Hello! It’s another lovely day of existence, which means I’m here to bring you another lovely day of biochemistry! I wasn’t so optimistic in my last post, but now that we’re inching closer and closer to the most interesting piece of molecular machinery I’ve ever seen, I’m a walking pep talk! I can barely contain my excitement!
Okay, that might be an exaggeration. I might just be excited because the weekend is close and I’m two days ahead in NaNoWriMo. Shush.
If your biology background is anything like mine, you probably have a very well-developed appreciation for the citric acid cycle as a thing that exists. I remember trying to learn it in eighth grade—I think that year was the first time I felt horror at the complexity of all this biology crud, and also the first time I realized that it was freaking cool.
However, perhaps less appreciated is another little thing called the electron transport chain (or the ETC). On the surface, it doesn’t appear too impressive—I mean, it takes electrons from reduced species like NADH, dumps them onto oxygen to make water, and pumps protons from one side of a membrane to another in the process. Big whoop. We’re changing a pH. What’s the use in that?
Well, reader, that’s where that fantastic piece of molecular machinery comes in. (I’m actually bouncing. I’m so psyched to write about that.) Unfortunately, before we can appreciate that enzyme in all its glory, we need to learn what makes it work.
The electron transport chain isn’t too shabby in its own right, anyway. After all, the ETC is the whole reason we need to breathe oxygen.
Okay, so I’ve done the intro bit that no one wants, but I’ve yet to properly introduce the function of the ETC. “Stop beating around the bush, June, and be straight with us for once!” Right, right, I hear you. Sorry. I’ve been spending the past five days pumping steroids into my NaNoWriMo word count.
Well, the electron transport chain is a stage of aerobic respiration that performs two very important functions in the mitochondrion. Firstly, and perhaps more simply, it takes all of that NADH that we’ve made by breaking glucose apart and pushing it through the citric acid cycle (what, that’s ten NADH in all, right?) and converts it back into NAD+. We need it to do that, since we need NAD+. You know. To pick up electrons.
Right, that brings us to the ETC’s second function. In addition to regenerating NAD+, it takes all the chemical energy in the NADH (and CoQH2) that we’ve built up will all of our respiration and uses it to pump protons out of the mitochondrial matrix. That doesn’t sound too exciting, but think about it this way: creating a charge gradient is like creating a battery.
All right, so how does the ETC do this? Well, as the name suggests, it involves a flow of electrons.
The whole premise of the ETC is the idea that we can string together redox reactions until, eventually, molecular oxygen is made into water using the electrons from NADH. It might seem a little arbitrary, to deem oxygen our final electron acceptor, but when we look at actual numbers, it seems significantly less so.
You see, the standard reduction potential for converting NAD+ into NADH is -0.32 V. The negative number means that NAD+ really doesn’t appreciate having to take on those electrons—my professor called it “shoving them down its throat.” However, beautifully enough, this means that NADH is really good at giving up its electrons, which is precisely what we want it to do.
On the other hand, the standard reduction potential for converting half a molecule oxygen into a molecule of water is 0.82 V. That’s really positive, which means oxygen really likes electrons. That’s also good, because that’s also what we want it to do.
When we subtract the standard reduction potential of NAD+ from the reduction potential of oxygen, we get a whopping 1.14 V. Knowing that the change in free energy is equal to -nFEº, we find that the energy released when NADH donates its electrons to half of an oxygen molecule is 220 kJ/mol.
Step aside, glycolysis. The ETC has gots this.
Now, as incredible as that is (and it is incredible), it doesn’t happen all at once, as the net reaction I mentioned above would suggest. Rather, the ETC uses four complexes to funnel electrons from NADH and CoQH2 to molecular oxygen. Those four complexes are named (get ready for this), Complex I, Complex II, Complex III, and Complex IV.
Yup, that’s right. They’re named for their order in the chain. Electrons from NADH will first flow through Complex I, getting dumped onto CoQH2. That CoQH2 will be sent to a pool of reduced and nonreduced CoQ in the mitochondrial membrane called the “Q Pool.” Complex II, on the other hand, takes succinate and oxidizes it into fumarate, transferring electrons first to FADH2, and then to CoQH2 that will get sent to the pool. (In fact, this is what facilitates step 6 of the citric acid cycle.) Complex III takes CoQH2 from the pool and transfers its two electrons onto two reduced Cytochrome c molecules, which then donate their electrons to Complex IV to be transferred to O2.
