Cell Respiration and Fermentation: Lecture Notes PDF

So, first thing I want to show everyone before I get started with drawing everything you need to know, like minimum for the test, is that, yes, it says that chapter 9 is 100 slides long for cell respiration, but I want to show you that the first 30 I'm calling old stuff from chapter 8, which is a pa...

So, first thing I want to show everyone before I get started with drawing everything you need to know, like minimum for the test, is that, yes, it says that chapter 9 is 100 slides long for cell respiration, but I want to show you that the first 30 I'm calling old stuff from chapter 8, which is a part down, like, here are the terms you need to know, if you have that kind of idea. But it is all talking about thermodynamics, all that fun stuff, first and second law, it's talking about chemical reactions, the endergonic exergonic with the videos and burning and Tom and Jerry again and a couple of reactions. All of that in chapter 8 was purely to set you up for chapter 9 and 10. You need to know endergonic exergonic, catabolic, anabolic. Still need to know hydrolysis, hydrolysis, dehydration, synthesis. You need to know coupled reactions. You need to understand proton pumps from the last chapter. You need to understand co-transport. You need to understand all of that stuff just to be able to do the electron transport chain in creb psych, I'm sorry, in mitochondria and chloroplast. So let me now draw exactly what you need to know. And I'm really hoping this program works, because it's not working for everything else I need. Good, it's working. Here is what I would like you to do. I would like you to take whatever sheet of paper you're doing and turn it sideways. And we're going to do cell respiration across the top half and a little bit of fermentation on the left and then we'll add photosynthesis and what's left. I also want you to do, and I'm going to try and write as neat as possible, so the first step is called glycolysis. Okay, glycolysis, breakdown sugar. If I am talking about aerobic respiration, I'm talking about mitochondria. If I'm talking about anaerobic respiration, I'm talking about fermentation. Glycolysis just is. It is the first step of aerobic or the first step of anaerobic. So glycolysis is the oldest thing that all life shares that is currently living today. There might have been other things that evolved, but glycolysis gave selective advantage and everything else died off. So from an evolutionary standpoint, glycolysis exists in every single thing deemed living today and that's one of the reasons why viruses aren't deemed living. They don't actually do metabolism. You do everything for them. I'm not going to write down everything you need to know. Do not memorize all of the enzymes. There's one enzyme in glycolysis I care about and I will point it out to you when I do the PowerPoint and there's one enzyme I care about in the electron transport chain and I will point out those names. I will not ask you about any other enzyme names at all, but you need to remember that to go from A to B to C, each one of those arrows is a different enzyme and we can do it better, but over time implies that you work with what already exists. It is not a reset the system in a living organism. So I am looking at it from an economic perspective. Inputs outputs. So input will become an output. If you want to write input and output, I just write I and O. We're going to focus on sugar, glucose specifically because that gives the most output of ATP. Anything you eat can go into multiple steps, but because glucose is the universal input, your system is primed to give the most output per molecule of glucose. Pound of fat is 3,600 calories worth of energy because of the number of carbon-carbon bonds. But they don't enter in step one, therefore we don't make as much ATP. It's just the number of bonds gives us more energy per pound of fat versus pound of glucose. But efficiency statement, purely based off of efficiency, glucose is the best input. So C6H12O6. Now I'm drawing a really cheap glucose molecule here. Each one of those points is a carbon, and I'm not writing the H's and the O's. What I need to do is cut those two bonds. If I cut two bonds, how many molecules will I now have? Two. So I'm going to have two of... And also, the reason why I'm writing C3 is I don't want you to memorize the goddamn molecular structure other than glucose is C6H12O6. Another name for this is going to be pyruvate. You might also see pyruvic acid. Then, for some reason, every time you break a bond, we're going to release an electron and a hydrogen. The hydrogen protons are extremely important in the electron transport chain. The electrons power the