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Good morning, class.

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I just wanted to spend the first
couple minutes clearing up three

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issues. None is a major conceptual
issue, but we like to focus on

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details and get them right,
get them correct here as well.

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Firstly, I misdrew a reaction
last time that described why RNA is

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alkali labile, i.e., if
we have high pH we call

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that an alkali pH, or
an alkaline pH, actually,

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to use the adjective. And we
said that hydroxyl groups can

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cause the cleavage of the
phosphodiester bonds of RNA but not

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DNA. And the way I described that
happening is that the alkali group

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causes the formation of this
five-membered ring right here,

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two carbons, two oxygens and
a phosphate. And that resolves

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eventually to this where there's
no longer any connection with the

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ribonucleoside monophosphate
below. And I drew it like this,

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without an oxygen, and
that's a no-no because,

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in fact, in truth, and
as many of you picked up,

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this reverts to a two prime hydroxyl.
So, please note there's a mistake

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there. There's also a couple
other mistakes. For example,

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in the textbook it gives you the
impression that when you polymerize

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nucleic acids you use a
monophosphate to do so.

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And, if you listened to my lecture
last time, that doesn't make any

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sense, because you need to invest
the energy of a triphosphate in

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order to create enough energy
to generate enough energy for the

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polymerization. The
textbook is incorrect there.

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Textbooks are written by
people, for better or worse,

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and as such, like everything else,
they are a mortal and fallible. So,

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the truth of the matter is, when
you're polymerizing DNA or RNA you

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need one of the four ribonucleoside
or deoxyribonucleoside triphosphates

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in order to donate the energy that
makes possible this polymerization.

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And please note that is a
mistake in the book. Recall,

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as I said last time, the
fact that ATP is really the

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currency of energy in the cell,
and that its energy is stored and

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coiled up in this pent up spring
where the mutual electrostatic

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repulsion between the three
negatively charged phosphates

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carries with it enormous
potential energy.

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And some of that potential
energy can be realized,

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during the synthesis of
polymerization of nucleic acids by

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cleaving this bond here. One
can also generate potential

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energy by cleaving this bond here.
This is the alpha, the beta and the

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gamma-phosphate. And
cleavage of either can create

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substantial energy, which in
turn can, as we'll indicate

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shortly, be invested in
other reactions. The reaction

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of polymerization. A second
point I'd like to make to

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you is the following,
and you'd say it's kind of

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coincidence. The currency
of energy in the cell is ATP,

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adenosine triphosphate,
we see its structure here,

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and this happens to be one of
the four precursors of the RNA.

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So, the same molecule is used in
these two different ostensively

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unrelated applications. One,
to polymerize to make RNA

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where genetic information
is stored and conveyed.

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Or, alternatively it's used here in
this context in order to serve as a

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currency for energy. High
energy as ATP. ADP with a

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little lower energy. AMP
monophosphate with even lower

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energy. And you might ask yourself,
scratch your head and say why is the

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same molecule used for
these two different things?

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In fact, there are yet
other applications of these

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ribonucleosides which also seem to
be unrelated to the storage or the

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conveyance of genetic
information. And it is believed,

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probably correctly, that the reason
why the same molecule is used for

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these totally different applications
is that early in the evolution of

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life on this planet there really
were a rather small number of

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biological molecules that existed.
Indeed, as we'll mention again

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later, it's probably the case that
the first organisms didn't use DNA

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as genomes. It's an article of
faith with us that one stores

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genetic information
in DNA molecules.

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And I implied that quite
explicitly last time. But,

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the fact of the matter is,
it's probably the case that the

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first organism, the first
pre-cellular life forms

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used RNA as the genetic material,
RNA to store things, replicating RNA

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via double-stranded RNA molecules
as a way of archiving genetic

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information. And only later during
the evolution of life on this planet,

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when that later was we can't tell,
but it could have been a hundred or

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two hundred years later.
Obviously, if we're talking about

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the origin of life as between 3.
and 3.5 billion years ago, we can't

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really localize that in time
very well, but only later was DNA

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assigned the job of storing,
in a stable fashion, genetic

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information. And as a consequence,
we come to realize as well yet

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another discovery, which is
that all the catalysts that

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we're going to talk about today,
the enzymes as we call them, almost

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all modern-day enzymes are proteins.
And we talked about them briefly

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before. But over the last 15 years,
20 years there's been the discovery

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that certain RNA molecules also
posses the ability to catalyze

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certain kinds of reactions.
When I was taking biochemistry,

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if somebody would have told me that,
I would have called the psychiatric

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ward because that was
such an outlandish idea.

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How can an RNA molecule
catalyze a biochemical reaction?

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It doesn't have all the side
groups that one needs to create the

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catalytic sites for reactions.
But we now realize, on the basis of

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research which actually led to a
Nobel Prize being awarded about five

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years ago, that RNA molecules are
able to catalyze certain kinds of

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reactions. And that begins to
give us an insight into how life

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originated on this planet because
RNA molecules may have stored

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genetic information, as I
said before, RNA molecules,

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or their precursors like ATP, may
have been their currency for storing

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high energy bonds,
as is indicated here.

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And RNA molecules may well have been
the first enzymes to catalyze many

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of the reactions in the most
primitive life forms that first

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existed on this planet. And,
therefore, what I'm saying is

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that as life developed in the first
hundred or two hundred million years,

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who knows how long it took,
gradually DNA took over the job of

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storing information from RNA and
gradually proteins took over the job

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of mediating catalysis, of
acting as enzymes to taking over

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the job from RNA molecules.
Today there are certain vestigial

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biochemical reactions
which we believe are relics,

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echoes of the beginning of life on
earth, which are still mediated by

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RNA catalysts. We think
that they are throwbacks

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to these very early steps, maybe
even in pre-cellular life form

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where RNA was delegated with
the task of acting as a catalyst.

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We're going to focus a lot today
on the whole issue of biochemical

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reactions and the issue of
energy. And this gets us into the

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realization that there really are
two kinds of biochemical reactions.

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Some of you may have
learned this a long time ago.

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Either exergonic reactions
that release energy,

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that produce energy as they proceed,
or conversely endergonic reactions

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which require an investment of
energy in order to move forward.

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So, here, obviously, if this
is a high energy state and

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we're talking about the
free energy of the system,

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which is one way to depict in
thermodynamic language how much

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energy is in a molecule, if we
go from a high energy state to

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a low energy state then we can draw
this like this and we can realize

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that in order to conserve energy,
the energy that was inherent in this

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molecule, the high potential energy
is released as this ball or this

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molecule rolls down the
hill. And, therefore,

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the reaction yields energy,
it's exergonic. And, conversely,

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if we want this reaction to proceed,
we need to invest free energy in

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order to make it happen. The
free energy happens to be,

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more often than not, in
the form of chemical bonds,

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i.e., energy that can be invested,
for example, by taking advantage of

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the potential energy stored
in these phosphodiester,

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in these phosphate-phosphate
linkages indicated right here.

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Here, by the way, is the
space-filling model of ATP

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just for your information.
That's the way it actually would

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look in life, and this is
the way we actually draw it.

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Now, having said that, if
we look at the free energy

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profile of various biochemical
changes then we can depict them,

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once again, in this
very schematic way here.

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And, by the way, free
energy is called G,

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the Gibbs free energy after Josiah
Gibbs who was a thermodynamic wiz in

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the 19th century at Yale in New
Haven. And here what we see is that

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the change in free energy between
the reactants and the products is

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given by delta G.
So, by definition,

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we start out the
reaction with reactants.

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And we end up at the end of
the reaction with products.

