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Course: MCAT > Unit 6
Lesson 15: Krebs (citric acid) cycle and oxidative phosphorylation- Krebs (citric acid) cycle and oxidative phosphorylation questions
- Oxidative phosphorylation questions
- Inhibiting the electron transport chain
- Regulating electron carrier molecules
- Heat generation in brown fat
- The citric acid cycle
- Krebs / citric acid cycle
- Regulation of pyruvate dehydrogenase
- Regulation of Krebs-TCA cycle
- Electron transport chain
- Oxidative Phosphorylation: The major energy provider of the cell
- Oxidative phosphorylation and chemiosmosis
- Regulation of oxidative phosphorylation
- Mitochondria, apoptosis, and oxidative stress
- Calculating ATP produced in cellular respiration
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Regulation of Krebs-TCA cycle
The citric acid cycle, always active to varying degrees, is crucial for ATP production. Acetyl-CoA enters the cycle, undergoes oxidations, and exits as carbon dioxide, producing FADH2 and NADH. This cycle is regulated through allosteric regulation and substrate availability, responding swiftly to the cell's energy needs. Created by Jasmine Rana.
Want to join the conversation?
- Should the CO2 have a 2 before it?(11 votes)
- Yes, because there are two molecules of CO2.(12 votes)
- I think you missed a step the Krebs Cycle. Isocitrate interacts with Isocitrate dehydrogenase which forms oxalosuccinate. (This step produces 1 NADH). The next step transforms Oxalosuccinate via the oxalosuccinate decarboxylase to a-ketoglutarate (this step produces 1 CO2). I know the goal was to simplify the krebs cycle but this neglects the formation of the NADH and makes students think that the Isocitrate dehydrogenase oxidizes isocitrate and releases CO2 which is simply not the case.(3 votes)
- Oxalosuccinate is an unstable intermediate which only exists bound to isocitrate dehydrogenase. It doesn't even appear in many detailed maps of the kreb cycle you can find with a quick google search. Seems like a pretty acceptable omission.(18 votes)
- In a few textbooks that I've read, and research that I've done (http://www.ncbi.nlm.nih.gov/pubmed/16097935) it states that ATP inhibits alpha-ketoglutarate dehydrogenase complex as well. I was wondering for the MCAT do we assume it is an inhibitor or not since in this video Ms.Rana states that it isn't.(4 votes)
- Both my biochem textbook and the Kaplan MCAT biochem book state ATP as an inhibitor for alpha-ketoglutarate as well. I think it is best to assume that all 3 of the enzymes mentioned in the video are inhibited by ATP and NADH.
I am sure if its role is controversial, the MCAT will specify in the passages.(4 votes)
- is it necessary to know every single enzyme for the citric acid cycle for the MCAT or just the big picture of 3 NADH, 1 ATP, and 1 FADH2 per turn or double for glucose?(2 votes)
- I haven't written the new MCAT yet but this would follow under biochemistry. If anyone else that has written it already that can clarify, that would be awesome. I would say yes, you know to know the reaction, products, and the enzymes involved. Kind of a downer but if you understand the reactions, it wouldn't be too difficult memorizing it. From the AAMC guide of biochemistry, this is what they want you to know from citric acid cycle:
Citric Acid Cycle (BIO, BC)
Acetyl-CoA production (BC)
Reactions of the cycle, substrates and products
Regulation of the cycle
Net molecular and energetic results of respiration processes(5 votes)
- Is NAD+ also an activator?(2 votes)
- Yes it is because it is a reactant in this reaction which indicates to the cell that is it ready for undergo the krebs cycle/needs energy.(2 votes)
- Alpha ketoglutarate...think I said that right....is synthesized from aa's from muscle cells during starvation. Is ATP not an allosteric inhibitor of alpha ketoglutarate dehydrogenase because cells are so lacking of ATP during starvation? To me this makes sense from an evolutionary perspective, as ATP would be in short supply during starvation and may be needed from the CAC at a greater level if ATP isn't being made elsewhere....just want to see if I'm thinking about this correctly!(2 votes)
- Alpha-ketoglutarate dehydrogenase complex is not an allosteric regluated enzyme, rather it is product-inhibited by NADH and succinyl CoA and possibly GTP. Similarly, citrate synthase is not allosterically regulated either, the rate is controlled by concentration of substrate and product, oxaloacetate and citrate respectively.
