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Practice English Speaking&Listening with: Lec 13 | MIT 7.014 Introductory Biology, Spring 2005

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Julia just mentioned that a few of you had commented,

when we were talking about the genetic code,

that some of you thought the fact that it

was degenerate, it had some redundancy in it,

like multiple codons or threonine,

that that was kind of cool, and some of you

thought it was sort of a waste and would have maybe designed

the thing differently.

That's, you know, part of when you study biology

you don't get to design it from first

principles.

You found out what happened during evolution and what got

selected for.

And once it gets selected for then that gets sort of fixed in

nature.

If there were four nucleotides then you could have one,

two and three-letter words.

And it's going to be a three-letter word to have at

least 20 then you've got some degeneracy or redundancy,

but that's not necessarily a bad thing.

And, in fact, if you go into the

evolution of the code more deeply, people are beginning to

suspect it evolved from a simpler one.

And there actually are some relationships between some of

the codons that go back to the similarities,

the chemical similarities between the amino

acids.

And it also allows some things for some cells,

for example, if they want proteins to be

present at very low levels they will use a

codon that has just a very low level of the corresponding tRNA.

And if they want to make a lot of the

protein they'll use a tRNA that it

makes in abundance.

And so it's sort of another way of

controlling levels of proteins.

There are a lot of different subtleties in here.

And also in biology redundancy is not

necessarily a bad thing.

It's just like on a space flight, if something

goes wrong and if there's some kind of redundant function then

you've got some backups,

too.

OK.

Well, in any case, today is a pretty

interesting first part of the lecture.

I've heard a few people express the view that why can't

I just teach what's in the textbook

and get on with it?

And I think this part, for those of

you who are following, really trying to understand

what I'm trying to do with this course,

I hope this will help you to see this.

Because what I've talked about,

this thing that Crick called the "central dogma"

which was the direction of information flow in biology

which was from DNA to RNA to

proteins.

And I'll just remind you, although

proteins do many things they are, for example,

enzymes that are biological catalysts.

And it was pretty well-established,

even by the time I was an undergrad that

this was the way information flow went in

biology and this was how it worked.

And there were various statements in

the literature that what was true for E.

coli was true for an elephant.

And it is still true today in a broad sense that,

as I've tried to emphasize throughout the course,

when you get down to a cellular molecule level there's an awful

lot in common and things look much

more alike than different compared to

what we see at a more macroscopic scale.

However, that doesn't mean that all the details are the

same.

And maybe you could begin to get a

glimmering of that when I told you that although the genetic

code is virtually universal.

That almost every organism, with

only a couple very tiny exceptions, uses exactly the

same genetic code to have nucleotides correspond

to three-letter words in the nucleic

acid alphabet correspond to particular amino acids in a

protein.

But the other languages that are written in there such as the

sequence to start transcribing a gene, making an RNA copy or

stop.

Those are different between different organisms.

Yeah?

Glycolysis enzymes are amazingly

similar.

They are very clearly, they arose once,

and they have stayed right through evolution.

You could, in principle, sometimes in

evolution you get something that creates a function and

something that starts out,

and then like what they call convergent evolution you

end up with two things that came from a different

evolutionary origin but have learned to do,

let's say, catalyze the same biochemical

reaction or something.

Glycolysis came once.

But if you were to look inside E.

coli or yeast, let's say E.

coli and look at how those enzymes are

regulated, the thing that says this is the start of

a gene, start making the RNA, it would look totally different

than if you looked in a mouse because

the language, the promoter does not have

the same sequence in an E. coli and in a human or in a

mouse.

And I'll tell you more about that today.

But there were -- I want to just now tell you

sort of three things that were sort of

exceptions to this general way of thinking.

Every one of them generated a Nobel Prize.

And this is a fun lecture for me to give

because the individuals involved in all of these things

had a very, very close association with MIT.

And when I told you when Crick called

this a central dogma he meant a hypothesis, or at least an idea

for which there was not reasonable

evidence.

And he learned later it was something a true believer cannot

doubt.

And once this gets established it does get in the

textbook and it does get in your thinking.

And so information goes down this way.

But there were a few oddities.

