Biochem discussion 2 | Chemistry homework help

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


Created by Brett Barbaro

A Short Course
Fourth Edition

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.


Created by Brett Barbaro

Chapter 3: Outline

3.1 Proteins Are Built from a Repertoire of 20 Amino

3.2 Amino Acids Contain a Wide Array of Functional

3.3 Essential Amino Acids Must Be Obtained from the

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.


Created by Brett Barbaro

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.


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.


Created by Brett Barbaro

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


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.


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.


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.


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.


Created by Brett Barbaro

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-

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

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.


Created by Brett Barbaro

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


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.


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.


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.


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.


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.


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.


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


Created by Brett Barbaro

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.


Created by Brett Barbaro

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.


Created by Brett Barbaro

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.


Created by Brett Barbaro

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


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