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PROFESSOR: All right, so let's
do our first clicker question.

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All right, let's just
do 10 more seconds.

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Interesting.
 

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So, in this problem you were
given the maximum rate, Vmax,

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which, by the way, you
calculated in class last time.

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And then said what will the
substrate concentration be when

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you have half of that rate.
 

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And so, when you have half
of the maximum rate, that's

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the definition of k m.
 

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So all you have to do is if
a k m is given, you just

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write down that value.
 

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So that's the level of question
you'll get on enzyme kinetics.

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All right, so that should be
a good tie breaker, too.

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All right, so in this little
review and we talk about the

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material from the second half
of the course, and why I think

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this material is really
important and cool, and that's

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because it all represents the
basic principles of

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how enzymes work.
 

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And as a biochemist, I
recognize this material

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is really important.
 

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So that's what interests
me particularly about it.

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And the point that I want to
make in general is that when

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you're studying introductory
material, sometimes it seems

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like you're never going to
really need that material

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again, but that's because you
haven't seen the connection

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between it in other topics.
 

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So, a lot of the things you've
learned will be related to

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things that you're going
to see you later on.

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So I'm going to give you
examples and review examples of

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how the material you've learned
will allow you to understand

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an enzyme, for example.
 

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So, we talked last time that
one reason why you care about

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understanding how an enzyme
works is because a lot of

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people want to inhibit enzymes.
 

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Well, why would you want to
inhibit enzymes, and that's

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because inhibiting enzymes
is very useful to treat

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a bunch of things.
 

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A number of you will, in the
next week, I'm pretty sure, be

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interested in ways to inhibit
enzymes to prevent headaches

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or to decrease headaches.
 

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And this is true of students
and faculty during finals week.

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And so, some of the treatments
for headaches that a number of

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those pharmaceuticals are
geared toward enzymes called

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prostaglandin synthesis, and
they inhibit those enzyme from

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working and that gets
rid of your headache.

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Arthritis, for example, is also
treated by a lot of the same

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medications that
treat headaches.

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Cancer, often chemotherapy or
you're giving people inhibitors

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of enzymes to decrease
tumor growth.

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And we talked last time about
inhibiting HIV proteases as

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part of a treatment for HIV.
 

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So, understanding enzymes is
very important for the

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pharmaceutical industry, and so
that's one example of why you

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need to know about chemical
equilibrium, why you need to

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know about acid based oxidation
reduction transition

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metals, and also kinetics.
 

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So, I'm going to give
you a case study.

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You've seen some of these
examples before, but we're

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going to put them
all together now.

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And I try in every lecture, if
I can, to mention vitamin B12,

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and here, we're going to tell
you about a vitamin B12

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dependent enzyme, and how
knowing what you know now about

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these topics would allow you to
understand how this

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enzyme works.
 

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So, first, kinetics, this
is easy, methionine

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synthase, it's an enzyme.
 

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So, what does this enzyme do?
 

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So this particular enzyme
converts an amino acid called

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homocysteine to another
amino acid, methionine.

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It also converts another
vitamin, a B vitamin, the

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methyltetrahydrofolate form to
tetrahydrofolate, so this

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folate is one your B vitamins.
 

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Why do you care?
 

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Well, methionine is needed for
proper formation of brain and

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spinal column, and it's
particularly important when

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women are pregnant that they
have enough folic acid so

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that they can make
enough methionine.

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If they do not have enough
folic acid, then you can

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have babies born with
neural tube defects.

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Also, as I mentioned before,
inhibiting methionine synthase

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raises homocysteine levels, so
you can't do this conversion,

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and that increases risk of
heart disease that homocysteine

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is actually a really good
indicator, high homocysteine

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levels of whether someone's
going to have heart

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trouble or not.
 

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This is also a target for
chemotherapy, because you need

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tetrahydrofolate to do DNA
biosynthesis, and tumor cells

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that are growing, tumors that
are growing, need a lot

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of DNA biosynthesis.
 

