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PROFESSOR: Today, we're going to talk
about a very exciting subject regarding molecules.
And this subject has to do with metals in biology.
Metals in biology, by the way, is actually
the name of one of the Gordon research conferences.
So if you get excited about this topic,
you can go to the Gordon research conference web page
and apply to attend the conference next summer
and learn about the latest developments in metals
in biology.
One of the things I want to impart to you today
has to do with where we usually find
metals inside of biomolecules.
So that leads me to talk a little bit
about nature's ligands.
In biological chemistry, we find that molecules sometimes
are quite a bit larger than we're
used to looking at in synthetic small-molecule chemistry.
So I'm going to talk about nature's ligands today
at sort of two levels of size.
Going to talk first about the porphyrin ligand.
And then next, we're going to talk about proteins.
OK.
First this porphyrin ligand is one
of the most pervasive small-molecule hosts for metal
ions within biomolecules.
And it's really quite a remarkable ligand type.
And I'd like you to appreciate it
at the level of being able to draw the structure of it
and to see just how this system can
provide a host for metal atoms.
It is a system that has four nitrogens that it
can donate to a metal center.
So it's a tetradentate ligand.
We talked about bidentate ligands earlier
in the semester.
This is a tetradentate ligand that nature
uses to hold metal ions very tightly where it wants them
in a biomolecule.
And first you draw the four nitrogens
at the corners of a square.
And now we're drawing in the carbon parts of the molecule.
You can draw four vertical lines like that and four
horizontal lines like this.
And then what we're going to do is, at each of the four corners
of this square-shaped molecule, we're
going to go ahead and complete five-membered rings.
Like that.
And then finally, we have four more carbons
to add to this structure.
And those four carbons are at the top, bottom, and left,
and right, like this.
OK.
So you can see that the porphyrin ligand is
a large ring-shaped macrocycle.
And where can a metal ion go?
It can go right in the center.
If you are going to figure oxidation states that involved
a porphyrin molecule, then you would
need to know the charge like we know that one chloride is
in a metal complex.
It carries a one minus charge.
And you need to know how many charges the porphyrin
ligand would carry if a metal were in there,
so that you could figure the oxidation
state and the d-electron count for the metal that would
be inserted into the porphyrin.
And to do that, we first recognize
that if you isolate a porphyrin without the metal in there,
then two of the four nitrogens have hydrogens attached.
OK?
And also this is a system-- you'll remember the graphite
structure that we looked at last time that
had all these p orbitals perpendicular to the plane
of the molecule.
And similarly, this is an unsaturated molecule
that has lots of pi bonding going on with the carbon
p orbitals that are perpendicular to the plane
of the blackboard here.
So it can be a quite flat molecule, but as you'll see
it can ruffle as well when it carries out
its biological function.
And so we'll go ahead and draw in the double bonds.
And this is the part where people sometimes get messed up
because one thing we don't want to do
is draw five bonds to a carbon atom.
OK?
And if you see a structure that's drawn that way,
you know that someone has made a mistake because they
violated the octet rule.
All right?
So let's draw in, starting here at the upper left,
we'll put in a double bond here, and here, and here.
And then this is where it gets interesting
because I could put a double bond here now or here
because this carbon's going to need a double bond.
I'm going to choose to put it here,
and then I'm going to use symmetry across the way
to put one there.
And having done that, I can now go here, here, here, here,
and-- so I didn't use symmetry across the way.
This is much easier to do and it's small.
OK.
So now you can see that these two nitrogens here
would have lone pairs that point into the center
of the porphyrin ligand and same across the way
by symmetry there.
And then when we remove these two hydrogens as H plus
and insert a metal ion, you'll see that the porphyrin is
actually behaving as a dianion.
When a metal ion and-- most typically,
we're going to see that the metal that
appears at the center of a porphyrin ligand
is an iron center.
And so the nitrogens provide four lone pairs
in the plane of the molecule that are directed at the metal
center.
So that's four out of the six positions for an octahedron
all in the same plane.
And because of the rigid delocalized structure
of the porphyrin ligand, what we find
is that a metal center that is in a porphyrin
is very difficult to take out of the porphyrin
because these lone pairs are forced at all times
to converge on the same point which is the metal ion.
OK.
You know that I enjoy giving lectures using shock.
But sometimes when the molecules are really big,
it's easier to use a computer to portray them quickly.
