So the big issue that I was trying
to take on yesterday,
and this is of really fundamental
importance to biology,
is that you saw from that molecular
composition of cells 80% water.
Of the rest of it about 50% of
what's there by mass is protein.
Proteins do most of the really
interesting stuff in the cell.
They're the ones that are able to
catalyze specific chemical reactions
with all this amazing chemistry
that's needed for life to take place
at physiological conditions.
They are structural components of
the cells.  They are all kinds of
amazing machines.
I showed you the little flagellar
motor that turns it,
but that's just one of many,
many nano machines that are
necessary for life.
They have exquisite specificity
when you get sick and you get an
immune response.
You develop antibodies and other
cells that are able to recognize
exactly some piece of that virus or
bacterium that has infected you and
mount an immune response.
But all of the things that are doing
that are proteins.
And the sort of, most of you I
think know that,
as we've sort of said that amino
acids are just a chain,
one amino acid joined to another
amino acid to another amino
acid and so on.
And so the backbone,
that peptide bond that I showed the
other day is absolutely regular
piece of backbone.
And what gives the amino acids
their character is the side chain
that hangs off.
And you'll have different side
chains hanging off depending on what
the amino acid is.
And you will not have to memorize
all of those structures.
But the important thing is that
these various amino acids fit into
chemical categories that give them
properties.  They either have a plus
charge and a negative charge,
they're hydrophobic, they don't like
to go with water,
they are polar, they cannot interact
with water and so on.
And it's clear from a couple of
your comments,
some of you are why are we going
through all of this?
Well, the reason we're going through
all of this is all amino acids look
like this.  It doesn't matter.
They're going to be an enzyme,
a part of a motor, a structural part
of yourselves.
They all consist of the same
backbone made up of those 20 amino
acids.  And what gives these,
makes the proteins so important is
the ultimate 3-dimensional structure.
I'm not sure what this sound is.
OK.  Let's try standing back here.
What gives all of these proteins
their individual character is how
this chain of amino acids,
you could just think of them like
this, folds up into some
3-dimensional structure that
ultimately is able to do the
biological function that we're
trying to understand.
And one of the real holy grails
still in biology is how to look at
the sequence of amino acids that
constitute a protein and figure out
what the 3-dimensional
structure is.
It's one of the holy grails that
hasn't been solved.
One of you may have a key insight
that will solve this.
If we could do that it would really
be a huge advance,
because what you can get out of the
genome sequences is you can read the
sequence of every gene and you can
predict the sequence of amino acids
in the protein.
But all it tells you is the linear
sequence of the amino acids.
It doesn't tell you what the
3-dimensional structure is.
And how an amino acid gets from the
sort of floppy chain linear
structure to the 3-dimensional thing
is complicated.
And you have to understand several
kinds of forces.
And so I introduced a few terms.
When we think about protein
structure, the primary structure,
that's just the linear sequence --
-- of amino acids.
So valine followed by a tryptophan,
followed by a proline, followed a
threonine, whatever it would be.
That doesn't tell you very much.
Then the first key part of
understanding how proteins get to a
3-dimensional structure was the
discovery of what's termed
secondary structure.
And these are the thing I introduced
to you to the other day.
There are two important ones.
An alpha helix and a beta sheet.
And this is a propensity of a
certain string of amino acids in
this linear sequence to adopt one of
two very common protein structures.
And the important thing about these
elements, the alpha helices and the
beta sheets is they are not
dependent on the side chain.
So they are not.
They are instead dependent
on hydrogen bonds --
-- between N-H and the carbon double
bond oxygen in the backbone.
And that was how Linus Pauling
figured out originally the alpha
helix.  He decided to ignore all the
side chains.  And he worked out that
you could arrange the backbone of a
protein, the peptide bonds into
these repeating structures that
would account for the reflections
he'd seen.  When we get to talking
about how Watson and Crick worked
out the structure,
that's how they started out, too.
They decided to ignore,
if you will, the side chains,
which are the As and Gs and Cs and
Ts, which turned out to be not a
productive way to go after the
structure of DNA.
But, in any case,
that was part of what Linus Pauling
did in working these out.
And so those little movies I showed
you, this is an alpha helix.
Now, what's been done in this
picture is all the side chains have
been taken off.
And so you can look at this in your
textbook, you'll see pictures,
but these hydrogen bonds are --
The amino acid is just in this helix.
It's coiling around.