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So if you inhibit this
enzyme, you can inhibit

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DNA biosynthesis,
so it's a potential

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chemotherapeutic target.
 

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There is some use
of this in Europe.

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Actually there is a treatment
that's given that's

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specifically supposed to
inhibit methione synthase, it's

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not used so much in this
country, but laughing gas will

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inhibit methione synthase.
 

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And so, in Europe some cancer
patients are treated with

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laughing gas as a way to
decrease their tumors.

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I'm not sure it's the most
effective therapy, but they're

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at least pretty happy with it.
 

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So that's the counterpart.
 

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So, this is an
important enzyme.

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And enzymes, of course, as we
know are catalysts and they

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catalyze reactions, so tell me
what you know about catalysts.

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Which is the following
statements about

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catalysts are true?
 

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OK, let's take 10 more seconds.
 

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Very good.
 

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All right, so going back to the
notes, statement 2 is true.

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So, catalysts work by lowering
the activation energy barrier

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for both the forward and
the reverse reaction.

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So both rates would be changed.
 

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And also, catalysts are
not going to affect the

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thermodynamics, they're
not going to shift the

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equilibrium toward products.
 

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What's something that you could
use to shift an equilibrium,

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say, to products or reactants.
 

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Temperature, yeah.
 

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So, just a little
review of kinetics.

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Again, a catalyst works by
lowering the activation energy

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barrier, or another way to say
that is by stabilizing a

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transition state, so it's going
to affect the activation energy

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for the forward reaction.
 

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And for the reverse reaction,
it's going to decrease both

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of them by the same amount.
 

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So if you know how much one is
decreased, you also know how

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much the other is decreased.
 

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And we also know that
it doesn't affect

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the thermodynamics.
 

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So, does it change the
equilibrium constant?

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00:10:06 --> 00:10:10
No, it doesn't change the
equilibrium constant.

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All right, so a little
review of kinetics.

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So now let's talk about
transition metals.

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So this particular enzyme
needs 2 different kinds

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of transition metals.
 

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It needs cobalt in the
form of vitamin B12 and

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it also needs zinc.
 

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So we talked about
methylcobalamin, so

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cobalamin is another
name for vitamin B12.

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00:10:34 --> 00:10:37
And here we have a methyl
ligand, c h 3 is a methyl

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ligand coordinated to the
cobalt in the center, and we

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saw before that when you have a
thing that forms attachments at

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more than one point, it's
called a chelate, so the corn

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ring here is a chelating agent,
and it's a tetradentate

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ligand because there are
4 points of attachment.

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So we can have monodentate,
bidentate, tetradentate,

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hexadentate, and tell you the
number of points of attachment.

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And again, this is a chelate,
and what do you know

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00:11:10 --> 00:11:12
about a chelate effect?
 

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I want someone to tell me what
the chelate effect is, and

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there's a special bonus prize
of a teeshirt for

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the best answer.
 

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Who wants to give it a
try and tell me what

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the chelate effect is.
 

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Any volunteers?
 

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Bonus teeshirt.
 

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Who wants to give it a try.
 

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Not very brave.
 

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STUDENT: [INAUDIBLE]
 

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PROFESSOR: OK, so chelate, it's
something that's going to be

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binding to a metal at multiple
points of attachment.

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And what do we know about how
stable or how favorable that

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kind of interaction is?
 

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STUDENT: It makes it more
stable because [INAUDIBLE].

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PROFESSOR: Are you
reading from your notes?

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Well, you know what, I didn't
say that was not allowed,

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so congratulations.
 

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Right, so chelates are
unusually stable due

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to entropic affects.
 

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So it's an entropy affect.
 

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So if you have a metal that's
free in solution, it's going

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to bind to a lot of water
molecules, and often, metals

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like to bind to thick things.
 

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You see a lot of
octahedral complexes.

