So today we are going to
continue where we left off last
time talking
more specifically about
variations on the theme of life.
And last year
I tried to do this lecture
using PowerPoint and it was a
total
disaster so I'm going back to
the board.
You will have the PowerPoint
slides.
They'll be on the Web to
download to summarize basically
what
I'm drawing on the board.
But it will be slightly
different on
the board.
But I found that for this
material it really doesn't work
to exclusively use the
PowerPoint.
So last time we talked about,
remember, my life on Earth
abridged where --
-- we had photosynthesis making 
glucose or organic carbon plus
oxygen?
And then the reverse of
this was respiration.
And then we had elements
cycling in the middle.
And I said this is
very, very abbreviated of how
all life on Earth works.
And so today
what I'm going to do is tell
you that that's not right.
That's
grossly oversimplified.
And there are some really
interesting
variations on the theme of how
to extract energy and carbon and
reducing power and electrons
from the Earth's system to
create life.
And it's mostly microbes that
have these diverse
possibilities.
And,
again, even what I'm going to
talk to you about today is
oversimplified.
If you go to a microbiology
textbook you'll find
just about every possible
combination of energy sources,
carbon sources and electron
sources in some microorganism
somewhere to
get through life.
So I'm giving you,
again, the
simplified version because
otherwise it gets way too
complicated.
So all
of life needs carbon and
energy, and a lot of other
elements, too,
but
these are the main axis upon
which we're going to order
our universe today.
So for carbon the choices are
inorganic or organic.
So this would be CO2 and this
might be glucose or
sugars, any sugars.
And then on the energy axis
they can use solar
energy, as in photosynthesis,
or they can use chemical
energy.
And within the chemical energy
sources they can be inorganic or
organic like sugars,
etc.
And often here you have reduced
compounds such as hydrogen
sulfide, ammonia,
and we'll talk about these.
So these are the ways we divide
up the possibilities for carbon
and
energy sources to be alive.
All organisms also need to have
an
energy currency in the cell.
And you've talked about this a
lot
already in the biochemistry
lectures so I'm,
again, just giving you the
impressionist view of this.
You know the details.
This is just to
get you organized.
And so all life uses redox
reactions.
And in your handouts for today
there's a primer on redox
reactions
just in case you want to review
that.
And one of the key reactions
we'll talk about today is the
conversion of NADP.
If you put
energy in you can reduce it to
NADPH.
So that's a reduction.
And the reverse you get energy
out when it's
oxidized.
Now, we're going to be talking
about oxidation and
reduction today.
And then they all use ATP which
you've talked a lot
about here.
And the couple here is ADP.
Put energy in.
You make ATP which is a high
energy
intermediate.
And in converting it back to
ADP that energy can be
released.
And this is used in the
biochemistry of the cell.
So all
cells have these two energy
conversion processes in common.
OK, so let's look at just
summarizing what we're going to
go
over today.
This is a summary of options
for life.
See also Freeman,
Chapter 25.
There is some discussion of
this.
And we can divide life here
between what we call autotrophs.
These are
organisms that can make their
own organic carbon.
In other words,
they can convert carbon dioxide
to organic carbon.
Heterotrophs are
organisms that can only use
organic carbon.
They rely on the guts of
other organisms in order to get
through life.
And so now we're going to
systematically go through these
processes that fall under each
one of these.
Oxygenic photosynthesis
is the one we've been talking
about last time and in my
abbreviated
version of life on Earth.
And this is carried out by
eukaryotic
organisms, plants,
trees, etc.,
and also by prokaryotic
organisms.
Those are the cyanobacteria,
microscopic photosynthetic
plants.
They use CO2 and sunlight.
So our first variant on this
theme we'll
get into is a group of bacteria
that do anoxygenic
photosynthesis.
Oxygenic means they evolve
oxygen.
These guys use solar energy but
they
don't evolve oxygen.
And we'll get into how that
works.
