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Lecture Comments (10)

2 answers

Last reply by: Swati Sharma
Sun Jan 14, 2018 10:03 PM

Post by Swati Sharma on December 22, 2017

Dear Dr Raffi

I have not at all understood the difference between left and right handed helix. Could you please explain how to find difference

Thank you

0 answers

Post by Sam Zanone on September 18, 2014

Professor Hovasapian:

Out of curiosity, could you possibly elaborate on 3D Structures of Proteins?  The Alpha Helix and Beta Sheet explanations are perfect, but our homework continually refers back to peptide chains, asking about which bonds join together to form Hydrogen bonds.  
ie:  "Which of the following peptide segments is most likely to be part of a stable alpha helix at physiological pH?" (with a multiple choice list provided of 5 different pentapeptides)

We also delve into the Ramachandran plot as well, and I was hoping you could explain that in a better organized mannerism than my professor had explained.

I'm not sure if this is too much to ask but here is my brief, or extensive depending on perspective, list of topics that I could use clarification on - and please forgive me if there are some on here that are provided further on in lectures:
1.  Ramachandran Plots
2.  Protein Chaperoning (GroEL & GroES)
3.  Beta Turns (the two common types and structural explanation)
4.  Proteostasis
5.  Example: Chris Anfinsen's Ribonuclease Refolding Experiment

I apologize if this is too many topics to amend to this lecture, but these are topics our professor is expecting us to know!

Thank you so much if you can assist in the explanation of these topics!  And keep up the fantastic lectures you are providing!  

1 answer

Last reply by: Professor Hovasapian
Wed Sep 17, 2014 10:14 PM

Post by Jenika Javier on September 14, 2014

So the amino acid that is likely to be found in the interior surface is the hydrophobic amino acid whereas the hydrophilic will be found on the surface of a globular protein?

1 answer

Last reply by: Professor Hovasapian
Sun Feb 9, 2014 3:33 AM

Post by nanette skiba on February 8, 2014

Yes, the last screen. How did you know to start at the blue string and not the red string? What did I miss?

1 answer

Last reply by: Professor Hovasapian
Sat Mar 30, 2013 5:21 PM

Post by ali aden on March 30, 2013

at the 9:11, when you draw the resonance of the peptide bond, it looks that you forget the + charge on the nitrogen atom because it has 4 bonds. Is that right?

Alpha Helix & Beta Conformation

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
  • Alpha Helix and Beta Conformation 0:28
    • Protein Structure Overview
    • Weak interactions Among the Amino Acid in the Peptide Chain
    • Two Principals of Folding Patterns
    • Peptide Bond
    • Peptide Bond: Resonance
    • Peptide Bond: φ Bond & ψ Bond
    • Secondary Structure
    • α-Helix Folding Pattern
    • Illustration 1: α-Helix Folding Pattern
    • Illustration 2: α-Helix Folding Pattern
    • β-Sheet
    • β-Conformation
    • Parallel & Anti-parallel
    • Parallel β-Conformation Arrangement of the Peptide Chain
    • Putting Together a Parallel Peptide Chain
    • Anti-Parallel β-Conformation Arrangement
    • Tertiary Structure
    • Quaternary Structure
    • Illustration 3: Myoglobin Tertiary Structure & Hemoglobin Quaternary Structure
    • Final Words on Alpha Helix and Beta Conformation

Transcription: Alpha Helix & Beta Conformation

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

Today, we are going to be talking about secondary, tertiary and quaternary structure.0004

Actually, we are only going to mention tertiary and quaternary structure towards the end.0010

I am not really going to discuss it too much; I wanted to concentrate on this lesson on the secondary structure, in particular, the alpha helix and the beta conformation or otherwise known as the beta sheet.0015

Let's just jump in and see what we can do.0026

OK, let's recap; we have talked about the primary structure of the primary structure of the protein.0030

The primary structure is its sequence of amino acids - that is it - just the lengthwise string of amino acids, alanine, glycine, leucine, isoleucine, whatever combination happens to be.0035

