#28 Biochemistry Citric Acid Cycle Lecture for Kevin Ahern's BB 451/551

Uploaded by oharow on 11.01.2012

Captioning by Disability Access Services
at Oregon State University.
Kevin Ahern: Okay folks, let's get started!
You're ready to go?
Student: My nemesis is back...
Kevin Ahern: Your nemesis is back?
Oh, I thought you were talking about me.
We're off to a great start.
That you see on the screen, you're looking at the class
schedule for winter of 2011 and that's because
I don't have the URL with me for 2012.
That was kinda dumb.
But it's the same basic content.
The figures might be slightly different
because it's volume six of the textbook
but I think you'll, we'll get through it.
Anyway, I'll get it fixed for next time.
Couple things.
First of all, I hope everybody had a good break.
How many of you have broken
all of your New Year's resolutions already?
Nobody has?
How many of you made New Year's resolutions?
So a few, a few.
I find that New Year's resolutions are good.
They make you feel good when you make them, right?
After that, well, you know.
But you feel, "This year, by golly,
"I'm going to win that Nobel Prize," right?
Drop those twenty-eight pounds that I gained over Christmas.
Alright, so, welcome to BB 451.
For those of you who were not in 450 last term,
I'm sure you've heard the horror stories.
But if not I will try to make it as unpleasant for you as I can.
Everything in the class is online.
When I get the correct URL for you I'll email it to the class.
I change it every year because I have to sort of manipulate
a page and I didn't realize it didn't have it with me,
that I don't have it with me.
At that page, in fact if you go back to this page
here that'll get you the right stuff.
That is this page, just instructions to slides for 451.
That'll get you the syllabus and the syllabus,
as people know, is required reading for the course
and so it's important to get that syllabus
and read through it and make sure you know what's in it.
And everything I do is up here on the screen.
So I will make videos available.
I videotape my lectures and I try to get them posted
within about twenty-four hours after I've given
the lecture so you can access those.
And you will see them on a page that looks
very much like this one where you can see videos
and you'll click to the links, et cetera,
and you'll get all that.
I don't keep specific office hours,
because I'm in my office a lot.
That may be changing slightly this term,
so I may post some specific office hours.
But as always, you're always welcome to come to my office
and if I'm free, you have priority.
So I will not be unavailable to you as much as I can.
If you want to schedule an appointment with me please feel free.
Send me an email and I'll be happy to schedule
something with you and if you need a tutor
or other assistance of any sort then of course
let me know, and I've got some excellent
students who tutor in biochemistry.
Yes sir?
Student: Here's the URL if you want it.
Kevin Ahern: There's the URL.
Oh wow, okay.
I guess it makes a difference if you put
winter12 there, doesn't it?
And Schedule.
I did remember it right I just forgot that winter12 thing.
Oh, what'd I do?
That was cool.
Go back here.
And Schedule, 451.
CW12, that's what I thought, okay.
Excellent, now we're up to date.
Thank you much, I appreciate that.
He's going to get an A.
I should probably get an F for not having the URL with me.
That was kind of dumb wasn't it?
So what we're going to see this term,
this term is an interesting term because
we sort of continue the metabolic processes
that we started last term and I think with this term
what you can see in metabolism is the sort of beautiful way
in which these processes relating to energy
are integrated with each other.
And you'll understand a lot more as we go through this,
how your body works.
You started to see that last term
with respect to glucose metabolism.
You're going to see it a lot more with respect
to citric acid cycle, electron transport
and oxidative phosphorylation and we will talk
for the first time about respiratory control.
And it's at that point that I think students
really begin to get that real appreciation
of the beauty of metabolism.
Metabolism is not simply a matter of memorizing
a bunch of reactions and enzymes and so forth
although there is obviously a component of that in what we do.
But the big picture of metabolism is a very important
thing and it's really a very interesting story.
We talk about metabolism essentially
for the first half of the term.
The second half of the term we go through molecular biology.
And so we get up close and personal with DNA replication,
transcription, and translation.
