BIOCHEM DISCUSSION 2

OK - so now we're going to start talking about amino acids, getting to the nuts and bolts of things.

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Created by Brett Barbaro

Biochemistry: A Short Course Fourth Edition

CHAPTER 3 Amino Acids

Tymoczko • Berg • Gatto • Stryer

© 2019 Macmillan Learning

This is what we will be talking about. Proteins are built from a repertoire of 20 amino acids - there are a few others, but 20 basic ones are shared between all organisms; amino acids contain a wide variety of functional groups, and I believe we talked about functional groups in the last chapter; and essential amino acids must be obtained from the diet. We are just going to touch briefly on that at the end, thanks.

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Chapter 3: Outline

3.1 Proteins Are Built from a Repertoire of 20 Amino Acids

3.2 Amino Acids Contain a Wide Array of Functional Groups

3.3 Essential Amino Acids Must Be Obtained from the Diet

So we are going to talk briefly now about different ways of depicting biomolecules. There are several different ways that we are going to talk about, and will be used in this course. At the bottom, you see a Fischer projection of alanine - and remember that it's actually tetrahedral, so the carbon in the center would be the center of the pyramid. And the horizontal bonds would be coming out of the page like the arms of a bear, chasing you. And the vertical bonds would be projecting behind the page. This would be an alanine molecule at neutral or physiological pH, because you can see that the nitrogen on the H3N group there has a positive charge, and the COO has a negative charge with no hydrogen on it.

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Two Different Ways of Depicting How Biomolecules Will Be Used (1/2)

• Fischer projections are useful for visualizing the constituent atoms of the molecule.

• Every atom is identified, and the bonds to the central atom are depicted as vertical and horizontal lines. The horizontal bonds are taken to project out of the plane toward the viewer, whereas the vertical bonds are assumed to project behind the plane away from the viewer.

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This is a stereochemical rendering of alanine, in which you can see a little bit more clearly the tetrahedral nature of the molecule, with the hydrogen sticking back with the dashed {wedge} at the top, and the CH3 group coming out of the page as a {solid} wedge, and the two straight lines are imagined to be in the same plane as the page.

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Two Different Ways of Depicting How Biomolecules Will Be Used (2/2)

• Stereochemical renderings are useful for visualizing the shape of the molecule.

• Wedges are used to depict the direction of bond projection. A solid wedge shows the bond projecting toward the viewer out of the plane. A dashed wedge shows the bond projecting behind the plane, away from the viewer. The remaining bonds are depicted as straight lines.

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Here are some more common ways of depicting alanine. At the top you have one of my favorites, this is the space filling model - the carbons are in gray, the oxygen in red, nitrogen in blue, and hydrogens in white. And that gives you a pretty good idea, I think, of what the molecule would actually look like as it's floating around in the cytoplasm. The spheres in this model represent electrons that are moving around, and it's kind of the electron clouds that would be surrounding the nuclei - the nuclei in this picture would be so small at this scale that you couldn't even see them - but it's the electrons that interact with each other and cause bonding and catalytic interactions, and therefore the electron structure is the most important thing to know, and you can see that pretty clearly in these depictions. The central picture here, sticks without hydrogens, is something that you might see - a lot of people leave off hydrogens because they think they complicate the picture, which is maybe fair - hydrogens are very mercurial, they tend to jump off and on quite readily - but I tend to like seeing where the hydrogens are because usually there are a ton of hydrogens associated with a molecule like you would see in the bottom one, sticks with hydrogens. And here you can see the hydrogen attached to the oxygen on the right and two hydrogens attached to the nitrogen on the left. Very strange, because this would not normally happen at any pH, so it's kind of an odd representation, but for some reason that's what they decided to do; but it’s a fair representation, I guess, of what the bonding structure of this molecule is.

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The balls and sticks model of alanine that we see on the top is a common representation, and it's good for showing where the nuclei are and what the bonding structure is, but not so good at depicting what the electron cloud would be like. But it is something that you would see a lot. Very strangely, also protonated on the {oxygen} not on the nitrogen, so in a rather unnatural state. The physical model is very much like a “balls and sticks” model, but one problem is that the hydrogens are attached directly to the nitrogens {and carbons}, so the bond lengths represented there are incorrect. Therefore, this type of model can be a little misleading. But another interesting thing, that you see on the right, is how the double bonded oxygen causes that carbon to have a planar triangular structure – it changes the tetrahedral nature of the carbon atom electron cloud into a planar triangle by making two bonds. Now, on the bottom, I have shown an alternate model of alanine and this is from the Journal of Irreproducible Results, and it is in fact a reasonable representation of alanine. With the body as the alpha carbon, the methyl group attached as the head, the carboxylic acid is the right leg and the amino group on the left leg and a single hydrogen coming off the middle. And why did I throw this in there? Because there are a lot of different ways of representing these molecules that I just want you to be prepared to encounter - you will encounter several different ways within this course that I haven't covered here. So I hope that they don't confuse you, but they are all fair representations and have their own advantages and disadvantages.

