Biochemistry Amino Acids

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

Today, we're going to start our discussion of biochemistry proper with the first of the biological macromolecules- the proteins, and proteins are made of amino acids.0004

Let's just jump right on in.0015

OK.0018

Of the biological macromolecules, proteins are the most abundant.0020

You have lipids which are your fats; you have the nucleic acids.0025

You have the carbohydrates, the sugars; and you have proteins.0028

Proteins are the most abundant.0032

Proteins are the ones that actually do everything.0034

They're the work horses of physiological systems.0037

Let's go ahead and write that down; let's do a blue ink today.0042

OK.0047

Of the biological macromolecules, proteins are the most abundant and the most diverse.0050

OK.0075

Proteins are made up of amino acids strung together like pearls on a string, like beads on a string.0076

Proteins are made up of amino acids strung together- that's it.0084

That's all a protein is.0098

It could be 2 or 3 amino acids strung together, or it could be a thousand amino acids strung together- that's it.0100

OK.0110

There are 20 common amino acids that make up the majority of proteins.0111

Well, they make up all the proteins, but I'll go ahead and just write the majority because that's the way I have it written.0128

OK.0139

All 20 are actually called alpha-amino acids and have the following structure.0143

OK.0166

Let me see where should I put this; that's fine, I'll go ahead and put it in the center.0168

We have C, COO, O^-; OK, we have an H, we have NH₃⁺ - did I put a plus, yes I did - and we have R.0173

OK, so this right here, this is called the alpha-carbon, and it is the alpha-carbon because it is the C that is attached to the carbonyl group; and the carbonyl group - you remember from organic chemistry - is this thing right here.0190

In this particular case, it is carboxylic acid because you have C, double bonded O, single bonded O, minus, the H has been taken off; it's usually COOH, and we'll talk about why I wrote the minus and the plus here a little bit later, but that's it.0223

It's called the alpha-carbon.0237

The alpha-carbon is not the first carbon in the chain.0238

The first carbon is the carbon of the carbonyl 1, 2, and as there are others; but the alpha-carbon is the one that's actually attached to the carbonyl carbon.0241

It's very, very important to distinguish that, and we'll talk a little bit more about that when we get into larger molecules and things like that, when we talk about alpha, beta, gamma, delta- things like that.0251

OK.0260

Now, the only thing that is different from one amino acid to the next is the R-group.0267

It's this thing right here.0294

That's the only thing that's different; everything else is actually still the same.0295

There is an alpha-carbon; there is an H attached to it.0299

There is an amino group, that's why we call it an alpha-amino acid.0301

This is the acidic group, the COOH or COO^-, it's the carboxylate, it has lost its hydrogen ion; so carboxylic acid, carbon alpha-amino acid- this is the only thing that changes for the 20 different amino acids.0306

OK.0324

Different R-groups give different properties, and this is what makes proteins so amazing.0327

The body coated in your DNA is, of course, the instructions for how to make the protein, and the protein is just based on a series of amino acids strung together - this one, this one, this one, this one - depending on how we string them together and how many we get different properties for the different proteins because different proteins have to serve different functions.0350

This is what's so amazing.0372

You have this incredible, incredible diversity of things that proteins do, I mean all kinds of things- things that you would never think are connected, and yet all of that is based on the properties of these 20 amino acids, 20, that's it.0374

I mean it's just as extraordinary as having those 4 bases that make up the DNA.0389

I mean it really is kind of extraordinary that you can actually have this level of diversity of function just from so few pieces.0393

OK.0406

Now, let's go ahead, let me redraw this structure here, just so we have it on the same page.0409

A C, O^-, there is an H, there is an R-group, and there is an amino group, and I'll put 3, and I'll put a positive charge on the nitrogen.0417

OK.0429

Notice that 4 different groups are attached to the same carbon.0430

The 4 different groups are attached to the alpha-carbon.0443

Let's go back to blue.0453

1, 2, 3, 4, you have the H, you have the carboxylic acid group, the carboxylate, you have the amino group, and you have the R-group- 4 different groups attached to a central carbon.0454

OK.0465

The alpha-carbon, the alpha C is a chiral center; and I hope that you remember what a chiral center is from organic chemistry.0470

Anytime you have 4 different groups attached to a single carbon, that carbon is a chiral center; and what that means is that, the arrangement of these 4 groups in space is such that you actually get two different versions of this particular molecule.0482

You get something called a left handed version, and you get something called a right handed version.0497