And then
there's a group of organisms
that still use CO2.
And in the very
similar pathway the Calvin
Cycle is photosynthesis.
But they use chemical energy in
order to make these
intermediates to
fix CO2.
OK, so let's talk about those
first.
And so we're going to
talk about the autotrophs.
And all of them share this
pathway, CO2 to C6H12.
This would be glucose.
And it takes ATP to run this
reaction and it also
takes reduced NADPH --
-- to run this reaction.
It also takes this enzyme
RuBisCO which
you've talked about I'm sure,
ribulose bisphosphate
carboxylase.
And this is the enzyme that
initially takes the CO2 from the
atmosphere and binds it to an
organic carbon.
Now, in a detailed version of
this is what's called the Calvin
Cycle or
the Calvin/Benson Cycle.
I don't know which one your
book calls it.
Calvin got the Nobel Prize but
Benson was the graduate student
that
did all the work,
so you should recognize that.
Anyway, you studied
this in great deal.
But an interesting factoid is
that RuBisCO
is the most abundant protein on
Earth.
That tells you how important
this reaction is for sustaining
life on Earth.
So notice that in order to
drive this reaction,
which is the Calvin
Cycle, it requires energy and
reducing power.
So where
do they get it?
Well, there are three ways that
autotrophs can get energy and
reducing power to drive this
reaction.
And the first is oxygenic
photosynthesis.
And the second is anoxygenic.
And the third is
chemosynthesis.
OK, those first three there.
So now
we're going to go through each
of these and look at how they
work
remembering that all of them
are generating ATP and NADPH in
order to
drive that.
So all of the autotrophs have
that in common.
Well, oxygenic photosynthesis
is the one that you know well
already.
You've studied it in great
detail in biochemistry.
So we're going to,
again, give you the abbreviated
version here just so you have a
template to map these other
ones onto.
These are what are known as the 
light reactions of
photosynthesis,
the Z scheme taking solar
energy,
splitting water,
evolving oxygen and
synthesizing ATP and NADPH.
This is
all familiar,
right?
Very familiar.
I'm just writing it in
a cartoon version.
OK, so this is the NADPH and
ATP
that goes to fuel that process.
OK, so now, well,
at least I can do it on that
board.
Let me do it on
this board. Anoxygenic --
-- is almost exactly like this
process, but instead of
splitting
water these guys oxidize
hydrogen sulfide.
So here's
our ATP and NADPH.
And they use sunlight to do
this.
So these are called
photosynthetic
bacteria.
And they were around very early
on the Earth.
Long before the
Earth's atmosphere was
oxygenated these were the guys
that were able
to use solar energy and make
organic carbon but without
evolving oxygen.
Then somewhere along the line
some cell evolved,
had some mutations and
somehow figured out that water,
this abundant source of water
was a much
better electron donor than
hydrogen sulfide.
And once the biochemistry
figured this out,
you can see the simple
substitution here,
the whole
Earth started going in a
different direction.
So this is an
interesting example of how a
small biochemical innovation can
dramatically change the whole
nature of the planet.
Now, these guys are still
around on Earth.
In fact, I'm going to show
you some.
I'll explain this at the end,
but I have some captured in
here.
See that little purple band?
Those are those guys.
I've got
other little tricks in here but
I'll save those.
Well, you cannot really see the
purple band.
But you can come up
later and look at it.
Those are photosynthetic
bacteria.
So they're
still around on the Earth but
they're stuck in places where
there's no oxygen.
So they have a rather
restricted niche on the
planet now, but they're still
extremely important.
What did I do?
Oh, here it is.
So one of the places that they
can
be found, and if you're
interested in them a great place
to go find
some is out at the Mystic Lakes
in Arlington which is a
permanently
stratified lake so the bottom
of the lake is always anaerobic.
There's
never oxygen there.
In a typical lake like that you
have a lot of mud
on the bottom and you have a
lot of hydrogen sulfide coming
out of the
mud from bacterial processes
that we'll talk about.
