Metabolic Diversity in Microorganisms

See if this works. See if it works if I click it up here. Okay, so I'm experimenting with some other capabilities that I found, which is why I was behaving a little differently. Today we're going to do a little work with some of this metabolic material. Just a few questions. But I would like you to get together with people around you, have conversations about them, make sure you understand the correct answer for each. I don't think it's going to reveal the correct answer to you when you're done with this or what other people's votes were. I was messing around with it, trying to figure that out, and I couldn't see it. I will be going around the room answering questions that you have, and I will be peeking to see what you guys are seeing because you've discovered, you work with different ways, maybe discover things I didn't. I just want to understand the behavior of how this works. Regardless, when we're done with the activity, we'll go through it together. And so we're all on the same page. So it's a little practice and application and making sure you're catching some of the things in the textbook work. And then we'll have time for class. So go ahead and start working together. Oh, and you should still be able to send me questions, and I haven't sent right now that other people want to. Oh. How are you feeling now? So the first one is the photo, hetero. That's what I got. I got a photo item. But it says, I'm able to do so many things. No, I know. I put flow in the middle. Wait, did I? Oh, shit. Sorry. Wait, did I? I don't know. It's 80 now. I don't know what I'm doing. That's okay. We can figure it out together. I don't know. Let's get to that together. So, what are you doing? Yeah. Yeah. Yeah, that's it. Can you put a hat around? Yeah. Yeah. Well, it says it uses light, and no light in this photo, and unable to use it for itself is the Hato bacteria. Which one following this correction? The Hato bacteria are photo hetero, so it uses light, but cannot make it its own, that use something or another. Yes, to the left. Thank you. I forgot. I am trying to see if we talk about the pain or the battery. I think we're right on the plug. I am lost. Thank you. Okay. I don't really know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don yes um I don't know. Okay. Light excites the factors. Light excites the keyword, which pumps protons and creates a proton motor. We're not doing the whole thing together. Are you on the phone? I think most of you are done. I realize that I need a way to know when you all are done and because I did things as percentages, which I like better, I couldn't tell the total number. So I added a slide at the end and it lets us do this as a slide just as a way to count who's done. But I think most of you are already done with it by the time I added the slide. So let's go ahead and go through these together and see how this works. So this first question, 89% of you thought that an organism that uses light energy for ATP but then can't use that ATP in order to make its own carbon molecule, its own sugar, is what? It is photo-heterotrophic, and that is correct. Very nicely done on that. This one looks a little bit more tricky. So the helobacteria are photo-heterotrocytes, bacteria rhodopsin, rather than an ETS, rather than an electron transport system, to set up a proton-motor force. So they do set up a proton-motor force. They're this weird organism that's mentioned in the text that reminds us that there's a lot of diversity out there and there's more than one way to solve a problem. And one of the big questions that we've had in biology, that always exists in biology, is what came first? So we've got these really amazing electron transport systems scheme that not only do you have this way of moving electrons and then pairing that to these transport proteins that various different mechanisms depending on the particular protein is effectively transporting a proton from one side to another to separate a battery. It's incredible that all this evolved. But then what's the point? How is any of this useful until you also have a way to make the proton gradient turn into ATP? That's really the thing that matters. So usually the way things work in evolution is you have the solution first and then you make it better and better and better and better. So in other words, it didn't start out as complicated as it is. So look at something like our blood clotting system, for example. We have all these proteins and factors that are involved in making sure our blood clots when it's appropriate and does not clot when it is inappropriate. So there's all these checks and balances. Well, blood clotting is really important So how did you get to the point of having blood clotting? How did you evolve all these schemes without any payoff, without anything to select for it, and then at the end put it all together? Evolution doesn't work that way. So in blood clotting, the hypothesis has been, well, There has to be a really simple way to make blood clot so that you have that and then once you have it you can improve on it and any improvement is selective. And then you go out in the animal world and you survey it and sure enough you find that there are animals that have much more simple blood clotting mechanisms that we do. You can kind of see the starting point. Well the same thing here. There was a hypothesis that said what you really have to have first is leukemia osmosis. Because why would evolution build all these things? Evolution is not intelligent. It doesn't plan for the future. It can't think, I'm going to build this now so that later on I'll be able to do this amazing thing. So the hypothesis is that you have the chemiosmosis first, and then you get better and better and better ways of doing it. So that was the hypothesis. And then eventually we discovered these archi- Halo bacteria, they're called halo bacteria because halo means salt and they grow in these really salty mud flats like you find around San Francisco. And then we call them bacteria because we didn't know about archae. They're actually archae. So they were called salt bacteria. But they've got this really simple system that uses a protein called bacteria redoxin. Here's the way it works. They've got a membrane. And that membrane has this protein in it called bacterial rhodopsin. And this protein, when it gets hit by a photon of light, it causes that protein to change shape in a way that moves a proton from here Over to here and this to just be the outside environment It's why they're restricted to these particular salty conditions that are acidic you have a lot of protein of a lot of protons in there and then they go into the interior of the cell and then they can use that gradient for ATP so they are using light and they are setting up the gradient and they are using for leukemia osmosis They have no electron transport system so you can imagine an ancestor had something like this and then eventually the electron transport system worked in there. Some people have hypothesized that photophosphorylation actually came before cellular respiration, partly for this reason, because we can see this connection. We don't know for sure though. Why am I spending time on this? Why do I give you guys these "random" appearing examples? Well, two reasons. Short term, it's cool. It's a reminder that we have to think outside the box. There's all these ways of solving problems. It's never just one answer. But more to the point, we are going to see this principle again and again in the course. This idea that a stimulus causes a change that has an action. It is the foundation of communication biologically. It is the foundation of all of our senses, how all of our neurons work to sense touch and smell and so forth. And specifically, this word bacteriorhodopsin ends in the word opsin. And opsin is a protein that reacts to light in order to achieve something. We