PROFESSOR: OK, well let's move on then, and just talk about
the amino acids.
Amino acids side chains.
And you won't have to memorize these structures.
We will give you a chart if you have a problem.
On the other hand, you need to get very familiar with them,
so they're old friends even if you can't quite remember how
many methylene are in a chain, or something like that.
And you will find that they fall into certain categories.
And I'm just going to try and give you examples of the major
categories.
There are negatively charged side chains.
An example would be amino acids known as aspartate, or
Asp, in which the side chain which corresponds to the R1 or
to the R2 over there, has a methylene group, and then a
carboxyl group.
But at pH sevenish, which is the pH that you find inside a
cell, that carboxyl group would be deprotonated so it
would have a negative charge.
The other negatively charged amino acid is glutamate, which
also, as you'll see has a carboxyl group.
There are positively charged amino acids.
A good one to illustrate this is Lysine, in which there's
four methylene groups, and then an amino
group at the end.
However, again, at pH 7, the kind of pH that you find
inside the cell, that amino group is going to get
protonated.
And so it will have a positive charge on.
If you have a Lysine side chain, and Arginine, and in
most cases, Histidine, are examples of other amino acids
that can have a positively charged group.
And why I'm going through all of this, I hope, will become
apparent in a few minutes.
Some of the side chains are not positive or negative
charged, but rather, they're polar.
And we just talked about polar bonds the last time, where you
have, the more electronegative an atom is, the more greedy it
is for electrons.
And if you recall, if you have a carbon carbon bond or a
hydrogen hydrogen bond that's nonpolar, and the electrons
were distributed equally, the oxygen is greedier for
electrons and so there is a little bit of a negative
charge there and a little bit of positive
charge on the hydrogen.
Well, that same principle applies to
amino acid side chains.
Take, for example, the amino acid Serine, which has a
methylene group and then a hydroxyl group.
Well, here we are.
There's an OH bond, so there will be a little bit of a
negative charge on oxygen with a positive charge on there.
There's another alcohol called threonine, which also has
hydroxyl groups.
And you can make amides of both Aspartate and Glutamate,
to give Asparagine and Glutamine, and both of these
are also polar too.
So what I'm hoping you're beginning to get a sense of,
you can do an awful lot with the properties of a peptide
chain, depending on which amino acids you
dangle off the side.
And ultimately, that order of amino acids is what's going to
be determined by what's in the gene encoding that protein.
Then there are quite a number of amino acids side chains
which are hydrophobic.
They're sort of fearing water, if you will.
The simplest is Alanine, or Ala, which is just a methyl
group, or Leucine, is perhaps, a little more obvious because
that's got this.
And you can see that that's a kind of--
draw it like that.
This is, very much, a kind of structure that's not going to
want to interact with water.
And then, another example would be Phenylalanine, or
Phe, and that one is a methylene group and, then, a
benzene ring.
So most of you know, have some sense of the properties of
benzene, a very, very organic solvent.
So here you put a side chain like this, it's very much a
residue that doesn't want to interact with water anymore
than Benzene wants to interact with water.
And then there are three special cases.
One of these is Glycine.
In this case, it's just a hydrogen.
One of the consequences of that is that since it's just a
hydrogen, that's going to be a very, very flexible place, if
we have a chain of amino acids and there's a Glycine there,
it's going to be very little of way of constraints
introduced, either by steric constraints or by
interactions.
Another very special one is one called Cystine, Cys.
And it's the same idea as Cyrine, there's an ethylene.
But instead of having an OH, it has an SH group.
And that may not seem to be a great consequence, the sulfur
is a little bit larger.
But sulfurs have--
a sulfide group here has a sulfhydryl group here has a
very special property, and that is, it can oxidatively
dimerize with another sulfhydryl.
So if you have a side chain, and there's a cystine that has
an SH group, and another, either part of the same chain,
or part of the different polypeptide chain that also
has a cystine, and they're in an oxidizing environment, and
they're also close enough together to interact, they can
form a bond like this, which is known as a disulfide bond,
and it's the only one of the amino acids that's capable of
reaching outside the chain in either hooking to a different
part of the chain or to a completely different protein.