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So as a little side note here, if you want to see how big a proton is compared to an atom, or an atom to a cell - if you want to just see the scale of things from Planck length to the size of the entire universe (that's the smallest possible measurement of length to the entire universe), this is a wonderful webpage and I think you can click it straight from this presentation. And I highly recommend you check it out.

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So - proteins are built from a repertoire of 20 amino acids (plus a few other ones). And you can see here the central atom is a carbon, which is called the "alpha carbon“. Then off of this alpha carbon, you have the amino group, you have the acid group, the COO-, you have hydrogen and you have your "R" group, which can be any one of 20 different things. And it is the "R” group that makes the amino acids different.

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Section 3.1 Proteins Are Build from a Repertoire of 20 Amino Acids

Learning objective 1: Identify the main classes of amino acids.

• An α-amino acid is composed of a central carbon atom called the α- carbon.

• The α-carbon is linked to an amino group, a carboxylic acid, a hydrogen atom, and a distinctive side chain, called the R group.

http://users.rcn.com/j kimball.ma.ultranet/Bi ologyPages/A/Ala.gif

So as we said, the amino acids contain a wide variety of functional groups. You might even say they are a wide array of functional groups - amino acids almost define what these functional groups are. Along the left you will see all of them, all 20 of them, and they are listed in order of reactivity, basically. The top ones, arginine and lysine, are very highly positively charged (that is what the blue means, is positively charged). The second two, aspartate and glutamate, are negatively charged - those are oxygens sticking off of there. Asparagine and glutamine are highly polar, but have negative and positive components. Cysteine and methionine both contain sulfur. Histidine is a special case. Serine, threonine have oxygen in them, and the rest are pretty much just nonreactive. Now, at the very bottom you will see proline, and that has caused a kink in the strand and we will get into that in a few minutes, but that's a very important quality of proline. Now, you have three letter abbreviations for all of these amino acids. You have one letter symbols for all of these amino acids. I'm not going to test you on that, but if you want to be a biochemist, you should learn them. And to the extent to which you learn these three-letter abbreviations, or one letter symbols, it will help you in this course, understanding more quickly the diagrams and pictures that we are talking about. As far as the actual structures of these are concerned, I am not going to test you on that either, but this is all stuff you can look up. So I mean, if need be, you can always look it up, but I think it's a good idea to get familiar with them, so we are going to do that right now.

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Section 3.2 Amino Acids Contain a Wide Array of Functional Groups

• The 20 amino acids found in proteins contain unique side chains that vary in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity.

• Amino acids have three-letter abbreviations and one-letter symbols. You are not responsible for memorizing these, or their structures. However, if you wish to continue studying biochemistry, it would be a very good idea.

• Amino acids can be sorted into four groups on the basis of the general characteristics of their R groups:

– Hydrophobic amino acids – Polar amino acids – Positively charged amino acids – Negatively charged amino acids

http://mgl.scripps.edu/people/goodsell/books/ MoL2figures/Figure2.7-reduced.jpg

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Figure 3.3 Hydrophobic amino acids.

Starting with glycine. Glycine is the smallest amino acid - and as a matter fact, it is only a hydrogen, which means that there's no stereocenter on the alpha carbon of glycine. It takes up very little space in protein chains and is good for tight corners and things. Alanine, a very simple straightforward CH3 sticking off of that alpha carbon, that is a nonpolar, hydrophobic group, but it's very small also. Valine is a little bit bigger. Why don't they have one that's just two carbons sticking off of it? Very interesting question. I don't know the answer to that. But basically, it's the same thing as the alanine, just larger. It's a hydrophobic group, it just takes up space. The same could be said for leucine - another carbon has been added on leucine, and the shape is a little bit different. Isoleucine is an isomer of leucine, which we get the name from, if you want to remember, which one is leucine and which one is isoleucine, I just remember at the top of the leucine, the three carbons there make a little "L" and on the top of the isoleucine, the two carbons make a little "I" and the next three carbons make a little "L", so it would be "L" and "IL", in case you're curious about that.

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Figure 3.3 Hydrophobic amino acids.

All right - Methionine. Methionine is actually a very important amino acid. It's the first amino acid that's ever laid down. It's encoded by the nucleotides AUG, which is your start codon, so whenever you make a protein in your body, it starts with methionine. And methionine has a little S in it - that is sulfur. Now, the hydrophobic nature of methionine - I challenge that, because the sulfur does have some electronegativity, so I would not say that it's completely hydrophobic, but it's not very hydrophilic, so I think that it's OK to categorize it among the hydrophobic amino acids. The next one, proline, is our very special one. What do you notice about this? It's a circle! That nitrogen, the only nitrogen in it, is not sitting out there alone as an H3N. It's now an H2N and it's combined to the other chain, to the side group. Now this gives it a very peculiar geometry, and introduces kinks in the protein structure, which is very important structurally, and we will talk a little bit about that later. Phenylalanine, is a big, honking, six carbon ring, sticking off of a carbon, and that guy has resonance structure, so it's actually hydrophobic and quite large. Even larger is tryptophan, and, although there might be a nitrogen in there, which gives it slightly hydrophilic character, tryptophan is overall very hydrophobic. And it's very important to know that these resonance structures interact with each other - they stack, and that creates another layer of connection between the various parts of a protein chain, that can affect its 3-D structure and its function.

