Ahern:...friday, and it will be like before so I want you
to sit every other one and so number 1 being here
and then every other one over.
Number 1 being here and then every other one over.
So if you count and you see that someone is sitting in 2,
don't move to 4.
They'll have to move.
Make sure you sit in the odd numbered seats
and then you'll be okay.
And then over here, same thing.
Starts and then moves over.
And the same is true over there.
That will align with everything down here.
The sooner we get seated, the sooner we can get started,
and that's important.
Let's see, the material that we will have on the exam,
everything I covered through Monday and on Monday,
I showed this slide but I only talked through
this one right here.
I'll talk about these reactions down here today.
You're not responsible for those on the reaction.
But you are responsible for this one up here.
So only the things that I talked through on Monday.
I did the review session last night, I have posted
the review session online, you can take a look at that,
if you weren't able to make it and you'd like to see that.
You'll notice on the review session that I say
that I am taking questions.
So I do this sometimes with students.
If you would like to submit a question for me to put on
the exam, or to consider putting on the exam,
I would be happy to do that.
I will take one student question and put it on the exam.
Send me your favorite question.
Send me what you would like me to put on there
and I will think about that and pick one
student question to put on there.
You need to have me that by tonight.
So if you get that to me by tonight when I finish writing
the exam, I'll make sure the one student question
is on the exam.
There was a question about did we sing loud
enough for the extra credit.
The answer is basically you did, yeah.
If there's any doubt, we're going to sing again today
so maybe that would help just make sure there's
going to be some extra credit or something,
that would be good.
So what I'm going to do today is actually kind of abbreviated.
I'm going to talk through some more of the glycolysis.
I'm going to talk about some consideration like other sugars
that enter and some health considerations relative to that.
And then I'm going to leave a little bit of time
for questions if you want to ask questions.
If you weren't able to come to the review session
last night and you would like to ask questions here today,
I will be happy to answer questions for you.
If you want to leave, that's fine too.
So whatever works for you.
Clear as mud?
Student: So you gave us the figure in Monday's lecture,
you had all the figures of the 10 steps,
but you only went over the steps up to 8.
Are we still responsible for the ones?
Ahern: His question has to do with the 10 steps of glycolysis.
That's what I was talking about here.
This is step number 8, that's where I've stopped.
So I'm not holding you responsible for steps 9 and 10.
Student: Even though you did give us the steps.
Ahern: Yeah, but I didn't talk about them.
Student: You said we need to know the figures
that were easy to remember and you mentioned
the first 4 of glycolysis.
And then you said "I might add some more figures to go along"
but you never did.
Ahern: I never did, would you like me to add some more?
Ahern: Okay, then I won't.
Student: So the variations of glucose and fructose pretty much.
Ahern: What I'm going to hold you responsible
for knowing the structures of in glycolysis for exam
will be the various structures of glucose and fructose, yeah.
Glucose and fructose molecules.
Like glucose-6-phosphate, fructose-6-phosphate, etcetera.
We'll keep it simple.
People last night said that they felt that the material
is greater than the material in the first exam.
Is that the general consensus in the room?
Ahern: Really, all right.
You know, it's always weird.
I never had that perspective, so I think, "oh, okay."
But then, I guess I look at it differently
than you do too, so that's fine.
The format of the exam will be exactly as the first exam.
Points may be slightly different for each section,
but you'll have a short answer section,
you'll have a problem solving section,
and you'll have a longer answer section.
So all three of those sections will be there.
I don't think time should be an issue.
I tried to keep it like like I kept the last exam
where hopefully time was not an issue.
Student: Will you tell us [inaudible] before the test again...?
Ahern: Well, since I haven't written the exam yet, I'm not sure.
It's not going to be significantly different
from what it was before.
There might be a few points here and there but I really don't
think it's going to be, not think,
I know it's not going to be significantly different.
I've written about three quarters of the exam,
so I know pretty much what's there.
Student: Can you post the curve from
the last exam online anywhere?
Ahern: I did.
Student: Oh, is it?
So it's on the schedule page.
One other thing with respect to grading.
The TAs have a big issue with being able
to grade it during next week.
So it means they got two monster exams
and they're not going to be able to have it
graded before Thanksgiving.