have opsins in our eyes that are tied to our sensory neurons, our photoreceptors. So we spend time on this stuff early on. Not just because it's interesting, although I hope some of you think it is, but because these principles apply so many places. I think I mentioned to you earlier, this whole idea of having a voltage and then letting things go through and it has an outcome, that is how our neurons function. So we're going to see these things again and again. Okay, so back to this question. So which of these statements is correct? Halobacter are primary producers. They are not. Why not? because they're not fixing carbon. So they are not a source of sugar. They can make energy, they can use it for their own purposes, but they are not a source of sugar in terms of the foundation of other things to just live on. Halo bacteria use kidney osmosis to generate ATP? They do. The key, how could you get that right? Proton-motive force. When you see proton-motive force, you see it inside the respirator, you see it in photophosphorylation, it means we're going to do chemiosmosis. So that's going to be correct. Halobacteria generate oxygen. I'm glad nobody picked that one. And then bacteria are adopted as a terminal electron acceptor. Not if we don't have an electron transport system. So that's how you can eliminate that one. So it is going to be this one. Okay, which of the following is correct about photosynthesis? It is a form of chemoautotrophy. No, chemoautotrophy is using energy from chemicals in order to do carbon fixation. Photoautotrophy is using energy from light. So, photoautotrophy is literally another word for photosynthesis. Photosynthesis is the process. If you are a photosynthetic organism, you are photosynthetic. Photo, energy from light. Auto can make your own carbon. It sometimes uses electrons stripped from water. It absolutely does. When it strips electrons from water, what do we call that? Oxygenic phototrophic over plus four or eight degrees. It is found only in plants. No, I'm glad very few of you picked that because it actually evolved in the oxygen form actually evolved in inside of bacteria. And that's where you carry out. That's where plants got it from in the first place. And then we have all these and oxygenic forms. So it was an oxygenic forms do not get their electrons from water and therefore they do not produce oxygen. So it is going to be the second option. It sometimes uses electrons to it from water. Okay, which of the following pathways do you use in electron transport systems? Select all that apply. So we are looking for the ones that specifically have this membrane that they're running electrons through in order to set up a proton-motor force and do chemiosmosis. It's going to be all forms of cellular respiration, and it's going to be the photosynthesis. What about other forms of photophosphorylation? Well, yeah, a lot of them are using electron transport systems too, but if you're doing photosynthesis, you're doing electron transport systems. This guy can't produce enough ATP to fix carbon. Not enough energy production there. Okay, this question about therabreath, which you might have seen in the store. So the therabreath is a mouthwash that claims to use the power of oxygen to invented by Dr. Harold Katz back in 1994 to defeat bad breath. Does it make sense? Some of you, 42%, think, yeah, it does make sense. Bad breath are likely anaerobic and We talked about how oxygen is really toxic to organs, so yeah, it makes sense. And then some of you are like, probably not. It is true that bad blood is caused by anaerobic bacteria, but why would oxygen matter? And then about 20% of you think, no way. This is actually extremely plausible, and there's a lot of evidence that this does work, this therapy does work. So remember, if you're an anaerobic organism, you probably can't really tolerate oxygen much. You might have survived some ability to evolve some ability to survive it, but oxygen is really, really toxic. And here's one way that I can help you remember this. You almost have to use oxygen in order to support the defenses against oxygen. Remember there's this weird thing that we always talk about how aerobic respiration is so efficient and it supports whole-cellularity because you get so much more ATP for every electron. Yeah, that's true, but people have really looked at this and studied reactive oxygen species and the... The massive toll those oxidants take on cells. You guys have heard you should have a diet with rich in antioxidants. It's true. You need to protect yourselves from all these reactive oxygen species that do a lot of damage. They're so damaging they can do things like if you leave your car parked for a long time, they will degrade the rubber on the tires and you get all those little cracks on the bottom. Oxygen is massively destructive. So when people really look at it, they go, yeah, it is true that oxygen boosts the yield, but most of that extra yield probably just has to go to support all of these processes. You're spending energy on this process to protect yourselves from the oxygen. So that's why I said last time, oxygen is both the problem and the solution. It's the source of both. So these anaerobic bacteria, they probably cannot produce enough energy to even tolerate oxygen since they're not doing aerobic respiration. So they tend to be limited to low oxygen conditions, and Dr. Harold Katz looked at this principle and said, maybe what we really should be using, putting in our mouthwash, aside from other possible things, is maybe we should just make sure we're flooding our mouth, all the little pockets of our teeth and gums with oxygen to help kill anaerobes. And it seems like it does work. None of these things are super effective outside of antibiotics, but the data show that it actually works pretty well compared to most other mouthwashes. Okay, so let's say you're digging. Some of you have had this experience. You're playing by a lake, a pond. You're digging down, building your sandcastle, and suddenly the soil turns dark and you smell rotten eggs really bad. I didn't expect you to know the answer to this, but it's something I wanted you to think about and bring up. What is going on here? Well, the answer is you've hit an anoxic zone. The oxygen is not penetrating down there. So oxygen is diffusing in. It's being absorbed, being used by aerobic respiration. Eventually, you go down. There's no oxygen. That's where the anaerobes can live. Why does it smell like rotten egg? because one of the common substrates that anaerobes use for their internal electron acceptor is sulfur compounds. And when they dump electrons into those sulfur compounds, they convert them to compounds like hydrogen sulfide, H2S, and that is the smell of rotten egg. So they're manufacturing that smell by taking sulfur from something that isn't stinky and converting it to a form that is stinky. So you know you've hit the anoxic zone when you get down in there, or at least hypoxic, low enough oxygen that they can now live there. Okay, this one, I had a mistake and you were only able to pick one, so some of you saw the version. Thank you to those of you who let me know about it, and it turns out we can fix it on the fly, which was kind of nice. So these numbers are not going to be accurate, but let's just go through this together. Which of these statements are correct? Only bacteria do fermentation. That is not correct. We also do fermentation. Eukaryotes do it too. The difference is we also do cellular respiration. Fermentation is our backup plant. Another example of fermentation is what yeast do. It's why yeast are useful for baking bread and producing beer, because they do fermentation, specifically alcohol, with carbon dioxide as a byproduct. A carbon dioxide byproduct adds some more to your cellular respiration, so that was a good conclusion. There are no photosynthetic archi. There absolutely are photosynthetic