electron transport chain. We need a molecule called NAD+, to merge with those, to become NADH. How many of you does this sound familiar from high school? The weird thing is that you need to break down two molecules of ATP to make four. This is where I look at it from an economic perspective. You give me $2, I hand you $4. You just got 100% return on investment. That's good for you, right? It feels like a pyramid scheme in my mind. The other reason why I think about it from an economic perspective is because the first half of glycolysis is called the investment phase, where you invest two ATP, and the second half is called the payout phase, where you make four ATP. You are going to see the terms investment phase and payout phase on the exam and in the mastering quiz. That's glycolysis. Yes, ma'am. Yes, that is a four. Just yell at me if my writing is bad, because the thing is, I'm zoomed in a lot to try and get it all on one screen, and it probably won't all fit on one screen. Any questions on glycolysis? Now, let's do aerobic respiration first. How many membranes surround a mitochondria? Two, so I would like you to draw a double line, and you could also add that glycolysis occurs in the cytoplasm. I'm not writing plasm only because I didn't give myself enough space. Now, the next part is called Krebs or citric acid cycle, whichever one you want. Well, pyruvate will enter the mitochondria, and we will break off one molecule of CO2 per pyruvate. So if there are two pyruvates, they each lose one, we break off two CO2s. And now it's going to bind with something else, and we're going to call it acetyl-CoA, which enters the top of the circle, goes around, and will all get broken down in the carbon dioxide. Yeah, capital C, little o, capital A, acetyl-CoA. That goes through the cycle and it gets broken down into carbon dioxide. Yes, ma'am? This? Krebs, K- R-E-B-S, because it's the Krebs cycle. Just think, I'm trying to write neatly here, okay? I blame the nuns. Yeah, for your left-handers, you understand. Now, I'm breaking carbon-carbon bonds, which means I'm losing electrons and hydrogen. That's an H+. That's a really bad H+. Well, I need to capture it. And so, NAD+, will become NADH. And there is another one called FAD, will grab the hydrogen and the electron, and become FADH2. I need those hydrogens and electrons in the next step. Yes? Did I write numbers? Then no. Because the thing is, in a perfect world, one molecule of glucose goes in, 36 to 38 ATP are made. Is the world perfect? So it is never, I don't want you to memorize, if I write a number down, I care. But here's an easy question. If glucose went in, how many carbon dioxides are released? Total. What was that, Elijah? Six. C6. I've got to balance my equations on both sides. Glucose is the carbon input. Carbon dioxide is the carbon output. The other thing is that one ATP is made per pyruvate. So I've made a total of two ATP in glycolysis, because I spent two to make four. That is also called substrate level phosphorylation in your book, because the phosphate is coming off a substrate. I've made two ATP total in Krebs, substrate level phosphorylation again. And that implies that the electron transport chain in I think 90 to 95% of the ATP needed or produced. How many of you had to remember every step of Krebs? Okay, that's Krebs. I will show the pictures, but there are no enzymes that I care about. If you take anatomy, pyruvate going in and breaking off a CO2 and combining with acetyl CoA, that's called the intermediate stage. I try and avoid that term in this class completely on the test. Pyruvate becomes acetyl CoA, gets broken down to carbon dioxide level for this course. Of course, I didn't leave enough room. So oxidative phosphorylation covers two processes. So I'm going to write it under Krebs, because I don't know how to scale correctly. So the first thing is going to be called ETC, electron transport chain. Input versus output. NADH is going to become NAD+. FADH2 is going to become FAD. That is going to break off electrons and hydrogen. Now, the electrons are going to pump hydrogen against the gradient. That active or passive? Okay, so we're creating a gradient. As we rip the electron and hydrogen off the NAD, the electrons will power a pump to pump hydrogen against the gradient. Electrons are pennies on the dollar. You all know what pennies are, right? In the US, because they got rid of them in Canada years ago. If a penny is worth 1 cent, it's 2.3 cents to make it. Seems stupid to continue it. There's an economic reason why. Still asks backwards, but it's a valid ask-backwards reason. I'm going to use electrons to pump hydrogen against the gradient, because the next step is called chemis osmosis. And there