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And, overall, if the reaction is
exergonic and will proceed forward,

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it releases energy. And the net
release of energy is indicated here

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by delta G. But,
more often than not,

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biochemical reactions that
are energetically favored,

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that are exergonic actually
can't happen spontaneously.

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They don't happen spontaneously
because, for various reasons,

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they have to pass through
an intermediate state.

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Which actually represents a much
higher free energy than the initial

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reactants posses. And
this higher free energy,

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that they need to acquire in order
to move over the hill and down into

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the valley, is called the energy of
activation, the activation energy.

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And, therefore, if I were to
supply these reactants with energy,

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for instance, let's say I were
to heat up these reactants and

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therefore give them a higher degree
of thermal energy which they might

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be able to use to move up
to this high energy state.

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I supplied them with free
energy by giving them heat.

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Then they might be able to move up
to here and then roll down the hill.

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But in the absence of actually
actively intervening and supplying

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them that energy,
they'll remain right here,

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and they may remain right
there for a million years,

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even though in principle, if
they were to reach down here,

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they would be much happier in
terms of reaching a much lower

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energy state. To
state the obvious,

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all these kinds of reactions wish
to reach the lowest energy state

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possible. But in real-time it can't
happen if there is a high energy of

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activation. Now,
what do enzymes do?

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As always, I'm glad I asked that
question. What they do is they

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lower the energy of activation.
And this is in one sense obvious,

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and in one sense it's subtle,
because enzymes have no affect on

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the free energy state of the
reactants, they have no affect on

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the free energy of the products.
All they do is to lower the hump,

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and they may lower
it very substantially.

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And because they
lower it substantially,

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it might be that some of
the reactants here may,

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just through a chance,
acquisition of thermal energy,

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be able to move over the much
lowered hump and move down into this

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state right here. Now, the
actual difference in the

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Gibbs free energy is
totally unaffected.

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All that happens is that the enzyme,
by lowering the energy of activation,

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make this possible in real-time.
The fact is that ultimately, if one

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were to plot many kinds of
reactions, many reactions,

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as is indicated here, have a
very high activation energy,

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and therefore we look at it like
this. But there could be other

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reactions which might have an
activation energy that looks like

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this, almost nothing at all.
And these reactions could happen

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spontaneously at room temperature
in the absence of any intervention by

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an enzyme. For example, let's
say we're talking about a

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carboxyl group which discharges
a proton. We've talked about that

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already. Well, that reaction
happens spontaneously

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at room temperature. It
doesn‘t need an enzyme to make

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it happen. It can happen
because there's essentially not

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energy of activation.
But the great majority of

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biochemical reactions do have
such an activation energy,

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and therefore do require a lowering
like this in order to take place.

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Now, let's imagine other versions
of the energy profile of a reaction.

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And keep in mind that what I'm
showing here on the abscissa is just

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the course of the reaction.
You could imagine I'm not really

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plotting time. I'm just
talking about a situation

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where to the left the reaction
hasn't happened and to the right it

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has happened. Can you see this
over there? Then I won't write over

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there. All right.
Let's see if this works.

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Boy, here we are in the 21st century
and we still haven't worked this out.

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OK. Everybody can see
this right here, right? OK.

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So, look. Let's imagine we have
a reaction that looks like this,

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a reaction profile that looks like
this, where these two energies are

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actually equivalent. OK?
I've tried to draw them on.

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Well, they're not exactly, but
they're pretty much on exactly

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the same level. And let's
say we start out with a

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large number of molecules right over
here. Now, if there were an enzyme

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around, the enzyme might lower
the activation energy and,

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in so doing, make it possible for
molecules to tunnel through this

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hill and move over here. The
fact that when a molecule gets

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over here it has the same free
energy as over there means that the

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catalyst may, in principle,
also facilitate a back reaction.

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What do I mean by a back reaction?
I mean going in exactly the

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opposite direction. And
so, once molecules over here

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are formed, the energy lowering
affects of the enzyme may allow them

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to move in both directions.
And, therefore, what we will have

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00:15:50,000 --> 00:15:54,000
is ultimately the
establishment of an equilibrium.

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00:15:54,000 --> 00:15:58,000
If these two energy
states are equivalent then,

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00:15:58,000 --> 00:16:02,000
I will tell you, 50% of the
molecules end up here and 50% of the

225
00:16:02,000 --> 00:16:06,000
molecules end up here. And
here we're beginning now to

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00:16:06,000 --> 00:16:10,000
wrestle between two different
independent concepts,

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00:16:10,000 --> 00:16:14,000
the rate of the reaction and the
equilibrium state of the reaction.

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00:16:14,000 --> 00:16:19,000
Note that the enzyme has no affect
whatsoever on the equilibrium state.

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00:16:19,000 --> 00:16:23,000
These two are at equal free
energies, the equilibrium state.

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00:16:23,000 --> 00:16:27,000
Whether the energy barrier is
this high or whether it's this

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00:16:27,000 --> 00:16:32,000
high is irrelevant. The
fact is if the enzyme makes

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00:16:32,000 --> 00:16:36,000
possible this motion back and forth,
the ultimate equilibrium state will

233
00:16:36,000 --> 00:16:40,000
be 50% of the molecules here
and 50% of the molecules there.

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00:16:40,000 --> 00:16:44,000
And, therefore, the enzyme really
only affects the rate at which the

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00:16:44,000 --> 00:16:48,000
reaction takes place. Will
it happen in a microsecond or

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00:16:48,000 --> 00:16:52,000
will it happen in a day or will
it happen in a million years?

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00:16:52,000 --> 00:16:56,000
The enzyme has no affect whatsoever
on the ultimate end product,

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00:16:56,000 --> 00:17:00,000
which in this case
is the equilibrium.

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00:17:00,000 --> 00:17:06,000
Of course, there is a simple
mathematic formalism which relates

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00:17:06,000 --> 00:17:12,000
the difference in free
energies with the equilibrium.

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00:17:12,000 --> 00:17:18,000
Here we might have a situation
where 80% of the molecules end up at

242
00:17:18,000 --> 00:17:24,000
equilibrium over here and 20% end
up here. Or, we might end up as a

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00:17:24,000 --> 00:17:30,000
state where 99. % of the
molecules end up here and 0.

244
00:17:30,000 --> 00:17:34,000
% of the molecules end up here.
But that ultimate equilibrium state

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00:17:34,000 --> 00:17:38,000
is no way influenced by the
enzyme. They just make it happen in

246
00:17:38,000 --> 00:17:42,000
real-time. And, therefore,
to repeat and echo a

247
00:17:42,000 --> 00:17:46,000
point I made last time, if most
biochemical reactions are to

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00:17:46,000 --> 00:17:50,000
occur in real-time, i.e.,
in the order of seconds or

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00:17:50,000 --> 00:17:54,000
minutes, an enzyme has to be
around to make sure they happen.

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00:17:54,000 --> 00:17:58,000
In the absence of such an
enzyme of its intermediation,

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00:17:58,000 --> 00:18:02,000
it just won't happen in real-time.
Even though, in principle,

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00:18:02,000 --> 00:18:06,000
it's energetically favored. So,
let's just keep that very much

253
00:18:06,000 --> 00:18:11,000
in mind in the course of discussions
that happen. And let's just begin

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00:18:11,000 --> 00:18:15,000
now to look at an important
energy-generating reaction in the

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00:18:15,000 --> 00:18:20,000
cell which is called glycolysis.
We already know the prefix glycol.

