Biochemistry Amino Acids, Continued

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

On the last lesson, we started talking about the amino acids and, we were undergoing the process of classifying those amino acids.0004

We are going to continue with that right now.0011

Let's just jump right on in.0013

OK.0016

We talked about the non-polar R-groups, and we talked about the aromatic R-groups.0017

The next group we are going to do is going to be the positively-charged R-groups.0023

Let's see.0029

Let's go ahead and stick with our blue here.0030

OK.0043

And again, at a pH equal to about 7, which is near the physiological pH.0045

OK.0052

The first one that we have is...let's go ahead and do C, COO^-, we have H, we have our amino with a positive charge.0053

And now, CH₂, CH₂, CH₂, CH₂, ⁺NH₃.0067

OK.0071

This is lysine, and it is Lys, and its single letter designation is a K.0080

Curious isn't it?0093

OK.0094

Our R-group that we're talking about is right here.0097

Lysine has 1,2,3,4 - I always forget how many - 3 or 4.0100

1,2,3,4, methylene groups CH₂, and then of course, you notice, you have another amino group and it is protonated.0105

OK.0116

Now, we'll do this one over here.0117

C, COO^-, H, ⁺NH₃.0123

Now, we have CH₂, CH₂ - this one is kind of interesting, we have an NH, we have a C, we have ⁺NH₂, and we have NH₂.0130

It's a bit of a curious one, all kinds of nitrogens in this one.0151

OK.0156

This is called arginine and it is Arg, and its single letter designation is an R.0157

Notice, on the alpha carbon, you've got 2 methylene groups, and then you have a nitrogen with a hydrogen, then you have another carbon; and then you have on this carbon, you have an NH₂ group, an amino group, and you have a protonated amino group.0167

That is arginine- positively charged.0185

Here is your positive charge on this R-group.; here is your positive charge on that R-group.0188

OK.0195

Let's see.0197

OK, that's fine; I guess I can do it here.0199

COO^-, H, NH₃- no changes here - this is an ⁺NH₃.0201

Alright.0212

We have CH₂, so that's N, that's C, that's N, and that's C, and double bond there.0213

Oops, why do you put a single bond, there is not a triple bond, definitely not a triple bond.0236

That is going to be a double bond.0240

This is going to be an H.0243

This is going to be an H.0245

Let me see if I've forgotten anything.0246

1, 2, 3, oh yes...we have an H here, 4, 3.0248

OK.0253

This is histidine, and we're going to be talking about histidine in just a little bit - very, very important - it is His; it is that.0255

Now, notice, we said positively charged R-groups, but you notice, I haven’t put a positive charge on here.0266

Here is why: that nitrogen, at a pH equal to about 7.0, which is what these are, notice that we've written this particular histidine with this not being protonated.0274

There is no hydrogen attached to it to give it a positive charge, so as it is, this is neutral - OK - pH7.0298

Although we wrote the R-group as neutral, this particular N is actually protonated to a fair amount.0308

It isn't completely protonated.0335

Some of it is deprotonated, but enough of it is protonated to where we can actually group it as in the ones that have a positive charge.0339

You can think of an H being attached there and there being a positive charge.0347

We just haven’t written it that way because it's not completely protonated like these are at pH7.0355

At pH7, some is protonated, most actually, is not, but enough is protonated to where we can consider it as part of this group.0361

OK.0371

As neutral, the N is actually protonated to a fair extent.0372

And again, all of these will make sense when we discuss the acid-base behavior.0381

OK.0387

Now, let's move on to the next group.0388

We have negatively charged R-groups, and I apologize for the tedium of not just putting a picture up and running through these.0391

This is more active; this is important.0402

OK.0407

Alright.0418

Let's do C, COO^-, H, ⁺NH₃, we have a CH₂, we have a C - I can never do that right on the angle, oh, I don’t want to be doing this is - negatively-charged; t7:33 his is a carboxylate.0419

There we go.0453

This is called aspartate, and it is Asp; and single letter designation is D.0454

The group is right here.0461

We have a methylene group, and notice, we have another carboxyl group.0466

This carboxyl group is not this one.0469

It's not attached to the alpha carbon.0472

This is the one that makes it alpha-amino acid, not this.0474

This just happens to be an extra carboxyl group, which is deprotonated at neutral pH.0480

OK, let me see.0488

And, let's do C, COO^-, H, ⁺NH₃, we've got CH₂, we've got CH₂.0492

So, we have 2 methylene groups, and then we have our other carboxylate again- this is glutamate.0506

Glutamate, Glu and single letter designation is E; and we have that as our R-group.0516

OK.0529

Let's go to uncharged but polar R-groups- R-group, I should say.0531

OK.0545

We've got C, COO^-, H, ⁺NH₃, and we have CH₂, and we have OH just like glyceraldehyde.0547

This is serine, Ser, S - a very, very, very important amino acid - plays a pivotal role in many, many, many enzymes.0564