I really wish we didn't have that happen,
but there's not really a way that we have around that.
So they've got biophysics and a biochemistry exam
both next week and they're not done with those until Wednesday
so there's no way to have the exam graded.
So you can go home and have Thanksgiving and you won't
hopefully think too much about your grade.
When you come back, I can assure you we will have
the exams ready for you when you come back on Monday.
But the exams will not be available next week unfortunately.
Student: Previous exams that were resubmitted for rescoring,
are those available in the office now?
Ahern: Previous exams for people who had regrading requests,
those are back in the BB office.
Well, let's get into this material.
I talked last time about this interesting enzyme,
phosphoglycerate mutase, and I pointed out to you that a mutase
has this odd system of operation where it adds a second
phosphate and then it takes off the phosphate that was on there
originally and as a result of that, there's an intermediate
that has 2 phosphates and that's how we get to 3-BPG.
So that's a really cool and interesting reaction.
One of the reasons that that rearrangement of the phosphate
is being made is to essentially create a high energy phosphate.
And that's what happens in the next step of glycolysis.
The next step is catalyzed by the enzyme known as enolase.
And enolase catalyzes the removal of water.
So water is taken out of this guy right here.
That creates a double bond next to this phosphate
and this phosphate is next to this carboxyl group.
Phosphoenolpyruvate, which you can abbreviate PEP,
and PEP has a lot of energy and PEP needs
a lot of energy and PEP has a lot of energy.
PEP is one of the highest energy molecules
that you will find in your body.
Very high energy and we recall of the earlier example
that I talked about in glycolysis where we have a molecule
that has a very high energy and it has a phosphate on it,
it can transfer that phosphate to ADP and make ATP by substrate
level phosphorylation and in fact,
that's exactly what happens in the last step.
In the last step, we see this high energy phosphate
being transfered directly onto ADP to make ATP
and that yields pyruvate.
Now, this last step is a really interesting step.
It's the step I like to refer to as the big bang.
The big bang.
Why do I call it the big bang?
Well this reaction right here has a very large,
negative delta G zero prime.
Very large negative delta G zero prime.
Now, notice that ATP is being made and in spite of that,
it still has a large negative delta G zero prime.
There's almost enough energy in this molecule to make two ATPs.
There's almost enough energy in the molecule to do that.
That's why I call it the big bang,
because when this sucker explodes,
it makes ATP and there's all this excess energy.
What happens when we have excess energy?
Student: Is that the metabolism of people?
Ahern: You're getting ahead of me.
So we have all this excess energy and we're not making ATP.
Well, what happens when we have excess energy in any reaction?
Well, that energy is just lost.
And we lose energy, we lose it as heat.
This big bang reaction gives off a lot of heat.
So one of the reasons that we get hot when we exercise
is we're going through a lot of glycolysis
and we're going through a lot of this reaction
and we're generating a lot of excess heat on the side.
So the reason we get hot is we're just not
100% efficient at making ATP.
That excess energy is given off as heat.
That's why we sweat and get hot whenever we're exercising.
Pyruvate kinase, I'll say a little bit more
about in a little bit and that may not happen actually
until Monday, but pyruvate kinase,
now this is very odd for glycolysis,
pyruvate kinase is the 3rd enzyme that's regulated.
This is the only metabolic pathway that I know
of where the last step is regulated.
It's actually regulated both allosterically
and by covalent modification.
It's very odd.
Now, there's a reason why.
I'm not going to tell you the reason today because
it's not going to make any sense to you,
but it makes sense when we look at the reversal of this pathway.
The reversal of this pathway involves the synthesis
of glucose and the synthesis of glucose
is called gluconeogenesis.
And it uses many of the steps of glycolysis.
It doesn't use this step, but it uses many steps of glycolysis.
It's important for the cell to be able to turn
this enzyme on and off.
If we think about it, we've got a very,
very large delta G zero prime.
If I can't turn this enzyme off,
what's going to happen whenever I've got PEP?
It's going to go almost completely to pyruvate.
Almost completely to pyruvate.
There will be times we don't want that happening.
So the short answer to the reason we want to regulate
this enzyme is because of the large delta G zero prime.
We really want to be able to regulate that enzyme.
