Respiration

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So why do we eat? I know some of you will just say, "Because I'm hungry." But again why? Why do I eat? Why do I like to go around and eat cow muscle or little corn babies? Well, part of it, the whole hunger side of it is because of instincts wheedled into my brain by natural selection. Because if I didn't like to eat, then I'd die. But why would I die?

Well it turns out we eat for two basic purposes: One, we eat food to get the building materials to make our bodies. The other is to get the energy we need. So like when I bite into this apple, which is simply an apple tree nutrients. My body is going to start going through a process that's going to turn the molecules of this, and convert them to an energy molecule called ATP.

Animals do this, plants do this. I mean we don't think about that a lot, but plants do this in order to get the energy that they harvested during photosynthesis, and use to make glucose. Because they need that energy to do cell division and protein synthesis, basically all the things that they need to do to stay alive and grow.

So just as a little side note, while I call this process of breaking down molecules to get energy, respiration. It's a different kind of respiration and some of you have heard of, which is the respiration of breathing. The sucking in of oxygen, and the breathing out of carbon dioxide. You will ultimately see however, there is a connection between these terms. So, I'm going to go through this process in depth with you today. You've hopefully already seen my overview of photosynthesis and respiration, but just in case I'm going to start off by going through the two different kinds of respiration to give you a big picture view of it.

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Then I'll go into that first step of respiration called glycolysis, and I'll discuss something called anaerobic respiration. Then, I'll follow that up with the second step of at least aerobic respiration, which is called the Krebs cycle. The last thing I'll do then, I'll discuss the electron transport system that ends the process known as aerobic respiration.

You know there is four different kinds of organic molecules. There is the proteins, fats, carbohydrates and nucleic acids. And if you paid any attention to nutrition or food labels, you know you can get energy out of pretty much all of them. But when we study respiration in textbooks, they're usually focusing on glucose, because that's one of the major carbohydrates. And it's kind of the generic breakdown molecule that you can be going through. But once you understand how glucose is broken down, then you can easily go back and see how this whole process could be modified to break down things like fats, in order to get their energy.

So let's dive into this. Now with respiration, there is two basic kinds; anaerobic and aerobic. I'm going to start off with aerobic respiration, the one that generates the most energy. And it's called aerobic because it requires the oxygen gas that's in air, hence the name, aerobic respiration. You can see here this is the chemical equation for aerobic respiration. C6H12O6 that's the chemical formula for glucose, plus 6 oxygen, O2 gas, yields 6CO2 + 6H20 + energy in the form of ATP.

So this equation by itself, if you can learn this, you can handle a number of the basic multiple choice questions that may be on aerobic respiration. And if there is a question in the essay question, you say this equation, you got yourself a point or two. But now let's go a little bit more in depth. What's the first step of aerobic respiration, whether aerobic or anaerobic? That step is called glycolysis.

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Glycolysis is the first step and its name tells you what it is. Glyco means sugar, lysis means to split. It's that first step where you take your six carbon glucose sugar, and break it on half to form a couple of pyruvic molecules, which have three carbon in it. When you do that, that happens in the cytoplasm of the cell. The cytosol to be a little more specific, the liquid that fills the cell. And when you do this, you get a little bit of energy in the form of ATP. You also have a couple of these little high energy electron carriers called NADH. And they are going to be carrying off that high energy electrons to hopefully another step in the process.

Now again if your doing aerobic respiration, you need to go to the next step which involves mitochondria. Here in the mitochondria, the inner compartment of the mitochondria, you have this location called the matrix. While around it on the inner surface, you have this inner membrane that has all these folds to increase its surface area to volume ratio, called the cristae. Floating around in the matrix are a number of enzymes. And what those enzymes do is they start taking the pyruvic and they break it apart, releasing all the carbons that have been in the three carbon, pyruvic. And then using the energy that's released by these to make ATP. But, most of what they're doing is they're putting the high energy electrons, that used to help hold the pyruvic molecules together. They're putting them onto some more of those high energy carriers NAD+, NFAD to make NADH and FADH2.

So what's the point of doing that? Well those high energy electron carriers, can then go off to the electron transport system. The electron transport system, is a series of embedded proteins and other molecules that are within the actual membrane of the cristae. And what they do is, they use the energy of those high energy electrons, to pump hydrogen ions across the membrane into this darkish region. And once those hydrogen ions are there, they ultimately will force their way back into the matrix.

