>> Okay, we're back.
Sorry a little slow
this morning.
We're going to finish up
terpenes today and then we're
on to cell singling
which is chapter nine,
the last chapter in the book.
This is one of my all time
favorite Botticelli's,
and that's saying a lot because
I'm a big Botticelli fan,
and I want to present you
with a mystery here which,
if you look closely, is the
color of the hair of these women
versus the sky over here.
So, anyway, a little
bit of a mystery,
will explain more very shortly.
Okay, take a quick look
at chapter nine,
just skim through it.
It has a ton of really useful
information especially if you go
on in biology or
anything bio related.
The goal of chapter nine is
to orient you in this enormous
and daunting sea of biological
literature, when you open
up science nature cell, it
seems like every new paper tries
to re-define cell signaling
and adds an additional
layer of complexity.
And the truth, is as a
chemist this the exact opposite
of the way we like to
think, chemistry we
like to have a few very
simple rules that we can use
to understand all of
cell biology and all --
sorry, all of chemical
reactivity.
Biology seems to be going
in a divergent direction,
but it needed to be that
complicated and so the goal
of chapter nine is to simplify
all of that daunting complexity,
strip it down into a
few essential elements
that if you learn then you
can understand anything
that you encounter in the
area of cell signaling,
and I'll be explaining
that very shortly today.
Okay, proposals, they're coming
up, they're due in two days,
48 hours, again attach a
self-addressed stamped envelope
if you want comments back,
if you don't want comments
back that's quite all right.
If -- it's essential though
that you follow instructions,
upload to turnitin.com as before
and if you're done at this point
and wondering how you
could possibly improve,
try to write more concisely.
So, concision is an essential
element of good writing,
the more concisely the
more precisely you write,
the fewer number of
words the better.
I told you, you can use up to
ten pages, but if you use five
and you're very affective at
arguing, so much the better,
okay, you'll be more
effective as a proposal writer
and someone being persuasive
if you can use fewer words,
fewer words is always
better than more words.
Okay, any questions
about the proposal,
this is your last shot.
Last chance for questions, okay,
let's start with you Sergio.
[ Inaudible Speaker ]
>> Oh, on the turnitin.com
website, oh on the --
[ Inaudible Speaker ]
Okay, well it really
is this Thursday --
[ Inaudible Speaker ]
Yeah, I assure you its Thursday,
I will take another look,
but honestly I'm going to hold
you to Thursday, so, okay,
but thanks for the heads up,
and then a question in the back.
[ Inaudible Speaker ]
No, no, no and thank
you for asking.
Okay, it's a completely
different format then the
journal article report.
[ Inaudible Speaker ]
Actually at the bottom of
the instructions posted
to the website, I tell you
exactly what kind of font
and margins I'm looking
for, so what I'm looking
for actually is double spaced,
12 point, one inch margins,
but I think it's all
specified on the --
sort of towards the end
of the instructions, okay.
But don't follow the
journal article report,
that's a different assignment,
for this assignment I'm looking
for a proposal, it has different
sections, etcetera, so,
sounds like you're
going to be busy.
Other questions, all right,
good luck, I cannot wait
to read your original
and creative ideas,
this is really one of the
most fun things for me
to do is actually read
about these clever schemes.
And I'll probably have them
back for you within a week,
so that one I can
return pretty quickly.
All right, oh, one
last announcement,
I don't think I have
a slide about this one
but I should announce it, please
fill -- please rate the class --
evaluate the class
through triple e,
this is especially
important if there's a chance
that I might be writing a letter
of recommendation for you.
When I write letters of
recommendation I always type
in the ID number, so that
I can get a complete --
I type in the ID number
and email addresses
and I do this just so
I get a complete record
of all the grades, and something
else that pops up is whether
or not the student
actually provided feedback
and that's randomized.
The feedback is stripped
from the ID
but it does give me a list
of all the names of everyone
who provided information
and so it also provides
me a second list of people
who didn't provide feedback.
And my feeling is if I'm going
to spend an hour or so working
on your behalf to help you get
into dental school or whatever,
you can spend ten minutes
working on my behalf
to help make the class a little
bit better for next generation.
Okay, so, if you want a letter
of recommendation from me,
be sure to fill out
those evaluation forms.
Any other questions about any
announcements, things like that,
where we're going, all right,
we're down to the
last two lectures.
We have so much to talk about,
so why don't we hop right in,
okay -- oh sorry, some
more announcements,
I will have office
hours tomorrow,
this is your final
all bets are off time
to ask me anything
about the proposal.
I imagine at that point you're
not asking me really crucial
questions, I'm hoping that at
this point your ideas are pretty
well set.
We will have discussion
sections this week,
and the discussion sections
again will have the format
of office hours, so you
can calmly have your
questions answered.
[inaudible] has been sick
for the last couple days,
but I'm hoping she'll
be back today,
get well soon [inaudible], her
office hours actually are today,
she tells me that she's
going to be there.
[Inaudible] has office hours --
[ Inaudible Speaker ]
Yeah, could you move this
to make it actually useful,
that would be great, thank you,
thanks, thanks [inaudible].
Okay, anyway, that's the last
of the announcements, all right,
so what we saw last time
is that the terpene class
of hydrocarbons that are
naturally synthesized
and they are astonishing
in their diversity
and their biological activity.
I should mention to you
that these are the compounds
that make perfumes smell good,
that make flavors taste good,
these are the compounds of life
that make life worth living
in a way, okay, these
are the things
that we sense and
we enjoy sensing.
So, these are all assembled
from isoprenes in head
to tail fashion and I'm
actually going to start this --
today's lecture by picking this
topic up again and looking at it
in a little greater detail.
And we talked about how these
linear isoprenoid pyrophosphates
such as [inaudible]etcetera, can
be cyclized by terpene synthases
and the terpene synthase
holds it up and then hits it
with this cyclization reaction
which was a [inaudible] cascade
that leads to these
complex natural products.
Today we're going to look at
the actual [inaudible] ions
as they go flying
through the air,
as they go on to make really
complex natural products,
and this is I think one
of those objects of wonder
that truly amaze me
about the natural world.
And then we also
discussed very briefly
that terpenes are often oxidized
after the cyclization step,
so after cyclization there is
a series of tailoring enzymes
that then took the skeleton of
the hydrocarbon and modified,
modified, modified
until an end you ended
up with this very bioactive
compound such as [inaudible]
which is used routinely
in anti-cancer therapies.
Terpene synthases,
as we discussed,
offer remarkable control
over ratio and [inaudible],
that's how you can
have one enzyme
that gives you a particular
ring fusion, say a 6-6 fusion
versus a 7-5 or even a spirafuse
where the two rings wrap
right angles to each other.
This is truly amazing chemistry,
and it requires a catalyst
that has been -- that has
evolved to have real control,
the catalyst really
exerts control
over this ratio and [inaudible].
Okay, I want to start with this
idea of head to tail fusion.
I kind of presented this
without really describing it
in great detail and I want to go
back over it just very briefly,
this is a familiar molecule
to us, the limonene,
this is derived from
two isoprene sub-units
and if we call this sort of --
this top part with the
two [inaudible] the head.
