#51 Biochemistry Gene Expression III Lecture for Kevin Ahern's BB 451/551

Uploaded by oharow on 12.03.2012

[Kevin laughing]
Kevin: Standing ovation, right?
[Kevin laughing]
I was talking to a colleague of mine the other day
on a committee and he looked at me and he said,
"You know when I was a student,"
he said, "I never had any idea the professors looked
"forward to the end as much as I did," and it's true.
So professors look forward to the end as well.
But I've really enjoyed working with you guys.
You've been a very good group.
And you guys have had the highest averages
I've ever had for a class, consistently.
So I'm very pleased, very impressed with that.
Very cool.
So today I'm going to finish up talking about regulation
of eukaryotic gene expression and as we will see
that occurs at several levels.
And I'm going to give you some examples
for each of those levels.
And then we'll move sort of slowly into sensory,
and the senses, the molecular basis of sensing.
When I finished last time I was talking about
the fact that enhancer sequences are tissue specific
and that certain tissues will have the protein
that may appropriately bind to that sequence and activate,
in some cases it can actually inactivate transcription
and these enhancers give some tissue
specificity for the expression of genes
that are needed by those tissues.
A very cool experiment is shown on the next
slide I want to show you to illustrate
the specificity of enhancer action.
What you see on the screen is a picture of a transgenic
chicken or a transgenic chicken embryo.
And this transgenic chicken embryo was transformed
taking an enhancer for a muscle protein
so that what they had done
was they had taken this enhancer for this muscle protein
and they linked it to the beta-galactosidase gene.
And the idea is that wherever the beta-galactosidase gene
is being expressed, if you apply X-Gal
to this developing embryo what you will see
are the locations in the developing embryo
where this muscle gene is being made.
Now the beauty of this technique and the beauty
of this experiment is you can actually see specific
places wherever the blues are where that gene
is being made because the blue corresponds
to where beta-galactosidase is cleaving the X-Gal.
And since this is an enhancer that's specific
for muscle tissue this is the place where the very earliest
expression of muscle genes is happening
during a developing embryo.
Well as you could imagine this kind of technique
is really useful for understanding gene expression
during the process of development
and so it's a very, very powerful technique.
And again, biochemists being lazy,
using blue color as a way of helping us to find things
really helps us in this case to understand how gene expression
is happening during the process of development.
Very, very cool experiment.
Regulation of gene expression in eukaryotes
happens in a variety of ways.
It occurs at the level of whether or not transcription
occurs and it occurs at the level of how stable RNAs are.
It occurs at the level of how accessible the chromosomes
are to the RNA polymerase and it occurs
also at the level of the stability of protein.
And there's many, I'm just listing a few here.
So I'm not going to come back and say list all the levels.
That's not my purpose in mentioning this.
But rather I want to show you this and say a little
bit about this particular method.
When we think about the regulation of gene expression
in eukaryotic cells two big things come to mind,
and these both involve covalent modifications of things.
The first of these as I'll talk about later today
is acetylation of lysine residues in histones,
that is putting an acetyl group onto lysines.
And as we will see the effect that that has
is to loosen up the chromatin structure to allow
an RNA polymerase and associated proteins
to get in there to start transcription.
Another covalent modification that occurs,
occurs not to the histone proteins
but to the DNA sequence itself.
And this modification that occurs in eukaryotic
cells involves methylation of a cytosine.
So methylation of a cytosine here gives us 5-methylcytosine
and the significance of this is that this methylation,
if this cytosine is present in a promoter
or a regulatory region for a gene,
will tend to silence the gene.
That is it will tend to inhibit transcription
of that particular gene.
So DNA methylation is an example of what we refer to
as an epigenetic modification that occurs in cells.
It's an epigenetic regulation.
And epigenetics refers to nongenetic changes
and these nongenetic changes such as putting a methyl
group on can actually be transmitted across generations.
So prior to our unraveling or understanding
of epigenetics we had the strong bias
or strong impression that everything that an organism had
was the product of the sequence
of its DNAs and as a result of our knowledge
now of these modifications that we see that control
how much of a gene is made we now know,
and the fact that they can be transmitted across generations,
we now know that there are other factors
involved in transmitting genetic information.
