Bio Chapter 9 PDF

Chapter 9 Life Is Work 1. Living cells require transfusion of energy from outside sources to do stuff. Energy enters through the sun, providing plants with energy to do stuff, the cycle continues, then the energy leaves as heat. 2. The chemical elements however are recycled,...

Chapter 9 Life Is Work 1. Living cells require transfusion of energy from outside sources to do stuff. Energy enters through the sun, providing plants with energy to do stuff, the cycle continues, then the energy leaves as heat. 2. The chemical elements however are recycled, like in photosynthesis Catabolic Pathways yield by oxidizing organic fuels 1. Complex molecules are broken down for energy Catabolic Pathways and Production of ATP 1. Organic molecules have potential energy, due to the arrangement of electrons in bonds. Exergonic reactions provide fuel. Some energy is used, rest dispersed as heat 2. Fermentation is partial degradation of sugars/fuels, but is not very efficient, since it doesn't use oxygen. Aerobic respiration is better, absorbing oxygen with the fuels as reactant. Some prokaryotes use something other than oxygen, but basically do the same thing as aerobic respiration, and are called anaerobic respiration. 3. For aerobic respiration, oxygen gets mixed with organic compounds, usually glucose, to make energy, and release CO2 and water. Glucose breaking down is an exergonic reaction, with the energy change of -686 kcal/mol. 4. Even though this process is catabolic and spontaneous, it does not directly do anything. It is the production of atp that aids in the cell working Redox Reactions: Oxidation and Reduction The Principle of Redox 1. To transfer e- around the cell, redox (oxidation-reduction) reactions literally go through a series of reactions that carry the e- where it needs to go. When e- are lost in a reaction, it is called oxidation, and when they are gained by the opposite side of the reaction, it is called reduction. Easy remember method is Leo Ger (loss of electrons is oxidation, Gain of electrons is reduction) 2. The substance giving up the e- is called the reducing agent, and the thing gaining the e- is called the oxidation agent 3. IDK if i explained the past 2 bullets correctly, if i did then let's go, if not then might have to read book 4. Sometimes the redox reaction might not even mean complete e- transfer, it might just mean that the e- gets pulled towards one reactant more than the other. When methane reacts with oxygen, the methanes e- go closer to the oxygens, thus causing a shift and a technical redox reaction 5. When an e- moves towards a more electronegative element, it loses potential energy, like a ball moving down a hill. Because of this, when trying to move an e- from an electronegative element it requires more energy. The higher electronegativity, more energy needed to remove. Oxidation of Organic Fuel Molecules During Cellular Respiration  1. So the main redox reaction that we're going to talk about is glucose+oxygen creating carbon dioxide, water, energy. The glucose is oxidized, and the oxygen is reduced here. Compounds with lots of hydrogen are preferred in for energy, since they have a lot of easy e- that can get pulled away and release energy.that energy that gets released in the reaction is used for ATP synthesis 2. This process cant just happen with body heat, instead if we swallow the sugar and lower the activation energy via enzymes, it makes it much easier to digest Stepwise Energy Harvest via NAD+ and the Electron Transport Chain 1. We can't just take sugar and use all its energy in one step, instead we cut it up into steps to slowly create ATP from the slowly exuded energy. It works by removing e- in each step of the glucose breakdown, allowing for energy production. The removal of that e- usually has a proton with it, aka a proton and an e- together are a hydrogen atom. But before that, they get handed off to an e- transporter called NAD+ 2. Enzymes called dehydrogenases remove 2 hydrogens from glucose. Then, an NAD+ gets slapped on with a proton and 2 e-. The last step is sending off one H+, or just a proton. The NAD+ now becomes NADH, as it gains 2 e- and an H+. When the e- from glucose goes to NAD+, and makes it NADH, it loses very little energy. The real energy is when it goes from NADH to oxygen, and then that energy can be used for ATP synthesis 3. To understand how the e- makes it from NAD+ to oxygen, we're gonna compare it instead to h2 mixing with o2. If both gasses were combined, and we did a spark, it would blow up. Instead, when we mix the h2 and o2 to get energy, we first get it from organic molecules, which makes it easier to control, and then we strip away the e- in an e- transport 4. The e- transport chain is usually made of proteins built into the inner membrane of eukaryotic cells and the plasma membrane of aerobically respiring prokaryotes. It cascades the electron down in a series of redox reactions until it can eventually allow it to connect with oxygen and hydrogen. 