No. Julia, Frank, Julia. no yeah Alexia sorry did you always sit here okay sorry Julia thought in this section Katie Griefer Katie All right guys, good afternoon. Let's go ahead and get started. All right, so if you haven't already scanned the attendance, today we are going to just finish the last section of chapter 6 and then we are going to jump into chapter 7. This is where we start delving into some of the...
these more complex processes. We're gonna be talking about cellular respiration. That's something, that's how cells harvest energy.
And so you guys are working on this in the labs this week and next week, so. Guys, can we try to keep it a little bit quieter here? Thanks.
All right. So chapter six, we're just going to finish off with the metabolism section. And then we are going to go through the majority of chapter seven. Hopefully today we'll get through the first four sections.
And so chapter seven is on cellular respiration. And so I really like how the book actually splits it into sections where cellular respiration is. isn't just one thing or one reaction, it's multiple things. Things happen in different parts of the cell, so just try to stay on top of it as I go through it, and we'll continue on with the rest of cellular respiration next, or on Friday.
But going back to metabolism for a second, we left off over here, we were talking about inhibitors, and they are substances that bind to the enzyme and decrease its activity. So there's There's two types, competitive and non-competitive inhibitors. And so a competitive inhibitor will interfere with the active site where the substrate has to bind, and therefore it doesn't allow the substrate to bind.
And a non-competitive inhibitor binds to an allosteric site, so another site on that enzyme that changes the shape of the enzyme so that the substrate cannot bind. So this allosteric term you'll be seeing a little bit more of, and so it just means it's another site on the enzyme. on the enzyme, that's not the active site.
And there are allosteric substrates that can either inhibit the activity of the enzyme or they can promote it. So there's differences there, but this example here is inhibition. And so all of the different chemical reactions that are carried out in an organism's body, that's what metabolism is.
So usually you might think of metabolism as when you're eating a meal, When you eat something and you digest it, you metabolize it, it's actually all the series of different reactions that happen in your body to harvest energy, break down molecules, make up molecules, all of that is metabolism. And reactions can be anabolic or catabolic. So an anabolic reaction or anabolism basically means that you are expending energy to build up molecules.
You're putting in energy. basically build something. So if you want to build, I don't know, a house, you got to put in some energy to do so. A catabolic reaction or catabolism means that you are harvesting energy or yielding energy.
You have an output of energy and that is by breaking down molecules. So the way that I remember this is anabolic starts with an A and adding starts with an A. So you're basically adding all of these components together.
By putting in energy, you're adding energy as well, and so then you have them bonded together to form the molecule. You're building up the molecule from these subunits. Catabolism, I think of cats, of course.
So I think of if you have a glass vase right here sitting on your counter and you have a cat at home, the cat's going to want to paw at it until it falls off. And so basically that's going to break, and there's going to be a release of energy. So you're harvesting energy.
by breaking down molecules. That's how I remember it. If it helps you, great. If not, that's fine.
And so a lot of reactions actually occur in a sequence. We call that a biochemical pathway. And essentially here, what I'm showing you is there's four enzymes here in the phospholipid bilayer membrane.
And the first enzyme has this first substrate, that's a circle, it goes in, but then it comes out as a triangle, so it's an intermediate substrate for enzyme 2. So then this will bind enzyme 2, it comes out as a square, so it's specifically going to bind with enzyme 3. So the product of one reaction is the substrate for the next enzyme. So usually there are many different steps that have to take place in different organelles. And so these reactions occur in a sequence.
And so that's kind of what cellular respiration is. It's a bunch of different reactions that encompasses enzymes, biochemical pathways, cannibalism, catabolism, redox reactions. So everything that we've learned so far...
far is going to kind of come together to explain cellular respiration. All right, and lastly I want to introduce you to this term called feedback inhibition, where similarly here we have three enzymes and each substrate becomes an intermediate substrate for the next one. And so eventually, if you make this end product and you don't want to just keep making it and wasting your resources, the cell actually stops or has mechanisms in place to stop making that end product. product so it's really advantageous for the cell to be only active when their products are needed so as the end product of the pathway increases in concentration the more product that is that is there means that it'll probably end up binding to an allosteric site as you see here and in the pathway and then it causes that to change shape so it can't bind normal substrates anymore.