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So if you have a metal bound to
6 waters, and you bring in a

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chelate that will blind with
multiple points of attachment,

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such as EDTA, which binds at 6
points of attachment, that

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1 molecule of EDTA will
displace 6 water molecules.

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So that is going to be
entropically favorable.

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6 things floating around in
solution have a lot more

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entropy than 1 thing floating
around in solution.

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And this makes
chelates very stable.

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And so, if you want to get --
if someone is poisoned with the

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metal and you want to get that
metal out of your system, you

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give them a chelate such as
EDTA, hospitals have EDTA.

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It's also good, as we learned,
for cleaning bath tubs.

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All right, so that's
the chelate effect.

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All right, so what about zinc.
 

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This enzyme has a zinc and
it has zinc in the plus

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-- zinc plus 2 ion.
 

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So, if you know that, you
can calculate a d count.

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And so again, we can go
to our periodic table.

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What group is zinc in?
 

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12.
 

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So what would be the d count?
 

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10.
 

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So 12 minus 2 equals 10.
 

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So what would you think would
be true about the color

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of this d 10 system?
 

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All right, so let's just
take 10 more seconds.

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All right, so it
would be colorless.

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00:14:55 --> 00:14:59
And so, all of the d orbitals
are going to be full, and so

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there's no transition from one
set of d orbitals to the other,

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00:15:04 --> 00:15:07
and so it would be a
colorless compound.

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00:15:07 --> 00:15:11
And that is, in fact, true that
it took years and years of

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00:15:11 --> 00:15:14
studying methionine synthase
before people realized that it

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00:15:14 --> 00:15:18
had a zinc in it, no one knew
that there was a zinc, because

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00:15:18 --> 00:15:19
they couldn't see it.
 

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It didn't add a color, and
so no one knew that a metal

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00:15:23 --> 00:15:24
was there for a long time.
 

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All right, so what about
oxidation reduction?

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So, this enzyme does a lot
of different oxidation

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reduction reactions.
 

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So, when it reacts with
homocysteine to form

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methionine, and the vitamin
B12, which is shown in a

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00:15:44 --> 00:15:48
cartoon form down here, goes
from a plus 3 state that has

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the methyl associated, it gives
the methyl group, the c h 3

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00:15:52 --> 00:15:54
group, up to homocysteine to
form methionine, and

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00:15:54 --> 00:15:58
then you're in a plus 1
state of cobalt here.

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But this state can lose an
electron, and you can have

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00:16:03 --> 00:16:04
a what's called [? cobe ?]
 

231
00:16:04 --> 00:16:08
2 form of the enzyme, which you
need to put another electron in

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00:16:08 --> 00:16:11
and reduce it to go back,
and you also need to

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methylate it again.
 

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00:16:12 --> 00:16:16
And the methyl group comes
from s adenosylmethionine.

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So, we need to think about how
we're going to reduce the

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vitamin to get it back in
its primary turnover state.

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00:16:23 --> 00:16:26
so, we know the redox
potentials for this.

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The standard reduction
potential for vitamin B12 is

239
00:16:30 --> 00:16:32
minus point 5 2 6 volts.
 

240
00:16:32 --> 00:16:35
The potential reduction
potential for flavodoxin, which

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is the protein that gives it
the 1 electron, and it's a

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00:16:39 --> 00:16:41
flavin protein, which
is another B vitamin.

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00:16:41 --> 00:16:46
And that's minus
point 2 3 0 volts.

244
00:16:46 --> 00:16:49
So, what do we
know about these?

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00:16:49 --> 00:17:34
Tell me which is the
better reducing agent.

246
00:17:34 --> 00:17:37
All right, let's just
do 10 more seconds.

247
00:17:37 --> 00:17:50
Click in your responses.
 

248
00:17:50 --> 00:17:55
OK.
 

249
00:17:55 --> 00:18:00
So, vitamin B12 is a
better reducing agent.