These are fit together in
head to tail fashion over here
and then I guess this is kind
of tail to middle fashion
on this side, but even
before the chemistry
that I'm showing
you is defined --
organic chemists have recognized
that terpenes always seem
to follow this head
to tail rule,
and this is actually a pretty
powerful way of figuring
out how these things are
chemically synthesized.
Or synthesized, not necessarily
chemically in a laboratory,
but synthesized by
microorganisms and plants
that have these terpene
synthase pathways, so,
the way this works is there's
the joining that we talked
about last time between
the heads and the tails,
and then we have a X
leaving group over here,
this is our pyrophosphate.
That leaves -- and that
sets you up for cyclization
to give you this limonene
compound and we'll look at it
in greater detail, but in short
this is going to set the stair
of chemistry, it's going
to set the [inaudible]
double bond that's going
to attack over here, etcetera.
Okay, so, very briefly
head to tail emerges
from how these things are
synthesized, so this tail
over here with the
pyrophosphate, the DMAPP,
the [inaudible] has
this good leaving group.
Good leaving group steps
out the door setting us
up with this [inaudible] and
then the head of the IPP,
the [inaudible] can attack,
that gives you naturally --
this is the tail over
here, head over here,
so head to tail jointing and
that happens every time, okay.
There's one really
important exception to this,
but for the most part these
things are held together
and attached together
in head to tail fashion.
And so, this gives us
a really important rule
for dissecting how
these things are built.
>> Quick question.
>> Yeah, yeah.
[ Inaudible Speaker ]
Yes.
[ Inaudible Speaker ]
Yeah but it's in residence
with this allelic position
to give you a [inaudible], but
only the primary is reactive,
the [inaudible] over
here is held distant
from this [inaudible] over here,
so because it's held away it's
not available for the reaction,
only the primary [inaudible].
And remember it's resonance,
so in the resonance structure
you're going [inaudible],
primary, [inaudible],
primary, [inaudible], primary,
but the primary gets
the reaction
and then [inaudible] principle
drives it on to completion.
Okay, so that kind of
sweeps it in one direction,
and I'll be honest, these --
this class of compounds seems
to ignore many of the rules that
you learned about in Chem 51
and again in sophomore again
in chemistry where we learned
about stability of [inaudible]
and how dominate the stability
of a [inaudible] is versus
secondary or primary.
And in this class of
compounds and this class
of synthases we find that the
enzymes themselves are capable
of overcoming those
biases and they overcome it
by stabilizing [inaudible] one
[inaudible] versus another,
and I'll show you --
I'll briefly [inaudible]
to imagine --
to speculate that the active
site would have something
hovering right above
this primary [inaudible]
to give it a little
extra stability.
For example you could imagine an
aromatic functionality up here,
a [inaudible] that
would be precisely poise
to do a [inaudible]
pie stacking event
and therefore stabilize
the primary [inaudible]
preferentially over the much
more beguiling [inaudible]
that otherwise would
be the dominant,
more stable [inaudible].
And I thank you for
asking because it's one
of the really intriguing aspects
of this class of compounds
and it blows me away every
time, okay, so when we look
at the structures that I
showed you last time notice
that these are all
joined together
in head to tail fashion.
So, we have tail, head, tail,
head, tail, head, tail, head,
tail, head, tail, head, tail,
head, tail, head, tail, head,
and this could go on
for a really long time
like N being 1000 in the
case of natural rubber,
but they're all joined
head to tail,
head to tail, one after another.
And they're all joined in that
fashion without, you know,
scrambling because that enzyme
that worms these bonds is
only set up to do a head
to tail joining and in synthetic
rubber chemists try to emulate
that kind of head to tail
fashion type of joining as well.
And so in synthetic rubber this
head to tail joining is set
into place by --
starting with some sort
of head based [inaudible],
so this is [inaudible],
this is basically a [inaudible]
attacks the tail of isoprene,
that sets you up with
a new [inaudible]
on this new head
carbon and that sets you
up to attack another
tail, etcetera.
Okay, so this actually works
really, really well, all right,
let's see, all right I want
to pick up our discussion
and show you a different
aspect of terpene chemistry
and the different aspect kind
of neatly leads us
towards cell singling
which is the final
topic of this class.
It turns out that the
localization of proteins
in the cell is vitally important
to dictating their function,
in other words you can have this
really, really active enzyme
that can turn on all kinds
of things in the cell,
but if it's not available, if
it's somehow squirreled away
in the cell then it
wouldn't have any effect
on cell singling.
So, getting the protein
to the correct place is a
really important challenge
in biochemistry and
chemical -- and cell biology,
and there's a couple
of different ways
that proteins are scooted to
the correct spot in the cell.
One way for example are
short peptide tags that act
as zip codes to direct
proteins to specific areas
within the cell, another way
is for proteins to be tagged
with isoprenoid derived --
isoprene derived tails, okay,
such as these [inaudible] that
are added on to the protein ras,
okay, regular ras is the GTPA's.
Okay, so here's the protein
over here, it has a [inaudible],
it has a phial, recall
the [inaudible] sets you
up to have [inaudible]
at Ph7 quite readily,
this phial can then attack
[inaudible] phosphate
as catalyzed by [inaudible]
and this will give you
a [inaudible] attached
to the phial.
Okay, so now you have this
greasy part over here,
where do you think this thing
gets localized to, okay,
we have a little bit
of greasy tail, yeah.
[ Inaudible Speaker ]
Membrane, indeed, right, the
membrane is a big greasy space
as well, so this acts as a
greasy spike that drives this --
that drives right
into the membrane
and anchors the protein
permanently
on that plasma membrane,
and that has [inaudible]
consequences.
I'm skipping over
some other stuff,
there's some other modifications
that take place as well,
but this basically takes
ras and confines it
to a two dimensional surface
on the upper half of the --
or two dimensional surface
on the barrier of the cell
and that kind of confinement
is really important
for its activity.
So, because ras plays a key role
in cancer base cell singling
there have been attempts
to derail this process
and inhibit [inaudible],
so this [inaudible]
is a important target
for anti-cancer therapeutics,
and unfortunately none
of those have worked
out in the clinic.
What ends up happening is
they're so non-specific
for ras getting [inaudible]
versus other proteins
getting [inaudible]
that they have not been very
effective in the clinic,
unfortunately, because
otherwise it looked
like a really promising
approach.
Okay, so if we can
disrupt this kind
of localization then we'd
have a way of dealing
with cell singling in many
different kinds of cells,
and here's another
example, this is an example
from the cell singling of
[inaudible], so [inaudible]
and [inaudible] are two types of
cells that control the build up
and break down of bone tissue.
So, the bones, the stuff that
your bones are made out of,
and this becomes especially
important as people age,
their bones tend
to get more brittle
and so it becomes really
important to inhibit [inaudible]
which are breaking down
the bones and so one way
of approaching that is
to inhibit [inaudible],
so if you inhibit this enzyme
here then you will be preventing
this [inaudible] and then
killing the [inaudible].
Okay, so the goal here is
to inhibit this process here
and the strategy is to
provide these kinds of drugs --
these are called
[inaudible] and these look --
I guess if you kind of
look really squinty-eyed
at these they kind of
look like the [inaudible].
Right, I mean you
really have to squint,
but you can definitely see that
in here into this [inaudible],
right, where there's a carbon
phosphorus bond hence the name
[inaudible], these [inaudible],
because they have two of these,
sort of look like
the [inaudible] --
the pyrophosphates
of [inaudible].
