BIOCHEMISTRY DISCUSSION 7
Leahh
20TheElectron-TransportChainb.pptxBiochemistry: A Short Course Fourth Edition CHAPTER 20 The Electron-Transport Chain
Tymoczko • Berg • Gatto • Stryer
© 2019 W. H. Freeman and Company.
Created by Brett Barbaro
Alright - so we talked about the harvesting of high energy electrons during the citric acid cycle (and other parts of glycolysis) in the form of NADH and FADH2. And now we’re going to show you where those electrons go, and how they are turned into energy that the body can use.
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Chapter 20: Outline
20.1 Oxidative Phosphorylation in Eukaryotes Takes Place in Mitochondria
20.2 Oxidative Phosphorylation Depends on Electron Transfer
20.3 The Respiratory Chain Consists of Proton Pumps and a Physical Link to the Citric Acid Cycle
Created by Brett Barbaro
This is the process of oxidative phosphorylation. And it takes place in the mitochondria, which is the same place as the citric acid cycle takes place. It depends on the transfer of electrons from those original substrates, the acetyl groups from the glucose, and it sends those electrons through a series of proton pumps. Those proton pumps establish a gradient which is then used to power formation of ATP.
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Oxidative Phosphorylation
Oxidative phosphorylation captures the energy of high-energy electrons to synthesize ATP.
The flow of electrons from NADH and FADH2 to O2 occurs in the electron-transport chain or respiratory chain.
This exergonic set of oxidation–reduction reactions generates a proton gradient.
The proton gradient is used to power the synthesis of ATP.
Collectively, the citric acid cycle and oxidative phosphorylation are called cellular respiration, or simply respiration.
DID YOU KNOW?
Respiration is an ATP-generating process in which an inorganic compound (such as molecular oxygen) serves as the ultimate electron acceptor. The electron donor can be either an organic or inorganic compound.
Created by Brett Barbaro
Another word that is used to describe this process is respiration, which is a little confusing to me because respiration, to me, means breathing. But you know, you need to be able to breathe to get the oxygen in there to accept the electrons and therefore, I guess, it’s kind of fair to use that term to describe this process as well. The NADH and FADH2 release their electrons into what’s called the electron transport chain, which is just a series of proteins that take these electrons and transform them into energy. This energy is stored in the form of a proton gradient. And then this proton gradient can be used to power the synthesis of ATP.
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Diagram of an Overview of Oxidative Phosphorylation
Created by Brett Barbaro
Figure 20.1 An overview of oxidative phosphorylation. Oxidation and ATP synthesis are coupled by transmembrane proton fluxes. The respiratory chain (yellow structure) transfers electrons from NADH and FADH2 to oxygen and simultaneously generates a proton gradient. ATP synthase (red structure) converts the energy of the proton gradient into ATP.
Here’s a diagram showing how that works. You start off with the tricarboxylic acid cycle in the matrix of the mitochondria (that’s what TCA means). Those electrons then go to the yellow protein which pumps the hydrogens out of the matrix and into the intermembrane space of the mitochondria. So you’re creating positive charge on the outside of the matrix.
And then the positive charges come back into the matrix via this red molecule, which is an ATP synthase. Now if you look at the charges there in the center on the top across the membrane, it’s got 4 positive charges, and 4 negative charges inside the matrix - every time you pump a positive charge out of the matrix, of course, you’re leaving a corresponding negative charge inside -that is creating a voltage across the membrane, a voltage just like you would find in a battery. And therefore the inner mitochondrial membrane is sort of like a battery; the whole mitochondrion is kind of like a battery. And you know, these are individual atoms, small charges - but they’re also in a very small space; and it turns out, actually, that the relative voltage created - it’s a very small voltage, in actual cells - but per unit area, for the concentration of this voltage in this small space, is actually similar to that of lightning. So we’re talking about having, you know, a very significant amount of charge being distributed here. And that’s what is going to power the formation of the ATP.
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Mitochondria Are Bounded by a Double Membrane
The outer mitochondrial membrane is permeable to most small ions and molecules because of the channel protein called mitochondrial porin.
The inner membrane, which is folded into ridges called cristae, is impermeable to most molecules.
The inner membrane is the site of electron transport and ATP synthesis.
The citric acid cycle and fatty acid oxidation occur in the matrix.
Created by Brett Barbaro
Let’s just talk briefly about the mitochondria. Remember, this has two membranes: there’s an outer membrane and an inner membrane. The outer membrane can let most small ions and molecules come through it because of channel proteins such as the mitochondrial porin, which just makes a pore in the membrane so stuff can get in and out.
The inner membrane, however, is impermeable to most molecules, normally impermeable to ions, and that’s where the electron transport and ATP synthesis takes place. And, you see, on a mitochondrion the folded internal membrane creates a great deal of more surface area on the inside of the mitochondria so that you can fit more of these proteins, and members of the electron transport chain, into that. Hydrogen ions are pumped out of the matrix during the electron transport chain and those then stick around because the matrix is negatively charged; and positives and negatives attract each other. So they don’t really leak out in the cell so much (otherwise you would make the cell more acidic). Now once they get pumped out, they really want to get back in, and that’s where you get energy from for the formation of ATP.