And in fact, proteins that tend to get excreted out into
the media, either by bacteria or other things, often have a
lot of disulfide bonds.
Because when you link the peptide chains together like
that, it tends to make a very tough protein that's hard to
break down and can be very, very robust.
And there is one other special category of, one other special
amino acid that's known as Proline.
You have the alpha carbon atom, the carboxyl group, and
then there's the amino group here.
But this carbon is linked by a little ring with three
methylenes to that amino acid.
Again, this may seem sort of an unnecessary detail or
something, but this is the way life evolved on earth.
This is an amino acid, but because of this ring
structure, this bond is not able to rotate.
So wherever a Proline shows up in the sequence, it puts some
structural constraints on the conformational space that that
chain is capable of getting itself into.
So when we study protein structure, this is at the
heart of how proteins work, we'll spend quite a bit of
time in the ensuing lectures talking about the central
dogma and the idea that the linear order of the amino
acids, in a protein, is determined by the sequence of
the DNA and how that's encoded.
But at the end, what you end up with is a linear sequence
of amino acids, all joined together by peptide bonds.
And there's an incredible number of
conformations possible.
These things could go all over the place in all kinds of
different ways.
Yet, only one form, in general, is the biologically
active conformation or maybe there's a couple of them and
it switches back and forth as part of a machine action, or
are part of what it does.
But by and large, for every protein there'll be one, or
just a couple of conformations.
And so understanding proteins, what many, many people are
interested in is trying to understand how you can get
from that linear sequence and determine the three
dimensional structure.
There are techniques, X-ray crystallography and NMR
techniques now, which enable us to get the structures,
solve the structures of proteins.
In fact, there's the structures of tens of
thousands of them are in a database
called the Protein Database.
And we're going to be talking about a little protein viewer
that you'll be using that, in fact, once you've used it in
your problem set, you could go open the structure of any
protein whose structure has ever has been solved, if you
want to do it.
But what we haven't yet figured out is a reliable way
of saying, here is a protein that consists of a particular
chain of amino acids.
I'm going to predict its three dimensional shape.
So we understand parts of it, but there's
parts we don't know.
And I'm going to take you through the first part of
understanding protein structure.
And before we do that, I want to just talk about the levels
of protein structure and the terms that are used to
describe these.
When people talk about the primary structure of a
protein, what they're talking about is the sequence of amino
acids, and it's possible I'll abbreviate those as AA, at
some point without thinking about it.
So just in case I do, that's a fairly commonly used
abbreviation for amino acids.
So that simply, Phenylalanine joined to a Proline joined to
a Glycine joined to two Cystines joined to something
else, but that's not terribly useful in terms of telling
what the protein does.
Then there's secondary structure.
These are regions of local folding and they're driven by,
guess what?
Hydrogen bonds.
And we'll talk about how that goes in just a moment.
Then the term, tertiary structure, is the term used to
describe the entirety of the folded protein.
If I went in and determined the structure of a protein
using x-ray crystallography, this is what I would see.
It would be the tertiary structure.
And there are other forces that we haven't discussed yet
that contribute to that tertiary structure.
And then, a quaternary structure means that there's
more than one polypeptide chain.
And it could be as simple as an enzyme that's got two
subunits and you've got to have them both there in order
for it to work, or as I think you're beginning to probably
get the sense from my use of the term protein machines,
there are structures that have multiple interacting proteins
and have complexities that rival some of the mechanical
things that we build ourselves.
So the interesting story, a little, bit how the insights
into secondary structure were first arrived.
Some of you may have heard the term Linus Pauling.
He was at Cal Tech, a Nobel Prize winner, very, very
influential scientist, in a variety of ways.
The key insight that Linus Pauling had
came in the late 1940s.
People had been doing X-ray crystallography on minerals
and things like that, and the basic idea was you had a
crystal of some type, you bounced electrons off, you got
a diffraction pattern.
Then you could work backwards and figure out the structure
that was generating the diffraction pattern.
And that had, then, been extended to proteins.
And it was discovered there were certain proteins that
would crystallize and you could bounce electrons off and
get a diffraction pattern.
