it is going to be CH2.0988

Our benzene and our hydroxy and here, we have the CH, CH3, and then we have CH2, CH3, that's our isoleucine.0994

And again, let me go ahead and put the hydrogens on the nitrogen, that's important, but notice that I've left the hydrogens off the alpha carbon, so this, sort of, is another way of representing it.1010

I think it is a really nice way of doing it.1021

Again N, C, C, N, C, C, N, C, C, but notice how the carbonyls, now, they alternate, one is down one is up.1023

That's it.1030

The line structure would look like this.1031

We will go ahead and put an N, and then we’ll do that, C, C, N, C, C, then N, C, C.1041

So again, you have something that looks like this.1055

To this day, it still confuses me; it makes me crazy.1058

I really just, really like to see my carbons.1061

Carbonyl is on the second carbon, N, C, C.1064

Carbonyl is on the second carbon; that one is taken cared off.1067

Here we have CH3; here we have the CH2, the benzene, the hydroxy, and then we have the CH, we have CH3, CH2 and CH3.1070

That's it.1088


When you have a peptide like this- let me go ahead and put my hydrogens on, it's probably very, very important; and again, let me go ahead and do my peptide bond.1091

My peptide bond is that one right there, the carbonyl carbon and the nitrogen.1102

Where is the next one?1107

The carbonyl carbon and the nitrogen, carbonyl carbon, nitrogen, carbonyl carbon, nitrogen- that's your peptide bond, very, very important.1110


Traditionally, what we do- let me go ahead and put a charge on here; this is a plus charge, better not forget that, there is a minus charge.1122


When we write our proteins, we write them from left to right, and on the left hand side, we put the free amino group, this in red; on the right hand side, we keep the free carboxyl group.1132

This right here, this is called the N-terminal amino acid.1143

In this particular group, the N-terminal amino acid is the alanine, also called the N-terminus.1154

It is the amino terminal group, the amino terminus, so we call it the N-terminus; and this is the C-terminal amino acid or the C-terminus, C standing for carboxyl.1164

That's it.1187

We always put the amino on the left and the carboxyl on the right.1188

We read from left to right.1191

This is the alanyl, tyrosyl, isoleucine.1193

That's it.1198


Let's see what else we can do here.1203

All right, OK.1207

Peptide bonds are very stable once they form, having average half-lives of about 7 years.1212

So, 7 years later, you'll still have half the proteins that were made 7 years ago.1242

That's all that means- under physiological conditions, 7 years under physio conditions.1248


Let's go ahead and redraw our peptide here.1263

I'm going to do it as blue.1268

We've got N, C, C, N, C, C, N, C, C, 3+, carbonyl, N, C, C, carbonyl, N, C, C, carbonyl, O-.1271

We had our alanine group, and we had our tyrosine group, and we had our isoleucine group - oops, not CH2, it is CH - and then we had a CH3 out there, we had a CH2 here, and we had a CH3 there.1289


Now, a peptide - notice - is just like an amino acid; I mean, you've got an amino end, you've got a carboxyl end; and in this particular case, you happen to have some groups in between that also have ionizable groups.1317

That's it.1328

It is just going to behave like a long amino acid.1329

It is going to have a pKa.1332

This group is going to have a pKa; this group is going to have a pKa, and, of course, in this particular case, because this is an ionizable group, it is going to have a pKa.1334

This particular tripeptide is going to have 3 pKas.1344

The titration curve for this one is going to be exactly what you think; it is going to have 3 plateaus, 1 for each pKa.1347

That's it.1356

There is nothing strange happening here.1359

It just behaves like a really, really long amino acid.1362

Ionizable groups behave the same way they would any others.1365

Now, the pKas like for this one and this one, are not going to be the same as the pKas listed for the 3 amino acids for alanine.1369

They’re probably pretty close, but obviously, it is going to be changing a little bit because now, the environment is different.1375


Let's see, what shall we talk about?1385

Ionizable groups, so in this particular case, we have 3 ionizable groups.1388


Let's see this list: terms we'll be using interchangeably.1394


Let me just go ahead and write this out.1410

We talk about peptide; we talk about protein.1412

We're going to talk about polypeptide.1418

We talk about oligopeptide.1424

Again, these are just all a bunch of different terms that mean a chain of amino acids- a peptide chain.1427

