Saturday, July 21, 2012

Protons: Where's the bias?

Executive summary: Complex I and Complex II are separate routes in to the electron transport chain. Glucose favours Complex I, fat favours Complex II. Now the extended version:

Here we have a nice schematic of the electron transport chain in a diagram of a mitochondrion taken from Wiki images.



The ATP Synthase complex shown on the upper left of the mitochondrial diagram allows protons from outside the inner mitochondrial membrane to pass back in to the mitochondrial matrix, generating ATP in the process. Under White Non Smoker conditions this electro chemical gradient might well have been maintained for free by the geochemistry of serpentinisation plus an acidic ocean. Nowadays the combined pH and electrical gradient which drives this ATP factory is maintained by the electron transport chain. This transports positively charged protons out of the mitochondrial matrix to maintain the gradient which is dissipated during ATP production.

In the diagram you can see two versions of the ETC being driven off of the citric acid cycle. On the upper right hand side a molecule of NADH provides electrons to Complex I. Complex I pumps some protons, hands the electrons to the Coenzyme Q pool (CoQ, marked as Q on the diagram) of electron transporters which then hand them on to Complex III. Complex II is not involved. The CoQ pool is a mobile reservoir of redox shuttles (electron transporters) which hands electrons to Complex III.

The second version, shown on the lower area, has succinate feeding in to Complex II. Complex II is actually the succinate dehydrogenase enzyme of the citric acid cycle. It is built in to the wall of the inner mitochondrial membrane and hands its electrons to the CoQ pool directly, no Complex I involved. Another difference is that Complex II doesn't pump any protons.

The proton pumping done by electrons passing through Complexes III and IV is independent of their route of entry to the ETC. Anything feeding in to the CoQ pool feeds onwards through Complexes III and IV. Mostly.

So we have the citric acid cycle processing acetyl-CoA to a ton of NADH for Complex I and a smidge of FADH2 within Complex II.

The FADH2 is quite tricky. It is embedded deeply within the succinate dehydrogenase enzyme and never, as far as I can make out, goes anywhere. It flicks between the FAD and FADH2 state as the citric acid cycle turns and basically acts as a bridge to transfer the effective oxidation of succinate to the reduction of the CoQ couple.

Another route in to the ETC, which seems sorely neglected, is Electron-Transferring-Flavoprotein Dehydrogenase, which sadly has no handy name. ETFD sits in the inner mitochondrial membrane and passes electrons to the CoQ couple, much as Complex II does, also without puming protons. ETFD gets its electrons from the FADH2 of an electron transfer flavoprotein which, thankfully, gets its electrons from the FADH2 of acyl-CoA dehydrogenase, the first enzyme of beta oxidation. Back on home territory.

Phew.

So fatty acid beta oxidation feeds in to the ETC at a "Complex II-like" membrane enzyme. It uses FADH2 to do this. It generates a small amount of NADH as well.

So we have two non-Complex I inputs in to the CoQ couple.

Aside: There are three if we include glycerol-3-phosphate dehydrogenase. Four if we include glycerol-3-phosphate oxidase Probably more. But let's keep it simple and stop at two... Actually glycerol-3-phosphate oxidase is really interesting as it specifically generates H2O2 enzymically. H2O2 production is generally considered to be a Bad Thing. Now what might the deliberate generation of H2O2 be signalling? Very interesting! Maybe another day.

So the citric acid cycle inputs just a few electrons through FADH2 at Complex II compared to the number it supplies using NADH at Complex I. Glycolysis is even more Complex I focused as it only adds NADH to its acetyl-CoA generation. However beta oxidation markedly inputs through the FADH2 of ETFD, with relatively little input using the NADH from the beta oxidation process, again in addition to generating acetyl-CoA. Obviously all acetyl-CoA generates the same ratio of NADH to FADH2.

The actual biases can be seen from these numbers, nicely posted by Lucas Tafur here. A direct quote:



As you can see glucose produces 5 molecules of NADH for each FADH2 where as fat produces only 2 molecules of NADH for each FADH2.

Glucose drives complex I significantly harder than fat does. Fat drives with a "Complex II-like" bias, supplying FADH2 from ETFD much as succinate dehydrogenase supplies some FADH2 from acetyl-CoA.