So the 3 enzymes in glycolysis that
are regulated are hexokinase, I said I won't say too much
about that one, phosphofructokinase,
which turns out to be the most important one for the most part,
and pyruvate kinase.
Not surprisingly, all three of those reactions
have a fairly negative delta G zero prime.
Now glycolysis as I said is unusual in being
regulated at 3 places.
And again, there are reasons why that's happening,
but as you can see with this example,
being able to turn off and reaction that has a large negative
delta G zero prime is important for the cell.
That's part of the reason why the cell has those three
different enzymes that are regulated.
Questions about that?
Student: With that being the bottom that
kind of chokes up things?
ending the final step of the glycolysis process.
Is there any kind of a storage or I guess battery area
for the PEP?
Ahern: Is there a place to keep PEP,
is that what you're saying?
Student: Yeah, is there somewhere where it's stored
until PEP need to be converted?
That's actually a very good question.
So his question is, "does the cell store PEP around?"
To my knowledge, it does not.
When we look at the metabolic pathways involved here,
we see that PEP goes to here and if we go backwards
to the synthesis of glucose, then PEP is driven that way.
I don't know of stores sitting around as such.
Student: What did you say were the two ways
that pyruvate kinase is regulated?
Ahern: Pyruvate kinase is regulated both
allosterically and by covalent modification.
And I'll talk more about those when I talk about regulation.
Student: Can you name the three things
that are regulated in glycolysis?
Ahern: The three enzymes?
The three enzymes regulated in glycolysis are hexokinase,
PFK, which is also known as phosphofructokinase,
and pyruvate kinase.
Those are the three regulated enzymes in glycolysis.
To come back to your question as I'm thinking through
my head about this, there are a couple of reactions
where the phosphate of PEP is donated to something.
So PEP in a couple of reactions, they're not major reactions,
but in a couple of reactions,
PEP serves as a high energy phosphate source kinda
like ATP does, but they're not central reactions.
Alright, so that's what's up with that.
We need to, there's the overall summary, blah, blah, blah,
no you're not going to memorize that.
We do need to consider some things about glycolysis
that are really important, though.
And it's one that I sort of glossed over,
but I want to come back and visit right now.
And that's a phenomenon known as redox balancing.
That's the first time you've heard that expression.
What in the world is up with redox balancing?
Well redox of course refers to reduction oxidation.
When I'm talking about balancing,
I'm not talking about the fact that every reduction gives
an oxidation and every oxidation gives a reduction.
That's not what I'm talking about.
So the balancing is something different from that.
When I'm talking about redox balancing,
I'm talking about the fact that cells have
a limited number of electron carriers.
Cells have a limited number of electron carriers.
So so far, we've been saying, "okay, well here's
“the glyceraldehyde-3 reaction, it gets oxidized
“to form 3-phosphoglycerate,
“I'm sorry, 1-3 diphosphoglycerate and NADH is produced."
And we didn't think anything more about it.
But what I'm telling you now is that cells
have a limited amount of NAD.
Cells have a limited amount of NAD.
When there's plenty of oxygen in our cells,
the NADH that's made goes and dumps off the electrons
in the electron transport system and becomes NAD again.
I'll repeat that because that's a very important point.
When there's abundant oxygen in our cells, the NADH
that's produced in oxidation reactions dumps
its electrons into the electron transport system
and becomes NAD again.
As long as we have plenty of oxygen,
we don't have to worry about balancing because
we're automatically grabbing the electrons here,
going over here, and dumping them
and then coming back as a NAD again.
We have to think about balancing when we don't
have sufficient oxygen.
We have to think about balancing when
we don't have sufficient oxygen.
And that's what you see depicted on the screen here.
If I don't have sufficient oxygen,
then NADH that's made here cannot dump its electrons
into the electron transport system.
We'll talk about that as a very important
consideration next term.
But sufficed to say in the absence of oxygen,
if we don't do something with that NADH,
it's going to accumulate and we're not going
to have any NAD left.
If we don't have any NAD left,
what's going to happen to that reaction?
It ain't gonna go.
We got trouble.
Well glycolysis is such an important pathway
for the cell because it makes all kinds of useful things
that we really don't, we really can't afford
to have that pathway plugged up.
