There was a little confusion
with dideoxies in one sense,
and some of these things like
the PCR you're going to have to
sort of sit down and actually
think about it,
but the principle of the
dideoxies, if we were making a
chain of beads that had a hook
on one end and a little hole on
the other, and we were joining
these things together,
we could make obviously,
a chain that went on.
And then we could hook another
one in, and so on.
And if we had a bunch of beads
like this every now and then we
threw in a very small number
that didn't have the hook on the
end, any time this particular
chain were elongating and we put
on one of these things,
the chain would stop because
you haven't got any where to
join onto it.
You added dideoxy into a
polymerase reaction.
A chain that gets the dideoxy
doesn't have anything to join in
the end, and that will stop.
If we only added this,
the entire reaction would stop,
and everyone would come at the
first time a dideoxy got
incorporated.
The trick is to put a little
bit in.
So, a few of the molecules
stop.
Everything keeps going.
The next time a dideoxy gets
incorporated,
the chain will stop there.
And out of this,
you will generate a family of
polymers that are of different
lengths.
Each one will terminate with a
dideoxy nucleotide,
and if the dideoxy nucleotide
we used in that particular
reaction was,
let's say, dideoxy ATP,
that means that an A was the
last nucleotide added to every
one of those.
And we can separate these on
the basis of size.
And if I ran them out on a gel,
I'd see something like that.
And that would tell me that
when that polymerase was coming
along, that was the first time
it saw an A.
A few stopped there,
polymerized a few more.
Then it put in another A,
put in some other things,
and so on.
And that by itself wouldn't
tell us the sequence.
But if I did that reaction four
times in a row,
then I could tell.
In the old days,
they didn't used to use dyes.
We just did P32 on it as a
label, and then you'd run the
four reactions side-by-side.
And this would be with dideoxy
ATP.
You'd see a pattern like that,
and maybe with dideoxy TTP,
you'd see something like this.
And when you got the rest of
them, you'd kind of end up
working out what the sequence
was by looking across the four
lanes.
This business of using the dye
is just one more step up in the
engineering side that enables
the thing to be done
automatically.
And it's pretty well explained
in your textbooks.
OK, PCR, someone was confused
as to why we didn't just let the
cell do it.
Well, the cell does a great
job, but if you are a molecular
biologist trying to understand
the basis of life or if you're a
biological engineer,
and you want to produce
something, you need to get hold
of a particular piece of DNA.
Or, if you're a forensic
investigator,
and you've got a tiny,
tiny sample of human DNA,
and you want to know whose it
is, you have to make more of it.
And, that's what PCR is all
about.
So I'm going to switch just
over to the net for a minute.
I think this first site,
I just want to show you
something, how somebody
functions in a lab now with all
these genes out there.
And then, I'm going to show you
a little animation for PCR that
will help.
So, if you just go to Google
and type NCBI,
that's the National Center for
Biotechnology Information.
And, the Dolan Learning Center
is a center that Cold Spring
Harbor Laboratory has set up to
teach people about DNA.
So let me just see here.
So, let's just go to,
OK, let's use,
whoops, this is going to seize
on us.
OK, let's find how it happens.
00:04:31
 
OK, so here's this National
Center for Biotechnology
Information.
There's all sorts of things you
can search for,
and I'm not expecting you to
know the site.
I just want to sort of give you
a demo.
If I was sitting in my office,
this is the sort of thing I can
do easily.
Rather than sequence looking
for DNA sequence,
I'm going to look for the
translated sequence of the
protein that's encoded by the
gene where the computer's gone
through and used the genetic
codes tell me the sequence of a
protein.
I told you about sequencing a
mismatch repair gene back in the
80s.
It was called MutS,
and I'll put in Walker GC,
and probably hopefully get us
to the thing.
And there, the very first hit
is DNA repair.
Protein MutS salmonella
typhimurium, that's the one I
sequenced.
So I'll just go to that.
It has various ways of
displaying the sequence.
I'm going to switch to Fasta,
which is a very easy way to see
it.
Now what you see is the
sequence of the protein using a
one letter code,
or one letter stands for each
amino acid.
K is lysine.
A is alanine,
and so on.
I'm just going to copy that,
that piece of sequence.
OK so that's the bacterial gene
for mismatch repair.
At the time I put that in the
database, there wasn't anything
else like it,
except for the gene that was
Streptococcus pneumonia.