is one enzyme called ATP synthase. So for once, it's named what it does. It synthesizes ATP. How many of you remember when going shopping, you put like a quarter or two quarters or a buck fifty into a thing and turn a handle, and it pops a gumball or a toy, right? That is what ATP synthase looks like. Hydrogen are the coins that go through it, and all it does is make ATP. I am not attaching a number to this, but in a perfect world, that'd be 32 to 34 ATP for the number of hydrogens pumped against the gradient. I am separating ETC and chemis osmosis, because ETC is creating the gradient which chemis osmosis uses to its advantage. That's the coupled reaction. The thing is, all of those hydrogen are still present, but more importantly, those electrons are de-energized, but they can still do damage. Therefore, the final electron acceptor is oxygen gas combining with some hydrogen and those really, really, really de-energized electrons to form water. Yes, ma'am? It's adding the hydrogen to itself and those de-energized electrons. It's just transporting it back. Yeah, it's just getting rid of it. NADH and FADH2 release the electrons in hydrogen to get pumped and charged the system. Oxygen kind of comes along and says, alms for the poor and takes everything left over at the end for itself. It just takes it on. Yes. Please notice, I'm trying to avoid the terms reduced and oxidized also. Are you familiar with redox reactions from chemistry? I don't care about them on this test. If you see a mastering biology question that asks something that is reduced or oxidized, look it up. I will not ask you about reduced or oxidized on this test. If I use the terms on this test, this will give you the answer. It just means I didn't have a better way of putting it. But reduced and oxidized, I'm not concerned about for this test. That's self-respiration. Now, if I were to cross off everything that is an input and an output, I want you to notice that I get glucose plus oxygen, give me carbon dioxide, water, and energy. You should probably know the equation for self- respiration, but I'm saying that this is an algebraic equation. Anything that was an input and an output just crossed off. NADH and FHDH2 is the shuttle bus going up and down to Rocky Top. One of them also goes to North Haven, the FHDH2, because it does more work. NADH and FHDH2 carry the electrons and the hydrogen to activate the electron transport chain. That is their job. They drop off the passengers, go back, and get more. Glucose goes in and is broken down into carbon dioxide. Water only matters as the very last... I mean, oxygen only matters as the very last step. However, if you don't get oxygen, you die because your body cannot survive on glycolysis and anaerobic respiration on its own. Now, let me throw up anaerobic respiration. Okay. Does anaerobic respiration exist in bacteria? Yes or no? Yes. Do bacteria have mitochondria? No, they do not. And so I'm going to write it here back in the cytoplasm. And I'm going to call it fermentation. Go. Yeah, I'll leave it in red. And let me get out of the way of it. Pyruvate comes in. I'm only writing C3. I don't got a lot of room. And it is going to become lactic acid. I'm doing lactic acid fermentation now. You ever work out and you feel the burn in your muscles? That's lactic acid buildup because you don't have enough oxygen in your system. You are doing anaerobic workout. Well, NADH is going to become NAD+, and the electrons and hydrogen are going to get bound back to C3 to become lactic acid. That's supposed to be an H+, and an electron minus. Because in bacteria, NADH is the limiting reagent. NADH in anaerobic fermentation. NADH is the limiting reagent for glycolysis. So the entire point of fermentation is just to make NAD+, again, to go back to glycolysis. Yes, ma'am? This arrow from NADH, that's the electrons and hydrogen breaking off the NADH and being added to the conversion of pyruvate to lactic acid. Because I was drawing it up above as the hydrogen and the electrons coming off, breaking the bond, to being joined with NADH. So it's them being broken off the NADH and being added to the formation of lactic acid. If you are reading a question and I'm asking you about alcohol, that is alcoholic fermentation, which is bacteria and yeast. If I'm asking you about human fermentation, there's no alcohol involved, and alcohol is not the answer. Sometimes it is, but it's not the answer to a test question. That is what you need to know for cell respiration and fermentation. That will answer probably 10 out of the 15 multiple choice questions right there, and I think it's at least one short answer potentially right there. I know that because I reviewed your exam last night and I wrote