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So today we are going to continue
where we left off last time talking

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more specifically about variations
on the theme of life.

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And last year I tried to do this
lecture using PowerPoint and it was

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a total disaster so I'm going back
to the board.  You will have the

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PowerPoint slides.
They'll be on the Web to download

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to summarize basically what I'm
drawing on the board.

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But it will be slightly different on
the board.  But I found that for

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this material it really doesn't work
to exclusively use the PowerPoint.

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So last time we talked about,
remember, my life on earth

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abridged where --

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-- we had photosynthesis making
glucose or organic carbon plus

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oxygen?  And then the reverse of
this was respiration.

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And then we had elements cycling in

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the middle.  And I said this is very,
very abbreviated of how all life on

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earth works.  And so today what I'm
going to do is tell you that that's

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not right.  That's grossly
oversimplified.

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And there are some really
interesting variations on the theme

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of how to extract energy and carbon
and reducing power and electrons

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from the earth's system
to create life.

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And it's mostly microbes that have
these diverse possibilities.

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And, again, even what I'm going to
talk to you about today is

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oversimplified.
If you go to a microbiology

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textbook you'll find just about
every possible combination of energy

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sources, carbon sources and electron
sources in some microorganisms

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somewhere to get through life.
So I'm giving you,

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again, the simplified version
because otherwise it gets way too

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complicated.  So all of life needs
carbon and energy,

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and a lot of other elements,
too, but these are the main axis

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upon which we're going to order our
universe today.

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So for carbon the choices are
inorganic or organic.

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So this would be CO2 and this might
be glucose or sugars,

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any sugars.  And then on the energy
axis they can use solar energy,

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as in photosynthesis, or they can
use chemical energy.

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And within the chemical energy
sources they can be inorganic or

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organic like sugars, etc.
And often here you have reduced

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compounds such as hydrogen sulfide,
ammonia, and we'll talk about these.

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So these are the ways we divide up
the possibilities for carbon and

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energy sources to be alive.
All organisms also need to have an

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energy currency in the cell.
And you've talked about this a lot

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already in the biochemistry lectures
so I'm, again,

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just giving you the impressionist
view of this.  You know the details.

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This is just to get you organized.
And so all life uses

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redox reactions.
And in your handouts for today

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there's a primer on redox reactions
just in case you want to review that.

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And one of the key reactions we'll
talk about today is the conversion

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of NADP.  If you put energy in you
can reduce it to NADPH.

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So that's a reduction.
And the reverse you get energy out

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when it's oxidized.
Now, we're going to be talking

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about oxidation and reduction today.
And then they all use ATP which

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you've talked a lot about here.
And the couple here is ADP.  Put

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energy in.

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You make ATP which is a high energy
intermediate.  And in converting it

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back to ADP that energy can be
released.  And this is used in the

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biochemistry of the cell.
So all cells have these two energy

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conversion processes in common.
OK, so let's look at just

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summarizing what we're going to go
over today.  This is a summary of

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options for life.
See also Freeman,

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Chapter 25.  There is some
discussion of this.

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And we can divide life here between
what we call autotrophs.

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These are organisms that can make
their own organic carbon.

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In other words, they can convert
carbon dioxide to organic carbon.

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Heterotrophs are organisms that can
only use organic carbon.

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They rely on the guts of other
organisms in order to

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get through life.
And so now we're going to

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systematically go through these
processes that fall under each one

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of these.  Oxygenic photosynthesis
is the one we've been talking about

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last time and in my abbreviated
version of life on earth.

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And this is carried out by
eukaryotic organisms,

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plants, trees, etc., and also by
prokaryotic organisms.

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Those are the cyanobacteria,
microscopic photosynthetic plants.

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They use CO2 and sunlight.
So our first variant on this theme

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we'll get into is a group of
bacteria that do anoxygenic

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photosynthesis.
Oxygenic means they evolve oxygen.

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These guys use solar energy but
they don't evolve oxygen.

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And we'll get into how that works.
And then there's a group of

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organisms that still use CO2.
And in the very similar pathway the

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Calvin Cycle is photosynthesis.
But they use chemical energy in

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order to make these intermediates to
fix CO2.  OK, so let's talk about

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those first.  And so we're going to
talk about the autotrophs.

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And all of them share this

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pathway, CO2 to C6H12.
This would be glucose.