So these epigenetic changes such as this,
such as the acetylation of lysines
and histones are very, very important factors
in us understanding how genes are expressed.
Well I want to spend a little bit of time talking
about one type of regulation we find in eukaryotic cells,
particularly things that affect multicellular organisms.
You recall from our discussion last term
that I talked about hormones.
We saw how, for example, epinephrine affected
glycogen metabolism and we saw how insulin affected
the metabolism of sugars and so forth
and the import of sugars.
Hormones do other things besides affect enzyme
activities and it's important for us to recognize
that hormones can also affect gene expression.
So estradiol is a female sex hormone
and it is an estrogen and it is a hormone that can,
as I said, affect the expression of certain genes.
So I want to spend a little bit of time
talking about how it works.
Estradiol works by interacting with a protein
called the nuclear domain receptor.
This nuclear domain receptor is a protein
that has two specific domains on it,
that is two specific structural regions.
One structural region is involved in binding DNA
and you see those little zincs right there
so I hope that you recognize that this guy
has some zinc fingers, to bind to a specific sequence in DNA.
So this nuclear hormone receptor,
nuclear domain receptor will in fact bind
to a specific sequence or specific sequences
in DNA and activate genes when this hormone
has bound an estradiol and its other domain.
So the other domain is a ligand-binding domain
and the ligand here is estradiol.
Now these two sites are separate from each other.
We can destroy the estradiol binding site
and the DNA binding domain site will still stay intact.
This figure shows schematically what happens upon
the binding of estradiol by the nuclear hormone
receptor and the nuclear hormone receptor
undergoes a significant change.
If you look at this little purple guy down here
you see that it lifts up and out of the way
after it is bound to an estradiol and that turns out
to be significant for the action that this hormone has.
So this structural change again, as we've been saying
for the past two terms, small changes in the structure
of a protein can have some fairly significant impacts
on the cell and such is the case here is well.
The nuclear hormone receptor does not
by itself activate transcription.
It's part of a series of steps that have to happen
in order for the genes regulated by estradiol to be expressed.
The binding of the receptor is the first
step in the process however.
So we see here that two nuclear hormone receptors
have bound to the specific target region of the DNA
and they have these two alpha helices,
that's the purple region that we saw before, sticking out.
And when there's no estradiol bound to those then
this other protein here called a coactivator is unable to bind.
However, when estradiol binds the two purple guys
sort of fold out of the way kind of like you saw
in the last figure and open up a binding site
that this coactivator protein can now bind to.
So this is an essential step in the activation
of transcription of genes that are controlled by this protein.
Now I'm going to show you a couple additional steps
in a minute but the critical thing from this slide
is that estradiol is favoring a change in the structure
of the nuclear hormone receptor and this change
in structure allows a coactivator protein to bind.
Everybody with me?
Tamoxifen is a compound that is used to basically
interfere with the function of estradiol.
And tamoxifen and its related compound raloxifene
can bind to the nuclear hormone receptor
and inhibit the binding of the coactivator.
So when tamoxifen or this guy right here binds
they can inhibit the binding of the coactivator
to the nuclear hormone receptor.
Well as you might imagine that has a fairly significant effect.
You can see the purple guy has moved out of the way
but this loop down here is not out of the way
and so the nuclear hormone receptor
is unable to bind to this coactivator
when tamoxifen is bound to it.
So that's a significant difference between the two.
So we could imagine that when we treat
with tamoxifen what we are doing is we are locking up
the nuclear hormone receptors and as a consequence
they will not be able to go ahead and activate
transcription of genes that otherwise
would be turned on by estradiol.
Well how does the overall process work?
The overall process works by virtue of the fact
that the coactivators, or the coactivator
that I showed you on the screen,
and there are several of these,
are actually enzymes and these enzymes
have a very important function.
These enzymes will take histones
and they will acetylate them.
They will specifically put an acetyl group
onto the lysine of histones.