And we'll be going through this in more depth
than what you've see in the others courses that you've had,
for the most part.
I talk fast.
I know that.
If I get talking too fast, as always,
"Kevin, slow down," or, "Repeat this," et cetera,
and I'll be happy to try to accommodate you the best I can.
Okay, before I get started any comments, questions?
Student: How was your holiday?
Kevin Ahern: How was my holiday?
Thank you for asking.
There's another A.
My holiday was very good.
Like everybody else I liked the length of the holiday.
It was wonderful.
I went and visited my mother in Oklahoma
and the main, good thing about going to Oklahoma
is you really appreciate coming back to Oregon, so...
[class laughing]
Oh boy I'll be in trouble now.
YouTube, all the Oklahomans will get me here.
I had a great time and, mainly I got caught up.
I had a ton of work to do but I actually feel
like for the first time in a long time that I got
on top of a bunch of things so that was very good.
So happy to be back.
It's always to me exciting, the first day of class,
and it's always exciting to get back
in front of people and get going through biochemistry.
So I really love that.
I really love this interaction.
And for me this is always really a special pleasure
because I get to carryover with a class that I worked
with last term, so I know what you guys have heard,
and what you're supposed to know, and I can actually build
on the things I talked about last term.
And so that's a nice connection for me.
I find that by the end of this term
I've gotten to know a decent number of you fairly well,
and I very much enjoy that.
And yes we'll have a song or two this term.
Student: What's your New Year's resolution?
Kevin Ahern: My New Year's resolution.
Thank you for asking.
As a matter of fact my New Year's resolution
is to run further than I ran last year.
Last year I finished off with, I think it was 1320K.
And this year, I'm hoping to do 1500K.
So if any of you are interested in running
and you want to run in the morning give me a holler.
I'm always looking for runners.
And it's fun.
I'm slow, I'm not fast.
But I can or speed up slow down
according to who I'm running with, a little bit.
Within limits.
We keep talking about this we won't have
to talk about biochemistry.
This'll be good, right?
Connie: Can we pick up our finals in the BB...?
Kevin Ahern: Can you pick up your final?
The finals are available in the BB office
and there's a key posted outside of my door.
Student: What was the average on the final?
Kevin Ahern: The average on the final was about 100 out of 150.
It was about 66 percent, yeah.
It's about 66 percent.
So it's a little bit lower than what there was on the,
I think on the second exam but it was still
not a bad overall performance.
Yes sir?
Student: Are those still available for review,
like for reconsideration on questions?
Kevin Ahern: If there's errors, yes.
Student: Okay.
Kevin Ahern: So much for all the pleasantries.
Now we get to talking about biochemistry, huh?
What's the ribbon for?
Does anyone know what the ribbons are for?
I'm going to screw up the universe here.
[class laughing]
I don't know what will happen.
They'll probably come cut my arm off.
All the Oklahomans will come get me or something.
Well, we're going to talk about a really interesting
process you've heard about in other classes.
And what you probably haven't gotten is you haven't gotten
that integration of this process, the citric acid cycle,
with respect to other metabolic pathways.
And that's one of the things I'm going to hammer home
to you is that integration.
And it's not complicated, but it's not really gone over
very well in other classes in my experience.
So let's start there.
The citric acid cycle is another cycle,
or another metabolic process that we refer
to as a central metabolic process,
meaning that it's central to the metabolism
of virtually every cell.
There are no absolutes with respect to metabolism,
but it's pretty darn central to most cells.
And by most it's probably 99.9 percent of cells
have a completely functional citric acid cycle.
The process is a cycle.
It goes like a wheel.
We start at one place and we end up at that same place.
And that is an important consideration
in understanding the citric acid cycle.
As you will see we can really break it into two main components.
Two components, the first component being the oxidation,
or the decarboxylation of...come on,
we're not going to do this, are we?
I guess we are.
Hit it?
[smacking clicker]
Alright, the decarboxylation which you see
are the two CO2's there, are the six-carbon intermediate.
