So, we're going to finish now by just talking more about this amazing
immune system we have, the adaptive immune system.
As I said on Friday, this is really an astonishing recognition system
that just plays a key role in us being able to survive in this world
that's full of bacteria, and yeast, and fungi, and viruses,
parasites. There are things just all the time
trying to do us in, and the reason we don't succumb is
because we have this amazing immune system. And there are several
features about it which I summarized the other day.
One is its diversity. It has this incredible ability to
recognize entities, including things that are
synthesized in a lab that had never been seen on Earth before.
It's amazing in terms of that side of it. Coupled with this is this
incredible specificity. As I indicated the other day,
for example, if it was seeing a benzene ring with a methyl on it,
it might be able to recognize this, but it could tell the difference
from having the methyl over here. It's got that level of
sophistication. In spite of that,
in spite of the fact that it can recognize everything else,
it's able to avoid self recognition,
which is a bit of a trick if you
think about it, that you have a system that's able
to see essentially anything, including things that never existed
before. And how does it avoid seeing all of our molecules,
and all the many, many things that makes us up? So,
it has to be able to tell self from non-self.
And then, I also talked about this memory aspects of the immune system,
that if you get exposed to a virus or bacterium or something,
but the first immune response is relatively weak.
But then if you get subsequently exposed, you get a very powerful
response. And that's the principle of a vaccine. If you think someone
is going to be exposed to chickenpox but they haven't had it,
if you could somehow elicit the initial response without making them
sick by using a killed virus or something like that;
polio is one of the examples you hear about in the paper right at the
moment. Then, if someone does encounter that virus
or that bacterium, because that's second response,
it's very quick and it's very powerful, and that's what vaccines
are all about. So, the issue,
I guess, today is how does that happen? And this is one of these
amazing insights into biology that's come by an application of all these
tools, recombinant DNA, and sequencing, and all the fancy
sort of things we've been talking about in the past few lectures.
So, the first part I need to let you know, is there are two parts to this
immune response, or two kinds of responses.
One's called the humoral response
and one's called the cellular response. And this takes place in
the plasma of your blood. So, in the liquid part of the blood
if you spin down the red cells and the white cells,
what you're left with is the plasma.
And, what this humoral response response does,
it's able to target bacteria, viruses, proteins.
And the recognition is done by a
special kind of protein called antibodies. And I'll tell you about
that in just a moment because they're a very important class of
protein in this Earth. And the cellular immune response is
carried out by a special kind of white blood cell.
For this lecture I think I'll just
abbreviate those as WBC if I need it. What this targets is not the actual
pathogen itself. But it targets cells that are
infected with a virus or a bacterium, etc. and that might seem to be even
a little bit more of a trick. It's hard enough probably to figure
out how to take something that's an entity like a virus that's floating
around your blood and figure out how to find something that binds to it.
What do you do if the thing's gone into one of your own cells and it's
hiding out in their replicating in the same way that,
let's say, a phage does or something like that
How do you see one of your own cells that's been infected by something
like that? And there is a special type of cells called cytotoxic T
cell that's very important. It's often abbreviated as that.
So let me first say a word about antibodies. These are proteins that
consist of four polypeptide chains. Two of the chains are bigger. So
they're called heavy chains. There's two of those. And there
are two chains that are smaller, so those are usually called light
chains. So, there's four of them altogether.
And, ignoring secondary structure and stuff for the moment,
let me just sort of give you an idea of how these are laid out.
These are the two heavy chains.
And these are joined together by disulfide bridges.
You remember disulfide bridges? If you had two cystines they can
form a covalent bond between them under oxidizing conditions.
So, those heavy chains are locked together. They're actually
physically covalently joined. In fact, there's the light chains
here. So, this is the light. And this part up here is highly
variable between different antibodies.
And the part down here is constant between antibodies.
And it's this huge amount of variability that the body produces
many, many, many types of antibodies, and then figures out which ones will
work to find the particular entity it's trying to recognize.
And I'll come back and tell you in a moment how that is done.