And that's what we're going to do today,
assuming my computer participates and cooperates
with me today.
And what I really want to do is to go through and show
you a tour of six really important metalloproteins.
And all of these, you'll see the heme
plays an important role, the iron in a porphyrin.
This unit together, when an iron is located inside
of a porphyrin, that is referred to as heme.
So you can have other metals in there,
and then it's not called a heme anymore,
but that would be very similar structurally.
OK.
So I'm going to take advantage of some really nice summaries
that have been put together on the protein data bank website.
So since the first crystal structure
was determined for a protein, the structural information
has been collected and put together in one site
so that researchers all over the world
can take advantage of this information
to advance science and medicine.
And since 2000, the protein data bank
has been collecting information about certain biomolecules
and putting out one new little short story or vignette
each month.
So you have their Molecule of the Month
portion of the protein data bank website.
So each month, you can go and look
and see which new molecule has been added
and learn more about it.
And I want to start out here with myoglobin.
OK.
And I'm going to give you this website information online
associated with today's notes.
So you're going to see that myoglobin was the first protein
structure.
There are many different ways to represent protein molecules.
Protein chains are composed of linear polimers
of the naturally occurring amino acids with polypeptide chains.
And they can sometimes be very, very large in length,
and then they fold up and make three-dimensional shapes.
And these are big ligands for metal ions.
And what you're going to see is that in many
of the most important proteins, the place where the reaction's
actually happened is that the metal center that's
embedded somewhere in the protein
chain as it has folded up around it to modulate function.
OK.
So this is a pretty small protein-- myoglobin is.
It's an oxygen storage protein.
So as you know, diatomic molecules like dioxygen
are important for life on Earth, and O2 in particular--
not only do we have hemoglobin that we'll talk about next,
but there are also oxygen storage molecules
like this myoglobin molecule.
And this was the first structure that was determined,
and that happened in 1960.
So we've been getting information
at the molecular level about how biomolecules work really
since 1960 using x-ray diffraction techniques.
So first, a worker in this area has
to obtain a large quantity of the protein in question,
get it purified, and then find conditions under which it will
grow single crystals so that you can impinge
upon it with an x-ray beam and then looked
at the intensities of the diffracted x-ray beams
and then work back to solve the crystal structure
and find out what arrangement of atoms in 3D space
could have given rise to that pattern of diffraction
intensities.
And that was first done for a protein in 1960.
You might find it interesting that this protein
was isolated from sperm whales.
OK?
Sperm whale muscles.
And in order to get a protein pure, as I said,
you need a lot of it.
And the muscles of sperm whales are very large indeed,
and so these workers were able to collect
large amounts of this red protein myoglobin
from sperm whale muscles in order
to finally get enough in pure form
to crystallize and solve the crystal structure.
And since this is involved in oxygen storage
and you know that whales and other marine mammals
can dive below the ocean surface for long periods of time,
they need to store lots of oxygen
so that they can use their muscles during the length
of a long dive.
And this protein is very abundant in muscles.
It gives meat its red color and so forth.
The color is coming from the heme units that
are embedded in the myoglobin.
And I'll step through a little bit of this,
but I would like to actually show
you some more of the features of this.
You'll see as you go through this website,
there are both static and interactive ways
to look at metalloproteins.
And sometimes the polypeptide chain
composed of the amino acids is just
represented here as sort of a tube,
so you can see the polymer has wrapped up.
And here they've chosen to represent
the heme unit as spheres to highlight it and accentuate it.
And in this first structure of myoglobin,
there was not an O2 molecule bound to the heme unit.
Instead, there was a water molecule
bound to the iron center of the heme unit.
And then down here, they rotate the structure perpendicular
so you can appreciate the square nature of the heme unit
together with when viewed edge on, its flat nature.
So that's the structure here.
And you can see how this myoglobin molecule,
this big protein polymer, has folded up
like a clam to grasp this heme unit that inside of it
will bind O2 and store it when oxygen comes to it.
And so later structures of myoglobin
have been carried out that do show you the position of the O2
molecule.
And in these two representations that we are given here,
we first see, once again, the heme unit
as spheres and the protein side chain just as tubes.
And then this representation in the bottom,
all the protein side chain atoms themselves
are represented as spheres.