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00:18:20,000 --> 00:18:24,000
Glyco refers to sugar. And lysis,
L-Y-S-I-S refers to the breakdown of

257
00:18:24,000 --> 00:18:29,000
a certain compound. I
am not going to ask you,

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00:18:29,000 --> 00:18:33,000
nor is anyone else in the room
going to ask you to memorize this

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00:18:33,000 --> 00:18:37,000
sequence of reactions. But
I'd like you to look at it and

260
00:18:37,000 --> 00:18:41,000
see what take-home lessons
we can distill out of that,

261
00:18:41,000 --> 00:18:45,000
what wisdom we can learn from
looking at such a complex series of

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00:18:45,000 --> 00:18:49,000
reactions. Perhaps, the first
thing we can learn is that

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00:18:49,000 --> 00:18:53,000
when we think about biochemical
reactions, we don't think of them as

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00:18:53,000 --> 00:18:57,000
happening in isolation.
Here I'm talking about,

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00:18:57,000 --> 00:19:01,000
for example, in this case I could be
talking A plus B going to C plus D,

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00:19:01,000 --> 00:19:05,000
and there might be a back
reaction to reach equilibrium.

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00:19:05,000 --> 00:19:09,000
And we're just isolating that simple
reaction from all others around it.

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00:19:09,000 --> 00:19:13,000
But in the real world in living
cells most reactions are parts of

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00:19:13,000 --> 00:19:17,000
very long pathways where each of
these steps here indicates one of

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00:19:17,000 --> 00:19:21,000
the others, a step in the pathway.
What we're interested in here is

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00:19:21,000 --> 00:19:25,000
how glucose, which I advertised two
lectures ago as being an important

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00:19:25,000 --> 00:19:30,000
energy source, is
actually broken down.

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00:19:30,000 --> 00:19:34,000
How does the cell harvest the
energy, which is inherent in glucose,

274
00:19:34,000 --> 00:19:38,000
in order to generate, among other
things, ATP, which we've said

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00:19:38,000 --> 00:19:42,000
repeatedly is the energy currency?
ATP is used by hundreds of

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00:19:42,000 --> 00:19:47,000
different biochemical reactions
in order to make them happen.

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00:19:47,000 --> 00:19:51,000
These other biochemical
reactions are endergonic,

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00:19:51,000 --> 00:19:55,000
they require the investment of
energy, and almost invariably,

279
00:19:55,000 --> 00:19:59,000
but not invariably, but almost
invariably the cell will grab hold

280
00:19:59,000 --> 00:20:04,000
of an ATP molecule, break it
down usually to AMP or ADP.

281
00:20:04,000 --> 00:20:08,000
And then utilize the energy, which
derives from breaking down ATP,

282
00:20:08,000 --> 00:20:13,000
it will invest that energy
in an endergonic reaction,

283
00:20:13,000 --> 00:20:18,000
which in the otherwise would not
happen. So, here we reach the idea

284
00:20:18,000 --> 00:20:23,000
that perhaps by investing energy
in a reaction, the equilibrium is

285
00:20:23,000 --> 00:20:28,000
shifted. Because by
investing energy, actually,

286
00:20:28,000 --> 00:20:33,000
the cell is able to lower the free
energy state between these two.

287
00:20:33,000 --> 00:20:36,000
And that makes it possible for their
equilibrium to be much more favored.

288
00:20:36,000 --> 00:20:40,000
Let's look at this glycolytic
pathway. Glycolytic refers,

289
00:20:40,000 --> 00:20:44,000
obviously, to glycolysis. And
here we start out with glucose.

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00:20:44,000 --> 00:20:48,000
We're drawing it out flat rather
than the circular structure we

291
00:20:48,000 --> 00:20:52,000
talked about last time. And
let's look at what happens here,

292
00:20:52,000 --> 00:20:56,000
again, not because anyone
wants you to memorize this,

293
00:20:56,000 --> 00:21:00,000
but because some of the details
are in themselves very illustrative.

294
00:21:00,000 --> 00:21:04,000
The goal of this exercise is
to create ATP for the cell,

295
00:21:04,000 --> 00:21:08,000
but the first step in the
reaction is actually totally

296
00:21:08,000 --> 00:21:12,000
counterproductive. Look
at the first thing that

297
00:21:12,000 --> 00:21:16,000
happens. The first thing that
happens is that the cell invests an

298
00:21:16,000 --> 00:21:20,000
ATP molecule to make glucose-6-phosphate.

299
00:21:20,000 --> 00:21:24,000
I've advertised the goal of
this is to generate ATP from ADP,

300
00:21:24,000 --> 00:21:28,000
adenosine diphosphate.
But the first thing here,

301
00:21:28,000 --> 00:21:32,000
this is an endergonic reaction in
which the cell invests energy to

302
00:21:32,000 --> 00:21:35,000
create this molecule here.
So, this doesn't make sense.

303
00:21:35,000 --> 00:21:38,000
But ostensively it must make sense,
at one level or another, because you

304
00:21:38,000 --> 00:21:42,000
and I, we're all here,
and everybody in this room,

305
00:21:42,000 --> 00:21:45,000
at least this moment
is metabolically active.

306
00:21:45,000 --> 00:21:48,000
All right. So, we've
got this molecule here,

307
00:21:48,000 --> 00:21:51,000
glucose-6-phosphate.
And this can isomerize.

308
00:21:51,000 --> 00:21:55,000
You see, here's glucose-6-phosphate, fructose-6-phosphate.

309
00:21:55,000 --> 00:21:58,000
And, the fact of the matter is,
there's no oxidation reduction

310
00:21:58,000 --> 00:22:02,000
reaction here. It's
just an isomerization.

311
00:22:02,000 --> 00:22:06,000
And this molecule and this molecule
are virtually in the same free

312
00:22:06,000 --> 00:22:10,000
energy state. It happens to be the
case that their profile will look

313
00:22:10,000 --> 00:22:14,000
very much like the one I drew you
before. Their energy profile will

314
00:22:14,000 --> 00:22:18,000
look like this. And one
needs an enzyme to lower it,

315
00:22:18,000 --> 00:22:22,000
but there's no energy that needs to
be invested in converting one to the

316
00:22:22,000 --> 00:22:26,000
other because they're very similar
molecules and therefore incomparable

317
00:22:26,000 --> 00:22:31,000
free energy states. Now
look at the next step.

318
00:22:31,000 --> 00:22:35,000
The next step is again
another ostensively totally

319
00:22:35,000 --> 00:22:39,000
counterproductive way of
generating energy. Because,

320
00:22:39,000 --> 00:22:44,000
once again, ATP, the gamma-phosphate,
its energy is invested in creating a

321
00:22:44,000 --> 00:22:48,000
dephosphorylated hexose, fructose
1, 6-diphosphate where the

322
00:22:48,000 --> 00:22:52,000
numbers refer obviously to
the identities of the carbon.

323
00:22:52,000 --> 00:22:57,000
And now we have a
dephosphorylated fructose molecule.

324
00:22:57,000 --> 00:23:01,000
And so here you can actually
see what the three-dimensional,

325
00:23:01,000 --> 00:23:05,000
what we would imagine closer to what
the three-dimensional structures of

326
00:23:05,000 --> 00:23:09,000
these molecules look like. And
we shouldn't focus this time on

327
00:23:09,000 --> 00:23:13,000
whether it's this or this.
For all practical purposes,

328
00:23:13,000 --> 00:23:17,000
let's just focus on this
pathway here. And here,

329
00:23:17,000 --> 00:23:21,000
for the first time, what now
happens is that this hexose

330
00:23:21,000 --> 00:23:25,000
is broken down into two trioses,
i.e., into two three carbon sugars.

331
00:23:25,000 --> 00:23:30,000
And this is a slightly
exergonic reaction.

332
00:23:30,000 --> 00:23:33,000
It yields, it happens without
the investment of energy.