There is a diagram of what I showed you, but of course these are
proteins. They have three-dimensional structures,
and so if you were to look at them with the secondary structure showing,
you can see the different, especially here, a lot of beta
sheets should be leaping out at you.
Now, the part where the recognition is done is up at this end.
So, it's essentially right here. And here's a little movie. You
could see how the thing looks in three dimensional space.
You see the part that's over on the left at the moment; that's the light
chain and the blue chain is that part of the heavy chain complex with
the light chain. And here is the,
it's been tilted up this way so this is the yellow and blue part
you were looking at And the recognition pocket is right
at the end of that. And at this picture,
it's showing how a particular protein was shown in red.
This is an anti-body that can very, very precisely recognize that
particular protein. You can't really tell it from the
three-dimensional shape shown on the left because it just shows the
secondary structure. But, if you could see the full
space filling model, you'd be amazed. The surfaces are
absolutely complementary. It goes back to one of those
principles I've said over and over and over again that so much of
biology works by having complementary surfaces.
And there's a little movie you could see how this thing is setting
up there at the top. So, these antibodies are produced
by a special type of what are called B cells.
These are cells that play roles in the humoral part of the immune
system. And they're called plasma cells. And each plasma cell makes
one particular antibody. And that's it.
So you have many different types of plasma cells, but each one only
expresses one particular gene that encodes one particular antibody.
So, for years, this is something that people struggled with just
conceptually. They could sort of calculate that there were so many
antibodies that if your entire genome was nothing but antibody
genes, we still wouldn't have enough DNA to account for all this ability
to recognize things. So, some other principle had to be
involved. And there are all sorts of speculations about what it was.
I had shown you, I'd managed to not get Bob Horvitz's thing on here,
but this then, who is our fourth Nobel laureate,
I've been sort of working through these.
Susumu Tonegawa, who is in the cancer center,
he's in the biology department. He's also heading, now, this
Picower Center of learning and memory. So, since doing this work
I'm telling you about on the immune system, he's gone to do some
wonderful stuff more on the big problem of how we learn,
and trying to get more molecular insights into that process.
But what Susumu managed to figure out was that this variation and
diversity in the immune system was, at its roots, a combinatorial sort
of process. So, if you look in the DNA of a zygote,
so that's the fertilized egg. We're just getting started with one of our
cells. You've got a single cell. We're looking in the DNA to see
what would happen. We come to the part of the DNA
that's involved in producing antibodies. What he found was that
if you looked along the DNA, there were sequences that looked
like part of the stuff that you'd find in antibodies,
but there were a whole series of them. So, he called this particular
segment V1, V2, V3, up to VN. There were a whole
set of these basically side by side by side by side.
There are about 300 of these in humans. And then down the DNA a
little bit he found another set of sequences that are all variations of
each other. And these were given D1, D2, D3, D4, up to DN.
And there are many of these. And then down the DNA a little
farther, there were three other sections that were called joining
segments. They were called J1, J2, J3. And a little bit farther
down there was a block of DNA coding the constant part of this
polypeptide chain that goes into an antibody.
And what Susumu Tonegawa was able to show, and this led to the Nobel
Prize. So, what happens during the development of these B cells is
there are rearrangements. And a lot of DNA is thrown around.
And the basic strategy is to take, if you think this as being column A,
you take one from column A, one from column B, just picking them randomly,
one from column C over here, and throw away everything else.
So you might have, for example, in one B cell,
you might have V32, D15, J2, and then the constant region.
And, what's in between is an intron that will be spliced out at the time
that the gene's expressed. In another B cell, you might
have V11, D22, J3. So, this rearrangement is random in
the sense of which V segment is chosen, which D segment is chosen,
and which J segment. I don't mean that it all just joins together in a
completely uncontrolled way. And then the rest of the DNA is
deleted.
So a consequence of this, is each B cell expresses only one
antibody. It's true that they're diploid, but only one chromosome
is expressed. So that's how they avoid,
you can imagine they might make to two. But they only make one.