Now, looking strictly at electron flow, you’ll notice that there’s no generation of ATP. In fact, there doesn’t really seem to be a purpose to it at all, other than to move electrons from NADH to O2. So, the question becomes, where is all of that 220 kJ/mol of energy that we’re supposed to be getting going, exactly?
Well, complexes I, III and IV span both sides of the membrane that separates the mitochondrial matrix (the inner part of the mitochondrion) from the inner membrane space. Here’s an image of a mitochondrion, just for help with visualization:
Now, every time electrons move through complexes I, III or IV, they pump protons out of the matrix and into the inner membrane space using the free energy released from the redox reactions they facilitate. Complexes I and III each pump four protons with each pair of electrons that flows through them, and Complex IV pumps two protons for every two electrons that flow through it to oxygen (every water molecule that is made). That means, for every molecule of NADH, ten protons are pumped from the matrix to the inner membrane space.
What, you ask, about Complex II? Well, remember, all it’s doing is oxidizing succinate into fumarate. If you think back to the citric acid cycle, you’ll remember that there’s no net release of energy in this reaction. Therefore, there’s no energy to pump protons with. Besides, Complex II is entirely on the inside of the membrane—even if it wanted to pump protons, it’s physically impossible for it to do so. Instead, it contributes CoQH2 to the Q Pool, which will eventually lead to the pumping of six protons out of the matrix (since it’s bypassing Complex I).
Now, wait, we do a lot of talking about NADH, but you’ll notice that Complex I took the electrons from NADH and put them on a molecule of CoQH2, as well. What’s up with that? Well, CoQ is a substituted benzoquinone, and it’s special in that it’s capable of forming radicals. What that means, practically, is that it can take on and give up one electron at a time. That’s important for Complex III, since it has to take individual electrons from CoQH2 and stick them on two molecules of Cytochrome c.
Cyctochrome c is, itself, a pretty amazing little thing. It’s a protein that contains a heme (hemoglobin, anybody?), which means it contains iron. However, this heme differs from the one in hemoglobin in two ways. First, its iron (before it takes on an electron) is in the +3 oxidation state, and, second, it’s covalently bound to its protein. Cytochrome c also contains four lysine residues (positively charged) that seek out negatively charged things, such as membrane protein complexes.
Okay, enough rambling about our electron acceptors. Let’s look at what each of these complexes do, shall we?
First in the ETC is Complex I, which takes electrons from NADH and funnels them to CoQ while pumping protons out of the matrix. This follows this net reaction:
NADH + H+ + CoQ + 4 H+in —> NAD+ + CoQH2 + 4 H+out
This whole thing really occurs in four steps. First, FMN (Flavin Mononucleotide) accepts a hydride from NADH, generating NAD+ and FMNH2. This species donates its electrons one at a time to clusters of Fe-S, which then donate their electrons one at a time to CoQ to make CoQH2. This is released to the Q Pool, where it will be used by Complex III.
This whole process releases over 70 kJ/mol of free energy. A portion of that is used to fuel the transport of protons from the inside of the matrix to the outside, which is really the whole point of this exercise.
Meanwhile, Complex II is oxidizing succinate into fumarate and storing the electrons it steals in FADH2. However, as said in the post on the citric acid cycle, FADH2 is covalently bound to succinate dehydrogenase. To get around this, it donates its electrons to Fe-S clusters, which in turn donate their electrons, one at a time, to CoQ. The product, CoQH2, is sent to play with all of the other CoQ molecules in the Q Pool. Here’s the net reaction:
Succinate + FAD (CoQ) —> Fumarate + FADH2 (CoQH2)
This process nets no free energy, so no proton pumping occurs. This is because succinate and FADH2 are equally enthusiastic about electrons, and thus one doesn’t fight the other for them (in contrast to NADH, which, in a relative sense, throws its electrons at anything that will take them).
All right, now we need something to use that CoQH2. Luckily, Complex III is more than happy to oblige. Here’s the net reaction for the shenanigans it pulls:
CoQH2 + 2 Cyt c (Fe3+) + 2 H+in —> CoQ + 2 Cyt c (Fe2+) + 4 H+out
This releases a good 37 kJ/mol, and thus, protons are moved out of the matrix. Additionally, this process uses up protons from the matrix, which further contributes to that mounting proton gradient. However, as I said above, this complex is pulling serious shenanigans. It’s not nearly as simple as that neat little reaction makes it look.
