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Hi. It's Mr. Andersen and welcome to Biology Essentials Video 31. This is on

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.

gene regulation in other words how we express a gene or not how we make a

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

protein or not and I want to start with a organism that lives in our intestine called ecoli ecoli is interesting in the it eats whatever we eat and so if I eat

it has to break down the proteins and the lipids in the bacon. If I have cereal it has

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

to break down the carbohydrates. If I have milk it has to break down the lactose. And so

the carbohydrates if I have milk it has to break down the lactose and so what's

what's interesting about an E. coli is that it can go from an organism that has 0 proteins

interesting about an e coli is that it can go from an organism that has zero

to break down lactose to one where 50% of the weight of E. coli is simply enzymes that

proteins to break down lactose to one where 50% of the weight of E coli is simply enzymes the deal with lactose and

deal with lactose. And it can do it like that. And so how do they do that? They do that through

it can do it like that and so how do

gene regulation. And so in this podcast I'm going to talk about gene regulation. Before

they do that they do that through gene regulation and so in this podcast I'm going to talk about gene regulation

I do that I want to get some terminology that I'm going to use a lot out of the way. And

before I do that I want to get some terminology that I'm going to use a lot

so a regulatory gene is going to be a gene on the DNA that regulates another gene somewhere

out of the way and so a regulatory gene is going to be a gene on the DNA that regulates another gene somewhere farther

farther down. A regulatory sequence will usually be found just above the gene. And so what

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

do I mean by that so if DNA looks like this the gene generally will be down

we want to express or not. A regulatory gene will be somewhere else in the DNA. It secretes

here that we want to express or not a regulatory gene will be somewhere else in the DNA it secretes something called

something called a regulatory protein which then can grab onto a regulatory sequence.

a regulatory protein which then can grab on to a regulatory sequence an example

An example of a regulatory sequence, I'll talk about is called a promoter. Once this

to of a regulatory sequence I'll talk about is called the promoter once this

is all set up then we can have an RNA polymerase actually make the gene. And so I'll go through

is all fit up then we can have an RNA polymerase actually make the gene and so

that terminology but what I'm talking about regulatory gene, regulatory sequence those

I'll go through that terminology but what I'm talking about regulatory gene regulatory sequence those both deal with

both deal with DNA. But when I am talking about a regulatory protein that's coming from

DNA but when I'm 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

somewhere else to help express the gene or not as far as gene regulation

of what we know now comes from bacteria. And so I'll talk about positive and negative control.

examples most of what we know now comes from bacteria and so I'll talk about positive and negative control positive

Positive control example I'll give you is the lac operon. That deals with lactose. And

control example I'll give you used the lac operon that deals with lactose

the negative control is the trp operon. It deals with tryptophan. And then finally I'll

and the negative control is the trip operon deals with tryptophan and then

show you what we know about eukaryotic gene regulation and how they use transcription

finally I'll show you what we know about eukaryotic gene regulation and how they

factors as activators, repressors to either express a gene or not. And so this is how

use transcription factors as activators repressors to either express a gene or not and so this is how genes are made or

genes are made or expressed. Remember we start with DNA and that DNA eventually makes messenger

expressed remember we start with DNA and that DNA eventually makes messenger RNA

RNA, mRNA, which eventually makes proteins and those eventually make you. And so any

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,

step along the way we can actually regulate the gene so we can regulate it post translationally post

post transcriptionally. So we can do it everywhere. But in general most of the regulation I am

transcriptionally so we can do it everywhere but in general most of the

talking about is just going to be from DNA to mRNA. Do we express the gene or do we not.

regulation I'm talking about is just going to be from DNA to messenger RNA do we express the gene or do we not and so

And so this is generally what goes on. You've got a gene like this. Upstream of that we

this is generally what goes on we'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.

have a regulatory sequence an example of this in eukaryotes would be the tatah

And the reason it's called a TATA Box is you have a thiamine adenine thiamine adenine and

box and the reason it's called the Tata box is you have a thymine adenine thymine adenine and on the other side

on the other side you'd have TATA backwards complimentary to that. And so this is simply

you'd have to add backwards complementary to that and so this is

a sequence above the gene that allows the RNA polymerase to get on. And so we have a

simply a sequence above the gene that allows the RNA polymerase to get on and

regulatory protein coming from somewhere else remember, another regulatory gene maybe downstream

so we have a regulatory protein coming from somewhere else remember another regulatory gene may be downstream or

or upstream from this whole gene. The regulatory protein, an example could be the TATA binding

upstream from this whole gene the regulatory protein an example could be

protein, this is found in us, it'll grab on to the TATA box, let me get rid of the writing,

the tatah binding protein this is found in us it'll grab on to the tata box let

and it allows RNA polymerase to grab on and actually express that gene. And so if we didn't

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

have the sequence if we didn't have the regulatory protein we couldn't make the

and we couldn't make the protein. And so that's basically how genes are regulated or not.