And you have light here.
And so you have a gradient here
of this is
oxygen and this is H2S.
And these photosynthetic
bacteria have to live
somewhere where there's enough
light to photosynthesize and
enough
hydrogen sulfide to use in this
part of the reaction.
But they're very sensitive to
oxygen so they cannot be in the
oxygenated
part of the lake.
So you find them in a layer.
It's called the
squeeze.
They have to have light so they
have to be up,
but they cannot
have oxygen so they have to be
down.
And they need hydrogen sulfide
so
they have to be down.
So they're layered in lakes.
OK.
So what
about these guys,
chemosynthesis?
They don't rely on solar
energy.
Again, they're still driving
the Calvin Cycle reducing CO2
from the
air into organic carbon,
but they're not using sunlight.
So what do they
do? They get their energy --
-- from redox reactions.
And let's just show you an
example.
Redox reactions couple to the 
conversion of oxygen to H2O.
So oxygen is involved in these
reactions.
And one organism,
for example,
can take ammonia and
convert it to nitrite.
Another type of organism can
take nitrite and
convert it to nitrate.
And there are other organisms
that
can take hydrogen sulfide and
convert it to sulfate.
And some can
take hydrogen sulfide,
oh, no, take iron,
ferrous iron,
Fe2+
and convert it to Fe3+.
So in all of these cases what
is
happening to these compounds?
Are they being oxidized or
reduced?
I
heard an oxidized.
Yes, they're being oxidized.
So these reduced
compounds, relatively reduced
compounds can be utilized
by oxidizing them.
The organism can release the
energy
that's needed.
ATP is generated here.
And NADPH is generated by any of
these redox couples.
So using this energy then the
cell
takes the reduced NADPH and the
ATP and it runs the Calvin
Cycle,
chemosynthesis.
OK.
Now, you may think that these
are kind of
strange, weird bacteria that
live in strange pockets of the
Earth where
there's no oxygen.
And who cares anyway?
They're outdated.
They dominated the Earth way
back in the early
stages of the Earth but they're
not so important now.
Well, that's not
true.
They're incredibly important.
In some ecosystems they're the
total base of the entire
ecosystem.
But also on a global scale,
as
you'll learn,
you should have a feeling for
this by the end of this
lecture, but also when we talk
about global biogeochemical
cycles you
will learn that these microbes
are really messengers for
electrons in
the environment.
Without them the redox balance
of
the Earth would not be
maintained, OK?
You cannot have nothing but
oxidizing reactions or nothing
but reduction reactions and have
a
system sustain itself.
So it's these microbes that are
playing a
really important role in
maintaining the redox balance of
the Earth.
OK.
Now, one system that I'm going
to
show you in that DVD,
that will do much better
justice to it than my
drawings here,
that's a deep-sea volcano in
case you didn't recognize
it.
And this is 2500 meters at the
bottom of the ocean,
very, very
deep.
And there is intense heat.
I mean just think of a volcano
on the
surface of the Earth.
Intense heat and reduced
compounds
are found in the Earth's mantle
that are ready to erupt through
this
deep-sea volcano.
And you have sulfate in the sea
water that
percolates through here.
And as it percolates in and
gets draw into the
volcanic stuff that's coming
out of here it's reduced to
hydrogen
sulfide coming out of the
volcano.
But you have oxygen in the
water in
the deep-sea.
And we'll be talking about this
when we talk about ocean
circulation.
But the oceans have a global
ocean circulation where the
surface water that's in
equilibrium with the atmosphere
actually sinks
and travels along the bottom of
the ocean.
So there is oxygen in the
bottom of the ocean,
unlike many lakes where you
don't have oxygen.
And we'll talk about that
difference.
And in the hot vents
the water coming out of here
can be very, very hot,
but there's a
gradient right as it comes out
meeting the colder sea water.