And then some of these even
have some greasy tails as well,
anyway, these compounds are
prescribed in large quantities
to women especially as they get
older, but also men as well,
depending on their
circumstances, and in order
to direct them directly to
bone often times they bind very
strongly to [inaudible] which
is one of the key prod --
key constituents for building
bone and bone density.
Okay, so this is an important
osteoporosis treatment,
questions.
All right, so I want to return
to where we left off last time
in terms of complexity, and
last time I showed you how the
terpene synthases worked,
but we didn't get a chance
to really zoom in and look at
the [inaudible] in cascades.
And so this seems like
an appropriate point
to pick things up,
so here's an example
of different terpenes
found in nature,
these include the
mono-terpenes which are C10,
so all of these consist of two
isoprene units joined in head
to tail fashion, the [inaudible]
terpenes which are C15,
again all of these
have three isoprenes
and then the die-terpenes,
C20's that have four
isoprene sub-units.
And again if we were --
if we spend time looking
at this we'll find that all
of these are -- all these
isoprene units are joined
in head to tail fashion,
sometimes it gets complicated,
[inaudible] but they're
definitely in there.
Okay, so how do you get this
rich structural diversity,
how do you control this compound
versus this compound or even
if you have something
like [inaudible]
versus this [inaudible]
over here, and the answer is
by controlling the
mechanistic pathways
of the cyclization processes
that synthesize these compounds,
and so the terpene synthases
that I described to you
on Thursday are exceptional
really at directing the outcome
of a really complicated
series of reactions.
And so the one I'm going
to start with is implicated
in the biosynthesis
of [inaudible],
so in this case the enzyme
[inaudible] takes this
[inaudible] and [inaudible]
it, okay, when it does
that the next step in
here is a [inaudible] --
or a cyclization
reaction where each one
of these electrons hops, hops
so it's starts here, hops here,
hops there and in the end you
end up forming one, two, three,
four, four carbon, carbon
bonds in one neat step.
Okay, I'm showing this to
you as a concerted reaction,
meaning all four bonds are
formed in a smooth pathway
and this is one of the areas
where chemists have been arguing
for years about whether all this
takes place in one step or not,
to my mind the definitive
experiment was done
by E.J. Corey who showed
pretty conclusively
that actually there sort
of multiple intermediates
that are formed during these
[inaudible] cyclization steps.
And so I'm showing
you all four er --
all five eras hopping
along at once,
it probably doesn't happen
exactly like that, okay,
all right, so after this
[inaudible] cycli --
after this cyclization cascade
this compound here [inaudible]
undergoes a series of methol
transfer events where hydrides
and methols all the
ones highlighted in pink
over here hop around
and move and migrate.
And by doing this , this gets
you to eventually [inaudible]
which then becomes
the basis for --
this becomes the basis then
for all human steroids, okay,
so this is a [inaudible]
cyclization that all
of you are doing even
as we speak, okay.
Let me just get you started
with where these
hydride shifts are going,
so after the cascade you end
up with a tertiary [inaudible],
right here so you have
this tertiary [inaudible],
the first hydride shift is
a one, two hydride shift
where this hydride in --
this H that's pink hops over
to here giving you a new
[inaudible] -- a new
tertiary [inaudible].
So, let's think about
this for a moment,
how might the enzyme
preferentially stabilize one
[inaudible] intermediate
over another
and then drive this
reaction onward.
I'll give you a hint;
I've already talked
about this today, Chelsea.
[ Inaudible Speaker ]
Indeed, well done
Chelsea, so you can imagine
over here there might be an
aromatic ring that's available
to do a [inaudible] pie stacking
to preferentially
stabilize this [inaudible]
over the other tertiary
[inaudible] up here,
all these things are directed,
you can't have, you know,
sort of random jumping
around the ring.
All of this is carefully
controlled by the enzyme
and in the absence of the
enzyme what's more likely
to happen is a beta
elimination and none
of these hydride migrations,
but these hydride migrations
are really profound, right.
Over here there used to be
a methol group over here,
it's not hopped over to here,
the methol group that was
over here was hopped over
to here, the hydrogen
over here is hopped over
to here, the hydrogen
that was here hopped
over to there,
so it's like a whole
series of one, two methol
and hydride shifts where
everything in the ring seems
to be on fire in some way.
And capable of migrating and
moving over and it's like a game
of musical chairs
where the final stop,
the final [inaudible] is
simply the most preferentially
stabilized likely
as Chelsea pointed
out through [inaudible] pie
stacking type interactions,
make sense.
All right, humans unfortunately
cannot synthesize retinoids
and this is a really important
-- a really big nutrition issue
in developing countries,
so the retinoids result
from an unusual tail to
tail joining event, okay,
so here's [inaudible]
die-phosphate
and a second [inaudible]
die-phosphate
and check this out, they're
going through an unusual tail
to tail joining event.
Okay, that almost never happens,
it happens in the super long
[inaudible] die-phosphate cases,
but for the most part
this is rare, right,
I mean every other isoprene
in here is joined in head
to tail fashion and
now here's two tails
that are coming together
as catalyzed
by [inaudible] synthase.
Okay, there's a couple of more
enzymes that go through here
and then boom you get down
to the familiar beta keratin
of carrots, right, that's that
nice orange color that we crave
so much, that color is
essential, it's not just
that it's colored
orange and makes --
I was going to make a joke
but it would have
been inappropriate.
But it's useful because it plays
important roles in human biology
and so for ex -- if you have a
diet that's missing this beta
keratin you end up with all
kinds of unusual diseases,
that aren't really seen in
developed countries like Europe
but are definitely important
in developing countries.
And so one of the challenges
is trying to come up with diets
that meet these nutritional
requirements, okay,
so for example if you're on
a rice dependent diet one way
to do this would be
to insert the genes
that synthesize beta keratin
into your rice resulting
in nice orange colored rice
that's called golden rice.
And using that as a way
of providing the nutritional
requirements for the people
in those countries, this
is really important,
this is something that I
think all of us should be
on the front lines working
on, this is the kind of thing
that makes a really big
difference in the world.
Okay, so a less weighty issue
but one that really surprised me
when I first encountered it,
this is a more trivial
application,
it turns out that farmed salmon
is farmed in a way to ensure
that you can actually
dial in the color
of the salmon that results.
And farmers -- fish
farmers do this
by feeding the salmon
these pre-cursors
to this [inaudible] pigment,
okay, so you could basically
with this salmon [inaudible] --
this [inaudible] fan
over here you can dial
in exactly the color
of salmon that is going
to be most appealing
to the market.
And if you go down to Albertsons
you're shaking your head,
but it's true, if you
go down to Albertsons
that salmon is a particular
shade of pink that's going
to best appeal to your
-- the Irvine consumer.
Okay, and it's all totally
controlled by simply feeding
in the right pre-cursor
chemicals so that
in the end the fish have this
[inaudible], this is necessary
because wild salmon
will eat lots of shrimp
that naturally make their own
[inaudible] and the shrimp --
the salmon that are farmed in
big pens don't encounter shrimp
as much and so end up with
a very different color.
You wouldn't want to eat
the non-pink salmon, okay,
it wouldn't be appealing,
so anyway same principle
as the beta keratin,
similar chemistry as well
and then again you just
dial in using dif --
you know dial in the final
color based upon different
concentrations of
these pre-cursors.