And then the other half of the cycle is rearranging
the four-carbon intermediate that results from that
back into the starting four-carbon intermediate.
So even though it's a cycle or a circle,
we do think about it having a starting point
and ending point which are the same.
And we'll see how that goes in just a bit.
The cycle is interesting in that
it is one of the major oxidative cycles of the cell.
That's shown in the part at the bottom with the eight electrons.
The eight electrons mean that we make
four reduced electron carriers,
three NADH's and one FADH2.
We also produce, with each turn the cycle,
one triphosphate, and that triphosphate is GTP.
Yes ma'am?
Student: What were the electron carriers again?
Kevin Ahern: There's three NADH's and one FADH2.
There we go.
Now I'm going to go through some details with those in a bit.
Now before, and I emphasize this,
before we talk about the electron,
before we talk about the citric acid cycle
we have to talk about how things get
to the citric acid cycle, okay?
It turns out there are many ways for compounds
to get into the citric acid cycle.
We're going to focus on one way to start,
and that one way to start is the entry
of a two-carbon intermediate known as acetyl CoA.
You've heard of acetyl CoA.
We talked about it last term.
And it is, for our purposes right now,
the primary entry point into the citric acid cycle.
This shows the cycle in a little more detail.
You can see what we think of a starting material,
for our purposes right now is oxaloacetate.
We talked about that last term as well.
Oxaloacetate has four carbons.
We combine a two-carbon piece with it.
That two-carbon piece is acetyl CoA.
That makes a six-carbon piece.
We have two decarboxylations.
That's those two CO2's you saw lost before.
That gives us a four-carbon piece.
And then the rest of that cycle is rearranging
that back into the original four-carbon piece.
So in a nutshell that's what's happening
in the citric acid cycle.
Now as I said we can't talk about the citric acid cycle
until we talk about how we get material into it, okay?
So I'm going to hold off on the citric acid cycle
for just a bit today and I'm going to tell you
about how it is that our cells,
or one way it is that our cells make acetyl CoA.
And in doing so we're actually linking
the citric acid cycle to glycolysis, okay?
So glycolysis, if you recall, it was at the end of last term.
I know it was a long time ago,
but if you recall from glycolysis what happens
is the end product of glycolysis was pyruvate,
and pyruvate, in order to get into the citric acid cycle,
has to be oxidized.
So that's our entry point to get things
into the citric acid cycle.
What I'm telling you here is not
a part of the citric acid cycle.
It's only how we get things to make acetyl CoA.
Blah, blah, blah, blah, blah.
Schematically it looks like this.
So what I'm getting ready to tell you is up here
you'll notice that up here is not
a part of the citric acid cycle.
So don't confuse what I'm getting ready to tell you
with the citric acid cycle
because it's not a part of it.
The entry of carbons from glucose
into the citric acid cycle requires an enzyme
that has a couple of names, okay?
And I think your book is not consistent
in how it deals with those names,
so I'm going to try to be consistent
in how I deal with those names.
There's acetyl CoA.
And the relevant part of this guy
is the red right there, okay?
All this big handle is used
simply to carry this little guy right here.
Well that little guy right there
is of a lot of interest to us because we have to make it
in order to get to those carbons to use for energy.
The enzymes that's used to break pyruvate down
into acetyl CoA is known as pyruvate dehydrogenase.
And your book is inconsistent
in the way it describes, it uses that name.
I'll tell you why as we get going along.
But the name of the enzyme that catalyzes
the conversion of pyruvate into acetyl CoA
is known as pyruvate dehydrogenase.
It's an interesting and it's a slightly complicated enzyme.
This is an electron micrograph showing
the appearance of this enzyme.
And you can see this enzyme looks
a little bit like dice, right?
It's cubic in nature and it has some
sort of bumps or balls that correspond to individual
subunits of the enzyme.
That right there is a little bit more clear depiction of that.
You're not going to have to draw that,
so don't worry about that, but I'm just showing you
what you're seeing in that electron micrograph, okay?
There are three primary subunits that comprise this enzyme.
Your book has very long names for them
and we're going to keep them very simple.