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And that forcing energy though is used to make a ton of ATP. Now if your paying attention on using high energy electrons to make an energy molecule. You know that energy can't be created nor destroyed, only transferred. So what happens to the energy on those electrons? It's being transferred to to the ATP. So now those electrons are called low energy electrons. We need to get rid of them on the electron transport system gums up. That's the job of oxygen. Oxygen gas from the air comes into the cell and ultimately winds up in the mitochondria where it's given these extra used up electrons. It grabs some hydrogen ions from the matrix and combines them to form water. And then that water goes away. But what if you don't have any oxygen, then you've got an issue because you can't do this process. That's where anaerobic respiration comes in.

Anaerobic respiration is the continuation of respiration but without use of oxygen. And because it's so important, all creatures on this planet can do anaerobic respiration, but most of those multicellular creatures can't survive on it for long. You've done it if you've ever been sprinting and you ran for longer than say ten seconds. You probably were taking yourself into anaerobic respiration just so you can keep running. But nobody that I know of can sprint for five hours, you just die.

So what is going on there is, glucose enters the cell in the cytosol, in the cytoplasm, glycolysis occurs creating our pyruvate. If there is plenty of oxygen, you go off to the mitochondria and you make your turn of ATP using anaerobic respiration in the mitochondria. But if there is no oxygen to allow you to keep going on, doing glycolysis which does generate some ATP a little bit but some, you can do anaerobic respiration through a process known as fermentation in the cytosol.

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And that's the two kinds of respiration. Aerobic and anaerobic.

Now that I've gone over the two basic kinds of respiration, let's start in on glycolysis. This process that is common to both aerobic and anaerobic respiration. Glycolysis means specifically, like I said before, splitting sugar and that's what it is. And if you remember photosynthesis' Calvin cycle, you actually already know a number of the steps of glycolysis, because it's like the Calvin cycle on some respects, run in reverse. If you want to find out what these steps look like, take a look at your textbook, because my summary here has skipped a number of steps. But it's very unlikely that, unless you're taking biochemistry, you want ten. It's very unlikely you're going to be having to memorize every step of the process.

So glycolysis begins with the spending of some energy. A couple of ATP molecules drop off their phosphate ions on the glucose, turning it into fructose-1,6-bisphosphate. What that means is that, it's a different sugar. There is a couple of reasons to do this. First, since it's a different sugar, this helps reduce the amount of glucose in the cell, so that the concentration gradient between the outside and the inside of the cell is maintained. So that glucose keeps diffusing in to the cell. Additionally, those phosphate ions make this a polar molecule, which means it can't get through the membrane. Last, this is a negative charge, that's a negative charge. Negative charges tend to repel, so this helps strain the molecule a little bit.

Now we can have some enzymes snap that six carbon molecule into a pair of three carbon molecules. Now, the three carbon molecule that's ultimately created is something called glyceraldehyde-3-phosphate. What are these numbers in the middle referring to? They are just little things that biochemists like to say, that tell you the address of the things that are on this. Like for example, notice the phosphates on the first and the sixth carbon, that's the 1/6 refer to.

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This molecule here glyceraldehyde-3-phosphate sometimes comes just written G3P then has some of it's electrons taken. You do that using NAD+. And the NAD+ grabs some of the most energetic electrons of G3P. And that makes a phosphate ion that's nearby floating around the the cytoplasm glum onto this, turning it into 1,3Bisphospoglycerate, lovely words aren't they? Now, this has two phosphates on it, let's pluck them back off. And we do that by putting them onto ATP. So we take them off here, take them off there and we wind up ultimately with making four ATPs, but we spend two in the beginning.

And here's another one of those evil science teacher tricks. I've seen it, I've done it myself and I've seen that on the national test, where they'll ask questions like; how many ATP molecules are synthesised during glycolysis? The correct answer is four, versus; what's the net product of glycolysis? There the answer is two. Or what's the profit of glycolysis, there it's two. You make four, but you spend two. Again, that means it's a profit of two.