Okay, so I'm going to switch
gears now, I've been talking
to you mainly about human
examples of terpenes;
I want to talk to
you just very briefly
about the non-human
examples, this is some
of my all time favorite
paintings anywhere,
these were done in
the 15th century
by the great Sandro Botticelli.
And they're truly sublime,
okay, this is 15th century
and these look astonishing
modern even today,
I mean they're just
exquisite portraits
of in this case this is
Venus, the birth of Venus
and this case is the
primavera that I showed
on the very first slide today.
Okay, so even the
best scientists
like to take vacations and
the great Conrad Black winner
of the Nobel prize in
chemistry for a lot
of the chemistry I've
been showing you today,
dealing with hydrocarbons,
working out things
like HMT [inaudible], working
out a lot of the synthesis
of cholesterol that
I've been showing
over the last two
lectures, that was all worked
out by the great Conrad Black.
Okay, so he's on vacation in
Florence, Italy and he's looking
at these paintings in real
life for the first time,
and the extraordinary thing
that he noticed was that all
of the models in these paintings
have blonde haired women
in them, okay, and this is
kind of a surprise to him
because if you're in Italy most
of the women have brunette hair,
that have dark brown hair.
And the thing that struck him
was that these were painted
in the 15th century where
as hydrogen peroxide
which is the most common
method for colorizing hair,
from converting from oxidizing
hair pigments from brunette
to blonde was not
invented until 1818,
so the synthesis hydrogen
peroxide was invented
by Thenard in 1818.
So presumably these
women did not have access
to large quantities of
peroxide, so an obvious question
to a biochemist like Conrad
Black is how did these women end
up with blonde hair, okay,
or maybe the artist completely
fabricated the whole blonde hair
thing, okay.
And if you look in
lots of other paintings
from the same time
period it's very clear
that blonde hair was
something of a craze, okay,
so Conrad's on vacation
and he likes mysteries --
oh and by the way he wrote a
sublime book called blondes
and venetian paintings
armadillos
and other medical mysteries,
highly recommended, great book.
Anyways so he's on vacation
and he starts looking
into this further and what
he finds is that the women
in that period would
spend a large amount
of time combing terpenes
into their hairs, okay,
so they would have this
kind of wet, oily solution
that they would comb into their
hair and then they would leave
that kind of wet hair
hanging out in the sun
for long periods of time.
And what happens is a very
inefficient chemical reaction
that results in production
of a tiny little bit
of hydrogen peroxide, and over
time this will gradually lighten
the hair color, okay, so
here's the way this works,
starting with [inaudible]
and chlorophyll, you know,
from the [inaudible] that
this is derived from.
Chlorophyll is a triplet
synthesizer that allows you
to do -- basically it
[inaudible] reaction
with the oxygen and then
here's the light over here,
so this converts the [inaudible]
oxygen to the triplet state
of oxygen -- the triplet
synthesizer giving you an
oxygen-oxygen double bond.
Recall that oxygen is --
almost all oxygen we're
breathing is oxygen-oxygen
single bond, anyways so this
gives you an oxygen-oxygen
double bond which sets you up
for this [inaudible] reaction,
giving you a proxy intermediate
that can then decompose
to form this super duper
stable aromatic compound
and releasing hydrogen peroxide.
Hydrogen peroxide can then dye
the hair a kind of blonde color,
you know, this is not exactly
blonde, blonde but it's,
you know, certainly
honey blonde, right,
and you know the process
might take a really long time,
but the results were
fashionable back then.
Okay, questions about this,
anyone want to do this
experiment for me, I'd actually
like to see this replicated,
I've been reading about it
for years, never
seen it replicated.
I understand it takes hours,
might be fun, all right,
let's talk about other
cyclization reactions.
The truth is things get really
complicated if you get into this
in greater detail, here
for example is the [inaudible]
pre-cursor to [inaudible]
and the [inaudible]
cyclization that this goes
through is pretty challenging,
right, and we're going
to do a [inaudible] attack
on a primary [inaudible].
We've seen that before, we've
saw that on an earlier slide
when we joined together the head
to tail isoprene pre-cursors,
there's then another cyclization
to give us a tertiary
[inaudible],
and then a beta elimination
over here.
So this beta elimination
gives us this [inaudible]
intermediate, [inaudible]
as an intermediate can then
be [inaudible] in a couple
of different places and this
is kind of an astonishing step,
okay, so what we're going
to see is a [inaudible]
of an [inaudible].
Okay, and just take a
moment to take a deep breath
and appreciate that
majestic [inaudible], okay,
because if you think about it
[inaudible] are not the great
basis, right, there's
really no way that this step
over here should take
place, but it does.
The enzyme has evolved
on a very effective acid
that can [inaudible] this
[inaudible] giving us a new
tertiary [inaudible] and setting
us up for the last cyclization
which then leads to
a beta elimination
to give us the [inaudible]
skeleton that becomes the core
for forming [inaudible].
Okay, this is really
astonishing chemistry,
this is pretty remarkable stuff,
okay, and then after you get
to [inaudible] over here you
get to [inaudible], all right,
anyone want to speculate on
identity of this acid over here,
okay, what kinds of acids
would you find in [inaudible],
someone not Chelsea,
yes Carl, what's that?
[ Inaudible Speaker ]
-- yeah so that would be
my first choice as well,
[inaudible] the problem
with those though is they have
oxygen [inaudible], right,
both of those [inaudible]
acids have oxygen's
and oxygen's are really
great [inaudible].
And the problem there is that
you have all these [inaudible]
that are flying all over
the place and oxygen
and [inaudible] don't
mix, the oxygen is liable
to go winging its way
down to the [inaudible]
and giving you a permanent
covalent intermediate.
So, instead when we look
closely at the structures
of terpene synthases
that do this type
of chemistry we find a
completely different acid
in [inaudible], it's not
[inaudible] or [inaudible],
so that was an excellent choice,
it was my first choice as well,
it turns out it's not the case.
Other choices, what other acids
would you find in an active site
of an enzyme, and I'll --
[ Inaudible Speaker ]
What's that?
[ Inaudible Speaker ]
-- yeah, yeah, so [inaudible],
that's a good choice as well.
Yeah, I can't argue
with that one,
all right, that's a good one.
I'll tell you [inaudible]
is actually the choice,
so [inaudible] which has a
[inaudible] side chain actually
acts as the acid to do
this [inaudible] step
and that's completely
[inaudible] because the PKA
of [inaudible] and [inaudible]
might be 10 or something
like that and here it
is acting as an acid
but [inaudible] something
that really doesn't
want to get [inaudible].
So you can imagine the
neighboring side chains must
in some way turbo-charge the
acidity of the [inaudible]
of [inaudible] making
this reaction possible,
this is pretty extraordinary
chemistry.
All right, any questions
about terpenes, [inaudible],
that class of molecules,
the class of molecules
we've been seeing.
Okay, questions about blondes
and Venetian paintings, Chelsea?