333
00:23:33,000 --> 00:23:37,000
And there's an enzyme, once
again, that's required in order

334
00:23:37,000 --> 00:23:40,000
to catalyze it. But
let's be really clear now.

335
00:23:40,000 --> 00:23:44,000
Now we have to follow
the fate of two molecules.

336
00:23:44,000 --> 00:23:47,000
The first triose and the second
triose. They have different names,

337
00:23:47,000 --> 00:23:51,000
but we're not going to focus on the
names. One thing you notice about

338
00:23:51,000 --> 00:23:54,000
these trioses is that they're
readily interconvertible.

339
00:23:54,000 --> 00:23:58,000
Once again, we can image
that we have a situation that

340
00:23:58,000 --> 00:24:02,000
looks like this. These are
flipping back and forth.

341
00:24:02,000 --> 00:24:06,000
And therefore, for all practical
purposes from our point of view,

342
00:24:06,000 --> 00:24:10,000
these two are equivalent because
they can be exchanged virtually

343
00:24:10,000 --> 00:24:14,000
instantaneously one with the other.
Now, so far we've actually expended

344
00:24:14,000 --> 00:24:19,000
energy. We haven't harvested
energy. But, keep in mind,

345
00:24:19,000 --> 00:24:23,000
the old economic dictum; you have
to invest money to make money.

346
00:24:23,000 --> 00:24:27,000
And that's what's going on here.
The first thing that happens is we

347
00:24:27,000 --> 00:24:32,000
have an oxidation reaction.
What's an oxidation reaction?

348
00:24:32,000 --> 00:24:36,000
We want to strip some electrons,
a pair of electrons off of this

349
00:24:36,000 --> 00:24:41,000
particular triose,
the 3 carbon sugar.

350
00:24:41,000 --> 00:24:46,000
And by stripping off a pair of
electrons we donate the electrons

351
00:24:46,000 --> 00:24:50,000
from NAD+ to NADH. And here
these structures are given

352
00:24:50,000 --> 00:24:55,000
in your book. But NADH, it
turns out, is the electrons are

353
00:24:55,000 --> 00:25:00,000
pulled away from the triose and
they're used to reduce NAD+ to NADH.

354
00:25:00,000 --> 00:25:04,000
Keep in mind that in an oxidation
reaction, one molecule that's being

355
00:25:04,000 --> 00:25:08,000
oxidized is deprived, is
denied a pair of electrons.

356
00:25:08,000 --> 00:25:12,000
The other molecule that's
being reduced, in this case NAD,

357
00:25:12,000 --> 00:25:16,000
acquires a pair of electrons.
And you can focus, if you want,

358
00:25:16,000 --> 00:25:20,000
about the charge of these molecules,
one or the other. But, keep in mind,

359
00:25:20,000 --> 00:25:24,000
that in these oxidation reduction
reactions, whether it's plus charged

360
00:25:24,000 --> 00:25:28,000
or minus charged is irrelevant.
The real name of the game is the

361
00:25:28,000 --> 00:25:31,000
electrons. Forget
about the protons,

362
00:25:31,000 --> 00:25:35,000
whether it has a plus charge or it's
neutral. The real name of the game

363
00:25:35,000 --> 00:25:38,000
here is that two electrons are being
used to reduce this molecule to this.

364
00:25:38,000 --> 00:25:42,000
By the way, third mistake
I forgot to tell you before,

365
00:25:42,000 --> 00:25:45,000
there's a double-bond in one of the
pyrimidines in the book that doesn't

366
00:25:45,000 --> 00:25:49,000
make any sense. Whoever
finds it gets a prize,

367
00:25:49,000 --> 00:25:53,000
but no one's figured out
what the prize is yet. So,

368
00:25:53,000 --> 00:25:56,000
this double bond gets reduced.
You see the difference between this

369
00:25:56,000 --> 00:26:00,000
and this over here. And
this NADH, it turns out,

370
00:26:00,000 --> 00:26:04,000
is a high energy molecule. The
street value of NADH is three

371
00:26:04,000 --> 00:26:10,000
ATPs, i.e., in the mitochondria NADH
can be used to generate three ATPs,

372
00:26:10,000 --> 00:26:15,000
and that's worth something. So,
NADH on its own is a high energy

373
00:26:15,000 --> 00:26:20,000
molecule. It can't be used for that
many things, but it can be pulled

374
00:26:20,000 --> 00:26:26,000
into the mitochondria where
it's converted to three ATPs.

375
00:26:26,000 --> 00:26:31,000
So, we say, well, we're starting
to make some money out of this

376
00:26:31,000 --> 00:26:37,000
investment because we've
made, in fact, these NADHs.

377
00:26:37,000 --> 00:26:41,000
See right here. Why
do we say two NADHs?

378
00:26:41,000 --> 00:26:46,000
Because there are two trioses we're
working with, and each one of the

379
00:26:46,000 --> 00:26:50,000
trioses gives you an NADH.
So, everything that's going on

380
00:26:50,000 --> 00:26:55,000
after this, starting from the top
here, is now double because we're

381
00:26:55,000 --> 00:26:59,000
looking at the parallel behaviors
of two identical three carbon sugars.

382
00:26:59,000 --> 00:27:04,000
So, here we've so far generated,
in principle, six ATPs.

383
00:27:04,000 --> 00:27:08,000
How much did we invest
already up to this point? Two.

384
00:27:08,000 --> 00:27:13,000
We invested two but we harvested
six. Already we're starting to make

385
00:27:13,000 --> 00:27:18,000
a little money because I told you
the street value of an NADH is three

386
00:27:18,000 --> 00:27:23,000
ATPs on the black market.
OK, so what happens next?

387
00:27:23,000 --> 00:27:27,000
Next is another good thing.
Each of the trioses, one can

388
00:27:27,000 --> 00:27:32,000
actually cause each of the
trioses to generate an ATP molecule

389
00:27:32,000 --> 00:27:36,000
from an ADP.
What happens here?

390
00:27:36,000 --> 00:27:40,000
It turns out that this phosphate
over here is actually in a pretty

391
00:27:40,000 --> 00:27:43,000
high energy state, in no
small part because of electron

392
00:27:43,000 --> 00:27:47,000
negative-negative repulsion. And
by stripping this phosphate off

393
00:27:47,000 --> 00:27:51,000
this high energy phosphate
stripped off of this molecule here,

394
00:27:51,000 --> 00:27:54,000
whose name we will ignore,
allows us to phosphorylate an ATP.

395
00:27:54,000 --> 00:27:58,000
And since there are two
trioses being converted, we're

396
00:27:58,000 --> 00:28:02,000
going to get two
ATPs. So, in effect,

397
00:28:02,000 --> 00:28:06,000
now we're actually ahead.
We started out investing two,

398
00:28:06,000 --> 00:28:10,000
we got six back from the NADHs,
and we're getting two back here.

399
00:28:10,000 --> 00:28:14,000
So, we've made two ATPs. This
is a good thing. Keep in mind,

400
00:28:14,000 --> 00:28:19,000
ADP is lower energy, ATP is
a high energy. Once again,

401
00:28:19,000 --> 00:28:23,000
we have an isomerization where
these two molecules are at comparable

402
00:28:23,000 --> 00:28:27,000
states here and here, where
the phosphate just jumps over

403
00:28:27,000 --> 00:28:32,000
to this state. And this
hydrolyzes spontaneously

404
00:28:32,000 --> 00:28:37,000
and we get this molecule right over
here, phosphoenolpyruvate at the end.