And you can see that when that's the case,
you can tell that the atoms of the protein
ligand really fill up space very well.
And what they're showing you with this circle here
is the location beneath that side chain of the dioxygen
molecule inside there.
And so they're trying to give you
the idea that when O2 is on the heme unit inside the myoglobin,
the myoglobin protein matrix actually covers that up.
And so in order for the O2 molecule to get into the heme
and also to exit from the metalloprotein,
this thing has to be flexible enough
to open up and allow the dioxygen molecule
to exit from its chamber inside the metalloprotein.
OK.
Now next, I would like to go over to the site
where we're actually able to look at things interactively.
And you need to be able to enter the code
for the protein in question.
And so this is a structure of the myoglobin molecule
that was obtained at molecular or atomic resolution.
So one of the parameters that you'll
see when people discuss protein structures
is the resolution to which the data have permitted
the structure to be determined.
And the best quality structures, the ones
where we know most precisely where the atoms are,
are the ones that have very low resolution numbers.
In other words, this one, if you looked at the introductory web
page there so that the resolution was
at the level of one angstrom.
OK?
So we're talking on the order of carbon-carbon bond distances
so that you can actually see all the individual atoms quite
clearly.
And this has to do with the quality of the crystal
and how large was the angle at which you could collect spots
from the diffracted x-rays as they came off of the crystal.
And so this is nice.
This one requires Java.
That's why I was not able to use Athena today.
But actually, I come in here, and I
see that the Athena terminal is down anyway,
so this was a good choice as it turns out.
And this is nice because you can actually
zoom on these structures.
One thing you notice is that this was crystallized
with sulfate present in the medium,
so there was some buffer present.
And it had sulfate, and the sulfates crystallized together
with the protein chains.
And as we look at representations of proteins,
you'll appreciate that this representation
shows the polypeptide backbone as these ribbons.
And that emphasizes that when proteins fold and go
into a three-dimensional shape that they
need for their function, they can usually
do so either by making coils like this
that look like springs-- these are called helices.
Or they can just form random coils as you can see out here.
And oftentimes you have these helices
that are like long springy tubes that are then
connected at their termini by coils of the protein side
chain.
And then, of course, here embedded within this structure
is our heme unit.
And one thing if you look at this one pretty closely,
you'll be able to see that this heme is a little more
interesting, a little more complicated,
than the one that I drew on the board
here because the one I drew on the board
was assumed to have just hydrogens at each
of these carbon positions at the periphery of the molecule.
But when we look at the one that's actually
been found in myoglobin at atomic resolutions--
so you see this one is actually with the O2 molecule present.
For some reason, no bond drawn there, but that's OK.
We've talked a lot about molecular representations,
and we understand what's going on here.
It's that people have decided that we would represent
the atoms over here without any detail at all just
showing them as ribbons.
And then here we're going to look at the atom positions.
And you can see the five-membered ring
here, here, here, and here at each nitrogen
corner of the heme unit.
There's the iron center.
And then, notice that the substituents,
instead of being just hydrogen or organic,
there's a carbon here.
This looks like a methyl group perhaps.
And this one looks like an ethyl group or maybe a vinyl group
here if this is one of the etioporphyrin ligand types.
And then coming out here, we have CH2, CH2.
We have something that looks like it might
be a ketone residue since we have
a single oxygen on a carbon there,
or alternatively, it could be some other oxygenated residue.
But over here, you see that there's
a link to this five-membered ring of the heme.
You have a couple of methylenes and then a carboxylate residue.
And so when you investigate these structures,
these metal complexes that are embedded in the protein
usually are held in position, both by the way
the protein folds up around the heme unit,
but also because, in this case, the heme unit is connected
to residues like this carboxylic acid residue that
can hydrogen bond to specific residues on the protein side
chain.
So if we were to look at the atoms involved in the side
chain right over here that's next to this carboxylate
residue, this probably has some hydrogen bond acceptor
that is interacting with this carboxylate residue-- and same
over here-- to hold this heme unit in its desired position
or in its required position for function.
So please keep that in mind as you go ahead
and look at different structures in the database.
And now let's go to the 2003 description of hemoglobin.
This is rather nice.
OK.
So myoglobin was a pretty small protein having a single heme
unit.
And hemoglobin is much more interesting.
It actually has four big pieces that come together,
and it has four heme units in it.
OK.