archi. So that one's false. All methanogens are archi. That is correct. Nitrogen fixation occurs among both the bacteria and the archi. That is also correct. We don't know any eukaryotes are able to do nitrogen fixation. So there are no eukaryotic diazotropes that we know of. So this slide was really reminding you about that pull-down menu. And again, when you're memorizing, look for a pattern. Which groups do all these really important metabolic processes? By the way, we've talked about a lot of other metabolic processes. These are the ones I picked because they're very important. Global biogeochemical cycles. They're a big deal. Nitrogen cycle, carbon cycle. Look at the pattern. It's basically everything, both the bacteria and the archaea do it, except methanogenesis. That one's only the archaea. And then the Eukaryotes just do a couple. So if you remember that, all you really have to remember is the one exception, which is Methanogenesis, and then which ones the Eukaryotes do. And then that makes it much easier to keep track of. It also now establishes more important principles, which I always care about more than rote memorization, although, again, acknowledging rote memorization is a skill. Okay, so we do have a solid 25 minutes. What can I help you all with? Take a moment to discuss with each other if that helps, and just start thinking about things that you'd like me to go over with you. I thought there was gonna be a way for me to enable you all to see the questions once we started. Okay, good, you're seeing them there now. I don't know if you can see questions other people are submitting, but we will at least see the ones that I'm putting up to the top. Okay, can I review fermentation once again? Yeah. So the issue is we are going to take electrons out of glucose to use them to produce energy by moving them somewhere else. How are we going to get the electrons out of glucose? Well, a glucose has these, like any organic molecule, has these carbon-carbon bonds. This pen is lousy. We had a good pen last time. Oh, maybe down here. So we have these carbon-carbon bonds. and they have their bounded things like hydrogens and occasionally they're bound to an oxygen with the hydrogen. But these bonds are electrons. We can get the electrons out. So that's what glycolysis is doing. That's what the citric acid cycle is doing after glycolysis. It's breaking the bonds and pulling the electrons out. In the case of glycolysis, the electrons are being pulled out and going into NAD plus turning into NADH. And then we're pairing that with this substrate level phosphorylation. In other words, we're pairing that with, let's use that energy of motion to put a phosphate group on a substrate. And then later on, we'll move that phosphate group to an ADP to make ATP. Fermentation is literally taking that NADH, getting the electrons back out, so that they can go back and pick up. So fermentation is a little side loop that recycles the NAD+ by taking the electrons out. Depending on the kind of fermentation you do, what they all have in common is we're dumping them into a waste product that we can't use anymore anyway. So we broke the glucose, we made a little fragment, we can't use that fragment for anything anyway, we just gotta dump it. Might as well dump the electrons into it first and then get rid of it. Depending on the exact kind of fermentation you do in the process, you produce something like alcohol. That's what yeast and certain bacteria and things do. Or you're producing something like lactic acid. That's what we produce in our muscles when they switch over to fermentation from a really respiration. Can I explain the steps of lactic acid fermentation? I can't. I don't remember the steps. I'm certainly not going to hold you all accountable to the steps. So I would like to think that the reason the questions are coming in slowly is because between the textbook and Wednesday's lecture, I did such a brilliant job explaining this that all of you have already mastered it. Unfortunately, I also know that it's Friday and you all are retired now. So can I go over the Krebs cycle again? So we are not really doing the Krebs cycle. Remember the other name cycle that I want you to start logging in because it's the much more common name now is the citric acid cycle or the carboxylic acid cycle. And what's really nice about those is they have the same acronym, TCA cycle. So almost always at the college level and higher, you're going to hear it called the TCA cycle. Although I think in high school, we still call it the Krebs cycle. And this just reflects, you're going to, you're going to cover this in medicine as well. We used to name a lot of things after the person who discovered it, or, in the case of medicine, often the person who was a victim, like Lou Gehrig's disease, for example, because Lou Gehrig got it. As a body, both in and outside of medicine, science is trying to no longer name things after people, because it doesn't mean anything. the Krebs cycle has to do with TCA, the Calvin Benson cycle has to do with carbon fixation. Let's just give them names and actually describe what they are. So the Krebs cycle is also known as the TCA cycle. The only thing you need to know about it, and I'm not even going to put this on an exam because I didn't really give you much information about it, but just to help you close this loop, when you break sugar, To get electrons out in glycolysis, you still have unbroken sugar bonds. So what the TCA cycle does is it breaks it down even further to get even more electrons out, to get even more ATP. So basically we're digesting it further to get more energy out of it. Ultimately, we break it all the way down to carbon dioxide, a single carbon with two oxygens attached. Now we can't break it any further than that. That's a super polar bond. We're not getting any more electrons out of that. So that's the TCA cycle that's producing the carbon dioxide when we breathe. Why would we expel carbon dioxide? Okay, can I explain the process of the membrane potential? Yes. So when we take protons... and move them across the membrane so that we have more positive charge on one side of the membrane than the other, that is called voltage. Voltage is the term you always hear about with electricity and batteries. In biology, probably actually also in electrical applications, I don't know for sure, but we also call that a membrane potential. Why do we call it a membrane potential? Well, I don't actually know the history of that, but it does make sense to me. If I had to guess, the reason is because this is a membrane, and we have set up potential energy across the membrane. That would be my guess. So it's referring to the fact that we charge a cellular battery across a membrane. So the bigger the membrane potential, the more potential you have to manufacture ATP. Bigger voltage separation to manufacture more ATP. And we're going to find out that this plays out in a really neat way in nervous function. Our neurons are doing this and they're controlling the voltage in order to get different outcomes and such. Can I explain a polar bond and a non-polar bond? Yes. So the first part of the chapter four goes through some basic chemistry. For those of you who are in chemistry, I hope it helps you. But you need to understand some basics to avoid having to memorize everything else. So the chemistry that you're given is very basic, but it really gets at some fundamental issues for why this whole system works. And here is the principle. Electrons achieve a more stable configuration whenever, number one, their negative charges are balanced by positive charges. In other words, we're not an ion. They're also in a better situation when their orbitals are full. So orbitals is something, I will be frank with you, I do not understand. I never understood it in chemistry, and I've never cared enough to try to really figure out why orbitals are the way they