So it shuts down the pathway and raw materials and energy are not wasted. So another example of feedback Inhibition in the context of like humans and human health, when a baby is being breastfed, basically if the baby stops like sucking for milk, it ends up your body just, the woman's body will not produce milk anymore. So you need the baby to want the milk for it to continue to be produced in the body.
So that's an example of like a feedback loop there. But that's, so yeah, but you guys just have to. you know know that the end product have getting really large and concentration in the cell isn't really advantageous unless it's needed so the cell can stop making the product by having that end product become the substrate for that allosteric site any questions Okay, so how are you guys finding the videos?
Are they helpful? Okay, I see a lot of nods. Yeah, so these are all going to be up on Blackboard as well.
So I'll play this one. Many of the enzyme-catalyzed reactions that occur in a cell, such as those involved in the biosynthesis of an amino acid, are carried out in a specific sequence called a biochemical pathway. In such pathways, the product of one reaction becomes the substrate for the next reaction.
If the end product of a pathway, such as an... amino acid becomes available in the environment, it is unnecessary and wasteful for the cells to continue to produce the product. Cells, therefore, have the ability to shut down a pathway when it is not needed.
In feedback inhibition, the end product of the pathway reacts with the first enzyme that is unique to the pathway. The reaction occurs at a site on the enzyme that is different from the active site, called the allosteric site. When the product binds to the allosteric site, the enzyme is released. The enzyme undergoes a conformational change and can no longer react with its substrate. There is no substrate for subsequent steps in the pathway and the final product is no longer synthesized.
Does that make sense? All right, great. So we're going to jump right in.
So cellular respiration, we're doing this in lab this week. If you've had lab yesterday, if not, you'll do it tomorrow. And we're going to continue it on next week.
as well. So cellular respiration is when you have glucose plus oxygen and then you produce carbon dioxide and water and energy in the form of heat and ATP. So over here we have glucose a six carbon molecule usually that is consumed in food molecules and then it'll undergo a series of reactions this is just kind of like a quick outline of what happens it undergoes a series of redox reactions releases cellular energy in the form of ATP just by showing you this is cellular respiration anabolic or catabolic You guys can shout it out loud. Catabolic.
Yeah, catabolic. Does anyone disagree? Alright, so yeah, it's catabolic because you are breaking down a glucose molecule and you are producing ATP.
So, easy there. So cellular respiration is a series of reactions. You start off with glycolysis.
You make pyruvate from that. You oxidize the pyruvate, and then it moves into the citric acid cycle. There's electrons and proton gradients that form. So we'll talk about all of that. But just to kind of give you a little bit more background, the way that organisms obtain their energy is classified as a cell.
and is termed respiration. So they can be classified in two ways, either as autotrophs or heterotrophs. So this is based on how they obtain energy, not food.
So autotrophs are able to produce their own organic molecules through photosynthesis, so auto, they have autonomy, they can do it on their own. And then heterotrophs live on organic compounds produced by other organisms. But all organisms will use cellular respiration to. obtain energy from organic molecules. Either they make their own or they live on the organic molecules from other organisms.
And cellular respiration is going to be a series of reactions and so I want to just I'll remind you of some terms that we learned already. They're going to come up now a lot more. Oxidation is the loss of electrons.
Reduction is the gain of electrons. The way to remember this is Leo the lion says ger, loss of electrons, oxidation. gain of electrons reduction. Another term I want to introduce is dehydrogenation.
Basically, it's the loss of a hydrogen atom because dehydrogenation, so loss of hydrogen. But A hydrogen atom is the first element on the periodic table. It's going to have one proton.
It's going to have one electron, right? So if you lose it, then there's going to be a lost electron as well that's accompanying the proton. So just keep that in mind. And so we'll come back to this in a few slides.
But to give you an overview, what I'm calling here is this is aerobic respiration. respiration. So aerobic respiration means that it's happening in the presence of oxygen. Anaerobic is without oxygen, in the absence of oxygen.