And at regular intervals there's
the opportunity for forming a
hydrogen bond.
And we can, with some success but
certainly not certainty,
predict that a particular sequence
of amino acids is going to form an
alpha helix.  And part of what
that's based on is there are some
amino acids that don't fit easily
into an alpha helix,
so they'll disrupt one if it ever
tried to form.
So that's one of the elements of
protein structure.
So what you might get from this is
the idea that somewhere along here
this little piece of the linear
sequence is apt to be an alpha helix.
And you can represent that as this
little sort of coil that you see in
these 3-dimensional structures.
The other one, which is the beta
sheet, now that involves
interactions between two pieces of,
two stretches of amino acids.  Maybe
there was a loop in between.
And then you can get interactions
between them.  And that,
oops.  Let me just go, there's the
beta sheet interaction.
Now, those are represented as
arrows.  You know,
it takes two of them to go.
So you've got to have, to represent
a beta sheet in a 3-dimensional
structure you have to have two of
those broad arrows.
And there was a question why were
there arrows on them?
Well, one of the things,
I think you can see if you look at
those backbones,
is that both nucleic acid and
protein backbones,
there's a polarity.
If you start in this direction,
the amino terminus, it's got a
particular direction.
It's not symmetric.  If you come
back the other way you find carboxyl,
amino, the alpha carbon.
And you'll find it in the opposite
order if you come back the other way.
So there's an inherent polarity.
The arrows aren't represented on
here, but they are when you look at
it in 3-dimensions.
And you can either form beta sheets
where the two strands have the same
polarity or, if in a case like that
where they loop back,
then of course if this one was
pointing in this direction as it
goes through the loop then the
opposite strand will be pointing in
the other polarity,
one going this way and one going
that way.  So this part
is sort of helpful.
You can make guesses that maybe this
part has a tendency over here to
form a beta sheet,
but you still haven't gotten very
far towards understanding how you
get to the 3-dimensional structure.
And just by putting on and
superimposing some amino acids onto
that alpha helix then you can see
what happens, that if you form an
alpha helix what happens is all the
side chains stick out.
And now I think you can see,
those of you who are engineers
anyway, if you wanted to build
something you have a cylinder and
you can stick amino acids out that
have particular chemical
characteristics.
And depending on the
characteristics of those amino acids,
whether they have charges on them or
if they hate water or something,
that will influence what happens to
that component of the protein
structure when it gets into a
3-dimensional thing.
And, as I think I showed you the
other day, when we caught it looking
down the end on this particular
example, here are a couple of
aromatic amino acids right here,
they're on the same side of the
helix and they would hate water.
Whereas, some of the other amino
acids up here are ones that have
charges so those would love water.
So what this would look like is a
cylinder part of which hated water
and part of which loved water.
And you might guess it folded up in
3-dimensional space.
The part that hated water might
fold towards the inside
of the protein.
And the part of the cylinder that
loved water would face to the
outside.  So that's sort of the
underlying principle.
So the rest of the other forces
that we had to understand in order
to get to what's called the tertiary
structure, this is the full 3D
structure, which we can now
determine by a variety of methods.
X-ray crystallography of proteins
is probably the most common.
The NMR, for example,
can be used to derive a
3-dimensional structure as well.
And the other forces then that go
into this are ionic forces.
Someone seemed confused by this,
but if you have a plus charge on
this part of an amino acid and a
minus charge here,
if in 3-dimensional space the plus
charge got somewhere near the minus
charge then that would
form an ionic bond.
And I think most of you know enough
electricity and magnetism that
wouldn't surprise you that those two
would be attracted.
The one that I think that has been
harder to understand is van der
Waals interactions that we talked
about the other day,
which is tricky in the sense that
for this course you don't
particularly really need to
understand the underlying
chemistry.
But the principal of it is that if
you have a nonpolar bond,
one that hasn't got any particular
attraction to it,
gets very, very close to another one,
then the transient fluctuations in
one induce something in the other
one that makes them stick together.
And the whole point about this is
if you get two molecular surfaces
that are very,
very close together,
about, you know, many two times the
length of a covalent bond or
something, then you can generate
very powerful forces.
Because even though each individual
interaction is weak,
about a quarter or a third of a
hydrogen bond,
summing them up can make them very,
very strong.  And so that's another
kind of force that's important when
a linear molecule is trying to
figure out how in space it's going
to fold up.  The point of the gecko
thing was it's only relatively
recently been discovered that the
reason those lizards can stick to
walls is they have sort of
incredible split ends.