That is referred to as the primary sequence; now, secondary structure occurs when the protein starts to fold.0050

Now, the complete folded protein, that is the tertiary structure, but before that, as parts of this polypeptide chain starts to fold and go this way and that way, there are certain patterns that develop simply by virtue of the nature of the peptide bond and the interactions that can take place and some of the constraints on bond rotation.0059

Two of those patterns are the alpha helix and the beta-pleated sheet.0082

That is what we are going to be talking about in today's lesson; this is our primary concern.0088

Now, the tertiary structure is, of course, the complete folded polypeptide chain, once this has taken on the final shape that it is going to take in free space.0092

Now, if you have more than 1 subunit in a particular protein, 2, 3, 4, 5, however many, when you put those individual units together, that constitutes the quaternary protein structure.0104

All proteins have primary, secondary, tertiary.0117

Some proteins that have multi-subunits, they are the ones that have the quaternary structure.0122

OK, let's get started.0126

Now, let's see.0131

Weak interactions among the amino acids in the peptide chain gives rise to the secondary and tertiary structures of a protein.0136

OK, in other words, secondary and tertiary structures just means its folded state.0178

A protein does not just stay as 1 long amino acid; it actually takes on some conformation.0188

OK, and again, let's go ahead and list these interactions.0194

Again, these interactions, what we call the weak interactions have a hydrogen bonding, which is probably the most important.0198

You have hydrophobic interactions probably the next most important.0215

Well, actually, you know what, I should not say that one is more important than the other; hydrogen bonding, yes, it is probably the most important, but the others, I would not necessarily classify them because they all participate.0226

We have polar interactions, and we have our ionic interactions.0236

Those account for the weak forces, the weak interactions.0250

Now, covalent interactions, there is some covalent interactions, but they are represented by only the sulfur-sulfur bond, the disulfide bond.0255

Covalent interactions, which facilitate folding, include the disulfide bond - that is about it - and we have talked about the disulfide bond when we talked about amino acids, no, primary sequence - OK - disulfide bonds.0266

OK, now, 2 principles govern the folding patterns we will discuss.0294

These are the 2 principles that you just want to keep in the back of your head.0318

Well, not necessarily just in the back of your head, but we are not going to discuss them more than just mentioning what it is that they are.0322

Two principles govern the folding patterns that we will discuss.0329

One of them is the hydrophobic amino acid side chains, they collect in the interior of a folded protein away from the aqueous solution.0333

Proteins are soluble; proteins are floating around in aqueous solution.0361

But again, hydrophobic means that they are afraid of water; they do not want to be near the water.0365

When a protein folds, it tends to have its hydrophilic amino acid side chains on the outside.0369

They can interact with the water; the hydrophobic, they tend to be on the inside as far away from the water as possible.0375

They collect in the interior of a folded protein.0381

It makes total sense; it is exactly what happens.0386

I will write "away from water".0391

OK, and 2: hydrogen bonds are maximized.0397

Again, hydrogen bonding, very, very important for protein folding, and hydrogen bonds, I will say, tend to be maximized.0402

OK, let's go ahead and recall the peptide bond.0417

The peptide bond, let me see; let me go to blue here.0422

Let's recall the peptide bond.0427

We have...remember our pattern?0438

We do N-C-C, N-C-C, right?0442

And let me see, N-C-C, the second carbon always know what, I need a little bit more room here, so let me redraw this, and in fact, I think I am going to do my resonance structure left and right instead of up and down.0450

Let me start over here on the left; let me go N-C-C, N-C-C, and the second carbon always gets the carbonyl, and let me see.0464

I will go ahead and do...well, let me see.0478

Yes, that is fine; I will go ahead and put some electrons there, and I will go ahead and just add a couple...well, you know what, that is fine.0484

I will go ahead and just leave it like that; it goes on, of course, in this direction and in that direction, but I was just concerned with a single peptide bond.0493

This is your peptide bond right here, the carbonyl connected to the nitrogen- OK, very, very important.0502