Ultimately you're making pyruvate a pair of them since this happens in parallel. This pyruvate if you're an aerobic creature, or you've got lots of oxygen, they off to mitochondria. And there they are ripped apart to make NADH and FADH2 and you pop out some carbon dioxide. If you're running out of oxygen however, you've got a problem, because mitochondria depends on oxygen to do this. And you're using the NAD+ here to make NADH, which means you're running out of the NAD+. And so while the mitochondria can take this NADH and convert it back to NAD+, again without oxygen, that just doesn't happen. That's why anaerobic creatures or those of us aerobic creatures who just don't have enough oxygen at this moment, will go through a process called fermentation.

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There is two kinds of fermentation. One is called alcoholic fermentation, the other one is called lactic acid or lactate fermentation. But the basic idea behind them is the same. Here is glycolysis. Going forward again, glycolysis ultimately creates an ATP and some Pyruvate. To do this it takes adenosine diophosphate and phosphate ion to make the ATP. But ATP is like money, this is spent money. It's always easy go get spent money, you just spend your money. But here, to go forward, the NAD+ is turned into NADH. In order to get that back what happens is that, in fermentation you drop the high energy electrons back on to the pyruvic. If you're an alcoholic fermenter, you break off the carbon dioxide molecule, and some menthol alcohol. Whereas in our cells, we don't make alcohol in our cells, which is a good thing because you go jogging and all of a sudden you're drunk and dead.

With us, we do lactic acid fermentation, where instead we drop off the high energy electrons again on the pyruvate, but the carbon dioxide doesn't fall off. Instead it just becomes a different three carbon molecule called lactic acid.

Now again that pyruvate molecule is not a good thing to have hanging around. It's actually fairly toxic. Lactic acid is not as toxic, but it's a little bit toxic. And that can be a problem for us because, let's suppose, like I said before, you're sprinting for ten seconds, you can handle that. You keep running for thirty seconds though, your oxygen levels in you're blood start to drop and your aerobic respiratory pathway simply can't keep up. And so they start producing a lot of lactic acid to keep you going, to at least recycle the NAD+, so you can get a little bit of ATP that your muscles need to keep you running. You try sprinting for five minutes, let alone the five hours I mentioned earlier, and you're going to discover you can't keep going because that not sufficient energy. And the lactic acid is starting to build up. And it is an acid

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It will start interfering with all the proteins and enzymes in your body, and then you've got a problem. Once you do stop however, you will keep galloping in air and using the oxygen that's coming in, to do aerobic respiration. And then you use the energy of the aerobic respiration to turn the lactic acid back to into pyruvate, and then ultimately convert it into energy. The amount of oxygen that you had to spend to turn this lactic acid back into pyruvate, that's something known as oxygen debt.

Again, to remind you with aerobic respiration, the pyruvate that just came out of glycolysis, goes off to the mitochondria, as does the NADH that was produced. The ATP, that gets used by the cell. Inside the mitochondria, the NADH is going to go off to the electron transport system while the pyruvate goes into the matrix of the mitochondria, to begin going through the biochemical reactions known as the Krebs cycle.

Now, as a side note, one of the problems that my students have, when they are starting this sort of stuff, is that there is all these names. Now things like glycolysis, sugar splitting, you can just look at the name and figure it out. But Calvin cycle and Krebs cycle, they are named after guys who studied this stuff. So there is no clues that really help you figure it out. What makes things worse is that the Krebs cycle is also called the Calvin cycle, Krebs cycle is called the citric acid cycle or the TCA cycle, tricarboxylic acid cycle. All these names, how can you keep them straight? With my kids I tell them think Calvin cycle.

Calvin cycle beginning with a C is found in the chloroplast, also beginning with a C. The Krebs cycle happens in the Mitochondria. Now, I chose Krebs cycle because of a mnemonic device, a memory trick that I came up with, that has only worked in 1999. But ever since then, it's never failed. Now let's see, Krebs cycle. So the Krebs cycle which begins with a K and a R, and that's the Krebs cycle we use in respiration, K and R.

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Now this is happening in the matrix of the mitochondria. If only there was some way to remember that KR was in the matrix. Wait a second Keanu Reeves was in the Matrix. See, it's goofy and kind of stupid, but it works. And for those of you who are movie geeks like me, what was the whole purpose of the matrix? Why were the robots using the humans? To get energy. Root.