However, isocitrate dehydrogenase is an allosterically regulated enzyme and is considered one of the rate limiting step for the TCA cycle. It show cooperative binding when isocitrate followed by ADP bind the isocitrate dehydrogenase. This cooperative binding decreases the Km of the enzyme in comparison to the ezyme bound to a single activator.
TCA regulation is tied to the rate of electron transport chain (ETC) primarily by NADH/NAD+ and ATP/ADP ratios.
The video was confusing which enzymes are allosterically regulated and which ones are regulated by substrate/product concentrations. The distinction is very important, at least for testing.(1 vote)
- would allosteric inhibition by NADH and ATP be considered negative feedback as well?(1 vote)
- Yes that is a form of negative feedback because NADH and ATP are products of TCA.(3 votes)
- Why is ADP an activator in Krebs Cycle, while AMP is an activator in Glycolysis? (Especially that both use ATP as an inhibitor)(2 votes)
- Don't amino acids enter the cycle as acetyl CoA? Why does it say here that amino acids enter the cycle as alpha ketoglutarate?(1 vote)
- Where amino acids enter the Krebs cycle depends on the amino acid.
Note that starting around5:40, Jasmine says "And in some cases amino acids can actually begin to break down from our muscles and enter in various places along the citric acid cycle. And one place they enter is, they actually are converted into alpha-ketoglutarate here. " (my emphases)
Khan Academy has more material on this here:
https://www.khanacademy.org/test-prep/mcat/biomolecules/fat-and-protein-metabolism/v/overview-of-amino-acid-metabolism
You should also find the section on amino acid catabolism from this wikipedia article helpful:
https://en.wikipedia.org/wiki/Protein_catabolism#Amino_Acid_Degradation
The diagram from that seems particularly helpful.(2 votes)
- She didn't mention FADH2. Is FADH2 an allosteric inhibitor as well?(2 votes)
- FADH2 is made indirectly by Coenzyme Q, which is reduced in the citric acid cycle. I don't believe that FADH2 serves to regulate the TCA.(0 votes)
Video transcript
- [Speaker] To save us
some time, I've went ahead and drawn out simplified
version of the citric acid cycle here and if you remember,
it begins with acetyl-CoA entering the cycle, and it
combines with this molecule oxaloacetate to form citrate. And this citrate undergoes
various conversions and oxidations, which
eventually cause the two carbons that entered with acetyl-CoA, because remember acetyl-CoA
is a two-carbon molecule. These two carbons exit as carbon dioxide. And as it's oxidized and
loses it carbon dioxide, acetyl-CoA also allows us
to produce the electron carrier molecules FADH2 and
NADH, which if you recall, go to the electron transport chain to allow us to produce ATP. So to summarize, let's go
ahead and write out the kind of overall chemical reaction
of the citric acid cycle. So we have as our reactants,
acetyl-CoA entering the cycle, we also have some co-enzymes
like NAD+ and FAD, and we also have a freed
GDP, remember GTP is formed in this cycle as well. And all of this eventually
will produce carbon dioxide from the oxidation of acetyl-CoA. We reduce our electron carrier molecules. So NADH and FADH2, we also form a GTP. Now the reason I wanted
to go ahead and write out this entire overall reaction
of the citric acid cycle is because when I was
first learning the cycle, I kind of often got stuck
in the individual reactions that were taking place in
this kind of merry-go-round. And getting confused by all
these names like isocitrate and succinyl-CoA, and I think
that when we're trying to understand in particular how this cycle is regulated, that is trying to
figure out when essentially, this cycle is in full
speed an when it's kind of slowing down, it's
actually nice to kind of step back and look at the big picture. Now the first point I want
to make is that in contrast to something like glycolysis,
which we usually think about as a metabolic pathway that
we really consider to be either on or off, the citric
acid cycle is something that we usually consider always to be on, but to various degrees,
depending on kind of the energy needs of the cell. And the reason it always has
to be on, right is because it needs to be delivering
these high-energy electron carriers to the