As long as you specify, as long as the person that you're talking to, your audience knows what it is that you're talking about, it doesn't matter what term you use.1437

Certain teachers, they prefer you to be really, really specific, and are a little bit more pedantic about that; but for all practical purposes, again, it is understanding that matters, not little things, so we have to definitely be able to distinguish between what is important and what is not.1445

If you have a teacher that wants you to differentiate between a peptide, a protein, an oligopeptide, a polypeptide, that's fine; but other than that, don't lose any sleep over it.1461


Now, let's talk about some biological activity.1473

Let's see, I think I'm going to start this one on the next page, maybe.1479

Yes, here we go.1484

You know what, let me go back to blue; I really like blue very much.1492

Biological activity of a protein or a peptide, biological activity and size of a peptide or a protein have nothing to do with each other.1499

You might have a peptide that is 3 amino acids long, 6 amino acids long, or you might have one that's 417 amino acids long.1524

The size itself does not correlate to biological activity.1534

The one that is small can have incredible biological activity, and the one that's huge can have incredible biological activity; so, size doesn't mean anything.1539

It does not make it more anymore important- let's put it that way.1548

Just as an example, there is this one peptide that you know very, very well - H3, N, C, C, N, C, C.1552

This is the carbonyl here, the carbonyl here.1567

Let's go ahead and do CH2, COO-.1571

Let's go ahead and put the H on the nitrogens, and this one is going to be phenylalanine, CH2, so the tyrosine without the hydroxy, so this is called L-aspartile-L-phenylalanyl - actually, it is phenylalanine, I should say - phenylalanine methyl ester.1579

I didn't do my ester.1615

OCH3, that's an ester R-group, carbonyl, oxygen, oxygen, this oxygen connected to another carbon.1618


This is NutraSweet.1626

You know that NutraSweet definitely has biological activity, and it is just a dipeptide- NutraSweet, otherwise known aspartame.1628


Some other examples: let's see, there is a protein called cytochrome-C.1641

It has 104 amino acid residues, and it consists of just 1 chain, so one long chain of 104 amino acids.1651


And then, there is something like hemoglobin.1666

Yes, OK.1677

Hemoglobin- let's see, that one has 574 amino acid residues, and it actually consists of 4 different chains.1680

So, in the case of hemoglobin, you have 4 separate chains that are associated with each other.1694


Hemoglobin is the protein that transports oxygen in the blood, just so you know.1710

Another example would be something like a protein called hexokinase or hexokinase, depending on your pronunciation.1721

It happens to have 972 amino acid residues, but it only has 2 chains.1731

Again, just because something has more amino acid residues, doesn’t mean there are going to be more individual chains associated with each other.1740

It has almost twice as many as the hemoglobin amino acids, but it only has 2 chains instead of a 4.1750


And, just so you know, this one happens to be an enzyme which converts glucose - oops, and we’ll definitely be seeing this one later in the second half of the course when we talk about metabolism, when we talk about glycolysis.1758

This one converts glucose to glucose-6 phosphate, the first step in the glycolysis cycle.1821


Now, let's see- hemoglobin, 4 chains, hexokinase 2 chains.1839

Let's talk about this a little bit.1849

Now, proteins like hemoglobin and hexokinase - you know what, I definitely need to slow my writing down just a little bit here - which have two or more individual chains, which associate noncovalently, that's very important, noncovalently, are called multi-subunit proteins.1852

So, if you have a protein like hemoglobin or hexokinase that actually consists of more than 1 chain, well, those chains are going to fold in a certain pattern, and those chains are going to interact with each other noncovalently.1864

Those kinds of proteins, we call them multi-subunit proteins, and each individual chain is called a subunit.1878

Now, there are proteins that actually interact covalently - separate chains - insulin being an example.1903

Insulin consists of actually 2 amino acid chains, but they are actually connected covalently.1912

We don't consider those, multi-subunit, because the interaction between the chains is covalent; but when they are noncovalent, we just happen to call them multi-subunit.1919