250
00:18:00 --> 00:18:05
If you have a large negative
number, then the reduced

251
00:18:05 --> 00:18:08
species is very reducing.
 

252
00:18:08 --> 00:18:14
So it wants to reduce other
things and get oxidized itself.

253
00:18:14 --> 00:18:16
So, that's interesting.
 

254
00:18:16 --> 00:18:20
It seems like vitamin B12
should be reducing flavodoxin

255
00:18:20 --> 00:18:22
and not the other way around.
 

256
00:18:22 --> 00:18:27
So we can look at how
unfavorable this process is,

257
00:18:27 --> 00:18:31
and we can calculate a standard
potential for this, and we can

258
00:18:31 --> 00:18:35
use this equation where we have
reduction minus oxidation and

259
00:18:35 --> 00:18:41
plug the values in, and so we
have a minus point 5 2 6 minus

260
00:18:41 --> 00:18:45
a minus of the floating
potential, and that gives us a

261
00:18:45 --> 00:18:48
negative value for delta e.
 

262
00:18:48 --> 00:18:51
So is this reaction
spontaneous?

263
00:18:51 --> 00:18:56
No, and that's because if you
have a negative standard

264
00:18:56 --> 00:18:59
reduction potential, then
you're going to have a positive

265
00:18:59 --> 00:19:03
value for delta g, so it
will not be spontaneous.

266
00:19:03 --> 00:19:06
And again, you can calculate
the value for delta g, so we

267
00:19:06 --> 00:19:09
have minus n, number of moles
of electrons, Faraday's

268
00:19:09 --> 00:19:13
constant times the difference
in potential, and it's a 1

269
00:19:13 --> 00:19:17
electron process, we put in
Faraday's constant and the

270
00:19:17 --> 00:19:20
calculated value for delta e,
and we get a positive

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00:19:20 --> 00:19:22
28 point 6.
 

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00:19:22 --> 00:19:26
And as I mentioned before in
class, the way this reaction

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00:19:26 --> 00:19:30
goes is that at the same time
an electron goes in, you also

274
00:19:30 --> 00:19:33
cleave s adenosylmethionine,
which gives the methyl group to

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00:19:33 --> 00:19:37
also return to the catalytic
cycle, and that process is very

276
00:19:37 --> 00:19:41
favorable minus 37 point
6 kilojoules per mole.

277
00:19:41 --> 00:19:44
So it drives the
unfavorable reaction.

278
00:19:44 --> 00:19:47
So in the body you will
have a favorable oxidation

279
00:19:47 --> 00:19:53
reductions and you'll
have unfavorable ones.

280
00:19:53 --> 00:19:56
All right, so what do you
a cell that requires

281
00:19:56 --> 00:20:01
energy to catalyze a
non-spontaneous reaction?

282
00:20:01 --> 00:20:03
So, that's an
electrolitic cell.

283
00:20:03 --> 00:20:08
And a cell that catalyzes
a spontaneous reaction?

284
00:20:08 --> 00:20:10
Galvanic, right.
 

285
00:20:10 --> 00:20:13
So again, with oxidation
reduction, it doesn't matter if

286
00:20:13 --> 00:20:16
you're talking about a battery,
or if you're talking about a

287
00:20:16 --> 00:20:20
cellular process, all the
same equations apply.

288
00:20:20 --> 00:20:26
All right, what about
acid based equilibrium.

289
00:20:26 --> 00:20:30
So in this particular -- in
this catalytic cycle, we are

290
00:20:30 --> 00:20:34
converting homocysteine to
methionine, and that chemistry

291
00:20:34 --> 00:20:38
involves acid base.
 

292
00:20:38 --> 00:20:41
So what is true about the
reaction is that the

293
00:20:41 --> 00:20:43
protonation state
of the substrate,

294
00:20:43 --> 00:20:45
homocysteine, matters.
 