are. And I don't know if anyone really knows that. It might be something we just... This is how the universe works. We figure it out, but we don't necessarily know why. Regardless, we've got these protons forming a nucleus. There's three protons in this case. And then around it, we've got these electrons that are in these orbitals. And they're not actually a circle like a planet going around the sun. It's like a three-dimensional space that they occupy. And this first one, this first shell made up of orbitals, can only hold two electrons. If we stop here, what do we have? We have an ion. This has got three protons, two electrons, one extra proton. It's got an additional charge. So it's a cat ion. It has a positive charge. Well, so we're going to need some more electrons to balance this thing out and make it more stable. Well, it turns out that first shell can only hold two. So we have to go out now to a shell that's further out. We're going to put one electron in there. Okay, great. We've just improved the situation because we're now in balance. We're no longer an ion, but now we've created a new problem. Two new problems. Problem number one is this electron is really far away from the protons. It would rather be closer. Problem number two... We don't have enough electrons in our outer shell. We're actually not in balance as far as our shells. It's better when they're full. So the solution to this will be to come next to another... that has the opposite problem. It has the problem of its shell, it's got three and it only needs one more. I shouldn't call it the opposite problem. It also doesn't have its shells full, but this one has one shell that's kind of extra, this one is missing, and they'll form a bond. They'll share their electrons so that this one now can share Three more. This one can share that one. It's actually the same electrons, but they're both sharing it. Okay, so now we can achieve even better stability. Well, what happens if this atom is basically the same kind of atom as that one, or something very similar in its tendency to take electrons? Then we result in a nonpolar bond. Both sides of the bond, the charge distributions are the same. But, and now the protons don't work anymore, so ignore that. But let's say this is carbon and this is hydrogen. That's non-polar because both carbon and hydrogen pull electrons about equally. In other words, they're both the same kind of electron hunger. Carbon, carbon, same thing. But what if this is oxygen? Now all the electrons tend to stay over here. Because they can get in really close to the positive charges, really close to the nucleus. And I don't know why that is, but that's why the periodic table is set up the way it is. It reflects these kinds of properties that we may be able to measure. So they're still sharing the electrons. Everyone is still in balance, but really oxygen, the electrons tend to stay around oxygen a lot more. So at any given moment in time, typically, I would say on average, you will find a partial positive charge here and a partial negative charge here, a partial positive charge here, because the electrons tend to stay here. And as weird as it sounds, when we don't like ions, it's not a situation of ionization. They're sharing electrons. They're both in balance. But because the electrons can get closer here, this is a more stable bond. So when you lie at a campfire, you're literally taking non-polar carbon-carbon-hydrogen bonds and you're moving the electrons into carbon dioxide, which is carbon-oxygen bonds, it's energetically favorable to move them that way. So that's why you're learning about polarity, nonpolar-polar. On Monday, we're going to talk about the properties of water. Polarity is a big deal, and why water behaves the way it does. So hopefully that will help close the loop as well. But this is the concept of nonpolar polarity. and why these energetics work out the way they do. Why oxygen is so good at killing electrons and not giving them up and such. Okay, I already explained the role of voltage in the electron transport system and chemionosis. Okay, that's basically the same question. Let's go through that again real quick. Voltage is separate, establishing the gradient. Protons on the outside. positive charge on the outside relative to the inside or vice versa. Doesn't matter which side has it in the application. That is the proton-motor force. The electron transport system is what does that. As the electrons move through, it moves the protons across. And the chemiosmosis is letting those protons go through ATP synthase channel to manufacture ATP. So it's an electrical current that you allow to flow through a protein, and the current is converted to chemical energy. Can I explain again why halobacteria aren't primary producers? Because they do not fix carbon. They cannot make their own sugar. They have to consume it from somebody else, just like we do. So we're not primary producers either. Is ETC the same as ETS? Yeah, it would be. Electron Transport Chain. We prefer the term electron transport system now because a chain can be a little bit misleading. It's not like a perfect chain. Although it's not very misleading, honestly. You'll see the same thing with food web versus food chain. That one, the food chain is a lot more misleading. Food web is definitely more accurate there. But yeah, it's the same idea. Can I explain the difference between aerobic and anaerobic cellular respiration? We're going to run electrons through electron transport chain, electron transport system. At some point, the electron has to go somewhere. Otherwise, our system gets all full of electrons. So we're going to dump it into something. If we dump it into oxygen, we're doing aerobic respiration. If we dump it into something other than oxygen, it doesn't matter what it is, it's anything other than oxygen, it's anaerobic respiration. And there's a lot of compounds that some prokaryotes have evolved to use in anaerobic respiration. Some of them are using sulfur compounds, some of them are using nitrogen compounds. Some of them are using literally iron, changing the valence of iron and such. I'm less interested in you guys memorizing that diversity. If you ever took a course in microbial physiology, we get really exposed to it and all the energetics of each different chain. I just want you to understand there's aerobic and there's everything else and what that key demarcating difference is. And by the way, I want to use this as an opportunity again to talk about exam strategy and principles. Let's say on an exam, I said an organism is using a nitrogen compound, I might even give you the name of the compound, as its terminelectron acceptor in a chemiosmotic scheme. What can you say about this organism? I know from experience that that can create panic. anything about this particular model you don't need to I'm describing something that's not oxygen look for an option that talks about an aerobic respiration right this is what I mean about don't try to memorize your drink it's another example memorize your way through look at what you know look at the principal and I'll apply it to a situation you haven't encountered before remember in college ultimately that's the skill we're really training you for Yes, there's a lot of memorization. There's a lot of stuff you just need to know, especially in this class, and I recognize that. But whenever you get a question, just think, what do I know about this? Don't worry about what you don't know about. What do I know about it? And if you've done your work, you know what you need to know to get it. Okay, can I explain water influx? So what it is, is water coming into something. Why it happens, we're going to cover in Chapter 7, when we talk about transport, which will include water uptake and movement by the wind. Okay, these are the questions that I've already answered. Are you guys done? Thank you for all of your hard work.