Just a quick note about the cristae inside of the mitochondria - the outer membrane of the mitochondrion is somewhat static, and the cristae, I believe, are just formed because the inner membrane grows a lot and there’s no space for it. So it starts folding in on itself, and so it turns out that the outer membrane is just basically holding the inner membrane in place.
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Electron Micrograph of a Mitochondrion
Created by Brett Barbaro
FIGURE 20.2 Electron micrograph (A) and diagram (B) of a mitochondrion.
So you can see here in this electron micrograph of a mitochondrion, the folded internal membranes of cristae, and you can see a little bit of the double bi-membrane of the outside membrane as well.
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Diagram of a Mitochondrion
Created by Brett Barbaro
FIGURE 20.2 Electron micrograph (A) and diagram (B) of a mitochondrion.
The space between the outer membrane and inner membrane is called the intermembrane space.
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Biological Insight: Mitochondria Are the Result of an Endosymbiotic Event
Mitochondria have their own genome. Sequence data suggest that all mitochondria are descendants of an ancestor of Rickettsia prowazekii, which was engulfed by another cell.
“No genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria.” http://www.nature.com/nature/journal/v396/n6707/full/396133a0.html
Here is an excellent Radiolab show about the birth of mitochondria: https://radiolab.org/podcast/cellmates/
Created by Brett Barbaro
Ok, now I’m going to tell you a story. This is a story about mitochondria.
A long time ago there were single-celled organisms, and that’s all there were, and they were floating around in the ocean. And for millions of years this is what happened. They just floated around - quite small cells - and they developed and grew and changed and did all kinds of crazy stuff. But there was a limit to how large they could grow because they only are able to take in a certain amount of food and process it, so they stayed fairly small.
Then, one day, some bizarre sequence of events occurred, very rare and one of these small single-celled organisms engulfed another single-celled organism. And so now you have a single-celled organism living inside another single-celled organism. Now, most of the time, this does not work out very well. But it just so happened, in this particular case, the single celled organism that was inside was able to get all of the nutrients that it needed from the other organism. And as a result, it produced ATP. And it produced more than enough ATP so that it started to give some ATP back to the larger organism, to the enclosing organism. So this kind of worked out for both of them.
The smaller organism no longer needed to look for food because it was just being supplied to it by the large organism. And it got a certain amount of protection, also, from the outside world. And the larger organism got the advantage of this smaller organism producing extra ATP because the smaller organism was able to use oxygen; it was an aerobic organism, whereas the larger one was anaerobic and could only get its ATP from glycolysis. And of course you get a lot more energy from aerobic processes like the citric acid cycle. I think it would probably be fair to say that the smaller organism used the citric acid cycle and the larger organism did not.
So perhaps the smaller organism previously depended on the excretions of the larger organism as its food source. As the larger organism was able to break down glucose into ethanol and lactic acid, those became the food sources for the smaller organism. Well, now they were integrated together, and the smaller organism was able to focus all of its energy on just taking those molecules and turning them into ATP. And the larger organism was happy because it got a whole lot more ATP out of the deal.
So over time the smaller organism was able to replicate, and there could be hundreds and thousands of these smaller organisms inside this larger organism. And the genomes of these smaller organisms started to change as well, because they didn’t need to have a lot of the genes that they had before. A lot of the genes they had before were necessary for survival out in the wild, but they weren’t in the wild anymore. They were inside this other cell where it was a totally different environment. So those genes faded by the wayside.
And the smaller organism was able to focus entirely on just making ATP. And as long as it kept making ATP that larger organism had more than enough energy to do everything that it needed to do. So what did it do with the rest of this energy? Well, the rest of this energy started doing other stuff. Just random stuff, growing new proteins and developing larger genomes, like new genes, replication of the DNA inside of these larger organisms, and mutations, and incorporations - and it led to just an explosion of new genes and new proteins and new processes that the larger organism can take advantage of to become more successful in the environment.
And it did. It was so successful, in fact, that it was able to multiply all over the place and then create so many of these things that they started to form multicellular organisms. And that is what eventually became plants and animals. Plants and animals all come from this symbiotic relationship between these two organisms that provide enough energy so that the larger organism can grow and experiment and try stuff. And that smaller organism’s able to focus entirely on ATP production.
Well, that smaller organism is what we call, today, mitochondria. Those are the smaller organisms that are living inside of the larger organism, which is our cells. And the mitochondria have their own genome. They’ve got their own DNA inside the mitochondria that’s separate from our human genome. And these mitochondria grow and divide and die inside of our cells just like little organisms would.