Let's write this out, each amino acid, except for glycine, and we'll see why later, because glycine, this R-group happens to be an H, so there are 2 hydrogens attached to the alpha-carbon, so it doesn’t come in an enantiomeric pair.0511

It doesn’t have a left handed, right handed version- it's just glycine.0534

Each amino acid exists as an enantiomeric pair, what we would call left handed and right handed- that's the best way to think about it.0550

In other words, what happens if I have a solution of, let's say alanine, some amino acid, if I have a solution of alanine and if I have separated that solution out into its left handed alanine, right handed alanine, if I pass some plain polarized light through that solution, one of them is going to rotate it to the left, one of them is going to rotate it to the right.0575

It has to do with how these 4 groups are arranged in space; and enantiomers, as you remember, are mirror images that are not super impulsible.0603

My left hand and right hand are mirror images of each other.0612

There is a mirror right here, but I can’t take my right hand, put it on top of my left hand, and have it match equally- it won't happen.0615

That's all that means, and you hopefully you remember that from organic chemistry; if not, I would definitely urge you to either go back and take a look through your books in the discussion about chirality, or take a look at the videos here at Educator.com for organic chemistry discussing chirality.0624

OK.0640

Let me go back to red here.0643

Configuration in biochemistry, in other words, configuration is just the arrangement of atoms or groups in space around the central atom; so, configuration in biochemistry is based on the D/L system and the reference molecule against which configurations for other molecules is decided.0645

OK, so let me see.0706

Configuration in biochemistry is based on the D/L system, and the reference molecule against which configurations for other molecules is decided is glyceraldehyde.0707

That’s just the convention that we have chosen- glyceraldehyde.0717

Now, let's go ahead and talk a little bit about glyceraldehyde.0725

When we decide on what this configuration of our protein is going to be, we're going to base it on what the configuration of glyceraldehyde is; and then we're going to decide whether it’s going to be a D-amino acid or an L-amino acid, and this is what we're going to discuss right now.0726

Let me go ahead and I wonder if I should draw it here.0741

No, let me go ahead and draw it on the next page.0745

Yes, let me go ahead and do it on the next page here so we have it on one.0748

Let me draw glyceraldehyde here.0752

This is C, this is going to be COH, this is going to be H, this is going to be CH₂OH and OH.0755

I strongly urge you to draw out these structures.0768

It's one thing to see them on a page, and it's one thing to see them as figures in your book; and you might be able to go through them, and after a couple of days of just sort of looking over them, looking over them, you might think that you actually have memorized them or understand them- I promise you, you don't.0772

There is a very big difference between being able to write out a structure- passive learning versus active learning .0787

You have to be able to actively draw out a particular structure.0794

That's the only way that your mind will ever really truly know that it understands something, if you could actually produce it, not actually say it's this, it's this, it's this.0797

OK.0809

This is something called L-glyceraldehyde.0810

OK.0819

This thing is actually something called a Fischer projection.0820

Yes, that's fine.0828

This is called a Fischer projection and it is equivalent to this.0830

C...you remember dashes and wedges from organic chemistry?0841

This is H, this is OH, and this is C - oops, sorry - this is C.0850

I'll go ahead and put that there and like that.0861

OK.0863

These wedges, that means that this group and this group, so this carbon right here this alpha-carbon, this is the alpha-carbon, because again, it is attached to the carbonyl group.0864

This carbon is in the plain of the page, but I hold a molecule at space - you remember, carbon is tetravalent, it has 4 groups on it, but those 4 groups are arranged in a tetrahedral arrangement, they're not just one on top of each other like a square, it isn't planar molecule, it is a 3-dimentional molecule.0877

When I hold that carbon like that, this H and this OH actually come out toward me.0894

They come out form the plain of the page toward me.0899

The dashes mean that it’s going away from me.0902

A Fischer projection is just a line version representing this.0905

Anything on the vertical axis, so this and this, it means they're pointing away from you; this and this, the H and the OH, they're coming out at you.0909

A Fischer projection allows us to just use lines without necessarily have to use this dashes and wedges.0920

That's all this means, so L-glyceraldehyde is this particular arrangement.0926

Now, let's go ahead and do D-glyceraldehyde right underneath.0932

I have C, I have COO, I have the H here, I'm going to leave the CH₂OH like that, but 'm going to put the hydroxy on the right, and I'm going to put the hydrogen on the left.0940

Notice, the only thing that i have changed is 2 substituents.0952

Anytime you switch the position of 2 substituents, you reverse the orientation, you change L to D, you change D to L.0954

If I switch the other 2 also, I switch it back to the original.0963

That's what it is; you have to switch 2 constituent and it changes the orientation in space.0967