I mean there were some viruses that had RNA inside

them.

They didn't have DNA.

So how where these handled?

Well, there turned out to be two

classes of RNA virus.

One that was studied quite heavily called,

it's a plant virus called the tobacco

mosaic virus.

And it had a coat.

And then it had in it a piece of RNA.

Now, you can see if that virus were to inject RNA in the cell

it could encode proteins.

But that genetic material has to be copied.

And the RNA was copied -- -- by an RNA dependent

RNA polymerase.

And so it's sort of just like the

RNA polymerase before, except instead of using DNA as

its template it can use RNA.

So that sort of somehow would be a little loop in

here about RNA being able to copy itself that hadn't been

anticipated.

And although this is an important virus in the plant

industry, for plants and agriculture,

it's not so important for humans.

But there's another class of RNA viruses that are very

important.

And these are called retroviruses.

And the reason these are so important is that the HIV-1

virus that's associated with AIDS is such

a retrovirus.

It's a virus that has a coat and it has an RNA that's its

genetic material.

And the person who worked out how

this goes was a person at MIT, Dave Baltimore.

He was a colleague of mine here for many years.

He was the person who founded the White-

head Institute and got that up and going.

And he then finally, to move

up one more administrative challenge, went to Caltech

to be president.

And that's where he is today.

And David was working on this

problem trying to figure out how these

retroviruses work.

And they're important.

Not only the HIV-1 virus, but there are certain

viruses that are associated with cancer.

In general, what they do is

they've picked up what's called an oncogene

which is sort of often a mutated version of one of your

normal genes.

And if that virus gets inside one of

your cells and brings in this mutated gene it's sort of kind

of the same consequence as

mutating one of your own genes along that

progression of cancer.

So it can kind of, say, bring in a cell that

screws up the control on when cells are supposed to replicate

and stop dividing and so on.

So David started to work on these, and what

he discovered was that these viruses encoded,

they had information encoding proteins.

And one of the proteins encoded in

their RNA is an enzyme he characterized which is given the

name "reverse transcriptase".

And what this can do is take an RNA

template and make the corresponding complimentary DNA

strand in this way.

So that if we took the -- We'll just take this RNA out of the

virus.

What this virus encodes then is an enzyme that's able to take

this RNA and make the corresponding DNA copy.

So there's the original RNA that was in the virus.

There is the RNA that it started out.

And so what is happening,

if you will in that case, is the information is

flowing in the other direction.

That was a marvelous discovery.

And it was discovered by someone who

wasn't willing just to take what was in the textbooks but

was trying to figure out what could possibly

be going on here.

Now, the way these viruses work then,

once they've done this it's not so bad because they've

got their information now in the form of DNA.

So this strand of DNA can be made into a double-stranded DNA

by just using the kinds of enzymes that

we've already talked about.

A DNA dependent DNA polymerase will

be able to copy the other thing.

And now you've got a DNA copy of

the information that used to be in the

virus.

But what happens to that is that you have a piece

of the host DNA.

And this viral DNA then inserts into

it, so you end up with this situation where you have DNA

from the host, and this is the virus

DNA.

So this is the DNA that encodes the information needed for the

virus.

And if this was our DNA then it would be inserted that way.

And there are just a handful of

health messages I've tried to drive home in

this thing.

I mentioned smoking the other day.

If you smoke -- If you stop smoking you

basically, well, let me try another way.

The risk of smoking is about equal

to the sum of everything else you can

possibly do in your life that will affect your chances of

getting cancer, leaving aside what you

inherited from mom and dad.

The one single thing to not do if you

want to avoid cancer, or to help loved

ones who smoke avoid cancer, is just don't smoke,

or if you do smoke, stop.

You freeze the risk of whatever increased risk you've got,

and then just live with that, but it doesn't

keep getting worse with time.

The other one is practice safe sex, and

this is why.

HIV-1 is a retrovirus.

If you get infected with it, it

makes a DNA copy of the RNA, it makes the other strand of

the DNA, and it sticks itself in.

So what you've got is your DNA here, your DNA there.

And HIV-1 is a permanent traveling

companion for the rest of your life.

There's no way of getting that out

of there right now.