And so eukaryotic cells in some aerobic prokaryotes, some prokaryotic bacteria, can produce the vast majority of their ATP this way in the aerobic respiration. Generally, cells will convert glucose and oxygen to carbon dioxide. and water and use the energy that's released.
That energy is held in electrons so all that the electrons that are being transferred through those redox reactions that energy then is released to make ATP. So it involves a complex series of reactions that remove energetic electrons and pass them eventually through an electron transport chain and so moving forward when I talk about cellular respiration the details of this process are going to be covered in in eukaryotes, so when it's aerobic. Because there's another kind that's anaerobic, and we'll talk a lot more about that in microbiology if you take that next semester.
So we're gonna start by just going through this first part, glycolysis. And so you'll notice that glycolysis is not, this is the mitochondria, this is the powerhouse of the cell, which is where ATP is generated. But glycolysis actually happens in the cytoplasm, it doesn't happen it's not in the mitochondria yet there's stuff that needs to happen in order for those products to be moved into the mitochondria and to make more ATP so a quick overview like Glycolysis just means you're splitting glucose.
So here we have a six-carbon molecule. This is glucose. And the general overview of just the outcome of glycolysis is that you're converting one glucose molecule, a six-carbon molecule, to two pyruvate molecules. Each pyruvate molecule has three carbons.
And this whole pathway is a 10-step pathway. In a couple slides, I'll break it down into two parts. So the first part is glycolysis.
five steps and the second five steps. The net production, the amount of ATP produced, that is basically two because there's ATP that needs to be put in as well so the net production, the amount that's produced overall, so you do on the product side how much ATP minus how much you put in as a reactant and you end up with two being produced overall. So that's done by by substrate level phosphorylation. I'm not gonna talk too much about that right now, but you also need to know that there's two ATP molecules produced and there's also two NADH molecules that are produced by the reduction of NAD+.
So the reduction of NAD plus means, Leo the lion says gerb, the gaining of electrons is a reduction. So if NAD plus gains electrons, then it's not gonna have any more positive charge because the. electrons are negatively charged so you end up adding electrons and protons and making NADH so that's where that's coming from but I'll explain that a little bit more further but it overviews that glucose 6 carbon molecule converting to pyruvate which is three carbons there's two pyruvate molecules the 10-step pathway occurs in the cytoplasm and net production of just that section that the glycolysis section is 2 ATP into NADH And so another really just important thing is, you know, when we talk about glycolysis and splitting glucose, we've said this before, glucose is the preferred source of energy for cells, you know, and we constantly have to make it. There's so many different pathways to help make sure that we are you know taking glucose and making something of it that is going to be really efficient and beneficial for the cells glucose molecules can be dismantled in many ways but primitive organisms actually evolved in glucose catabolizing process that will release enough free energy to drive the synthesis of ATP in these enzyme-coupled reactions.
So this happened evolutionarily through primitive organisms, and so it's a really important process to know for this class and for others. Alright, so here's a quick video. Cells derive energy from the oxidation of nutrients such as glucose. The oxidation of glucose to pyruvate occurs through a series of steps called glycolysis.
The energy released during these oxidation reactions is used to form a benzene triphosphate, ATP, the energy currency of the cell. The initial steps in glycolysis are the addition of two phosphates to the glucose molecule at the expense of two molecules of ADP. The result is a six-carbon sugar diphosphate molecule and two low-energy adenosine diphosphate molecules, or ADP.
This six-carbon sugar diphosphate molecule is then split into two three-carbon molecules. Each of the three carbon molecules is converted through a series of steps. pyruvate. During these reactions, electrons are transferred to the coenzyme NAD plus to form NADH, and ATP is formed.
Under aerobic conditions, the pyruvate is further oxidized to yield more ATP, and under anaerobic conditions, the pyruvate is converted into lactic acid. Alright, any questions on that? So you're saying that glucose is outside of the mitochondria?
Yeah, it's still in the cytoplasm. And there's two ATPs that are from there? Yeah. Yeah, so that's a good point because we always say mitochondria is the powerhouse of the cell.
That's where all the ATP is generated. There's actually ATP that's generated elsewhere, but the majority of the ATP is generated in the mitochondria, so that's why. Anything else?