Now I mentioned that earlier.
Now I'm going to tell you a little bit more
about the significance of that.
So it actually is putting on a lysine onto the side chain,
I'm sorry, putting an acetyl group onto the side chain
of lysines in the histones.
Well if we look at the unmodified lysine in chain
we see of course that it has a positive charge.
And when we add the acetyl group, we see it over here,
we see that the positive charge has disappeared.
So we've converted a protein that had a positive
charge to a protein that has a zero charge.
Well obviously DNA is negatively charged,
the protein is positively charged.
There's a nice tight interaction that happens
as a result of that attraction of the positive to the negative.
If I remove the positive or I cover up the positive
as I do here then what happens is that attraction
between the histone and the DNA is not nearly so tight.
It's not nearly so tight.
So as a consequence of that the interaction
between the histone and the DNA loosens
and that loosening is very important in ultimately
allowing access of the proteins in transcription
to come in and do their thing.
So this acetylation that's favored by the coactivator,
and yes a coactivator is a histone acetylase,
that interaction is, that modification favors
now transcription ultimately of the gene.
Well we can see that, oh but before I say that
one of the things I should point out is that the acetyllysines
that you see as a result of that modification are targets
for proteins that have a specific structure
called a bromodomain.
So proteins that have a bromodomain will recognize
and bind to acetyllysines.
Proteins that have a bromodomain will recognize
and bind to acetyllysines.
Well the histones have an acetyllysine so this protein
with a bromodomain binds to it.
Well what might a protein like that be like?
Well one of the proteins that does that
is called a remodeling engine.
So now I'm going to show you the whole process
in the activation of a gene.
So let's start at the very beginning.
So we have a transcription factor, in this case
the nuclear hormone receptor,
that is bound to a specific sequence of DNA.
In this case the transcription factor has bound
to estradiol and as a result of binding to estradiol
a coactivator can bind to that nuclear hormone receptor.
That's what's happened right here.
The coactivator is a histone acetylase so it starts
putting acetyl groups on lysines in the region
where this has been bound.
And as a consequence of that proteins that have a bromodomain
now can find those acetyllysines and bind to them
and one of them that has a bromodomain is called
a remodeling engine.
I love that name.
A remodeling engine.
That sounds like something you'd run through your kitchen
when it's really time to fix it up, right?
So the remodeling engine has a very important function.
Its function is to clear away a space for all
of the transcriptional proteins to come in.
So the remodeling engine opens up access of the promoter
to all these other proteins that's necessary for transcription.
As a consequence, the binding of the nuclear hormone receptor
leads to binding of several proteins that ultimately
lead to activation of transcription.
If tamoxifen binds to the nuclear hormone receptor
over here none of these steps happen.
Therefore transcription does not get activated.
And if those genes are necessary for cellular proliferation
and cellular proliferation is what you're worried about
because you have a cancerous cell that is responding
to estrogen, what you have done is you have just found
a way to turn off the replication of that cancer cell.
A very cool thing.
Good place for me to stop and take questions.
Yes sir?
Student: How localized is the area of effect
of this histone acetylase?
Is it within ten to twenty base pairs or can it act
a long long ways away like some nuclear enhancer sequences?
Kevin Ahern: Yeah, so his question is how far away can this guy act.
It really is limited only by the accessibility of the bending of the DNA.
So it can actually act over a region of several hundred base pairs.
Other questions?
Am I that clear or are you guys that tired
with that tenth week?
So that's one example of how gene expression
in eukaryotes can be regulated.
There are hundreds of others.
I'm not going to go through those.
But I do want to talk about a couple of other schemes
for controlling gene expression in eukaryotes.
So not all gene expression in eukaryotes is controlled
at the level of whether transcription occurs
or how much transcription occurs.
There are other control mechanisms and some
of these are translational in nature.
And that's one of these right here.
So I want to sort of make a left turn now
and talk about another gene that is important,
and there are a couple of genes in cells
that are important and also very interesting.