But I would like you to get together with people around you, have conversations about them, make sure you understand the correct answer for each. I don't think it's going to reveal the correct answer to you when you're done with this or what other people's votes were. I was messing around with it, trying to figure that out, and I couldn't see it. I will be going around the room answering questions that you have, and I will be peeking to see what you guys are seeing because you've discovered, you work with different ways, maybe discover things I didn't. I just want to understand the behavior of how this works.

Regardless, when we're done with the activity, we'll go through it together. And so we're all on the same page. So it's a little practice and application and making sure you're catching some of the things in the textbook work. And then we'll have time for class. So go ahead and start working together.

Oh, and you should still be able to send me questions, and I haven't sent right now that other people want to. Oh. How are you feeling now?

So the first one is the photo, hetero. That's what I got. I got a photo item. But it says, I'm able to do so many things.

No, I know. I put flow in the middle. Wait, did I?

Oh, shit. Sorry. Wait, did I?

I don't know. It's 80 now. I don't know what I'm doing. That's okay. We can figure it out together.

I don't know. Let's get to that together. So, what are you doing? Yeah. Yeah.

Yeah, that's it. Can you put a hat around? Yeah.

Yeah. Well, it says it uses light, and no light in this photo, and unable to use it for itself is the Hato bacteria. Which one following this correction? The Hato bacteria are photo hetero, so it uses light, but cannot make it its own, that use something or another.

Yes, to the left. Thank you. I forgot. I am trying to see if we talk about the pain or the battery.

I think we're right on the plug. I am lost. Thank you.

Okay. I don't really know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don't know if this works out.

I don't know if this works out. I don't know if this works out. I don yes um I don't know.

Okay. Light excites the factors. Light excites the keyword, which pumps protons and creates a proton motor.

We're not doing the whole thing together. Are you on the phone? I think most of you are done. I realize that I need a way to know when you all are done and because I did things as percentages, which I like better, I couldn't tell the total number.

So I added a slide at the end and it lets us do this as a slide just as a way to count who's done. But I think most of you are already done with it by the time I added the slide. So let's go ahead and go through these together and see how this works. So this first question, 89% of you thought that an organism that uses light energy for ATP but then can't use that ATP in order to make its own carbon molecule, its own sugar, is what? It is photo-heterotrophic, and that is correct.

Very nicely done on that. This one looks a little bit more tricky. So the helobacteria are photo-heterotrocytes, bacteria rhodopsin, rather than an ETS, rather than an electron transport system, to set up a proton-motor force.

So they do set up a proton-motor force. They're this weird organism that's mentioned in the text that reminds us that there's a lot of diversity out there and there's more than one way to solve a problem. And one of the big questions that we've had in biology, that always exists in biology, is what came first?

So we've got these really amazing electron transport systems scheme that not only do you have this way of moving electrons and then pairing that to these transport proteins that various different mechanisms depending on the particular protein is effectively transporting a proton from one side to another to separate a battery. It's incredible that all this evolved. But then what's the point? How is any of this useful until you also have a way to make the proton gradient turn into ATP? That's really the thing that matters.

So usually the way things work in evolution is you have the solution first and then you make it better and better and better and better. So in other words, it didn't start out as complicated as it is. So look at something like our blood clotting system, for example. We have all these proteins and factors that are involved in making sure our blood clots when it's appropriate and does not clot when it is inappropriate. So there's all these checks and balances.

Well, blood clotting is really important So how did you get to the point of having blood clotting? How did you evolve all these schemes without any payoff, without anything to select for it, and then at the end put it all together? Evolution doesn't work that way. So in blood clotting, the hypothesis has been, well, There has to be a really simple way to make blood clot so that you have that and then once you have it you can improve on it and any improvement is selective. And then you go out in the animal world and you survey it and sure enough you find that there are animals that have much more simple blood clotting mechanisms that we do.

You can kind of see the starting point. Well the same thing here. There was a hypothesis that said what you really have to have first is leukemia osmosis.

Because why would evolution build all these things? Evolution is not intelligent. It doesn't plan for the future.

It can't think, I'm going to build this now so that later on I'll be able to do this amazing thing. So the hypothesis is that you have the chemiosmosis first, and then you get better and better and better ways of doing it. So that was the hypothesis.

And then eventually we discovered these archi- Halo bacteria, they're called halo bacteria because halo means salt and they grow in these really salty mud flats like you find around San Francisco. And then we call them bacteria because we didn't know about archae. They're actually archae.

So they were called salt bacteria. But they've got this really simple system that uses a protein called bacteria redoxin. Here's the way it works. They've got a membrane. And that membrane has this protein in it called bacterial rhodopsin.

And this protein, when it gets hit by a photon of light, it causes that protein to change shape in a way that moves a proton from here Over to here and this to just be the outside environment It's why they're restricted to these particular salty conditions that are acidic you have a lot of protein of a lot of protons in there and then they go into the interior of the cell and then they can use that gradient for ATP so they are using light and they are setting up the gradient and they are using for leukemia osmosis They have no electron transport system so you can imagine an ancestor had something like this and then eventually the electron transport system worked in there. Some people have hypothesized that photophosphorylation actually came before cellular respiration, partly for this reason, because we can see this connection. We don't know for sure though.

Why am I spending time on this? Why do I give you guys these "random" appearing examples? Well, two reasons. Short term, it's cool. It's a reminder that we have to think outside the box.

There's all these ways of solving problems. It's never just one answer. But more to the point, we are going to see this principle again and again in the course.

This idea that a stimulus causes a change that has an action. It is the foundation of communication biologically. It is the foundation of all of our senses, how all of our neurons work to sense touch and smell and so forth. And specifically, this word bacteriorhodopsin ends in the word opsin.

And opsin is a protein that reacts to light in order to achieve something. We have opsins in our eyes that are tied to our sensory neurons, our photoreceptors. So we spend time on this stuff early on.

Not just because it's interesting, although I hope some of you think it is, but because these principles apply so many places. I think I mentioned to you earlier, this whole idea of having a voltage and then letting things go through and it has an outcome, that is how our neurons function. So we're going to see these things again and again.

Okay, so back to this question. So which of these statements is correct? Halobacter are primary producers.

They are not. Why not? because they're not fixing carbon. So they are not a source of sugar.