Both FADH2 inputs do exactly the same thing to the CoQ couple, they reduce it. A reduced CoQ pool has major implications for electron transport and free radical generation.

I rather like eating fat. What does that do to Complex I?

It's probably not the obvious answer.

Peter

30 comments:

Aaron said...

Quick question -- I like the fact that you have gotten all technical in your posts, but I'm always left wondering if you are just posting information about a particular cycle or if you have some comment on what is going on.

It would be more informative, if you even feel like doing it (i understand this is your blog) -- to comment on what you actually think is going on in this post with your fat metabolism -- do you think these mitochrondrial diagrams support your thesis to eat high fat?

I understand if you want to just use your blog for personal musings for your own personal headspace -- that is your choice.

George Henderson said...

Hepatitis C Virus core protein blocks complex 1 and this is where mitochondrial ROS generation is stepped up, blocking Fox01 phosphorylation and producing the characteristic DM2 symptoms.
So sidestepping Complex 1 as far as possible - well, it works for me.
http://hopefulgeranium.blogspot.co.nz/
Thanks for this insight; another piece of the puzzle turned up.

Peter said...

Aaron, I usually get to some sort of conclusion (not always, I keep meaning to go back to why macrophages specifically generate lipid peroxides and no, it's not to kill us!) but it's a multi step process. If I just write that "superoxide is essential to normal physiology and core to what goes wrong in T2DM", it doesn't get me very far in setting out (and in some way preserving, I think that's why I blog) my own impression of how metabolism works.

I'm quite lucky in that, so far as I can see, I'm in the correct paradigm, so things are very likely to pan out. At least as far as we have the information, there are always bits missing. The drive in this series is that reducing the CoQ couple does very interesting things to Complex I. So does running the ETC backwards, a standard procedure under hypoxic conditions. Mitochondria as consumers of ATP, and a price to pay. We call this reperfusion injury. At what point does the transition from physiology to pathology occur? Physiological insulin resistance vs T2DM. Both superoxide driven.

George, still driving at physiology vs pathology. It's interesting how pathology is usually physiology driven beyond any reasonable limits. Then we label the debris as diseases...

BTW, someone commented that fat storage is the default state and we wouldn't live very long if it wasn't. This is a very nice comment, can anyone remember who said it and where?

Peter

Eva said...

Man this blog gets harder every day LOL! Probably I need to go buy some chemistry books and study! Still interesting though..
;-P
-Eva

fortune said...

Hi Eva:

I think Peter's point here is that insulin resistance begins at the mitochondria level, when we have superoxide build-up.

This kind of build-up is most reliably produced by a glucose-oriented metabolism, not a fat-oriented one, due not only to the down regulation of genes, but more importantly due to the basic nature of the mitochondria's own chemistry.

This is an important point to refute those such as Guyenet and other conventional wisdom people who argue that eating fat causes insulin resistance. Peter is showing how the detailed chemistry of the mitochondria disproves this assertion.

And it's interesting because the conventional wisdom people always accuse Taubes, Lustig, etc. of not understanding biochemistry. Yet when you look at the textbooks available on Goole, what you can find seems to support the fat-oriented view.

I wonder why actual biochemists never speak up in these situations. There must be someone who is expert in how mitochondria work, but you never hear from them. They seem to have nothing to say in the nutrition arena - they just study their little cycles and don't seem to feel it has any relevance in larger human issues.

Why does no one just ask a professor of biochemistry to comment and get the whole question over with?

twitchyfirefly said...

@fortune:

"I wonder why actual biochemists never speak up in these situations."

Check out Richard Feinman.
http://rdfeinman.wordpress.com/

George Henderson said...

Bears can hibernate for up to 7 months without eating, if they've stored enough fat. Pretty good illustration of a default state.
Polar bears don't hibernate, though they're descended from grizzly bears that do. Polar bears have a zero-carb diet, unlike grizzlies; maybe they couldn't get fat enough if they tried. However, some baleen whales manage a similar feat on their migrations, without sleeping, while feeding their young, from stored fat. And some birds fatten at an incredible rate before setting out obese on long flights.
And it doesn't seem to cramp their flying style at all.

Peroxisomal beta-oxidation yields little ATP and much heat; carbs can't enter this pathway; so is this the safety valve that makes fat over-supply less fattening than carb?

Kindke said...