And as you go through this website,
you'll find out about why blood is red versus blue.
It's actually red in the oxygenated form and blue
in the deoxygenated form.
And there are many crystal structures
of different hemoglobins and mutants of hemoglobins
in the database and both with and without the oxygen
molecules.
There's a discussion here of artificial blood.
And as you'll see what the premise is
here for the design of artificial blood
motivated by a desire to have blood
available for transfusions and so forth that would not
be contaminated, would be just synthetic--
would be just pure hemoglobin in fact.
But what happens is that without the protective casing
of the red blood cell, the four parts of the hemoglobin
molecule fall apart from each other,
and they don't do their function properly anymore.
And we'll learn more about the function in a moment.
So people have actually made mutants
wherein you make covalent bonds between the four
different subunits of the hemoglobin
so that they can't fall apart.
And that's one of the approaches to the synthesis
of artificial blood.
And then this is a rather nice little video
which comes from two different hemoglobin crystal structures.
If you imagine different crystal structures,
like crystal structure of hemoglobin when
it has O2 bound verses when it does not have O2 bound,
as snapshots of the molecule in motion,
then you can generate a little movie
like this one shown here from the experimental data
on the crystal structure.
And so the really remarkable thing here
is that-- see when the O2 molecule is bound
to the heme, then the protein itself,
this large unit that is comprised of four parts, as one
confirmation, one structure, and it changes quite a bit.
You see how much it is moving around when the dioxygen
molecule comes off of the heme.
And that is related very much to its function.
In fact, it turns out that, in hemoglobin,
when the deoxyhemoglobin arrives at a place in your body
where there is a lot of oxygen, the first O2 molecule binding
event is very difficult to achieve because it involves
a big change in the structure of the entire protein molecule.
But once that first O2 molecule has bound,
the whole protein molecule has changed its structure such
that the next three hemes take up their O2 molecules
rapidly in rapid fire succession after the first one has
done it.
So the heme goes into a place of high-oxygen concentration
and it rapidly loads up with four O2's.
And then it moves on.
And then when it gets to a location that needs oxygen,
the first one comes off, and then the next three fire
off in rapid succession because of the change in the protein
shape.
And so hemoglobin is, therefore, very
good at collecting four O2 molecules at a time
and then delivering them to where they're needed.
And this is just a beautiful example of the way protein
crystallography can teach us about mechanisms
of biomolecules.
OK.
And then also you can learn about disease mechanisms
in the data bank here because this
is from a different crystal structure where
a mutation has occurred in the protein side
chain of the hemoglobin.
So this is one hemoglobin molecule.
And it turns out that when that mutation is present,
unfortunately, it causes hemoglobin molecules
to aggregate and stick together and clump together like that.
And that phenomenon is associated with diseases
like sickle cell anemia.
OK?
So the structure of the protein is
changed when one residue of the amino acid side chain
is changed to a different amino acid.
And then these things all aggregate together
instead of forming nice disks as normal red blood cells do.
They stick together and form these different shapes
that are not good at functioning the way they're supposed to.
And then here is a close-up on where the action takes place
in the hemoglobin molecule.
And this, again, is from the two crystal structures
that we were talking about-- the one that
has the oxygen molecule bound to the iron of the hemoglobin
and the one that does not.
And one thing that you'll notice is
that when the O2 molecules is absent, this iron in yellow
represented here as this yellow sphere is sort of dipping
down on one side of the hemoglobin--
the heme plane toward the nitrogen of this histidine.
So this is part of the amino acid protein side chain.
And a histidine residue has this Lewis space group here that
is coordinated to the iron.
And so in that form, this is a five-coordinate metal center
with five ligands of square pyramidal geometry.
It's an octahedron missing one of those six ligands.
And then when the O2 ligand comes in and binds and becomes
the sixth ligand in the coordination
sphere of the iron, the iron responds to that
by moving up to the other side of the porphyrin plane,
and it draws with it the histidine ligand.
So the iron moving up pulls the histidine up.
And that structural change at the iron center
is then propagated throughout the amino acid side
chain to which this is connected and then,
ultimately, throughout the entire protein
to give you that huge conformational change that we
saw when O2 is bound versus when it's not.
So the coordination chemistry of the iron
here is really controlling the peptide confirmation
and the function of this protein.
OK.
So these bio molecules actually accumulate
quite a lot of the concepts that we've
talked about all semester.