[ Inaudible Speaker ]
Oh, okay, so [inaudible] is
a really effective antibiotic
that kills off the
neighboring microbes,
so microbes will
synthesize this as a way
of killing off their neighbors
to compete, but we chemists,
and medicinal chemists
and pharmacists
and physicians prize [inaudible]
because it's very effective
at inhibiting [inaudible]
and [inaudible] and the fact
that it's very effective
in anti-cancer therapies,
so it prevents cells
from dividing and ends
up killing breast
cancer cells for example.
All right, are there any other
thoughts, all right, moving on,
I want to switch gears now,
we're now on chapter nine,
the final chapter, the
final topic for the book,
and in a way I've kind of
saved the best for last.
We really had to
learn everything
that we've learned this quarter
so that we can understand
at a systems level how
cells really work, okay,
so we can now put together all
of the information I've
been giving you all quarter
and now think about cells
in a really chemical way.
Okay, and specifically
we've been talking
about the central dogma of
biology and we're now ready
to talk about how
natural products
and synthetic molecules can get
in and disrupt key processes
in different steps of
this central dogma.
And again because natural
products are synthesized
by enzymes, these enzymes down
here are synthesizing things
and we're going to be
most interested in those
that are interfering
with transcription.
Small molecules in general offer
some really powerful abilities
to control processes
in the cell,
for one thing you have control
over when they're applied, okay,
so what this means then is you
can have an organism that's
grown to a certain
stage of development
and then you give it the
chemical compound and you shut
down a pathway at specifically a
certain stage in its development
and that allows you a really
powerful tool to ask, all right,
so at this stage in development
how does this protein pathway --
how does this pathway
actually impact the development
of the organism.
For that matter you also
have spacial control,
so what I told you about
was temporal control,
spacial control meaning that you
can dose in a specific type --
a specific site in the organism,
for example you might be
interested in understanding,
I don't know, just kidney's,
okay, or let's just say liver
and how signaling by liver
cells effects other organs.
So you can imagine with small
molecules you have a way then
of just dosing in just the
liver and not the other pathways
in the organism,
so this temporal
and spacial control is
really powerful and one
of the great strengths of using
synthetic molecules as tools
to dissect these pathways.
And so that's what we're
going to be talking
about for the next
couple of days
as we discuss small molecule
control over the central dogma.
This has been done for thousands
of years, okay, there's evidence
of this that goes back to
writings on Egyptian papyrus,
you can actually find
descriptions of small molecules
that are isolated from
plants like this one.
So, for example from this
plant, this weird looking plant
over here, you can actually
isolate [inaudible],
which is isolated again from
the plant depicted over here,
this is known as [inaudible],
night shade, [inaudible]
and it has a structure
-- this structure here,
notice that it's structure
mimics the structure
of [inaudible], okay and this
is one you don't really have
to squint at.
These two look really
similar to each other,
especially when you draw
them like this, okay,
and then here's the
structure of [inaudible],
another related compound in
this and so these compounds act
as agonists for [inaudible]
receptors,
and these compounds are found
in really high concentrations
in seeds and berries
of these plants
because it encourages animals to
grab onto the seeds and berries
and move them around
thus spreading the plant
and making it more successful
as a Darwinian evolved creature.
Okay, so we humans are also very
big on psychedelic experiences
and so we also prize these seeds
and berries, I will tell you
that you should definitely
read the warnings
if start experimenting with
these, these are really --
come down very, very serious
side effects and even death.
But for centuries these have
been used and they work again
by targeting [inaudible]
receptors
which I believe we talked
about in the context
of paralysis, right.
So, for example witches for
centuries were thought to fly,
they were probably flying
metaphorically using compounds
like these isolated from
[inaudible], night shade
and other plants, okay, and
the straight forward way
that they would do this
was they'd take these seeds
and put them in various
membrane passages, right,
so up your nose etcetera.
And actually they
work surprisingly --
there's a high concentration of
these compounds in these things,
okay, in addition to humans
wanting to spread these things,
small molecules are used
by other animals to
signal each other.
So, for example the avocado
seed moth shown here responds
to this pheromone,
this compound over here
and this is actually a
powerful way that we can use
to trap the pest to attract it,
this is a pheromone that it uses
to attract it's mates,
okay, so signaling
by small molecules is used for
therapeutics, it's used to --
by organisms to signal each
other, it's used recreationally,
it's used in all kinds
of different context.
And it's pretty much universal.
Every organism that we find,
even the most simple organisms,
even something like [inaudible]
use small molecules to talk
to each other, so this
really is a universal mode
of communication and
it's kind of astonishing
that we humans actually
use different modes
for communication, we're
not so dependent upon this,
but your dog, your
dog is very dependent
on small molecule
signaling as evidence
that it spends all it's
time sniffing, right,
your dog sees a rich universe
of small molecules all around it
when it samples sense
in the air.
Okay, before I get into how
these small molecules work,
we have to have a
little chat about arrows,
this is [inaudible] experience,
I know that this is one
of the big hang-ups that
organic chemists have
when they start diving
into cell signaling.
Arrows in chemistry and arrows
in biology have two
fundamentally different
meanings, okay, in the
chemistry world we have arrows
that indicate transformations
from reactants going
to products often
with some catalysts,
these areas can be
[inaudible] arrows,
they can be single point arrows
indicating no return reaction,
but this a familiar area to us.
For that matter we're also
very familiar with arrows
that show electrons or
overlap of orbital's
from the highest
occupied orbital the homo
of this [inaudible] pair
to the lowest occupied
[inaudible] orbital
of the [inaudible] over here.
Okay, so these are arrows
that we use conversationally
all the time, in this class
and in other classes,
and I've been using these
since the very beginning
of this class,
I've used them today
multiple times,
they're totally understood.
Arrows in biology mean
something different, okay.
First, when there is an arrow
the arrow means directly act --
direct activation, okay, so for
example this arrow indicates
that this [inaudible] binds
to its receptor over here
which in turn binds to this
[inaudible] protein over here.
Further more if this [inaudible]
protein does some transformation
it's going to be
acting as a catalyst
and they way we indicate it's a
catalyst is the way we indicate
it's a catalyst if it's
chemical transformation
by simply placing it in
the center of the arrow.
Okay, now there's a whole bunch
of other arrows that we find
in biological communication,
so for example an arrow
that has a terminator
at the end,
I don't even know what
you would call this,
anyone want to take
a crack at this,
what would you call
this end point one.
All right, the perpendicular
line,
it indicates a direct
inhibition, okay,
so this would be --
so some how this guy
over here directly inhibits
this protein over here,
oh if it's a dotted line it
indicates indirect inhibition
meaning maybe there's an
[inaudible], so this guy binds
to this guy which binds this
guy which somehow inhibits this.
Okay, so dashed lines
indicate indirect effects
and solid lines indicate
direct effect,
and then finally there is the
arrow that has the arm on it
that indicates --
activates transcription.
Okay, so all of these arrows,
this is kind of the language
of biology, they follow these
conventions, they're really not
that daunting if we take a
moment to think about them.
All right, within cell signaling
there's three scenarios --
so we're all good on the arrows,
arrow business we don't have
to talk about that
anymore, okay,
we're going to be using them,
that's the convention
we're going to follow.
Within cell singling there's
going to be three kinds
of scenarios for cell
signaling and each
of these scenarios evolve
depending on their requirements
of that type of cell,
for example on the left you
can imagine the signal arrives
and then the cell has
to immediately respond,
in that case the cell
will release something
that is pre-synthesized and
no transcription is required.