Let me go ahead and put this hydrogen in here, and I will go ahead and put my electron pair there.0510

Now, this electron pair, there is resonance going on here.0515

This electron pair actually jumps here, creates a double bond and pushes these electrons onto oxygen.0520

Another resonance structure for the peptide bond is the following: N-C-C, N-C - oops, not there - N-C-C jumping the gun a little bit.0526

So, we have something like this; we have this single-bonded between the carbonyl and the nitrogen, but it has double bond character because of this resonance structure.0545

Because of this double bond character, this peptide bond, it cannot rotate like a single bond.0555

This is fixed; this H, this N, this C and this O, they all lie in a plain.0560

H, N, C, O, they are in a plain that cannot rotate, precisely because of this resonance structure, because it has partial double bond character.0566

It is not a complete single bond; it is not a complete double bond.0576

It is a resonance; there is resonance going on.0579

Electrons can move because of resonance, the peptide bond, the bond between the carbonyl carbon and the next nitrogen, but peptide bond, itself, is not free to rotate.0583

This has profound consequences for protein structure and life and physiology, in biology.0614

OK, we have the following.0627

We have the following.0633

We have N-C-C, N-C-C, N-C-C, N-C-C, N-C-C.0642

I think I will do 1 more; I think I have 4 of them altogether, N-C-C.0654

Carbonyl is on the second of the pattern, N-C-C here, and, of course, this goes on in both directions.0660

Notice, this carbon right here, I will do it in red.0667

This is the alpha-carbon; it is the carbon that is attached to the carbonyl carbon.0672

Here, this is the alpha-carbon; here, this is the alpha-carbon.0679

OK, now, we said that the peptide bond is not free to rotate, right?0682

This is a peptide bond right here.0690

This is a peptide bond right here.0694

Sorry; this whole peptide structure, the peptide bond is actually this one right here between the carbon and the nitrogen.0698

Sorry about that.0705

There is another peptide bond right here; OK, those bonds are not free to rotate, we just said.0710

Now, the bonds that are free to rotate are the bonds to either side of the alpha-carbons.0716

In other words, carbon, this bond is free to rotate; that bond is free to rotate- that, that, that, that.0745

Those bonds are free to rotate.0754

Now, by convention, the bond, which is nitrogen carbon alpha is called the phi bond, greek letter phi.0759

OK, the bond C, alpha to the C carbonyl, it is called the psi bond or psi as you know it.0774

OK, in its fully-extended state, this one right here - if you just...N-C-C, N-C-C, N-C-C, N-C-C, fully-extended not folded - phi and psi are said to be at a 180°.0793

That is just convention.0825

This bond right here, this N-C, the phi bond, it can go like this, and this other one right here, the C, CO bond, it can go like this.0832

We have these 2 bonds that can rotate in its fully-extended state.0844

This bond is 180°; this bond is 180°.0849

Well, you can see that we can start rotating things, but eventually, things are going to bump into each other.0853

Theoretically, we can go all the way around; we can go from -180 to +180 or 180 down to 0 to -180.0858

That gives us a full 360° turn all the way around.0866

Real proteins do not do 360° turns, and the reason they do not is because of steric hindrance.0872

Things just start to bump into each other; again, these line structures, they do not give you an idea of just how closely packed these atoms are.0878

Just by convention, we said, phi and psi for a fully-extended peptide chain at 180°, that is really all you need to know.0886

OK, now, let's talk about secondary structure.0896

OK, excuse me.0900

Actually, you know what, I think I am going to go back to blue here.0909

OK, well, secondary structure by definition is the conformation of part of the peptide chain.0925

There are certain parts of the peptide chain that tend to take on certain patterns of folding, and that is what we are going to discuss.0948

That is secondary structure.0953

Not the whole peptide chain, that would be tertiary.0957

Now, given the constraints of bond rotation that we just discussed and side chain interaction - I remember we had side chains on these amino acids, they are going to interact with each other, and they are going to bump into each other - which is both good and bad.0961