Now I started this discussion by saying I was going to tell you a story, and scientists would now ask “Is this story actually true?” Well, nobody knows for sure, but this is our best guess, my best guess, at least, of what actually happened. And there’s a lot of evidence to support it. There’s a great episode of the show Radiolab that covers this story, and I’ve included a link for you there on the page. It was actually showed to me by one of the students of this class.
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Section 20.2 Oxidative Phosphorylation Depends on Electron Transfer
Learning objective 1: Describe the key components of the electron-transport chain and how they are arranged.
The electron-transport chain is a series of coupled redox reactions that transfer electrons from NADH and FADH2 to oxygen.
Created by Brett Barbaro
All right, so, the electron transport chain is a bunch of redox reactions, which means that electrons are passed from one place to another, and in this case they are passed from NADH and FADH2 to oxygen.
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Electron Flow Through the Electron-Transport Chain Creates a Proton Gradient
Energy is released when high-energy electrons are transferred to oxygen.
The energy is used to establish a proton gradient.
Created by Brett Barbaro
So in this process of transferring high energy electrons to oxygen, a good deal of energy is released. You can see at the top reaction there, half of an oxygen (just 1 oxygen atom) would take 2 electrons from NADH and it would also take a hydrogen ion and make water and that would release, you know, flying bolts of energy which gets translated with all of these equations into 220.1 kJ/mol. That’s the final number.
And if you remember, the energy in a single ATP is about 30 kJ/mol. So the transfer of these two electrons releases enough energy to create several ATP molecules. And the way they do this is to establish a proton gradient.
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The Electron-Transport Chain Is a Series of Coupled Oxidation–Reduction Reactions (1/2)
The electron-transport chain is composed of four large protein complexes.
The electrons donated by NADH and FADH2 are passed to electron carriers in the protein complexes.
The carriers include flavin mononucleotide (FMN), iron associated with sulfur in proteins (iron–sulfur proteins), iron incorporated into hemes that are embedded in proteins called cytochromes, and a mobile electron carrier called coenzyme Q (Q).
Created by Brett Barbaro
The electron transport chain is composed of four large protein complexes. The electrons are donated from NADH and FADH2 to electron carriers in these complexes, and then passed along to pump hydrogens out into the mitochondrial intermembrane space. Now proteins themselves, the amino acids do not have a great deal of room for absorbing electrons, so they use prosthetic groups to actually do the electron transport. And those prosthetic groups include the flavin mononucleotide, there’s iron that’s associated with sulfur in these iron-sulfur proteins, much like what we saw with isocitrate synthase in the last chapter, and there’s iron that's incorporated into hemes and proteins that use these are called cytochromes, and then there is also a mobile electron carrier called coenzyme Q.
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Diagram of the Oxidation States of Flavin Mononucleotide
Created by Brett Barbaro
Figure 20.5 The oxidation states of flavin mononucleotide. The electron carrier component is the same in both flavin mononucleotide and flavin dinucleotide (FAD).
Flavin mononucleotide is very similar to FAD in its structure and it can be reduced by having two electrons and their associated hydrogens attached to it.
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Structure of Iron–Sulfur Clusters
Created by Brett Barbaro
Figure 20.7 Iron–sulfur clusters. (A) A single iron ion bound by four cysteine residues. (B) 2Fe-2S cluster with iron ions bridged by sulfide ions. (C) 4Fe-4S cluster. Each of these clusters can undergo oxidation–reduction reactions.
Iron sulfur clusters come in several flavors - you can have one iron with four sulfurs, two irons with six sulfurs, four irons with eight sulfurs. I’m actually not sure why iron and sulfur are such good partners. Maybe they just fit well together. But remember these irons atoms are ions, they are charged and so the charge is distributed over this whole complex.
Now where does the sulfur come from? And how does this get incorporated into proteins? Well, cysteine -remember cysteine? It is the amino acid that’s responsible for the disulfide bridges in the tertiary structure of proteins. And so they can form disulfide bridges, but they can also interact with iron and hold these sulfur iron complexes in place. And it turns out, because of their positive charge, because it’s an ion, they are very good for transporting electrons. Iron is able to very easily change from a +2 state to a +3 state. And so it’s that feature that allows the electrons to come and go so easily.
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Structure of a Heme Component of Cytochrome c Oxidase
Created by Brett Barbaro
Figure 20.8 A heme component of cytochrome c oxidase.
And here is a heme. Which also uses iron as its electron transport. You’re familiar with heme from hemoglobin. That’s the same molecule that is important for transporting oxygen inside the blood. Interestingly, this is also used to transport electrons in the cytochrome elements of the electron transport chain. And let’s think about that for a second - “cyto” means cell, “chrome” means color. So you would think that these cytochrome elements of the electron transport chain were responsible for the color. Well, they are. Turns out that this iron atom actually gives it sort of a red color. And that’s the same color that you see in your blood. That is created by the heme groups in your blood. So you might want to think of the cytochrome (cytochrome c for example) as kind of the hemoglobin of the mitochondria.