In the process, as you can see, that part is random. Furthermore,
the joining events are what I think you could call sloppy.
And this leads to even more variation than you would have
imagined simply looking at the number of segments.
So, what this part of the process does is it explains why the system
can be has the diversity it has, because it's using this
combinatorial process. If you know the number you can
calculate how many possible combinations there are.
But then there's much more variation because when it joins
together a little segments that are joined are done in a sloppy way so
that the DNA sequence that shows up where the joints occur doesn't look
like anything that was in the DNA at all. It was something like a
polymerase that wasn't very faithful copying and making mistakes
as it went along. So what the system does,
is it doesn't get you a response. It just explains why there is so
much diversity, and why it is that I can go into the
lab and synthesize a compound that's never been on this earth before,
inject a rabbit to it, and the rabbit will probably produce an
antibody that's able to recognize that. That's because it's made this
whole set of them. And they all are going to have
somewhat different surfaces. And they make so many that one of
those surfaces is going to fit the molecule that I'm testing.
You can sort of see, that's only part of the trick.
So, how do you now get an immune response? Because you've got
millions of these things. But what you now need is a whole
lot of one particular antibody that's going to recognize the
pathogen that you are being exposed to. And the principle of that is
really cute. It's a process called clonal selection.
And the idea is that each
B cell displays
a sample of its antibody on its surface. So, we might think of it
this sort of way, that after this process is through
we have one B cell. Of course, these are way out of
proportion. The cells would be huge, and these would be molecules.
So, they're small. But here would be an antibody that can recognize
squares, say, this one would have an antibody that could recognize
triangle. This one would have an antibody that
could recognize a semicircle and so on, millions and millions of
different shapes. And these cells don't divide,
though. They've been made, and they just sit there.
And then, when you stimulate them with an antigen,
and I used that word the other day, an antigen is just anything that
will elicit an immune response. It could be a piece of a foreign
protein, carbohydrate, just about anything that's a small
molecule you've made in the lab. But let's say we exposed now this
individual to an antigen, which in this case can fit into that
receptor. And what happens, then, this one becomes stimulated to
divide. So what we have now is this B cell
that has this antigen stuck into its binding pocket on the sample of its
antibody. And then, the cells divide and they give rise
to two populations. They give rise to the plasma cells,
which are very short-lived, on the order of a few days.
And what these do, so they would look like this,
what they do is secrete antibodies into the plasma.
So what you end up with, then, are a lot of these antibodies
that have exactly the specificity that the original sample had on the
outside of that particular B cell. This takes a few days. So back
when we were talking about the discovery of DNA,
I was telling you about Streptococcus pneumonia,
and you get infected by the Streptococcus.
And there would be this period of five or six days where this person
was very sick, and then either they'd survive or
they didn't survive. If they survived, they'd been able
to mount an immune response and make these antibodies before they got
killed by the bacteria. And the reason it takes a few days
is when you start out there could be just one B cell that's able with an
antibody, makes an antibody that is capable of recognizing the capsule.
Maybe there are a few. Anyway, but they were very,
very tiny number, and there were probably a lot of bacteria.
So what had to happen, then, is that the original cell or small
number of cells that could recognize the Streptococcus had to be
amplified. They had to make a lot of plasma cells that have the
potential to make the antibody, and then they had to secrete the
antibody into the plasma. And I'll tell you in just a minute
some of the strategies that that uses to help kill the pathogen.
And the other population, just before I go on there,
are what are called memory cells. There's not as many of these made,
but they're very long-lived. And so, what they have is exactly the same
capacity to make the same antibody, but they're not actively dividing.
They'll just sit there,
float around in your bloodstream, and then if you get a second
exposure to the antigen, you get a very fast and strong
response because the selection for finding the cells that had
antibodies that can recognize the antigen has already been done.
And there's already a few of them around, and then after you do that
then you're able to make, once again, the binding of the
antigen stimulates these guys to start dividing.
They make a lot of plasma cells. And going back to the principal of
vaccination, your first response is fairly modest.