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And it takes ATP to run this
reaction and it also takes

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reduced NADPH --

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-- to run this reaction.
It also takes this enzyme ribisco

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which you've talked about I'm sure,
ribulose bisphosphate carboxylase.

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And this is the enzyme that
initially takes the CO2 from the

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atmosphere and binds it
to an organic carbon.

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Now, in a detailed version of this
is what's called the Calvin Cycle or

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the Calvin/Benson Cycle.
I don't know which one your book

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calls it.  Calvin got the Nobel
Prize but Benson was the graduate

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student that did all the work,
so you should recognize that.

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Anyway, you studied this in great
deal.  But an interesting factoid is

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that ribisco is the most abundant
protein on earth.

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That tells you how important this
reaction is for sustaining

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life on earth.
So notice that in order to drive

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this reaction,
which is the Calvin Cycle,

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it requires energy and reducing
power.  So where do they get it?

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Well, there are three ways that

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autotrophs can get energy and
reducing power to drive this

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reaction.  And the first is oxygenic
photosynthesis.  And the

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second is anoxygenic.
And the third is chemosynthesis.

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OK, those first three there.  So
now we're going to go through each

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of these and look at how they work
remembering that all of them are

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generating ATP and NADPH in order to
drive that.  So all of the

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autotrophs have that in common.
Well, oxygenic photosynthesis is the

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one that you know well already.
You've studied it in great detail

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in biochemistry.
So we're going to,

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again, give you the abbreviated
version here just so you have a

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template to map these
other ones onto.

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These are what are known as the

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light reactions of photosynthesis,
the Z scheme taking solar energy,

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splitting water,
evolving oxygen and synthesizing ATP

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and NADPH.  This is all familiar,
right?  Very familiar.  I'm just

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writing it in a cartoon version.
OK, so this is the NADPH and ADP

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that goes to fuel that process.

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OK, so now, well,
at least I can do it on that board.

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Let me do it on this board.
Anoxygenic --

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-- is almost exactly like this

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process, but instead of splitting
water these guys oxidize hydrogen

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sulfide.  So here's
our ATP and NADPH.

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And they use sunlight to do this.

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So these are called photosynthetic
bacteria.  And they were around very

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early on the earth.
Long before the earth's atmosphere

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was oxygenated these were the guys
that were able to use solar energy

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and make organic carbon but without
evolving oxygen.

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Then somewhere along the line some
cell evolved, had some mutations and

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somehow figured out that water,
this abundant source of water was a

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much better electron donor than
hydrogen sulfide.

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And once the biochemistry figured
this out, you can see the simple

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substitution here,
the whole earth started going in a

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different direction.
So this is an interesting example

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of how a small biochemical
innovation can dramatically change

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the whole nature of the planet.
Now, these guys are still around on

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earth.  In fact,
I'm going to show you some.

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I'll explain this at the end,
but I have some captured in here.

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See that little purple band?  Those
are those guys.

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I've got other little tricks in
here but I'll save those.

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Well, you cannot really see the
purple band.  But you can come up

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later and look at it.
Those are photosynthetic bacteria.

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So they're still around on the
earth but they're stuck in places

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where there's no oxygen.
So they have a rather restricted

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niche on the planet now,
but they're still extremely

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important.  What did I
do?  Oh, here it is.

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So one of the places that they can
be found, and if you're interested

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in them a great place to go find
some is out at the Mystic Lakes in

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Arlington which is a permanently
stratified lake so the bottom of the

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lake is always anaerobic.
There's never oxygen there.

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In a typical lake like that you
have a lot of mud on the bottom and

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you have a lot of hydrogen sulfide
coming out of the mud from bacterial

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processes that we'll talk about.
And you have light here.

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And so you have a gradient here of
this is oxygen and this is H2S.

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And these photosynthetic bacteria
have to life somewhere where there's

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enough light to photosynthesize and
enough hydrogen sulfide to use in

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this part of the reaction.
But they're very sensitive to oxygen

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so they cannot be in the oxygenated
part of the lake.

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So you find them in a layer.
It's called the squeeze.  They have

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to have light so they have to be up,
but they cannot have oxygen so they

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have to be down.
And they need hydrogen sulfide so

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they have to be down.
So they're layered in lakes.

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OK.  So what about these guys,
chemosynthesis?

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They don't rely on solar energy.
Again, they're still driving the

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Calvin Cycle reducing CO2 from the
air into organic carbon,

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but they're not using sunlight.
So what do they do?  They get their

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energy --

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-- from redox reactions.
And let's just show you an example.