But I told you that there are times that cells run out
of oxygen and they have to be able to adapt to that.
So they've adapted a mechanism that you see here
where the NADH instead of dumping off its electrons
to the electron transport system,
dumps its electrons onto the pyruvate.
When it dumps its electrons onto pyruvate,
a couple of things can happen.
If you're a bacterial or bacterium or yeast cell,
that's the reason, that's what fermentation is all about.
That's what they're making is ethanol.
Notice that the byproduct of that is more NAD.
And that NAD now can be reused back up here.
We've just balanced the equation.
So we've balanced it, we've regranted the NAD
that we need and we didn't even have to have oxygen for it.
That's why making beer, making wine is occurring
in an environment where there's no oxygen,
because the cell has to do what it can,
and so it starts making ethanol and at the same time
making NAD that it can use to keep this process going.
Ahern: Her question is, "isn't ethanol bad for cells?"
I'm talking about yeast in bacteria here, first.
We do something different.
But yeast in bacteria also don't like this too much.
You can get up to maybe 12 to 15% ethanol before they knock out.
The reason we distill liquor, we distill the alcohol
in liquor is because the yeast and bacteria can't make it
at a high enough concentration.
They die by the time it gets to that point.
They use a still to pull out the ethanol
and make vodka and all the various things that are there.
So the bacteria in yeast don't like it either,
but they tolerate it a lot more than now do.
We don't make ethanol.
I'm going to show you something like that in just a second.
In stead, we convert pyruvate into lactate.
So when I showed you that 3 fates earlier of pyruvate,
I said one was it could acetyl-CoA if we have oxygen,
I said it could go to ethanol if you're a bacterium or a yeast.
The third thing is it can go to lactate if you're an animal.
Lactate is known as lactic acid.
Some people like to think that because
when you exercise heavily, excess lactic acid is produced
and that's what leads to sore muscles.
Other people dispute that so whether that's true or not,
I won't try to weigh into that argument.
But sufficed to say, lactic acid is a byproduct
of heavy exercise because your muscles are using energy
faster than oxygen can come to them.
They've got to make something to keep
that glycolysis process going.
Questions about that?
Student: The site's just choking down the reaction
with not having any NAD plus left over
as an electronic receptor.
If that actually occurred,
would that be the major consideration or is the fact
that you also have NADH that's in excess and runs around
willy nilly reducing stuff in the cell?
Ahern: His question is "are there other considerations
“besides the fact that you run out of NAD here?
“Can the NADH dump its electrons to other things?"
The answer is basically not, no.
What will happen is NADH will just accumulate
but nothing else will happen.
Keep in mind that I describe this as running out of NAD, right?
But remember that NADH is a product
and NAD is a substrate, right?
So we could imagine that if we let that NADH get even a little
bit too high, we're going to favor the backwards reaction.
So that's the bigger consideration with NADH.
So we get too much NADH, even if we haven't used all
of the NAD, that reaction isn't going to go forward
for very long because the product is going to accumulating
and the delta G is going to becomes positive.
Student: You mentioned in a previous lecture I believe
that during these conditions that lots of the electrons,
like the cell uses NAD to get rid of the excess electrons
in these conditions . . . in reaction [inaudible.],
more then a normal amount of electrons escape it, so to speak.
Ahern: I'm not sure I understand your question.
Student: So in this condition, when there's low NADH,
is there a possibility of some of the electrons not being picked
up and going around causing problems
like you talked about before?
Ahern: Okay, so his question is if you run out of, well,
if you run out of NAD, the question is
"do the electrons go somewhere else or do they cause problems?"
I would say no.
So you're basically going to stop the reaction when you start
tipping the balance of products and reactants.
That's really what's going to determine whether or not
that reaction is going to go forwards.
I wanted to say just a word about what happens inside
of us and this is always something of interest to students.
Here's the same thing on the screen that
I showed you schematically on the last figure.
We see, again, the same sort of phenomenon.
We see that NADH is produced by this
oxidation reaction over here.
It gets used again when we're out of oxygen
to remake NAD and we're back here.
This again depicts what happens inside of bacteria and yeast.
You don't see lactate on there.