electron transport chain, to allow at least some constant
flow of ATP production, which is vital to a lot of
the tissues in our body. In contrast, you can probably
think of a case when, you know a theoretical
case perhaps, where someone might not have any glucose in their diet. And of course glycolysis
then could be off, but the body might be
able to use fatty acids and other kind of sources of kind of fuel to enter the citric acid cycle. And indeed, kind of a
clinical proof of this is that there are kind of disease
states that involve mutations of enzymes in glycolysis, for example. But you would be hard
pressed to find a living individual who has a mutation
in their citric acid cycle because this cycle is so vital to life. So that brings me to my
first point, which is that there is no hormonal control
in the citric acid cycle, because it's on regardless
of whether we're in the fed state or the fast state. Instead the major form of regulation of the citric acid cycle is
through allosteric regulation. So I'll remind you that
allosteric regulation is simply the ability of a molecule
floating around in the cell, to bind to a specific enzyme
that's part of this pathway, and it binds through a part
of the enzyme that's not the active site, and
essentially by doing this, it causes the enzyme to undergo
a conformational change, and it can either make
the enzyme work better, in which case we call it
an allosteric activator. Or it can make the
enzyme not work as good, in which case we call it
an allosteric inhibitor. And the way that I remember
that allosteric regulation is the major kind of
form of regulation in the citric acid cycle, is I remind
myself that since this cycle is always on, it still kind
of wants to be able to adjust on a minute to minute, so rather fast way to the kind of energy needs of the cell. So I'm gonna go ahead and write
that here, wants to respond to the energy needs of the cell. And they way that it can
figure this out is by looking at the molecules it has floating around. And these molecules are
often those that are involved in regulating this pathway allosterically. And finally, a third way
that this cycle is regulated is by looking substrate availability. And this is exactly what it sounds like. Essentially, if the body
doesn't have a lot of acetyl-CoA around for example, remember
this is one of the major kind of substrates for this pathway. Then it makes sense of course
that the speed by which this NADH and FADH2 is
produced is gonna slow down because there's just not
enough to enter the cycle. Now one high-yield example
of this is when citrate, under conditions of high
ATP generally shuttles a lot of it's acetyl-CoA
into the cytoplasm for fatty acid synthesis. And of course when this
happens, it's taking the citrate out of the cycle, and so it will slow
down the overall cycle. On the flip side, let's
say our body was in a very starving state, we haven't
had food for quite some while. And in some cases amino
acids can actually begin to break down from our muscles
and enter in various places along the citric acid cycle. And one place they enter is,
they actually are converted into alpha-ketoglutarate here. And suffice to say that the
general idea here is that if you have of this substrate
around, it's gonna push the cycle to go faster which
makes sense in this case right, because the body is
alerted to the fact that it's starving, and so it
wants to be able to produce more NADH and FADH2 to produce more ATP. Alright, so that's kind
of a general overview of substrate availability,
but now I wanna talk more in depth about this
allosteric regulation. Now you wouldn't notice if I
had told you, but it turns out that there are three reactions
in the citric acid cycle that have a very large negative delta G. And remember large negative
delta G means that these reactions are largely
irreversible, which means that they are good targets for
regulation because once these reactions essentially
occur, it's usually like a ball rolling down a hill
and will allow everything else to occur. And these three reactions
are the conversion of oxaloacetate and acetyl-CoA into citrate, as well as the conversion from isocitrate to alpha-ketoglutarate,
and alpha-ketoglutarate to succinyl-CoA. Now to go ahead and keep
this kind of diagram as clear as possible, I'm