Good points fortune, I think the pieces of the puzzle fit together a bit.

Obese people typically burn a higher % of carbs than fat compared to lean people as shown by respiratory quotient analysis ( if someone has a graph of that please link it ) , So if carb oxidation produces more oxidative damage you would expect obese people to have higher IR because they are burning more carbs for energy.

As it happens I found this study today and already posted it on guyenets blog, I think this study atleast supports the idea that insulin resistance can start at the mitochondrial level.

One has the wonder if it is complex I activity damaging those mitochondrial proteins thus making lon protease work overtime! Obviously there are other ways to get IR, but anyway, does someone else have some thoughts on this possible connection?

George Henderson said...

As why macrophages making ROS isn't such a bad thing; this is done by a process called the respiratory burst:
http://www.ncbi.nlm.nih.gov/pubmed/10975851
"These results suggest that monocytes have a specific GSH transporter that is triggered by the release of H2O2 during the respiratory burst and that induces the uptake of GSH into the cell. Such a mechanism has the potential to protect the phagocyte against oxidant damage."

Eva said...

Thanx Fortune! Really I think one big prob is humans are pack oriented creatures by nature. Most feel a strong urge to follow the pack decisions and shy away from directions that will stir up trouble. Thus trying to change the direction of the public can feel a lot like trying to steer the Titanic. The main place of change is with the younger generation which tends to feel a strong urge to break with the older generation. So if you are trying to teach that the old generation has been wrong, the young generation is typically the most ready to listen. Of course, they will make a new pack of stubborn humans with stubborn opinions, but at least some of the opinions will be different ones! We can only hope eventually, progress gets made. Perhaps it feels glacially slow at times, but if you look at how far human tech and knowledge has come in just 100 years, it's really quite amazing when you think about it!

feinman said...

"they just study their little cycles and don't seem to feel it has any relevance in larger human issues" is very different from "Why does no one just ask a professor of biochemistry to comment and get the whole question over with?"

If you ask me, I will tell you what I know. This is my area of professional interest but biochemists don't always jump in because 1) it is not obvious that everybody is comfortable with a detailed biochemical discussion, and 2) we don't always know how to generalize from the details to nutrition -- what we know is much less than what we don't know. The difference between science and medicine is that in science, if you don't know, you don't know. In medicine, with a patient etherized upon a table, if you don't know, you still have to do something. It is why we think highly of doctors because few of us want to shoulder that responsibility. It is different from science however.

Hyperlipid's discussion doesn't make any sense to me. That doesn't mean it is wrong but it would have to be explained with some detail.

Some of my thoughts -- it seems this is an advanced discussion but I will keep it as simple as possible: The mitochondrion is the structure in the cell that carries out oxidative metabolism. You can look at my black box picture of the processes at http://wp.me/s16vK0-648 The gist of it is that there are roughly two fuels, glucose and the small molecule, acetyl-CoA. Acetyl-CoA is the main fuel for the Krebs cycle and it is oxidized to CO2 by oxidative coenzymes (NAD and flavins). The coenzymes get re-oxidized by oxygen in a sequence -- the electron transport chain is a kind of fire-bucket-brigade of redox reactions where oxygen is at the final oxidation You get acetyl-CoA from both glucose and fat but the separation described above doesn't ring true (again, maybe there's something I don't know).

One of the ways in which NAD gets into the line is through a protein called complex I which is a flavin-containing protein. So NAD generated in the Krebs cycle goes in mostly through complex I although 1 step is through complex II. Beta-oxidation of fats uses both a flavoprotein like complex II but NOT complex II and also NAD which goes through complex I. Glucose supplies pyruvate which goes to acetyl-CoA which goes into the Krebs cycle but also supplies NAD through a mechanism using mitochondrial glycerol-3-P dehydrogenase which is another flavin enzyme.

So, the idea of complex I and complex II substrates is not part of normal biochemistry that I ever heard of.

For those readers who are familiar with this, I will add something in a separate comment...Well, you asked.

feinman said...

Again, for those interested or familiar with this:

There are several flavin-proteins in the inner mitochondrial membrane. They all accept electrons from substrates and pass them on to CoQ.

Complex II (succinate dehydrogenase)
Fatty acyl CoA dehydrogenase
glycerol-3-phosphate dehydrogenase

feinman said...