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Redox reactions couple to the

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conversion of oxygen to H2O.
So oxygen is involved in these

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reactions.  And one organism,
for example, can take ammonia and

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convert it to nitrite.
Another type of organism can take

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nitrite and convert it to nitrate.
And there are other organisms that

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can take hydrogen sulfide and
convert it to sulfate.

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And some can take hydrogen sulfide,
oh, no, take iron, ferrous iron,

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Fe2+ and convert it to Fe3+.
So in all of these cases what is

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happening to these compounds?
Are they being oxidized or reduced?

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I heard an oxidized.  Yes, they're
being oxidized.

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So these reduced compounds,
relatively reduced compounds can be

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utilized by oxidizing them.
The organism can release the energy

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that's needed.  ATP
is generated here.

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And NADPH is generated by any of

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these redox couples.
So using this energy then the cell

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takes the reduced NADPH and the ATP
and it runs the Calvin Cycle,

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chemosynthesis.  OK.  Now, you may
think that these are kind of strange,

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weird bacteria that life in strange
pockets of the earth where there's

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no oxygen.  And who cares anyway?
They're outdated.

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They dominated the earth way back
in the early stages of the earth but

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they're not so important now.
Well, that's not true.  They're

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incredibly important.
In some ecosystems they're the

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total base of the entire ecosystem.
But also on a global scale, as

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you'll learn, you should have a
feeling for this by the end of this

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lecture, but also when we talk about
global biogeochemical cycles you

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will learn that these microbes are
really messengers for electrons in

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the environment.
Without them the redox balance of

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the earth would not be maintained,
OK?  You cannot have nothing but

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oxidizing reactions or nothing but
reduction reactions and have a

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system sustain itself.
So it's these microbes that are

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playing a really important role in
maintaining the redox balance

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of the earth.  OK.
Now, one system that I'm going to

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show you in that DVD,
that will do much better justice to

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it than my drawings here,
that's a deep-sea volcano in case

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you didn't recognize it.
And this is 2500 meters at the

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bottom of the ocean,
very, very deep.  And there is

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intense heat.  I mean just think of
a volcano on the surface

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of the earth.
Intense heat and reduced compounds

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are found in the earth's mantle that
are ready to erupt through this

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deep-sea volcano.
And you have sulfate in the sea

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water that percolates through here.
And as it percolates in and gets

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draw into the volcanic stuff that's
coming out of here it's reduced to

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hydrogen sulfide coming
out of the volcano.

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But you have oxygen in the water in
the deep-sea. And we'll be talking

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about this when we talk about ocean
circulation.  But the oceans have a

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global ocean circulation where the
surface water that's in equilibrium

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with the atmosphere actually sinks
and travels along the bottom of the

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ocean.  So there is oxygen in the
bottom of the ocean,

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unlike many lakes where you don't
have oxygen.

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And we'll talk about that difference.
And in the hot vents the water

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coming out of here can be very,
very hot, but there's a gradient

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right as it comes out meeting the
colder sea water.

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And so what you have here is a
perfect incubator for chemosynthetic

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bacteria --

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-- that use the hydrogen sulfide in
chemosynthesis to fix carbon dioxide

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using the oxygen here.
And that forms the base of the

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entire food web in the deep ocean
because there's no light down there.

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There's no photosynthesis.  There's
only chemosynthesis.

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And just a little story that goes
back to when I first came to MIT as

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an assistant professor in 1976.
You weren't even born.  But when I

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was young we used to go the Muddy
Charles Pub periodically after work

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and have beers.
And there was a professor,

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in this department actually,
John Edmond, who passed away several

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years ago but who used to be there.
It was sort of like our Cheers.

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And I'll never forget the day he
came back from a cruise.

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He came to the pub.  He was a
chemist and I'm a biologist.

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And he said you will not believe
what we found on the bottom of the

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ocean.  He had gone down in Alvin,
this two-person submersible vehicle.

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And he started talking about these
giant clams and these giant tube

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worms and all of these things,
and I thought he had had one too

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many beers.  I found it hard to
believe.  Well,

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it turned out that that was the
first discovery of these deep-sea

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vents and he was on that expedition.
And through that collegial

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relationship I actually ended up
with one of the clam shells from the

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clams there, which is one
of the giant clams.