The gene that you see on the screen
is a protein called ferritin, F-E-R-R-I-T-I-N,
and ferritin is a protein that has a very important function
inside of cells.
It binds to iron.
It will bind to iron.
And there's a few thousand iron atoms that an individual
ferritin can sequester in a structure that looks like this.
Well why do cells do that?
Well iron turns out to be a fairly toxic compound
for cells but cells need it also.
So iron because of its ability to be in the plus two,
plus three state, it has two different oxidation states,
and if left free in the cell it can produce
reactive oxygen species.
So cells are very careful to try to sequester iron
as much as they can.
If they're unable to sequester iron, they're much more likely
to have oxidative damage happen to them.
So it's important therefore that cells make
the appropriate amount of ferritin to handle
the amount of iron that they have.
Well it turns out that there are two proteins to consider
when thinking about iron within a given cell.
Once the iron is in the cell we want to have ferritin
to gobble it up.
Well how do we govern how much iron gets into a cell?
And that happens as a result of action
of another protein called transferrin,
and specifically the transferrin receptor.
So the transferrin receptor is a protein on the surface
of the cell that facilitates the input of iron into the cell.
So the two proteins that we're interested in are
the transferrin receptor and ferritin.
Ferritin holds the iron once it gets in.
The receptor controls how much gets in by
the more receptor we have, the more iron will come in.
The less receptor we have the less iron will come in.
So cells have to literally balance the two
of these and they do it in a very interesting way.
They do it by regulating both the translation of genes
and the stability of messenger RNAs.
We're gonna see both examples as we examine these genes.
These two processes, the translation and the stability
of the gene are regulated as a result of action
of something called the iron response element.
The iron response element, looky there.
There's a structure kind of like you've seen before.
You guys are going to get tired of seeing hairpins.
And you'll discover that hairpins can do a variety of things.
This guy doesn't have anything to do with
termination of transcription.
It doesn't have anything to do with termination
of transcription but instead it's a target for binding
by a protein that recognizes this structure.
Now in the past I've called this protein IREBP
which is kind of a mouthful,
and I'm going to call it IRP, iron response protein.
It's going to make you IRP.
Haha, Okay.
So IRP is a protein that can recognize this structure
and bind to it.
IRP is a protein that can also do something else.
It can bind to iron.
Now IRP, if it binds to iron, will not recognize
this structure and will not bind to it.
If IRP is not bound to iron it will recognize
this structure and it will bind to it.
Are we clear?
Two situations.
Low iron or high iron.
If we have low iron IRP is going to bind.
If we have high iron IRP is not going to bind.
I'm sorry, if we have high iron, yeah it's not going to bind.
Student: When you say "this structure"
which structure do you mean?
Kevin Ahern: This stem-loop.
Student: [inaudible]
Kevin Ahern: I'm sorry?
Student: [inaudible]
Kevin Ahern: This is the messenger RNA for ferritin.
So we're looking at the messenger RNA,
if I didn't say that I should say that.
It's the messenger RNA for ferritin.
Now this structure is present in
the messenger RNA for ferritin.
Now what happens?
Let's imagine we've got low iron.
Low iron, that means that the IRP is not going to be bound
to iron which means it is going to be bound here.
If the IRP is bound here the ribosome comes along and says,
"Okay I'm going to translate this guy,"
and it hits the protein that's sitting right there
and it can't go any further.
When the protein is on there the ribosome gets stuck
and will not translate this gene.
It will not translate, it will not make ferritin.
And that makes a lot of sense because if we have low iron
we don't want to waste energy making ferritin.
If we have low iron we don't want to
waste energy making ferritin.
If we high iron then what happens?
Well when we have high iron the IRP binds to iron.
It doesn't bind to this structure.
This structure is therefore left open.
The ribosome comes along and yes it can translate
and it goes all the way through there and it says,
"I'm making plenty of ferritin,"
and it's making ferritin where iron is high
which is what the cell needs to do because the cell doesn't
want to have all this iron floating around freely.
High iron, low iron, the cell is either making
or not making ferritin.
With me?
Questions on that?
You are a quiet group today.