295
00:20:45 --> 00:20:49
So, you can have a protonated
homocysteine, and here's the

296
00:20:49 --> 00:20:51
structure of homocysteine, a
deprotonated homocysteine

297
00:20:51 --> 00:20:55
where the sulfur does not
have a proton anymore.

298
00:20:55 --> 00:20:57
So we have an s minus here.
 

299
00:20:57 --> 00:21:01
And this protonated form of
homocysteine can be converted

300
00:21:01 --> 00:21:05
to methionine where there's a
methyl group attached

301
00:21:05 --> 00:21:07
to the sulfur here.
 

302
00:21:07 --> 00:21:13
So, we want to know at
physiological p h 7 point 4,

303
00:21:13 --> 00:21:16
how much of the homocysteine
is deprotonated?

304
00:21:16 --> 00:21:20
And here, if you're asking how
much of something is in a

305
00:21:20 --> 00:21:24
protonated state, how much of
something is in a deprotonated

306
00:21:24 --> 00:21:29
state, what you are asking is
what is the p k a

307
00:21:29 --> 00:21:32
of homocysteine.
 

308
00:21:32 --> 00:21:34
So what is the p k
a of homocysteine?

309
00:21:34 --> 00:21:38
That's what you need to know to
figure out how much would be in

310
00:21:38 --> 00:21:40
the protonated state, how
much would be in the

311
00:21:40 --> 00:21:41
deprotonated state.
 

312
00:21:41 --> 00:21:45
So here, the p k a is 10.
 

313
00:21:45 --> 00:21:48
So now, without doing any
calculations, I want you to

314
00:21:48 --> 00:21:53
tell me what you expect about
how much is protonated and how

315
00:21:53 --> 00:21:57
much is deprotonated at
physiological p h if

316
00:21:57 --> 00:22:36
the p k a is 10.
 

317
00:22:36 --> 00:22:57
All right, let's just
take 10 more seconds.

318
00:22:57 --> 00:23:00
I hope that I mentioned
that acid base will

319
00:23:00 --> 00:23:02
be on the final exam.
 

320
00:23:02 --> 00:23:05
So good thing we're
reviewing it right now.

321
00:23:05 --> 00:23:13
All right, so now let's
look at the math.

322
00:23:13 --> 00:23:17
So if you're given a p k a and
p h and asked about a ratio of

323
00:23:17 --> 00:23:21
protonated to deprotonated it's
OK to pull out your favorite

324
00:23:21 --> 00:23:24
Henderson Hasselbalch equation,
which gives you a sense of the

325
00:23:24 --> 00:23:27
ratio, can predict the ratio,
again it's approximation,

326
00:23:27 --> 00:23:30
but predict the ratio of
protonated to deprotonated.

327
00:23:30 --> 00:23:33
H a, of course, being an
abbreviation for protonated,

328
00:23:33 --> 00:23:36
a minus for deprotonated.
 

329
00:23:36 --> 00:23:40
And so we can calculate here
that if you have a p h of 7

330
00:23:40 --> 00:23:45
point 4, p k a of 10, you
get a ratio of 400:1.

331
00:23:45 --> 00:23:48
So that's the math, but you
can also just think about it

332
00:23:48 --> 00:23:49
in terms of what you know.
 

333
00:23:49 --> 00:23:52
So let's just do
a brief review.

334
00:23:52 --> 00:23:55
So the answer here is that free
homocysteine is protonated

335
00:23:55 --> 00:23:58
and non-reactive at
physiological p h.

336
00:23:58 --> 00:24:00
But let's just think about
this question a little more.

337
00:24:00 --> 00:24:02
So this is not a figure in
today's handout, but you've

338
00:24:02 --> 00:24:06
seen this a few times, so let's
just look at it for a minute.

339
00:24:06 --> 00:24:09
So, we talked a lot about
acid based titrations.