Let's take a look at something.1930

This is a picture of hemoglobin; this is hemoglobin.1935

I just wanted you to see a picture of it, and see…now, don’t worry, as far as the spirals are concerned and things like that, we're going to be talking about that a little bit later- what they mean, what they represent.1944

When we talk about protein structure, specifically, we are going to get into more detail about that; but I just wanted you to see of a multi-subunit protein.1956

Notice, this red is 1 subunit; this red 1 up in here, the top right and on the bottom left, this is another subunit; and, of course, you have the 2 blues, that's a third subunit, that’s the third chain, and the fourth chain is right there.1965

So, each one of them has a series of amino acids they fold; and those 4 subunits, they come together and they form the total protein which we call hemoglobin.1981

That’s all that’s going on here.1992


Let's see.1996

Now, let me go back to blue.2006

Now, some proteins contain permanently associated chemical groups attached, and they're called prosthetic groups.2010

A protein could be just a long string of amino acids that has been folded into a protein, and there is nothing else that's involved with it.2045

It is a protein; it does what it does, nothing else, but there are some proteins that don’t just have the amino acid portion, but they actually have other groups that are attached to them, and these groups are called prosthetic groups.2055

Some examples would be - let's see, let's…oops…make sure these lines aren’t there - an example would be lipoproteins.2070

You know what, let me classify this a little bit better.2087

I’m going to give you the class name, and then I'm going to give you the prosthetic group.2090

So, if I talk about a particular lipoprotein, well, the prosthetic group, the thing that happens to be attached to that particular protein, is going to be a lipid, a fat, a lipid, a fat of some sort- that's it.2103

Another class is the class called glycoproteins, a huge, huge class of proteins; and the prosthetic group, a thing that happens to be attached to the protein, they're going to be carbohydrates, otherwise known as sugars.2122

There are things called hemoproteins where the thing that is attached to the prosthetic group is heme; and heme is an iron porphyrin.2144

And again, don't worry about these words; we’re going to be coming back to hemoglobin.2160

We are going to be discussing heme and iron porphyrin and things like that, so right now, I just want you to see the words and see what's going on.2164

A hemoprotein, where the prosthetic group is actually something called a heme group, and it is actually a porphyrin molecule that has an iron in the center; and this hemoglobin is actually a perfect example of a protein that has a prosthetic group, and if you look carefully, you can actually see the - let me do this one in black - you can see the heme groups right here.2170

See, they're actually inside and I know that you can see them in green.2195

There is one there; there is one in this subunit, and I think I see one in this subunit, too, right in there, if you look carefully.2199

Hemoglobin is an example of a hemoprotein.2210

It is a protein, multi-subunit, and each one of the subunits has a prosthetic group.2215

The whole protein has 4 prosthetic groups.2220


There is also another class, the metalloproteins, and it is exactly what you think it is.2226

The prosthetic group happens to be metal ions, for example, maybe zinc, maybe calcium, calcium 2+, maybe magnesium- whatever it happens to be.2232

Let's take an example.2250

Let's take a look at a metalloprotein to see what it might look like.2251


This enzyme is carbonic anhydrase; and I will write down the reaction in just a minute.2257

This is a metalloprotein.2270

This is a particular protein that has a zinc ion, actually, as its prosthetic group; and if you look really carefully, you can actually see the zinc.2272

It is right there, right in there.2283

Now, what I've done is I’ve taken this, and we’ve blown it up a little bit, so that you can actually see the interactions.2286

If we go deep inside the proteins, here is our zinc, and as you can see, its interaction is a noncovalent interaction with what looks like 3 histidine residues and this thing which looks like a hydroxy group.2291

That's what’s going on.2314

This is an example of a metalloprotein.2315

Now, carbonic anhydrase, it catalyzes the following reaction, just so you know, just to have it for information.2319

CO2, + H2O, HCO3, yes HCO3- + H+, so it catalyzes this particular equilibrium- the equilibrium between the CO2, H2O, and bicarbonate, and acid.2333