Well how about the transferrin receptor?
If we look at the coding or the messenger RNA
for the transferrin receptor which we see here
we see that it also has iron response elements
located in it and look at this it's got a whole bunch of them
at the 3' end of the gene.
Now in this case what the IRP does is when it binds
to an element it stabilizes the messenger RNA
and allows it to exist for a longer period of time
meaning you'll make more of it.
And when there's no IRP bound here the nucleases will start
chewing it back and destroy the gene.
So this mechanism which uses the IRP is controlling
how much stable messenger RNA there is
for the transferrin receptor.
I'll step you through it in a second about how it works.
So no IRP bound, message unstable,
decreasing amounts of messenger RNA.
IRP bound, message relatively stable,
more messenger RNA around.
Well let's use our information about
low iron/high iron conditions.
Under low iron conditions is IRP going to be bound here or not?
Low iron, IRP is going to be bound.
Message is going to be stable.
What's going to happen to the production
of transferrin receptor?
It's going to be favored.
That makes sense.
When we have low iron the cell wants to bring in more
so it's going to make receptor to bring in more iron.
When iron concentrations are high, on the other hand,
there's no IRP bound to these guys.
This message gets destroyed and we make less
transferrin receptor.
That makes sense.
We don't want to be making more receptor to bring in more iron
if we already have plenty.
So one protein can control,
in the first case with the ferritin,
how much protein is actually translated.
In the second case, the same protein can control
how much messenger RNA there is to be translated.
They work in opposite ways but because of the balance that
they have cells have the proper amount of iron within them
and that iron is ideally sequestered in a safe way.
Questions about that?
Do I see a question or is that a...?
Student: [inaudible]
Kevin Ahern: The thing that brings in the iron
is the transferrin receptor.
Student: So once it gets on the outside of the cell [inaudible]
degradation process because otherwise [inaudible]?
Kevin Ahern: Yeah that's a very good question.
So basically her question is once you get it out
in the cell membrane is it there forever,
I think is part of what you're implying.
And the answer is there's many other levels of regulation.
So no it's not there forever
and proteins will get broken down over time.
That's superimposed on top of this, but yes,
that's a consideration.
It's also a consideration for ferritin.
So the stability of the protein is ultimately important
in governing these as well.
And I'm just simply showing you this mechanism
or these two mechanisms as ways that cells can control things.
But yes the cell has to govern how much
of those individual proteins are present.
Student: Does anemia affect [inaudible]?
Kevin Ahern: I'm sorry, I can't hear what you said.
Student: Oh, does anemia or lack of iron affect the system?
Kevin Ahern: So her question is does anemia affect
these systems in any way.
That would be a really good exam question.
What do you think?
Will anemia affect this?
I see some heads shaking yes.
What would be your prediction?
A person's not getting enough iron.
What are we going to see happening in these systems?
So what are you going to be making the most of
if you have low iron?
You're going to be making transferrin receptor
and you're making very little ferritin.
So yes that will affect things indeed.
There went the exam question.
Now I can't use it.
I'll have to think up something harder.
Ha ha ha ha.
You're so funny Kevin.
Other questions?
Student: Is this RNA less stable at the 3' end?
Is that why it's stabilized so much
by these iron response elements all being at that end?
Kevin Ahern: Yeah his question is, is this guy fairly unstable
at the 3' end and the answer is yes it is.
And the stabilities of different messenger RNAs
aren't completely understood in terms of
what makes them exactly, you know, rock stable.
Longer poly-A tails will affect that
but then the question is,
well why do some get a longer poly-A tail than others?
What's the governing principles in that?
And that's not a completely understood phenomenon.
Student: Does IRB preferentially bind to
the iron over ferritin?
Kevin Ahern: Yeah so the question is does IRB preferentially
bind iron more than ferritin does?
Is that what you're saying?
The IRB has a pretty high affinity for iron.
It has to because it is literally competing
with ferritin for that iron.
And you don't mind if ferritin wins that battle basically,
but if there's a small concentration of iron
that's not bound by ferritin you'd really like to be able to
get that regulation there as quickly as you can.