405
00:28:37,000 --> 00:28:42,000
And, once again,
we harvest two ATPs,

406
00:28:42,000 --> 00:28:47,000
one ATP from each of the trioses.
And we end up, at the end of this

407
00:28:47,000 --> 00:28:52,000
reaction, with pyruvate. And
you'll say this is terrific

408
00:28:52,000 --> 00:28:57,000
because we invested two ATPs, we
harvested four, plus we got six

409
00:28:57,000 --> 00:29:03,000
from the NADHs, right? Two
NADHs, each NADH gives us three

410
00:29:03,000 --> 00:29:11,000
each, so let's do the arithmetic.
Let's do the balance sheet. We

411
00:29:11,000 --> 00:29:18,000
invested to begin with, with
the one glucose, we invested

412
00:29:18,000 --> 00:29:26,000
two ATPs. That was early on. Then
the return was first two NADHs,

413
00:29:26,000 --> 00:29:33,000
which I've told you equals six ATPs.
Because an NADH is worth three ATPs.

414
00:29:33,000 --> 00:29:39,000
This is so far good. And now
subsequently we've made four ATPs so

415
00:29:39,000 --> 00:29:46,000
that the net yield looks pretty
useful. Six plus four is ten minus

416
00:29:46,000 --> 00:29:52,000
two, a profit of eight ATPs
from one glucose molecule.

417
00:29:52,000 --> 00:29:59,000
This is terrific you may
say, but there's a rub.

418
00:29:59,000 --> 00:30:04,000
There's a catch. If
glycolysis is occurring in the

419
00:30:04,000 --> 00:30:10,000
absence of oxygen, if that
happens, then we have a

420
00:30:10,000 --> 00:30:15,000
problem here, because the only way
that these NADHs can generate ATP is

421
00:30:15,000 --> 00:30:21,000
if there is oxygen around to take
these electron pairs and use them to

422
00:30:21,000 --> 00:30:27,000
reduce an oxygen molecule.
That is, by the way, part of the

423
00:30:27,000 --> 00:30:32,000
reason we breathe. Keep in
mind that when you generate

424
00:30:32,000 --> 00:30:36,000
an NADH from an NAD molecule,
you need to regenerate the NAD.

425
00:30:36,000 --> 00:30:40,000
You can't just accumulate more and
more NADHs. You need to regenerate

426
00:30:40,000 --> 00:30:44,000
the NAD. And,
therefore, this NADH,

427
00:30:44,000 --> 00:30:48,000
with their electron pairs, the
electron pairs have some to be

428
00:30:48,000 --> 00:30:52,000
disposed of. You have to regenerate
NAD. You can't just make more and

429
00:30:52,000 --> 00:30:56,000
more and more of this. So,
how do cells get rid of it?

430
00:30:56,000 --> 00:31:00,000
Well, how they get
rid of it is simple.

431
00:31:00,000 --> 00:31:05,000
You take the electron pairs
and you slap them onto oxygen,

432
00:31:05,000 --> 00:31:10,000
and that's really called combustion.
And you get a lot of energy out of

433
00:31:10,000 --> 00:31:16,000
that. But what happens if all of
this is occurring anaerobically?

434
00:31:16,000 --> 00:31:21,000
Anaerobically means the reaction is
occurring in the absence of oxygen.

435
00:31:21,000 --> 00:31:27,000
Well, if you have a yeast that's
growing 14 feet underground,

436
00:31:27,000 --> 00:31:31,000
this is happening anaerobically.
If you have a yeast that's

437
00:31:31,000 --> 00:31:35,000
fermenting in a big keg to make
wine or beer, it's also probably

438
00:31:35,000 --> 00:31:39,000
happening anaerobically. If
you start running in a 100 yard

439
00:31:39,000 --> 00:31:43,000
sprint, or let's say you had to
run a mile, then initially there's

440
00:31:43,000 --> 00:31:47,000
enough oxygen, there's
a lot of oxygen around to

441
00:31:47,000 --> 00:31:51,000
allow you to get rid of these NADHs
and dump the electrons that they

442
00:31:51,000 --> 00:31:55,000
have acquired onto the oxygen
molecule. And that's fine.

443
00:31:55,000 --> 00:31:59,000
That's worth a lot because,
in effect, what you're doing is

444
00:31:59,000 --> 00:32:03,000
you're taking oxygen and hydrogen
and you're combusting them together.

445
00:32:03,000 --> 00:32:07,000
And that's great. But as
you start running down the

446
00:32:07,000 --> 00:32:12,000
street, soon the oxygen supply to
your muscles is going to run out,

447
00:32:12,000 --> 00:32:16,000
and soon a lot of the energy
production in your muscles happens

448
00:32:16,000 --> 00:32:21,000
anaerobically. Why?
Because you can't get oxygen

449
00:32:21,000 --> 00:32:26,000
quickly enough to your muscles,
and therefore, for a period of time,

450
00:32:26,000 --> 00:32:30,000
you start feeling that burning
sensation in your muscles because

451
00:32:30,000 --> 00:32:35,000
oxidation of NADH isn't happening.
And these NADHs instead are

452
00:32:35,000 --> 00:32:40,000
regenerated by another way.
How are they regenerated? The

453
00:32:40,000 --> 00:32:45,000
electron pairs of the NADHs,
must be, are dumped back onto this

454
00:32:45,000 --> 00:32:50,000
molecule right here, pyruvate.
They're not used to make

455
00:32:50,000 --> 00:32:55,000
ATP because they can't be used to
make ATP because there's no oxygen

456
00:32:55,000 --> 00:33:01,000
around to accept the electron pairs
that these NADHs have acquired.

457
00:33:01,000 --> 00:33:05,000
And so, what happens
with these valuable NADHs?

458
00:33:05,000 --> 00:33:09,000
Under anaerobic conditions
this doesn't happen.

459
00:33:09,000 --> 00:33:14,000
These NADHs are used instead,
their electrons are donated to our

460
00:33:14,000 --> 00:33:18,000
friend pyruvate here,
these three carbon sugar.

461
00:33:18,000 --> 00:33:23,000
And what happens, when they are
donated back to the pyruvate,

462
00:33:23,000 --> 00:33:27,000
in order to regenerate NAD you need
more NAD to pick up to use later in

463
00:33:27,000 --> 00:33:32,000
the reaction, to use over
again in another reaction.

464
00:33:32,000 --> 00:33:36,000
When you donate the electrons
from NADH back onto pyruvate,

465
00:33:36,000 --> 00:33:41,000
what happens? You get lactic acid.
Lactic acid is what makes your

466
00:33:41,000 --> 00:33:45,000
muscles burn when you're running
very quickly and you can't get

467
00:33:45,000 --> 00:33:50,000
enough oxygen into them to
begin to burn up the NADH.

468
00:33:50,000 --> 00:33:55,000
So, instead of using NADH to
generate ATP, it's diverted to make

469
00:33:55,000 --> 00:34:00,000
lactic acid. That's in one sense
good because you regenerate NAD.

470
00:34:00,000 --> 00:34:04,000
Why do you need to regenerate
NAD? Because you need a lot of NAD

471
00:34:04,000 --> 00:34:09,000
around for the earlier steps
in the reaction. Keep in mind,

472
00:34:09,000 --> 00:34:13,000
early in the reaction you need NAD
here. If you don't regenerate it

473
00:34:13,000 --> 00:34:18,000
then glycolysis grinds to a halt.
So, even though you make NADH and

474
00:34:18,000 --> 00:34:23,000
it's a good thing in principle,
in practice it has to be recycled.

