Proteins, levels of Structure, Non-covalent Forces, excerpt 2 | MIT 7.01SC Fundamentals of Biology
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Proteins, levels of Structure, Non-covalent Forces, excerpt 2 | MIT 7.01SC Fundamentals of Biology

November 14, 2019


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.

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  1. I knew there were 20 basic amino-acids, but this video has lots of interesting info about their interconnection in order to form proteins. Thx, MIT

  2. Excellent!! Can anybody tell which one is the primary textbook for this curse, please? The description of different protein folding structures based in their chemical bonds is excellent. I got very impressed with the spatial constrain that some bonds offer to the whole protein structure. What is the Professor’s name, please? 

  3. Wow he talks.and acts human. Most of my Prof. were dried up old farts that went through the process on muscle memory..makes me want to go back. Lucky kids to have him.

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