I noticed a couple of you came to
Bob Full's talk the other day and
you got to hear the full treatment.
But because the hairs on their feet
are so split they're very fine and
the molecules are able to make very
close interactions,
van der Waals interactions with the
surface.  And that's what's holding
the gecko to the wall.
And there are just so many of them
that it can support a whole gecko.
And that's what could be the basis
of, he said to me,
a $30 to $50 billion adhesive
industry, a self-cleaning dry
adhesive.  And it's not something
magic only the gecko hair will do.
You can design synthetic molecules
that have the same property and are
able to make these millions of van
der Waals interactions.
So that's two of the other things.
And the final thing, which isn't
really a force but goes into this,
is this hydrophobic effect.
And that is that if we have things,
amino acids such as valine or
something that doesn't like to mix
with water, then when the protein
folds up, the things that don't like
to interact with water will kind of
go together just the way if you put
a lot of oil in the water it will
sort of pull together.
Because any time you have something
that gets stuck in water,
it disrupts hydrogen bonds and
that's energetically unfavorable.
So the things that hate water will
tend to lump together.
And you're all used to seeing
little drops of oil and stuff
floating around.
And let me switch over to this
other thing now.
So this was just showing you one of
these protein chains that's folded
up into a 3-dimensional structure.
This happens to be something with
an enzymatic activity.
But the important thing for right
now is what's been colored in here
are the amino acids that if you look
back on the list of amino acids and
what categories are,
you'd see some of them are said to
have hydrophobic side chains.
You can see quite strikingly how
the amino acids in the interior part
of this protein have clustered
together.  They don't like to
interact with water.
They interact very well with each
other.  Just like you can mix butter
and oil, they mix together
very well.
And so that is another factor that
contributes to the 3-dimensional
structure of these proteins.
So understanding what proteins are
all about means ultimately
understanding their 3-dimensional
structure.  And,
as I say, a big unsolved problem
right at the moment is how do you
get from a linear chain of amino
acids to one of these 3-dimensional
structures?  And you can imagine
with 20 different side chains
there's an unbelievable number of
combinations that you can make.
Yet almost every protein in nature
has one unique or one or two or
something confirmations that takes
out, out of all the kinds of things
that you could do.
And it's this combination of forces
that does that.
You know, let me just go back for
one second.  So the final thing that
ones talks about when you're talking
about proteins are quaternary
structure.
And what that means is when you have
more than one polypeptide chain,
so if we have two different proteins
that interact,
this is protein number one and this
is protein number two,
then there has to be some sort of
interaction between each of these
three dimensional structures in
order for the proteins
to stick together.
Something like that flagellar motor
that let's the bacteria swim,
has many, many parts, all of which
have to fit together just the same
way all the different parts of an
engine have to fit together.
Now this next little movie is just
a dimer.  It's actually a
heterodimer so it's made of two
proteins.  They're different but
they've come together and they're
interaction.  So what you will first
see is the 3-dimensional structure
of each protein showing the alpha
helices, the beta sheets,
and nothing else is shown.
The side chains aren't shown.
The molecular surfaces aren't shown.
You can just see the backbone.
You'll see alpha helix a turn, some
beta sheets, just the kind of stuff
you were seeing the other day.
But you'll see that the two
proteins are together.
And this is actually a movie made
by Tom Schwartz who's a
crystallogram who just started on
our facility this fall in the
biology department.
It's one of the proteins he studied.
And then after that he rotates it
around so you can see it.
After that he then puts on the side
chains and then traces the surface.
So this is what they call the van
der Waals surface.
So this is what the protein would
actually look like.
And what I think you'll see from
this is how incredibly well the
proteins fit together.
The theme I'll probably keep saying
all the way through the course is
biology works from fitting shapes.
And things have to work incredibly
well, and that's also why these van
der Waals forces become
so important.
Because evolution has ended up
making things that just go together
just like a hand in a perfectly fit
glove.  That's the way most of these
interactions are.
So watch this little movie.
So the light blue is one of the
proteins.  There's an alpha helix.
There are a lot of alpha helices in
this one.  And the purple one is the
other protein.
And you can see that in between
them there's an interface.
And so those must be interacting.
But when he superimposes now all the
amino acids in the surface,
now what he's going to do, he's
going to pull those apart so you can
see where they were interacting.