But I found out,
someone else is sequencing by
phoning around in the field.
I'm going to go back to the
main site and I'm going to use a
program called Blast,
which lets you search the
entire database.
I'll use a protein blast.
I'm going to take a protein
sequence, and I'm going to ask
what else is out there in terms
of protein sequences?
I'll paste in this bacterial
sequence, and then I'm going to,
if I can, manage this thing.
Let's see if I can get myself
down here.
OK, over here I'll probably do,
OK, so I'm going to limit it,
let's just search the human
genome.
That's all we've got to do.
And what did I have to do to
get this thing to fit?
Which button?
Go to the right.
Can you just come up here for a
second to help me get this set
up?
I'm computer limited here
apparently.
OK, that one,
OK, great, so why do we not try
this again?
PAUSE]
Sorry about this.
We'll see if we can get this
thing to go.
I have what?
Yeah, that's OK though.
That should be fine.
Try again.
Let's see if I can get the
thing to work.
OK, so it's got it now.
It'll tell me.
It's searching all the sequence
that's out there.
There's just an unbelievable
amount of sequence.
That's just how long it took.
It's showing me here a
diagrammatic representation of
the things.
Then I can see that the very
first it was MutS homolog three
for humans.
And if I go down here,
we can actually see on
alignment of the bacterial gene
on the top line,
and the lines below is the
sequence of that particular
human homolog.
And you can see in between all
the things that are in common,
and particularly down at the
C-terminus of the protein,
you can see there's very strong
conservation.
You may not think that that's
impressive, but remember for
every one of those positions,
there's 20 possibilities.
So, if you get that many in a
row, that's the same gene
basically.
And when you take the
structure, the structure's going
to be very, very similar.
And it does mismatch repair in
both.
Just to try and give you an
idea of how you do sequence now,
because with all these genomes
done, you do the vast majority
of it by computer,
rather than some other way.
I want to take you and show you
this.
DNA learning:
if you go there,
the second thing is a set of
animations.
Go to the animations.
There's one on polymerase chain
reaction.
And, I'm going to just show you
this because this is a nice
little, let's see if we can get
this thing to center.
OK we'll have to see whether
this is going to work.
OK, so this is the principle
of, you can go do this at your
leisure, but the idea is to heat
the DNA up, the strands come
apart.
Then, were going to take these
two little primers,
not promoters,
which I think someone was
confused about,
a little piece of DNA that
complimentary,
and anneal them.
Than we added DNA polymerase.
You know what happens then.
We extend those primers.
That was the first cycle.
Do the same thing again.
Go to the second cycle.
This is what I was drawing on
the board the other day.
Now are going to denature the
DNA.
The strands come apart.
Let's let the polymerase extend
them.
Let's go to the third cycle,
denature the DNA,
anneal the primers,
extend the primers,
and now for the first time,
we've got what we were shooting
for.
We have a double-stranded copy
of just the DNA that was defined
between those primers.
OK, I think this actually,
I'm going to go back one.
Oops, OK.
If you go, then,
to the amplification graph,
what they're doing here is
they're showing you what happens
as you do successive cycles.
So, at the first,
oh, it's down here.
Just a minute.
If we do the first cycle,
we end up with two DNA copies.
That's just plotting what I
showed you.
The next one:
we have four.
We haven't yet got to this
target sequence.
By the next cycle,
we now have two copies of the
target sequence plus these other
things.
But if you keep going,
let's say by the time we're at
seven cycles,
the number of targets is up to
114.
The number of DNA copies is
128.
But, if we keep going like
this, we'll find out that the
target copies become the vast
majority of the sequences that
are in there.
So, by the time that you're up
in the 30 cycles,
or something like that,
there's only a handful of the
original things,
or almost all,
and that, I hope will help some
of you who might have had
problems with understanding the
PCR.
So, what I'm going to do is
tell you a few more things about
what you can do with recombinant
DNA, this recombinant DNA
technology, because it's just so
powerful.
And I can only sort of give you
a few ideas, and show you a few
variations.
But, most of these things are
just taking principles that
you've already learned as part
of the basic biology I'm trying
to tell you, and then using them
like an engineer to achieve some
applied purpose.
For example suppose I wanted to
produce a human protein,
and try and produce it in a
bacterium.
That would be great.