So it has a fairly high affinity for iron as a result of that.
Yes, question over here?
Student: So IRB will bind the first hairpin
which is on the left of the coding region, right?
Kevin Ahern: IRB will bind, in the case of ferritin, yes.
Student: Is it the same code as for the transfer?
Kevin Ahern: It's basically the same sequence here
as there was at the 5' end of the other one, that's correct.
Kevin Ahern: Yes, back there.
Student: [inaudible]
Kevin Ahern: How is the iron removed from the ferritin?
Now there's a question that you should be thinking about.
How do we remove noncovalently bound molecules?
Nobody remembers from last term?
What happens to them?
Student: I thought they just come apart naturally
every once in awhile.
Kevin Ahern: So they come off every now and then.
So there's always an on and off and an on and off process.
If it's not a covalent interaction it's not stuck there
permanently and so as it comes off it can be grabbed
by something else and that's how that happens.
Very good.
Student: Is this sort of as straightforward as it looks
as far as the binding and the affinity or is it under
allosteric control like hemoglobin that changes its affinity
in different parts or different situations.
Kevin Ahern: His question is, is there a cooperativity
to the binding of iron here and the answer is no there's not.
As far as I know it's a single protein.
It's not a multisubunit protein.
Student: Is one IRP sufficient enough to stabilize
that 3' end or does more than one IRP-
Kevin Ahern: Yeah good question.
Is one IRP necessary or is it more stable with more on there?
The answer is the more that there are on there,
yes the stabler it will be.
And these are all relative things so it's not
an absolute on or off but I'm going to have more
if I have more of these guys bound.
Student: So the more IRPs there the more mRNA?
Kevin Ahern: The more IRPs there are the more messenger RNA
will be there, that's correct.
It's a dose effect.
Well the last thing I want to talk about-let's see
that was the IREBP which I am now calling IRP.
You can see it there versus low iron, blah blah.
And the last thing I want to talk about with respect
to regulation is actually, I put it under translation but
it's more under the effective stability
of messenger RNAs as well.
And this is the action of a set of RNA molecules
that have been relatively recently understood.
These have happened in the past ten years.
They're known as microRNAs and microRNAs are synthesized
by cells as a way of controlling,
and this seems very odd but it's true,
as a way of controlling how much of a given RNA,
a given messenger RNA they have that's stable.
So the cell goes to all the way through the trouble of making
a messenger RNA and then it decides how much of this
do I really want to have?
It seems wasteful and yes, it is wasteful,
but it provides the cell with an additional way
of regulating how much messenger RNA it has.
How does it work?
Well cells synthesize small single stranded RNAs
called microRNAs that get processed,
and they get processed into little pieces of 22 nucleotides.
And those 22 nucleotides are generally specific
for specific messenger RNAs
meaning that they are complementary to them.
So if I make a microRNA that's complementary to, let's say,
a gene for globin for which I need hemoglobin,
that complementary microRNA will pair with it inside
of a protein called argonaute and the argonaute will
cleave that messenger RNA thereby rendering it nonfunctional
or at least less functional.
Now this might seem like it's an odd mechanism
but there are at least 700 human genes
that are regulated exactly this way.
The more of a given microRNA is made,
the less stable the messenger RNA
that's complementary to it will be.
Very interesting stuff.
So it's an important control mechanism again
for regulating how much messenger RNA a cell has.
We can imagine this could occur again at a variety of levels.
It could occur at the level of tissue,
different stabilities in different tissues.
We can imagine it could occur as a result of hormone action,
a variety of things that would govern how much
of a given messenger RNA is present in a given cell.
Okay, questions about that?
Yes, Connie?
Student: How is that different from siRNA?
Kevin Ahern: How is that different from siRNA?
So siRNA is related in a sense.
siRNAs arise as a result of, the silencing action arises
from double stranded RNA and double stranded RNA gets,
one of the strands gets peeled away
and bound by another protein called RISC.
I'm just telling you this because you asked.
You don't need to know this.
And the RISC complex actually goes
and does a very similar thing.