And
so what you have here is a
perfect incubator for
chemosynthetic
bacteria --
-- that use the hydrogen
sulfide in chemosynthesis to fix
carbon dioxide
using the oxygen here.
And that forms the base of the
entire food
web in the deep ocean because
there's no light down there.
There's no photosynthesis.
There's only chemosynthesis.
And just a little story that
goes back to when I first came
to MIT as
an assistant professor in 1976.
You weren't even born.
But when I was
young we used to go the Muddy
Charles Pub periodically after
work
and have beers.
And there was a professor,
in this department
actually, John Edmond,
who passed away several years
ago but
who used to be there.
It was sort of like our Cheers.
And
I'll never forget the day he
came back from a cruise.
He came to the
pub.
He was a chemist and I'm a
biologist.
And he said you will not
believe what we found on the
bottom of the ocean.
He had gone down in
Alvin, this two-person
submersible vehicle.
And he started talking about
these giant clams and these
giant tube
worms and all of these things,
and I thought he had had one
too many
beers.
I found it hard to believe.
Well, it turned out that that
was
the first discovery of these
deep-sea vents and he was on
that
expedition.
And through that collegial
relationship I actually
ended up with one of the clam
shells from the clams there,
which is one
of the giant clams.
Their meat is blood red because
they
have a special kind of
hemoglobin that they use to keep
the oxygen
tension perfect for these
chemosynthetic bacteria.
If the
oxygen is too high they cannot
do this because it will
spontaneously
oxidize the H2S.
So the oxygen tension is very
critical.
And they have a special kind of
hemoglobin that does that.
So these
clams had symbiotic
chemosynthetic bacteria.
Well, since then these
vents have been discovered
everywhere and ecosystems
similar
have been discovered on the
surface.
And there are all kinds of
different vents.
You're going to learn about not
only hydrothermal
vents, hot vents in this video,
but also cold seeps they're
called where
you have methane bacteria that
are really important.
OK.
So these are the main ways in
which organisms can get energy
to convert
CO2 to organic carbon.
Then you have all these
heterotrophs,
the
ones that use the organic
carbon, and they have various
ways of doing
that.
You've learned in biochemistry
the primary way,
which
is very powerful,
and that is using aerobic
respiration to do that.
And so we are just going to
abbreviate that here.
That's our
reverse of photosynthesis.
So heterotrophs.
So we have first aerobic.
And let me jump ahead
with the slides.
OK, there you are.
So this is a cartoon version of
aerobic respiration.
So we'll just put glucose,
we'll come down to the
Krebs' Cycle.
And we are going to let
electrons flow here and have
oxygen be the final electron
acceptor creating water.
So we've really just
accomplished the absolute
reverse of
photosynthesis and we've made
NADH in doing this and we've
made ATP.
So these guys are getting the
energy out of the glucose that
all of the
other organisms made.
And oxygen is the terminal
electron acceptor when
there's oxygen around.
But there are lots of
environments,
as we've talked about on Earth,
where there isn't oxygen.
And there
are bacteria that can take
advantage of those environments.
And instead
of having oxygen be the
terminal electron acceptor there
are a number
of other elements that they can
use, compounds that they can
use.
For
example, there are some that
use nitrate and they reduce
it to nitrous oxide.
N2.
Ammonia.
All the relatively
reduced forms of nitrogen.
And so this called anaerobic.
And this process is called 
gentrification.
And if it weren't for these
bacteria, these anaerobic
bacteria that can reduce
nitrate, nitrogen
would never return to the
atmosphere.
Remember last time we
talked about nitrogen fixation,
how specific types of microbes
can take
N2 from the atmosphere and pull
it into the ecosystem?
Well, if you
didn't have these bacteria
doing this process that nitrogen
would
never get back to the
atmosphere.
They're central to closing the
nitrogen cycle.
Then there are some that can
use sulfate and reduce it
to hydrogen sulfide.
As you can imagine,
these are critical to
creating the hydrogen sulfide
that's used in these other
processes.