Now, this equivalent would be, just draw it out, and again you want to definitely draw as many of these as possible - oops sorry 1, 2, 3, 4, 1, 2 ,3, 4 - let's go ahead and do some wedges there and this time the hydroxy is on the right, the hydrogen is on the left and we have CH₂OH.0972

OK, this is D-glyceraldehyde.0997

There you go.1005

OK.1007

Now, let's go back to blue.1009

OK.1011

All amino acids and biological proteins - well, all proteins are going to be biological, biological proteins, sorry, that's a little redundant but OK - are the L-enantiomer or enantiomer.1014

The pronunciation is irrelevant; it's the chemistry that's important.1040

Their configurations, for all of the amino acids, match L-glyceraldehyde.1046

When we say amino acid, we're talking about an alpha-amino acid, we're talking about an L-alpha-amino acid - that's it - but we're not always going to say L-alpha-amino acid; we just want to know what it means and what are these that we are dealing with if the question of stereochemistry actually does come up.1063

Sometimes it does; sometimes it doesn't.1081

OK.1084

Now, let’s go ahead and draw out the structures.1086

Let me redraw L-glyceraldehyde here on top.1088

This is C, this is a COH - and please, please, please confirm my structures, sometimes we get so carried away with drawing out these carbons, and hydrogens, and oxygens, and sulfurs, and nitrogens, that we're going to make mistakes, so by all means, please confirm these structures, we're all human.1093

OK.1115

Our H is on the left for glyceraldehyde, our hydroxy is on the right, and we have the CH₂OH, so this is L-glyceraldehyde.1116

Now, our proteins look like this.1124

Let me do the amino acids; I'll do these in red.1129

This is C, this is COO^-, this is H, this is NH₃⁺, and this is the R-group.1133

Notice, this is the alpha-carbon of L-glyceraldehyde, this is the alpha-carbon of the amino acid, the carbonyl group is on top, hydroxy on left, amino group on the left, hydrogen on the right, hydrogen on the right, this group CH₂OH, R-group.1144

This is why glyceraldehyde is the reference molecule.1164

The configuration of an amino acid is based on L-glyceraldehyde.1167

This is what all amino acid in your body look like.1172

This is an L-amino acid, and let me go ahead and draw the equivalence one last time.1176

OK.1187

And again, when you see these lines you are looking at a Fischer projection- anything on the vertical axis is pointing away from you; anything on the horizontal axis is coming out towards you.1188

You have H, you have NH₃⁺, you have the carboxylate, and of course, you have the R-group, whatever that happens to be.1199

OK.1211

Now, just so you know - let me go ahead and do this one in blue - just so you know, when you guys took biochemistry, and you guys were studying stereochemistry, you didn't learn the D/L system; what you learned was something called the R/S system.1212

In other words, you took those 4 groups on there and you assigned each one of a priority based on the molecular weight of the atom that's attached to the carbon.1229

For example here, the hydrogen would be the lowest priority, the nitrogen would be - oh actually, let's go - nitrogen would be first priority, and then this carbon would be second priority, the R-group would probably be third priority, and hydrogen would be the last priority.1239

You take that molecule and you arrange it in such a way that the hydrogen is pointing away from you, out of the page, and then when you look at the other 3 groups, you count 1, 2, 3 or 1, 2, 3.1257

If it goes clockwise, we call it S-configuration, if it goes counter clockwise, we say S-configuration.1270

If when you're looking at it, it goes clockwise, it's called the R-configuration.1279

So, just so you know, L-amino acids, they correspond - it doesn't matter- they correspond to S-enantiomers in the R/S system, so just so you know that this R/S system exist, we didn't just throw it out; it's just in biochemistry, they tend to use the D/L based on glyceraldehyde.1283

OK.1312

I wonder if I should...no that's fine.1318

Well, you know what, let me go ahead and draw it out.1323

OK.1325

If I had a carbon and if I had hydrogen pointing straight back behind me so that I can't see it, it’s actually blocked by this carbon, this is going to come out NH₃⁺; what you would be looking at is something like this.1326

OK.1346

This is first priority, this second priority, this is not an H, this is the R-group.1347

Sorry, see, I told you.1354

That’s the R-group; R-group is going to be third priority.1357

We are moving in a counter clockwise direction when we count 1, 2, 3- S-configuration.1359

Again, not a big deal.1366

It's L-glyceraldehyde that is the standard, but thought you should know this just in case.1368