475
00:34:23,000 --> 00:34:27,000
And if it's not recycled to make
more new NAD to allow this step to

476
00:34:27,000 --> 00:34:32,000
happen then the whole glycolytic
reaction will shut down

477
00:34:32,000 --> 00:34:37,000
and you're in a
mess. However, sadly,

478
00:34:37,000 --> 00:34:41,000
in the absence of oxygen, the
only way to recycle this is to

479
00:34:41,000 --> 00:34:46,000
dump these electrons not onto
oxygen which is energy rich,

480
00:34:46,000 --> 00:34:50,000
it's dump them back onto pyruvic
acid creating lactic acid.

481
00:34:50,000 --> 00:34:55,000
So, you reduce this bond
right here. So, you get CH,

482
00:34:55,000 --> 00:35:00,000
COH. This bond right here is
reduced and you get lactic acid.

483
00:35:00,000 --> 00:35:04,000
So, instead of a carbonyl bond
here you have CH and COH right here,

484
00:35:04,000 --> 00:35:09,000
that's a reduction reaction. And
now you're able to regenerate the

485
00:35:09,000 --> 00:35:13,000
NAD. And now you say that's a
great thing. But, keep in mind,

486
00:35:13,000 --> 00:35:18,000
that now the entire glycolytic
reaction, how much is our net profit

487
00:35:18,000 --> 00:35:23,000
now? Before I was gloating about
the fact that we made eight ATPs,

488
00:35:23,000 --> 00:35:27,000
we netted eight ATPs out of this.
What are we back down to now?

489
00:35:27,000 --> 00:35:32,000
What's the whole net yield
now? Well, the TAs can't answer.

490
00:35:32,000 --> 00:35:36,000
It's two, because we invested
two and we got out four.

491
00:35:36,000 --> 00:35:40,000
And it's only two. Now,
why is this so interesting?

492
00:35:40,000 --> 00:35:45,000
Well, until about six hundred
million years ago there wasn't that

493
00:35:45,000 --> 00:35:49,000
much oxygen in the atmosphere.
And in the absence of oxygen this

494
00:35:49,000 --> 00:35:54,000
is almost the only reaction that
could be used in order to generate

495
00:35:54,000 --> 00:35:58,000
energy. And about six hundred
million years ago more and more

496
00:35:58,000 --> 00:36:03,000
oxygen from photosynthesis
became dumped into the atmosphere.

497
00:36:03,000 --> 00:36:08,000
And soon oxygen became available
to organisms like our ancestors.

498
00:36:08,000 --> 00:36:13,000
And then they could actually begin
to recycle this NADH in a much more

499
00:36:13,000 --> 00:36:18,000
productive way. And as a
consequence what happened,

500
00:36:18,000 --> 00:36:23,000
instead of having glycolysis
yielding two, we could go up to this

501
00:36:23,000 --> 00:36:28,000
theoretical eight because the NADHs
could now deposit their electrons on

502
00:36:28,000 --> 00:36:33,000
oxygen, which is
much more profitable.

503
00:36:33,000 --> 00:36:39,000
In fact, I've just told you now
that in the absence of oxygen you can

504
00:36:39,000 --> 00:36:45,000
only make two ATPs. I will
tell you, without providing

505
00:36:45,000 --> 00:36:51,000
it to you, that in the presence
of oxygen you can make 34 ATPs.

506
00:36:51,000 --> 00:36:57,000
And 34 is, we can agree,
much better than two in the

507
00:36:57,000 --> 00:37:01,000
presence of oxygen. Higher
life forms could not evolve

508
00:37:01,000 --> 00:37:05,000
until this much more effective
way of generating energy became

509
00:37:05,000 --> 00:37:09,000
available. And, therefore,
if our ancestors who

510
00:37:09,000 --> 00:37:13,000
lived longer than six hundred
million years ago were very sluggish

511
00:37:13,000 --> 00:37:17,000
and they weren't very smart,
the reason why they were sluggish

512
00:37:17,000 --> 00:37:21,000
and they weren't very smart is
because they couldn't generate the

513
00:37:21,000 --> 00:37:25,000
energy that was required to
efficiently drive metabolism.

514
00:37:25,000 --> 00:37:29,000
The metabolism,
anaerobic metabolism, i.

515
00:37:29,000 --> 00:37:33,000
., occurring in the absence of
energy, is extremely inefficient.

516
00:37:33,000 --> 00:37:39,000
It just doesn't happen very well.
Now, what actually happens if we

517
00:37:39,000 --> 00:37:45,000
have oxygen around? Well,
what happens is something

518
00:37:45,000 --> 00:37:51,000
like this. We take the pyruvate,
which is the product of glycolysis

519
00:37:51,000 --> 00:37:57,000
and which is this much
more primitive pathway,

520
00:37:57,000 --> 00:38:02,000
and we dump it into the mitochondria.
And now we generate through this

521
00:38:02,000 --> 00:38:08,000
cycle here, which I'm not
asking you memorize, please,

522
00:38:08,000 --> 00:38:13,000
don't do that. We generate the
reactions which go from here and get

523
00:38:13,000 --> 00:38:19,000
us up to this 34 ATP yield per
glucose. And the essence of the

524
00:38:19,000 --> 00:38:24,000
citric acid cycle, which
happens in the mitochondria,

525
00:38:24,000 --> 00:38:30,000
keep in mind that the
mitochondria look like this.

526
00:38:30,000 --> 00:38:34,000
Keep in mind that the mitochondrion
are the decedents of bacteria which

527
00:38:34,000 --> 00:38:39,000
parasitized the cytoplasm of cells
probably 1.5 billion years ago.

528
00:38:39,000 --> 00:38:43,000
But if we now look at what
happens in the mitochondrion,

529
00:38:43,000 --> 00:38:48,000
the pyruvate that we generated in
the cytosol, in the soluble part of

530
00:38:48,000 --> 00:38:53,000
the cytoplasm is now pumped into
the mitochondria, and there's a whole

531
00:38:53,000 --> 00:38:57,000
series of reactions that go on
here, which takes this three-carbon

532
00:38:57,000 --> 00:39:02,000
sugar. The first thing
that happens is that

533
00:39:02,000 --> 00:39:06,000
carbon is boiled off. Carbon
dioxide, that's released.

534
00:39:06,000 --> 00:39:10,000
Now we're down to a two carbon
sugar. And then this two carbon

535
00:39:10,000 --> 00:39:14,000
sugar is added to a four carbon
sugar and progressively oxidized.

536
00:39:14,000 --> 00:39:19,000
And as it's oxidized what's spun
off? Well, what's spun off is,

537
00:39:19,000 --> 00:39:23,000
for example, there's NADH
which is spun off, there's ATP.

538
00:39:23,000 --> 00:39:27,000
See, there's an NADH which is spun
off. Here's an NADH that's spun off.

539
00:39:27,000 --> 00:39:32,000
Here is a cousin of NADH.
It's called FADH which,

540
00:39:32,000 --> 00:39:36,000
once again, generates a high
energy molecule. Once again,

541
00:39:36,000 --> 00:39:41,000
the carbon molecules are oxidized,
electrons are stripped away and used

542
00:39:41,000 --> 00:39:45,000
to create these high energy
molecules, FADH and NADH.

543
00:39:45,000 --> 00:39:49,000
By the way, FADH, a cousin of NADH,
is only worth two ATPs on the open

544
00:39:49,000 --> 00:39:54,000
market. Whereas, NADH, as
I've told you repeatedly,

545
00:39:54,000 --> 00:39:58,000
is worth three. And by the time we
add up all of the NADHs that have

546
00:39:58,000 --> 00:40:03,000
been generated by this cycling
and the carbon dioxides that are

547
00:40:03,000 --> 00:40:07,000
releases, at the end of this cycle
here we start with two carbons,

548
00:40:07,000 --> 00:40:12,000
add it to four and we
get a six carbon molecule.