There are 2 patterns of folding that tend to appear most often in proteins.0995

One of them is called the alpha helix, and the other one is called the beta conformation or the beta sheet; and I will explain the difference between beta sheet and beta conformation.1017

Most of the time, they are used synonymously; the beta sheet actually comes from several strands of the peptide chain lying next to each other to give you this thing that looks like a sheet- that is all.1036

OK, let's go ahead and talk about the alpha helix first.1049

Alpha-helix, I am going to go ahead and talk about a little bit, and then, I will go ahead and show you some images.1053

Now, the peptide backbone, and by backbone I mean the N-C-C, N-C-C, N-C-C, it wraps itself around an imaginary axis, not unlike a single-stranded DNA.1063

It wraps itself around an imaginary axis through the center of the helix, in fact, exactly like single-stranded DNA.1094

Well, I probably should not say single-stranded DNA, but you will see what we mean in just a minute.1116

OK, now, this twist is right-handed.1122

This twist is right-handed, and I will discuss what right-handed and left-handed helices mean in just a minute; and the R-groups that are on the alpha-carbons, they protrude out and away from the helix.1128

OK, let's take a look at our first image here.1159

Let's see; where is it?1163

OK, here we go; as you can see, let's take a look at this one over here on the left.1166

You see this pattern; you have got this N-C-C, N-C-C, N-C-C, N-C-C.1171

Actually, because of the constraints on the fact that the peptide bond cannot rotate, but the phi and psi bond can rotate, you end up with this pattern.1184

Well, you see the interactions, when it actually starts to curve this way, it is going around and around.1195

It is going up like this, like a spiral staircase, and that is exactly what is happening; and there is an axis right down the middle, and here, you can see the R-groups.1202

They are protruding out from the top.1212

OK, 1 complete turn accounts for about 3.5 amino acid residues.1215

Two turns for 7 complete amino acid residues, that is how they tend to arrange themselves.1222

And over here, you can see the hydrogen bonding that stabilizes this alpha helix structure- very, very common secondary structure.1230

Alpha-helices show up in a multitude of proteins.1239

Now, that is not a guarantee; we are not saying that all proteins have an alpha helix somewhere in their structure.1244

It just happens to be one of the structures that shows up in a lot of the proteins.1250

It is a motif; it is a pattern that develops, but that is no guarantee that it exists in every single protein.1254

Different proteins do different things, so some of them actually do not have alpha-helices at all so definitely distinguish that.1262

Here is another version of it; there you go.1268

You have your N-C-C, N-C-C, N-C-C, N-C-C, N-C-C pattern that wraps itself around an imaginary axis.1272

Here, you had your carbonyl, oxygen interacting with the hydrogen on the nitrogen.1282

You have got hydrogen bonding, hydrogen bonding that stabilizes this alpha helix- very, very stable arrangement, works out quite beautifully.1291

Now, let's go ahead and take a look at one more image of this.1300

Again, when you see this little ribbon-like thing and a helical structure, that is a schematic diagram of the protein.1304

What you are going to see when you see protein diagrams in most pictures is you are not going to see all these individual atoms.1314

You are not going to see ball and stick stuff; what you are going to see is individual twists.1321

That is a schematic; this twist right here, that is not part of the protein.1325

That is a schematic representation of the actual amino acid peptide chain - that is it - as you can see very clearly, this helical pattern.1330

OK, now, let's talk about this whole right-handed and left-handed helix.1340

Here is what right-handed and left-handed mean.1348

From your perspective, you are looking at this picture right now; if you take your hand and you run it away from you to the right and up, if your thumb in pointing up, it is a right-handed helix.1352

That is what this is; that is what alpha-helices are.1366

The alpha helix pattern is right-handed, notice, going away from you, going to the right away from you and up.1368

OK, notice, it is going up.1377

If your right hand follows that ribbon and if your thumb is pointing up, that is a right-handed helix.1381

If you happen to have another helix and if it is your left hand that goes to the left away from you and up and if your thumb in pointing up, then, it is going to be a left-handed helix, and that is exactly right.1390