Bottom line: "Glucose drives complex I significantly harder than fat does. Fat drives with a "Complex II-like" bias..." is not part of normal biochemistry but I like Hyperlipid's blog and it is from an article that is clearly an opinion. For people who are truly corrupting biochemistry and putting whacko ideas in people's head, you can't do better than Rob Lustig... for example: alcohol is not metabolized, in any way, like fructose. This kind of nonsense is very damaging because it obscures the need for reducing carbohydrate not just fructose. Lustig is not a scientist although he has played one on Alec Baldwin's show.

Jane said...

Peter, is it your position that glucose oxidation produces more superoxide than fat oxidation does?

Another interesting question is how mitochondrial superoxide is detoxified. It gets converted by MnSOD into hydrogen peroxide, which goes to the nucleus and induces transcription of some very helpful genes. This is supposed to be how extra copies of MnSOD make fruit flies and worms live longer.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246264/

This suggests MnSOD might not be working properly in insulin resistance and diabetes. It was shown recently in a mouse model of hemochromatosis that excess iron, which is implicated as a cause of diabetes in humans, prevents entry of manganese into mitochondria so MnSOD has no Mn and doesn't work. The mice had diabetes which could be prevented by extra manganese.
http://www.ncbi.nlm.nih.gov/pubmed/18317567

Elliot said...

Professor Feinman,

While I'm still trying to wrap my head around the biochemistry involved in all of this and so don't have much to say about it (Thanks, by the way, for the posts on your blogs about basic biochem!) but as long as you're here I'm actually curious if you have any thoughts on the recent study everyone has been talking about that seemed to show a caloric advantage to maintaining weight-loss on a low-carb diet.

George Henderson said...

Perhaps the HCV model can offer some insights; HCV core protein specifically inhibits Complex 1.

In this paper
http://www.sciencedirect.com/science/article/pii/S0168827810008329
the steatosis (that resulted from enhanced delta-9 desaturase activity) was attenuated by EPA and AA (and I imagine that DHA would have been more effective that EPA, but it was not tested).
But interestingly, the authors thought that finding some way of adding pyruvate to the mix was preferable.
See the tables attached to the abstract.

"This lipid metabolism disorder was associated with NADH accumulation due to mitochondrial dysfunction, and was reversed by the addition of pyruvate through NADH utilization."

It's not that beta-oxidation doesn't supply NADH for complex 1 to deal with, but that it supplies less, proportionately to ATP generated.
Would that be a correct interpretation of Lucas Tafur's stats?

Peter said...

Hi Prof Feinman,

Thank you for the input. There are two more post currently cooking and possibly several more after that which may either clarify what I am thinking or show it to be complete garbage!

Jane, of course not. Glucose must, by necessity, produce the least superoxide. At least without hyperglycaemia and when well controlled by physiological levels of insulin. Next two post will explain why. I guess you already know this. No one would argue that elevated ferritin is bad, on some other set of posts I might go at what might increase iron absorption. I think the current state of play is that it is "not well understood". This interests me more than the catastrophe which occurs in the aftermath.

George, there's a lot more to come in this series, we might be able to fit a bit together.

Bed time. Children are on school holidays, my wife is in London for a week and my older son is here to stay. I'm off work for a week. I need a beer. Ok, a glass of wine would do.

Peter

Edward J. Edmonds said...

I look at mitochondria as a sort of catalytic converter of sorts burning extra oxygen instead of having it hanging around causing potential damage; turning the oxygen into CO2 and water which we get rid of. I think some organisms can make ATP via the peroxisomes, but this doesn't happen as far as we know in mammal peroxisomes. The environment is glucose rich, yet we have the mitochondria which are damn fine fat burners. It would seem wasteful to have mitochondria unless there was a distinct advantage to burning fat...

George Henderson said...

Just to muddy the waters;
mitochondria also play a role in innate antiviral immunity
http://www.pnas.org/content/102/49/17539.full.pdf

Why is the MAV on the mito?
Does it need ROS, or some Citric Acid Cycle intermediate?
Or is it evolved from an archaean defense?
Only time will tell. But it seems Sex, Power and Suicide is no longer the full story...

George Henderson said...