I could take the one gene.
I could grow a fermenter load
of E.
coli, and if I got it right,
then I'd be able to make a lot
of this protein instead of
trying to isolate it from some
human source or something like
that.
There's a couple of problems.
We talked about them.
One is the problem of
promoters.
Another one is that human DNA
would have introns in it.
And, bacteria doesn't recognize
the human promoters.
It wouldn't start to make an
RNA in the right place,
and it doesn't know what to do
about splicing out the intron.
So, let's address the intron
first.
There is a way of handling that
that's quite easy.
And that's what's called to
make cDNA library.
So, if we have DNA,
and then we get the RNA,
we get the RNA copy [SOUND
OFF/THEN ON]
including these intron
sequences.
And then what happens,
this is RNA splicing that we
talked about.
And what we get out of that
would be an mRNA,
in which the introns have been
removed.
So, eukaryotic cells,
my cells, know how to express
the gene, so they make the RNA,
they know how to get rid of the
introns.
So, if I were to isolate a
messenger RNA.
That's been spliced from me,
or you, or anything,
what we would have is a
population of RNA molecules that
don't have introns anymore.
Anybody remember any way we
could get from RNA back to DNA?
Reverse transcriptase.
So, if we used reverse
transcriptase,
that protein that David
Baltimore discovered and
viruses, and which retroviruses
use, now we would have a signle
stranded DNA copy of the mRNA.
And then, we could use an
ordinary DNA polymerase to get
ourselves to double-stranded
DNA.
We'd be doing,
in essence, exactly what one of
these retroviruses does.
This would give us what's known
as a cDNA library,
where the genes don't have
introns anymore.
So, if I wanted to get at one
of my proteins,
one of my genes,
and think about expressing it
in E.
coli, what I would do is go
looking in a cDNA library using
a sort of approach as we've
done, trying to find my gene of
interest, because if I use the
cDNA library now it would just
be like a bacterial gene.
You could see the ATG start.
You could get out your handy
little genetic code,
and you could walk along,
and read out the sequence of
the protein.
So, that's part of what you
need to do if you wanted to
make, say, a protein inside of a
bacterium.
The other one which we talked
about was since the promoters
are not a universal language,
what E.
coli RNA polymerase sees is
different than what human RNA
polymerase sees as a start site.
I would have to add in a
promoter that would drive the
expression of this open reading
frame if I wanted it to work in
E.
coli.
And that's fairly easily done,
too.
A general thing that's for this
is called expression cloning.
And it would be more or less
the same idea.
We'd have a vector that had a
cloning site.
It has an origin of
replication, and maybe there's a
selectable marker such as the
drug resistance.
That's the basic kind of factor
that I talked about before.
However, if I clone in a piece
of DNA into that,
it has to have a promoter that
can be read in the organism
working with,
because it's just out whatever
nature gave it,
whatever promoter that would be
in front of that.
But, if I were to now into this
vector put an E.
coli promoter right there,
now, if I just downstream of
that put any open reading frame,
human protein lets say,
which we've gotten rid of the
introns, the human genes minus
its introns, which you got from
the cDNA library,
now when the bacterial
polymerase came along,
it would be copying,
making it a messenger RNA for
human protein,
and we could get it out of
that.
And the beauty of that,
suppose we took the front part
of the Lac operator,
we would have a regulated
promoter.
It would be just everything we
studied about Lac if we were to
starve it for,
you know, we have to get rid of
glucose, and then if we added
lactose or some kind of
synthetic inducer,
we can turn the promoter on and
off.
So, you could grow an entire
fermenter load of bacteria
without expressing the gene.
And then, once you had the
bacteria all grown up,
you could throw in something
that would normally induce the
expression of the Lac regulatory
system.
And now, instead of making beta
galactosidase,
instead it would make the
protein that you are interested
in, you with me?
It's very pretty.
And in fact,
so much of what you can see in
this is, these really basic
studies, since the Lac system
was one of the first to really
be worked out in detail,
we use its parts.
And, there are many vectors
around now that have exactly
that.
They have the Lac promoter,
and you can turn things on and
off in a regulated way,
so not only provide a promoter
that works in the organism,
but it also gives you a measure
of control.
There's another very cute
trick, and what we've done sort
of here is we took,
say, the promoter for Lac in
the regulatory region.