I'll tell you something that will surprise you.
We have in our bodies abundant alcohol dehydrogenase.
Why don't we make ethanol?
Wouldn't that be a really cheap Friday night?
[Class laughing.] Just hold your breath, right?
And you'd have, you'd start producing this stuff, right?
Well, it turns out that we don't have,
this process actually takes this reaction right here
and this enzyme we don't have.
At least the enzyme that produces acetaldehyde.
We have an enzyme that produces a related compound
but we don't have the enzyme that produces acetaldehyde.
So why do we have alcohol dehydrogenase?
Student: For breaking down ethanol,
acetaldehyde is the first product for metabolizing ethanol.
Ahern: So his answer, he says that you're breaking down ethanol
and the answer is basically yes.
Ethanol as we've described is not
very compatible with our cells.
No matter how much of the stuff we drink,
our body is actually detoxifying or trying to detoxify ethanol
with this enzyme and it's running the reaction
backwards to acetaldehyde.
Oh, just a minor problem that acetaldehyde causes hangovers.
Yeah, so if you wondered why you get a hangover,
you can blame that enzyme.
Now at this point, someone always says,
"now let's see, if I go and exercise real heavily
“and my oxygen is low, what's going to Happen?"
There's all kinds of schemes with that.
I'm not going to go into that.
The thought of running heavily after you've drunk
a bunch of beer just doesn't sound like a very fun idea to me.
Student: Isn't acetaldehyde more toxic than ethanol naturally?
Ahern: Acetaldehyde is fairly nasty, yeah.
Where were we?
So there's our pyruvate fates again to remind you
of what I showed you earlier.
Pyruvate going now to acetaldehyde and ethanol.
That's happening in bacteria and yeast.
Lactate happens inside of us.
Acetyl CoA, if oxygen is available in any of these cells,
assuming they're all aerobic like most bacteria
are aerobic as well.
I will talk about this reaction actually right
here beginning of next term.
Where am I at?
Ethanol formation, there you go.
Blah, we don't need to do that.
Lactate formation, that reaction is again one that we have.
We have the enzyme lactate dehydrogenase.
You notice the difference in this reaction compared
to what's happening in bacteria and yeast is in bacteria
and yeast we're from a 3 carbon compound to a 2 carbon compound.
In us, we're making lactic acid.
And lactic acid turns out to be pretty much
a biological dead end.
We don't really convert lactate into anything else.
Well then what happens when it accumulates?
When it accumulates, we've got a whole bunch
of lactic acid sitting here and it's not very useful for us.
Our body has to wait until we catch up in
the oxygen department and then it runs
the reaction backwards to make pyruvate.
It turns out that this cycle actually is very important
when we're exercising heavily.
Our body has a very cool way of dealing with lactate
where parts of our body have oxygen and other parts don't.
I'll explain that to you next term.
What else did I want to say here?
Fermentation options, and I won't talk about that.
Next, I'll talk about other sugars and then
I'll finish for today and I'll open it up to questions.
Glycolysis is a central metabolic pathway.
That central metabolic pathway is central
to most cells on the face of the earth.
Almost every cell on the face of the earth has it
and it's useful because it allows us to oxidize
not only glucose, but it allows other sugars
to enter that pathway as well.
So for example, there are enzymes that will,
through a series of steps, convert galactose
And that turns out to be very useful because when we drink milk,
we're getting a lot of galactose.
Milk contains lactose, lactose is a disaccharide
that contains both glucose and galactose.
So we have to be able, ideally,
to convert galactose into something that's useful for us.
We do that in a process I'll show you in just a second.
Fructose not surprisingly is something that we can convert into
fructose-6-phosphate and metabolise inside of glycolysis and,
if I have time, I will tell you briefly why
I think we have an epidemic of obesity relative to fructose.
In fact, I'll start there.
This is, I'm going to give you Kevin Ahern's pet theory
about why America is growing fatter and fatter and fatter.
This is Kevin Ahern's pet theory.
There's no evidence for this theory
other than what I'm going to argue for you on the screen.
But I think it's not an illogical argument.
One of the things that's happened in the American
diet over the past 20 or 30 years has been the increasing
use of fructose inside of materials for sweetening.