So glycolysis, another word for it is glycolytic pathway. So I said there's 10 steps, and you're going from glucose to 2-pyruvate molecules. ATP, but what's happening in between those.
So the first half consists of five sequential reactions that convert one molecule of glucose into two molecules of G3P. It's another three carbon compound. We're not at pyrolysis. yet. And so these reactions actually require the expenditure of ATP.
You have to actually use ATP to do this. So if you see over here you're putting in ATP to get to that G3P which is I believe right here. G3P. So you have to put in some ATP to get there. And then the second half consists of five more reactions that convert that G3P into pyruvate and that's where you end up yielding energy.
So you end up having four ATPs that are being generated in the second half. So that's why we have a net yield of two ATP molecules, because you have two that are put in and four that come out. So four minus two, you have a net output of two. That's what I was trying to explain earlier. Does that make sense?
Okay. So back to this for a second. We're also trying to make sure we think about where that energy is coming from in order to make the ATP, and that is happening through these redox reactions. these oxidation reduction reactions. So I have it kind of, I literally have the glossary definition here of what NAD is.
It's nicotinamide adenine dinuclide, NAD. It's a molecule that becomes reduced to NADH as it carries high energy electrons from oxidized molecules and delivers them to ATP producing power. ...in the cell.
So NADPH, when NADP plus ends up getting reduced to NADPH, that NADPH holds all that energy of the electrons and then it gives it to... the molecules that need to make ATP. So it's like an intermediate that carries the energy for the molecule that needs to make the ATP. So this is all an enzyme catalyzed reaction, so kind of similar to what we were talking about. We have an energy-rich molecule here.
This is the substrate, and it has two protons on it. That will bind here. NAD plus is actually a cofactor.
We didn't really talk much about them, but it's just another factor that binds to the enzyme. So this enzyme needs two substrates. It's not binding to an allosteric site or anything like that.
It's just a cofactor. And so basically the energy-rich molecule and the NADP. NAD plus bind and then you have this oxidation reduction reaction where two electrons and a proton are transferred to NAD plus forming NADH. The second proton is donated to the solution. So we'll talk about that.
The video that I'm going to show you next is going to help explain that better. But then the NADH will diffuse away and then it can donate the electrons to the molecules that need to make ATP. Alright, let's see this. Cells obtain energy during cellular respiration by oxidizing food molecules such as glucose.
The energy derived from these oxidation reactions is used to form ATP. Oxidation can be defined as the removal of hydrogens from a molecule. Since a hydrogen consists of a proton and an electron, a proton and an electron are removed during oxidation.
Whenever a molecule is oxidized, hydrogen is removed. Another molecule must be reduced, hydrogen is added to it. During an oxidation-reduction reaction in the cell, an enzyme is involved in transferring the hydrogen proton plus electron to a coenzyme called NAD+.
This enzyme has a binding site for both the substrate and NAD+. Once the substrate is removed, the NAD+. and NAD plus are bound with the enzyme, the hydrogen is transferred from the substrate to the NAD plus. In other words, the substrate is oxidized, loses the hydrogen, and the NAD plus is reduced to NADH. As with all enzyme-mediated reactions, once the reaction is complete, the products separate from the enzyme and the enzyme can be used again.
NADH, a high-energy electron carrier, diffuses away and is available. to donate the hydrogen to other molecules. Alright, any questions on that? I'll give you a second to let it sink in. Can you guys hear me okay in the back?
Okay. Alright, so in order for respiration to continue, the NADP, or I keep saying P because I'm thinking of photosynthesis, NAD plus has to be regenerated. So, for glycolysis to continue. The NADH has to be recycled back to NAD+. And there's two ways that this could happen.
And obviously those two ways are dependent on oxygen, like I said before. Aerobic respiration means oxygen is available. and oxygen is that final electron acceptor. So if you remember back to electronegativity in chapter 2, oxygen has a high affinity for electrons so that's where this is now being used. That affinity for electrons makes it a really strong electron acceptor from the NADH.