But the difference being that a silencing RNA,
an siRNA, starts out as a double stranded RNA.
This guy's starting out as a single stranded RNA.
And cells have a mechanism for dealing with this
probably because you think, well when do we have
double stranded RNAs present in our cells?
I don't have double stranded RNAs except for my loops
of my tRNA or my loops of my ribosomal RNA.
When would cells have double stranded RNAs?
Well many viruses that are RNA viruses actually have
double stranded RNAs as part of their lifecycle
and so it's probably a protective mechanism
that when the cell recognizes this double stranded RNA,
if I make silencing, if I take a piece of this
I can silence genes of the virus.
So it's probably a protective mechanism against that.
Does that answer your question?
Student: [inaudible]
Kevin Ahern: That's a good question.
This process as far as I know takes place in the nucleus.
Good question.
So that's where we finish talking about gene expression.
It provides us a perfect opportunity for a song.
This is just a general song.
It has nothing to do with gene expression
but it does have to do with how you might be studying.
And I know there's some people who couldn't make it today
which is why I thought of this song.
So it's to the groove of Feelin' Groovy.
[singing Online Movie]
Lyrics: Oh no!
I missed my class
Someone ought to kick my ass.
Perhaps there is some hope for me
Did Ahern make an online movie?
Nanananana online movie...
Doctor Kevin's always blowin'
Tellin' me I should be knowin'
All that biochemistry
I hope there is an online movie
Nanananana online movie...
Got sweat on my brow
I'm starting to weep
I fire up my laptop, I'm white as a sheet
As Firefox is downloading I'm feeling neat
'Cause I just found the online movie
Okay, a short one today.
Mercifully short given my singing.
Well now we turn our attention to some bigger systems
and these bigger systems are, we can start understanding them
because we've now got the tools of biochemistry
at the molecular level to begin to understand
how senses actually work.
So this is kind of cool stuff.
We're going to talk about smell.
We're going to talk about taste.
We're going to talk about vision
and we're going to talk about hearing and touch.
So we've got five senses there that we'll be talking about
and smell is where I will start.
This schematically shows the various senses.
Of course you know where all these senses are located.
And we see some connection to various regions
of the brain that allow us to process the information
that our senses are telling us.
As we will see, the individual senses have very different
strategies for functioning,
very different strategies for telling us
what it is that they have detected.
And some of these are really cool and interesting.
Smell is particularly interesting.
Here are some things that we can smell.
There's almond.
There's skunk.
I think I'll stay away from that one.
There's rose and there's zing-, zing-,
zingiberene, ginger.
I can't even say that.
You can't look at it and say,
"Well I think I know what that is,"
with the possible exception of this guy right here.
Thiols tend to have a fairly strong scent.
But nothing else on here really jumps out at us
in terms of structure telling us
what this smell will actually be.
Look at these guys.
They're identical in structure.
They are simply stereoisomers.
Identical chemicals except for the orientation
of the things in three dimensional space.
The orientation of this carbon right here determines
whether it's spearmint or caraway,
R-carvone versus S-carvone.
Pretty cool.
So this tells us that, no surprise,
the structure of the molecules are very very important
in our ability to have proteins and other things
interact with them and in this case send signals to our brain.
This is the same thing I just showed you before
but now it shows us up close and personal
what the nasal epithelia look like.
Nasal epithelia have on their surface,
they have neurons that terminate at the location
where these scents are coming into the brain.
And it's these termini that are the places where
the signal that gets sent to our brain starts.
If we look at the various things that we can smell
we discover that we have various
specific receptors for smells.
So we've got about thirty active receptors.
But we can smell more than thirty things
so what does that mean?
It means that any given smell that we have may be binding,
and in fact usually is binding, to more than one receptor.
And the efficiency with which it's binding to any given
receptor tells our brain a different signal.
So we get more than thirty smells.
The smells that we see are blends of those
that our brain basically builds for us.
If we compare us to all the other mammals that are out there
we see that we are on the low end of the scheme.