340
00:24:09 --> 00:24:11
We talked about so here we
have a weak acid tritrated

341
00:24:11 --> 00:24:13
with a strong base.
 

342
00:24:13 --> 00:24:15
In the beginning it's a weak
acid problem, at the

343
00:24:15 --> 00:24:18
equivalence point it's a weak
base problem, because we've

344
00:24:18 --> 00:24:21
added enough moles of our
strong acid to convert all of

345
00:24:21 --> 00:24:24
our weak acid to its
conjugate base.

346
00:24:24 --> 00:24:27
And in the middle when you've
added half the number of the

347
00:24:27 --> 00:24:32
moles, you've converted half
of your weak acid to its

348
00:24:32 --> 00:24:35
conjugate, then the p h is
equal to the p k

349
00:24:35 --> 00:24:36
a at this point.
 

350
00:24:36 --> 00:24:38
So that would be right
in the middle of this

351
00:24:38 --> 00:24:39
buffering region.
 

352
00:24:39 --> 00:24:42
Again, in a buffering region
you have quite a bit -- you

353
00:24:42 --> 00:24:45
have quite a bit of your weak
acid and quite a bit of a

354
00:24:45 --> 00:24:47
conjugate, so it can buffer.
 

355
00:24:47 --> 00:24:51
If strong acid is added, then
it can be used up, if strong

356
00:24:51 --> 00:24:54
base is added, it can be used
up without changing

357
00:24:54 --> 00:24:55
the p h very much.
 

358
00:24:55 --> 00:24:58
That's a buffer, so the p h
curve is flat in here in

359
00:24:58 --> 00:25:00
that buffering region.
 

360
00:25:00 --> 00:25:05
And so, when you think about
this, if you're at p h's that

361
00:25:05 --> 00:25:09
are below the p k a, then
you're going to be more

362
00:25:09 --> 00:25:13
protonated, and p h is above
the p k a, you'll be

363
00:25:13 --> 00:25:14
more deprotonated.
 

364
00:25:14 --> 00:25:18
So let's look at the figure
now that's in today's handout

365
00:25:18 --> 00:25:19
and think about this.
 

366
00:25:19 --> 00:25:24
So when the p h equals the p k
a, you will have equal number

367
00:25:24 --> 00:25:30
of moles, of something that's
protonated as deprotonated.

368
00:25:30 --> 00:25:33
And if you're at p h's
above the p k a, you'll

369
00:25:33 --> 00:25:34
be more deprotonated.
 

370
00:25:34 --> 00:25:39
P h's below the p k a,
you'll be more protonated.

371
00:25:39 --> 00:25:44
And in the particular example I
gave, we have a p k a of 10, so

372
00:25:44 --> 00:25:49
at 7 point 4 we're at a p h
that is below the p k a, and so

373
00:25:49 --> 00:25:52
here they'd be more protonated.
 

374
00:25:52 --> 00:25:54
So if you do the
math it's 400:1.

375
00:25:54 --> 00:25:57
But even if you aren't doing
any math, you should think

376
00:25:57 --> 00:26:00
about the fact that that
would have more of the

377
00:26:00 --> 00:26:05
protonated form than
the deprotonated form.

378
00:26:05 --> 00:26:09
All right, but the enzyme has
a problem, because only the

379
00:26:09 --> 00:26:11
deprotonated form is active.
 

380
00:26:11 --> 00:26:15
The p k a of the free
homocysteine is 10, and you're

381
00:26:15 --> 00:26:18
at physiological p h, so this
reaction doesn't seem

382
00:26:18 --> 00:26:19
like it should go.
 

383
00:26:19 --> 00:26:23
But again, it's an enzyme, and
enzymes catalyze reactions.

384
00:26:23 --> 00:26:26
So they do things to make
that reaction go faster.

385
00:26:26 --> 00:26:30
And what this particular
enzyme does is it lowers

386
00:26:30 --> 00:26:33
the p k a of homocysteine.
 