That is all that is happening here; that is all that means.1401

OK, now, let's see.1406

I will write it on this page.1411

Interactions among the side chains can stabilize or destabilize an alpha helix.1416

Again, not all peptides have alpha-helices- very, very important.1446

OK, now, let's talk about the beta sheet, a little stranger to wrap your mind around because there is just a little bit more to keep track off in terms of what is interacting with what.1462

I am going to try my best to represent a good pattern that you can always follow, and when we actually look at some structures, we are actually going to do one by hand, do a couple by hand because it is very, very important that you would be able to do it by hand not just look at it.1480

For the most part, I think for the exams that you would take, I do not think you are going to be asked to draw out a beta conformation either parallel or anti-parallel, but at the very least, you certainly should be able to recognize it; but it is very nice to be able to draw one out because I think it helps crystalize it in your mind, solidify just what the arrangement is.1495

OK, beta sheet, OK, the peptide backbone - again, it is the backbone we are concerned with - arranges itself in a zigzag pattern resembling pleats, and if you do not know what pleats are, just think of an accordion or your pleated pants, sort of, that zigzag up and down, up, down, up, down, up, down- things like that.1517

OK, now, it is actually the beta conformation.1564

It is actually a conformation; this idea of sheet comes from the following.1575

When 2 or more peptide strands lay next to each other and interact, the structure, it begins to look like a pleated sheet.1583

Really what it is is if it is just a single strand or at most, 2 strands, what you have is something called a beta conformation.1625

OK, a single strand can actually arrange itself in this zigzag pattern, but when you lay multiple strands next to each other - let's say this is a strand, this is a strand, this is a strand - when you lay them next to each other, it looks like a sheet.1635

That is what is happening; really, what it is is when we speak about beta sheet, we are talking about beta conformation.1649

A single peptide chain can have a beta conformation.1654

Multiple strands either from the same peptide chain that is looped around or maybe a different peptide chain lying next to each other, that is what gives rise to the beta sheet.1658

You want to think in terms of beta conformation; that is what it is.1669

You do not want to think of beta sheet; you want to think conformation.1674

OK, now, the 2 or more segments/strands that are lying next to each other can be either parallel or antiparallel; and, of course, we are going to draw all of this out, so do not worry at all.1678

We are going to talk about this in a reasonable amount of detail and show you how to actually produce it yourself, not just recognize it on a sheet of paper.1712

Let's take a look here.1720

Aha, here we go; in a parallel arrangement, this right here is the peptide chain.1727

This segment of the peptide chain from here to here, all of a sudden, assumes a beta conformation.1734

In ribbon diagrams of proteins that you see, whenever you see some flat arrow, that is a beta conformation.1740

Well, this beta conformation, let's say the segment of - let's say, I do not know - 30 amino acids all of a sudden achieves a beta conformation, which we will talk about in a second.1749

I will show what it looks like, and then, you have the peptide chain that has just, sort of, random, and then, it comes around again; and then, it lays right next to this strand.1758

Now, you have, again, another beta conformation.1766

Well, if they arrange themselves like this, this we call parallel.1770

If, in fact, it ends up, let's say, having a beta conformation from here to here and then, just some random arrangement of the amino acids, but then, it loops around itself tightly; and now, it lays next to this one except going in this direction, we call that anti-parallel- that is it.1775

This is parallel, and this is anti-parallel; that is all that means.1790

That is all that means.1794

OK, now, let's see; I have got the image of the anti-parallel.1798

I have got the image of the parallel beta sheet; this is the anti-parallel beta sheet.1802

Now, let's go ahead and take a look at...aha, OK, now, this is a diagram of the parallel arrangement of the peptide chain.1810

This is 1 segment of the peptide chain; it is looped around, and this is another segment of the peptide chain.1825

See how they are next to each other; if you have, let's say, several of these, it starts to appear like an extended sheet structure- flat.1833

It is going to be like this and like that, like that, like that, like that, like that, and here is what is happening here.1842