And if we compare it to something like a mouse or a rat
we discover that they've got way more than we do.
Well it turns out we have the same genes
that mice and rats have for smell.
It's just that many of our have been inactivated over time.
Well we're not quite as dependent upon smell
for finding food as a mice or a rat is.
Human beings do use smell but not in the same way that a mouse
or a rat does which is why mice and rats are what they are.
This schematically shows one of the proteins involved
in the reception of smell
and as you can see it's a transmembrane domain protein.
You can see that it goes across 7 times meaning it's a 7TM.
And this shows us how the process works
at the level of smell.
So here's an odorant.
What is an odorant?
An odorant is one of those molecules I showed you before
and specifically an odorant is something that will bind to
and stimulate an olfactory receptor protein.
We see that olfactory receptor protein
up close and personal here.
It looks just like we saw before where we had
the epinephrine receptor which was known as
the beta-adrenergic receptor.
It was a 7TM.
In this case the odorant is binding to
the receptor and guess what happens?
It induces a small change in the structure of that protein.
That small change activates a G protein
just as we saw before for epinephrine.
That causes the G protein to let go
of its GDP and bind to GTP.
That activates it.
The activation of that protein activates,
causes it to interact with adenylate cyclase.
Adenylate cyclase synthesizes cyclic AMP
and now in the case of this particular nerve cell
the cyclic AMP binds to a receptor
and lets in sodium and calcium.
Letting in of sodium and calcium you recall
from our talk about nerve cells disturbs
the electronic environment.
It changes the voltage, in other words,
and a signal has just started.
So we've just, this cell has just said,
"Okay, I have bound to something that is an odorant.
"I'm going to tell the brain that I've got it.
"I'm going to fire it."
So this guy is now firing.
This wave of voltage will move down the nerve cell ultimately
telling the brain that it is bound to something.
Now what the brain's going to do is it's going to look
at the pattern of all the receptors that gives this signal.
Here's receptor number eleven and this receptor number eleven
is firing at about 10% of the cases
but receptor number twenty-nine is firing at about 75%
of the cases and now your brain says,
"Oh I know what that is."
Your brain picks, basically draws that picture
for you that you perceive as smell.
We don't need to talk about that.
This is what I wanted to say.
So this illustrates a little bit about what
I was saying before in terms of different receptors
and the effect of different molecules
on the binding of those receptors.
We see, for example, here's an odorant, a C7,
seven carbons long with a hydroxyl group,
and we can see it really does interact
with receptor number one.
It does some interaction with receptor number two,
none with number three, none with number four,
a little bit over here, and that's the pattern
that this guy illustrates.
If we look across this we see very little similarity
of the overall pattern of any given one that's here.
Here's a C8 that looks kind of like a C7
but even there the C8's firing number fourteen
and C7 isn't firing.
C7's firing this guy here.
What you see on the screen is why you can smell
so many different things.
It's really cool.
It's really interesting that the brain
is drawing those pictures for us.
And I call them pictures because I can't think of any other
way to describe what the brain is doing except
making this up for you to give you the impression of smell.
The various olfactory senses do converge in a given,
what's called a bulb, and that bulb then coordinates
a signal that goes to the brain.
So that coordination of the signal is important
as you can imagine and allows us to detect, again,
very specific things but also to get a wide range
of things that we're able to detect.
That's probably a good place to stop for today.
I'm going to stop there and I'll talk about
taste and vision next time.
[class murmuring]
Student: For 332, when should the course synopsis write-up
if we want our current grade, what day should it go through?
Kevin Ahern: Thursday.
Student: Through Thursday?
And you want it by when?
Kevin Ahern: Oh I'm sorry.
It'll go through Tuesday.
I want it on Thursday.
So I'm going to talk tomorrow.
Thursday's going to be mostly just a discussion.
It's not going to be anything new.
Student: Are those the notecards?
Kevin Ahern: Oh yeah, notecards.
If you didn't get a notecard, get a notecard!
How are you doing?
Notecard, okay.
One please, one please.
Everybody can take one, yep.
Student: Thank you.
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at Oregon State University