Do you get the idea now of how
beautifully these things have folded
up in 3-dimensional space in
positions so that they can fit
together and work together as a
machine?  Just the same way if you
were building a machine and you
needed to have two parts that you
had to join together you've got a
tool thing so that the surfaces go
exactly together.
That's what nature does.
That's also why I'm making such a
deal out of this 3-dimensioanl
structure of proteins and how it got
there.  I could just say it gets
there by magic,
but it doesn't.  It's determined by
this set of forces.
And one of the things we cannot do
at this point is predict.
Here's a linear sequence of amino
acids.  Here's the 3D structure.
That would be a huge advance in
biology if one of you guys could
figure out how to do that
during your career.
OK.  So I just want to reiterate
some of the things that proteins do
because we'll be talking about them
as we go along.
One thing they do,
they act as enzymes which are
catalysts for biological reactions
that take place under physiological
conditions.  And we'll give you a
lot of examples of those enzymes
starting very soon.
They play structural roles.
Our hair, our fingernails are made
of protein.  The hairs on the
gecko's feet are made of keratin
which is the same stuff our hair is
made of, except they basically got a
whole lot of split ends.
They're finer hairs to begin with
and a lot of split ends.
And that's what makes these very,
very fine things that can make van
der Waals interactions
with surfaces.
They play roles in specificity.
For example, I mentioned the
antibodies.  And we'll talk about
the immune response in some detail
at the end of the course.
And one of the really magic things
that we've come to understand in
biology recently is how it is that
your body has this immune system
that's able to recognize literally
any molecule, any molecule.
It doesn't matter whether it is
existed or you and your PhD thesis
in chemistry synthesize something
the world has never seen before,
your immune system can create an
antibody or something that will very,
very specifically recognize that
particular shape in just the same
sort of way that you saw the shape
on that movie.
And you might think you'd need to
code a zillion millions of DNA in
order to do that.
But there's a trick using
combinatorial functions and mutation
that lets your body do that.
Another example, which I was
showing you, that can do all sorts
of little motors and machines,
I showed you the bacteria swimming
around.  These are just E.
coli.  And you cannot see the
flagellar motors,
but you can see them buzzing around
just under a cover slip.
Some of them are stuck to the cover
slip.  There we go.
In this one, which was taken by
Howard Burge who is a professor at
Harvard, I just took this off his
website, you can see the bacteria
swimming by having these flagella
which are basically like sort of
propellers more or less that they
turn.  Here's one where he used the
strobe so you can get a little bit
better view of it.
And I showed you this picture in
the first lecture.
So that's the machine,
but every single part of that
machine is made of a protein that's
got a very certain 3-dimensional
space.  And we're going to start
talking about energetics,
how does this cell get energy?
And one of the things you might
wonder is if you were to design such
a nano machine how would you power
it?  They exist.
I mean it's here.
But that's why in part I'm going to
start talking about energy and how
cells make energy,
because this is one of the things
they have to do.
And that was, as I said,
was an average electron micrograph
of a lot of those motors.
So you can see that although,
you know, that's the textbook thing,
the actual thing is pretty much the
same shape.  This is not at a
resolution where you can make out
the individual proteins that put it
together, but some of those are
starting to be known in
3-dimensional detail.
And I thought you might enjoy
seeing this just to convince you
it's a motor.  In this thing,
what Howard Burge did was he stuck
the propeller,
if you will, the flagellar to a
cover slip using an antibody.
And then he let them do their thing.
And normally they would be turning
the propeller and swimming,
but if the propeller is attached the
same thing would happen if you held
onto the propeller of a boat and
turned on the motor the boat would
start twirling around.
And what you're seeing here is
bacterial that are twirling around
because their flagellar
are stuck on.
And those of you who are observant
will notice even that they change
direction.  And that's part of the
system that bacteria use so they can
swim towards a food source or away
from another one.
OK.  Here's just something to let
you think about it.
If anybody can figure this out send
me an email.  Here's something else.
The phenomenon I'm going to show
you is due to a protein made by a
soil bacterium called Pseudomonas
syringae.  You don't
need to know that.
It associated with plants.
And what you're going to see is a
little movie made by a couple of
post-docs in my lab where they took
pure water.  And if it's pure water
you can cool it below freezing.
You can get it down to, I don't
know, minus eight degrees centigrade
and it still will be a liquid,
even though you know water freezes
at zero degrees centigrade.
