Lecture 6A - Control of Gene Expression

Hi. I'm Dr. Lesley Blankenship-Williams, and in this lecture we are going to explore the control

of gene expression. Previously we learned what gene expression is. We know that it is a two-step

process, transcription and translation, and we also learned about the rules of gene expression.

In other words, if I give you a DNA sequence, you should be able to predict the RNA copy

and, therefore, also the protein structure. Now we're going to take a look at control.

You have lots and lots and lots and lots and lots of genes in every cell. How does

your cell or body know which genes to turn on and which genes to leave alone?

So what do I mean by turn on a gene? Turn on a gene is synonymous with gene expression.

So we have lots and lots and lots of genes in our cells, but only a small fraction of them

are expressed at any given time. So basically our overarching question is, "How does the cell

know which genes to turn on and which genes to leave alone?" Let me give you an example.

If I take your cheek cell, I'm going to have all the DNA for the blueprint of your entire body,

including a gene that codes for the hormone insulin, but your cheeks don't make insulin.

They don't express it. That gene for insulin is there, but it is turned off.

How is it that your cheeks ignore that gene, but your pancreas, which do make insulin,

know to turn on that gene so that they can make and secrete insulin? It's a simple question with

an incredibly complicated and detailed answer. Unfortunately, we're just going to scratch the

surface of that answer in this lecture. Okay if we think about gene expression as a two-step process,

we first need to understand that both steps have to happen in order for gene expression

to be complete. If you were to somehow block transcription, then you would not make RNA. If

you did not make RNA, the ribosome would have no instructions to build a protein,

so you would not make proteins. If you were to block translation, then your body would still not

make any proteins. You would make all of this RNA, but the RNA would just be floating

around in the cell and it wouldn't actually be translated by the ribosome into a polypeptide.

So both steps have to happen. One step represents the control. In other words,

it is the step that controls whether or not the entire process happens. And it turns out that,

from an efficiency standpoint, the control is the first step. So we say that gene expression

is controlled at the transcriptional level. Well what does that actually mean? If we know that

transcription is the process of RNA polymerase reading a DNA strand, and making the MRNA

transcript copy, then technically what we're really saying is RNA polymerase controls which

genes get transcribed and which genes do not. The translation part of it is generally on autopilot.

In other words, once you make the RNA, it's going to be translated. If you make the RNA,

you've turned on the gene. If you don't make the RNA, the gene is off. And what controls

whether or not the RNA gets synthesized? Well, RNA polymerase, of course. Let's watch a quick video

that shows how RNA polymerase makes that RNA, just to give us a visual idea of

transcription.

Now while that is a very interesting video, unfortunately what is not

shown in the video is how RNA polymerase knows where to start, and where to end.

In other words, there is a lot of DNA out there, lots and lots and lots and lots and lots of DNA.

So how does RNA polymerase know where to start? Let's address that question here.

When we take a stretch of DNA from the human cell, only about one percent of that DNA

actually has genes on it. The rest of it does other stuff. So here I've marked off three areas,

coded for in blue highlighter, and they are my hypothetical Gene A, Gene B,

and Gene C. And I also have my RNA polymerase. My RNA polymerase wants to know where to go.

Now if RNA polymerase just went wherever it wanted and started transcribing, it would be a

disaster. It might start in the middle of a gene. It might actually transcribe something that's not

even a gene. You would have no consistency, no control, and the cell would probably die.

So the first thing we need to do is give RNA some direction about where the genes actually are.

And this is done with a special region in front of each gene

that is called a promoter. So a promoter is actually a region of DNA that precedes

every gene, and the promoter is where RNA polymerase is always going to start.

But now we have another problem. Which promoter does it go to?

Does it go to the promoter in Gene A? Gene B? Or Gene C? You don't want to be transcribing

all of the genes, just the ones that the cell needs.

So RNA polymerase is going to need some more information to know which promoter it needs to

sit down on and start transcribing, and this is where additional signaling molecules come in.

The cell is going to need a way to direct RNA polymerase to transcribe only the gene that it

wants. So the way that this works is there are other regions of DNA, highlighted in green here,

that are actually in front of the promoter. And these regions bind special molecules

that end up drawing RNA polymerase into the promoter region. So in a simplistic example,

assume that it takes three of these molecules, we'll call them transcription factors,

in order to get RNA polymerase to come to the promoter. So what happens is is the cell gets a

signal. Let's say it's a star, and the star is going to bind to this green area here, but not

all the green areas, only the green areas in front of specific genes, genes that the star

would want to trigger the start of transcription. So here I've put a star in front of A and B.

Now we get another transcription factor, and it's a heart. And the heart is attracted to Gene B

and Gene C, but it didn't bind to Gene A. And then a third transcription factor arrives, the diamond,

which binds to C and B. And now we have three transcription factors

in front of the promoter for gene B. This attracts RNA polymerase to that promoter region,

and now RNA polymerase is going to go ahead and start transcription of Gene B.