I'll use R to stand for
regulatory region,
and then this would be the LacZ
sequence.
What we've really done,
is we've taken a gene from
somewhere else,
let's call it gene X that had a
promoter from gene X.
And, in essence,
is cutting each of them here.
And, now we take the regulatory
promoter region from Lac and we
put down below it gene X.
And, now we've got this gene
whose products we're interested
in producing in a fermenter
under the control of the Lac
operon.
Well, there's another kind of
thing we can do.
We can do the other way around.
We could take LacZ,
which makes beta galactosidase.
We could put it under the
promoter regulatory region of
gene X.
Well, what will happen then?
If that construct is sitting in
a cell, anytime that the cell
decides to make gene X,
instead it will make beta
galactosidase,
which is really easy to assay
for.
And, this sort of strategy,
you'd use something like LacZ
as a reporter.
In this case beta galactosidase
synthesis, which you can assay
for, reports when is the
promoter of gene X is
functioning.
This reporter gene now has the
regulatory characteristics that
are imposed upon it by that
particular promoter.
So, there's this picture that
I've showed you,
this little movie I showed you
early on.
You've seen it a couple of
times.
In this case,
the reporter is green
fluorescent protein.
What Barbara Meyer,
who made this particular
construct, did was they took the
gene for green florescent
protein which started out in a
jellyfish as you may remember.
And, the protein folds up,
and ends up being fluorescent.
So, we can tell when it's
expressed very easily.
And in this case,
you'll notice not all of the
genes in the whole worm isn't
glowing.
And so, it's under the control
of the promoter regulatory
region that is expressed only in
specific body parts.
And so, you can see where that
promoter is working by just
looking at the worm.
In the case of something like
the mouse that we talked about,
it's a pretty uniform
expression at least in the skin.
So, that was probably,
in that case,
the green fluorescent protein
was probably put in a promoter
that's expressed in probably
most of the cells in the body,
at least certainly all the ones
in the mouse cell.
I don't know the details of
that.
Ditto over here.
It was probably something that
was expressed in most of the
body cells, but you also could
have put something that was just
expressed in some very little
bits.
So, depending on how you do the
construct, there are a lot of
different things that people can
do in this sort of thing.
OK, one more category that
comes out of the sort of thing,
is if we have a gene of some
type, I don't know what it does
but I'd like to find out.
You know, at least budding
geneticists, know what we'd like
to do.
We'd probably just like to
disable that gene very
specifically,
and then look at the live
organism to see what happens.
And, the principle is the same
whether you're doing it in E.
coli or a mouse.
It gets a little more
complicated for technical
reasons doing it in a mouse.
But the idea is exactly the
same.
And here's the strategy.
So, we'll just take a piece of
DNA from the organism.
And sitting at here is this
open reading frame that we've
seen.
We don't know what its function
is.
We think if I could knock it
out, get rid of its function,
I'll look at the organism.
Maybe I can make a guess then.
So, if we were to cut the gene
somewhere with a restriction
site, and then we were to take,
for example,
a gene encoding a drug
resistance or something like
that, and insert it at that
point, what we would end up with
is this piece of the organism's
DNA.
The first part of gene X,
then a drug resistance,
then the last part of gene X,
and some more sequence from the
organism.
Now, this would be,
we'd have this in a test tube.
We could do it by the kind of
recombinant DNA manipulations
that we have.
And what would happen if I were
to put, now, let's keep it with
bacteria where it's easy to see.
If I were to take that piece of
DNA, put it inside a living
cell, what's going to happen?
Well, let's make this,
say, here's the end of it.
That's all we've got.
Well, inside the living cell,
we of course have the entire
genome.
And then we come to this part.
We have gene X.
Then we'd have this going.
That would be the whole thing.
Well, this particular piece
doesn't have an origin of
replication.
It's not joined to a vector.
It's just sitting there.
So, if the cell divides,
it's not going to get
replicated.
So, if I select for a drug
resistance that's on that piece
of DNA, unless something happens
I'm not going to get a
drug-resistant bacteria.
But you do know a way that this
thing could join to an origin of
replication.
It could join to the origin of
replication that's on the
bacteria chromosome.
And, the way to do it would be
by undergoing genetic
recombination over here,
because this DNA is exactly the
same as on that side,
and over here it's the same
thing.
This DNA is the same as that
side.