We're going to call them E1, E2, and E3.
E1, E2, and E3.
As we will see these have individual functions,
and we will talk individually about those.
There are the mouthful names that are there.
And you can see already that the book has gotten off
on the wrong foot by giving it this name
"pyruvate dehydrogenase component."
Most people call this subunit "pyruvate decarboxylase."
And that's confusing because this enzyme
is overall catalyzing a decarboxylation.
But as we will see the decarboxylation
is only one part of what this enzyme does.
So E1 is pyruvate decarboxylase.
You're not even going to need to know that.
If you know it as E1, E2, E3, I'm happy.
But each of these subunits has a function
and as I talk about the mechanism of the enzyme,
I'm going to show you those functions.
Look at the number of those chains that are in there.
Twenty-four in E1.
Twenty-four in E2.
Twelve in E3.
It's no wonder it's big enough we can see it
in an electron microscope.
This is a pretty big honking enzyme.
What we're going to focus on for the most part
are coenzymes that this enzyme uses.
There are five coenzymes that this enzyme uses.
I'm going to give you those coenzymes first
and then as we go through the mechanism,
I'll point out to you where they're used.
The five coenzymes, you can see two of them on the screen.
Thiamine pyrophosphate which you are welcome to call TPP,
and lipoic acid which I will also let you call lipoamide.
When it's linked to one of the proteins it's lipoamide.
When it's free it's called lipoic acid.
But I'll use, I'll let you use either one of those terms.
Student: How do you spell that?
Kevin Ahern: Lipoamide?
I said there were five, okay?
The third coenzyme is coenzyme A.
When we talk about acetyl CoA,
it's the CoA part that we're talking about.
So the third coenzyme is coenzyme A
or you can also call it CoA.
Sometimes we write CoA as C-O-A-S-H,
and we'll see why that's the case in just a bit.
The fourth coenzyme is NAD and the fifth coenzyme is FAD.
So we have two coenzymes involved in oxidation reduction.
They're both essential, they're both important.
So those five coenzymes allow
the decarboxylation of pyruvate to occur,
and the oxidation reactions to also occur.
Student: Can you repeat that?
Kevin Ahern: I'm sorry?
Student: Can you please repeat that?
Kevin Ahern: So, repeat what the five coenzymes do?
Student: Just the last sentence.
Kevin Ahern: Let me remember my last sentence.
So my last sentence was that these five coenzymes
allow the decarboxylation to occur
and the oxidation reactions to occur.
I think that was my last sentence.
In my age you can't remember things.
You know, you remember something that happened
back when you were about fourteen
but you can't remember something you said two minutes ago.
The same thing happens when you take an exam, right?
You can't remember what...
It's a sign of old age, folks.
Well, I've been talking, I will tell you that mechanism.
I haven't done that so let's now overview the mechanism.
It's not going to be the mechanism we talked about
with respect to the serine protease,
so don't worry about that.
In fact this is probably going to be as deep
of a mechanism as you're going to see this term, right here.
Let's look first of all what's happening in this process.
Pyruvate is getting converted from a three-carbon compound
into a two-carbon compound linked to a CoA.
So we're going from pyruvate over here on the left
to acetyl group linked to a CoA on the right.
That means we have to lose a carbon in the process,
and that carbon that we're losing is lost
in the very first step.
The very first step.
We can think of the decarboxylation,
this is where E1 is important.
E1 is essential for the decarboxylation.
Now this decarboxylation is really interesting
because you will notice that the decarboxylation
is not directly linked to an oxidation.
The oxidation follows in a subsequent step.
So the decarboxylation is not the oxidation step.
It's a step that's independent of that.
And that turns out to have some very big importance.
In our cells we automatically go
from decarboxylation to oxidation to transfer.
We don't have any to short circuiting this.
If we had a way of short circuiting this,
we would save an awful lot of money on happy hour.
Because bacteria and yeast,
one of the ways in which they ferment,
is they short circuit.
Instead of going through the oxidation step
they take this guy here and make ethanol.