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Diagram of the Components of the Electron-Transport Chain
Nice animation:
https://www.youtube.com/watch?v=LQmTKxI4Wn4
Attached to Succinate dehydrogenase
(prosthetic group)
(aka succinate dehydrogenase)
Created by Brett Barbaro
Figure 20.6 Components of the electron-transport chain. Electrons flow down an energy gradient from NADH to O2. The flow is catalyzed by four protein complexes. Iron is a component of all of the complexes as well as cytochrome c. [After D. Sadava et al., Life, 8th ed. (Sinauer, 2008), p. 150.]
So here is an overall diagram of the electron transport chain. And the four main components, you can see, are numbered 1, 2, 3, and 4, using roman numerals. And then, there are a few other elements like the ubiquinone, cytochrome c, and oxygen which interact with these four. NADH enters the electron transport chain at the first of these enzymes, which is the NADH-Q oxidoreductase complex. Q is also known as ubiquinone and is represented in this diagram by that second small purple {blob – sorry, it’s not a protein!}.
Now there’s a loss of energy that is associated with the transfer of those electrons, and that energy that is lost is actually used to transport protons (but we’ll get into that a little bit later).
FADH2 enters the chain at succinate dehydrogenase {also known as succinate-Q reductase}, which you might recall is one of the enzymes in the citric acid cycle. It’s the enzyme that is membrane bound in the citric acid cycle. Succinate dehydrogenase removes the hydrogens from succinate, and along with that the high energy electrons, and then passes those electrons on to ubiquinone.
From ubiquinone, or Q, all of these electrons go through Q-cytochrome c oxidoreductase, which is the third in the series of enzymes in the electron transport chain. This complex pumps more protons out and passes the remaining energy on in electrons to cytochrome c, which then passes the electrons to cytochrome c oxidase, which pumps out the final protons into the intermembrane space and passes the electrons on to oxygen, creating water.
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The Electron-Transport Chain Is a Series of Coupled Oxidation–Reduction Reactions (2/2)
Coenzyme Q binds protons (QH2) as well as electrons and can exist in several oxidation states.
Oxidized and reduced Q are present in the inner mitochondrial membrane in what is called the Q pool.
Created by Brett Barbaro
All of these elements are embedded in the inner mitochondrial membrane. We’re going to talk a little about coenzyme Q which is one of the first shuttles that passes electrons around. And remember when you’re passing electrons there’s two charges, so, you know, those negative charges are balanced by positive charge on the hydrogens. But the hydrogens are just protons they don't really have energy to contribute to these reactions. The energy is all stored in the electrons. So really, you can consider it the carbon-hydrogen bond that is holding these high energy electrons - I guess that would be considered a high energy bond. Which makes sense - of course you remember fats, they’re a bunch of carbon-hydrogen bonds and that’s where you get your energy from. So, yeah I’m still trying to figure this stuff out too. :p
Now, coenzyme Q is basically the shuttle which transports these high energy electrons around in the membrane, the inner mitochondrial membrane, and also the hydrogens. And that’s the same coenzyme Q that you see in these dietary supplements that you can buy at the health food store. I guess if you want to make sure that you’re able to pass your high energy electrons around well enough - I don’t know if that really gets into your system or not, but I think that’s why people take it. And there’s a bunch of this coenzyme Q in the inner mitochondrial membrane, swimming around, and some of it has the electrons and hydrogens on it, some of it doesn’t. The ones with the electrons and hydrogens are the reduced forms and the oxidized forms are the ones that don’t. So all of these together we call the Q pool.
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Diagram of Oxidation States of Quinones
Semiquinones are radicals – aka Reactive Oxygen Species (ROS)
http://examine.com/supplements/coenzyme-q10/
Created by Brett Barbaro
Figure 20.9 Oxidation states of quinones. The reduction of ubiquinone (Q) to ubiquinol (QH2) proceeds through a semiquinone intermediate (QH•).
Coenzyme Q, as you can see in the upper left, is actually a hydrophilic head group associated with a very long hydrophobic tail which keeps it embedded in the membrane. In the remaining parts of this diagram, we can see on the far left the oxidized form of coenzyme Q, which is also called ubiquinone. And that does not have any of the hydrogens or electrons on it. And you can add the high energy electron and hydrogen and end up with the semiquinone intermediate, which is a radical. You can see there on the bottom of that diagram there is an O with a dot by it. That dot represents the radical, which means that it’s a single electron and that electron is able to balance the nuclear charge of the oxygen so that the whole atom there is neutral. But electrons like to be paired with each other (you might remember from your chemistry). So a single electron is actually very unstable and can react with things very easily. That’s why these radicals are so dangerous, is because they can interact with other molecules and break them apart when you don’t want them to be broken apart.
To make matters even worse you can lose the hydrogen, and follow the arrow up, to the semiquinone radical ion and that’s a fairly dangerous situation. But you can also gain another electron and happily pair that free electron with another electron and hydrogen to make the reduced form of coenzyme Q which is ubiquinol. So because it goes through a free radical intermediate, this is one of the more dangerous parts of the electron transport chain. And also the harvesting of energy from glucose.