And what it has to do in order to
turn into ice,
somewhere you have to nucleate the
formation of an ice crystal.
And once it goes,
going.  So, anyway,
what you're going to see is some
super- cooled water they've made.
You can see there is zero degrees
there.  And this is Metchitaga,
one of the post-docs in my lab.
That's the super-cooled water.
She's taking a little bit of
culture of this Pseudomonas syringae,
and she's just going to put it in,
give a little tiny squirt, a few
micro-liters into that water.
Now it's going all cloudy.
And now you might wonder what's
happening there.
But, as you'll discovery,
what happened is that what was
liquid water is now ice.
That is due to one protein that this
bacterium makes and displays on its
surface.  And here's a controlled
experiment.  This is putting in a
little bit of rhizobium meliloti,
another soil organism, and the same
amount of bacteria.
It didn't happen.
OK.  So that's due to a protein
that was on the surface of that
bacterium.  Anybody have any idea
what that could do?
Send me an email.  OK.
There's one last class of
[UNINTELLIGIBLE] macromolecule.
Those are lipids.
These are a little different in the
sense that this is not know a long
chain made by joining together
subunits as you see with the
proteins and nucleic acids,
but putting together the parts
necessary to make a lipid involve
the same principle,
that you end up splitting out water
molecules.  That's a theme you've
heard over and over again.
And if we take three long chain,
three fatty acids, some number of
carbons --
Some number of carbons.
Just some arbitrary number here.
And then we take a three carbon
compound that has three hydroxyl
groups.  Now, this is not a
carbohydrate because you'll notice
there's not a double bond oxygen as
you saw in the carbohydrates.
It's actually an alcohol that's
known as glycerol.
And if we split out water like this
what you get is a fat,
something you're familiar with from
beef fat.  Or if you get something
like olive oil,
you've heard the term unsaturated
fats.
Maybe you'll recall from the second
lecture that if we had a single
covalent bond,
or if we had a double or a triple
bond that was called an unsaturated
bond.  So if you have an unsaturated
bond in here somewhere then you end
up with an unsaturated fat.
And most of you know probably
something like beef fat is solid.
If you put it in a refrigerator
something like peanut oil
will stay liquid.
And that's because if you have just
saturated side chains from this then
they pack together very tightly and
they will form a solid.
If you put a double bond in then
there's a kink in the backbone and
it's hard for these things to pack
together.  And that's why they're
called unsaturated fats.
Now, there's a very particular kind
of lipid that's of unbelievable
importance in biology known
as a phospholipid.
And the reason that's so important
is that that is the boundary that
determines the outside of a cell.
So every cell, every organism
either is a single cell or is made
up of multiple cells.
And, as I said in the first lecture,
that one of the secrets to life is
having a boundary that goes around
your insides it separates your
insides from all the rest
of the universe.
And the way these membranes,
as they're called, are made of is
what's known as a phospholipid
bilayer.  And it's the same
principle as before.
It uses a glycerol, except that one
of the fatty acids is replaced by a
phosphate group that will have some
kind decoration added onto it.
And the other will have fatty acids
at the other two positions.
Now, you'll notice by splitting out
water here, the kind of bond that we
have created, the chemical name of
this is an ester bond.
And if we wanted to break it we
could add water back across it.
So what's important about this
molecule is this part of the
molecule, if you will,
is water-loving because the very
polar bonds here,
the oxygen here would have a
negative charge under physiological
conditions.
And this part is,
if you will, water-hating.
So phospholipids are often
represented in the following way
where this is the water-loving and
then this would be the water-hating
part here.
And so if you take phospholipids and
you just try and disperse them in
water, they spontaneously
self-assemble into structures that
bring the water-loving parts
together and the water-hating parts
together.  And by so doing this they
form what's known as a
phospholipid bilayer.
And that's what this membrane is
made of.  Membrane of bacterial cell,
membrane of our cells virtually the
same thing.  It has the property
that is not permeable to very much.
Water can get across a very limited
number of other chemical compounds,
but most things cannot.
And so, by having this membrane,
what the cell is able to do then is
control who comes in and who comes
out.  And the way it does that is it
has to put particular importers or
exporters imbedded in the membrane
that can carry out those functions.
Because, as you would guess, any
system would have to bring stuff in,
get rid of waste, you'd have to be
able to go back and forth.
The things that do all those
transports across the membrane are,
what kind of molecule do you think
it likely to be?