387
00:26:33 --> 00:26:37
So when homocysteine is bound
to the enzyme, it's p k a

388
00:26:37 --> 00:26:42
is no longer 10, but
now its p k a is 6.

389
00:26:42 --> 00:26:44
So, how does the
enzyme do this?

390
00:26:44 --> 00:26:46
Well, that's where
the zinc comes in.

391
00:26:46 --> 00:26:49
So, the zinc binds to the
homocysteine and it acts as

392
00:26:49 --> 00:26:54
a Lewis acid as it binds
to the homocysteine.

393
00:26:54 --> 00:26:56
So the homocysteine is your
donor ligand, and you have

394
00:26:56 --> 00:26:59
your metal as the Lewis
acid, your acceptor.

395
00:26:59 --> 00:27:05
And that alters the p k a, so
it actually associates, zinc

396
00:27:05 --> 00:27:09
associates with this sulfur,
and that changes the p k a.

397
00:27:09 --> 00:27:13
So, I just wanted to mention
again, I was having dinner with

398
00:27:13 --> 00:27:16
some of my faculty colleagues
who teach organic

399
00:27:16 --> 00:27:17
chemistry here.
 

400
00:27:17 --> 00:27:21
We were interviewing another
job candidate, and they looked

401
00:27:21 --> 00:27:23
at me and said, they're
teaching organic this semester

402
00:27:23 --> 00:27:25
and they said we asked our
class about p k a's, and they

403
00:27:25 --> 00:27:29
all insisted that they had
never heard about p k a's

404
00:27:29 --> 00:27:30
in their freshman
chemistry course.

405
00:27:30 --> 00:27:35
And I, of course, said, well,
they did not take 511-1 then.

406
00:27:35 --> 00:27:39
So just remember, especially
when it's Barbara Imperiali

407
00:27:39 --> 00:27:43
asking, did you hear about
p k a's, the answer is?

408
00:27:43 --> 00:27:45
STUDENT: Yes.
 

409
00:27:45 --> 00:27:46
PROFESSOR: Thank you.
 

410
00:27:46 --> 00:27:50
OK, so just this week.
 

411
00:27:50 --> 00:27:55
So it alters the p k a here.
 

412
00:27:55 --> 00:27:57
So now what's our situation?
 

413
00:27:57 --> 00:28:03
Well, now at physiological p h,
we have a p k a of 6, and so

414
00:28:03 --> 00:28:05
that gives us a very
different ratio.

415
00:28:05 --> 00:28:08
Instead of 400:1, we have 1:25.
 

416
00:28:08 --> 00:28:13
So most of the homocysteine is
deprotonated at physiological

417
00:28:13 --> 00:28:17
p h, which means
that it can react.

418
00:28:17 --> 00:28:21
So, if we go back to this
now, our p k a is now 6,

419
00:28:21 --> 00:28:26
and so physiological p h
is now above that p k a.

420
00:28:26 --> 00:28:30
So when you're above the p
k a, you should have more

421
00:28:30 --> 00:28:32
deprotonated than protonated.
 

422
00:28:32 --> 00:28:37
So that's how you can
rationalize these things.

423
00:28:37 --> 00:28:40
All right, now I have to
ask, all right, we do

424
00:28:40 --> 00:28:42
not need a tie breaker.
 

425
00:28:42 --> 00:28:46
So at the end of the lecture,
we will announce the winner.

426
00:28:46 --> 00:28:51
But let's first do
chemical equilibrium.

427
00:28:51 --> 00:28:54
Chemical equilibrium.
 

428
00:28:54 --> 00:28:57
So we didn't talk too much
about this in chemical

429
00:28:57 --> 00:29:01
equilibrium, but enzymes can
have alternate conformation,

430
00:29:01 --> 00:29:05
so the enzyme can change its
shape during chemistry.