You might’ve heard of reactive oxygen species. Those are the free radicals and this is an example of one of them. And this is why you take your antioxidants. They are chemicals that are supposed to help clean this up a little bit so that it won’t damage the cell.
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Section 20.3 The Respiratory Chain Consists of Proton Pumps and a Physical Link to the Citric Acid Cycle
Learning objective 2: Explain the benefits of having the electron-transport chain located in a membrane.
Electrons flow from NADH to O2 through three large protein complexes embedded in the inner mitochondria membrane.
These complexes pump protons out of the mitochondria, generating a proton gradient.
The complexes are:
NADH-Q oxidoreductase (Complex I)
Q-cytochrome c oxidoreductase (Complex III)
Cytochrome c oxidase (Complex IV)
An additional complex, succinate Q-reductase (Complex II), delivers electrons from FADH2 to Complex III.
Succinate-Q reductase is not a proton pump.
Created by Brett Barbaro
So electrons flow from NADH down to molecular oxygen through the three major protein complexes of NADH-Q oxidoreductase, Q-cytochrome c oxidoreductase, and cytochrome c oxidase. You can tell by the names of these pretty much what they do. NADH-Q takes electrons from NADH and puts them on Q. Q-cytochrome c takes electrons from Q and puts them on cytochrome c. And then cytochrome c oxidase finally oxidizes the cytochrome c. But we can call these by their simpler names: we can call them Complex I, Complex III, and Complex IV.
Now where’s Complex II? Well, that’s the one that interacts with FADH2. That’s the one that is embedded in the inner mitochondrial membrane.
Now the complexes 1, 3, and 4 are proton pumps. So when they pass electrons through them, they will pump protons out of the matrix and into the intermembrane space. Complex II, however, does not pump any protons. And it ends up delivering the electrons to Q without pumping any protons. So that’s why FADH2 does not generate as much ATP as NADH. And you might want to remember at this point that Complex II is the membrane bound element of the citric acid cycle.
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The High-Potential Electrons of NADH Enter the Respiratory Chain at NADH-Q Oxidoreductase
The electrons from NADH are passed along to Q to form QH2 by Complex I. QH2 leaves the enzyme for the Q pool in the hydrophobic interior of the inner mitochondrial membrane.
Four protons are simultaneously pumped out of the mitochondrial matrix by Complex I.
intermembrane space
Created by Brett Barbaro
So let’s go through this whole process step by step. The first step we’ll talk about is the electrons coming from NADH get passed along to Q to make QH2 by Complex I. QH2 has a little bit less energy than NADH and that energy is used to pump four protons simultaneously out of the matrix and into the intermembrane space of the mitochondria.
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Diagram of Coupled Electron-Proton Transfer Reactions Through NADH-Q Oxidoreductase
Created by Brett Barbaro
Figure 20.11 Coupled electron–proton transfer reactions through NADH-Q oxidoreductase. Electrons flow in Complex I from NADH through FMN and a series of iron–sulfur clusters to ubiquinone (Q), forming Q2−. The charges on Q2− are electrostatically transmitted to hydrophilic amino acid residues (shown as red and blue balls) that power the movement of HL and H components. This movement changes the conformation of the transmembrane helices and results in the transport of four protons out of the mitochondrial matrix. [After R. Baradaran et al., Nature 494:443–448, 2013.]
This diagram shows in two steps how this occurs. It begins with the removal of high energy electrons from NADH at the top, and those electrons get passed down through a series of iron-sulfur clusters to the Q, which is there in orange. The first step of this opens up passages allowing hydrogens to be taken into the central parts of these associated complexes, which have negative interiors. During this part, a single proton is also pumped from the matrix into the intermembrane space.
Now if you take a look at the iron-sulfur clusters and the FMN, it kind of looks like a wire going down. Well, I think that’s exactly what it is, as a matter of fact. You know how electrons travel along a copper wire, well in this case the electrons are traveling along an iron wire that is mediated by the iron-sulfur clusters. And that’s kind of something you’ll see in a lot of these parts of the electron transport chain. If they need to get an electron from one part of the protein to another, the best way to do that is to send it through this stream of iron. And actually there is some copper in it as well.
So the entry of these electrons and their passing along induces a conformational change in these three associated proteins, and ends up releasing hydrogen ions into the intermembrane space.
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http://www.rcsb.org/pdb/101/motm.do?momID=144
A bacterial complex I is shown here, from PDB entries 3m9s and 3rko, which is composed of 14 protein chains.
Human complex I is one of the largest membrane-bound protein complexes that has been discovered, composed of 46 chains.
FMN
Created by Brett Barbaro
Here’s a more realistic representation of the Complex I. This is actually Complex I from a bacteria, which is much more simple than the one that we have in our own bodies, but you can see the FMN prosthetic group up at the top in green, and then a series of iron sulfur clusters which pass the electrons down to the remainder of the protein. You can also see on the left the green protein has an arm that extends across the purple and blue proteins, which creates a physical link between the various members of this complex.