it two months ago. Now, I'm going to erase the screen. It's on the recording, and I will ask you to take out a sheet of paper in the beginning of the next class and write it from memory, and every class that will ask you to take out a sheet of paper and write it from memory. Now, photosynthesis is easier. There are two... Oh, and by the way, when I'm saying if this was my sheet of paper, I should be able to write like glycolysis there, fermentation here, crib, ETC, and chemi here, and then I would go something like this, and photosynthesis can go part one and part two can fit right there in the bottom of the sheet. I just was not correctly expanding it or shrinking it on my view, okay? There are two parts to photosynthesis. The first part is called the light... Let me get back to black. Do you want to write this in green because it's photosynthesis? Which implies you might want to color pens while you're doing this as a study skill. Light dependent reaction. Input and output. Why am I so far down? Okay, what's the energy source for this? Light. Light. It's light dependent. Now, I will tell you that water is split right away to oxygen, and coming off of that is electrons and hydrogen. Oh shit, this looks familiar. By the way, the purpose of photosynthesis is to make sugar. Oxygen is the farts of plants. It is a byproduct that if it builds up too much in the plant, they will die. The primary sole purpose is to produce sugars. Well, we got to capture those, which means we need NADP. Oh, and by the way, those hydrogen are pumped against the gradient via an electron transport chain, which produces ATP. And NADP captures them to become NADPH. And ADP becomes ADP. Half the time I forget to write the inorganic phosphate, the P little i. I do have that in the exam questions, and I know you will see it in the mastering questions. I can't give a number to it because in the Amazonian rainforest and the Great Barrier Reef and the coral reefs, those are the highest net primary productivity on the planet, ecology now, because they have unlimited sunlight, the rainforests are wet, and plants grow like mad because it's good temperature for enzymes. Therefore, I can't actually put a number to the number of ATP produced. Because if there's water and sunlight and good temp, it is doing it all the time at max efficiency. Now, the next step is the light independent reaction or the dark reaction or the Kelvin cycle. But I'm trying to stick to light dependent versus light independent when I'm talking. Well, the inputs versus the outputs, NADPH is going to become NADP. ATP is going to get broken down to ADP plus pi. NADPH. Sorry, I better. Okay. Imagine if this entire class was a chalk talk with me in this board. Yes, ma'am? Yeah. They come off and CO2 is combined with the hydrogen and the electrons and the ATP exergonically releasing the energy. Therefore, the CO2 is endergonically storing it in a molecule called G3P. And if I add two G3Ps together, I get glucose, G3P. You'll see what it stands for in some way. Oh, yeah, there should be a line there. Thank you. CO2 is combined with the electrons, the hydrogen, and the energy from the ATP being broken down into G3P, and two of those will make us glucose. Yes, ma'am? G3P equals glucose. Yes? However many CO2s are needed, yes. Notice I'm not putting numbers on because I don't want people to worry about how many numbers. Unlimited water, unlimited sunlight, good temperature, unlimited sugar supply. Yes, ma'am? Yeah, in the chloroplast. Like, the actual parts? Like, the actual parts? Yeah. Okay, that probably will be more mastering questions than exam questions. Okay. Yes, ma'am? Yes. By the way, your PBL is on photosynthesis next week because all of you hate photosynthesis. If you can write this stuff out and use it on the test, you should get an 80% or higher. Of all of the exams, the third test this semester, the average is always the highest because the first exam, you don't know what you're getting into with me. The second exam, some people improved, some didn't. The third exam is only two chapters and it's after the withdrawal date and therefore if you're staying, you ask better study, you do well on it. The fourth exam, yes, is cardiovascular respiratory neuro, but it's also during finals week, even though it's a fourth exam, only not a cumulative final and you're all stressed out about finals. Now, across the last, I don't know, nine years I've been teaching this course, there are more hundreds on the third test than any other test. Because it's two chapters and if you can draw this stuff out on the back of one sheet of paper and use it, you should get at least an 80 or higher. Now, I'm going to stop the recording and you can't leave yet.