We talked about high fructose corn syrup.
The American obesity epidemic, you can literally trace
to about the time we started putting that into our food.
High fructose, we've got high fructose.
Well fructose is just a sugar, we just oxidize it like glucose,
we've got the glycolysis pathway, what's the deal?
I'm going to argue with you here that there is a big deal.
The big deal is what you see on the screen.
The last pathway didn't show you what you see here.
The last pathway shows you fructose going to
fructose-6-phosphate and then on into glycolysis.
I argue that if that pathway occurs, not a big deal.
I also argue that if we overload that pathway,
that this pathway causes some problems.
Now let's think about this.
First I need to tell you what's happening in this pathway.
Fructose, we've got a lot of fructose in our body.
A lot of fructose floating around here.
There's an enzyme called fructose kinase
that will convert fructose into fructose-1-phosphate.
Then there's this enzyme called
Notice that aldolase is kinda like
the aldolase we saw in glycolysis.
It splits this 6 carbon molecule into 2 3-carbon molecules.
One is glyceraldehyde and one is DHAP.
That's the same as we saw in glycolysis.
And we say, "oh, glyceraldehyde, that's the problem."
Well no, we can convert glyceraldehydes
So at this point, we have two things exactly
the same thing as glycolysis.
Why are we obese?
There's something very important we've neglected.
Anybody know what it is?
We've talked about it.
I'll give you a hint.
That last pathway showed going in through
This is not going in through fructose-6-phosphate.
Student: Where's the phosphate?
Ahern: It's not that.
It's not the absence of phosphates.
I'll tell you the answer.
The answer, at least from Kevin Ahern's pet theory
on why Americans are getting obese, a good acronym right?
My pet theory about this is that we have just
bypassed the phosphofructokinase step.
Phosphofructokinase was a regulatory enzyme.
We've bypassed the regulatory enzyme and now what are we doing?
We're force feeding the cell with these compounds
and when we start force feeding the cell with these
compounds, we're going to start force feeding
glycolysis all the way through.
We start making lots of pyruvate.
Pyruvate is a precursor of acetyl-CoA.
And when we have a lot of energy, as we do when we have
a lot of sugar, acetyl-CoA is made into fatty acids.
High fructose corn syrup, by this argument,
the Kevin Ahern pet theory about why Americans
are getting obese, okay?
Say that real fast.
By this idea, we're force feeding glycolysis
and as a consequence, making fatty acids and making fat.
For what that's worth.
Clear as mud?
It pays you to look and see if you have
high fructose corn syrup that you're eating.
It's pretty hard to find stuff that doesn't have it.
Student: What gets converted into the fatty acids again?
Ahern: So pyruvate is the end product of glycolysis.
Pyruvate can be converted to acetyl-CoA.
And when we have lots of energy, acetyl-CoA goes
straight to fatty acids.
Student: This would be the same net effect you would see
if someone who had a knock out mutation of PFK.
Ahern: He says it would be the same net effect you would
see if you had someone with a knock out mutation of PFK.
I think you had somebody who is dead if they had a knockout
mutation of PFK, but yeah.
That would be worse.
Student: Is there any research going on looking into
the problem with [inaudible] obesity epidemic?
Ahern: Say that again?
Student: Is there any research going into this,
like not this specifically...
Ahern: Oh yeah, a lot of people are interested
in high fructose corn syrup and the link to obesity.
And there are really some really suggestive things that
there is in fact a link between the two.
Student: So is there anyone looking at biochemical pathways?
Ahern: All of these are used, so this is only my own pet theory.
Student: There are some people that say it isn't.
Ahern: There are some people that say the sky is made
from green cheese, I mean, so you can't go on
what some people say, right?
Student: You're bouncing.
Ahern: Oh, I'm bouncing.
I thought we might, instead of going into galactose,
do a song and then call it a day.
And then I'll take questions for stuff.
Does that seem reasonable?
I've got a song about glycolysis that's a lot of fun.
It's to the tune of "These Are a Few of My Favorite Things."
Here we go.
Aldehyde sugars are always aldoses and
If there's a ketone, we call them ketoses.
Some will form structures in circular rings.
Saccharides do some incredible things.
On to a glucose, we add a "P" To it.