5. The normal transfer of the e- from NADH to oxygen has an energy change of -53 kcal/mol, making it exergonic. The cells slowly this energy with the redox reactions, slowly having more electronegative compounds until it reaches oxygen, so more energy can be released slowly The Stages of Cellular Respiration: A Preview 1. The 3 main metabolic steps are glycolysis, citric acid cycle, and oxidative phosphorylation. Glycolysis doesn't really count inside the cellular respiration portion, since all cells do it, and it actually makes the starting material, pyruvate, for the citric acid cycle. 2. Glycolysis occurs in the cytosol, breaking glucose into 2 pyruvate molecules that get shipped to the citric acid cycle. The citric acid cycle is in the mitochondrial matrix, and oxidizes a derivative of pyruvate into co2. The third step, oxidative phosphorylation,  occurs as atp is synthesized from the steps in citric acid and glycolysis, as energy is taken and used to make atp. It is powered by the redox reaction going on in the ETC 3. oxidative phosphorylation consists of 2 parts, one being electron transport and the other being chemiosmosis. They both occur in the inner membrane of the mitochondria, and in the plasma membrane for bacteria. Oxidative phosphorylation accounts for almost 90% of the ATP produced by respiration. The other 10% is made directly from steps in glycolysis and citric acid cycle, and it is called substrate level phosphorylation. This happens by an enzyme moving a phosphate from a substrate over to ADP, instead of adding an inorganic phosphate 4. Substrate molecules are an organic intermediate during catabolism of glucose. For each molecule of glucose turned into carbon dioxide and water, the cell generates 38 ATP from respiration. Each ATP has 7.3kcal/ mol of free energy. Glycolysis harvests chemical energy by oxidizing glucose to pyruvate 1. Glucose gets split into 3 carbon groups, gets oxidized and jumbled into pyruvate. Glycolysis has 2 steps, the energy investment and the energy payoff. Energy investment uses ATP, energy payoff produces ATP from substrate level phosphorylation, and NAD+ is reduced to NADH by electrons. Net gain from glycolysis is 2 ATP and 2 NADH 2. Glycolysis happens with or without oxygen, but in respiration oxygen is necessary for the pyruvate and NADH to continue on their path to the citric and ox phosphorylation Look at page 168-169 cause I refuse to depict that, maybe if i have time, make sure to study the steps ATP is produced in. The citric acid cycle completes the energy yielding oxidation of organic molecules 1. Glycolysis produces very little energy, the pyruvate has to get broken down further to extract its energy. This happens in the mitochondria or cytosol for pro cells. The pyruvate enters the mitochondria via active transport, then gets turned into acetyl coA. 2. That process of pyruvate turning into acetyl Coa occurs in 3 reactions. First the oxidized carboxylic is removed (coo) and let off as carbon dioxide, leaving the pyruvate as a 2 carbon fragment (acetate). The electrons are removed from that fragment, and slapped onto some NAD+, reducing them into NADH. That acetate is taken, and a coenzymeA is attached to it using a very unstable bond, causing the entire product to become heavily energy reactive. This product is known as acetyl CoA 3. The acetyl CoA is shipped off to the krebs cycle, and used to produce one atp from substrate level phosphorylation. 2 pyruvates create 2 atp, but most of the energy is actually made by transferring e- to the NAD+ and FADH during the cycle 4. The cycle has 8 steps 2 carbons are entering in the reduced form of an acetyl group, and 2 are leaving the oxidized form of a Co2 molecule Acetyl group is from Acetyl CoA, and attaches to oxaloacetate, making citrate, and then it all cycles back to oxaloacetate  5. For each acetyl group, 3 NADH are produced, in steps 3,4, and 8. Instep 6, FAD gains 2 protons and 2 electrons to become FADH2. Step 5 sometimes makes GTP, ATP copycat, can make atp by substrate level phosphorylation, ripping of its phosphate and giving it to ADP 6. The NADH and FADH2 made are used in the etc, which is a part of oxidative phosphorylation During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis 1. So far glycolysis and citric only create 4 atp per glucose molecule, all by substrate level phosphorylation. 2. Now that all the NADH and FADH2 have taken e-, they can be put into the etc to make atp. The PAthway of Electron Transport 1. Etc is on the inner membrane of the mitochondria, or on plasma membrane for pro, and the inner membrane has a bunch of folds called cristae that increase surface area so that thousands of chains of reactions can occur. 2. Most components of the etc are proteins with some prosthetic groups attached to them that help in the catalytic functions of the enzymes 3. Basically a giant gradient of reduction and oxidation, where the electron falls down all these proteins toward a more electronegative neighbor. 4. First we look at the beginning protein complex 1, which starts with the flavoprotein. It accepts the 2 e- from NADH, and becomes reduced. It then passes it to an iron-sulfur protein, and then gets passed to ubiquinone, or q. Q is small and hydrophobic, not a protein. It is individually mobile, so it can move around the membrane instead of just sticking around. 