If nature was going to design
something that was a pump to get
something in or something that would
get something out,
any idea what kind of molecule?
Take a guess given what I've said
so far.  Protein.
Yeah.  Absolutely.
And let me just sort of show you a
couple little pictures here.
So here's a representation of this
phospholipid bilayer.
This is pretty standard stuff.
This is what you'd put on a
blackboard.  Here's in gray now the
phospholipid.  And here's one of
these proteins,
a picture of one of these proteins
that functions to get things across
the membrane.  And hopefully what
you can see now is that it's made up
of a whole lot of alpha helices,
and they pack together to give sort
of a cylinder made up of different
alpha helices that weave in out like
this.  And then by this sort of
trick the protein is able to create
a channel that runs up and down the
middle of this protein that's
imbedded in the membrane.
And then, depending on the
characteristics that channel,
it can either be used to bring stuff
in or get rid of it.
There is a more fanciful depiction
of it.  This is not reality,
but there you are with the
water-loving parts.
Here are the fatty acids going in.
And this is supposed to be one of
these membrane proteins.
Now, this next movie is trying to
pretend here that it's looking at
one of these membrane proteins
colored here in red as it
spans the membrane.
So here's looking from the membrane
surface on.  And now it's going to
dive into this thing as it crossed
the membrane.  And basically what
this movie is letting you do is feel
like if you were the molecule that's
being transported across the
membrane you'd see how you'd go
right down through a channel in the
middle of the protein.
So that's one of the underlying
principals then,
is that you have a phospholipid
boundary that's critical for life.
But then to have everything else
that needs to happen the cell makes
a series of proteins that function
either to bring stuff in or to bring
it out.  Or in the case of something
like the flagellar motor we talked
about it has to imbed a part of the
machinery right in the membrane.
And one last picture I just want to
show you.
Usually, even on that movie,
you tend to see the cell represented
something like this with a membrane
and every once in a while there's a
protein.  This is a cartoon but it
is much closer to a to-scale drawing.
This is an E.
coli cell.  Now,
they have an extra membrane that we
won't worry about right for the
moment.  But right there,
this little piece that we can see
little bits of, is the
cell's membrane.
And what this picture is showing is
that this membrane is just
absolutely studded with membrane
proteins that are going to carry out
various functions.
And here actually we're seeing that
motor which is imbedded both in the
inner and outer membrane.
And there's the motor going off.
But a couple of things maybe you
can take home from this is there are
a lot of proteins stuck in those
membranes that control what goes in
and out.  You also get a sense in
here of how crowded
the cytoplasm is.
The proteins are really at amazingly
high concentrations when they're
inside the cytoplasm.
OK.  So that's sort of a quick
survey.  It's nothing more that a
really superficial introduction to
the four classes of biomolecules.
But to go any farther we're going
to have to think a little bit now
about of the characteristics
of living cells.
I don't know if any of you know if
any of you know what this is,
but this is bakers yeast.  If you
were making bread you know you put
some yeast in it and it divides and
it gives off carbon dioxide as a
waste product and makes the bread
rise.  And what's happened in that
little movie you just saw were two
cells dividing to give four,
and four dividing to get eight,
and I don't know what we're up to
here, but you can see a cell grow.
That's sped up.
It takes probably something closer
to an hour for a cell division to
take place.  But this is the kind of
thing that microorganisms do when
they grow, is you can start with a
single cell and it will make two
cells that are identical to itself
and those will make four.
And what happens when we start out
as a single cell,
we start out initially like this.
And we make cells that are identical
at the beginning.
And those are the famous embryonic
stem cells, because at this point
they can become any cell in your
body.  And if you're a yeast it
doesn't matter.
Everything you make is the same.
If it's a human, once you start
dividing at some point cells are
going to have to start making
decisions and the progeny will have
to start to be different of each
other so that you can have something
that's an eye and another cell
that's in the liver and so on.
And we'll talk a little bit about
that as we go on.
But the major point,
right at this point, is that all of
life involves one cell dividing and
giving a couple of other cells,
and then those going on.  So these
cells, as we've said,
characteristics of organisms which
are to be true at their cellular
level as well is that they carry out
metabolism, they undergo
regulated growth.
And you have a nice example of yeast
undergoing regulated growth and they
reproduce, which in the case of a
single-celled organism is the same
as cell division.
