Biochemistry Alpha Helix & Beta Conformation

Hello and welcome back to Educator.com, 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 are...you 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 gets...you 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