They can make energy, they can use it for their own purposes, but they are not a source of sugar in terms of the foundation of other things to just live on. Halo bacteria use kidney osmosis to generate ATP? They do. The key, how could you get that right? Proton-motive force.

When you see proton-motive force, you see it inside the respirator, you see it in photophosphorylation, it means we're going to do chemiosmosis. So that's going to be correct. Halobacteria generate oxygen.

I'm glad nobody picked that one. And then bacteria are adopted as a terminal electron acceptor. Not if we don't have an electron transport system. So that's how you can eliminate that one. So it is going to be this one.

Okay, which of the following is correct about photosynthesis? It is a form of chemoautotrophy. No, chemoautotrophy is using energy from chemicals in order to do carbon fixation.

Photoautotrophy is using energy from light. So, photoautotrophy is literally another word for photosynthesis. Photosynthesis is the process. If you are a photosynthetic organism, you are photosynthetic. Photo, energy from light.

Auto can make your own carbon. It sometimes uses electrons stripped from water. It absolutely does. When it strips electrons from water, what do we call that?

Oxygenic phototrophic over plus four or eight degrees. It is found only in plants. No, I'm glad very few of you picked that because it actually evolved in the oxygen form actually evolved in inside of bacteria.

And that's where you carry out. That's where plants got it from in the first place. And then we have all these and oxygenic forms.

So it was an oxygenic forms do not get their electrons from water and therefore they do not produce oxygen. So it is going to be the second option. It sometimes uses electrons to it from water.

Okay, which of the following pathways do you use in electron transport systems? Select all that apply. So we are looking for the ones that specifically have this membrane that they're running electrons through in order to set up a proton-motor force and do chemiosmosis. It's going to be all forms of cellular respiration, and it's going to be the photosynthesis. What about other forms of photophosphorylation?

Well, yeah, a lot of them are using electron transport systems too, but if you're doing photosynthesis, you're doing electron transport systems. This guy can't produce enough ATP to fix carbon. Not enough energy production there. Okay, this question about therabreath, which you might have seen in the store.

So the therabreath is a mouthwash that claims to use the power of oxygen to invented by Dr. Harold Katz back in 1994 to defeat bad breath. Does it make sense? Some of you, 42%, think, yeah, it does make sense. Bad breath are likely anaerobic and We talked about how oxygen is really toxic to organs, so yeah, it makes sense. And then some of you are like, probably not.

It is true that bad blood is caused by anaerobic bacteria, but why would oxygen matter? And then about 20% of you think, no way. This is actually extremely plausible, and there's a lot of evidence that this does work, this therapy does work.

So remember, if you're an anaerobic organism, you probably can't really tolerate oxygen much. You might have survived some ability to evolve some ability to survive it, but oxygen is really, really toxic. And here's one way that I can help you remember this. You almost have to use oxygen in order to support the defenses against oxygen. Remember there's this weird thing that we always talk about how aerobic respiration is so efficient and it supports whole-cellularity because you get so much more ATP for every electron.

Yeah, that's true, but people have really looked at this and studied reactive oxygen species and the... The massive toll those oxidants take on cells. You guys have heard you should have a diet with rich in antioxidants.

It's true. You need to protect yourselves from all these reactive oxygen species that do a lot of damage. They're so damaging they can do things like if you leave your car parked for a long time, they will degrade the rubber on the tires and you get all those little cracks on the bottom. Oxygen is massively destructive.

So when people really look at it, they go, yeah, it is true that oxygen boosts the yield, but most of that extra yield probably just has to go to support all of these processes. You're spending energy on this process to protect yourselves from the oxygen. So that's why I said last time, oxygen is both the problem and the solution.

It's the source of both. So these anaerobic bacteria, they probably cannot produce enough energy to even tolerate oxygen since they're not doing aerobic respiration. So they tend to be limited to low oxygen conditions, and Dr. Harold Katz looked at this principle and said, maybe what we really should be using, putting in our mouthwash, aside from other possible things, is maybe we should just make sure we're flooding our mouth, all the little pockets of our teeth and gums with oxygen to help kill anaerobes. And it seems like it does work. None of these things are super effective outside of antibiotics, but the data show that it actually works pretty well compared to most other mouthwashes.

Okay, so let's say you're digging. Some of you have had this experience. You're playing by a lake, a pond.

You're digging down, building your sandcastle, and suddenly the soil turns dark and you smell rotten eggs really bad. I didn't expect you to know the answer to this, but it's something I wanted you to think about and bring up. What is going on here? Well, the answer is you've hit an anoxic zone.

The oxygen is not penetrating down there. So oxygen is diffusing in. It's being absorbed, being used by aerobic respiration. Eventually, you go down.

There's no oxygen. That's where the anaerobes can live. Why does it smell like rotten egg?

because one of the common substrates that anaerobes use for their internal electron acceptor is sulfur compounds. And when they dump electrons into those sulfur compounds, they convert them to compounds like hydrogen sulfide, H2S, and that is the smell of rotten egg. So they're manufacturing that smell by taking sulfur from something that isn't stinky and converting it to a form that is stinky. So you know you've hit the anoxic zone when you get down in there, or at least hypoxic, low enough oxygen that they can now live there. Okay, this one, I had a mistake and you were only able to pick one, so some of you saw the version.

Thank you to those of you who let me know about it, and it turns out we can fix it on the fly, which was kind of nice. So these numbers are not going to be accurate, but let's just go through this together. Which of these statements are correct? Only bacteria do fermentation.

That is not correct. We also do fermentation. Eukaryotes do it too. The difference is we also do cellular respiration. Fermentation is our backup plant.

Another example of fermentation is what yeast do. It's why yeast are useful for baking bread and producing beer, because they do fermentation, specifically alcohol, with carbon dioxide as a byproduct. A carbon dioxide byproduct adds some more to your cellular respiration, so that was a good conclusion.

There are no photosynthetic archi. There absolutely are photosynthetic archi. So that one's false. All methanogens are archi. That is correct.

Nitrogen fixation occurs among both the bacteria and the archi. That is also correct. We don't know any eukaryotes are able to do nitrogen fixation. So there are no eukaryotic diazotropes that we know of. So this slide was really reminding you about that pull-down menu.