So, the signal never
reaches down to the level
of transcription of DNA, an
example of this I'll show you
on the next slide,
it's the release
of [inaudible] by goblet cells.
Another type of signal is signal
arrives, the cell then has
to synthesize a bunch of
new proteins and respond
to that signal, transcription
is required,
if transcription is required
things slow down, okay,
so this is a slow type
of signal over here.
For example, skin cells that
have to fill in a wound, okay,
so you cut your finger with some
paper or something like that,
the skin cells nearby have
to [inaudible] and fill
in that injury and so
-- this is not going
to happen instantaneously,
right,
you know that it takes a couple
of days for the paper cut
to heal, right, it doesn't
happen instantaneously.
It doesn't have to happen
instantaneously for that matter,
and so this is a slow
type of cell signaling.
Commonly there's both a
slow and a fast response.
For example a response
to insulin,
so the insulin won't rise
the cell immediately starts
responding using the glucose
transporters that we discussed
when we talked about [inaudible]
biology a few weeks ago.
But in addition the cell has
to respond to this insulin
by synthesizing new proteins
and having a slow response,
so this hybrid is also a
very common mode as well
and so we're going to see
these three different scenarios
play out.
The first scenario is this
business about [inaudible],
so for example [inaudible]
agonists buys a [inaudible]
stimulates intestinal goblet
cells to spill out [inaudible]
in a rapid response,
okay, so this is you,
you're eating something, you
counter something that's bitter,
like buys a [inaudible] and
you have to immediately respond
to that, you know, your stomach
doesn't like bitter stuff.
And so the stomach and
the intestine respond
by secreting all this
[inaudible], we've talked
about the structure of
[inaudible], it's an [inaudible]
and that helps smooth the
passageway and get rid
of this bitter tasting compound.
Okay, so here's the
goblet cells over here,
they've already stored up
all the [inaudible], okay,
it's already over
here so as soon
as [inaudible] you
immediately start spewing
out the [inaudible], it
flows out into the intestines
and it's already
been pre-synthesized.
So, no DNA transcription
is required,
you've got an immediate
response, okay,
now I'm also trying to
systematize self signaling
so also on the level
of systemization,
cells can either be talking to
each other, to different kinds
of cells or they
could be talking
to the same class of cells.
And these two different classes
of cell signaling are referred
to as either [inaudible] or
[inaudible] is communication
between cells of
the same type, okay,
so if those goblet cells
are stimulating each other
that would be [inaudible],
if however they depended
on a different class of
cells to stimulate them
that would be [inaudible],
okay, make sense.
Okay, now it turns
out that within all
of biology there's really
only seven different types
of cell signaling, okay, and
I want to make this point,
this is super duper important
because when you pick
up the literature
in cell biology
and signaling it's insanely
confusing and complex.
Cut through all that
complexity, all that matters is
that there are seven different
types of cell signaling,
if you learn these
seven different types
of cell signaling you
will understand all
of the different kinds of
pathways that are written
about in the current
literature, okay.
And one of the problems with --
okay, so I'm starting to get
off the track, I can't resist.
Okay, so one of the things
that makes this difficult is
when biologist write about
their own pathways they always
describe how their pathway's
unique and how it does --
nonsense, okay, every single
pathway can be fit into one
of these seven categories
over here.
And as a chemist I want to know
the seven simplest examples
and then I want to be able
to apply those seven
simple examples
to every other example that's
out there, and I promise you,
you can do this, this
will make sense of all
of cell signaling, okay.
So, all we have to do
over the next couple
of days is simply learn
about these different types
of receptors and [inaudible]
and their cell signaling
transduction pathways
that modulate transcription
and this is going
to simplify an otherwise
ridiculous level
of complexity, okay.
Let's get started, this is --
so this diagram is really
basically all you have to know,
this shows the seven different
types of cell signaling starting
with the most common
nuclear receptors,
so nuclear receptors are
controlled by [inaudible]
that reach directly into
the nucleus and turn
on transcription, hence the
name nuclear receptors, okay.
And I'll show you
examples of each of these,
also at the top are
two component pathways
where you have a
[inaudible] event up here
that eventually reaches down to
transcription, and note again
that these dashed lines
indicate indirect effects,
so in this case the
[inaudible] is going
to go all the way
into the nucleus.
In this case though it's
going to have a whole bunch
of [inaudible] that are
going to have multiple steps
to eventually get
to the nucleus,
in addition we have receptor
[inaudible] depth receptors,
G protein couple receptors,
ion channel receptors
and finally gas receptors.
And from there all of
cell signaling can fit
into these seven
categories, so all we have
to do is learn these seven
and then I hope everything
else will make sense,
okay, sound like a plan.
Let's get started, I'm going
to start on the most common
which are nuclear receptors and
then we'll step systematically
through each of these, oh, okay,
before I get to that I have
to introduce a couple
of more terms.
The first of these are terms
that are taken directly
from the area of genetics.
The terms are forward genetics
versus reverse genetics,
and the best example I can
give to this are [inaudible],
so fruit flies naturally
have red eyes, okay,
and if you radiate a whole
population of fruit flies
or you feed them some sort
of chemical mutagen you will
eventually find fruit flies
that have white eyes, they
will have this white phenotype.
Okay, they look like
this, red eye, white eye,
and then if you spend
time looking
at the different
mutations that result
in the white eye you will figure
out that actually this results
from impaired mutations that
prevent the pigment pre-cursors
that result in the
red eye from getting
across the cell membranes, okay.
So, white eyes result
from mutations
that prevent those
pigment pre-cursors
that eventually result in
the red eyes over here, okay,
so this approach is
called forward genetics,
you make a whole series
of random mutations
and then you look at the types
of phenotypes that result
from those random mutations
and use those different random
mutations to dissect the biology
that results in those
phenotypes.
Okay, that's called forward
genetics, you make mutations,
you look for response,
you then understand how
that response occurred, okay,
the opposite would be reverse
genetics, not exactly opposite
but it's complimentary.
Before I get to reverse,
any questions
about forward genetics, okay,
so forward genetics
random mutations,
hope for an interesting
phenotype,
this a strategy that's worked
well for over 100 years,
biologists have been doing
this for a really long time.
Chemists have in the last
couple of decades applied a --
actually no, no, no, I'd
say this has been going
on for a much longer
time than that,
let's say at least five
decades maybe even longer,
chemists have been applying
a chemical analog of --
on forward genetics called
forward chemical genetics
where you apply a bunch of
different small molecules
to introduce random
changes and you hope
to find an interesting
phenotype, okay.
So maybe you have your fruit
flies you apply a bunch
of chemicals to the fruit
flies and you look for ones
that give you white eyes,
chemicals that result
in white eyes and then that
identifies chemicals that are
in some way preventing the
pigments from reaching the eyes
to give you the red color
of the fruit flies, okay.
Here's one example of this,
this is a compound called
[inaudible] isolated
from Easter island soil,
so soil from Easter islands
out in the pacific, this
compound in the very center acts
as the glue in a
molecular sandwich
between FK106 binding protein
12, it has a molecular weight
of 12 [inaudible] and another
compound called [inaudible],
okay.