And that phenomenon is going to continue
as I take you through a tour of a couple more
of these important molecules.
Now the first one was a small one
that we looked at, myoglobin, and I'm
going to continue that sort of progression
by now talking about another small protein.
This one may even remind you in its appearance of myoglobin.
But instead of serving to store O2,
like myoglobin, cytochrome c, which
has a single heme unit in it here,
serves as a shuttle for electrons.
OK?
The pathway that electrons take in the whole process
of respiration in organisms is really quite fascinating.
We require reducing agents.
We eat food.
Those are reducing agents.
And then we go ahead and burn that fuel
using the oxygen molecule.
And that's where we get our energy.
We don't burn the fuel literally by having us burst into flames,
but we do it in a controlled manner, in a stepwise manner.
And we take advantage of those steps
to carry out the processes of life.
And so there are proteins like these small cytochrome
c proteins that are developed expressly
for the purpose of moving electrons from one
place in the body to another.
So it's like a little electron shuttle protein.
And these are just two views of it.
And if you read this part of the website,
you'll also learn that this one has remained
virtually unchanged over eons.
It's a very ancient protein.
OK.
And this picture shows you cytochrome c protein
and where it picks up its electrons
and then where it goes to drop them off.
So here's an enormous protein relative
to cytochrome-- cytochrome c is the little teeny one here
with just a single heme unit.
OK?
Look at this thing.
This thing is-- I don't know what this looks like,
but it looks like a bizarre-shaped entity,
shall we say.
And this yellow stripe that goes across the page
here is actually a membrane.
So proteins are often classified as to whether they
are membrane proteins-- meaning that they don't move around.
But they're embedded or fixed in a membrane
with one part of their molecule on one side of the membrane
and the other part of the molecule
up on the other side of the membrane
and then the part of the molecule
that's actually located within the membrane, and then
non-membrane proteins like cytochrome c
that are actually mobile and can move about within a cell.
And cytochrome c goes over to this large protein
which has lots of different cofactors shown here
in red which incidentally are hemes themselves.
And so this molecule-- the big protein
here embedded in the matrix is called cytochrome bc1.
And it is a protein involved in this process of respiration.
It is producing electrons.
And cytochrome c comes over here, and as you can see,
it fits really well into this spot right here
on cytochrome bc1.
And that's a feature of protein-protein interactions
that they often contain residues on their surface
that are hydrogen bonding residues, for example,
that make their surfaces complimentary.
And it means that when cytochrome c comes in
into cytochrome bc1, it actually locks in in one particular way.
And this complex between cytochrome c and cytochrome bc1
has been crystallized.
And the crystal structure of it's in the database,
and that's where we get this representation shown here.
So you can actually go through-- if you're a crystallographer--
and look at all the different complimentary interactions that
holds cytochrome c into place on cytochrome bc1
when it docks there.
And what I'm going to tell you in a moment
is that as electrons are originating
within cytochrome bc1 here, they have
a pathway through which they move
and they get up into this heme unit.
And then when cytochrome c docs, the heme unit within it
can get close enough to this heme unit
that their wave functions can overlap,
and the electron can tunnel right
across into the cytochrome c which accepts it.
And then it goes off, and it's looking for this protein
next which has also been crystallized and characterized
in the database.
And we'll talk about it next.
This is called cytochrome C oxidase
because it oxidizes the reduced form of cytochrome c.
And let me just say that probably one
thing we won't have on the final will
be working the molecular orbital diagram of this molecule.
As you can see, we've got up to a position
here where the number of orbitals
is kind of prohibitive to do that sort of thing.
Now you can understand why the computational chemists have
quite a big challenge as they try
to understand at a molecular level all of the processes
of life and, really, a long way from doing that actually.
When people attempt to do that these days,
they're usually making some big approximations with the protein
side chain because that's the electronically uninteresting
part of the system.
Where the metals are is where everything is happening.
Let's go down here and see what else we can learn.
OK.
Here's a close-up with a different representation
of when cytochrome c molecule docs on
to the cytochrome bc1 complex.
And here we've got the polypeptide chain of cytochrome
c represented as these pink tubes, and then
as these yellow tubes down here, this little part
of the cytochrome bc1 molecule that is reaching up
to interact with cytochrome c.