But if you get a second response, what you're doing now is the memory
cells are already there. They have the specificity for
recognizing the antigen in question. And you can make a whole lot of
them. So, if you had chickenpox when you were little,
you have memory cells that know how to recognize the chickenpox virus.
And then when your kid gets chickenpox like mine did,
I didn't get sick because I had memory cells that were able
to recognize that. OK, so what happens if you get an
antibody? How does this help the organism, or in our case someone
like you or me, avoid getting sick?
So there are a couple of strategies. One we might think of
is bind and block. For example, you are a virus and you
get covered by antibodies. Viruses: it's exactly the same
logic as bacteriophage, except that instead of affecting a
bacterial cell a virus would be infecting one of our cells.
And as the virus has receptors or something, it has to recognize
something on my cell, in order to attach and then to
inject its DNA. So if we've got an antibody sitting
here, then it can't find its way to the host cell.
And then, there are a couple of other ways. They can target for
destruction. And there's basically two ways. There's something called
the complement system, that if it is able to recognize,
say, the bacterial cell and their antibodies are sticking to the
outside, what the complement system does is it's able to make little
pores in the membrane of the pathogen.
And I think one of the things I hope you will remember is that one of the
secrets of life is that we have to keep that membrane around there.
We have to keep all of our insides in, and the rest of the world
outside. We have hydrogen ion gradients across the membrane.
So, if you want to kill a cell and you, say, insert a protein that has
a little hole and it, and that thing sits and sticks in
the membrane, that cell is dead. It can't maintain an ion gradient,
and things can leak out through the hole.
So that's one of the ways of killing it. The other ways are macrophages.
These are a type of white blood cell, as well,
are very good at recognizing bacteria that have antibodies stuck
to the outside. And in fact, that was the principle
of that. We have the Streptococcus, and we have the capsule.
And you may remember that little movie I showed of a white blood cell
that was trying to eat it, and it couldn't get hold of the
thing, whereas we saw another example where a bacterium without a
capsule, there was sort of principle I said is that the white blood cell
was able to recognize the bacterium and then it pinches it off inside of
a membrane bubble. And I sort of said at least in
principle that there is another little bubble with poisons,
and it brings it together so that you have the bacterium and the
poison together inside of some intracellular compartment,
so that macrophages know how to kill a bacterium if they bring it inside.
The problem in the case of something like Streptococcus was
being able to recognize it because it couldn't get hold of that capsule.
So, those antibodies that guy made during that five day thing decorate
the outside of the capsule because their specificity is to recognize
the capsule and bind to it. But a macrophage,
even if it couldn't get hold of the bacterium with a capsule is able to
ingest something that has antibodies stuck on the outside.
And once it gets inside, it can kill the bacterium.
In fact, immunologists call this process opsinization,
which is derived from the Greek words for seasoning,
like putting salt on your food. And the idea was that when they were
giving that word, with these macrophages,
which liked to eat bacteria, they have a little seasoning that
they have these little antibodies decorating their outsides.
So here you can see it least in the humoral response how you generate a
whole lot of diversity. Then this principle of what's called
clonal selection identifies a B cell that's able to make an antibody that
can recognize the particular pathogen or molecule that you're
being exposed to amplify that, make a lot of antibodies, and then
it can either just stick to the pathogen like a virus and mess it up
that way, or it can decorate it if it's something like a bacterium,
and then pull in a couple of other systems that are capable of killing
the pathogen. I mean, it's an absolutely amazing system.
It sounded like science fiction when I first heard about it.
When I heard people talking about it, everyone could see there was an
information theory problem. How do you encode all that
information with just this amount of DNA in a cell?
Now we understand. And there's even another part that
I'm leaving out here. But once this whole thing has been
selected, there's another whole round of sort of refinement where
the cells do kind of a very kind of localized mutagenesis one base pair
at a time in the vicinity of this binding pocket.