And again, when you're memorizing, look for a pattern. Which groups do all these really important metabolic processes? By the way, we've talked about a lot of other metabolic processes. These are the ones I picked because they're very important.

Global biogeochemical cycles. They're a big deal. Nitrogen cycle, carbon cycle.

Look at the pattern. It's basically everything, both the bacteria and the archaea do it, except methanogenesis. That one's only the archaea.

And then the Eukaryotes just do a couple. So if you remember that, all you really have to remember is the one exception, which is Methanogenesis, and then which ones the Eukaryotes do. And then that makes it much easier to keep track of. It also now establishes more important principles, which I always care about more than rote memorization, although, again, acknowledging rote memorization is a skill. Okay, so we do have a solid 25 minutes.

What can I help you all with? Take a moment to discuss with each other if that helps, and just start thinking about things that you'd like me to go over with you. I thought there was gonna be a way for me to enable you all to see the questions once we started. Okay, good, you're seeing them there now.

I don't know if you can see questions other people are submitting, but we will at least see the ones that I'm putting up to the top. Okay, can I review fermentation once again? Yeah. So the issue is we are going to take electrons out of glucose to use them to produce energy by moving them somewhere else. How are we going to get the electrons out of glucose?

Well, a glucose has these, like any organic molecule, has these carbon-carbon bonds. This pen is lousy. We had a good pen last time.

Oh, maybe down here. So we have these carbon-carbon bonds. and they have their bounded things like hydrogens and occasionally they're bound to an oxygen with the hydrogen. But these bonds are electrons.

We can get the electrons out. So that's what glycolysis is doing. That's what the citric acid cycle is doing after glycolysis. It's breaking the bonds and pulling the electrons out. In the case of glycolysis, the electrons are being pulled out and going into NAD plus turning into NADH.

And then we're pairing that with this substrate level phosphorylation. In other words, we're pairing that with, let's use that energy of motion to put a phosphate group on a substrate. And then later on, we'll move that phosphate group to an ADP to make ATP. Fermentation is literally taking that NADH, getting the electrons back out, so that they can go back and pick up. So fermentation is a little side loop that recycles the NAD+ by taking the electrons out.

Depending on the kind of fermentation you do, what they all have in common is we're dumping them into a waste product that we can't use anymore anyway. So we broke the glucose, we made a little fragment, we can't use that fragment for anything anyway, we just gotta dump it. Might as well dump the electrons into it first and then get rid of it.

Depending on the exact kind of fermentation you do in the process, you produce something like alcohol. That's what yeast and certain bacteria and things do. Or you're producing something like lactic acid.

That's what we produce in our muscles when they switch over to fermentation from a really respiration. Can I explain the steps of lactic acid fermentation? I can't. I don't remember the steps.

I'm certainly not going to hold you all accountable to the steps. So I would like to think that the reason the questions are coming in slowly is because between the textbook and Wednesday's lecture, I did such a brilliant job explaining this that all of you have already mastered it. Unfortunately, I also know that it's Friday and you all are retired now. So can I go over the Krebs cycle again?

So we are not really doing the Krebs cycle. Remember the other name cycle that I want you to start logging in because it's the much more common name now is the citric acid cycle or the carboxylic acid cycle. And what's really nice about those is they have the same acronym, TCA cycle. So almost always at the college level and higher, you're going to hear it called the TCA cycle.

Although I think in high school, we still call it the Krebs cycle. And this just reflects, you're going to, you're going to cover this in medicine as well. We used to name a lot of things after the person who discovered it, or, in the case of medicine, often the person who was a victim, like Lou Gehrig's disease, for example, because Lou Gehrig got it.

As a body, both in and outside of medicine, science is trying to no longer name things after people, because it doesn't mean anything. the Krebs cycle has to do with TCA, the Calvin Benson cycle has to do with carbon fixation. Let's just give them names and actually describe what they are. So the Krebs cycle is also known as the TCA cycle. The only thing you need to know about it, and I'm not even going to put this on an exam because I didn't really give you much information about it, but just to help you close this loop, when you break sugar, To get electrons out in glycolysis, you still have unbroken sugar bonds.

So what the TCA cycle does is it breaks it down even further to get even more electrons out, to get even more ATP. So basically we're digesting it further to get more energy out of it. Ultimately, we break it all the way down to carbon dioxide, a single carbon with two oxygens attached. Now we can't break it any further than that.

That's a super polar bond. We're not getting any more electrons out of that. So that's the TCA cycle that's producing the carbon dioxide when we breathe.

Why would we expel carbon dioxide? Okay, can I explain the process of the membrane potential? Yes. So when we take protons...

and move them across the membrane so that we have more positive charge on one side of the membrane than the other, that is called voltage. Voltage is the term you always hear about with electricity and batteries. In biology, probably actually also in electrical applications, I don't know for sure, but we also call that a membrane potential.

Why do we call it a membrane potential? Well, I don't actually know the history of that, but it does make sense to me. If I had to guess, the reason is because this is a membrane, and we have set up potential energy across the membrane.

That would be my guess. So it's referring to the fact that we charge a cellular battery across a membrane. So the bigger the membrane potential, the more potential you have to manufacture ATP.

Bigger voltage separation to manufacture more ATP. And we're going to find out that this plays out in a really neat way in nervous function. Our neurons are doing this and they're controlling the voltage in order to get different outcomes and such. Can I explain a polar bond and a non-polar bond?

Yes. So the first part of the chapter four goes through some basic chemistry. For those of you who are in chemistry, I hope it helps you.

But you need to understand some basics to avoid having to memorize everything else. So the chemistry that you're given is very basic, but it really gets at some fundamental issues for why this whole system works. And here is the principle. Electrons achieve a more stable configuration whenever, number one, their negative charges are balanced by positive charges. In other words, we're not an ion.

They're also in a better situation when their orbitals are full. So orbitals is something, I will be frank with you, I do not understand. I never understood it in chemistry, and I've never cared enough to try to really figure out why orbitals are the way they are. And I don't know if anyone really knows that. It might be something we just...