And at least a category of these proteins, and analysis
of the diffraction pattern suggested it was some kind of
helix, and there was a repeating element of about 5.4
angstroms, roughly.
And so, Linus Pauling was very
interested in protein structure.
And I think it was in late 1948, he was visiting England
and he caught the flu, just like some of
you have been catching.
And he spent a few days reading detective stories and
then he got bored.
And so he tried to take on this--
think about this problem.
While he was lying in bed.
And he made a simplifying assumption.
He said let's just forget about all the side chains.
Maybe they don't really matter in terms
of this basic property.
Maybe it's determined by the backbone of the peptide chain.
So he took a strip of paper, started pleating it.
And he was a very good chemist, so he knew about this
partial double [? blind ?]
character of the peptide bond and the constraints that it
put on the structures that the protein could take.
And in doing this, he realized that if he folded the thing
into a helix, kind of like this, into a right handed
helix, that things worked out such that the carboxyl group
in the backbone was just beautifully positioned to form
hydrogen bond that was on one of the nitrogens.
He called this an alpha helix.
There were 3.7 amino acids per turn.
And the distance from here to here was 5.4 angstroms.
And if we just--
sorry, I meant to put that up
earlier, or did I go backwards?
Anyway, there are all the amino acids and
they're in your book.
Here is just the backbone of an alpha helix.
And the orangey yellow colored bonds are the hydrogen bonds.
And I hope you can see how the spiral goes.
And you can also see, as it goes by, you can look right
down the hole down the middle of the helix.
So let's put on some amino acids now.
And again, you'll see, as it goes by, you can look right
down the helix.
But you see how the amino acids stick out onto the side.
And if you look, for example, there is a Phenylalanine and a
Tyrosine, they're aromatic groups that are very
hydrophobic.
And up here there's a Lysine, so that's this side of the
helix is charged.
That's a glutamate.
So there's a couple of charged amino acids on
this side of the helix.
Up here we've got a water hating part and somehow this
is, I think, reminding me that I left something out.
Let me just fix that up while I'm at it.
The other hydrophobic amino acids, I forgot to say those
are Isoleucine, Valine, Methionine, Tyrosine, and
Tryptophan.
Those are in your book.
Those are other examples of hydrophobic amino acids.
But I think, even in this little example of an alpha
helix, you can see, depending on which amino acid was where,
along that little region of alpha helix, it would very
much influence what that part of the protein
was capable of doing.
There's a second region of secondary structure that's
very important.
It's called a beta sheet.
The one I'm showing you is an example of an anti-parallel
beta sheet, although you can have parallel
beta sheets as well.
But what I've done here is to take one strand of a
polypeptide chain and I've written it out this way.
And then I've taken a second--
what has happened?
Oops.
That's interesting.
The stool just broke.
OK.
Fortunately, I noticed.
So what we have here is that the possibility for hydrogen
bonding between this hydrogen of amino group and this
oxygen, again, so we can get hydrogen
bonds formed like this.
And this makes what are called a beta sheet structure.
And they can build up as well.
This next one gives-- you can see how you can put one beta
sheet on top of another.
And both of these are two major types of secondary
structure and the way an alpha helix is represented is
something like this.
This would be an alpha helix.
And a beta sheet is written as an arrow like that.
And so most proteins tend to have structures that consist
of, for example, an alpha helix, some kind of turn,
maybe a beta sheet, another turn, another beta sheet.
Now maybe a turn, maybe an alpha helix going this way,
some combination of regions of secondary structure.
And I've got just a couple of examples of that.
Here you can see a domain of a protein with some beta sheets
in purple, alpha helix in green.
Where that's a piece of a protein coming from what's
known as the bracket one gene.
Some of you may be aware there's a familial
susceptibility to breast cancer that was discovered.
It's a complex protein.
Part of it, and a very, very important part of it, is this
piece known as the BRCT domain.
It's the bracket one c terminal domain, consists of
beta sheets alpha helix.
Here's a protein I've already shown you the structure of,
but maybe you recognize now, that green fluorescent protein
is mostly beta sheets.
It's the only beta sheets is going down here.
There's a little bit of an alpha helix up there.
