Gene Regulation

Hi. It's Mr. Andersen and welcome to Biology Essentials Video 31. This is on
gene regulation. In other words how we express a gene or not. How we make a protein or not.
And I wanted to start with a organism that lives in our intestine called E. coli.
E. coli is interesting in that it eats whatever we eat. And so if I eat bacon for breakfast
it has to break down the proteins and the lipids in the bacon. If I have cereal it has
to break down the carbohydrates. If I have milk it has to break down the lactose. And so
what's interesting about an E. coli is that it can go from an organism that has 0 proteins
to break down lactose to one where 50% of the weight of E. coli is simply enzymes that
deal with lactose. And it can do it like that. And so how do they do that? They do that through
gene regulation. And so in this podcast I'm going to talk about gene regulation. Before
I do that I want to get some terminology that I'm going to use a lot out of the way. And
so a regulatory gene is going to be a gene on the DNA that regulates another gene somewhere
farther down. A regulatory sequence will usually be found just above the gene. And so what
do I mean by that? So DNA looks like this. The gene generally will be down here that
we want to express or not. A regulatory gene will be somewhere else in the DNA. It secretes
something called a regulatory protein which then can grab onto a regulatory sequence.
An example of a regulatory sequence, I'll talk about is called a promoter. Once this
is all set up then we can have an RNA polymerase actually make the gene. And so I'll go through
that terminology but what I'm talking about regulatory gene, regulatory sequence those
both deal with DNA. But when I am talking about a regulatory protein that's coming from
somewhere else to help express the gene or not. As far as gene regulation examples, most
of what we know now comes from bacteria. And so I'll talk about positive and negative control.
Positive control example I'll give you is the lac operon. That deals with lactose. And
the negative control is the trp operon. It deals with tryptophan. And then finally I'll
show you what we know about eukaryotic gene regulation and how they use transcription
factors as activators, repressors to either express a gene or not. And so this is how
genes are made or expressed. Remember we start with DNA and that DNA eventually makes messenger
RNA, mRNA, which eventually makes proteins and those eventually make you. And so any
step along the way we can actually regulate the gene. So we can regulate it post translationally,
post transcriptionally. So we can do it everywhere. But in general most of the regulation I am
talking about is just going to be from DNA to mRNA. Do we express the gene or do we not.
And so this is generally what goes on. You've got a gene like this. Upstream of that we
have a regulatory sequence. An example of this in eukaryotes would be the TATA Box.
And the reason it's called a TATA Box is you have a thiamine adenine thiamine adenine and
on the other side you'd have TATA backwards complimentary to that. And so this is simply
a sequence above the gene that allows the RNA polymerase to get on. And so we have a
regulatory protein coming from somewhere else remember, another regulatory gene maybe downstream
or upstream from this whole gene. The regulatory protein, an example could be the TATA binding
protein, this is found in us, it'll grab on to the TATA box, let me get rid of the writing,
and it allows RNA polymerase to grab on and actually express that gene. And so if we didn't
have the sequence, if we didn't have the regulatory protein we couldn't make the RNA polymerase
and we couldn't make the protein. And so that's basically how genes are regulated or not.
And so let's talk about how this works is the lac operon in bacteria because this the
first one we really started to understand. So the way they tweak what I just said is
that the neat thing about bacteria is instead of just having one gene they'll have a number
of genes. And so they'll have three genes. All the genes required to deal with lactose
will be put right next to each other. And so we've named those the lac Z, Y & A gene
but they each make a protein and they each help break down lactose. Above that they'll
have a regulatory sequence called a promoter. Remember that's going to be where RNA polymerase
grabs on. And the other thing they'll have in an operon is called an operator. An operator
sits right between the promoter and the genes. And the way I like to think about it is it's
like an on-off switch. And so it can either be set in an on position or it can be set
in an off position. And so it regulates whether or not we turn the genes on or we don't. The
other thing that I'm going to add here is something called a repressor. A repressor
will plug right into the operator, so it's going to fit right here, and as long as the
repressor is available, RNA polymerase can't get on. And so this would be, when the repressor
is here the operator is now in the off position. In other words we can't make these genes.