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Ubiquinol Is the Entry Point for Electrons from FADH2 of Flavoproteins
Succinate dehydrogenase of the citric acid cycle is a part of the succinate-Q reductase complex (Complex II).
The FADH2 generated in the citric acid cycle reduces Q to QH2, which then enters the Q pool.
NUTRITION FACT
Coenzyme Q is frequently marketed as a dietary supplement, often called CoQ 10. Its proponents assert that it boosts energy, enhances the immune system, and acts as an antioxidant. Clearly, people who lack the ability to synthesize CoQ and consequently suffer from neuromuscular disorders due to defective mitochondria benefit from CoQ supplementation. Moreover, some evidence is beginning to accumulate showing that CoQ supplementation may benefit people undergoing severe physiological stress—for instance, from heart disease or cancer. However, no studies have established that CoQ supplementation will help a well-nourished person in any activity. In fact, because of its antioxidant effects, CoQ supplementation may actually negate the beneficial effects of exercise.
Created by Brett Barbaro
Succinate dehydrogenase, which is a component of the citric acid cycle, is part of the succinate-Q reductase complex which transports high energy electrons from FADH2 to Q to make QH2. But remember this doesn’t pump any protons, so that’s why the FADH2 does not generate as much energy as NADH does.
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Electrons Flow from Ubiquinol to Cytochrome c Through Q-Cytochrome c Oxidoreductase
Electrons from QH2 are used to reduce two molecules of cytochrome c in a reaction catalyzed by the Q-cytochrome c oxidoreductase or Complex III.
Complex III is also a proton pump.
https://en.wikipedia.org/wiki/Cytochrome_c
Created by Brett Barbaro
Electrons then flow from ubiquinol (or QH2) to cytochrome c, which is another carrier protein. The cytochrome c protein can only carry one electron. So it takes two of them to gather both of the electrons from QH2. This puts the electrons in a lower energy state than they were. And where did that energy go? It’s been stored as a pumping of protons. So the energy from the electrons is now in the form of a greater proton gradient.
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The Q Cycle Funnels Electrons from a Two-Electron Carrier to a One-Electron Carrier and Pumps Protons
QH2 carries two electrons, whereas cytochrome c carries only one electron.
The mechanism for coupling electron transfer from QH2 to cytochrome c is called the Q cycle.
In one cycle (which processes four electrons), four protons are pumped out of the mitochondria and two more are removed from the matrix.
Created by Brett Barbaro
So the electrons are passed from QH2 to cytochrome c one at a time. And in this case they’re not passing the hydrogens along with it, actually. The hydrogens are actually being released from the QH2 into the intermembrane space. And that’s the mechanism by which this particular complex pumps the protons - we haven’t gotten into the actual mechanism by which the other complexes pump protons, but this one’s pretty straightforward. So it’s got to transfer these electrons one at a time, and there’s an interesting mechanism for doing that, which they call the Q cycle. A full cycle involves the oxidation of two QH2 molecules and the pumping of 4 protons, so that’s 1 proton per electron.
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http://www.rcsb.org/pdb/101/motm.do?momID=137
https://en.wikipedia.org/wiki/Cytochrome_c
http://examine.com/supplements/coenzyme-q10/
Created by Brett Barbaro
So electrons are passed from coenzyme Q (on the left top) through Complex III and onto cytochrome c. And in this illustration you can see some of the prosthetic groups, the hemes, and the iron-sulfur groups that are involved during the transport of these electrons. The electrons flow through the iron atoms and remember the hemes are the ones that give it the color.
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Diagram of the Q Cycle
Created by Brett Barbaro
Figure 20.12 The Q cycle. In the first half of the cycle, two electrons of a bound QH2 are transferred, one to cytochrome c and the other to a bound Q in a second binding site to form the semiquinone radical anion Q•–. The newly formed Q dissociates and enters the Q pool. In the second half of the cycle, a second QH2 also gives up its electrons, one to a second molecule of cytochrome c and the other to reduce Q•– to QH2. This second electron transfer results in the uptake of two protons from the matrix. The path of electron transfer is shown in red.
So the first half of the Q cycle starts with your Complex III associated with 1 QH2 and 1 Q. And the two hydrogens are released from the QH2 into the intermembrane space and that’s your pumping of the hydrogens, basically there. The electrons that were associated with those hydrogens, one goes up into the cytochrome c, which is in the intermembrane space, and reduces the cytochrome c. The other electron gets passed along into the other Q forming that unstable intermediate with the free radical on it.