So, if that genetic exchange
happened, what would happen,
even if it happened rarely,
was this piece of DNA would
replace the piece of DNA that's
in there.
I'd be able to tell it was
there because I'd just select
for drug resistance.
And even if it only happened
only one in 500,000 cells,
it wouldn't matter because up
would growth the colony that now
has the drug in the middle of
gene X.
Gene X is gone,
and I could look at the
organism if it's alive and see
if it has a phenotype.
If it's an essential gene,
that strategy obviously won't
work, and when people do the
more complicated thing of doing
this kind of experiment to make
a transgenic mouse,
it takes about a year to go
from our DNA manipulation all
the way to the live mouse with a
disrupted gene.
And sometimes what they find
after spending half of your PhD.
is that that was an essential
gene.
And, there's no live mouse,
or it made it two days into
being an embryo and it tanked at
that point.
But, this again,
you could see,
we talked about going back and
forth between gene,
protein, and trying to figure
out function.
All I can sort of do is give
you the flavor of what's going
on.
But one sort of overarching
thing I hope you remember going
through this is DNA sequencing,
PCR, all these kinds of
manipulations we're talking
about are just exploiting these
basic cellular components that
we learned about studying,
how does DNA replicate?
How is information coded?
How do genes get expressed?
How does genetic information
gets sorted between cells?
It's simply applying those
relatively well understood
tools, or sort of biological
principles and parts that we
learned about,
and now using them as tools in
an engineering way,
and have just completely
transformed the way biology has
been done in the last couple
decades.
And it's just,
as I say, things are changing
so, so fast.
It's almost breathtaking.
So, the last little bit of sort
of technique oriented stuff,
I just want to at least make
sure I've mentioned what are
called microarrays.
You often hear these referred
to as DNA chips.
The principle here is this is a
way that lets you ask,
not only whether one gene is
being expressed or not under a
particular condition,
whether its RNA is being made,
and in most cases that means
making protein,
or whether it's off,
or whether it's at some
intermediate level.
A microarray lets you do that
experiment with many,
many, many genes at once.
And here's the principle.
You take some surface,
and there will be a bunch of,
if you will,
sites on the surface,
on this chip or whatever.
And, what will go to be
attached here would be a little
piece of DNA from gene one.
I mean, let's say,
maybe a hundred nucleotides:
that would be far more than
enough to make it absolutely
specific that they could only
hybridize to a messenger RNA
from gene one,
and not from anything else.
And, this one,
then, would have from gene two,
this one, from gene three,
and so on.
Then, if we were to take a
messenger RNA preparation from,
say, an organism if it's a
little one, or maybe a tissue,
or something like that,
anywhere you could isolate RNA
from.
And then, we'll label it in
some kind of way,
and we can label it
radioactivity,
we can label it with dyes.
It's usually done with dyes,
and there are a variety of
variations on this.
Those are sort of technical
details how to do it.
But here's the principle.
Let's just, for the moment,
just consider that it's got a
label on it.
So if we take the messenger
RNA, and take this little chip
that has samples in the extreme,
it could be a sample of every
single gene that's in the genome
of that organism,
we take this labeled RNA,
actually what we would usually
do is to use this to make a
labeled cDNA preparation,
which would be a copy of each
one of these things.
That the technically easy way
to get label into it.
But what we do have is if the
gene was on, its messenger RNA
would be on, and we'd have a
bunch of stuff corresponding to
gene one that had label on it.
And if we give it a chance,
that will, then,
hybridize here.
And there would be some way of
detecting this label.
If gene two was off in that
sample, there won't be any
hybridization.
There won't be any signal.
You can sort of see in
principle what you're doing is
you're interrogating each gene
in the extreme,
each gene in the organism under
some condition.
Is it on?
Is it off?
If you did various samples,
and you could see maybe it's in
an intermediate level,
and so on.
So, the chips look like that,
50-100,000 genes perhaps,
something like that.
These things are really small.
Here's sort of a display of a
simple one, and this is one
where they're taking RNA.
The samples are from two
conditions.
One's labeled with a dye that's
green, and one's labeled with a
dye that's red.
And, if you get equal amounts,
it looks yellow.
So, they mix the two things
together, and if the gene is the
same under two conditions it
would be yellow.
Under one condition,
if the gene was on in condition
one than it would be green,
and off in two,
and back and forth.