5. After q, it's basically a long line of proteins called cytochromes that have a prosthetic group of heme, essentially iron atoms that donate electrons. Each of these cytochromes has a slightly different electron carrying heme group, until after the cytochrome a3, where oxygen atoms are present and accept the electron. The oxygen also gets hydrogen ions that make water. 6. FADH2 also drops off electrons, but drops them lower on the chain at protein complex 2, and the etc provides ⅓ the amount of ATP when it comes to FADH2 instead of NADH. Chemiosmosis: The energy-coupling mechanism 1. The inner membrane of mitochondria has many proteins called ATP synthase, the enzyme that makes atp from ADP and inorganic phosphates. The synthase is using the already occurring ion gradient to help produce Atp. that is the H+ imbalance on either side of the inner membrane, also being the ph difference between the sides, This way of producing ATP is called chemiosmosis 2. ATp synthase has 4 main parts, each made of multiple polypeptides. Protons attach themselves in such a way to one part( the rotor) that causes the synthase to spin and put together the ADP and inorganic phosphate  3. The way the rotor spins is essential in it either being atp hydrolysis of atp synthesis 4. Basically what's going on is the exergonic reactions on the etc are used to pump protons aka H+ out of the mitochondrial matrix into the intermembrane space. Afterwards, H= wants to get back in, the only way back is through the atp synthase, and so the rotor is able to spin and make the atp 5. The H+ are able to make it out of the mitochondrial matrix to the inner membrane through points in the etc, that accept the protons(H+) and shove them out. This is called the proton motive force. 6. In chloroplasts and prokaryotes, the proton motive force is also used, and in prokaryotes, it is used to move the flagella and pump/dump things over the membrane An Accounting of ATP production by cellular respiration 1. In general, the list goes from glucose, to NADH, to etc, to proton motive force, to creating ATP 2. ATP yield per glucose molecule is 4 from substrate level phosphorylation, and 32-34 from oxidative phosphorylation. Each NADH’s transfer of e- equates to around 3 ATP produced. HOWEVER, some numbers are not exact. One reason is the redox reaction in the etc and the phosphorylation of ATP are not directly coupled. So there is no exact ration 3. This means that it is more generalized, where we must simply infer how the process works. For 1 NADH(technically 2 e-), 10 H+ are shoved out using the proton motive force into the inner membrane. 3-4H+ then enter back into the cell, through the ATP synthase channel to generate 1 ATP. so for every 10 h+ shipped out, 3-4 are shipped in. 10/3=3.3, and 10/4 is 2.5. So for every one NADH, we make an approximate 3 ATP. 4. For FADH2, even though it has the same # of e-. Since those e- are dropped off later in the etc, the etc is unable to pump as much H+ out, making the less ATP, only around 2 ATP. Just think if you were in a race with some random guy, and you get paid based on how far you sprint, if you ran more distance, you made more profit. The random guy started a third of the way there already, so why the hell should he get paid more? Anyway, bad tangent but good analogy i think 5. Another reason for inexactness of how much atp is being produced is the type of thing carrying electrons from NADH produced in the cytosol. It can either go to FAD or Nad+, and depending on which ch it gets handed to , it will again change how much atp is produced. Think Of it like this: you can hand some money to a responsible kid(me ) who will go and drop it off wisely in someone's hands( start of etc), or you can hand it to some dummy(yusuf) who might drop it off to some random guy( next step of etc) and so the guy who got it first can spend it more efficiently. Think that analogy sucked at the end but wtvr idc 6. The last reason is the division of power. The cell needs to bring in pyruvate using the proton motive force too, so it can't dump all its energy into making ATP, but if it did, it could make a total of 38 ATP, instead of 36. The cell can either dump all its effort into  one hw and get a hundred on that and a 0 on something else, or it can split up its energy and do 2 hw but only get a 90 on both 7. So, after all we've been through, we can now understand how efficient respiration is with its 3 steps. It's around 40% efficient in changing the chemical energy of glucose into ATP. the rest is given off as what. In comparison, a car is only about 25% efficient in generating energy from the gasoline it burns. Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen 1. Oxygen is essential for respiration since it helps the etc in oxidative phosphorylation, pulling the e- so they can help pump protons that make ATP later. But some cells can survive without oxygen, via anaerobic respiration and fermentation 2. For anaerobic respiration, instead of oxygen pulling electrons down etc, some other element/compound can be used. For example, some prokaryotes use sulfate to pull the e- down the gradient, and when the protons connect with the ion, H2S is produced, instead of when oxygen connects with the protons and creates water 3. For fermentation, there is no etc or oxygen. Instead what is going on is stuff being oxidized, or losing electrons, to other stuff. Glycolysis is an example of this, where glucose is broken down into pyruvate as e- are lost to NAD+, no oxygen/etc needed. Even though there is no oxidative phosphorylation to produce a lot of atp, it still makes 2 net no matter what 4. However, for this to be feasible, there has to be a way to recycle the NADH after being made in glycolysis so that the cycle can restart again, or else the NADH would stay filled forever and not restart. And that's where the types of fermentation come into play Types of fermentation 1. Fermentation is glycolysis and a way to regenerate NADH aside from dumping e- into the etc. that way the NAD+ can get reused to do more glycolysis and make more atp, even if its just 2 net at a time 2. Alcoholic fermentation turns pyruvate into ethanol. Glycolysis makes the pyruvate, then co2 is dragged off of the pyruvate, making it acetaldehyde. The acetaldehyde is then able to be reduced and turned into ethanol 3. Lactic acid fermentation just reduces pyruvate into lactate, so the NADH is dropping its stuff onto pyruvate and getting recycled Fermentation and Aerobic Respiration 1. Basically everything is the same for fermentation and aerobic respiration up until the pyruvate stage, even using the same e- acceptor (NAD+) but the difference comes from how the NADH can get recycled, and who the final acceptor is. The final acceptor in fermentation is an organic molecule or acetaldehyde, but in aerobic its oxygen. Aerobic is better because it is able to take the energy from pyruvate and use it though 2. Some organisms are obligate anaerobes, which means they can not survive in oxygen, only doing fermentation. Some are facultative anaerobes, where they can make enough ATP through fermentation and aerobic respiration.our muscles are facultative, since they  can turn pyruvate into acetyl coA or make lactate. The rate at which fermentation occurs needs to be fast to match the rate needed that would normally be got from respiration The evolutionary Significance of glycolysis 1. Glycolysis happens in all living things, since it does not require oxygen that early earth's atmosphere did not have. This is simple, but the textbook loves to yap. Campbell when i catch you Glycolysis and the citric acid cycle connect to many other metabolic pathways The Versatility of Catabolism 1. So we don't just come across glucose in nature. Duh. but we do come across a bunch of stuff like proteins, fats, and carbs. We can get stuff like carbs in starch or polysaccharides like glycogen, which can be hydrolyzed into glucose and then used in glycolysis 2. Proteins in excess can get turned into intermediates, by being converted into amino acids, and then turned into intermediates of glycolysis and the citric acid cycle. The cell can excrete the NH3 produced as ammonia or urea. 3. Fats can be turned into glycerol and 3 fatty acids, with glycerol being turned into Glyceraldehyde 3 phosphate., an intermediate of glycolysis. Most of the energy is actually in the fatty acids though, because they have lots of hydrogen and e-, so through beta oxidation the fatty acids can get chopped up into 2 carbon fragments, which enter as acetyl coA. NADH AND FADH2 can also be made from those e- on the chain, and can go to the etc. Fats make around 2 times more atp per gram compared to glucose. Biosynthesis (Anabolic Pathways) 1. When we break stuff down, we can repurpose the parts instead of just eating them as fuel. Instead with amino acids we can add them to our own proteins. But sometimes we need specific molecules that don't come from food. Instead we have to make them by diverting intermediates of cycles like the citric acid, and build off of them. Regulation of Cellular Respiration via Feedback Mechanisms 1. Stuff can stop the making of the same stuff if there's too much stuff. Negative feedback loop as the stuff turns off the reaction making it after a certain point. This also works for catabolism, if the cell is using a lot of something, let's say atp, the process (respiration\) will speed up to match the output needed. Phosphofructokinase, an enzyme in the glycolytic pathway, can be turned off and on easily by many things. After its made stuff, it has to continue down the glycolysis pathway, so it's a good point to turn on or off. 2. It can be inhibited by ATP and citrate, and stimulated by AMP. As ATP builds, the enzyme becomes inhibited and stops working, and if AMP is sensed it will speed up the reaction. Again, if citrate is accumulating, it will stop the enzyme, and if it gets consumed, the enzyme stops. 3. Energy is released not produced from the stuff we eat or wtvr, he just yapping, think he master oogway Thank god, i finished yippee