We can't do that.
Yes sir?
Student: Does E1 stabilize that tertiary carbanion
that forms since that's a pretty unstable species?
Kevin Ahern: No.
E1 does not stabilize that.
TPP actually stabilizes that.
And I'll talk about that.
TPP is part of the E1 but E1 itself, no.
That's where the coenzymes are very very important
in that stabilization process.
Okay, now.
Looking at this mechanism we've got carbon dioxide produced,
we've got E1 that's catalyzed it, and, as noted up here
this guy right here is a very unstable species.
We don't want it floating around
and we don't have it floating around.
In fact, in our cells we never have it floating around.
This is what's called a, reactive acid aldehyde.
Reactive acid aldehyde.
Acid aldehyde we talked about last term.
Why did we talk about reac-, acid aldehyde last term?
Student: Hangover.
Kevin Ahern: Hangovers!
Very good.
The one thing we remember from last term, hangovers.
[class laughing]
So a reactive acid aldehyde basically has extra electrons here.
We've got to deal with this guy.
We don't have that being free.
We don't want this reacting so in fact upon decarboxylation
this guy is transferred to thiamine pyrophosphate, TPP.
This is why that first coenzyme is necessary.
It's actually carried.
TPP carries and hangs on to this guy.
Now, the next step of this process is where oxidation occurs.
What's happening in the next step of the process?
What we're making in the next step of the process
is we are transferring this guy right here,
this reactive guy right here, from TPP to lipoic acid.
So this oxidation occurs during the transfer
to the lipoic acid or the lipoamide.
What's happening in that process?
Well we see electrons being lost.
We see a minus here; we see a plus over here.
Loss of two electrons are occurring.
And what's happening in that process is that
if you look at that structure of lipoic acid that I show you,
showed you, you will see the lipoic acid has a disulfide bond.
Two sulfurs linked together.
In this process, whats happening is that disulfide bond
is getting reduced because it's accepting the electrons
from this activated intermediate.
That leaves two sulfhydryl groups,
I'll show you this in a second also,
and it results in the oxidation of this compound right here.
Alright, now.
Last, and I'm going to show you these things separately also
last, this oxidized acetate, as it were,
is transferred to coenzyme A.
It's transferred to coenzyme A.
That's occurring on E3.
So we can think of this as E1, E2, E3.
E1, E2, E3.
Now, E2 has some other things going on with it as we shall see
that are important to understand the overall process.
If we simply did this right here, we would have problems because
we haven't accounted for what's happening to these electrons.
If we simply left that lipoamide in the reduced state
we couldn't do another cycle of decarboxylation, right?
Well, let's look to see now individual reactions
of what's happening.
Here is that initial decarboxylation reaction.
The decarboxylation reaction actually results directly
in the attachment of that hydroxyethyl-TPP right there
where we've linked this red portion of the molecule
to this ring right here.
The CO2 has been lost.
There's a mechanism.
We're not going to go through the mechanism, don't sweat that.
Then we transfer this guy right here,
which is this reduced intermediate, to lipoamide,
and look what's happening to the lipoamide.
We're breaking the disulfide bond.
When we add electrons to a disulfide bond
we create sulfhydryl bonds.
There's an S-H.
And as we'll see this'll become an S-H as well.
And then we transfer this guy over to a CoA
and now we're left with two disulf-,
two sulfhydryl bonds.
It's this structure that we have to resolve.
We have to get this guy back to the disulfide state
if we want to have this enzyme continue its reaction.
That happens as a result of transfer of electrons
from the lipoamide residue to FAD.
That converts FAD into FADH2.
It also regenerates the lipoamide.
In addition, excuse me,
the electrons from FADH2 are transfered to NAD
creating NADH and resulting in FAD.
Ultimately the electrons from NADH
will be dumped into the electron transport system
and we will regenerate NAD.
But in terms of this enzyme
this is an ending point right here
because we've regenerated the lipoamide disulfide bond
and the enzyme is ready for another cycle of catalysis.
That's a mouthful.
I'm going through it quickly.