All the systems for dealing with AIDS are just

managing the infection.

So when someone is HIV-1 positive, they've

got those viral genes now permanently integrated

into their DNA.

So it's extremely important that you

be aware of that, or if you know people who don't

appreciate this because they haven't got so

much of a biology background that you help

them understand that.

OK.

So I just wanted to show you, I found one

other picture last night.

And this is you see all these old scientists,

right?

Of course, David didn't look like this when he was doing his

work.

In fact, I think he's fairly cleaned up here.

I found this one in the Cold Spring Harbor

archives last night.

I've seen pictures of him looking considerably more shaggy

and perhaps disreputable and stuff.

But anyway, when David was making all these

discoveries he was still quite a young man.

I believe he got his Nobel Prize when he was still

in his thirties.

And so many of these discoveries are made by people

that are not all that much older than

you.

But, again, it's trying to understand why we know what we

know and then trying to fit other

things into it.

Now, the next thing I want to tell you about that has some of

this same character, I've sort of told

you that you have a piece of DNA.

Let's say there's a gene here and

this is the coding region, and then we make

a mRNA copy, and then we use the genetic

code and we make the protein.

And so if we sequence the DNA and

find the beginning of this protein we can read along using

that genetic code and away it should go.

And that was beautifully worked out,

understood, just like I sort of finished up telling you the

other day.

So Phil Sharp who got a Nobel Prize for this work and is a

colleague in the Biology Department.

He's in the Cancer Center just across the street from the

building I'm in.

That was the cancer center that Salvador Luria,

who Jim Watson trained with,

had founded.

And Phil was studying this process.

It was before we could sequence DNA.

It was in the mid '70s.

And he was working with the tools we had

then trying to map the relationship of an

RNA to a gene that was on a virus.

It was a DNA virus, not an RNA

virus, so don't get yourself mixed up with that.

But what he had was basically a fragment of DNA

that he knew encoded the gene.

So he knew somewhere on this piece of DNA

there was a gene somewhere in here, and he

had isolated the mRNA.

And one way you could map, physically see the

relationship of an RNA and a DNA would be to take,

let's just take away one of these strands.

So we have the complimentary strand

of the DNA to the RNA.

And if we mix them together and let them

slowly cool down they will form hydrogen bonds.

They'll form a DNA-RNA hybrid just the same

way two strands of DNA come on.

And so if the gene was a little shorter

than the piece of DNA then you might have

expected to see something that looked like this.

And the way you'd see this, if you looked in an electron

microscope -- -- perhaps it would look sort

of like this.

You cannot actually see the two strands, but you'd see a

thick part.

That would be the RNA duplex.

So this would be just DNA.

And the thick part is RNA base paired with a single strand of

DNA.

You got it?

That's what textbooks said you should have seen.

And so this is more.

This is data from Phil's paper describing this.

And let me focus on this one in

particular.

That's what he actually saw.

You guys got any idea what's going on?

Why don't you take a minute, find somebody who's near you

and see if you can come up with any ideas.

Here's the hybrid.

Forget about this little bit at the 3 prime end.

That's not a worry.

Here is the thing.

And this, I think, is a

piece of single stranded DNA sticking out the end.

But it looks a bit more complicated.

Any ideas?

Most people put this data in their drawers.

Phil didn't.

Phil and his colleagues didn't.

What they realized was, I'm going to try and redraw

this just very slightly to help you see what's

going on.

What they were seeing was something that looked rather

like what they were expecting.

They were seeing a region of hybrid DNA and they were

seeing a region of single-stranded DNA like this,

but what it looked like was there were little

loops of single-stranded DNA sticking out.

And what Phil had discovered was a phenomenon we now know

as RNA splicing.

And here's what goes on.

In bacteria, with very few exceptions,

you can look at the DNA, you can find the open reading

frame and you can just read off the sequence

of the protein.

You find the ATG, AUG,

methionine codon, and then it keeps going no

stops, and finally you come to a stop codon and you see

there is the protein.

So the coding information is essentially

continuous in almost all bacterial genes.