So this is FKEP on the left in
purple, [inaudible] on the right
in green and you can see that
the [inaudible] is acting
as the meat in the sandwich
to bring together this complex
and then that result is
once this complex forms the
[inaudible] prevents,
amongst other things,
t-cells from forming.
And so [inaudible] is a really
important amino suppressor,
I think we talked about
this before actually,
maybe a couple times in this
class, this is a molecule
that prevents the immune
system from responding
to say liver transplants.
Okay, so again this is called
forward chemical genetics
because we're going to
use random compounds
that are isolated
from some [inaudible],
from like a distant island
and then we're going to look
for ones that have
interesting effects,
in this case the phenotype of
suppressing the immune system
and then we use the compound
to study how these immune
system pathways work.
So [inaudible] has been a really
powerful compound for figure --
for dissecting these pathways,
and in recent years has also
had an important effect --
important tool -- it's been
an important [inaudible]
in studying aging and diet
and other types of pathways.
Okay, so small molecules
offer control
over otherwise unavailable
phenotypes and so
for this reason they're --
they've come to the floor
as really good power tools
in cell biology, so for example
the classical genetics approach
starts to break down
when you get mutations
that kill the organism, okay.
So for example this [inaudible],
if you make mutations
to [inaudible] you end
up with these, you know,
embryos that are hugely
distorted and really incapable
of living, okay, so the
classic genetic forward genetic
approach, not going to work.
So instead what you do is
you identify a small molecule
inhibitor, a [inaudible] and
then that offers a solution
that inhibits [inaudible]
and gives you a way
of studying this
otherwise lethal phenotype.
So that way you can dissect
how the protein actually works.
Okay. All right.
Now of course doing this
requires some way to look
for interesting phenotypes,
right, we need some way to go
out and identify in forward
chemical genetics weird cellular
phenomena and so chemists
have been very clever
about doing this.
This is an experiment done by
Tarun Kapoor and Tim Mitchison
and what they did is
they had a whole library
of different compounds.
Here's one compound shown here.
And they start with 16,000
compounds and in a plate
that has a large number
of wells they look
for some mitotic signature.
Okay, which has this
dark blue color, okay,
so they set up an
assay that looks
for a particular phenotype, dark
blue, under that assay, okay,
and then they take the compounds
that light up in this assay
and look for the effect --
look for the compounds that can
stabilize microtubule formation,
okay.
So earlier we talked
about [inaudible],
here's a [inaudible] stabilizes
microtubules, here's another set
of compounds, 52 of these
de-stabilize microtubule
formation, one stabilizes
it and the compounds
that are positive here then go
on to florescence
microscopy experiments.
Over here these are
low [inaudible],
over here these are
high [inaudible],
over here you have
16,000 compounds,
down here you have less than
100, okay, staring at cells
under a microscope,
that's hard work, okay.
Over here though just looking
for the one dark spot out of,
you know, thousands
-- tens of thousands
of dark spots, that's easy.
This step over here
can be done by robots,
this step over here can
be done by robots as well,
but sometimes the
robots miss stuff,
sometimes the imaging software
misses really interesting
effects, okay.
And what Kapoor and
[inaudible] found is
that this compound called
[inaudible] has this really
astonishing effect
on the [inaudible]
which is this assembly
of chromosomes during
cell division, okay,
so normally the chromosomes
line up kind of like on the --
I'm forgetting my football
analogy, scrimmage --
line of scrimmage, sorry.
Okay, so everything
lines up on this line
of scrimmage during
cell division
and then these chromosomes
are pulled apart
into the two daughter cells,
[inaudible] explodes the
whole thing and so instead
of having chromosomes in
the center, microtubules
on the sides, instead you end up
with chromosomes on the outside
and those crazy microtubules
in the center.
And that's absolutely
fascinating;
it turns out that this
compound is an inhibitor of one
of the motor proteins that
drives the chromosomes
and pushes and shoves
the chromosomes
into place during
this process and so
that gives you a
really powerful tool
for dissecting how cell
division takes place.
Okay, so any questions
about using small
molecules in this, yeah?
>> Yeah, so this division
that they wanted to figure
out if they could interfere
with [inaudible] divisions --
>> Exactly --
>> They dyed the chromosomes
blue and then checked a bunch
of molecules to see if any
of them were disrupted.
>> Exactly.
And I'll be honest, they
didn't expect to have,
you know, something like this.
Like, they weren't
looking for this pattern,
they were just looking for
weird patterns in the same way
that you'd look for white eyes
or just weird colored creatures
in the case of the fruit
flies, the [inaudible].
You're just simply looking
for something that's abnormal
and then once you find that
abnormal thing, then you go in
and you use this
as a tool to figure
out how this process works
and what proteins
must be implicated.
So this implicated motor
protein called [inaudible],
this particular type of
[inaudible] in this process
that otherwise it wasn't clear
exactly what it was doing,
sound good, powerful tool.
Okay, yeah, question
in the back.
[ Inaudible Speaker ]
Yes --
[ Inaudible Speaker ]
Yeah --
[ Inaudible Speaker ]
Well if it's a dominant mutation
then you cross breed the
dominance together and then
you would definitely see it,
if it's recessive then you would
see it in one out of every four,
you know, daughters -- one
out of every four progeny,
that's the genetics.
Also it's complicated
because it also depends
on how many mutations
are required,
it starts to get
complicated quickly,
but my genetics friends could
tell you all about that,
but it makes sense right,
that yes you'd see those
mutations coming through,
whereas if you use a
small molecule, you know,
once the small molecule
is metabolized --
once it's hydrolyzed or whatever
-- oxidized, it's game over,
it's effects disappear.
And that too is powerful, right,
so you apply the small molecule
and then it goes away and
you go back to wild type,
and so you can see what it looks
like if the small
molecule's not there
in exactly the same organism.
Okay, all right, so
I want to get back
to the seven different kinds,
now that we understand how
small molecules are going
to play important roles, I'm
going to highlight the import --
the rules of the small
molecules as we start looking
at the seven different
pathways for cell signaling.
One of the most common of these
cell signaling pathways are the
nuclear hormone -- or the
nuclear receptor based pathways,
there are some 28
nuclear receptors,
only eight have well
identified known [inaudible],
as recently as a
couple of years ago.
Okay, so these eight
are depicted here,
so some of these are familiar
to us, I believe we talked
about the [inaudible] -- these
[inaudible] hormones earlier
in the quarter, we
talked earlier today
about the processes of
synthesizing estrogen
which eventually can be further
modified to give us [inaudible].
Here's testosterone over here,
here's [inaudible] over here,
these are all steroid
receptors, right, all these guys
up here are steroids, these guys
down here, [inaudible] acid,
[inaudible], these
are other hormones,
these hormones bind directly to
nuclear receptors and as we see
in a moment the nuclear
receptors directly carry the
signals all the way
to the DNA level.
Note that when these things
are bound, when these hormones
over here are bound,
they're completely engulfed
by the protein, the protein
throws a big old' sloppy bear
hug around the steroid over here
and it's completely
buried, okay.
So in this space-filling model
you don't see any yellow, okay,
it's completely covered up.
The thing is heavily
buried by receptor.
The receptor changes it's
confirmation upon binding
to the hormone and that in
turn allows it to do stuff,
like get into the nucleus and
start effecting transcription.