Nope, as life would have it, Complex III uses a complicated cycle called the Q-cycle to move electrons from CoQH2 to Cyt c. I won’t get into explicit details, but here’s the general gist of the two stages that it takes to move the electrons:
Cyt c (Fe3+), CoQH2 and CoQ all bind to different parts of Complex III. One electron is transferred from CoQH2 to Cyt c (Fe3+), making Cyt c (Fe2+), which is released. The other electron is transferred to CoQ, making that radical that I mentioned, CoQ*. Two protons move out of the matrix, and CoQ is sent to the Q Pool.
Another Cyt c (Fe3+) binds, and the whole thing starts again. An electron is transferred from another molecule of CoQH2 to the Cyt c (Fe3+), making Cyt c (Fe2+). The other is transferred to CoQ*, which takes up two protons to make CoQH2. Two protons are moved from the matrix, and all of the CoQ (reduced and oxidized) is sent to the Q Pool.
Jeez Loise. Confusing, much?
Finally, we’re at the complex where the magic happens: Complex IV!
Complex IV, our friend, finally does something we’re semi-comfortable with: it uses electrons from Cyt c (Fe2+) to reduce oxygen, something we’re perfectly familiar with, to water, something else we’re familiar with. Here’s the net reaction for a molecule of NADH (2 electrons):
2 Cyt c (Fe2+) + 1/2 O2 + 4 H+in —> 2 Cyt c (Fe3+) + H2O + 2 H+out
Now, like you’re expecting, it’s not as simple as slapping electrons on oxygen and calling it a day. That’s because doing that generates species called Reactive Oxygen Species, which are really bad for you. Turns out, every intermediate between oxygen and water that results from a single electron addition really wants to murder-kill everything in sight.
Take molecular oxygen and add an electron, and you get superoxide, a radical. Superoxide takes another electron and two protons to make hydrogen peroxide, which is equally horrifying. Hydrogen peroxide picks up another electron to make a water molecule (oh, nice), and a hydroxyl radical, which loves to tear apart all the lipids~! It’s only after you add another electron and proton to this thing that it’s palatable (that makes water, after all).
These species are so bad for you that your body has enzymes that exist only to hunt them down and kill them. It also has compounds that accomplish this. You may have heard of them once or twice—they’re called antioxidants.
(In fact, our bodies weaponize reactive oxygen species. White blood cells swallow up bacteria that are infecting us and generate superoxides with the explicit goal of killing all the things.)
Right, so what’s a Complex IV to do? Sit there and stare at it until it all comes together without killing everything in the process?
Of course not. As my professor said today, our cells are smarter than we are. This little thing gets clever, and it cheats the system using copper and iron.
Here’s how it works. Cyt c binds to the surface of a subunit of the complex in the inner membrane space. It transfers its electron to the iron (III) at a site that contains iron (III) and copper (I). The iron reduces to iron (II). Now, what does that iron (II) make us think of?
Yup, oxygen is on that sucker like Sapphire on Netflix. (I’m sorry, it’s a bad analogy, but it’s true.) The iron (II) transfers two electrons to whichever atom of the oxygen is nearest it, generating a ferryl oxo adduct (Fe4+=O2-). Meanwhile, the copper (I) donates electrons to the oxygen nearest it, one from another Cyt c and one from the copper. It picks up a proton from a tyrosine on the enzyme, becoming HO–-Cu. The hydroxide picks up a proton and is released as water.
To finish out (which requires another two electrons, or another NADH), an electron is given to both the iron and the copper, resetting them so that they can accept another molecule of oxygen. The O2- picks up two protons, then is released as water.
Holy freaking cow. If that isn’t awesome, I don’t know what is.
Well, there you have it folks. It took us a lot of time and effort, but we finally managed to regenerate our NAD+ and pump ten electrons per NADH into the inner membrane space. Of course, now the question becomes, how are we going to use all of that built up concentration and charge? Well, dear readers, that’s where the chemiosmotic hypothesis comes in. I promise, you won’t be disappointed.
Questions? Comments? Tears? Salt? There’s a little box down there. You know how to use it~!