431
00:29:05 --> 00:29:08
And that those conformation
of the enzyme can

432
00:29:08 --> 00:29:09
be in equilibrium.
 

433
00:29:09 --> 00:29:13
So the enzyme itself can be an
equilibrium with different

434
00:29:13 --> 00:29:16
conformational states.
 

435
00:29:16 --> 00:29:19
So here, there are a lot
of states of the enzyme.

436
00:29:19 --> 00:29:21
It needs to react with
homocysteine, it needs to react

437
00:29:21 --> 00:29:23
with methyltetrahydrofolate and
with s adenosylmethionine.

438
00:29:23 --> 00:29:30
And when the structure was
determined to this enzyme, here

439
00:29:30 --> 00:29:34
in green is the vitamin B12,
and red is the methyl group.

440
00:29:34 --> 00:29:36
You see that the methyl group
is pretty buried, you can

441
00:29:36 --> 00:29:40
barely see it, but yet it needs
to interact with homocysteine

442
00:29:40 --> 00:29:43
to give it a methyl group, it
needs to take a methyl group

443
00:29:43 --> 00:29:46
off methyltetrahydrofolate, it
also needs to take a methyl

444
00:29:46 --> 00:29:48
group off s adenosylmethionine.
 

445
00:29:48 --> 00:29:50
But it doesn't seem like
there's any room for any of

446
00:29:50 --> 00:29:52
them to actually get in there.
 

447
00:29:52 --> 00:29:55
So, this was a sign that
there has to be some kind

448
00:29:55 --> 00:29:57
of change in the structure.
 

449
00:29:57 --> 00:29:59
So here's another picture
of the structure.

450
00:29:59 --> 00:30:02
Here's the vitamin B12 in
green, the methyl group in red,

451
00:30:02 --> 00:30:05
and there's this whole protein
part up here that has to get

452
00:30:05 --> 00:30:08
out of the way to
do the chemistry.

453
00:30:08 --> 00:30:11
And, in fact, we do know from
experimental data that it

454
00:30:11 --> 00:30:14
does move so you can
do the chemistry.

455
00:30:14 --> 00:30:17
So that means that the enzyme
has to have a number of

456
00:30:17 --> 00:30:19
different structures.
 

457
00:30:19 --> 00:30:20
It's modular.
 

458
00:30:20 --> 00:30:23
Here's the vitamin B12 binding
domain, the vitamin B12,

459
00:30:23 --> 00:30:27
there's this region that have
to move called the methyl cap.

460
00:30:27 --> 00:30:29
It needs to interact, the B12
here needs to interact with

461
00:30:29 --> 00:30:32
a folate domain, a
homocysteine domain, and an

462
00:30:32 --> 00:30:35
activation domain.
 

463
00:30:35 --> 00:30:40
So you need to have at least
these 4 different structures,

464
00:30:40 --> 00:30:45
and these 4 structures will be
in equilibrium with each other.

465
00:30:45 --> 00:30:48
So you need to have a structure
with folate, a binding domain

466
00:30:48 --> 00:30:53
on top of the red B12, you need
to have homocysteine in yellow

467
00:30:53 --> 00:30:56
on top of the B12, you need to
have a resting state where

468
00:30:56 --> 00:30:59
those helices are on top of the
B12, and you need to have an

469
00:30:59 --> 00:31:01
activation state where
the [? adomet ?]

470
00:31:01 --> 00:31:05
domain is on top of the B12,
and all of these states are

471
00:31:05 --> 00:31:08
going to be in equilibrium with
each other, and they're going

472
00:31:08 --> 00:31:12
to be moving, which means that
enzymes are dynamic, which

473
00:31:12 --> 00:31:15
means that chemistry
is dynamic.

474
00:31:15 --> 00:31:19
Chemistry in the body is
not in the solid state.

475
00:31:19 --> 00:31:24
Chemistry in the body
is in solution.

476
00:31:24 --> 00:31:24