With that out of the way, let's go into the details of the Krebs cycle.

Now technically, before the Krebs cycle actually begins, that pyruvate is converted into a molecule called acetyl-CoA. How does that happen? Well a pyruvate, a three carbon molecule has a couple of its high energy electrons taken away by an NAD+, turning into NADH. When that happens, one of the carbon dioxide falls off and that creates a two carbon molecule called acetyl group, which is attached to something called co-enzyme A. Co-enzyme A, that's just a kind of helper molecule, that's helping some of the enzymes here do their work. It's kind of like the guy who holds the board when the karate guy is doing his board breaking. He's not breaking the board, but he helps hold the board. And if he just kind of tosses up in the air, karate guy will be just kicking the board somewhere else, instead of breaking it.

So co-enzyme A holds on to this carbon group, forming something called acetyl-CoA. With that out of the way, I now have to apologise. I'm about to hit you with a whole snowstorm of different names. And do you need to memorize every step of the Krebs cycle? Probably not. It would help, just in case they happen to have an essay question where they are giving a turn of points out for knowing every step of the Krebs cycle. Or if you've got an evil teacher like me, who actually asks his students to memorize these steps. But in general you don't need to.

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I means heck, as biology majors in college we don't bother memorizing until later on as upper division students. And we haven't bothered to memorize it, it's just we've had to go through it so many times looking at the textbooks to find out the names, that we just know it. So to help you out if you are going to focus on learning these names, I'm going to give you a mnemonic at the end. But what I would really like you to understand is, the logic of what's going on. Because once you get the logic, these all becomes simpler. If not, it's kind of trying to memorize a speech in Swahili. I can't speak it. So it would be almost impossible. So let's get into this.

So here we see the acetyl group, that two carbon molecule, is attached to a four carbon molecule called oxaloacetate. That makes a six carbon molecule called a citrate. Sometimes it's called Citric acid depending on the pH of the mitochondria. And that's one reason why an alternative name for the Krebs cycle is the citric acid cycle.

Well, what happens to the citrate is it then turned into a different molecule called isociterate. Now I've grossly simplified these diagrams to help you focus on what's going on with the carbons. So what's the difference between these guys, is the arrangement of the other atoms and molecules, where the hydrogen and oxygen are. Are those details important? No. But I'm telling you the names because that's the kind of thing that may appear on the AP essay.

Next step, the isociterate comes along and the enzyme strips off a couple of its energy electrons, giving them to NAD+ to form NADH. When this happens, one of the carbons falls off, and goes away as carbon dioxide. What happens to the carbon dioxide? It has a non polar small molecule floats away in the matrix, passes through the cristae, passes through the outer membrane of the mitochondria into the cytoplasm of the cell. And unless it is a plant cell that can use the CO2, the carbon dioxide just goes out ultimately from the cell, into the bloodstream and gets breathed out into the air.

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This makes a molecule called alpha ketoglutarate. Alpha ketoglutarate, that alpha is a Greek letter because they just couldn't stay to the English Language. Here we do a next step where we again strip off some of the high energy electrons that were holding on carbon dioxide. So that gets released and we had six now we're at five, finally we're at a four carbon molecule. And this one is called a succinyl CoA. CoA what's that referring to? Remember our buddy co-enzyme A, it plays a part up here, it also plays a part in here, and that's what we see going on here.

Now that co-enzyme A holds succinyl in just the right way so we can just turn it to succinate. Now, why bother going through this step? Because this rearrangement allows you to create another energy molecule, an ATP. But you look at this and you see, "No we're making GTP." If you happen to mention during an AP Biology essay, that during a Krebs cycle you're actually technically making a GTP, you got yourself another point. That's the kind of thing that impresses the writers.

That GTP, which is guanosine triphosphate can easily transfer its third phosphate to a ATP, adenosine triphosphate, or this cell can use that GTP if it's doing something like DNA replication which actually needs GTP as well as TTP and CTP.

So now we have our succinate, what happens to that? Well, we pop off a couple of its electrons forming fumerate. Now remember we added in two carbons up here, we've already popped them out. So now as we're stripping out the last of the high energy electrons, no more carbons fall off. But something to help you with this, notice, every time a carbon dioxide comes off, you're making so many NADHs. So that one way to help minimise the amount of memorizing you have to do.