Let's go through this very, very carefully.1850

I am going to describe what is happening on this image, and then, we are going to actually reproduce this image ourselves.1855

We want to be able to create one by hand; start at the top and repeat the N-C-C pattern, notice, N-C-C, N-C-C, N-C-C, parallel, N-C-C, N-C-C, N-C-C, again, N, C to the left, C, N, C to the left, yes, N, C to the right, C.1859

This is the parallel arrangement; all you have to do is double up the N-C-C pattern, the N-C-C pattern this way.1883

We will say start at the top, and repeat our N-C-C pattern going down in parallel.1890

OK, the carbonyl is on the second carbon, notice, N-C-C, carbonyl, N-C-C, carbonyl, N-C-C, carbonyl, and notice, they alternate, in-out, in-out; but you will get that anyway.1909

The carbonyl is the second carbon.1925

OK, now, along the inside, when you do this for 2 strands in parallel, these match, N-N, C-C, C-C, N-N, C-C, C-C.1938

They match; that is parallel.1952

Along the inside, the nH hydrogen bonds to the carbonyl, oxygen.1953

OK, that is what you have here, this nH hydrogen bonding to this carbonyl.1968

Notice, the hydrogen bonding is staggered; it is not straight across.1976

It is staggered, OK, down, up, carbonyl, the hydrogen, carbonyl, the hydrogen, carbonyl, hydrogen, carbonyl, hydrogen.1980

When you see something like this, when you see a parallel arrangement, you can recognize parallel multiple ways.1994

You can recognize the pattern of the N-C-C, N-C-C and then, the literal mirror image.1998

Actually, I am sorry, not a mirror image, just a copy of it right next to it, N-C-C, N-C-C, and you can also notice the staggered arrangement of hydrogen bonding between the carbonyl and the hydrogen on that nitrogen.2003

Now, the R-groups, they alternate - out of the page, into the page, out of the page, into the page - and last but not least, the pleats are on the alpha-carbons.2019

The pleats are here.2055

Go ahead and do this in black; that is a pleat.2060

That is a pleat; that is a pleat.2067

That is a pleat; what is happening here is these - 1, 2, 3, 4 - they are going down.2072

1, 2, 3, 4, they are coming up.2080

1, 2, 3, 4, they are going down; 1, 2, 3, 4, they are coming up.2084

If you look at it from the side, you will get something that looks like this, boom, boom, boom, boom, boom, boom, just a pleated pattern.2090

These R-groups, they are going to stick out.2100

These R-groups are going to go down; these R-groups are going to stick up.2105

These R-groups are going to go down; that is all that is going on here.2111

OK, let' see if we can actually do one of these by hand; it is really, really important.2117

We do N-C-C, N-C-C, right?2124

Let's do one more: N-C-C.2130

Carbonyl is on the second carbon; it is out, out and out.2136

OK, let's go ahead and do another one: parallel.2141

We have N-C-C.2146

We have N; we have C.2153

We have C, and we have N.2155

We have C, and we have C, N-C-C, carbonyl, N-C-C, carbonyl, N-C-C, carbonyl.2159

The nitrogen has hydrogen; the nitrogen has hydrogen.2167

Our hydrogen bonds in blue, hydrogen bonds there, hydrogen bonds there- that is it.2174

That is the pattern; you do your N-C-C.2184

You start at the top; the carbonyl is on the second carbon.2185

Along the inside, the nH, hydrogen bonds to the OH.2188

The R-groups alternate, out of the page, into the page, and the pleats are in the alpha-carbons.2191

There is an R-group out of the page; there is an R-group out of the page.2198

There is an R-group in the page; there is an R-group in the page- out of the page, out of the page and all the way down, and the pleats are along there, there, there, OK, there, there.2202

And if you were to look at this from the side, you would see that, that, that, that, and on the cusp, you would see an R sticking out here and then down here at this cusp, this.2224

You would see the R sticking out down here; that is what is going on.2235

This is the beta conformation; if you have multiple strands, you can have another strand and another strand and another strand.2239