Off to a great start, aren't we?
You guys look asleep!
Yes, question back there.
Student: So each stage is stabilized by E1, E2, E3
by providing pockets for this reaction to take place?
Kevin Ahern: E1, E2, and E3 are providing active sites
for this reaction to occur, that's correct.
The stabilization is really more,
I would describe more as being done
by the coenzymes themselves.
But they're components of E1, E2, and E3, yes.
Yes sir?
Student: So NAD takes both the electrons from FADH2?
Kevin Ahern: NAD takes both electrons from FADH2.
Virtually every transfer of electrons
we will see this term are occurring in pairs.
Virtually everything we see with electron transfer
is electron transfer occurring in pairs.
Now that's just a blah, blah, blah, blah, blah.
As I said, this reaction in us,
once we start with pyruvate
we have to go all the way through to the end.
We can't short circuit.
Bacteria and yeast can short circuit,
and if you think back to last term
when I talked about the different fates of pyruvate,
one of the fates of pyruvate in animals if we didn't have oxygen
was that we could convert it to lactate, right?
If you think, the thing I showed you for yeast
and bacteria one of the fates was pyruvate went to ethanol.
Now you know how it goes to ethanol.
Because acid aldehyde can be reduced to ethanol by NADH.
That regenerates NAD and that's necessary
for what cycle, or what process?
Why are cells going through fermentation?
Student: Anaerobic.
Kevin Ahern: They're anaerobic but why,
what are they trying to do.
What are they trying to keep going?
Student: Glycolysis.
Kevin Ahern: Glycolysis.
They're trying to keep glycolysis going
because glycolysis needs that NAD.
If there's no oxygen the only way to make NAD
is by this process right here.
That's why bacteria and yeast are making ethanol,
so they can keep glycolysis going.
That's why we make lactic acid.
So we can keep glycolysis going.
If we stop glycolysis we're going to be in trouble.
There's lipoamide.
It's called lipoamide when it's connected to the protein.
It's actually connected trough a lysine bond in the protein.
There's the structure.
And there's, if that's helpful to you,
I'm not going to expect you to regurgitate this,
this cycle right here anyway, but,
you should know the basics of the cycle.
I would certainly say that you should know that
initial basic diagram that I showed you,
those three steps where E1, E2, and E3 play a role.
You should certainly know the functions
of the coenzymes in this process.
Now this process that you see here
is all occurring inside of the mitochondria.
Inside of the mitochondrion.
In fact we're going to spend a fair amount of time inside
the mitochondrion because that's where
the citric acid cycle occurs.
That's also where the fatty acid oxidation occurs.
So these processes are occurring-
Gesundheit, in the citric acid cycle.
Student: So is it accurate to say that it never lets go
of the intermediate?
So if a TPP is attached to those two carbons
it would never let that go?
Kevin Ahern: Very good question.
Is it accurate to say it never lets go?
And the answer is you're correct, it does not let go.
It literally is passing them from one component to the next
so they're not released in a free form
because they are fairly reactive intermediates.
You've got it.
That is the pyruvate dehydrogenase complex.
So, that went, I guess I'm going fast today
so I should slow down, give people a chance
to catch their breath, give me a chance to catch my breath.
Okay enough of that.
[class laughing]
That's a joke, folks.
Alright, let's talk about the citric acid cycle.
So as I said, those reactions I just described to you
are not a part of the citric acid cycle
but now we are talking about reactions
that are part of the citric acid cycle.
The cycle is circular, as I noted.
Technically it doesn't have a starting and an end point
but we're going to define this for our purposes
as a starting point.
It will also become the ending point
when oxaloacetate is eventually remade over here.
We saw that last term.
Where did we see oxaloacetate last term?
Does anyone remember?
And where was gluconeogenesis occurring?
It's occurring in the liver.
In the cell, where's it occurring?
The first step occurs in the mitochondrion.
The last step happens in the endoplasmic reticulum,
everything else occurs in the cytoplasm.
Why is that important?
That's important because?