gonna go ahead and kind of abbreviate the names of
these enzymes, but of course you can always go to
Wikipedia or a textbook and remind yourself what
these enzymes are called. But of course this
enzyme from octyl acetate and acetyl-CoA to citrate,
is citrate synthase, and isocitrate to alpha-ketoglutarate is isocitrate dehydrogenase,
so I'm gonna say ID. And then alpha-ketoglutarate
to succinyl-CoA is alpha-ketoglutarate dehydrogenase. Now the allosteric regulators
that these three enzymes can end up being kind of a long list, but my hope in this video
is to just be a resource for you to come back to
and to kind of justify why certain things are
allosterically inhibiting or activating these enzymes. So why don't we start off with
the allosteric inhibitors, and one kind of easy allosteric
inhibitor to remember is NADH because it allosterically inhibits all three of these enzymes. And the reason it does this,
and it should be apparent to you why this is so, is
that, notice that NADH is a product of the overall
citric acid cycle, right? So it's a product right here. And so if we're building
up NADH, it's essentially a sign to the body that the
citric acid cycle is going faster than the, essentially
the electron transport chain, which is using up these NADH,
can consume those NADHs. And so it's time for the
citric acid cycle to slow down. Now another allosteric
inhibitor that should make some sense to you is ATP. So if we have a lot of ATP in
the body, it makes sense that this would be an allosteric inhibitor of processes that produce energy right, Because we want to conserve
energy and not kind of make more energy than our body needs. So in this case, it turns
out experimentally for some reason, only two of
these enzymes have been shown to be inhibited by ATP
and those are citrate synthase and isocitrate dehydrogenase. Now the final allosteric
inhibitors to talk about are actually products that
form in the citric acid cycle and these products, if they
accumulate in excess amounts, can actually negatively
feed back by allosterically inhibiting some of these enzymes. And the two notable products
that do that are first, citrate, which can
allosterically negative feed back on it's enzyme citrate synthase,
as well as succinyl-CoA, which not only negatively
allosterically feed backs onto the alpha-ketoglutarate
dehydrogenase, but it also can actually
negatively feed back on the citrate synthase enzyme as well. And one way that I kind of
remember why succinyl-CoA might wanna kind of feed
back all the way back to the citrate synthase
is to recognize that the citrate synthase is the kind
of first kind of point of entry into the citric acid cycle. And so, if it can stop the
citric acid cycle sooner, it will essentially waste
less energy so to say. Alright so that kind of sums
up the allosteric inhibitors, but what about the allosteric activators? The first allosteric
activator that always comes to my mind is ADP. Remember that ATP is
hydrolyzed by a water molecule into ADP, and a free phosphate group. So if ADP levels accumulate
in excess of ATP, then it's basically a
sign that the cell is running out of it's power,
it's running out of it's ATP, and it will therefore
need to produce more ATP. And so, if it needs to produce
more ATP, it makes sense that it would want to activate the enzymes in the citric acid cycle. And it's easy to remember
because it activates the same enzymes that ATP inhibits. So those are citrate synthase
and isocitrate dehydrogenase. Alright, so we're hitting
the home stretch here and there's actually only
one more allosteric activator that we need to talk
about, and that is calcium. So why might calcium be
an allosteric activator? Well remember that our muscle
cells require an influx of calcium to contract. So presumably you know, if
we're exercising really hard, of course our energy needs
go up, but our calcium levels inside of our cell are also going up, because of all that muscle contraction. So, this is essentially
a way for the body, especially in skeletal
muscles to essentially couple muscle contraction
with producing more ATP to meet the needs of
those contracting muscles. And again, this is experimental evidence, but calcium has been shown
to allosterically activate isocitrate dehydrogenase, as well as alpha-ketoglutarate dehydrogenase.