OK.1373

Now, let's go ahead and talk about the classification of amino acids.1374

Now, we classify amino acids - well, let me just go ahead and write this out first and talk about it...classification of amino acids - we classify amino acids for any number of reasons; a part of it is to help you memorize them, so it's much easier as you know to memorize things in groups.1380

If I have 20 things that I have to memorize and you will certainly have to memorize the structures and the names for these amino acids, it's easier to memorize it in groups, so there is a utilitarian reason.1402

There is also another reason: we can classify them based on their chemical properties, so there are some that are going to be polar, some that are going to be aromatic R-groups, some that have charged R-groups, some that have uncharged R-groups.1413

The truth is there is a bunch of ways to actually classify depending on what it is that you're trying to do.1430

Again, there are 20 amino acids, and they, for the most part, behave the same way; but there are reasons why, later on you'll see, certain proteins have certain amino acids in certain specific places when we talk about enzymes.1435

Again, classification of amino acids is just something that we do.1450

Our classification is going to be based on the following: we will classify according to properties of the R-group, and we are going to basically break this up into 5 different groups.1456

Our first group is going to be the nonpolar R-group.1466

Our second is going to be the aromatic R-group, and then we’re going to have polar R-group, and then we're going to have positively charged R-group, so there is a group of amino acids that have a positively charged R-group under normal pH conditions, under normal physiological pH, which is in the range of about 7-7.4 - and again, we will talk about that in a minute - and negatively charged R-group.1475

OK.1542

What I'm going to do is, I'm going to draw out these structures by hand, of the 20 amino acids; and I'm going to designate the group.1543

I’m going to give you the 3 letter short hand designation, the single letter designation for each of these amino acids.1550

I’m going to be drawing these at the way that these amino acids are found under normal pH conditions for the body, which is again, in the range of about 7-7.4 or about 7.3.1556

We're going to talk about pH and acid base behavior of amino acids a little bit later, so don't let the these charges or why it is that certain things are charged and why there are not.1570

Don't let that throw you; it will make sense after the fact.1583

Right now, I just want to talk about the classification of these amino acids.1585

OK, so let's go ahead and start out with the amino acids with nonpolar R-groups.1589

I wonder if I should start here or that's fine; let's go ahead and go red.1596

I guess I can start here: amino acids with nonpolar R-groups.1604

Alright, so, the first one we want to look at, this is C, this is COO^-, and I'm not going to draw up a double bond, I'm just going to write this group, the carboxylate group, the COO^- - hopefully you know now that it's a carboxylate group - COO^-, pH is here, NH₃⁺, and H.1620

This is glycine; its three letter designation is Gly, and its single letter designation is a G.1648

The particular group is an H; this one does not come in an enantiomeric pair.1660

It’s the only one that doesn't because the H and the H are the same.1664

OK.1668

The next one, let's go ahead and do...if the R-group is a CH₃⁺, so now, our R-group is right there; this is called alanine, and it is Ala, and its single letter designation is A.1670

OK.1696

Let's go ahead and do the third one- H.1697

Notice, this part is all the same, the only thing that’s changing here is the R-group.1706

We have the CH, we have CH₃, and we have CH₃.1711

Our R-group is right there.1720

This is called valine or some people pronounce it as valine.1723

Again, pronunciation is irrelevant; what's relevant is the chemistry.1728

So, that's 3 of them: glycine, alanine, valine- I say valine, anyway.1734

OK.1739

And, let's do, there is a fourth and a fifth so should I do leucine?1740

Yes, it's fine, I'll go ahead and do leucine next.1748

C, it's a C, COO^-, H, NH₃⁺, and I hope you'll forgive me for repeating myself; I'm going to repeat myself several times because by repeating myself, when you hear it enough, it will start to sink in- you have to draw this by hand.1751

You're probably wondering why don't I just put up a nice figure of this and just run through them - glycine, valine, proline, leucine, isoleucine - because that's nice.1773

A couple of reasons: 1, I'd like to encourage you to actually refer to your book.1785

Biochemistry books are beautifully written, all of them are beautifully written and beautifully illustrated, so I encourage you to use these videos along with your book, and take a look at the figures in that book; that way you'll have 2 sources that solidify the information.1790

Another reason I don't do that is, again, because of passive learning.1807

We can convince ourselves that we can look at something and we can understand what's going on.1810

We don't understand it unless we are able to produced it with our hand.1813

There is a connection between what the hand does actively, and what the mind actually understands and knows.1816

You need to draw these out.1820

Is it tedious?1822

Yes, maybe; but it's absolutely worth it.1823

There is nothing, nothing, nothing like knowing that you can actually produce any molecule under any circumstance that is full command of your biochemical knowledge.1826