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Figure 3.4 Polar amino acids.

All right, polar amino acids - those guys have an electronegative atom. It's usually an oxygen, which is the most electronegative atom that we will be running across in most of these organic compounds, and one of the most electronegative atoms around, second to fluorine, I think. So those electronegative oxygens are very reactive, and they're hydrophilic, for one thing, and they tend to get phosphorylated and have other groups added to them, which makes them important in signaling. So these guys are actually kind of important. I mean, they're all important - but threonine and serine and tyrosine are all very important for cell signaling and for other catalytic interactions.

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Figure 3.4 Polar amino acids.

Now, the polar amino acids cysteine, asparagine, and glutamine, are all kind of special, actually. Cysteine is important for forming disulfide bonds, which stabilize the structure of the proteins, (the tertiary structure), and we will be talking a little bit more about that in a moment. Asparagine and glutamine are very similar residues, containing both an electronegative oxygen and an often-charged nitrogen group, so they have a negative and a positive charge associated with them, which makes them very useful for active sites in enzymes.

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Figure 3.5 Positively charged amino acids.

Lysine and arginine are your two positively charged amino acids. Very important for cell signaling, for catalytic interactions. These can be modified by a number of enzymes and are important reactive elements of proteins.

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Figure 3.7 Negatively charged amino acids.

Aspartate and glutamate - these are your negatively charged amino acids, with acidic side chains. They're almost identical, except for aspartate has two carbons in the side chain, whereas glutamate has three, which gives them slightly different geometry and slightly different reach in protein. And once again, these charged groups, the carboxylic acid groups, are very important for signaling and for catalytic interactions.

Histidine - now, this one is kind of special, because it can be charged or it can be uncharged at neutral (or physiological) pH. So it's very important in the active sites of enzymes, because it can be used to pass protons around.

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Figure 3.6 Histidine ionization. Histidine can bind or release protons near physiological pH.

And this is just an example of how that works. Your proton (in blue on the left, attached to that nitrogen ... and stabilized on the left by a resonance structure), can get released and {the electrons can} change into a double-bond on the right, where there is no charge. So the left-hand form is positively charged and the right-hand form is not charged - and the pKa of that is about six, so that is something that can happen quite readily in physiological systems. {At pH 7, about 1 in 10 histidines would be protonated.}

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Diagram of Histidine Ionization

So this is just a chart to give you an example of how strong these various charges are on these amino acids. The most electronegative is actually the terminal alpha carboxyl group that's at the top there, and that's the one that's attached to the alpha carbon. That's the one that all amino acids have. Aspartic acid and glutamic acid are next, and they're a little bit less negatively charged. Histidine is your one that can switch back-and-forth at around physiological pH. The alpha amino group, which is on every amino acid, that's what gives it its name, that also can switch around physiological pH. Cysteine would tend to be neutral at physiological pH, as would tyrosine, so that's why they're not listed as charged, but they can lose those protons very easily. Lysine actually tends to be charged, and arginine also, at physiological pH, so that is why they are considered the positively charged amino acids.

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The Ionizable Side Chains Enhance Reactivity and Bonding

Figure 3.8 A child suffering from kwashiorkor. Note the swollen belly and limbs. This swelling (edema) is due to fluid collecting in the tissues because there is not enough protein in the blood.

Now, 11 of those amino acids you can actually manufacture in your body from other elements. But nine of them, called the essential amino acids, you cannot manufacture within your body and therefore you need to eat them. If you don't, then you can get very sick, such as this child suffering from kwashiorkor. His swollen belly and limbs are actually due to fluid collecting in the tissues, because there's not enough protein in the blood. Due to the lower concentration of protein in the blood, osmotic pressure develops and water flows into the more protein-saturated tissues.

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Section 3.3 Essential Amino Acids Must be Obtained from the Diet

And here is just a list of the nonessential and essential amino acids. You're not going to be responsible for remembering these, but I thought I would include them just because they are important to know for your nutrition.

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Table Listing the Nonessential and Essential Amino Acids

Table 3.2 Basic set of 20 Amino acids Nonessential Essential Alanine Histidine Arginine Isoleucine Asparagine Leucine Aspartate Lysine Cysteine Methionine Glutamate Phenylalanine Glutamine Threonine Glycine Tryptophan Proline Valine Serine Tyrosine

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