And there's a bit of one over here?
Here's an example of a protein that's mostly alpha helix.
What's this one do?
This is a protein we'll talk about when we talk about DNA
replication.
It's involved in recognizing mismatches in DNA, for
example, the G improperly got paired with the T during DNA
replication.
There's a system comes along and repairs those mismatches
gives you another several thousandfold increase in
fidelity, and if you mutate it in that kind of protein in a
human, you have a familial
susceptibility to colon cancer.
So it doesn't matter what their function is, when you
get down to regions of secondary structure, you'll
see these recurring things -- alpha helices, beta sheets.
And if you understand their properties, you begin to
understand some of the basic structure of forces that are
giving the proteins their properties.
That's an enzyme called chymotrypsin.
What it does, it's an enzyme that catalyzes the cleavage of
peptide bonds in other proteins.
But there it is.
Got a lot of alpha helices, beta sheets, turns.
You can go on and on.
I just said, one more up there.
That's the Ras protein.
That's an oncogene.
Mutate that in a particular way, you have a
susceptibility to cancer.
But it doesn't matter, when you get down to the protein
structure, most proteins have beta sheets, alpha helices.
OK.
Go back to that one in a second.
So we have to understand the rest of the
structure of proteins.
We have to be able to talk about the other forces that
are important for making a protein.
And the third force is pretty simple.
That's an ionic bond, and it's just this simple, that if you
had a peptide chain that had, for example, an Aspartate with
a negatively charged amino acid on it, and we had, say, a
Lysine, four Methylenes, and the NH3 plus that was attached
somewhere else on that polypeptide chain, then we can
get an ionic bond, because of the attraction between the
negative charge on here and a positive charge on that.
So that is one of the things that then a force that can
influence the structure of proteins.
The next one is a harder one to understand.
It's known as the van der Waals interaction.
And here's basically what's going on is that a non-polar
bond can have a transient polarity.
Sorry about this.
And it can induce polarity in a nearby non-polar bond, and
that can then give an attraction.
These things need to be very close together, about 0.2 to
0.4 nanometers apart, the two non-polar bonds, in order for
this to happen.
Does anybody remember the length of the covalent bond,
the 0.15 to 0.2 nanometers, so within one or
two covalent bonds.
They have to be that close.
Their strength is about one third, one quarter to one
third, to that of the hydrogen bond.
And if you remember, the hydrogen bond was about one
twentieth of the force of the strength of the hydrogen bond.
But nevertheless, you can have a lot of them because, if you
have an extended surface of a protein that's very close
together, you can get a lot of these van der Waal
interactions.
And I'd always found this a somewhat
esoteric kind of force.
But in fact, we're familiar with these because that's how
a lizard manages to go up a surface.
It uses van der Waals interactions.
And as I'll show you in a minute, the trick is it's got
little hairs on the bottom of its feet that have about a
billion split ends and they're so tiny they're able to make
van der Waals interactions with the surface.
In a minute, I think there's a shot from underneath.
I got these movies from Robert Full at Berkeley,
who's worked on these.
You could see the lizard kind of peeling its foot off.
And here they've made a little robot that can work by van der
Waals forces and it will climb up the wall
kind of like a lizard.
And here's what's going on at the molecular level.
These are the toe pads on a lizard like this.
We're going to be just zooming in now.
And you'll see they're covered with hairs, and you keep
zooming in more, there's more hairs.
And we keep zooming in more, get down to a single hair,
there is a 30,000 fold magnification.
There's 115,000 magnification.
And in the end, a gecko, such as you've got here, has a
billion 0.2 micron tips.
And just to compare it to a human hair, over on the edge,
then you can see what the gecko hair is like.
It's a very, very fine hair and it's able to use van der
Waal interactions to stick to the surface.
Bob actually made a Band-Aid by collecting this little
hairs out of the thing.
And he made a little joke of putting it in a Band-Aid box.
But this is interesting because it
isn't affected by water.
You can peel it off.
You can put it back down.
And he thinks there were commercial possibilities for
using van der Waals interaction.
So, OK, I think we have one more force to go, but I think
we will call it a day right here.