ATP energy ought to renew it.
Quick rearranging creates F6P
Without requiring input energy.
At a high rate
Add a phosphate
F1,6BP is made up this way
So we can run and play
da da da da.
Aldolase breaks it and then it releases
DHAP and a few G3Pieces
These both turn into 13PG
Adding electrons onto NAD
Phosphate plus ADP makes ATP
While giving cells what they need energy
Making triphosphate's a situation
Of substrate level phosphorylation
Lose a water
PEP gets a high energy state
Just to make pyruvate
So all the glucose gets broken and bent
If there's no oxygen cells must ferment
Pyruvate lactate our cells hit the wall
Some lucky yeast get to make ethanol
This is the end of your glucose's song
Unless you goof up and get it all wrong
Break it, don't make it to yield ATP
You'll save your cells from futility
We will definitely have an extra credit question on the exam.
If there are people who would like to ask question
for a mini review session here,
I would be happy to take questions.
I see a hand back there.
Student: Really quickly, when we're looking at
the insulin signaling probably,
Student: There's one enzyme that has a really long name
and could you give us a nickname for the highlight
because it's phos...pho- inosit...
Ahern: Yeah, I know what you're talking about.
Student: Do you think you could write one
you could use for the test?
Ahern: As a matter of fact,
Where's my thing here?
I am happy to grant that request.
Every year, I get this request and it looks like it's made it
into my highlights and so fourth,
so let's take a look at that pathway and come up with a name.
I will let you guys name it, how about that?
So let's think, hold on just a second now.
Insulin signaling right here.
This is the name, do you want this one,
or do you want this one?
Students: The green one.
Ahern: You want the green one?
That's usually the one people want to rename.
Student: That's the one you said was like longer
in your highlights thing.
You said it was like phosphor...
Ahern: What do you want to call the green one?
The green one?
I like that.
Can anybody beat the Hulk?
The hulk it is.
So, for this exam, phosphoinositide-3-kinase
will be known as the Hulk.
And you may also call it phosphoinositide-3-kinase,
we will not count that against you.
But if you call it the Hulk outside this class,
please don't tell anybody where you got that name from.
It didn't come from me, right?
Are there other real questions?
Student: Ribose, does it have an alpha and beta?
Ahern: Does ribose have an alpha and beta?
Anything that has a Haworth structure will
have an alpha and a beta.
And you may notice, I didn't mention
Haworth structure in class.
I did put them in the highlights.
So you should know Haworth means ring.
Fissure structure means straight chain.
Probably got that in organic chemistry
but I just forgot to mention it the day I talked about those.
Other questions, Yes?
Student: For the catalytic [inaudible],
we talked about the catalytic triad
and then that was the active site
and then the oxyanion hole in the S1 pocket.
And the S1 pocket is what binds the substrate.
But I thought the definition of the active site
was what [inaudible.]
Ahern: So her question is, that's a very common one
that Karen's asking.
So the question that she's asking is I talked about
the catalytic triad being the active site
and then I talked about separate things like
the S1 pocket and the oxoanion hole.
So really, it's a very semantic argument
we're talking about here.
So you're correct.
These are all in essentially the same place.
So I simply used the three amino acid side chains
to describe the active site because
that's where the reaction is catalyzed.
But you're right, the substrate will be held at the active site.
And that substrate specifically is held in the S1 pocket.
So all I care about is you know the S1 pocket
is right there at the active site.
Whether we call that part of the active site
or not is just a semantic argument.
That's a very common question.
I get that the most common question of
that material from students.
Student: I wanted to check something about SH2 domains.
Ahern: Yes, SH2 domains.
Student: I think it says that both the Hulk
and IRS have SH2 domains and they're like both that
allows them both to recognize phosphate . . .
Ahern: So when you see portions of a protein recognizing
phosphotyrosines, they have SH2 domains, that's right.
Student: Okay, so they both do that.
Ahern: They both do, yeah.
Student: Can you say that one more time?
If it has a SH2, it recognizes . . .
Ahern: When you see something recognizing a phosphotyrosine,
which is what these are recognizing,
it usually involves an SH2 domain, yeah.
We've got 10 more minutes.