And they're able to make, if they're given more time and more
exposure to the antigen, they can make a better and better
binding surface until you begin to approach sort of the theoretical
maximum. Now, the T cell, in this case this
involves the cytotoxic T cells, and they have a specific recognition
molecule on their surface. It's called the T cell receptor.
And in this case, it's attached.
So, this is the membrane of the T cell. And this is the cytoplasm
down on this side. There's a little bit of the protein
that goes into that. And then there's an alpha helix
that goes through, and then a segment that comes up
like this. And there's another chain that does the same thing.
So, there are two segments that span the membrane.
This thing is anchored in the membrane.
And then it's essentially the same principle as with antibodies.
There's a variable region, and there's a constant region.
And to a first approximation anyway the logic by which the cell
generates a huge, diverse set of T cell receptors is
the same logic that underlies the generation of a whole lot of
different antibodies by taking segments, joining them,
picking them randomly out of column A, column B, and then joining them
together, sloppy joining all the other processes to increase the pool
of diversity. Now, what these B cells are able to
do, then, these T cells are able to do is something quite remarkable.
We have on our cells, this is, say, one of my cells,
little sort of proteins that function as sort of display cases or
something. And what they do is they show samples of all of the different
proteins that are inside us at any given moment. Proteins are turned
over, and chopped up, and things are recycled and so on.
So there are always little peptides, little pieces of proteins around.
And, the display case, if you will, has got a major
histocompatibility complex, which is usually abbreviated as MHC
because it's such an unwieldy name. And there are many,
many alleles of MHC in the population, which means that we each
have, for the most part, a sort of individually designed
display case for showing these peptides. The property of these
display cases, they take some little piece of a
protein just a few amino acids long, it binds into the display case, and
that sticks on the outside of our cell. And so we have
a lot of these. And so on the surface of our cells
are these little individualized MHC display cases showing little samples
of the peptides of the proteins from the proteins that are inside us.
So, if everything is fine, all of the peptides that are in the display
cases are our own. And I'll tell you in a minute why
that doesn't cause a problem. But then if you get infected by a
virus, and it injects DNA or its RNA inside of you and then starts to
replicate, now you have some virus proteins that don't belong to you.
They get chopped into pieces, and they begin to appear on these
major histocompatibility display cases. So if you think here,
this could be, perhaps, a little piece of, let's call it self protein,
it could be a little piece of my own DNA polymerase or something
like that. And over in this one,
let's say we have a little piece of a viral protein.
So that's something that would not be normally there.
So what this T-cell receptor does is it recognizes, so this
is non-self or foreign. What the T-cell receptor does is it
recognizes these foreign peptides. But it does it in the context of
the display case. Otherwise the peptides would be
floating around. So, in essence, the T-cell receptor,
if this is a cytotoxic T cell it's able to see the individual display
case with a bit of viral protein in it.
And then it knows that it should kill that cell because it's got
something in it that shouldn't be there. I mean,
it's a brutal but very effective strategy. If we applied it here,
I go around if I found any of you had a cold, I could just take a gun
and shoot you and it would cut down on the number of sick days for the
rest of us because it wouldn't spread the infection.
But in essence, at a molecular level,
that's the strategy. Try to identify a cell that's got something
inside it that shouldn't be there, and then the cytotoxic T cells kill
that. And let me just show you a couple of quick movies of this.
At this point, these will be the last protein structures you're going
to see from me, I think. Here's a representation of that T
cell just as a cartoon as you see it in a textbook.
Here it is. This is the binding pocket up here.
And there's a little tiny peptide, nine and amino acids from the HIV
virus bound in here. Somebody did a crystal structure,
and was able to work that out. And, if you look at it in three
dimensions, you'll see how beautifully this little binding
pocket and the peptide lies in there.
So that red part is the piece of chalk, and the other part is what
I'm describing as my hand. It's not a bad analogy, actually,
even on a structural level. And then, here's another representation.
This is sort of showing the hand with a piece of peptide in it.
And then the T cell is able to see this whole thing in recognize it.