Where are we?0580

And again, I encourage you to double check these structures.0581

I am not using a figure and running through it.0584

I'm actually drawing these things out, so please confirm that I have actually drawn them correctly.0588

We are all human; we all make mistakes, so by all means, this is actually a great way for you to actually look at a figure in your book; and make sure that I'm actually drawing it out correctly, and I'm matching the right amino acid, with the right name and the right three-letter symbol and the right single-letter symbol, rather than just taking my word for it.0593

OK.0613

Let's go: C, C uncharged…OK, that's fine0615

Let's do C, COO^-, this is H, this is ⁺NH₃, and now, we've got a C here, we have a hydroxy, we have that, and we have CH₃.0623

OK, this is threonine.0641

So, you notice the C here, you have the OH attached here, there is another C, this is just another CH₃ group, threonine, this is Thr and this is a T.0646

Our R-group is right there, and here, our R-group is right there.0657

That is threonine.0664

OK.0666

The third one in this group: COO^-, H, ⁺NH₃, we have CH₂, and we have SH, sulphur- this is cysteine, Cys and C.0668

We’ll talk more about cysteine in just a little bit.0692

Let's do C, COO^-, this is an H, this is our⁺NH₃, and then we have our CH₂, and then we have C, and double bond O.0696

Now, we have an NH₂.0713

So now, instead of a carboxylate here, we have the amide.0716

This is asparagine.0721

It is Asn, and its single letter designation is that.0727

OK.0734

Now, asparagine is the amide of aspartate, the one that we had before in the previous.0740

It's just, instead of a carboxyl right here, we have replaced that O minus, that OH group, where the H is deprotonated.0746

We've replaced it with an NH₂.0753

So, whenever you have a carbon double bonded to an oxygen in that same carbon of the carbonyl carbon, is bonded to a nitrogen, that's called an amide or an amide.0755

Again, pronunciation doesn't matter.0763

Now, our last one is COO^-, H, ⁺NH₃, now, we have a CH₂, CH₂, C.0767

I should really draw this a little bit... you know what, I’m just going to do it horizontally, How is that...NH₂, and this is glutamine.0785

This is glutamine; it is Glm, and it is a Q for a single-letter designation.0802

Asparagine is the amide - I actually prefer to say amide myself - well, let me do it in red.0811

This is your group; these are your groups- it's the R-group.0822

In the case of asparagine and glutamine, they happen to be amide of aspartate, and the amide of glutamate, the 2 other amino acids.0828

OK.0843

There you go.0844

Those are our 20 common amino acids broken down into groups.0845

In this particular case, we happen to choose a group of 5.0851

That's it.0856

Now, let's go on and talk a little bit about these.0858

Some things you should know about the amino acids, there are thousands of things that you should know about the amino acids, but we don't have all the time in world.0861

We'll worry about that as you go on in your biomedical career, but a couple of things that you should keep in mind as we begin our discussion of proteins and amino acids: you should know about the amino acids.0874

OK.0893

Cysteine easily diamerizes, and diamerize means 2 molecules come together to form a single molecule.0896

A dimer made up of 2 pieces diamerizes to form something called interestingly enough, cysteine, Ine.0908

That's why it was different.0922

It's written with an EI instead, so the dimer version is the one with the Ine.0923

Let me go ahead and write out this reaction in structural form.0929

C, COO^-, H, ⁺NH₃, we have CH₂, and we have SH.0935

We are going to add it to another one, so let me just go ahead and write it from left to right this way.0946

COO^-, H, CH₂ and SH.0952

And, what happens is the following.0958

Now, I'm going to write this vertically.0963

OK.0964

So, let's go ahead and do C, COO^-, ⁺NH₃, this is going to be CH₂, this is going to be S, this is going to be S, this is going to be CH₂; this is going to be another alpha carbon - yes, that's right – this is going to be COO^-,COO^-, this is going to be ⁺NH₃, and there is an H, S, S.0965

There you go.1005

OK.1006

I'll go ahead and make the arrows a little bit longer and I'm going to introduce just a little bit of biochemical notation.1009

A little arrow going out, 2H⁺ + 2 electrons; or if they're coming in this way, 2H⁺ + 2 electrons.1017

What happens is the following.1029

When these diamerize, what ends up happening is this H plus an electron goes away.1033

This H plus an electron goes away and this S bonds with this S to form a dimer.1038

Here is one of them; here is the other.1047

OK.1052

This right here, this is called the disulfide bond.1053

Profoundly important - we'll be talking about this in a couple of lessons - a disulfide bond.1058

This is how long chains of amino acids, actually they bend and fold, and when a cysteine in one part of the protein chain, and there is a cysteine on another part of the protein chain, when they tend to come together, they end up actually forming a covalent bond, this disulfide bonds.1065

So, what you have is this loop, and there might be other places where it's connected.1084