549
00:40:12,000 --> 00:40:16,000
We spew off some carbon dioxides
here and go back to four carbon

550
00:40:16,000 --> 00:40:20,000
sugar. Add another two, go
up to six carbons. Go around

551
00:40:20,000 --> 00:40:24,000
again, spin around the wheel.
And each time we do that we

552
00:40:24,000 --> 00:40:28,000
generate a lot of NADHs,
we generate a lot of FADHs,

553
00:40:28,000 --> 00:40:33,000
and we generate a lot of ATP.
In all cases, these are highly

554
00:40:33,000 --> 00:40:39,000
profitable reactions simply because
the NADHs and the FADHs can be used

555
00:40:39,000 --> 00:40:45,000
in the mitochondrion to generate
ATP. So, let's look at the energy

556
00:40:45,000 --> 00:40:51,000
profile of the entire thing. Put
it all together. This is where

557
00:40:51,000 --> 00:40:57,000
we started out at the beginning,
and this is the end of glycolysis,

558
00:40:57,000 --> 00:41:02,000
OK? So, now we're
adding up the energy

559
00:41:02,000 --> 00:41:06,000
profiles of the whole sequence
of reactions that constituted

560
00:41:06,000 --> 00:41:10,000
glycolysis, which begins up here
and ends right here because pyruvate,

561
00:41:10,000 --> 00:41:14,000
as you will recall, is
the product of glycolysis,

562
00:41:14,000 --> 00:41:18,000
the first step. The
Krebs Cycle happens,

563
00:41:18,000 --> 00:41:22,000
or sometimes it's called
the Citric Acid Cycle. So,

564
00:41:22,000 --> 00:41:26,000
let's just get these words straight.
Citric Acid Cycle because it

565
00:41:26,000 --> 00:41:30,000
happens to be one of the cycles,
or it's sometimes called the Krebs

566
00:41:30,000 --> 00:41:35,000
Cycle after the person who
really discovered it, Krebs.

567
00:41:35,000 --> 00:41:39,000
The Krebs Cycle begins here.
You see how the shading changes

568
00:41:39,000 --> 00:41:43,000
from pyruvate. And here
we go all the way down

569
00:41:43,000 --> 00:41:47,000
there. And let's now look at what
happens in terms of energy exchange.

570
00:41:47,000 --> 00:41:51,000
Recall that early on we needed to
invest ATPs to kick up the energy

571
00:41:51,000 --> 00:41:55,000
state up to here. We
invested ATPs at this stage

572
00:41:55,000 --> 00:42:00,000
right here, and then we
began to get some back.

573
00:42:00,000 --> 00:42:04,000
We got these two NADHs, one
NADH coming from each of the

574
00:42:04,000 --> 00:42:08,000
three carbon sugars. We got
some more ATPs here and we

575
00:42:08,000 --> 00:42:12,000
got some more ATPs here, but
these NADHs could not be used

576
00:42:12,000 --> 00:42:17,000
productively for generating
ATP in the absence of oxygen,

577
00:42:17,000 --> 00:42:21,000
but in the presence of oxygen
now we can begin to use these very

578
00:42:21,000 --> 00:42:25,000
profitably. Each of these makes
three ATPs and each of these,

579
00:42:25,000 --> 00:42:30,000
obviously, makes ATPs. And
then let's look at what happens

580
00:42:30,000 --> 00:42:34,000
in the mitochondrion. Keep
in mind here's the borderline

581
00:42:34,000 --> 00:42:38,000
between the cytosol, the
cytoplasm and the mitochondrion.

582
00:42:38,000 --> 00:42:42,000
Here is where the oxygen is
actually used and here we generate

583
00:42:42,000 --> 00:42:46,000
all these NADHs here, here
and here, FADHs. And I keep

584
00:42:46,000 --> 00:42:50,000
saying, and it's still true,
just in spite of the fact I keep

585
00:42:50,000 --> 00:42:54,000
saying it, that these NADHs
can be converted to ATPs,

586
00:42:54,000 --> 00:42:58,000
and the ATPs can then be diffused,
transmitted throughout the entire

587
00:42:58,000 --> 00:43:02,000
cell where they're then used
invested in endergonic reactions.

588
00:43:02,000 --> 00:43:06,000
Here we see all these NADHs.
And look at the overall change in

589
00:43:06,000 --> 00:43:11,000
free energy. The initial steps
in glycolysis didn't really take

590
00:43:11,000 --> 00:43:15,000
advantage. Glucose has inherent in
it almost 680 kilocalories per mole

591
00:43:15,000 --> 00:43:20,000
of energy. It's pretty high up here.
But by the time we get from here

592
00:43:20,000 --> 00:43:25,000
down to here, there's an
enormous release of energy,

593
00:43:25,000 --> 00:43:30,000
it's harvested in the form of these
molecules which are then reinvested.

594
00:43:30,000 --> 00:43:34,000
In the absence of oxygen, this
entire procedure can only go

595
00:43:34,000 --> 00:43:38,000
from here down to here. And
a lot of this drop from six to

596
00:43:38,000 --> 00:43:42,000
seven is futile because we
have to reinvest this NADH.

597
00:43:42,000 --> 00:43:47,000
These cannot be used,
actually, to generate more ATPs,

598
00:43:47,000 --> 00:43:51,000
as I've said repeatedly. So,
this means in the end that we can

599
00:43:51,000 --> 00:43:55,000
generate an enormous amount
of energy in the form of these

600
00:43:55,000 --> 00:44:01,000
coupled reactions.
Having said that,

601
00:44:01,000 --> 00:44:08,000
let's actually look at what
happens inside of the mitochondria.

602
00:44:08,000 --> 00:44:15,000
Inside of the mitochondria there
are actually different physical

603
00:44:15,000 --> 00:44:22,000
compartments. See the blue space
there, the intermembrane space,

604
00:44:22,000 --> 00:44:30,000
the blue spaces there? The
matrix is on the inside.

605
00:44:30,000 --> 00:44:35,000
The intermembrane space is between
the two, the inner and the outer

606
00:44:35,000 --> 00:44:40,000
membrane, and outside is the
cytoplasm. The outer membrane,

607
00:44:40,000 --> 00:44:45,000
the inner membrane, in between it.
So, look what happens, actually, in

608
00:44:45,000 --> 00:44:50,000
the mitochondrion. Those
NADHs are used to pump

609
00:44:50,000 --> 00:44:55,000
protons from the inner space of the
mitochondrion into the intermembrane

610
00:44:55,000 --> 00:45:00,000
space. I'm not showing
you that happening.

611
00:45:00,000 --> 00:45:05,000
But you'll have to take it on my
word. So, protons pictured here are

612
00:45:05,000 --> 00:45:10,000
extracted from NADH and FADH, and
they're used to pump protons out

613
00:45:10,000 --> 00:45:15,000
here. And, therefore, protons
are moved from here to here.

614
00:45:15,000 --> 00:45:20,000
Obviously, when you pump protons
out the pH gets lower on the outside

615
00:45:20,000 --> 00:45:25,000
than it does on the inside,
and because there's a gradient,

616
00:45:25,000 --> 00:45:30,000
there's a higher concentration of
protons here than on the inside.