Now, it becomes this beta sheet; this is not necessarily a beta sheet.2245

It is only 2 strands; it is a beta conformation.2250

It tends to become a beta sheet; OK, this is the parallel arrangement.2252

Alright, now, let's go ahead and take a look at an anti-parallel arrangement.2260

OK, now, the pattern for this image is actually from the bottom up.2267

So, what I am about to describe and what I actually draw is going to be from the top down.2271

The top down, this picture, we put it on this page in such a way that the particular pattern that I use, because I wanted to base on going from top to bottom, and because I wanted to maintain that N-C-C pattern just to make it easy and analogous to everything that came before, in this particular case, the way this image was arranged, is actually going to be from the bottom up.2277

Let me go ahead and just start, and we will talk about it.2303

Again, we are going to start at the top, and we are going to write our N-C-C pattern.2308

But again, for this image, it actually is going to begin from the bottom.2312

Notice, here is your N-C-C, N-C-C, N-C-C.2316

And again, the same thing, let's see, N-C-C.2321

Yes it goes down; the second C has the carbonyl.2330

Let's see, N-C-C, N-C-C, N-C.2331

OK, and then, we have...OK, now, when you arrange this one in this N-C-C pattern and then, what you do because this is anti-parallel, since you started with the N-C-C pattern, all you want to do is you want to reverse that pattern and go C-C-N, C-C-N.2339

If you were drawing this, you would go N-C-C, N-C-C, but then, you would go C-C-N, C-C-N because now, it is anti-parallel.2361

You are going to end up with the same arrangement, just keep going, just put together a second strand, put together another strand.2370

What you are going to discover is that now, again, the carbonyl, oxygen and the hydrogen on the nitrogen are going to hydrogen bond again, but this time, it is straight across- that is it, again, along the inside of the pattern.2376

Notice, we have N-C-C, N-C - I am sorry - C-C-N.2395

You are just reversing it; that is the anti-parallel part.2402

You are still going to end up with an arrangement, but this time, you are going to notice that the carbonyl and the hydrogen on the nitrogen are actually aligned with each other straight.2404

They are not going this way or this way; that is what characterizes this behavior.2412

OK, let's see what we have got here, N-C-C.2419

Let me see; what is the best way to do this?2426

N, C, should we go C-C-N?2430

Maybe, N outside, carbonyl, we have got N-C-C, C.2436

I am wondering if I know what, I am actually going to describe my pattern, and I think it would actually work out best.2458

Let me go ahead and do that; let me go ahead and do it here.2469

I am going to say, start at the top.2472

Let me see, 2, C, C, C-N, C-N.2483

Yes, that is fine; OK, start at top and write the pattern N-C-C.2491

This time...actually, you know what, no, I think this is going to be a lot more confusing.2508

My apologies; we will not go ahead and do this.2515

We will just go ahead and rely on this particular picture.2517

The only thing that you need to recognize with respect to this, I think the parallel is a lot easier.2521

The anti-parallel is a little strange, but again, the only thing that you really need to know is the N-C-C, N-C-C pattern, that is the same for one of the strands.2525

Anti-parallel just means reverse that; write it as C-C-N, C-C-N.2534

And then, when you do that, like we said before, you will end up, along the inside, you will have the carbonyl oxygen directly in line with the hydrogen on the nitrogen, and this is the anti-parallel beta conformation; and when you, let's say, do another strand here, which is going to be...if this one if we say it is this direction, since this is anti-parallel, it is this direction.2540

If you have another strand, it is going to be this direction because now, this and this have to be anti-parallel, and if you add another strand, it is going to be in that direction because this and this have to be anti-parallel.2566

Well, the hydrogen bonding takes place in between the strands.2576

When you have multiple strands, now, you have something called the beta sheet, other than that, this is the anti-parallel beta conformation just for 2 strands.2580

And again, N-C-C, N-C-C, C-C-N, C-C-N, everything else is the same.2592

You are going to treat it exactly the same.2597

In the N-C-C pattern, the carbonyl appears on the second carbon.2601

In the C-C-N pattern, the carbonyl is on the first carbon because it is C-C-N, right?2605