And here's the heme unit of cytochrome bc1
that is right at the surface of that protein
so that it can overlap it's wave function with the heme unit
of cytochrome c to permit an electron to transfer and reduce
cytochrome c.
OK.
And so now we'll go on to cytochrome c oxidase.
OK.
So in reading about cytochrome c oxidase,
you're going to learn more about oxygen.
And this piece of today's story, together
with the one that I'm going to go
to next, which will be with respect to photosystem
one and photosystem two, are sort of the two ends
of the chain of respiration.
Because with photosynthesis, that we'll talk about next,
we use light energy to create O2.
And most organisms on the planet have these cytochrome so
that they can use O2.
In fact, what they do is they take
electrons that are derived from food
and get energy by combining them with oxygen,
reducing them-- reducing the oxygen molecule-- to water,
and at the same time pushing protons
across a membrane which stores energy
that can be used for other processes like building up ATP.
And so, the cytochrome c oxidase is getting its electrons
from cytochrome c and it's using those electrons
to reduce the O2 molecule.
And for that reason, cytochrome c oxidase
should have somewhere in it a place for the dioxygen
molecule to bind.
Just like is the case for hemoglobin.
We found out where oxygen binds in hemoglobin.
And notice that as you go through they'll
make an analogy here to charging of a battery
or actually of a capacitor as you're reducing the O2
molecules with these electrons coming in from the cytochrome c
shuttle, and making water and pushing protons
across a membrane that is being likened to charging a battery
or charging a capacitor.
And this is a membrane-bound protein
just like the bc1 complexes.
And here's a nice graphic that shows a number
of the important cofactors.
A cofactor is just something that's
an integral part of a protein but isn't
part of the amino acid backbone of the polypeptide chain.
And usually it's something like a heme,
but here not only do we have hemes, but here's a heme that
is thought to be involved in the electron transport
chain within the cytochrome C oxidase molecule.
And over here is a heme that is thought
to be important in binding the O2 molecule.
And also this one has copper.
So these 3D transition elements are turning out
to be pretty important in biology.
The iron is frequently the site for the binding
of a diatomic molecule, but look at this.
This structure that's in the Cambridge database here,
its PDB entry 1OCO, actually has a carbon monoxide
ligand bonded to the iron in the active site
where O2 is supposed to bind when this enzyme functions.
So this is a poisoned form of the enzyme.
CO comes in and binds and shuts this enzyme down,
and that's what they were able to purify and crystallize
and get the 3D structure of.
And then here you have a heme iron
which interacts with the carbon end of carbon monoxide.
And then positioned over here, and also ligated by residues
from the protein side chain, is copper,
referred to as copper b.
So this is a copper ion.
And that means that when a diatomic molecule
goes in and binds to the heme at one end,
it's other end is binding simultaneously to copper b.
And that diatomic molecule is serving
as a bridge between two metal ions-- the iron
heme and the copper b up here.
And then also up here is a copper
a site, where you have a pair of coppers.
And this site is referred to and thought
to be the port of entry of the O2 molecule
into cytochrome c oxidase.
That O2 somehow comes in and may bind here first, but then
go over here and electrons are coming
in through this other heme unit into the one that binds the O2
and ends up reducing it to generate water.
So that is a really pretty picture
of how complicated the machinery of an enzyme
can be to take advantage of all this lovely transition element
chemistry and redox chemistry to carry out life function.
And also-- let's see-- OK, so what they're doing here
is analyzing this.
This cytochrome c oxidase is composed
of a number of different protein chains
that are all packed together into the overall complex,
and they're coloring each of these residues a little
differently here.
And then when you get down to the bottom of this page,
they're comparing a subunit of cytochrome c oxidase
to an actual cytochrome c oxidase that
is found in bacteria molecules.
Bacteria organisms.
So bacteria have their own cytochrome
c oxidases and this looks like the central core
of our cytochrome c oxidases.
And the idea is that mitochondria in cells
may, at some point way, way back in evolution,
have been the result of bacterial invaders into cells.
And then these bacteria became integral parts of ourselves,
and we added new proteins on and elaborated
to change the function as we deemed necessary
through evolution.
But these ways of comparing structures
of simpler or ancient proteins to ones that are more modern
is an interesting way to learn about how life
has evolved on this planet.
OK, and-- so cytochrome c oxidase
is a pretty remarkable protein.