That's the first step of gluconeogenesis, what are we making?
We see that oxaloacetate can readily be made
inside the mitochondrion if it's needed.
Oh there's our friend.
Goodbye, friend.
I use that in a sarcastic nature.
Oxaloacetate can be made in the mitochondrion very easily.
Plenty of oxaloacetate there.
We will see oxaloacetate is one of the most ubiquitous molecules
to be found in metabolism.
We see it in gluconeogenesis.
We see it in the citric acid cycle.
We see it in the metabolism of many amino acids.
So it's a very interesting and important compound.
In this first step we're taking that four-carbon oxaloacetate
and we are converting it into a six-carbon molecule
known as citrate.
I don't care if you know it as citryl CoA.
I never even refer to that myself at all.
Oxaloacetate, OAA.
Acetyl CoA, ACCOA.
Goes to citrate.
Now this reaction is an energetically favorable reaction.
In fact it's fairly energetically favorable.
The enzyme that catalyze,
and by the way I'm not going to require you to memorize
all the structures of the citric acid cycle.
Like last term I will require you to know the names
of all the enzymes and the names of all the intermediates.
You should also know how many carbons they have, okay?
But I'm not going to require you to know the structure.
The name of the enzyme that catalyzes this reaction
is called citrate synthase.
A very easy name.
Synthase means synthesizes, right?
It synthesizes citrate.
Citrate synthase catalyzes this reaction.
As I said this reaction is energetically fairly favorable.
That'll turn out to be important when we get to the other side
of the citric acid cycle.
Putting two molecules together isn't always
a very favorable process, but this process
is energetically fairly favorable.
Why is this energetically fairly favorable?
It's because it uses an activated intermediate.
Anybody remember what that was from last term?
What's an activated intermediate?
Or give me an example of an activated intermediate
you saw last term.
Does anybody remember last term?
[class laughing]
Yes, over here.
Student: UDP-glucose.
Kevin Ahern: UDP-glucose was an activated intermediate.
An activated intermediate, I will remind you
since you're looking a little sleepy,
is a molecule that has a high energy bond.
Kevin Ahern: You okay?
Student: I was thinking in my head but I was way off
on what it is.
Kevin Ahern: It has a high energy bond
and it uses the energy of that bond
to donate a part of itself to something else.
That's what an activated intermediate was.
Last term we saw UDP-glucose had a high energy bond.
It would use the energy of that bond
to put a glucose onto a growing glycogen chain.
You probably don't remember but I mentioned last time that
acetyl CoA is also an activated intermediate.
This bond between the sulfur of the CoA and the acetyl group
is a high energy bond.
The energy of this bond is what makes this reaction favorable.
Acetyl CoA is an activated intermediate, has high energy,
and uses the energy of itself to help put this two-carbon piece
onto this four-carbon piece, thereby making citrate.
Excuse me.
Now as I said, the energetic favorableness of this reaction
is important as we come back around to the other side.
In the second step of the process of, the citric acid cycle,
the six-carbon citrate intermediate is rearranged.
It's rearranged to make an isocitrate.
And that rearrangement, as you can see,
simply moves a hydroxyl group from one position to another.
Instead of being in the middle
it's moved to a top one as you can see here.
This is an isomerization as it were.
It's a rearrangement of the position of things
relative to the molecule.
And what the cell is getting ready to do
is its getting ready for the first oxidation.
The enzyme that catalyzes this reaction is the only enzyme
in the process whose name-
excuse me, doesn't tell you what it does.
The enzyme name is aconitase.
And yes it has that intermediate
but I don't even expect you're going to know the intermediate.
I only care about the beginning and the end there.
Aconitase catalyzes the conversion of citrate into isocitrate.
We're still at six-carbons.
We started at six.
All we've done is we've rearranged the things around there to make,
that new six-carbon molecule
Student: How do you spell aconitase?
Kevin Ahern: Aconitase is right there.
The third step of the citric acid cycle
involves the oxidation of isocitrate.
It's catalyzed by an enzyme known as isocitrate dehydrogenase.