By using these special binding molecules, these transcription factors, which bind to

regions of DNA in front of the promoter, we can direct RNA polymerase specifically

to particular genes and only turn on those genes. Now that we've looked at my simple animation,

let me show you a more complicated, but accurate, picture of transcription factors. So transcription

factors are going to be these additional molecules that bind to parts of the DNA,

or bind to each other. They create what is called a hairpin loop in the DNA,

and collectively all of that brings RNA polymerase to this specific promoter, rather than any of the

other promoters. And then once RNA polymerase binds to that promoter, it begins transcribing.

And what is not discussed is that there is also a region at the end of a gene, where RNA polymerase

runs into it and knows to fall off. So effectively gene expression is controlled by some sort of

chemical binding here to this promoter region, that allows RNA polymerase to bind and start

transcribing. So now that we've covered the, kind of, basics of how gene expression is controlled,

let's start looking at how eukaryotes and prokaryotes do things differently. So here I have

a partial human genome map. I don't expect you to read anything on there, I'm just showing this

for you so that you can see just how detailed and complicated it is, and this is just a partial map.

So when the human cell gets ready to turn on a gene, it's rarely one gene. Rather we're looking

for some outcome, so the human cell gets a signal that says, "Hey, I want you know the body says

Hey, I want you to do something." And so we've got this outcome, and there are actually multiple

genes involved that all need to be turned on in order to achieve that outcome. So for instance,

let's say this was a stem cell, and the body got a signal for that stem cell to divide and create

two daughter cells via mitosis. Well one step in cellular division is to copy all of the DNA,

and it turns out there are multiple, multiple enzymes that are involved in copying that DNA,

such as topoisomerase, DNA gyrase, DNA polymerase, DNA primase. Of course, you don't need to know

any of those, I'm just pointing out that there are many enzymes that are going to be needed to

replicate the DNA, and those enzymes are scattered at different spots on the chromosomes. In other

words, they're not located in one central spot. It's not like the cell has here's a

chromosome 4 and here's section chromosome 4 that has all of the DNA replication genes on it.

So I'm going to give you a real example. DNA primase is one of the many enzymes needed

to achieve cellular replication, so if I want to replicate my DNA, I must have DNA primase.

So where is the gene for DNA primase? Well it turns out DNA primase is made up of two

subunits. So it has quaternary structure because it's two subunits put together,

and the subunits are coded for on different genes. One subunit is coded for on chromosome 6,

and the other subunit is coded for on chromosome 12. So the two genes that must be turned on in

order to make DNA primase are actually located on totally different chromosomes. So I'm going

to need to send RNA polymerase to chromosome 6 at the gene for DNA primase subunit 1, and I'm going

to need to send RNA polymerase to chromosome 12 for the other subunit for DNA primase.

If I only turn on the gene in chromosome 12, I'm only going to make part of DNA primase,

and I won't have the complete working protein, so it won't work. So I have to be able to turn

on both of these in order to get DNA primase. So now that I've used that as an example,

let's kind of summarize what this means in eukaryotes. The related genes that all are

kind of going to the same outcome are spread about on different chromosomes, and what that means is

that you're going to have to draw RNA polymerase down to each one of those genes independently.

And the analogy that I want to give you for this is, imagine if I were in control of all of the

lights on the Las Vegas strip, and each light had its own independent switch. So if I wanted

to turn on the strip or the lights on the strip, I would have to go and turn on all of these lights,

which is independently. There's that one, and that one, and that one, and that one, and that one.

It's really time consuming, very cumbersome, but it does have an advantage. The advantage is,

let's say that one of the hotels is closed or one of the billboards doesn't have

anything that I want to advertise. Well the advantage is I could just choose not to turn

on that one right now, and save some energy. So even though I have to go at these one at a time,

I do get some benefit in getting control over which ones I decide to turn on, and for how long.

Now the reason I am stressing this is because prokaryotes take a more simplified approach.

In prokaryotes, all of the genes that go for some outcome are clustered together,

one right after another. I'm not even going to say they're on the same chromosome because, remember,

prokaryotes only have one chromosome. So they've got their one chromosome,

but instead of having it here and here and here, they're just boom boom, one, two, three,

right in a row. So if there are three genes for an outcome, they're located one right behind another.

And not just that, there is a single control switch. In other words, if you have Gene A, B,

and C that all go for the same outcome in a prokaryote, there is one master switch,

one promoter in front of all of the genes. And if RNA polymerase sits down at that promoter, they're

all made. If RNA polymerase does not, none of them are made. So it's an all or nothing situation,

and we can think of this like having a master switch. So going back to my Las Vegas example,

instead of controlling each individual light one at a time, I would have one switch. When

I turn it on, all of the lights are on. When I turn it off, all the lights are off. You could

see that that's a much more efficient and simple way to do things, but I lose my ability to modify

and control individual lights that way. We are going to pick up this idea of how prokaryotes

arrange their genes in tandem in what is called an operon in the next lecture. Thanks.