Student: Where on the G protein is the interaction
with the beta adrenergic receptor?
Does it bind with all the beta [inaudible]?
Ahern: Her question is "where on the G protein does
“the G protein interact with the beta adrenergic receptor?"
So, on the beta adrenergic receptor,
you've got all three present that's there.
So the interaction that's there is not precluded
by the covering of the beta and the gamma.
The beta and the gamma; however, have to move away in order
for the G protein to interact with the adenylate cyclase.
So all three are present in the beta adrenergic when it binds
to the beta adrenergic receptor.
Student: And then when it takes GTP, it sheds the beta....
Ahern: The binding of GTP causes it to lose the beta
and the gamma, which is what enables it then to go
and bind with the adenylate cyclase.
Student: So there's no actual binding of the GTP
to the other subunits, is there?
Ahern: There's no initial of the GTP to the other subunits.
The other subunits in fact don't bind GTP at all.
So it's only the alpha sub unit that will bind GTP.
Student: It's also called PI3K in the book,
can we use that, too?
We've already named it for our study guides.
Ahern: So the book calls it PI3K?
Ahern: Oh, why not?
PI3K, we've got phosphoinositide 3-kinase,
my key is going to be this long, the TAs are going to kill me.
Yeah, go ahead, that's fine, I'm sorry.
Student: What are your TAs going to think when
the Hulk is an acceptable answer?
Ahern: Every year, I rename that enzyme.
One year we renamed it Larry.
[Class laughing.] Last year, I think we called in Malcolm.
The Hulk is the best name we've had though, I have to say.
So one year I forgot to tell the TAs that I had done this.
And so I always say this thing with my TAs,
and I say, "You know, give me a call if
“there's something unusual on the exam."
And then I give this call late one night and he goes,
"what the hell is Malcolm?"
So I shouldn't tell them, right?
Just leave it as the Hulk, right?
Student: It's Malcolm in the Middle.
Ahern: Malcolm in the Middle, yeah.
I shouldn't open this up, should I?
Student: I'm a little confused about G proteins.
It seems like there's a part of a G protein
and then there's a difference between a G protein,
GTP and GDP, and which one is binding where
and I'm sort of really confused.
Ahern: So the term G protein, to hopefully alleviate
your confusion, the term G protein simply means
protein binding guanine nucleotide.
It can bind GTP, it can bind GDP.
And that's where we talk about ras being a G related
protein because it also binds GTP or GDP.
Student: What are GDP and GTP?
Ahern: Guanine nucleotides.
GTP is ...
Student: Those so are nucleotides then.
Ahern: Yeah, yeah.
GTP is like ATP except for it has guanine
instead of adenine on it
Student: Oh, okay.
Ahern: Sorry, yeah.
Ahern: Okay, yeah.
Student: How come?
Ahern: How come?
So her question is one of the problems in the book.
And the problem in the book says that if you take
small concentrations of PALA and you treat ATCase with it,
you discover that you've actually increased
the activity of the enzyme.
If you used high concentration of PALA,
you completely kill the enzyme.
The question is why.
Student: is it because when it binds to the one site,
the other sites are still available?
Ahern: Her answer is exactly right.
So the answer to the question is in low concentrations,
only one or two of the sites get bound,
locking the enzyme in the R state, right?
Locking the enzyme in the R state and then those ones
that aren't bound to PALA are just as active as they can be.
That's exactly right, yeah.
Student: Did you send an email out about an error? Someone.
Ahern: Oh, I had an error on a sign on a Delta G.
Student: Oh, okay.
Can you pull the figure up for me?
The original one I modified so it's not even on here anymore.
But I can show you where it was.
So it was actually the highlights for...
it was the one, let's see, is that right?
Yeah, it was this one right here.
So on the original one, I had written this reaction backwards.
So I had written it creatine phosphate + ADP goes
to creatine + ATP and I left the sign as plus,
and it should've been negative.
Whenever you reverse the direction of an reaction,
you have to change the sign.
I hadn't done that.
So I just went back and rewrote it in the same way
that you saw it in class, which is the way,
this is the way I showed it in class.
You guys feel confident for this one?
I want to see everybody make an A on this one.
Ask you again on Friday.
Okay, have fun, see you on Friday.