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Their meat is blood red because they
have a special kind of hemoglobin

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that they use to keep the oxygen
tension perfect for these

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chemosynthetic bacteria.
If the oxygen is too high they

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cannot do this because it will
spontaneously oxidize the H2S.

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So the oxygen tension is very
critical.

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And they have a special kind of
hemoglobin that does that.

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So these claims had symbiotic
chemosynthetic bacteria.

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Well, since then these vents have
been discovered everywhere and

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ecosystems similar have been
discovered on the surface.

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And there are all kinds of
different vents.

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You're going to learn about not
only hydrothermal vents,

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hot vents in this video, but also
cold seeps they're called where you

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have methane bacteria that are
really important.  OK.

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So these are the main ways in which
organisms can get energy to convert

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CO2 to organic carbon.
Then you have all these

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heterotrophs, the ones that use the
organic carbon,

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and they have various ways of doing
that.  You've learned in

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biochemistry the primary way,
which is very powerful, and that is

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using aerobic respiration
to do that.

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And so we are just going to
abbreviate that here.

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That's our reverse of
photosynthesis.  So heterotrophs.

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So we have first aerobic.

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And let me jump ahead

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with the slides.

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OK, there you are.
So this is a cartoon version of

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aerobic respiration.
So we'll just put glucose,

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we'll come down to the Krebs' Cycle.
And we are going to let electrons

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flow here and have oxygen be the
final electron acceptor

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creating water.
So we've really just accomplished

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the absolute reverse of
photosynthesis and we've made NADH

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in doing this and we've made ATP.
So these guys are getting the

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energy out of the glucose that all
of the other organisms made.

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And oxygen is the terminal electron
acceptor when there's

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oxygen around.
But there are lots of environments,

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as we've talked about on earth,
where there isn't oxygen.

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And there are bacteria that can
take advantage of those environments.

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And instead of having oxygen be the
terminal electron acceptor there are

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a number of other elements that they
can use, compounds that they can use.

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For example, there are some that
use nitrate and they reduce

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it to nitrous oxide.
N2.  Ammonia.  All the relatively

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reduced forms of nitrogen.
And so this called anaerobic.

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And this process is called

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gentrification.
And if it weren't for these bacteria,

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these anaerobic bacteria that can
reduce nitrate,

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nitrogen would never return to the
atmosphere.  Remember last time we

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talked about nitrogen fixation,
how specific types of microbes can

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take N2 from the atmosphere and pull
it into the ecosystem?

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Well, if you didn't have these
bacteria doing this process that

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nitrogen would never get
back to the atmosphere.

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They're central to closing the
nitrogen cycle.

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Then there are some that can use
sulfate and reduce it to hydrogen

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sulfide.  As you can imagine,
these are critical to creating the

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hydrogen sulfide that's used in
these other processes.

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There are some that use CO2 and
convert to methane.

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These are methanogenic bacteria,
and they're incredibly important in

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the global carbon cycle and
in the methane cycle.

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Methane is a really powerful
greenhouse gas,

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and we're going to talk about that
later.  And then there are some that

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can take Fe3+ and reduce it to Fe2+.
And the same for manganese.

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So you should be starting to sense a

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sort of symmetry here,
right, that these anaerobic bacteria

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are fulfilling functions on the
earth.  Let me write these down.

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These are sulfate reducers,
these are methanogens, and these are

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iron reducers and manganese
reducers.

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So these will all become extremely
important when we talk about the

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global biogeochemical cycles of all
of these elements.

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It's these microbes that make sure
that the cycles can continue and

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don't run into a dead end of
oxidation or reduction.

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OK.  Before we go to the movie,
I just want to say if you look at

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Table 25.2 in your textbook,
I think it's that one.

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I'm assuming I'm using the most
recent version.

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You'll see a variation of this
theme in which there will be some

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entries of organisms that don't fall
into these categories that

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I've just shown you.
And that is to say that there are

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organisms that use light energy and
organic carbon energy at the same

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00:33:41,000 --> 00:33:46,000
time.  For every variation that's
possible there's an organism that's

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00:33:46,000 --> 00:33:51,000
evolved to take advantage of it.
I've just oversimplified it here,

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but you should know that.  And the
bottom line is if it's

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thermodynamically possible.
And, again, this whole lecture could

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00:34:01,000 --> 00:34:06,000
have been done in a thermodynamic
mode.  We could have looked at which

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redox couples were energetically
possible and then assigned those to

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particular microbes.
But for now I just want you to get

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00:34:17,000 --> 00:34:22,000
the overview.  But for anything
that's thermodynamically feasible

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00:34:22,000 --> 00:34:28,000
there's a microbe out there
that's doing it.