For us reproducing is a lot more
complicated because we have to make
a whole other multicellular organism
where the cells have differentiated
functions, but the point about that
is there has to be an unbelievable
amount of synthesis.
The DNA in our body,
we start out with two meters in a
fertilized cell,
and we have ten to the fourteenth
cells by the time we're an adult.
So we've had to make a tremendous
amount of DNA let alone protein and
everything else.
And something almost all of you
know from your engineering
background from this place is that
you need energy in order
to synthesize material.
And what we'll start to talk about
in the next phase of this course
then is how do cells make energy and
how do they carry out metabolism.
So I'm going to, just before we do
that, introduce to you very quickly,
to close out here, two classes of
organisms that we find in nature.
We find organisms that are known as
autotrophs.  These are certain
bacteria, and they're able to make
everything they need starting with
CO2, ammonia, phosphate,
water, a few things, but that's all
they need.  So,
for example, an organism that lives,
a bacterium that lives out in the
open ocean is able to make
everything from those very,
very simple basic building blocks.
Heterotrophs need to eat --
-- some things made by
other organisms.
An example of a heterotroph that
you're familiar with,
that I'm familiar with is us.
You probably remember your mother
reminding you,
as you're about to have yet another
hotdog, that it was important to eat
your vitamins.
The reason you need to eat vitamins,
those are things we absolutely need
for our life but we cannot make them
ourselves.  Vitamin C is
one you probably know.
It has an interesting history how
people figured this out.
It was sailors at sea got really,
really sick.  Their teeth would
start to loosen,
they would start to bleed and they
would die.  Some of the famous sea
voyages you heard about in high
school, I think the Cape of Good
Hope, on that trip where that was
discovered 100 out of the 160
sailors died at sea because of
scurvy.  Now, scurvy turns out to be
due to not having vitamin C.
And there was finally a guy,
Lind, I'm just blanking on his first
name at the moment,
in about the 1700s who was a naval
surgeon in the British Navy who
actually figured out that if you
gave sailors lemon juice that they
didn't get scurvy.
It was a controlled experiment.
It took about 50 years.  I think it
was 1795 when they started to
finally give the sailors lemon juice
and stopped having this terrible
sickness amongst their sailors.
And then in about 1950 they
substituted lime juice.
And some of you may still know the
British sailors are called ìlimeysî.
And that was because of this
solution they found to avoiding
scurvy.  And what was really
happening was they were finding a
way to provide vitamin C which is in
fresh fruits and vegetables which
wasn't part of the classic sailor
diet which was sort of biscuits and
dried meat during long voyages at
sea.  And there are several other
vitamins, but the reason they're
called vitamins is they're things
that you body cannot make but other
organisms can.
The other thing that we cannot make,
we can make some of our 20 amino
acids, but there are eight amino
acids that we cannot make,
lysine, methionine, lucien,
isoleucine, valine, threonine,
phenylalanine and tryptophan.
And this actually has consequences
for us because those of you who are
vegetarians probably know you have
to be kind of careful about your
diet.  If you're eating animal
protein you're getting essentially
all the different amino acids,
but if you're a vegetarian you have
to be careful because the major food
crops such as wheat and rice,
for example, are very low in lysine.
So if you just eat those you end up
with a lysine deficiency that's not
good.  But, on the other hand,
beans, lentils, the various
leguminous plants,
which also are those ones that form
the special associations with
bacteria that let them convert
atmospheric nitrogen into ammonia,
legumes are high in lysine but low
in methionine.
So peoples all over the world
figured this out by trial and error.
So the Mexican diet is rice and
beans.  There's a reason for it.
What's happening actually is just
in the rice you're low in lysine,
but by having beans at the same time
you're balancing out the two.
Or the Native Americans in this pat
of the country had ìthe three
sistersî with the corn, the
squash and the beans.
And again they were balancing out
the diet by making sure that they
got the various amino acids,
a balance of all the amino acids
that were necessary for life.
It also actually was really good
gardening practice because the beans
were able to convert atmospheric
nitrogen into ammonia,
which was fertilizer, and the squash
leaves shaded the ground so that the
ground didn't dry out,
and the corn could grow even when it
was short on water.
But what was really happening,
as people grew without even
understanding about chemistry,
they were compensating for the fact
that we're heterotrophs and needed
to do this.  So we'll start in the
next lecture on trying to talk about
how cells make energy and how it
makes some of this amazing
stuff happen.