This produces a significant amount of ATP which is you know really good for the cell that's what they want or wants. and The second type of this recycling back to NAD plus is anaerobic respiration or we call it fermentation. It occurs when oxygen is not available and usually it's an organic molecule that's the final electronic step.
or not oxygen because obviously oxygen is not available. Fermentation is really important. That's how the yeast can be used to make beer and wine. And so there's also a lot of bacteria in our gut that undergo anaerobic respiration or fermentation that produce a lot of really important metabolites and short chain fatty acids that are good for health.
But that's just a tangent that I'm going on. But for the rest of this class, we're going to be talking about it in the context of aerobic respiration and the presence of oxygen. So we've gone through glycolysis, we've made pyruvate.
Now when oxygen is present, pyruvate usually is oxidized to acetyl-CoA, or acetyl-CoA, which... then enters the mitochondria here, and that's where it enters the citric acid cycle. So the citric acid cycle has also been simultaneously called the...
Krebs cycle or the tricarboxylic acid cycle. Krebs is just the name of the person I think that identified it. And tricarboxylic acid or TCA cycle is another one you may have heard. But that's all the same thing.
In this class, I'll be referring to it as citric acid cycle or Krebs cycle because one of the videos calls it that. But this is aerobic respiration. So usually when oxygen is not present, pyruvate is then reduced in order to oxidize.
NADH back to NAD+, that's through fermentation. But at this point we are, we have the pyruvate and in order for it to enter the citric acid cycle, it has to go through a step of pyruvate oxidation and that's in the mitochondria. This is when it goes to the mitochondria. So another quick overview of me kind of saying the same thing. In the presence of oxygen and green, the pyruvate gets shuttled into the citric acid cycle.
but there has to be this oxidation step where it becomes acetyl CoA before it can do that. Whereas without oxygen you just have the NADH being reduced and there's just other processes. This is the ethanol, this is one of those products that's provided when you have pyruvate and then you end up with an alcohol.
So we're going to focus on the part with oxygen and that's where pyruvate is being oxidized to acetyl-CoA. So this is a eukaryotic cell. This is happening... in the mitochondria and so this part here is important because this requires a multi-enzyme complex called pyruvate dehydrogenase so pyruvate is actively transported into the mitochondria for the rest of the processes of cellular respiration.
This multi-enzyme complex, if you remember, it's just a bunch of subunits of enzymes that work together to form a molecular machine. And usually unwanted side reactions are prevented, and all reactions are controlled as a unit. And so that's what this pyruvate dehydrogenase enzyme complex is called. That's what's catalyzing this pyruvate oxidation reaction.
Remember the term dehydrogenation, that's what this is all about. We're talking about removing a hydrogen, moving electrons, and so a lot of that begins to happen here. Pyruvate holds a lot of energy that needs to be harvested.
And cells do this in two steps. The first step is the oxidation of pyruvate. The second step is the citric acid cycle. So because pyruvate just holds so much energy, it can't just run through and get to the citric acid cycle and just harvest all that energy.
The cell splits it into these two steps. The first is this oxidation step, where each 3-carbon pyruvate molecule produces... one carbon dioxide molecule, one NADH molecule, and one acetyl CoA molecule.
So in this case here we are in the mitochondria and you have pyruvate and then you have the NAD plus being reduced to become NADH. So now NADH has a lot of energy because it's holding those electrons and you have the release. of CO2 and then you end up with acetyl CoA.
It's just acetyl with a coenzyme attached to it. So if pyruvate's a three carbon molecule and acetyl CoA is a two carbon molecule, where did the other carbon go? We don't know. Think about it.
Pyruvate, each pyruvate is a three carbon molecule and you end up with acetyl CoA. And acetyl CoA is a two carbon molecule. The CoA is just coenzyme A, don't confuse that with a carbon. But there's two carbons there. So where did that third carbon go that was in pyruvate?
It's got to go somewhere, it doesn't just disappear. Yeah? Was it released from the...
Yeah, and what does it become released into? What does it become? Like where is it now?
CO2. There you go. You guys, it's right there. This is CO2. So that's just something to keep straight because you're always counting carbons and making sure you're going, you know, you're going sequentially in a reaction and you can account for all of them.