And I want to see if I can get this thing up interactively
because the structure is quite impressive.
And I'm using this carbon monoxide substituted variant.
When these structures have many thousands of atoms,
sometimes these things take a little while to load.
So hopefully this won't take too long.
The viewer that-- there are actually several viewers
that you can choose from on this protein data bank web page,
and they possess features that allow
you to turn on or turn off different parts
of the molecule.
You can subtract away the cofactors,
or subtract away some of the loops or the helices,
and that allows you to explore the structure in quite
some detail.
Now, each of these are different protein residues,
different residues of this enormous protein.
So let's come down here, zoom in a little bit.
OK, if I notice that-- there I can subtract away
the coils that hold together the various loops, OK?
Or you can take away, in fact, all of those things.
And notice the cofactors themselves are these heme units
and they have some interesting and complicated side chains.
But they're the same sort of heme units
in general that we see in myoglobin or in cytochrome c.
OK?
Let's see .
Actually-- there are orientations
of this molecule that you can access
that shows you how this thing fits nicely into a membrane.
This is one of them.
You see all these different helices that
are aligned with one another.
This is the part of the cytochrome c oxidase
that resides in the membrane.
And all of these residues are lipophilic,
so they interact with the non-polar interior
of the membrane very well allowing this protein
to just stay in as part of the membrane.
And then these loops that extend on one side of the membrane
or onto the other contain polar residues
that would prefer to interact with water
or with charged things in solution.
And so that's an important aspect of the way
a membrane protein like this is the structured.
If I could just take away the loops here,
the coil, that becomes quite clear.
So now, with the few minutes we have left,
I'm going to go ahead and talk about photosystem I
and II at the other end of the chain of respiration
where organisms are actually-- you know,
they realize that eventually you would run out
of all the food on the planet and everything would die.
And so they learned to absorb light
and to use light energy to carry out processes of life
instead of just using the energy that you
get when you add electrons to water, to two oxygen
and make water.
And so let's go look first at photosystem I.
Photosystems I and II are different parts
of the photosynthetic pathway and of the electron utilization
chain, electron transfer chain.
And what you see is that photosystem I and II are both
going to be membrane proteins.
These, incidentally, are usually much harder
to obtain in large quantities and much harder to crystallize,
and their structures much harder to characterize.
So there are a lot of important membrane proteins
whose structures are not very well known yet.
In photosystem I it's a trimer.
There's one piece right here, it's shaped like a big disk.
Here's another piece and here's another piece.
And then if you flip it by 90 degrees
to look at it edge-on you can see here
it is sitting in the membrane.
And these have colorful cofactors.
These now have porphyrins, many porphyrins,
that contain instead of iron, contain magnesium.
And these are the chlorophylls that are present in here
as light gathering entities.
And then-- OK.
OK, with this picture I can tell you
quite a bit about photosystem I. Here, you can see,
is the part of the molecule that is embedded in the membrane.
And what we have is the ability to extract electrons
from a molecule that is hard to oxidize.
OK, so in photosystem II you'll see
that the source of electrons is water.
And so photosystem II is capable of pulling electrons out
of water, generating dioxygen, the most important
photosynthetic reaction on our planet.
In the case of photosystem I, the source of the electrons,
instead of being water, is a little protein
called plastocyanin.
So plastocyanin comes up here and it is oxidized.
And it's a little bit like the LED
we talked about last time, because what
happens is there's a pair of heme units here,
they're not hemes of chlorophylls, the special pair,
that when light energy is absorbed and excitation occurs,
it sends an electron to high energy.
And normally, after such an absorption of light occurs,
that electron would just drop back down
and the molecule would go back to its ground state.
But what this molecule has been built to do
is to take that high energy electron
and descend it through a series of redox active molecules.
And it actually goes all the way through here,
and these are little iron four s four cubes.
So these are beautiful little inorganic molecules, Fe4 S4
cubes.
The electron pathway goes through these redox
active units and jumps from one of these Fe S4 cubes
to another, and finally jumps out to a protein that
docks up here to accept it, which is a ferredoxin protein.
So after light comes in and you get a high energy electron,
you get a hole, the hole is filled through oxidation
in the case of photosystem I and plastocyanin
in the case of photosystem II of water, and so the chain goes.
Now, having run out of time here,
I will talk about photosystem II at the beginning of next hour.