I guess if the peroxisomes can produce heat, then there's less need to waste ATP generating it. So peroxisomal fat oxidation is actually energy-efficient.
Metabolic heat is important to us.
Temperature control is the most amazing act of homeostatis. We walk a very narrow tightrope every day of our lives, yet it can be swung upwards into fever when required - but only so far.

Unknown said...

Hi Dr. Feinman:

"If you ask me, I will tell you what I know."

Ok, then, please Dr. Feinman - does eating fat cause such oxidative problems to the mitochondria that we become insulin resistant, as Guyenet claims? Is eating fat harmful? Will it lead irrevocably to insulin resistance unless we count every single calorie to insure we never have excess?

Or is it glucose that clogs up the mitochondria to cause insulin resistance? If neither, what then is the true cause of insulin resistance? Does it start in the cells or elsewhere?

Is insulin a fat storage hormone or a fat-loss/satiety hormone? Surely there are known answers to these questions - they are fundamental to biochemistry.

Why will no one just tell us the answer? When I google biochemistry textbooks, they all agree that insulin is the fat-storage hormone. But I can't get an actual biochemist to just flat out say this.

Why not? Please help us all out here if you can.

Thanks!

Jane said...

Peter, have you seen this paper about saturated fat increasing iron absorption and decreasing manganese absorption?
http://www.ncbi.nlm.nih.gov/pubmed/11697763

I suspect this is how saturated fat causes insulin resistance.

ItsTheWooo said...

@feinman I too am growing tired of Lustig's antics lately, I used to have more respect for him but lately he has become more sensational to the point of meaninglessness. I suppose his comparison of alcohol to fructose relates to the fact that both in excess can be hepatotoxins. Alcohol ingestion will raise ketones and inhibit glucose production in the liver; fructose doesn't do this so they even aren't alike in post ingestion outcome.

Saying alcohol and fructose are similar because liver abnormalities can result from both is like saying all drugs are the same because at a high enough dose the liver will become damaged.

@unknown pretty sure Guyenet thinks it is body fat that is the problem not dietary fat. Being fat in your fat tissue causes IR and all diseases of obesity, end mystery - Dr Guyenet.
Also, Peter's hypothesis is that fat metabolism generates free radicals that promote transient insulin resistance, and this is actually a good thing which helps the body adapt to a fat metabolism on a ketogenic or very low carb intake.

Insulin is both a storage hormone and a satiety hormone in normal physiology, it's not an either or proposition. In obesity, however, it is causing pathological storage of nutrients which is why insulin suppression via diet or drugs helps obesity. A pathological lacking of insulin leads to hyperphagia and rapid weight loss as in type 1 diabetes.

The party line is that insulin is facilitative and the cause of obesity is a defective personality that can't control food, a sort of mental illness of excessive food consumption, so no you won't hear anyone say that insulin is very important and pathological in obesity, for the same reason you won't hear industrialists and capitalists promoting unionization of workers. It's very much a social and moral and financial issue behind this cognitive dissonance.

Peter said...

Jane,

That's me f*cked then!

Its, the word is physiological. Next post is getting there. The one after is also cooking.

Peter

George Henderson said...

@ Unknown
"When I google biochemistry textbooks, they all agree that insulin is the fat-storage hormone."

I keep waiting for CIH skeptics to announce that it's time to rewrite the textbooks.

NAFLD alone has multiple causes
"Fat can accumulate in the liver in five different (though often simultaneous) ways."
http://principleintopractice.com/2012/07/23/liver-and-lipids/

It is naive to expect a single causation that applies to every case of diabesity, but fortunately it is apparent that much the same things aggravate or relieve it in most cases.
Insulin is not the only hormone regulating fat storage. As Guyenet says, adrenaline is one of many hormones that also plays a(n opposing) role.
But you inject adrenaline if you eat a peanut you are allergic to.
If you can't convert sugar to fat or anything else, you inject insulin.
Nothing else.
Q.E.D.

Unknown said...

Wouldn't SOD produced hydrogen peroxide also raise O2 levels? Is this O2 concentration rise available for Complex IV to deliver H+ into the intermembrane space? Would that also favor the gradient for ATP synthase?

George Henderson said...