So, without trying to get lost
in the technical details right
now, which doesn't matter,
the principle of this thing is
that you can take,
you can sort of,
by making a preparation of RNA,
then you can use these DNA
chips and say,
is each gene on and off?
Or if I switch conditions,
who comes on and off?
So, it's a little like,
I think of it this way.
It's like having,
all right, who's on today?
And a number of hands go up,
or something.
And the rest of you would be
off.
But, come back on Monday,
and I say to the something or
other, and a different set of
you would put up hands.
And what I'm kind of looking at
are the changes between that.
And the sort of thing where
this has been so powerful,
for example,
is there are kind of cancers
for which there is a treatment,
but it was only 20% successful.
And, when people started to
study these cancers and then
looked to see what genes were
on, what they realized was even
though physicians had given
these cancers a particular name,
if you looked at which genes
were being expressed,
they fell into two classes,
class A and class B.
And what they then realized was
that the treatment they were
using was 100% effective of
tumors of class A,
and wasn't doing anything for
the tumors of class B.
The physician couldn't tell the
difference between these two
types of tumors,
but a microarray can say it.
And once you have that kind of
insight, if somebody has a tumor
of the type A,
you can use the treatment.
It's very effective.
And of course,
when people are trying to do
now would be to develop an
equivalently effective treatment
for something for the tumor of
type B.
So, again we have so little
time in this class.
I could go on basically for
ages.
There's the output of the real
sort of DNA chip.
You can see things are very
dense, and the great cleverness
in doing these things,
people now use the technology
that goes with LaserJet printers
to actually synthesize little
pieces of either DNA or proteins
starting on a little spot on
each membrane,
or on the chip,
or whatever.
You put it on one nucleotide
and then you put it on the next,
and the next,
and the next.
You could sequence it using
technology that's already around
for inkjet printers at that kind
of thing.
So here you've seen a fusion of
different types of engineering.
OK, the last thing I'm going to
tell you about is a little bit
about the immune system.
We've run into this.
This is a movie that some of
you liked, got the biggest aw I
think of the last part of the
course anyway.
But what we are seeing here is
a white blood cell pushing aside
from red blood cells,
which are stationary,
and chasing a bacterium.
It's obvious that it can trace
it.
It's able to recognize some
things, and at some point,
then, it took it up.
The principle of what happened
there was this white blood cell
had a capacity to recognize the
bacteria, then bind to it.
And then, its membrane,
this is the membrane,
and this is a white blood cell.
There's many types of these,
and it pinches the membrane
off.
So you have the bacterium.
This is the bacterium.
And, it's inside a little
membrane compartment,
as if the bacteria is in a
little soap bubble.
And the principle of what
happens is the white blood cell
has another soap bubble that's
full of poison.
And, if you took two soap
bubbles and push them together,
you know what happens.
They'll fuse,
and you'll get a bigger soap
bubble.
And that's, in essence,
how these white blood cells
normally kill bacteria.
They would bring together these
two compartments.
Now you have a bacteria and a
poison within a white blood cell
at the bacterium,
would get killed.
And we talked about how
bacteria fought back.
That was a streptococcus that
has a capsule.
And the capsule,
by having polysaccharide on the
outside, prevent the white blood
cell from being able to grab
hold of some feature of the
bacteria, that starts this
process of killing it.
And when I told you the story
of how DNA was found,
it was people studying
pneumonia.
If you remember,
it was streptococcus.
If the streptococcus had a
capsule, and the people would
get very sick.
And after five or six days,
there would be a crisis where
they either lived,
or they died.
And what would happen in that
time is that,
the last thing I'll tell you
about, what's called the
adaptive immune system would
have generated special
recognition molecules called
antibodies that would have
learns to recognize the capsule
at that bacterium.
And once those were there,
now those white blood cells
would be able to capture the
bacterium, because the
antibodies give it a hand in
recognizing there was something
there that needed to be killed.
The way this adaptive immune
system works,
it's almost like science
fiction.
And I'll tell you the molecular
basis of it.
The key insight came from
Susumu Tonegawa,
another member of the MIT
faculty biology,
and also runs Picower Center,
who got a Nobel Prize for
understanding the basis of the
diversity of the immune system.
What I just want to do for the
moment is just sort of point out
the key features of what's
called the adaptive immune
system.