Disulfide bond is very, very important in the overall structure of a protein.1088

Now, 2H⁺ + 2 electrons, or you can think about it as 2 hydrogen atoms, either way.1093

This right here.1104

When these are lost, what you have is oxidation- fixed oxidation.1107

You're taking away electrons or another way to think about oxidation is removing hydrogens.1112

By adding electrons, adding hydrogens, you're reducing it.1117

Two cysteine amino acids oxidize to a cysteine dimer.1122

A cysteine dimer reduces to 2 cysteine amino acids.1127

OK.1131

So, our lost, so we call this oxidation.1133

This is oxidation.1137

This is oxidation.1140

OK.1144

Now, tryptophan and tyrosine.1148

I will let you look up their structures- tryptophan and tyrosine.1153

I'll give you a hint: they are in the aromatic group- tryptophan and tyrosine.1157

So again, this is just some basic information on some of the amino acids, just some things to keep in mind that we should know.1167

To some extent phenylalanine, they absorb, because they had aromatic groups, they absorb ultraviolet light strongly.1172

There is a very strong absorption - no, I'm not going to use that symbol for at, I'm just going to go ahead and write AT - at about a wavelength of 280 nanometers.1195

OK. This explains why proteins absorb UV light.1217

It's because of the tryptophan, tyrosine and the phenylalanine content in that particular protein.1231

And of course, this gives us an analytic tool by which to do something, measure things with proteins, analyze proteins.1238

It gives us another thing that we can measure or identify.1246

OK. Now, let's go back to blue.1253

OK, so, there are other amino acids, in fact, a few hundred amino acids floating around on the cell, that are not so common.1258

OK.1277

Some are derived from common amino acids and they do show up in proteins, but are modified after the protein has been synthesized- after protein synthesis.1280

In other words, there are some uncommon amino acids that you do find in proteins, but they're not incorporated while the protein is being built one amino acid at a time, strung together as beads on a string.1311

They use these particular uncommon amino acids.1324

The protein is built using the 20 common amino acids, and then after that, there is a modification.1329

There is something added; there is something subtracted to a particular amino acid residue, to a particular amino acid on the protein chain.1337

I'm just going to list a couple of them, just so you know.1345

And again, you'll find more on your book and I would certainly urge you to take a look at them just structurally.1348

They are very, very interesting1354

So, the first one we're going to take a look at is, well, let me go ahead and draw this structure first, and I'm going to draw it linearly like horizontally.1356

Let's go, C, CO^-, H, ⁺NH₃, we have CH.1366

OK.1391

I've got CH₂, CH₂, I've got CH₂, I've got a hydroxy there, I've got CH₂, and I've got ⁺NH₃, 1,2,3,4.1392

OK.1414

This is called 5-hydroxylysine.1416

You'll see it as one word normally, the hydroxylysine or the small L.1425

I tend to separate them, that's just my personal preference.1428

Don't worry, you're not going to get points taken away you shouldn't, unless your teacher specifically says keep it as one word.1432

I know some teachers like that.1438

So, 5-hydroxylysine...this is the 1-carbon, this is the 2-carbon. this is the 3-carbon, this is the 4-carbon, this is the 5-carbon, right?1440

We said the carbonyl carbon is the first carbon. So 5-hydroxy...there is an OH on the 5-hydroxylysine.1450

This is originally lysine, so if I block out this hydroxy, what I’ll have is the normal amino acid lysine.1458

So the protein is synthesized, lysine is put on there, and then after that, the hydroxy is put on there.1463

This is one carbon, this is the alpha carbon.1474

This is the beta carbon, this is the gamma carbon.1478

This is the delta carbon, so it's also called delta-hydroxylysine.1481

And again, number 1 and alpha are not the same.1487

Alpha, beta, gamma, delta, epsilon, and so forth; 1, 2, 3, 4, 5...so, you'll see them both.1491

OK.1499

This is found in collagen, a connective tissue protein- a very, very, very, very important protein.1504

It's what keeps skin soft and supple, elastic.1519

OK.1538

Another one would be something like this.1539

Let's do a C; let me write it a little farther out.1545

This is going to be the final example of an uncommon amino acid.1551

This is the alpha carbon.1559

I always like to designate that, so that I know where it is.1562

CH₂, this is CH, this is CO^-, there is a CO and O^-.1567

So, this is alpha, this is beta, this is gamma, so this is called gamma-carboxyglutamate.1589

Let me go to blue...alpha, beta, gamma.1602

On the gamma, there is another carboxyl group, COO^-, and then of course, this rest of the molecule happens to be the normal glutamate.1605

That's it, just a couple of uncommon amino acids that you should know about, nothing too fancy, nothing too difficult.1617

OK.1624

Thank you for joining us here at Educator.com and Biochemistry.1625

We’ll see you next time for discussion of the acid-base properties of amino acids.1630

Take care, bye, bye.1632