Mitochondrial complex I regulates SIRT1-dependent response to fructose

Activation of complex I of the mitochondrial electron transport chain increases NAD+/NADH ratio through increased NAD+ production as well as increasing ATP production from ADP (Voet & Voet 1994). Fructose induced gluconeogenesis through a SIRT1-mediated mechanism in parallel with increasing NAD+/NADH ratio (Figs 1 and 2) and ATP levels at 6 h (Supplementary Figure 3A, see section on supplementary data given at the end of this article). Therefore, we tested whether changes in SIRT1 resulted from increased complex I activity by using rotenone, a potent complex I inhibitor. Rotenone inhibited fructose-induced increases in NAD+/NADH ratio (Fig. 5A), ATP levels (Fig. 5B), SIRT1 protein (Fig. 5C), and SIRT1 activity (Fig. 5D). Rotenone also inhibited fructose-induced increases in hepatocyte glucose production (Fig. 5E), PEPCK activity (Fig. 5F), and mRNA levels of Pck1 (Fig. 5G) and Pgc1α (Fig. 5H). These results suggest that the changes in NAD+/NADH ratio and SIRT1 in response to fructose occur through increased activity of complex I of the mitochondrial electron transport chain.

Abstract (link to free fulltext)

This nicely ties in with the idea that fructose toxicity is carbohydrate-dependent.

http://rdfeinman.wordpress.com/2012/07/27/flawed-studies-ii-occams-razor-and-how-to-reduce-fructose-consumption/

feinman said...

I am behind in answering some questions. I will get to them as quickly as possible. I usually get follow up notices.

feinman said...

@Elliot I have not read Ludwig's paper in detail yet but metabolic advantage is supported by other data and, in particular, by a thermodynamic analysis showing it is possible and that it unambiguously occurs in animals (although in the opposite direction; mice get fatter (calorie-for-calorie on high fat diets even if there is no carbohydrate (http://bit.ly/MfzgYY) and by the fact, that in humans, it always seems to favor low-carb.

feinman said...

"Is insulin a fat storage hormone or a fat-loss/satiety hormone? Surely there are known answers to these questions - they are fundamental to biochemistry.
Why will no one just tell us the answer? When I google biochemistry textbooks, they all agree that insulin is the fat-storage hormone. But I can't get an actual biochemist to just flat out say this."

I'm an actual biochemist and insulin is one of the fat-storage hormones and generally one of the satiety stimuli but if you look through the biochemistry textbooks, you see how complicated it is. If you wanted a grand principle of biochemistry it would be that there are hardly any metabolites that don't have feedback, that, is a response that goes in the opposite direction. Most important, insulin is at the top of a cascade of many responses. The bottom line is that most biochemists say flat-out that insulin is an anabolic hormone -- generally favors fat-storage, glycogen-storage and protein synthesis -- but you can't make generalizations that apply to every situation -- you always have insulin but you need to know what else is going on to make any prediction. I describe metabolism to students as analogous to American football. We tend to follow the ball-carrier but the key to the play may be down-field blocking or, more likely, the whole thing. That's why we are not comfortable with flat-out. With all those disclaimers, it is most impressive, how far we can get with insulin. That is the point of my Occam's Razor post, http://wp.me/16vK0 where, if you consider metabolism as Y=A+B+C+D+..., you may be able to understand things with just A and you shouldn't drag in B, C, D, E, etc. unless you have to but sometimes you have to.

So, for your questions:

"Ok, then, please Dr. Feinman - does eating fat cause such oxidative problems to the mitochondria that we become insulin resistant, as Guyenet claims? Is eating fat harmful? Will it lead irrevocably to insulin resistance unless we count every single calorie to insure we never have excess?"

You absolutely must know what else is going on. As some other comment said. Insulin resistance responds to fatty acids in the blood, not the diet. But if you are exercising, the fatty acids are your fuel and will reduce insulin resistance. From first principles, (the A term) eating fat may be harmful in you accompany it with carbohydrate and are inactive... but once you are talking individual reactions and system response (B, C and D), it may not be and we, flat-out don't know why not.

"Or is it glucose that clogs up the mitochondria to cause insulin resistance? If neither, what then is the true cause of insulin resistance? Does it start in the cells or elsewhere?"

The mitochondria are not plumbing and we don't know what causes insulin resistance. We have lots of ideas about what contributes -- that's why the textbooks are so thick and expensive -- but we don't have the answer. That's why I still have a job.