N-C-C, the carbonyl shows up here on the second carbon if you are doing that.2609

Well, going backwards, parallel, it is C-C-N.2616

It is OK.2621

Sorry; we are going down, C-C-N because again, the carbonyl, second carbon from the nitrogen.2627

Because you have a peptide chain that has a bunch of carbon-nitrogens, carbon-nitrogens, the carbonyl carbon is attached to a nitrogen, but the alpha-carbon is attached to the carbonyl carbon; and that is also attached to the nitrogen on the other end.2639

Because you are running them together, you have to choose a place to start.2652

You have to choose your basic unit; it is up to you.2656

You can choose nitrogen-carbon-nitrogen if you want to.2658

I prefer 3 atoms, N-C-C, and when I reverse that, you have to start in 1 place and go down or go up, as long as you are consistent.2663

I prefer going up to down, so if I do N-C-C, going from up to down, my anti-parallel is going to go C-C-N from up to down- that is it.2675

And because the carbonyl is on the second carbon away from the nitrogen, here, the nitrogen, it is on the second carbon away from the nitrogen.2687

It is just a question of consistency; you just have to keep track of that.2693

That takes care of the anti-parallel beta conformation.2699

OK, now, let's go ahead and finish up with just a couple of words on tertiary and quaternary structure, and we will be all set.2703

Tertiary structure, alright, the final folded spatial arrangement of a single polypeptide chain- that is it.2712

Once it is finally achieved, once it has gone through its alpha-helices and its beta sheets and it has taken on its final shape, that is the tertiary structure.2744

Now, quaternary structure, as we said before, when a protein has 2 or more subunits - in other words, separate chains - the combined form...actually, I will say this.2754

If a protein contains 2 or more, when a protein has 2 or more subunits or separate chains, the overall combination, that is what constitutes quaternary structure- that is it, nothing too complicated.2806

Let's take a look here; I think we have an image of myoglobin here.2832

This is myoglobin.2840

Let's see where it starts; it starts here, goes through an alpha helix, a little bit of just random arrangement of the amino acids, goes through another alpha helix, turns, goes through another alpha helix, turns, alpha helix, alpha helix, and then, it ends, or you can start here and go this way.2846

It does not really matter; this is myoglobin.2863

This is tertiary structure; myoglobin is a single polypeptide chain that happens to fold, and you notice, certain segments of it, in this particular case, there are no beta sheet, you have just this, just a series of alpha-helices and free fragments that have no general discernible pattern.2867

Here, we have the hemoglobin.2886

You have 1, 2, 3, 4 subunits.2893

This would constitute quaternary structure because now, all of the subunits started to interact, so you have just this whole protein that does what it does.2898

That is quaternary structure; OK, now, let's see here, one final word.2909

This is just some random protein; it is the ribbon diagram of some random protein.2917

OK, and we have mentioned this before, but alpha-helices are represented precisely by/as helical ribbons.2923

OK, and beta conformations or beta sheet patterns, beta conformation patterns are represented as flat arrows.2944

Let's go ahead and start and see what we can do.2968

We begin here; we have some random amino acid sequence.2972

It does not really seem to strike a pattern, and then, here, it has an alpha helix; and then, it goes here.2978

The polypeptide chain continues, and then, this segment, notice, it is a flat arrow, so it is in a beta conformation, turns around.2985

It goes into, again, another beta conformation this way.2993

OK, and then, this way, another beta conformation up to here, and then, it comes around random sequence and then, a final alpha helix and then, another random sequence; and it finishes here.2997

This is the COO- end; this is the amino end.3015

This is the NH2 end; more than likely, we generally start with the NH2 and end with a COO-- that is it.3027

When you see a ribbon diagram, flat arrow is beta conformation.3036

The helix is the alpha helix, and that is it; most of the protein structures that you will see will be given to you in ribbon conformations.3040

Thank you so much for joining us here at; we will see you next time, bye-bye.3048