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Remember every time I see a two falls off, I'm also getting an NADH carrying away some high energy electrons. Now how can you remember that FAD helps form fumarate? FAD, helping form fumerate. The FAD becomes FADH2 and it too goes off to the electron transport system, just like the NADHs. What happens to our fumarate? Well it becomes malate. We're almost done, not quite, but almost there.

What happens to the malate, it ultimately becomes our starting material, oxaloacetate. hat's why this is aT cycle because we wind up back where we started. To turn malate into oxaloacetate, we take last of the high energy electrons that had been ultimately way back in the beginning, put in to this molecule by the process of photosynthesis. We take last of our high energy electrons off in the form of NADH. So this is the Krebs cycle.

And again, do you need to memorize all these names? No you don't. Not to do okay on the AP BIology exam. And even if you did spend the time on this, the chances of them giving you points for every single name, not that high. But again if you need to, let me show you a way to remember these names. I'm going to give you another mnemonic, another memory trick. And in this one, the first letter of each word corresponds to the first letter in each these names.

So the mnemonic is Oxes Are Crazy In Kansas. No offence to those of you who live in Kansas, So Should Foxes Marry Oxes.

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'Oxes' is our oxaloacetate, 'Are' is our acetyl-CoA, 'Crazy', that's our Citarate, In, that's our Isociterate, 'Kansas', that's our alpha Ketoglutarate because I'm going to start writing in Greek. 'So' is our succinyl CoA, 'Should' is our Succinate, Fumerate is our 'F', Malate is our 'Mary' and we are back at our starting Oxaloacetate. For those of you who are English die-hards, I know it's supposed to be oxen, but this makes it rum with foxes. And I know the way the brain works and if it rhymes, you can remember it better.

So if you don't like this, come up with your own and if it's better than this one, email it to me. I'd love to hear them. So this is the Krebs cycle, now we're ready to move on to the last step.

So far we've been working pretty hard to try to get all those electrons off the glucose molecule. So let's take a look at how much we've actually made. Remember when glucose went through glycolysis, it poured off a couple of high energy electron carriers in the form of NADH, carrying some high energy electrons going off to the ETS. For every glucose that enters, we get a pair of those pyruvates. And as those pyruvates go through the Krebs cycle, we wind up cranking out one plus three more. Or for the two that go through, a total of eight NADHs here. We also get a couple of those FADH2 and all these go over to the electron transport system to drop off those high energy electrons. Let's take a look at how that looks.

Here we see the cristae. We've zoomed in right there and we can see this membrane here has embedded within a number of specialised proteins. Some of them are proteins that pump hydrogen ions, others are cytochromes that are transferring the electrons from one to the next. NADH comes along here to this first guy and drops it off it's high energy electrons.

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The energy of those electrons is used to grab a hydrogen ion, and shelve it into the space between the inner and outer compartment of the mitochondria. Moving it from the matrix, away from the enzymes who are not dumping a bunch of acid, or hydrogen ions on top of our enzymes, that might cause them to have problems. That electron is then passed on here to this next hydrogen ion pop. It too grabs a hydrogen ion and shelves it across the membrane.

Finally the electron winds up here and there, again hydrogen ions are being shelved across the membrane, and now the energy of the electrons is gone. We need some place to dump these or otherwise it's kind of a water slide with the kids you don't just get off the slide. It starts clogging up, that's where our buddy oxygen gas comes along. It comes along, takes those electrons and uses those electrons to grab still more hydrogen ions from the matrix, to form water.

Now you notice that happens here. FADH2 it drops its electrons off here in the middle pump. That's one of the reasons why FADH2 doesn't wind up transferring as many hydrogen ions across the membrane, and is ultimately responsible for making less ATP. Just as a little quick side note, hydrogen ions, I keep calling them that because it's easier for kids to hear. Alternately, you could simply call them protons because you know hydrogen atom has one proton and one electron. You remove that to make an ion all you're left with is a proton. I stay away from that because when I start talking about protein, proton pumps, kids go. So I'll stick with calling them hydrogen ions.