Oh, by the way, I told you
that these are the eight
that are known, the other
twenty sort of unknown,
it's not that those
other twenty bind
to various metabolites weekly,
okay, meaning not very strongly
and so that binding is thought
to be a little non-specific
and a way of sampling many
different states in the cell.
So different steps
along metabolism
and other intermediate
compounds as well, okay.
So why don't we take a
look, there are two modes
of nuclear receptor signaling
that we need to learn about,
one of these is illustrated
by estrogen.
So here's estrogen over
here, in the hypothalamus
and the hypothalamic
neurons in this --
the estrogen binds to
the estrogen receptor.
The estrogen receptor
then dissociates
from the heat shock
protein, and that freeze
up the estrogen receptor
to eventually make its
way to the nucleus, okay.
What you need to know about this
is the estrogen receptor binds
to the estrogen, to the steroid
and then it gets all the way
to the nucleus, it doesn't
get to the nucleus before then
because it's kind of covered up
by these heat shock proteins.
And furthermore it has to bind
to this [inaudible] beta --
[inaudible] beta molecule
over here to make it
through the nuclear pore and
be imported into the nucleus,
once it's there it [inaudible]
trigger transcription
of the [inaudible]
receptor hormone gene, okay,
so this triggers the
transcription and then
in turn then allows the cells
to respond to the estrogen.
Okay, something else
that's notable about this,
notice that this has a
homo [inaudible], okay,
these are two identical
molecules
of estrogen receptor alpha over
here and then estrogen receptor
over here and they're
both identical.
Contrast that against
the other mode
of nuclear receptor signaling
which involves hetero
[inaudible], same principle,
the molecule diffuses, in this
case the molecule's [inaudible]
acid structure is here,
oh, and by the way,
again this is structure of
[inaudible] again synthesized
from [inaudible] acid over
here can directly sneak its way
across the plasma membrane,
through the cytoplasm,
through the nuclear
membrane and get all the way
over to this receptor
for the [inaudible] acid.
So this is the [inaudible]
receptor alpha,
and this also binds to
the [inaudible] receptor
and then the two of
these get together
and hetero [inaudible]
before leading to production
of these [inaudible]
en-coated proteins, okay.
So this leads to transcription
and expression eventually
of these [inaudible]
proteins, okay,
so in both cases we
see a similar effect,
you have this greasy
little hormone molecule,
the greasy hormone molecule gets
in through the plasma membrane,
binds to the receptor and
then the receptor sneaks
into the nucleus where it
can cause transcription.
Okay, so in this case the
signaling molecule is taking a
short cut to get all the way to
the nucleus, sound good, okay.
Let's look at a structure,
so this is a structure
of the [inaudible],
this [inaudible] binding
to [inaudible] acid
receptor alpha bound also
to this [inaudible] over here,
[inaudible] and [inaudible] acid
in yellow up here, and
then also binding to DNA.
So, this is an example again
of hetero [inaudible], blue,
purple, [inaudible] and then
this hetero [inaudible] can
interrogate the DNA using
exactly the same sort
of transcription factor
event that we talked
about when we talked
about proteins binding
to DNA many weeks ago, in
fact maybe over a month ago.
It seems like a really long
time, earlier in the quarter,
and again notice that
this has its alpha helix
that could snuggly fit
into the major groove
and interrogate the sequence,
so this thing will then look
for a particular sequence of DNA
and then activate transcription
of a particular gene -- a
particular open reading frame
of that DNA leading to the
turning on of specific proteins,
the production of
specific proteins.
Make sense, okay, so
much to talk about here,
and unfortunately I
just don't have time,
we're running out of time.
So if I were to say
chemists have spent a lot
of time thinking about ways
to control nuclear receptors
because if you can then you
can dramatically control gene
transcription and in turn that
can have dramatic consequences
for controlling the growth of
cells, the mortality of cells,
the differentiation
of cells, etcetera.
And this has been done
classically for well
over 50 years now,
for example isolated
from the [inaudible]
yam, this compound --
check out this [inaudible],
this thing is enormous, right,
that's a whole [inaudible]
down here,
this is what the
yam tree looks like,
it's just one monster
[inaudible].
You can isolate from
this [inaudible],
this compound [inaudible]
and from [inaudible] you
can make [inaudible],
you can make a whole
bunch of other steroids
and you can imagine
wanting to make this
for birth control pills,
for hydrocortisone,
for anti-inflammation,
[inaudible],
other inflammation
effects, etcetera, okay.
Now a days, so back in the
50's and 60's a whole series
of chemists -- a whole
generation of chemists went
to Mexico where the [inaudible]
yam has been cultivated
for centuries, they
went to Mexico
and they isolated directly out
of these very high percentages
of the pre-cursors like this one
for synthesizing these hormones.
Nowadays we found that
even though they're present
at lower concentrations in soy
beans because soy beans are
so -- are grown so [inaudible]
and at such high levels
in the United States
that we can regulate --
we can much more simply isolate
[inaudible] directly from soy,
and so the ultimate
source nowadays of many
of our steroids is
from soy [inaudible].
Okay, so rather than
the [inaudible] yam,
which is too bad because the
yam has a wonderful cultural
heritage, other non-steroidal
[inaudible] nuclear receptors
include these [inaudible]
compounds, [inaudible],
and [inaudible] over here,
the important thing to know
about this is that both of
these compounds are derived
from [inaudible], this
iodinated [inaudible],
and these are important
for regulating the
basil metabolic rate.
And so if your diet does
not have enough iodine
in it you could run into all
kinds of complications, okay,
including [inaudible]
that's shown here,
and I put the picture up
because I suspect no one
in this classroom has seen
a case of [inaudible].
This used to be totally
common until all the salts
in the country, except for
kosher salt, was iodized, okay.
So what this means is that
there's a low concentration
of sodium iodide mixed in
with the sodium chloride,
and it turns out that it
doesn't require a very high
concentration of iodine --
iodide in the diet
to get just enough
to synthesize naturally these
[inaudible] derivatives.
All right, questions, anything
dealing with nuclear receptors,
okay, one last thought
[inaudible].
This compound over
here requires UV light
for an [inaudible]
ring opening reaction.
So you start with [inaudible]
the compound does this very
weird six pile electron
[inaudible] ring opening,
electrons are going
to bounce, bounce,
bounce and this gives you a ring
opening, and then there's a one,
seven [inaudible] shift shown
by these arrows over here.
Which you might have to go
home and convince yourself
of yourself, but long story
short this gives you vitamin D3,
if you have a deficiency in
vitamin D this leads to rickets,
the bow-legged phenomena,
it's just one
of the many manifestations of
this really terrible disease,
but again the key that in our
diets we get enough vitamin D3
this leads to liver enzymes
and kidney enzymes that convert
into [inaudible] and then
[inaudible] binds directly
to nuclear receptors.
Okay, final thought,
last slide of the day.
If for example you
have a mutation
in the [inaudible] receptor,
the mutation of this [inaudible]
over here to [inaudible].
You could chemically synthesize
-- I'm talking like you do this
at a laboratory and then, you
know, give it to a pharmacist
who gives it to a physician,
you could have a chemically
synthesized derivative
of [inaudible] that then fills
in the mutation over here,
binds the receptor and gives
you normal cell signaling.
Okay, well why don't
we stop here.
When we come back next
time we'll be looking
at the other six types
of cell signaling.
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