And there's a few, some genes like

that in eukaryotes, but many eukaryotic genes are

constructed, it's almost as if you took the

gene you'd find in a bacterium and then

you'd cut it in a bunch of places and stuck extra DNA in

between all of the pieces.

So you'd get something like this where there's,

in the DNA there'd be coding information.

And then non-coding information and another block of coding

information.

And then a block of non-coding and say another one of coding

information.

So this is a double-stranded DNA.

And what happens then when the cell

makes RNA is the whole thing gets copied into

what's known now as a pre-messenger RNA.

And so there's a bit of coding stuff here, there's a bit of

coding stuff here, and there's some more

coding stuff there.

But what the cell has is sort of like your unedited

footage from your family summer vacation when you were running

the video camera.

And maybe you don't want to show everybody ever second of

video that you took during the thing.

So what you do, you get in there and you

edit it.

In the old days you used to have to take the film and splice

it.

And now you can all do it with iMovie or something like that.

But what you do is take the pieces

of information you want, and this is

what the cell is doing.

It takes this part of the RNA.

And this part of the RNA, and joins it together,

and then this part.

And when it's done it has the mRNA that now looks like the

kind of mRNA that you would find in a

bacterium where you can find the start codon.

And then you could read in three-letter words all the way

through to the end of the protein.

So, in essence, what Phil found was

that in many organisms at least there's another step in here

where we get RNA splicing.

And only after that you get down to proteins.

What was quite remarkable about this result and why I'm kind of

hammering on it a little bit is this is

the data that's out of Phil's paper.

You can look it up on the Internet.

Type in Phil Sharp 1977 and you'll

find this original paper with that figure in it.

The moment Phil realized what it was and talked

about it at a meeting, a whole lot

of people suddenly sort of almost simultaneously discovered

RNA splicing because they opened

their drawers and there were all these

uninterpretable electron micrographs they had.

And they were in very short order able to save it in the

system.

The same thing was going on,

but it was just confusing, it didn't fit,

and to some extent most people's

minds were set by this paradigm, this

central dogma as something that a true believer cannot doubt.

And you had to have a flexible enough

mind to be able to see that.

And so this is an important piece of biology that hadn't

been anticipated.

And it can be quite remarkable.

I'm just going to give you a couple of extreme

examples.

Well, not even extreme examples.

But just show you how much non-coding information there can

be.

Factor 8 is a protein that plays a part in blood clotting.

And the gene is 200 kilobase pairs.

And the pre-mRNA is just a direct

copy, so it's 200 kilobases.

It's just a single strand so it's not a

base pair.

And the actually spliced mRNA when it's done is 10 kilobases.

So that means that only 5% of the gene is coding information

and 95% of that information gets thrown

away when the RNA gets spliced.

And even a more extreme example is a protein called dystrophin.

This is what's affected in a human

genetic disease known as Duchenne

Muscular Dystrophy.

In this case, the gene is two mega- base

pairs.

So of course then the pre-mRNA is also two megabases

but the pre-RNA is 16 kilobases.

So in this case less than 1% of the

gene has coding information for making a protein.

There are a lot of interesting reasons as to why it would be

like this.

One this, things can evolve more rapidly sometimes because

you have parts of proteins that are sort

of like modules and evolution can probably connect them.

In fact, it also provides ways of regulating because we now

know there are alternative ways of

splicing RNA.

So you can take one RNA and then splice it in different

ways in different cells and end up

generating different proteins that were all encoded by one

particular gene.

And so it gives cells different kinds of regulatory

strategies they can use.

Now, the third sort of thing that

came out that falls in this same kind of thing of people

having their minds open and not fixed by the

current understanding or bounded by

the current understanding is the discovery that RNA can act

as an enzyme.

And I've already talked to you about that and I've told it was

ribozyme, but it was discovered by Tom Cech.

Tom is currently president of the Howard Hughes

Medical Institute, but he did his

post-doctoral work at MIT with Mary Lou Pardue.

I'd been a post-doc at Berkeley when he was just finishing his

graduate work, and I met him out there.

And then he came to MIT to do his post-doc.

And a year later I got a job so I'd become friends

there and became friends when we started here.

So I had a pretty close link to this particular

story.

Here's a picture of Tom together

with Phil.