Now moving these hydrogen ions off from one side to the next, that's creating a pretty strong difference in charge. It's kind of like I used to entertain myself and piss off my third grade teacher, and I would shuffle across the carpet of the classroom and give static shocks to my buddies. You can use that to do work besides exploding skin cells on someone's ear.

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And not only is it an electrostatic gradient a difference between all these positives here, and the negatives there, it's also a concentration gradient. We've got a lot of hydrogen on one side, not so many on the other. This difference in both charge and concentration, is called a chemiosmotic gradient. And as we've seen before with photosynthesis.

So what we have here is a special tunnel with a structure attached to it. That is technically called the F1 particle or more simply, the ATP synthex. And it uses the driving force of these hydrogen ions going down the chemiosmotic gradient, to make the F1 particle at this bottom part to start to spin, turning the driving kinetic energy of the hydrogen ions, into a kinetic energy. That's used by the HP synthase enzyme, to slam phosphates onto adenosine diophosphate, turning them into ATP. Remember, that's the big pay off here.

Just as another interesting side note, many of you have probably have heard of the poison called cyanide. The way cyanide works is it actually puts holes in the cristae. Now, you can kind of think of the ATP synthase channel as a bridge. It's a toll booth bridge where the hydrogen ions have to pay a toll in form of ATP, in order to get across. Well the cyanide potholes are kind of like a free bridge. If you had two choices, you can go across the bridge and pay money, or go across another one that's for free. Which one would you do? The free one. So if you accidentally start eating some cyanide, instead of you getting ATP, you get sleepy and then you get dead. So let's take a look at all the totals here, we've been working so hard now we've got our pay off.

For every NADH that drops off its electrons, it kind of depends but generally you make roughly three ATP molecules. All those FADH2 only make two. How can you remember that? FADH2.

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So here we see the electron transport system winds up making, if you did the Mathematics here. You'll find you'll make up somewhere between 32-34 ATP. Part of that variation is because these NADHs here wind up loosing some of their energy as they pass it across the membrane, in most cells of your body. So electron transport system makes 32-34 ATP. Remember, for every turn of the Krebs cycle we made one GTP, which we can translate to one ATP and glucose made it spin twice, that's our two. And then here is our 2ATP profit that came out of glycolysis.

You do the add up, 2 plus 2 plus 32 to 34, that's a grand total of somewhere between 36 to 38 ATP. That's a whole lot better than those wimpy little anaerobic bacteria out there, that are struggling on the 2ATP of anaerobic respiration. So yes it takes more time, yes it requires oxygen, but it's a big advantage for us.

Respiration isn't that hard. Yeah there is a lot of chemical names to remember but, the key thing to do, is to focus in on the basic ideas. It all begins with glycolysis. You take your six carbon glucose you split it into half. If you've got not much in the way of oxygen, then you send that off to fermentation, so that you can at least recycle back the NAD+ that glycolysis required.

If you do have oxygen however, then you can go from the cytosol where glycolysis happened, into the mitochondria, where the pyruvate is ripped in down to little tiny beats to give off the carbon dioxides, to release all the high energy electrons that were used to assemble the pyruvate in the first place. These high energy electrons are dumped on to those high energy electron carriers; NAD+ and FAD, to form NADH and FADH2. Those ultimately go the electron transport system, where those high energy electrons are used to power the formation of a chemiosmotic gradient, the pumping of hydrogen ions across the membrane.

[0:32:00]
And then that chemiosmotic membrane drives chemiosmotic phosphorylation, which is simply the synthesis of ATP using that ATP synthase channel, as the hydrogen ions go back down their gradient. The used up electrons are then dumped on to some oxygen gas from the air and turned into water. That's it. You wind up making the 2ATP profit from glycolysis, 2 more ATP mention the GTP for a point, and then 32-34 ATP for the electron transport system. This gives you usually you'll see the number 36 ATP on test as the profit for aerobic respiration, versus anaerobic respiration's profit of 2ATP.

Now I recommend strongly that you watch this lecture a few times. Just go through and really make sure you get it. Then additionally, if you check your bonus materials folder, you'll see there is links for the official AP labs that are focused in on respiration. If you do that, you'll be well and advanced of probably about 75% of the students who actually take the AP Biology exam. Because again, this is what they consider one of the harder topics. But if you invest the time, you'll see massive pay off in your essay scores and your overall score on the AP.