This is how the universe works. We figure it out, but we don't necessarily know why. Regardless, we've got these protons forming a nucleus.

There's three protons in this case. And then around it, we've got these electrons that are in these orbitals. And they're not actually a circle like a planet going around the sun.

It's like a three-dimensional space that they occupy. And this first one, this first shell made up of orbitals, can only hold two electrons. If we stop here, what do we have?

We have an ion. This has got three protons, two electrons, one extra proton. It's got an additional charge. So it's a cat ion.

It has a positive charge. Well, so we're going to need some more electrons to balance this thing out and make it more stable. Well, it turns out that first shell can only hold two. So we have to go out now to a shell that's further out. We're going to put one electron in there.

Okay, great. We've just improved the situation because we're now in balance. We're no longer an ion, but now we've created a new problem.

Two new problems. Problem number one is this electron is really far away from the protons. It would rather be closer.

Problem number two... We don't have enough electrons in our outer shell. We're actually not in balance as far as our shells.

It's better when they're full. So the solution to this will be to come next to another... that has the opposite problem. It has the problem of its shell, it's got three and it only needs one more.

I shouldn't call it the opposite problem. It also doesn't have its shells full, but this one has one shell that's kind of extra, this one is missing, and they'll form a bond. They'll share their electrons so that this one now can share Three more.

This one can share that one. It's actually the same electrons, but they're both sharing it. Okay, so now we can achieve even better stability.

Well, what happens if this atom is basically the same kind of atom as that one, or something very similar in its tendency to take electrons? Then we result in a nonpolar bond. Both sides of the bond, the charge distributions are the same. But, and now the protons don't work anymore, so ignore that.

But let's say this is carbon and this is hydrogen. That's non-polar because both carbon and hydrogen pull electrons about equally. In other words, they're both the same kind of electron hunger. Carbon, carbon, same thing. But what if this is oxygen?

Now all the electrons tend to stay over here. Because they can get in really close to the positive charges, really close to the nucleus. And I don't know why that is, but that's why the periodic table is set up the way it is. It reflects these kinds of properties that we may be able to measure.

So they're still sharing the electrons. Everyone is still in balance, but really oxygen, the electrons tend to stay around oxygen a lot more. So at any given moment in time, typically, I would say on average, you will find a partial positive charge here and a partial negative charge here, a partial positive charge here, because the electrons tend to stay here.

And as weird as it sounds, when we don't like ions, it's not a situation of ionization. They're sharing electrons. They're both in balance. But because the electrons can get closer here, this is a more stable bond. So when you lie at a campfire, you're literally taking non-polar carbon-carbon-hydrogen bonds and you're moving the electrons into carbon dioxide, which is carbon-oxygen bonds, it's energetically favorable to move them that way.

So that's why you're learning about polarity, nonpolar-polar. On Monday, we're going to talk about the properties of water. Polarity is a big deal, and why water behaves the way it does.

So hopefully that will help close the loop as well. But this is the concept of nonpolar polarity. and why these energetics work out the way they do. Why oxygen is so good at killing electrons and not giving them up and such.

Okay, I already explained the role of voltage in the electron transport system and chemionosis. Okay, that's basically the same question. Let's go through that again real quick.

Voltage is separate, establishing the gradient. Protons on the outside. positive charge on the outside relative to the inside or vice versa.

Doesn't matter which side has it in the application. That is the proton-motor force. The electron transport system is what does that. As the electrons move through, it moves the protons across.

And the chemiosmosis is letting those protons go through ATP synthase channel to manufacture ATP. So it's an electrical current that you allow to flow through a protein, and the current is converted to chemical energy. Can I explain again why halobacteria aren't primary producers?

Because they do not fix carbon. They cannot make their own sugar. They have to consume it from somebody else, just like we do. So we're not primary producers either. Is ETC the same as ETS?

Yeah, it would be. Electron Transport Chain. We prefer the term electron transport system now because a chain can be a little bit misleading.

It's not like a perfect chain. Although it's not very misleading, honestly. You'll see the same thing with food web versus food chain.

That one, the food chain is a lot more misleading. Food web is definitely more accurate there. But yeah, it's the same idea. Can I explain the difference between aerobic and anaerobic cellular respiration?

We're going to run electrons through electron transport chain, electron transport system. At some point, the electron has to go somewhere. Otherwise, our system gets all full of electrons.

So we're going to dump it into something. If we dump it into oxygen, we're doing aerobic respiration. If we dump it into something other than oxygen, it doesn't matter what it is, it's anything other than oxygen, it's anaerobic respiration. And there's a lot of compounds that some prokaryotes have evolved to use in anaerobic respiration. Some of them are using sulfur compounds, some of them are using nitrogen compounds.

Some of them are using literally iron, changing the valence of iron and such. I'm less interested in you guys memorizing that diversity. If you ever took a course in microbial physiology, we get really exposed to it and all the energetics of each different chain. I just want you to understand there's aerobic and there's everything else and what that key demarcating difference is.

And by the way, I want to use this as an opportunity again to talk about exam strategy and principles. Let's say on an exam, I said an organism is using a nitrogen compound, I might even give you the name of the compound, as its terminelectron acceptor in a chemiosmotic scheme. What can you say about this organism?

I know from experience that that can create panic. anything about this particular model you don't need to I'm describing something that's not oxygen look for an option that talks about an aerobic respiration right this is what I mean about don't try to memorize your drink it's another example memorize your way through look at what you know look at the principal and I'll apply it to a situation you haven't encountered before remember in college ultimately that's the skill we're really training you for Yes, there's a lot of memorization. There's a lot of stuff you just need to know, especially in this class, and I recognize that.

But whenever you get a question, just think, what do I know about this? Don't worry about what you don't know about. What do I know about it?

And if you've done your work, you know what you need to know to get it. Okay, can I explain water influx? So what it is, is water coming into something. Why it happens, we're going to cover in Chapter 7, when we talk about transport, which will include water uptake and movement by the wind. Okay, these are the questions that I've already answered.

Are you guys done? Thank you for all of your hard work.

Transcript for:Metabolic Diversity in Microorganisms

Transcript for:
Metabolic Diversity in Microorganisms