RNA polymerase and we couldn't make the protein and so that's basically how genes are regulated or not and so let's

And so let's talk about how this works is the lac operon in bacteria because this the

talk about how this works in the lac operon in bacteria because this is the

first one we really started to understand. So the way they tweak what I just said is

first one that we really started to understand so the way they tweak what I

that the neat thing about bacteria is instead of just having one gene they'll have a number

just said is the the neat thing about bacteria is instead of just having one gene they'll have a number of genes and

of genes. And so they'll have three genes. All the genes required to deal with lactose

so they'll have three genes all the genes required to deal with lactose will

will be put right next to each other. And so we've named those the lac Z, Y & A gene

be put right next to each other and so we've named the the lack zy and aging but they each make

but they each make a protein and they each help break down lactose. Above that they'll

a protein and they each help break down lactose above that they'll have a

have a regulatory sequence called a promoter. Remember that's going to be where RNA polymerase

regulatory sequence called a promoter remember that's going to be where RNA

grabs on. And the other thing they'll have in an operon is called an operator. An operator

polymerase grabs on and the other thing they'll have in an OP operon is called an operator an operator sits right

sits right between the promoter and the genes. And the way I like to think about it is it's

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

like an on-off switch and so it can either be set in an on position or it

in an off position. And so it regulates whether or not we turn the genes on or we don't. The

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

other thing that I'm going to add here is something called a repressor. A repressor

that I'm going to add here is something called a repressor a repressor will plug

will plug right into the operator, so it's going to fit right here, and as long as the

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

repressor is available RNA polymerase can't get on and so this would be when

is here the operator is now in the off position. In other words we can't make these genes.

the presser is here the operator is now in the off position in other words we can't make these genes this repressor

This repressor I'm going to show you is showing what's called positive control. And what do

I'm going to show you is is showing what's called positive control what do

we mean by positive control. What I said was when lactose shows up we want to make all

we mean by positive control what I said was when lactose shows up we want to

the proteins to break down and deal with lactose. And right now there's no lactose present and

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

so it's off. But let's say lactose shows up. In other words I drink a glass of milk. Now

let's say lactose shows up in other

there's lactose. So the lactose shows up. The lactose you'll notice is going to fit

words I drink a glass of milk now there's lactose so the lactose shows up the lactose you'll notice is going to

perfectly into that repressor. And when it fits in the repressor it changes the confirmation

fit perfectly into that repressor and when it fits in the repressor it changes

or the shape of that protein. In other words, now the repressor doesn't fit in the operator

the conformation or the shape of that protein in other words now the repressor doesn't fit in the operator anymore

anymore. In other words it lacks these little prongs we'll say that fit in the operator.

in other words it slacks these little prongs will say that fit in the operator

Okay. So lactose is present. Repressor is now off. Well who can grab on? RNA polymerase

okay so lactose is present repressor is now off well who can grab on RNA

now fits. RNA polymerase can fit. There's no repressor. RNA polymerase is going to run

polymerase now fits RNA polymerase can fit there's no repressor RNA polymerase

down. It's going to make each of the mRNAs for each of those lac genes. Each of those

is going to run down it's going to make each of the messenger RNAs for each of those lac genes each of those are going

are going to make a protein. And each of those are going to break down the lactose. And so

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

we can deal with a lactose and we can metabolize that lactose so now the

what's happening to our repressor? It's going back to that original shape. And so it's a

lactose is gone what's happening to our repressor it's going back to that original shade and so it's a cool way we

cool way we can have positive control. If lactose shows up, then we make all of the

can have positive control lactose shows up then we make down make

proteins that can actually deal with that lactose. It shows up again? We're going to

all the proteins that can actually deal with that lactose shows up again we're

get rid of that repressor and we continue. And so that would be positive control. What's

gonna get rid of that repressor and we continue and so that would be positive

an example of negative control? Well a negative control we learned about from the trp operon.