OK.1836

No more lecturing- not for a while.1837

OK.1840

We have CH₂, and we have CH, CH₃, CH₃, so you notice this one actually just like valine except that extra carbon group there.1841

This is leucine, and it is Leu, and it's single letter designation is L, and this is your R-group right here; and last but certainly not least, a very unusual amino acid.1856

So, we will go ahead and put an NH₂⁺ - notice, this one is not an NH₃, and I'll tell you why in just a minute - this is going to be C.1877

Let's go, I'm going to draw a C here and a C there, and that's there, so this is going to be CH₂, this is going to be H₂, and this is going to be H₂.1888

The reason I have 2 hydrogens on this one, it's still a plus charge, is because again, nitrogen, this time, it's actually connected; this amino group is actually connected to the R-group.1900

The R-group is right here, but it happens to be connected, so, tetravalent nitrogen has a positive charge here, 3 hydrogens, and one of them is bonded to carbon, here nitrogen is bonded to 2 carbons that's why it only has 2 hydrogens here.1911

This one is called proline, and it is Pro, and its single letter designation is a P.1924

OK.1934

These things - the glycine, alanine, valine, leucine and proline - they represent the first group of nonpolar R-groups.1935

There is no polarity here; there is no electronegative element to create a dipole, so that's it.1944

OK.1952

Let's go ahead and do our...actually you know what, we have a couple of more.1953

I'm sorry.1962

We have 2 more, yes, all right.1965

Let's do C, COO^-, we have H, and we have NH₃- getting ahead of ourselves, sorry about that.1967

Now, we have a C, CH₃, H, CH₂, CH₃- this one is called isoleucine.1979

There is no capital in there.1997

This is isoleucine, and it is Ile; and its single designation is I, and this group is right there.1999

There you go.2011

Leucine, isoleucine, iso just means we've rearrange that, so 1, 2, 3, there are 4 carbons, 1, 2, 3, 4, just one of those carbons is arranged differently- that's all.2012

And, let's do methionine.2023

OK, so we've got C, COO^-, H, NH₃⁺; we have CH₂, CH₂, sulfur, and CH₃.2026

This is called methionine, and still nonpolar, Met; and its single letter designation is an M.2048

Let me draw out the group; there we go.2062

This is the first group of amino acids, the ones that are have nonpolar R-groups.2066

OK.2072

Let's go ahead now, and move on to the second group: the amino acids that have aromatic R-groups.2073

OK, aromatic R-groups.2079

OK.2089

Let's do C, COO^-, H, N, H.2090

You know what, I'm going to do this in blue.2099

I think blue is my favorite color.2105

I know it doesn’t matter, but for some odd reason, I just think that it looks better in blue, I don't know why- personal taste, I guess.2110

We have blue, so aromatic R-groups: C, COO^-, H, we have our NH₃⁺, and we have CH₂, and then we have this benzene ring; and this is phenylalanine, and it is Phe, and its single letter designation is F.2118

OK.2155

I wonder if I should do...that's fine, I guess I can do it over here.2157

OK.2163

C, COO^-, our H, our NH₃⁺, and now, we'll do CH₂, we have our benzene ring again, and we also have a hydroxy attached to that benzene ring.2164

This is going to be tyrosine, three letter designation is Tyr, single letter designation is a Y.2181

OK.2192

Now, let's do C, COO^-, H, NH₃, again, a very unusual amino acid because you have an indole group actually attached to this.2194

Let's go, C, let me draw it out this way, like that, I will put a nitrogen, yes, that's fine I'll put a nitrogen there, and then I'll go that way, that way, that way.2213

I'll go ahead and do my aromatic ring like that, and H; and this is called tryptophan.2233

Tryptophan, three letter designation is Trp, and curiously enough the single letter designation is W.2245

Let's make sure we have this right: double bond, this is aromatic, there is a hydrogen on there, 2, 3, so this a carbon, it has an H attached to it.2253

These are all carbons, of course; this is a benzene ring.2264

So, this whole thing right here is an indole.2268

Our R-group here is that one; our R-group here is that one, and our R-group here is this one.2270

We have 3 amino acids that have aromatic R-groups.2279

OK.2283

I'm going to go ahead and stop at this lesson here for today, and the next lesson, we're going to continue with our classification of amino acids; and we'll get into more properties of those amino acids.2284

Thank you for joining us here at Educator.com and Biochemistry.2295

We'll see you next time, bye-bye.2298