But not to worry! That free radical is not going to be released into the pool so that it can be doing damage to everything. It stays stuck to the Complex III. And then the Q that was there gets released into the pool and joins everyone else. Now another QH2 molecule comes in and that also gets stripped of its two protons, and also its two electrons. And once again, one of the electrons goes up to cytochrome c (this is a different cytochrome c - the first one has dissipated away and a new one has taken its place) and the other electron goes down and joins the free radical there reducing the Q to QH2 and that absorbs two hydrogen ions from the matrix and then all of those Qs and QH2s are released back into the Q pool
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Cytochrome c Oxidase Catalyzes the Reduction of Molecular Oxygen to Water
Cytochrome c oxidase accepts four electrons from four molecules of cytochrome c in order to catalyze the reduction of O2 to two molecules of H2O.
In the cytochrome c oxidase reaction, eight protons are removed from the matrix. Four protons, called chemical protons, are used to reduce oxygen. In addition, four protons are pumped into the intermembrane space.
Created by Brett Barbaro
The last step in Complex IV (cytochrome c oxidase) takes the electrons from cytochrome c and transfers them into waiting protons. It starts with 4 cytochrome c that have been reduced and combines with 4 hydrogen ions from the matrix {yes, 4! The other 4 are pumped} and molecular oxygen, creating water. In the process 4 more protons are pumped into the intermembrane space. So this is just another example of the energy of oxidation being harnessed in the form of a proton gradient.
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Diagram of the Cytochrome c Oxidase Mechanism
Created by Brett Barbaro
Figure 20.13 The cytochrome c oxidase mechanism. The cycle begins and ends with all prosthetic groups in their oxidized forms (shown in blue). Reduced forms are in red. Four cytochrome c molecules donate four electrons, which, in allowing the binding and cleavage of an O2 molecule, also makes possible the import of four H+ from the matrix to form two molecules of H2O, which are released from the enzyme to regenerate the initial state.
And here’s a diagram showing how the electrons are passed from cytochrome c to water. In the upper left we can see that cytochrome c will dock on this cytochrome c oxidase and the electrons will be passed from a copper metal ion, down to a heme, and finally to a different copper metal ion. This is done twice, leaving electrons on that copper B ion and also the iron in heme a3. At this point you’ve got a couple of extra electrons, and an oxygen will float into that space and interact with these two metal ions, creating a peroxide bridge. The addition of two more electrons from two more cytochrome c and also two protons turns that peroxide bridge into a pair of hydroxyl groups.
At this point two more hydrogens are able to combine with those hydroxyl groups, releasing water and resetting the enzyme. On the right, we can see a diagram of the active site where this takes place. And it turns out that that the copper and the iron are exactly the right distance away to capture the oxygen molecules. Unfortunately, they’re able to also capture carbon monoxide molecules. And that’s one of the ways that you get carbon monoxide poisoning. Carbon monoxide can get into that gap and then prevent oxygen from getting in there.
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Diagram of Proton Transport by Cytochrome c Oxidase
Created by Brett Barbaro
Figure 20.14 Proton transport by cytochrome c oxidase. Four protons are taken up from the matrix side to reduce one molecule of O2 to two molecules of H2O. These protons are called “chemical protons” because they participate in a clearly defined reaction with O2. Four additional “pumped” protons are transported out of the matrix and released on the cytoplasmic side in the course of the reaction. The pumped protons double the efficiency of free-energy storage in the form of a proton gradient for this final step in the electron-transport chain.
So this is an overall diagram of the whole process starting with 4 reduced cytochrome c molecules at the top, and changing to 4 oxidized cytochrome c molecules. 4 protons are pumped through the enzyme, and 4 protons are combined with oxygen to make water. Those are called chemical protons because they are involved in the chemical process.
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http://d6igaq6njxgjh.cloudfront.net/content/physrev/95/1/219/F1.large.jpg
Created by Brett Barbaro
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The electron-transport chain. High-energy electrons in the form of NADH and FADH2 are generated by the citric acid cycle. These electrons flow through the respiratory chain, which powers proton pumping and results in the reduction of O2.
This illustration shows the whole process with Complex I, II, III, and IV, and also the little Q molecules wiggling around there in the membrane - those are the yellow little guys. And yeah, interestingly they can pass all the way through from the inner leaflet to the outer leaflet of the membrane because of that long tail of theirs. That’s what makes them such effective distributors and carriers of these electrons.
So starting on the left, you have the NADH interacting with Complex I, dropping off its two electrons. And those electrons flow down the iron wire down to a Q which is waiting there. And it also absorbs a couple of hydrogens from the matrix. (Now, in this case, the matrix is on the top, the intermembrane space is on the bottom.) And that causes a conformational change, which ends up transporting four protons total from the matrix into the intermembrane space.
The Q molecule is now a ubiquinol, and it’s able to wiggle around until it bumps into Complex III - and that’s where it can drop off its two electrons and release its two protons into the intermembrane space. Now, simultaneously, succinate is interacting with Complex II and being oxidized to fumarate and dropping off electrons that flow down the wire in the middle to another ubiquinone molecule, therefore reducing it and making it into ubiquinol where it picks up another couple of hydrogen ions from the matrix. And then that ubiquinol also is able to float around until it encounters Complex III and drop off those electrons there.