And, if you look at it in a structural form, here's
the little peptide. This is the part,
the display case you're looking at. And here's the T cell receptor now
fitting down in seeing the peptide in the context of this major
histocompatibility antigen. And again, these things are all
beautifully complementary a three dimensional level.
Again, at the heart of this is the principle of complementary surfaces
fitting together that underlies so much biology. What's this?
This is a tumor cell. These are cytotoxic T cells that
have recognized this tumor cell is doing something it shouldn't that a
normal cell wouldn't do. And it's attacking it, and it's
killing them. So, not only does the cellular immune
response help us against things like infections from virus and bacteria,
it also will help prevent cancer. So obviously there must be some
trick here to why we don't see our own peptides. This is the self
versus non-self And it's a relatively simple principle.
So, distinguishing self versus non-self is a problem throughout
this whole part of the immune system.
And here's the principle. During embryogenesis, the cell
makes, the organism I guess, makes the assumption. I mean
obviously it's not thinking about it.
This is a way of understanding what's happening.
It makes the assumption that no pathogens are present.
Any B or T cell recognizing something must be recognizing itself.
And so, it deletes those B and T cells. This process is given a name.
It's called education. And it happens in this organ called
thymus. So, and then after birth, then it switches. And now B and T
cells, if they recognize something, the body makes the assumption it
must be a pathogen. And it goes after it.
We have this huge human disease where that goes awry: rheumatoid
arthritis, or multiple sclerosis are cases where the self versus non-self
recognition has broken down. OK, so for example multiple
sclerosis, a very difficult disease, because there's a gradual
deterioration of the nervous system.
And what happens is the body of the person with that mounts an immune
response against the sheath that covers the nerves,
and then that sheath gets destroyed, and that the nervous system,
somebody with multiple sclerosis, starts to break down. And so, if
you lose this self versus non-self you get what's called an autoimmune
disease. You may have heard that phrase. It's very important.
It's a very tough thing if you have one of these. But that's what lies
at the heart of it. And people still don't know,
but there is certainly some evidence for some of these that are triggered
by a bacterial infection. So, it could be that perhaps maybe
a bacterial protein looked close enough to one of your own proteins,
that somehow you got antibodies against the bacterium,
and then it turned out it could also recognize something in your body.
There are some other immune diseases you probably heard of,
the baby in a bubble kind of thing. There are a few people who were
born who have no immune response at all because one of the basic pieces
for doing those DNA gymnastics I talked about isn't there.
Those people have no B cells or T cells. They die unless they are
absolutely shielded from everything else. And that's one of those cases
when gene therapy, if you could get that gene into that
person, they'd have an immune system and they could live.
There are other kinds of immune deficiencies that are less extreme,
but nevertheless, people will be susceptible to infection.
The other one which I've already talked about, but now you can see in
another context is AIDS, Acquired Immune Deficiency Syndrome.
And I told you what the HIV virus does is it injects its RNA.
That makes a DNA copy. It goes into protein. The cells that it
affects our special type of T cell called T helper cells.
What they are doesn't matter so much, but what's important to know
is they're needed for both branches of the immune system.
They play roles in the humoral response and cellular response.
So, someone who gets infected with HIV, what happens is the virus is
replicating in these helper T cells. And so their immune system is
slowly, slowly being knocked away. And the last thing, which I won't
have time to talk about, but if you have an allergy,
that's an overreaction of the immune system. So this is my last lecture.
I've got to let you guys go. It's been a true pleasure to talk to you;
A real honor to meet many of you. And many of you put a lot of effort
into those little answers. I really, really appreciate that.
For those who'd rather not be here, I hope that somewhere down the line
when you're confronted with a medical situation dealing with your
parents, your child, yourself, whatever it is,
that some of the stuff that you heard will reemerge to help you with
those decisions. And I wish you the best of luck for
the rest of the course, and the rest of your careers at MIT
and beyond. Thanks very much. And as I leave,
too, I've had the pleasure of just having an incredible teaching staff.
I don't think you guys know how hard they work behind the scenes,
but thanks to all of you for being with me.