The active site of this enzyme -again, we have this as zinc ion - is coordinated to 3 histidine residues; and again, this protein has folded in on itself, but these R-groups, they are sticking out, so this particular active site, there are 3 histidine residues in different places, that have positioned themselves in such a way that they can actually trap that zinc ion, histidine resides, and what looks like a hydroxy group and NOH-.2353

That's it; that's all that's going on here.2398


Now, and again, as far as these little twists and turns, these arrows, these ribbons, these lines, we are going to be talking about that a little bit later.2404

Right now, what's important, I just wanted you to see some proteins, see some interactions, things like that.2414

We are going to be talking about what those mean, and they do mean specific things when we talk about protein structure- very, very important.2418

Now, let's go ahead and actually talk about protein structure just globally, real quick, and do a couple more examples of some proteins; and then later on, we'll discuss all of these in a little bit more detail.2427


A protein has 4 levels of structure.2446

Normally, it has 3 levels of structure, but the multi-subunits, they are the fourth level of structure.2450

The first level of structure - let me go ahead and use, that's OK, I'll go stick with black, OK - the primary structure of a protein is its amino acid sequence.2454

That's it.2465

Alanine, tyrosine, isoleucine, leusine, valine- whatever it is, that's the primary structure, the amino acid sequence.2466

Now, the amino acids, once we actually form a peptide chain, there are certain portions of that peptide chain that are going to take particular configurations.2474

Two of those configurations happen to be alpha-helix and beta-pleated sheet.2487

So, those spirals that you see, like for example over here, that means that section of the protein, the backbone, is taking on a spiral shape.2492

These flat sections like these flat sections with little arrow heads on them, that means individual amino acids have arranged themselves in something called a beta-pleated sheet; and again, we will talk in greater detail about these a little bit later.2502

This is called the secondary structure.2517

The secondary structure is where it actually folds on itself, individual portions of the amino acid chain to achieve certain basic structures that keep showing up over and over and over again; and primarily it is going to be the alpha-helix and the beta-sheet.2520


Now, the tertiary structure of a protein, the third level is once this is formed, and a little bit of this is formed, and whatever else is happening along the chain, that chain is going to start folding in on itself.2537

Perhaps a cysteine residue from here and a cysteine residue from there are going to bind and form a disulphide bridge.2550

Maybe there is going to be other interactions.2556

When it is actually folded, that single chain, when it has come to its final folded position, that is called the tertiary structure.2562

That is the 3-dimensional structure, and that's what we've been looking at.2567

An example of a tertiary structure protein is this one right here.2573

Notice, we have some alpha-helices; we have some beta-pleated sheets.2578

These are just regular lines; that means there is nothing is going on.2583

That is just straight amino acids, just a straight chain.2586

There is no particular uniform structure there.2590

It is just amino acid after amino acid.2593

That is this particular structure right here, just a long peptide chain.2596

So, the whole thing, this is an example of tertiary structure.2600

This happens to be the protein firefly luciferase.2604

It is an enzyme- ASE ending tells you it's an enzyme.2615

This protein is a protein that is responsible for the firefly actually being able to glow the way that it does.2617

This is an example of a tertiary structure.2625

This is a single chain.2629

It is a single chain that has folded and has taken up a particular configuration- that's the tertiary structure.2631


Now, when you have a multi-subunit protein, when you have, let's say, 4 chains like hemoglobin, each one takes a particular shape; and then those individual proteins actually associate noncovalently to form the entire protein.2638

When you have a multi-subunit protein, that's the fourth level of structure.2656

That is the quaternary structure.2661

So, primary, secondary, tertiary, quaternary- just wanted you to be aware of this particular setup in terms of structure; and then we are going to be talking about these in future lessons in rather great detail.2664

Let's go ahead and check out one more.2680

Again, in this particular case, this is going to be an example of quaternary structure.2684

This is hemoglobin, again, the one that we saw before.2689

You have your 1 chain right there, another chain, another chain, and another chain.2695

Each one of those represents the tertiary structure.2704

When they come together to form the entire final protein, you have your quaternary structure.2707

That's it.2711


Thank you for joining us here at and Biochemistry.2714

We'll see you next time, bye-bye.2717