That's actually my wife right there who was in this picture.

But Tom actually looks much more like that.

He's very colorful, very fun, a very interesting

person.

But anyway, when Tom left MIT to take a

faculty position at Bolder he was interested

in trying to understand the biochemistry of RNA splicing.

And so he went -- He did what a good scientist will

do.

They'll try and find an experimental system where the

question they want to address is simple enough you can

actually get an answer.

There's a kind of way of doing science where you pick a

system that's too complicated and you never actually get an

answer.

It sounds very important because you're working on

something that's important but you cannot,

you don't have the tools you need to get to

the answer.

So Tom wanted to work on the biochemistry of RNA splicing

because that had just been discovered.

And so he went to a small little tiny organism called

tetrahymena.

And the reason he looked at that was because it had a

ribosomal RNA, so

it was an RNA that was made in great abundance within the

organism.

And it only had one of these

non-coding regions.

I'll tell you the words for these coding and

non-coding.

To me they're non-intuitive, but I

guess you should know them.

The coding region is called, the

part that codes is called an exon and the non-coding part is

called an intron.

So, anyway, Tom worked on this organism because the pre-mRNA

was basically this.

Or the pre-mRNA before the splicing

looked like this.

This was going to give this like that.

He could get large quantities of this RNA,

so he was all set to make extracts of the

cells of this organism and then start cooking up this RNA

substrate with all sorts of cell

extracts.

And then his plan was to purify the

enzymes that did the RNA splicing.

And so I first heard about this, Tom

was working on this when he was here.

And he went off to, I guess

it was Denmark to learn how to grow this organism.

Then they were back and he was off at Bolder.

And we used to play squash all the time.

And whenever I got out to Bolder we'd try and get in a

squash game.

So I was out there at a meeting and we were sitting around in

the locker room.

And I said so how's the splicing biochemistry project

going?

Tom says, well, it's going OK,

I guess.

There's only one little problem,

he says.

The controls are splicing.

Now, what he meant was if you were trying to

add cell extract and get this thing to

go what you would start out with is the RNA in a tube

basically.

And that would be your control.

And then you'd start adding stuff to it

and start looking for splicing.

And what Tom was finding was that if you

just took this RNA and let it sit in a test tube that the

splicing happened without him putting

anything in.

And here he was already to find all the

enzymes, the proteins that did it.

And Tom did an absolutely gorgeous piece of

science to prove that what was happening was the RNA was

catalyzing its own splicing.

And he had to work very, very hard to prove that it

wasn't a contaminating protein.

Remember we had this sort of discussion?

We were talking about is DNA the

genetic material and how would we

know that it wasn't just a little tiny bit of something

else in our DNA perhaps that was doing it.

Tom had to go through pretty much a

similar exercise, but this was one of these key

insights that lead to the proof that RNA could

function as a catalyst, what we now

know as a ribozyme.

And I've shown you now we now sort

of accept that the actual ribosome itself is a ribozyme

and that the formation of the peptide bond,

the thing that's the heart of all

proteins is made by a ribozyme, not catalyzed by ribosomes and

not by a protein.

OK.

So the next topic that I want to try on which sort of

we've already set up from this is that if the information is

all in DNA to begin with then if you

make an RNA copy you're only taking a

segment of that information at a time.

And that gives the cells a lot of possibilities for regulating

how they respond to the environment

or just controlling what genes are

expressed.

And there are basically two kinds of strategies that are

involved in these regulatory decisions.

They can either be -- Can either be reversible

changes.

For example, a bacterium and a food source.

If you're a bacterium and you've got enzymes that let you

eat a hundred different kinds of food

and you're in an environment where there's only one of them

there, you're really wasting energy if

you make the proteins to make the other

99.

So you might guess that somehow evolution has selected for

systems that have learned how to turn

on and off the things they need to eat

certain food sources depending on whether the food source

is available.

We only carry umbrellas when it rains.

If you had to carry an umbrella and a snowsuit and a

surfboard, everything all the time, it would slow you down in

evolution.

So the other type, which we've talked about as

well when we talked about starting as a single cell

and going to the 10^14 cells that make

us up, then many of those changes, as those cells go along

and progressively more specialized

need to be irreversible.