And this is one of the reasons
that we are able to live.
And even though we get sick
from time to time,
and we've all had one thing or
another get us for a little
while during the semester,
the reason we aren't sick all
the time, and the reason we
recover when we get sick,
as we have what's called an
adaptive immune system.
What happens when people get
infected with HIV virus is the
cells that it lives in and
destroys are key players in your
adaptive immune system.
And to some people don't die
from the H1V infection itself,
they died because lots of
things that we just,
bacteria or fungi,
whatever things we just have on
us and we live with all the time
suddenly become killers because
you lack the immune system that
fights them off.
So the so-called adaptive
immune system is absolutely
amazing.
So several features,
it's got an incredible
diversity, there is a general
word that's used to describe
some sort of all sorts of
chemical entities,
and it's called an antigen.
So anyway, this can recognize
many, many what are called
antigens.
And at the moment I think you
can just think of them as some
kind of chemical entity.
It could be a carbohydrate.
It could be a little piece of
an organic molecule.
It could be a few amino acids
on a protein.
But it's something that's
potentially capable of being
recognized by your immune
system.
So, there are many,
many, many things.
And the amazing thing is I can
go into a lab and synthesize a
molecule that's never been seen
on this Earth before and
challenge somebody with it,
and you'll produce an immune
response that will be mounted
against that even though it's
never been on Earth before.
It's also the specificity.
It is completely amazing.
If I were to take a protein,
and then, let's say,
put on a phenyl ring with a
methyl there,
inject it into someone,
the immune system would figure
out how to recognize this thing
with the phenyl ring,
and the methyl.
But, the response it generated,
it would see this but not,
let's say, that if I wanted to
get an immune system,
something with methyl here,
I'd have to put that into the
organism and let the immune
system figure out a response.
So, the specificity is at the
same kind of level that you are
used to here.
If restriction enzymes can read
different sequences in DNA or
protein can tell one optical
isomer of a small molecule from
another, it's this fitting of
complementary shapes.
So, with the immune system is
all about is figuring out how to
get a complementary shape
somehow that's able to recognize
essentially any kind of chemical
shape and structure you can
think of.
It's just mind blowing.
And, you could already see
right from the beginning,
where the fundamental problem
people could see from the
beginning.
It sounds like we would need a
genome that's infinitely big,
full of things that are ready
to recognize anything.
And so, one of the real
surprises is,
and now we know,
is there is 20,000 genes are so
in the human genome.
There can't possibly be a
zillion genes,
each one specific for one of
these structures.
There had to be some underlying
principle that we had to learn.
And that was one of the big
challenges in the immune system
for a long time.
Another one was that if you
have an organism that has this
capacity, and you could
recognize it,
why don't you do yourself in?
Because you yourself are full
of entities that could,
in principle,
generate an immune system.
So, one of the other things the
immune system had to deal with
was avoiding self recognition.
If you're able to recognize
anything, how do I not avoid
killing my own selves?
So, that is another really
fundamental problem in this
immune system.
This is exciting.
We can all stop and watch,
but I think I'll just try and
keep soldiering along for the
last minute or so.
So, one other feature that was
interesting about the immune
system, is it has a memory.
And I'll tell you more about
antibodies at the beginning of
next lecture.
But, these are the kinds of
molecule that's able to
recognize these different
entities.
And you've all heard the term
in your ordinary life.
But, if we look at the level of
antibodies that are made in the
body,
if the first exposure to an
antigen that would get some kind
of response that comes up upon
the first exposure,
and this is time here.
If we let there be some delay,
it could be even into years,
and then we get a second
exposure, the antigen,
the response is much higher.
And this could be a log scale.
So, it could be dramatically
higher.
So, what was the basis of that?
How does it work?
You see right there the
principle of vaccination in the
sense that if you ever got
chickenpox as a kid,
your body has learned how to
make antibodies.
So if you ever see it again,
it mounts a really big immune
response.
If you want to have a disease
something like tetanus that you
haven't seen,
you go to the doctor and they
squirt and a bit of the stuff
that doesn't make you sick,
but it gives you the initial
immune response.
Then, if you ever step on a
rusty nail, you get a very
powerful response against
tetanus.
And that sort of the underlying
principle of vaccination is this
concept of memory.
We'll pick that up on
Wednesday.
So, have a great Patriots Day
weekend.