So now, acetyl-CoA can proceed to the citric acid cycle. And the thing that a lot of books probably should include more of is that acetyl-CoA is the molecule that links glycolysis in the cytoplasm and the reactions of the citric acid cycle in the mitochondria. I could very well see this being a quiz or a test question. Any questions? Alright.
So, the next step, again, pyruvate holds a lot of energy, and the second step is through, to harvest that energy is the citric acid cycle, and again, we're still in the mitochondria here. And then this basically oxidizes the acetyl group in the acetyl CoA, so that two carbon molecule. It occurs in the mitochondria, and it's a biochemical pathway. It's a cycle. that keeps going continuously and it's split it's nine steps but we split that into three kind of segments and so you don't really need to know the little details of everything that's happening in those nine steps I learned it that way and I found that it was harder to retain information and remember why glycolysis was important for ourselves and respirations important because I was so honed in on the details that I just forgot after the exam so you guys should know the main details but I'm not going to have you guys memorize every single little thing.
And so the three steps are, the first one is you have the acetyl-CoA. That acetyl group ends up being added to an oxaloacetate, which is a four-carbon molecule, to make citrate, which is a six-carbon molecule. That citrate gets rearranged and decarboxylation, so you're losing carbon dioxide.
You're eventually making carbon dioxide because you're losing a carbon molecule and it's becoming carbon dioxide. And then you have to regenerate oxaloacetate so that this cycle can continue and it can bind to acetyl-CoA and then make another six-carbon molecule and so on. I mentioned that the citric acid cycle is also called the tricarboxylic acid cycle or TCA cycle.
That's just because, FYI, citrate is a... carbon tri-carboxylic acid so that's where that name came from but just an FYI so this video kind of helps show that and not overwhelm people with all the details During glycolysis, one molecule of glucose is broken down into two molecules of pyruvate. A two-carbon fragment of pyruvate is then used to form acetyl-CoA.
During the conversion of pyruvate to acetyl-CoA, carbon dioxide is produced and a molecule of NADH is formed by the reduction of NADH. NAD+. The acetyl-CoA enters the Krebs cycle, which occurs in the mitochondrion of eukaryotes or the cytoplasm of bacteria and archaea. For the Krebs cycle, the two-carbon acetyl portion of one acetyl-CoA is transferred to a four-carbon molecule known as oxaloacetate, producing a six-carbon compound called citrate.
The CoA carrier molecule is released. Carbon dioxide is then released from the six-carbon molecule, forming a five-carbon compound. In this step, this carbon compound is oxidized, transferring a hydrogen and an oxygen. electron to NAD plus to form NADH.
Next, a second oxidation and decarboxylization occurs, again producing NADH and carbon dioxide. In addition, a molecule of ATP is produced. As a result of these reactions, a four-carbon molecule is formed in the Krebs cycle.
Finally, this four-carbon molecule is further oxidized to form a third NADH and one NADH. These reactions regenerate the oxaloacetate, the four-carbon molecule that initially reacted with acetyl-CoA. It is for this reason that this metabolic pathway is referred to as a cycle.
Let's consider the overall yield from the Krebs cycle from one molecule of glucose. Each glucose molecule is broken down into two pyruvate molecules during glycolysis. Then, each pyruvate is converted to acetyl-CoA, which enters the Krebs cycle.
Thus, for each glucose molecule, the Krebs cycle must complete two full cycles to completely break down the two pyruvate molecules. One cycle generates two molecules of CO2, three molecules of NADH, one molecule of FADH2, and one ATP molecule. Therefore, the total yield from one glucose molecule is 4. CO2, 6 NADH, 2 FADH2, and 2 ATP.
So why is he saying that the total yield from two cycles, like why do we need two cycles? Did you guys catch that? To break down the two pyruvate molecules that come from one glucose molecule. So that's two full cycles is the one glucose molecule being broken down fully.
So yeah. Does that make sense? Okay.
So I'll leave you with that. Please review this before next week because we're just going to keep moving on with the rest of the details. It's just going to get more and more detail-oriented.
So review everything before Friday, and we'll finish up then.