Whenever you see, hear the word dehydrogenase in an enzyme
it is always an oxidation reaction that it catalyzes.
Isocitrate dehydrogenase is catalyzing the oxidation
of isocitrate starting with a six-carbon molecule,
again forgetting the intermediate,
getting over here to a five-carbon molecule,
Oxidation reactions release electrons.
We don't want those electrons floating around.
Electrons are taken by an electron carrier.
In this case the electron carrier is NAD, making NADH.
You guys are looking a little tired.
Student: We need a song.
Kevin Ahern: You need a song?
Student: We need a song.
Kevin Ahern: You want a song?
Will you sing loud if I pull up a song?
Class: Yes!
Kevin Ahern: Alright, we'll have a song.
Now, A, you have to sing loud.
B, I know that everybody's been very,
very upset of the fact that it's been so dry lately
so I thought we'd sing about that.
Kevin Ahern: Everybody know the song,
"Let It Snow, Let It Snow, Let It snow?"
Class: Yes.
Kevin Ahern: Alright, let's go with this one.
[all singing]
Oh the Oregon weather's dowdy
'cause the sky is mostly cloudy
You can't stop it if you complain
So let it rain, let it rain, let it rain
It doesn't show signs of slowing
And it's rarely right for snowing
Though it's driving some folks insane,
Let it rain, let it rain, let it rain
When it finally turns out dry
We'll be putting away our rain gear
It will probably be July
But I'll surly miss the rain dear
'Cuz the sound of the falling rain
Pitter pattering down the drain
Makes music inside my brain
So let it rain, let it rain, let it rain
Kevin Ahern: Alright.
Student: Woo!
Kevin Ahern: Don't encourage me.
[class laughing]
Now that the blood's flowing
we can go further in the citric acid cycle.
How's that?
Okay, let's do one more reaction and I tell you what,
we'll actually finish early today.
How's that?
[class murmuring]
One more reaction.
This last reaction, I've saved the best for last
because this is a cool reaction
and it's an interesting reaction.
You can see it on the screen here.
Alpha-ketoglutarate is going to get oxidized.
There's an NAD.
And there's a CoA.
And it's going to get, transfer the four-carbon product
to the CoA's catalyzed by react-,
an enzyme known as alpha-ketoglutarate
and by the way you can call alpha-ketoglutarate,
alpha-KG if you want, alpha-ketoglutarate dehydrogenase.
This also is a decarboxylation.
It's also a decarboxylation.
It's also an oxidation.
We produce NADH as we produced before.
And the energy of that oxidation
is creating another activated intermediate.
Look at this.
Here's that S bond to the C.
Succinyl CoA, activated intermediate.
Well why is this a cool reaction?
This is a cool reaction because this enzyme,
alpha-ketoglutarate dehydrogenase,
which you can call alpha-KGDH,
alpha-ketoglutarate dehydrogenase
has a structure that's almost,
people are noisy out there,
almost identical to pyruvate dehydrogenase.
It's almost identical.
Indeed, if we look at what it's doing,
it's catalyzing a reaction almost identical to it.
There's an alpha-keto acid.
Pyruvate is an alpha-keto acid.
In pyruvate oxidation we see loss of the carbon
off of the keto group.
It's exactly what we see here.
We see the transfer of the acetyl group to a CoA.
Here we see the transfer of a succinyl to a CoA.
The steps are almost identical.
The structure of the enzyme is almost identical.
The five coenzymes are identical.
The reaction mechanism is identical.
Cells are very efficient.
Evolving enzymes, if you've solved the problem once,
you don't always have to go resolve it again.
They've done it with this enzyme and modified it slightly
to use a slightly different substrate,
but the same basic reaction occurs.
Questions about that?
Okay one last thing.
Now you guys heard those guys out there.
They're noisy.
You are too, when you come in here.
When you come in in the section outside of the classroom,
and there's a classroom in here, whisper.
Be polite.
Don't speak loudly, okay?
I don't want to have to come along and shush people.
Thank you.
Alright, see you around.