And this is particularly important

in development.

We don't want a cell in our retina suddenly deciding

it should be part of a heart and start to make a heart in the

middle of your eye or something like

that.

So things in development tend to be

once you're off you're off or once you're on you're on or

something.

And just to give you another little look at that picture I've

shown you before of the nematode.

And at the time, the first time I

showed you this, I was just trying to emphasize

that we could take the gene encoding green fluorescent

protein and put it in anything and

it would go green.

In this case, Barbara Meyer who is at

Berkeley now but used to be my office-mate

at MIT for many years, what she's done is

she's taken that green fluorescent protein,

the gene for that, and

she's put it under the control of a regulatory system,

a gene that is made to be expressed in the

esophagus of the worm.

And so even though that gene is present in all the cells of that

organism, it's under the control of a system that usually

permits the genes to be made that are

needed for making esophagus but not in other

parts of the body.

So you probably didn't pick that part up now but

sort of take another look at that same thing and see

something different.

So how do we learn about gene regulation?

The key work, like so many of these things,

started kind of inauspiciously,

if you will.

There were two French scientists, Jacques

Monod, who is a biochemist, Francois Jacob who was a

geneticist.

And they were working on the

metabolism of lactose by E. coli.

Lactose is galactose, beta 1,4 glucose.

And you don't have to know exactly the structure.

You can just remember there were a lot of

different hydroxyls, and that was one particular

linkage.

And there's an enzyme that cleaves this

into galactose and glucose.

And this can go right into glycolysis and

make energy for the organism.

And the galactose undergoes a couple of different

transformations, and it

can get in there as well.

But in order to get at the energy that's in

those carbohydrates, this linkage has to be broken.

And it was broken by an enzyme called

beta-galactosidase.

That's a protein that's able to catalyze

the cleavage of those two sugars.

That's what Jacques Monod and Francois Jacob were studying.

They were helped out in this

exercise.

I guess part of the reason they got

going on this was people had noticed for many years that if

you grew E. coli in glucose there was no

beta-gal.

I'm going to abbreviate this as beta-gal just so I won't have to

keep writing the same thing.

But if they grew E. coli in lactose

beta-gal was present.

And they had to be able to assay for this enzyme.

And they used -- There were standard types of

biochemical assays you could use.

But some chemists that helped design a very cleaver kind of

substrate that helped them,

that could be used in these kinds of studies,

and I'll show you one of them.

What this enzyme really looks at is it looks

at, let's see, galactose.

What it sees is sort of the galactose side of this linkage,

and then it reaches in and catalyzes the

cleavage of what's joined to it.

And it turns out not to be specific

for whether glucose is on the other side.

It can accept substrates that have other things as well.

So some chemists made some variants like

this.

This is a compound that's commonly known as X-gal.

If you talk about it in the lab it's

got a longer chemical name.

But what happens if beta-galactosidase is there,

it's able to cleave this substrate

so you get galactose, which is colorless.

But if you get just X, this is colored,

but up here this original material is also colorless.

So this is very convenient because if you

use a substrate such as this you could put the cells on a

plate with this indicator.

And if they are colored, and the

color is blue, you'd know they were making

beta-galactosidase.

And if you don't see a color,

you know they're not.

There are a variety of ways of assaying for this

enzyme.

With that I'm just trying to give

you a little bit of flavor of one of the different ways that

they could assay for it.

Now, one of the issues was it looked as though E.

coli didn't have any beta-galactosidase activity if

lactose was absent when growing in glucose.

And they made it if lactose was present.

Well, that would be kind of what you would expect

evolution would have figured out how to do,

only make the enzyme for metabolizing lactose if the

lactose is present, but they had to

figure out what the molecular basis of this

was.

And one of the possibilities was that the protein was made

that it was all sort of unfolded,

and when the substrate came in then it

folded all around it and then it could cleave it.

Or another possibility, which would be the kind we're

talking about now, is the protein is not made

until the lactose is present, and then it

makes it new.

So they had to figure out, between these two,

which of these two was true.

When you see the lactose present, is it just

beta-galactosidase is already made but it's inactive,

or is it being made de novo when you add the

lactose?