control what's an example of negative control well a negative control we learned about from the trip operon trip

trp operon instead of just having three it actually has five different genes. But they're

operon instead of having just three it actually has five different genes but

put right next to each other in the same way. The way it works is it's actually off when

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

tryptophan or whenever that chemical is present. And so tryptophan remember is an amino acid.

that chemical is present and so tryptophan remember is an amino acid we

We need it to make proteins and so bacteria, as long as tryptophan is present they don't

need it to make proteins and so bacteria as long as tryptophan is present they

want to have to make tryptophan on their own. And so the way it works here is that the actual

don't want to have to make tryptophan on their own and so the way it works here

tryptophan fits in the repressor. It gives it a shape that actually blocks the RNA polymerase

is that the actual tryptophan fits in the repressor it gives it a shape that actually blocks the RNA polymerase are

or the making of those proteins. But let's say for example that your diet doesn't have

the making of those proteins but let's say for example that your diet doesn't

tryptophan. So you're not getting tryptophan in your diet. What does the bacteria do? Well

have tryptophan so you're not getting tryptophan in your diet what does the

now the repressor is going to change shape. It's going to change shape that allows RNA

bacteria do well now the repressor is gonna change shape it's going to change

polymerase on. RNA polymerase is going to quickly make those 5 proteins and then those

shape that allows RNA polymerase on RNA polymerase is going to quickly make those five proteins and then those five

5 proteins are going to make more tryptophan. So the tryptophan fits again and it's going

proteins are going to make more tryptophan so the tryptophan fits again

to turn off. And so what that gives us is really cool control, as far as the bacteria

and it's going to turn off and so what that gives us is really cool control as

goes, on if we have positive control in the case of lactose whenever it shows up, then

far as the bacteria goes on if we have positive control in the case of lactose whenever it shows up then we want to

we want to break it down or tryptophan control, negative control, when it's there then we

break it down or tryptophan control negative control when it's when it's

want to turn it off. So simple, neat engineering solution to a real world problem. Now we don't

there then we want to turn it off so simple neat engineering solution to a real-world problem now we don't have

have operons. Remember in between each of our genes we'll have long stretches where

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

there's actually junk quote unquote DNA and so the way it works in us is a

different. We use what are called transcription factors. So RNA polymerase is here but RNA

little bit different we use what are called transcription factors so RNA

polymerase can't get on until we have a number of transcription factors present. And so let's

polymerase is here but RNA polymerase can't get on until we have a number of transcription factors at present and so

say we want to make a protein as well in eurkaryotes. To do that we have regulatory factors. Those

let's say we want to make a protein as well and eukaryotes to do that we have regulatory factors those are

are actually made by regulatory genes that could be somewhere else in the DNA or they

actually made by regulatory genes that could be somewhere else in the DNA or

could even be outside the nucleus in the cytoplasm. So in order for us to transcribe a gene it

they could even be outside the nucleus in the cytoplasm so in order for us to transcribe a gene it takes a little bit

takes a little bit more, it's a little more in depth. First of all the transcription factors

more it's a little more in-depth first

will allow the attachment of RNA polymerase. We'll have other transcription factors that'll

of all the transcription factors will allow the attachment of RNA polymerase will have other transcription factors

actually hold it in place but you can see that we're not actually making the gene. And

that will actually hold it in place but you can see that we're not actually making the gene and so in order to make

so in order to make the gene, the DNA upstream of that will actually have to fold. It'll

the gene the DNA upstream of that will actually have to fold it'll get more

get more transcription factors and you'll notice that still nothing's going on. We still

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

don't have transcription until that actually folds back and activates that

can it go now and make that protein or make the RNA and then eventually make the protein.

RNA polymerase can it go now and make that protein or make the RNA and then eventually make the protein and so how

And so how does it work in us? We don't really have these on/off switches, I don't know if

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

you can see my hands but what happens is the DNA actually folds back on itself and it can activate genes and other places along the genome and so it's a

different form of control it's more

more complex form of control, but it really requires input from all these other transcription

complex form of control but it really requires input from all these other

factors. So that's gene regulation and I hope that's helpful.

transcription factors so that's gene regulation and I hope that's helpful