Now in this diagram you can see on Complex III there’s 2 Q; one of them is ubiquinone and one of them’s ubiquinol – one of them is oxidized, and one of them is reduced. The one with the electrons, the reduced one, would be the one toward the bottom there, and that’s dropping off its electrons and the hydrogens are being released into the intermembrane space. One of the electrons is flowing down to cytochrome c, and the other is flowing up to the ubiquinone to reduce that.
The cytochrome c is then able to diffuse off (and that’s, I think, true - I don’t think cytochrome c is membrane bound, I think it’s able to just diffuse), and then it reaches Complex IV where it’s able to drop off that electron. And the electron flows down the wire into the iron and copper center there, where it’s able to interact with oxygen, turning oxygen into water. And that also powers the pumping of another proton.
Toxic Derivatives of Molecular Oxygen Such As Superoxide Radical Are Scavenged by Protective Enzymes (1/2)
Partial reduction of O2 generates highly reactive oxygen derivatives called reactive oxygen species (ROS).
ROS are implicated in many pathological conditions.
ROS include superoxide ion, peroxide ion, and hydroxyl radical.
Two to four percent of oxygen molecules consumed by mitochondria are converted into superoxide ions.
DID YOU KNOW?
In mammals, the mutation rate for mitochondrial DNA is 10- to 20- fold higher than that for nuclear DNA. This higher rate is believed to be due in large part to the inevitable generation of reactive oxygen species by oxidative phosphorylation in mitochondria.
Created by Brett Barbaro
And that’s pretty much the end of the electron transport chain. I debated as to whether or not to even include this last part, but reactive oxygen species are extremely important in health and I think that people have a great deal of interest in them. So we’ll talk about them for a little bit. As I mentioned, the process of making the electrons pump the protons out creates some dangerous intermediates. Those are your free radicals. And a free radical can interact with just about anything, and it passes that free radical along and it propagates throughout the mix. And so, those are dangerous and cause a lot of diseases and mutations in the DNA. And as a matter of fact, we’ve talked about mitochondrial DNA (mitochondria have their own DNA) and, you know human DNA mutates at a certain rate - well the mitochondrial DNA mutates about 10-20 times faster than our human DNA because of these free radicals that get released during this process. That’s what happens when you play with electricity!
As a result, your mitochondria will die a lot of the time, and then they get digested by the cell, into lysosomes, and recycled. And they divide, of course, so they’re able to reproduce - and so there’s a constant turnover of these mitochondria. And I think in a way that is what protects our DNA from having to be exposed to all of these free oxygen radicals. All of these things are contained in the mitochondria so they’re not exposed to the rest of the cell. And the mitochondria can die and be recycled, and therefore ‘take the hit’ / the damage from this extremely powerful and somewhat dangerous process. Three of the reactive oxygen species that are created are the superoxide ion, the peroxide ion, and the hydroxyl radical.
Two to four percent of the oxygen molecules that are consumed by mitochondria can turn into superoxide ions, for example - so that’s a major problem. So how does the mitochondria deal with that?
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Toxic Derivatives of Molecular Oxygen Such As Superoxide Radical Are Scavenged by Protective Enzymes (2/2)
Superoxide dismutase and catalase help protect against ROS damage.
DID YOU KNOW?
Dismutation is a reaction in which a single reactant is converted into two different products.
Created by Brett Barbaro
In order to deal with all of these free radicals we have an enzyme called superoxide dismutase, which can take free radical oxygens and combine them with protons to make regular oxygen and peroxide. And the peroxide can then be broken down by catalase into oxygen and water.
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Table 20.3 Pathological and Other Conditions that May be Due to Free-Radical Injury
Created by Brett Barbaro
So free radical injury can actually lead to an enormous number of pathological conditions. Just as the mitochondria are responsible for our great advancement in growth and power as organisms, they are also responsible for a lot of the problems that we might have. In fact there’s a gentleman called Doug Wallace who used to be at UCI, where I did my graduate work, and he pretty much ties ALL disease to the mitochondria.
But I mean, look at this list, it’s crazy. Emphysema, bronchitis, Parkinson’s disease, muscular dystrophy, cervical cancer, alcoholic liver disease, diabetes, down syndrome… I mean, all of these things may be due to, or at least related to, free radical injury of the mitochondria; and possibly, I guess, other parts of the cell due some failure of superoxide dismutase or catalase to properly deal with these free radicals. There’s also a theory that aging is the direct result of the breakdown of the mitochondria - the mutation over time of the mitochondrial genome such that it stops working properly. So it’s a fascinating area of research.
So now we’ve talked about how we pump the protons out of the matrix of the mitochondria, and we’ve established this crazy voltage, this enormous source of power. So how do you make use of that power to create ATP? Well, as it turns out, you use it to drive little motors - and that’s what we’re going to talk about in the next section.
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