617
00:45:30,000 --> 00:45:34,000
The protons begin to accumulate
outside here in the intermembrane

618
00:45:34,000 --> 00:45:39,000
space. Are they in the cytoplasm?
No. They're in the space between

619
00:45:39,000 --> 00:45:44,000
the inner and the outer membrane.
You start to accumulate in this

620
00:45:44,000 --> 00:45:49,000
blue space lots of protons.
And this pumping of protons into

621
00:45:49,000 --> 00:45:54,000
the space between the two
membranes requires energy,

622
00:45:54,000 --> 00:45:59,000
and the energy comes from
our friends NADH and FADH

623
00:45:59,000 --> 00:46:04,000
as it turns out. They are
responsible for causing

624
00:46:04,000 --> 00:46:08,000
this accumulation of protons in
the space between the inner and the

625
00:46:08,000 --> 00:46:12,000
outer membrane. So, now
we get lots of protons out

626
00:46:12,000 --> 00:46:16,000
there. And what happens now,
the protons like to flow back in

627
00:46:16,000 --> 00:46:20,000
because there is a higher
concentration here as they are

628
00:46:20,000 --> 00:46:24,000
inside the space that's called
the mitochondrial matrix,

629
00:46:24,000 --> 00:46:29,000
on the inside of the
mitochondrion. So, what happens?

630
00:46:29,000 --> 00:46:32,000
Here, yet another Nobel Prize
winning discovery is the discovery

631
00:46:32,000 --> 00:46:36,000
of a very interesting molecule, or
complex of proteins I should say,

632
00:46:36,000 --> 00:46:40,000
that looks in three-dimensions
roughly like this.

633
00:46:40,000 --> 00:46:44,000
And what this complex does is as
the protons flow through the inner

634
00:46:44,000 --> 00:46:48,000
channel here, they're moving
down an energy gradient.

635
00:46:48,000 --> 00:46:52,000
They're going from a state of high
concentration to a state of low

636
00:46:52,000 --> 00:46:56,000
concentration.
What that does,

637
00:46:56,000 --> 00:47:00,000
that diffusional pressure
actually yields energy.

638
00:47:00,000 --> 00:47:05,000
And this complex right here harvests
that energy in order to convert ADP

639
00:47:05,000 --> 00:47:10,000
into ATP. So, when I
talk about NADH as being

640
00:47:10,000 --> 00:47:15,000
worth, each of them being worth
three ATPs, what I'm really talking

641
00:47:15,000 --> 00:47:20,000
about is the fact that NADHs can
be used to pump protons in the

642
00:47:20,000 --> 00:47:25,000
mitochondria outside here, and
these protons can then be used,

643
00:47:25,000 --> 00:47:31,000
can then be pumped, can then flow
in this way through this proton pump,

644
00:47:31,000 --> 00:47:36,000
which then uses ADP in the
inner cavity of the mitochondria

645
00:47:36,000 --> 00:47:40,000
to create ATP. And
here we get finally the

646
00:47:40,000 --> 00:47:44,000
conversion of ADP into ATP. We
can realize, finally, this much

647
00:47:44,000 --> 00:47:48,000
promised benefit. And then
these ATP molecules are

648
00:47:48,000 --> 00:47:52,000
exported from the mitochondria
throughout the entire cell and used

649
00:47:52,000 --> 00:47:56,000
to drive many reactions.
We've already encountered one

650
00:47:56,000 --> 00:48:00,000
important set of reactions,
and those reactions are the

651
00:48:00,000 --> 00:48:04,000
polymerization of nucleic acids.
Now, one final point I want to make

652
00:48:04,000 --> 00:48:08,000
is the following. We've
just talked about metabolic,

653
00:48:08,000 --> 00:48:12,000
we've talked about the pathway
of energy production in the cell.

654
00:48:12,000 --> 00:48:16,000
And you might have had the
illusion, for a brief instant,

655
00:48:16,000 --> 00:48:20,000
that those are all, that's the sum
of all the biochemical reactions in

656
00:48:20,000 --> 00:48:24,000
the cell. But, in fact,
if we plot out all the

657
00:48:24,000 --> 00:48:28,000
biochemical reactions in the cell,
they're much more complicated. Here

658
00:48:28,000 --> 00:48:31,000
is the glycolytic pathway. You
see it right down here where

659
00:48:31,000 --> 00:48:35,000
nothing is named? Here is
the Krebs Cycle right here.

660
00:48:35,000 --> 00:48:39,000
And we're not even talking about
energy here. And as molecules move

661
00:48:39,000 --> 00:48:43,000
down this pathway from here
to here to here to here,

662
00:48:43,000 --> 00:48:46,000
some of these molecules are
diverted for other applications.

663
00:48:46,000 --> 00:48:50,000
Not for energy production
but for other applications.

664
00:48:50,000 --> 00:48:54,000
And what happens out here, they
are converted through a series

665
00:48:54,000 --> 00:48:58,000
of complex biochemical steps
into other essential biological

666
00:48:58,000 --> 00:49:02,000
molecules. What
do I mean by that?

667
00:49:02,000 --> 00:49:06,000
If you give E. coli, a bacterium,
you give it a simple carbon source

668
00:49:06,000 --> 00:49:10,000
like glucose and you give it
phosphate and you give it a simple

669
00:49:10,000 --> 00:49:14,000
nitrogen source like
ammonium acetate or something,

670
00:49:14,000 --> 00:49:19,000
E. coli can, from those simple
atoms generate all the amino acids,

671
00:49:19,000 --> 00:49:23,000
can generate the purines and the
pyrimidines, can generate all kinds

672
00:49:23,000 --> 00:49:27,000
of different complex biological
molecules just from those

673
00:49:27,000 --> 00:49:33,000
simple building blocks. And
so, the process of biosynthesis

674
00:49:33,000 --> 00:49:40,000
involves not only the
creation of macromolecules,

675
00:49:40,000 --> 00:49:47,000
these steps of what are called
intermediary metabolism are used to

676
00:49:47,000 --> 00:49:54,000
synthesize all the other biochemical
entities that one needs to make a

677
00:49:54,000 --> 00:50:01,000
cell. They're used to synthesize
purines and pyrimidines.

678
00:50:01,000 --> 00:50:05,000
They're used to synthesize lipids,
they're used to synthesize amino

679
00:50:05,000 --> 00:50:09,000
acids, and they're used to
synthesize literally hundreds of

680
00:50:09,000 --> 00:50:13,000
other compounds. And when
we see this chart like

681
00:50:13,000 --> 00:50:18,000
this, and nobody on the face of the
planet has ever memorized this chart,

682
00:50:18,000 --> 00:50:22,000
each one of these steps, going
from one molecule to the next,

683
00:50:22,000 --> 00:50:26,000
represents another biochemical
reaction. And the vast majority of

684
00:50:26,000 --> 00:50:31,000
these biochemical reactions
going from A to B to C to D.

685
00:50:31,000 --> 00:50:35,000
Each one of these steps requires
the intervention of an enzyme,

686
00:50:35,000 --> 00:50:39,000
a catalyst that is specialized
for that particular step.

687
00:50:39,000 --> 00:50:44,000
So, this begins to give you an
appreciation of how many distinct

688
00:50:44,000 --> 00:50:48,000
biochemical steps one needs in a
cell. The numbers probably to make

689
00:50:48,000 --> 00:50:53,000
a simple cell, you probably
need about a thousand

690
00:50:53,000 --> 00:50:57,000
distinct biochemical reactions,
each of one of which requires the

691
00:50:57,000 --> 00:51:02,000
involvement of an enzyme.
And many of these steps,

692
00:51:02,000 --> 00:51:06,000
importantly, many of these
biochemical steps are endergonic

693
00:51:06,000 --> 00:51:11,000
reactions. Where do they get the
energy for driving these reactions

694
00:51:11,000 --> 00:51:15,000
forward if they're endergonic?
ATP. So, the ATP from the energy

695
00:51:15,000 --> 00:51:20,000
generating furnace down here is the
then spread throughout the cell to

696
00:51:20,000 --> 00:51:25,000
power all of these energy consuming
reactions. Have a great weekend.