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And, in fact, microbiologists
actually comb through redox tables

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00:34:32,000 --> 00:34:37,000
and put together different redox
couples and hypothesize.

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I ought to be able to find an
organism that does this in that

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00:34:41,000 --> 00:34:46,000
environment.  And then they go out.
And they can almost always actually

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00:34:46,000 --> 00:34:50,000
find it.  So they're incredibly
versatile.  And it gives you a

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00:34:50,000 --> 00:34:55,000
really good strong feeling for the
power of thermodynamics in driving

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00:34:55,000 --> 00:35:00,000
the evolution of these biochemical
processes.

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Finally, before we show you the
movie I want to show you what this

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00:35:07,000 --> 00:35:15,000
thing is all about.
There was a Russian microbiologist

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00:35:15,000 --> 00:35:23,000
back in the previous century
named Winogradsky --

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00:35:23,000 --> 00:35:33,000
-- who wanted to isolate some of

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00:35:33,000 --> 00:35:39,000
these photosynthetic bacteria.
And knowing what their

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00:35:39,000 --> 00:35:45,000
characteristics were he went out and
got himself some mud and some pond

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00:35:45,000 --> 00:35:52,000
water.  And he set up what we've
come to call a Winogradsky column.

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00:35:52,000 --> 00:35:58,000
This is a Winogradsky juice bottle,
but it works the same.  And what you

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00:35:58,000 --> 00:36:05,000
do is you put mud in the bottom and
you put pond water here.

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00:36:05,000 --> 00:36:09,000
And the pond water has basically an
inoculum.  It has representatives of

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00:36:09,000 --> 00:36:13,000
all different types of bacteria.
They might be spores.  If they

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00:36:13,000 --> 00:36:17,000
don't like the environment they're
in they sporulates and then they

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00:36:17,000 --> 00:36:21,000
just don't germinate.
But presumably in pond water you

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00:36:21,000 --> 00:36:25,000
have everything that could possibly
grow in here.  And in the mud you

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00:36:25,000 --> 00:36:29,000
add a source of sulfate.
And so you might add calcium

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00:36:29,000 --> 00:36:33,000
sulfate and you might add a little
organic matter,

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00:36:33,000 --> 00:36:38,000
you know, plant parts or something
just to jumpstart it.

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00:36:38,000 --> 00:36:45,000
And eventually you set up a gradient
here of hydrogen sulfide and oxygen.

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And over time the organisms grow
along that gradient.

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00:36:53,000 --> 00:37:01,000
So you'll end up down here with the
anaerobic respiration.

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00:37:01,000 --> 00:37:08,000
In fact, the organisms generate this

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00:37:08,000 --> 00:37:12,000
gradient.  When you start out the
whole thing is oxygenated.

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00:37:12,000 --> 00:37:16,000
And what you should think about in
this context is what happens.

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00:37:16,000 --> 00:37:20,000
How do these gradients get
generated when you start out with a

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00:37:20,000 --> 00:37:24,000
completely mixed system,
everything in there, everything

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00:37:24,000 --> 00:37:29,000
oxygenated?  Eventually
you have anaerobic --

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00:37:29,000 --> 00:37:33,000
First you'll just have anaerobic
respiration, right?

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00:37:33,000 --> 00:37:38,000
Anything that can use organic
carbon and oxygen is going to go

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00:37:38,000 --> 00:37:42,000
like mad, and that's what's going to
draw the oxygen down.

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00:37:42,000 --> 00:37:47,000
Then you'll have anaerobic
respiration here.

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00:37:47,000 --> 00:37:51,000
You'll have photosynthesis up here,
evolving oxygen.  You'll have

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00:37:51,000 --> 00:37:56,000
chemosynthetic bacteria here because
they need a little bit of oxygen but

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00:37:56,000 --> 00:38:00,000
they also need some of this hydrogen
sulfide and photosynthetic

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00:38:00,000 --> 00:38:07,000
bacteria here.

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00:38:07,000 --> 00:38:11,000
Well, they're like down here.
Because they need light but cannot

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00:38:11,000 --> 00:38:16,000
have oxygen.  And so you can set
these up.  And this purple band here

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tells you that you've got your
photosynthetic bacteria.