There are some that use CO2 and
convert to methane.
These are
methanogenic bacteria,
and they're incredibly
important in the global
carbon cycle and in the methane
cycle.
Methane is a really powerful
greenhouse gas,
and we're going to
talk about that later.
And then there are some that
can take Fe3+
and reduce it to Fe2+.
And the same for manganese.
So you should be starting to
sense a
sort of symmetry here,
right, that these anaerobic
bacteria are
fulfilling functions on the
Earth.
Let me write these down.
These are sulfate reducers,
these are methanogens,
and these are iron
reducers and manganese
reducers.
So these will all become
extremely
important when we talk about
the global biogeochemical cycles
of all
of these elements.
It's these microbes that make
sure that the
cycles can continue and don't
run into a dead end of oxidation
or
reduction.
OK.
Before we go to the movie,
I just want to say if you
look at Table 25.2 in your
textbook, I think it's that one.
I'm assuming I'm using the most
recent version.
You'll see a
variation of this theme in
which there will be some entries
of
organisms that don't fall into
these categories that I've
just shown you.
And that is to say that there
are
organisms that use light energy
and organic carbon energy at the
same
time.
For every variation that's
possible there's an organism
that's
evolved to take advantage of
it.
I've just oversimplified it
here,
but you should know that.
And the bottom line is if it's
thermodynamically possible.
And, again, this whole lecture
could
have been done in a
thermodynamic mode.
We could have looked at which
redox couples were
energetically possible and then
assigned those to
particular microbes.
But for now I just want you to
get the overview.
But for anything that's
thermodynamically feasible
there's a
microbe out there that's doing
it.
And, in fact,
microbiologists
actually comb through redox
tables and put together
different redox
couples and hypothesize.
I ought to be able to find an
organism that
does this in that environment.
And then they go out.
And they can
almost always actually find it.
So they're incredibly
versatile.
And
it gives you a really good
strong feeling for the power of
thermodynamics in driving the
evolution of these biochemical
processes.
Finally, before we show you the
movie I want to show you what
this thing is all about.
There was a
Russian microbiologist back in
the previous century named
Winogradsky --
-- who wanted to isolate some
of these photosynthetic
bacteria.
And
knowing what their
characteristics were he went out
and got himself
some mud and some pond water.
And he set up what we've come
to call a
Winogradsky column.
This is a Winogradsky juice
bottle, but it
works the same.
And what you do is you put mud
in the bottom and you
put pond water here.
And the pond water has
basically an
inoculum.
It has representatives of all
different types of bacteria.
They might be spores.
If they don't like the
environment they're in they
sporulate and then they just
don't germinate.
But presumably in pond
water you have everything that
could possibly grow in here.
And in the
mud you add a source of
sulfate.
And so you might add calcium
sulfate
and you might add a little
organic matter,
you know, plant parts or
something just to jumpstart it.
And eventually you set up a
gradient
here of hydrogen sulfide and
oxygen.
And over time the organisms
grow
along that gradient.
So you'll end up down here with
the anaerobic
respiration.
In fact, the organisms generate
this gradient.
When you start out the
whole thing is oxygenated.
And what you should think about
in this
context is what happens.
How do these gradients get
generated when
you start out with a completely
mixed system,
everything in there,
everything oxygenated?
Eventually you have anaerobic
--
First you'll just have aerobic
respiration, right?
Anything that
can use organic carbon and
oxygen is going to go like mad,
and that's
what's going to draw the oxygen
down.
Then you'll have anaerobic
respiration here.
You'll have photosynthesis up
here, evolving
oxygen.
You'll have chemosynthetic
bacteria here because they need
a
little bit of oxygen but they
also need some of this hydrogen
sulfide
and photosynthetic bacteria
here.
Well, they're like down here.
Because they need light but
cannot
have oxygen.
And so you can set these up.
And this purple band here
tells you that you've got your
photosynthetic bacteria.