This repressor I'm going to show you is showing what's called positive control. And what do
we mean by positive control. What I said was when lactose shows up we want to make all
the proteins to break down and deal with lactose. And right now there's no lactose present and
so it's off. But let's say lactose shows up. In other words I drink a glass of milk. Now
there's lactose. So the lactose shows up. The lactose you'll notice is going to fit
perfectly into that repressor. And when it fits in the repressor it changes the confirmation
or the shape of that protein. In other words, now the repressor doesn't fit in the operator
anymore. In other words it lacks these little prongs we'll say that fit in the operator.
Okay. So lactose is present. Repressor is now off. Well who can grab on? RNA polymerase
now fits. RNA polymerase can fit. There's no repressor. RNA polymerase is going to run
down. It's going to make each of the mRNAs for each of those lac genes. Each of those
are going to make a protein. And each of those are going to break down the lactose. And so
we can deal with the lactose and we can metabolize that lactose. So now the lactose is gone and
what's happening to our repressor? It's going back to that original shape. And so it's a
cool way we can have positive control. If lactose shows up, then we make all of the
proteins that can actually deal with that lactose. It shows up again? We're going to
get rid of that repressor and we continue. And so that would be positive control. What's
an example of negative control? Well a negative control we learned about from the trp operon.
trp operon instead of just having three it actually has five different genes. But they're
put right next to each other in the same way. The way it works is it's actually off when
tryptophan or whenever that chemical is present. And so tryptophan remember is an amino acid.
We need it to make proteins and so bacteria, as long as tryptophan is present they don't
want to have to make tryptophan on their own. And so the way it works here is that the actual
tryptophan fits in the repressor. It gives it a shape that actually blocks the RNA polymerase
or the making of those proteins. But let's say for example that your diet doesn't have
tryptophan. So you're not getting tryptophan in your diet. What does the bacteria do? Well
now the repressor is going to change shape. It's going to change shape that allows RNA
polymerase on. RNA polymerase is going to quickly make those 5 proteins and then those
5 proteins are going to make more tryptophan. So the tryptophan fits again and it's going
to turn off. And so what that gives us is really cool control, as far as the bacteria
goes, on if we have positive control in the case of lactose whenever it shows up, then
we want to break it down or tryptophan control, negative control, when it's there then we
want to turn it off. So simple, neat engineering solution to a real world problem. Now we don't
have operons. Remember in between each of our genes we'll have long stretches where
there's actually junk quote unquote DNA. And so the way it works in us is a little bit
different. We use what are called transcription factors. So RNA polymerase is here but RNA
polymerase can't get on until we have a number of transcription factors present. And so let's
say we want to make a protein as well in eurkaryotes. To do that we have regulatory factors. Those
are actually made by regulatory genes that could be somewhere else in the DNA or they
could even be outside the nucleus in the cytoplasm. So in order for us to transcribe a gene it
takes a little bit more, it's a little more in depth. First of all the transcription factors
will allow the attachment of RNA polymerase. We'll have other transcription factors that'll
actually hold it in place but you can see that we're not actually making the gene. And
so in order to make the gene, the DNA upstream of that will actually have to fold. It'll
get more transcription factors and you'll notice that still nothing's going on. We still
don't have transcription. Until that actually folds back and activates that RNA polymerase
can it go now and make that protein or make the RNA and then eventually make the protein.
And so how does it work in us? We don't really have these on/off switches, I don't know if
you can see my hand, but what happens is the DNA actually folds back on itself and it can
activate genes in other places along the genome. And so it's a different form of control. It's
more complex form of control, but it really requires input from all these other transcription
factors. So that's gene regulation and I hope that's helpful.