So what they did was they grew cells in glucose plus

radioactive C14-leucine for a long time.

So all the proteins -- -- were radioactive.

And once they got, that's going for a long

time.

So every protein being made is radioactive.

Then they add excess unlabeled leucine.

So this means that from now on any new proteins that are

made will not be radioactive because you're just going to

swamp out any radioactive stuff with this.

And they added glucose, excuse me, now

they added lactose to the cells.

And then they isolated the beta-gal enzyme.

It was actually pretty easy to do.

It's a huge enzyme and it's a tetramer.

So very large.

Even in those days it was fairly easy

to isolate this enzyme.

And then they looked to see is it

radioactive?

If it's radioactive it was there all

along and it's refolded to become the active enzyme.

Or if it had been only after lactose then it would be made de

novo in response to it.

And what they found was that it was non-radioactive.

Which implied that it was made after

you added the lactose.

So they knew then that they were

studying a system in which a protein was only made after the

cells had experienced a particular growth

substrate.

And so a lot of work went into figuring out how this

system worked.

Let's see.

We're a little short on time.

So I'll tell you what I'll do.

I'll tell you, I'll just put out

quickly the mechanics of what they saw, and

we'll start in on the regulation on how this works.

And some of you may be able to figure it out.

What we now know is that the gene that

encodes beta-galactosidase is in a stretch of DNA that's

pretty interesting.

It's got three genes.

It's the gene lacZ.

This is the gene for beta-galactosidase.

And another gene called lacY and

lacA.

There's a promoter.

That's a start signal for transcription.

Remember that?

So there's a sequence here that says start

transcription.

Down here is a terminator.

Another word written in the nucleic acid alphabet that means

stop making mRNA.

And there is one long mRNA, as you can see,

that has the peculiarity of encoding three

different genes.

So if you have more than one gene in a single

message then that's called an operon.

You've got one mRNA.

But, in any case, so whenever beta-galactosidase

was being made then RNA has to start being made here,

goes to there.

And we won't worry about the

functions of these other two genes.

But, as you might guess from the way evolution has selected

for it, they have related activities to what

beta-galactosidase does.

And for bacteria it's a very efficient

way to control the expression of a bunch

of genes at once.

Then there was another gene up here known as lacI

that had a promoter and a terminator, and it made

an mRNA as well.

And that mRNA encoded a protein that's known as the lac

repressor.

And what that lac repressor does,

it's a protein that has the ability to recognize a very,

very specific DNA sequence and bind there.

And I'm just going to kind of blow up

this part of the thing.

So what we have here is the, this is

the promoter here.

And it happens that the binding sequence --

-- for lac repressor overlaps with

the promoter.

Weird, right?

Maybe not.

So I'll tell you, well, you can think about this

over the weekend, if you haven't run into this

system before.

So this gene gets made all the time.

So this protein gets made all the time.

What does that protein do if it's just like

this?

Its job in life is to look for this

sequence and bind to it.

If it binds to it, it covers

up the promoter.

And the beta-galactosidase gene is

not expressed because the cell cannot make mRNA.

So this may seem a little obscure,

but there's something very important here.

Now the conditionality on whether

this gene is expressed or not is controlled by a protein,

right?

It's controlled by this lac repressor.

If it's on there the gene won't be made.

And if it's off the gene now you can make

it.

There's a promoter and the RNA polymerase will see it.

And so you've learned something about

proteins.

They can bind various things.

And so what lac repressor has, it's got a little binding

site that lactose is able to bind to and

change the confirmation of the lac repressor.

So why don't you take those pieces of information and

see if you can figure out how the circuitry goes.

Yeah?

Did I do something wrong?

Sorry.

Oh, sorry.

Excuse me.

Yes, Z-Y-A.

Excuse me.

OK?

We'll walk through that on Monday,

but focus on the fact that if the repressor is

there and lactose isn't, it binds to this sequence.

The repressor is made all the time, but this repressor is

something that can tell you whether lactose is

there or not.

So you can put the circuit together, OK?

The Description of Lec 13 | MIT 7.014 Introductory Biology, Spring 2005