Bio Ch. 9

How ATP synthase works

1.) H+ ions flowing down their gradient enter a channel in a stator, which is anchored in the membrane. 2.) H+ ions enter binding sites within a rotor, changing the shape of each subunit so that the rotor spins within the membrane 3.) Each H+ ion makes one complete turn before leaving the rotor and passing through a second channel in the stator into the mitochondrial matrix 4.) Spinning of the rotor cases an internal rod to spin as well. This rod extends like a stalk into the knob below it, which is held stationary by part of the stator 5.) Turning of the rod activates catalytic sites in the knob that produce ATP from ADP and inorganic phosphate

Introduction

Catabolic pathways release stored energy by breaking down complex molecules. Energy flows into an ecosystem as sunlight and ultimately leaves as heat, while the chemical elements essential to life are recycled. Photosynthesis generates oxygen and organic molecules that are used by the mitochondria of eukaryotes as fuel for cellular respiration. Respiration breaks this fuel down, generating ATP. ATP drives most cellular work. Respiration's waste products, carbon dioxide and water, are the raw materials for photosynthesis. 3 key pathways of cellular respiration: glycolysis, the citric acid cycle, and oxidative phosphorylation. Fermentation is simpler pathway coupled to glycolysis.

Fermentation, anaerobic respiration, and aerobic respiration

- All 3 use glycolysis to oxidize glucose and other organic fuels to pyruvate, with a net production of 2 ATP by substrate-level phosphorylation. - NAD+ is the oxidizing agent that accepts electrons from food during glycolysis. - In fermentation, the final electron acceptor is pyruvate (lactic acid) or acetaldehyde (alcohol). IN cellular respiration, electrons carried by NADH are transferred to the ETC. In aerobic respiration the final electron acceptor is O2; in anaerobic respiration it's a different electronegative molecule. - Fermentation yields 2 ATP. Aerobic respiration yields up to 32 ATP per glucose molecule. - Obligate anaerobes carry out only fermentation or anaerobic respiration and can't survive in the presence of oxygen, which can actually be toxic if protective systems aren't present in the cell. - Facultative anaerobes can make enough ATP to survive suing either fermentation or respiration. Muscle cells behave as facultative anaerobes. Pyruvate is a fork in the metabolic road that leads to the citric acid cycle under aerobic conditions or lactic acid fermentation under anaerobic conditions. - Early prokaryotes are thought to have used glycolysis to make ATP before oxygen was present in Earth's atmosphere. Cyanobacteria produced O2 as a byproduct of photosynthesis. Glycolysis is the most widespread metabolic pathway among organisms. Glycolysis doesn't require membrane-enclosed organelles.

Chemiosmosis (the energy-coupling mechanism)

-ATP synthase, located in the inner membrane of the mitochondria (plasma membrane for prokaryotes, chloroplast membranes for plants), makes ATP from ADP and inorganic phosphate. Works like an ion pump in reverse by using the energy of an existing hydrogen ion gradient to power ATP synthesis. - ATP synthase is powered by a difference in H+ concentration on opposite sides of the inner mitochondria membrane. - Chemiosmosis: the process in which energy stored in the form of and H+ gradient across a membrane is used to drive cellular work. - ATP synthase is a multisubunit complex with 4 main parts each made of multiple polypeptides. Protons move one by one into binding sites on the rotor, causing it to spin and catalyze ATP production from ADP and inorganic phosphate. - The ETC establishes the H+ gradient, using the flow of electrons from NADH and FADH2 to pump H+ across the membrane from the kitochnorial matrix into the inter membrane space. The H+ has a tendency to move across the membrane, diffusing down its gradient, and the ATP synthases are the only sites providing a route through the membrane for H+. Thus, the energy stored in an H+ gradient across a membrane couples the redox reactions of the ETC to ATP. - Certain parts of the ETC release and accept H+ (from the aqueous solutions inside and surrounding the cell) along with electrons; the transfer of electrons causes this change. Electron carriers are arranged so that H+ is accepted from the mitochondria matrix and deposited in the inter membrane space, resulting in a H+ gradient called a proton-motive force. - Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work. In mitochondria, the energy for gradient formation comes from exergonic redox reactions, and ATP synthesis is the work preformed. Chloroplasts use chemiosmosis to generate ATP during photosynthesis, and light drives the electron flow down the ETC and forms the H+ gradient. Prokaryotes use chemiosmosis to rotate their flagella and pump waste and nutrients across their membrane.

Redox Reactions

- Catabolic pathways decompose organic molecules by transferring electrons during the chemical reactions, releasing energy stored in the organic molecules that is then used to synthesize ATP. - In an oxidation-reduction (redox) reaction, the loss of electrons (substance becomes more positive) is called oxidation and the gain of electrons (substance becomes more negative) is called reduction. - The reducing agent reduces the other substance, and is oxidized itself. The oxidizing agent oxidizes the other substance, and is reduced itself; oxidizing agents are often very electronegative. - Some redox reactions involve the complete transfer of electrons, others change the degree of electron sharing in covalent bonds, e.g. methane combustion. - The more electronegative an atom, the more energy is required to take an electron away from it. An electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative atom. A redox reaction that moves electrons closer to a very electronegative molecule, such as oxygen, releases chemical energy that can be put to work.

Chemiosmosis overview

- Chemiosmosis couples ETC to ATP synthesis. - During the ETC, NADH and FADH2 shuttle high-energy electrons extracted from food during glycolysis and the citric acid cycle into the ETC built into the inner mitochondria membrane. Electrons are passed to a terminal acceptor, O2, forming water. CoQ and Cyt c move electrons between the large complexes. As the complexes shuttle electrons, they pump H+ from the mitochondria matrix into the inter membrane space. Chemical energy is transformed into a proton-motive force, a gradient of H+ across the membrane. - In chemiosmosis, the protons flow down their gradient via ATP synthase, which is built into the membrane and harnesses the proton-motive force to phosphorylate ADP, forming ATP. ETC and Chemiosmosis make up oxidative phosphorylation.

Catabolic pathways

- Compounds that can participate in exergonic reactions, are complex and organic, are rich in potential energy, and therefore act as fuels, are degraded by enzymes to simpler waste products that have less energy. Some energy is used to do work; the rest is dissipated as heat. - Fermentation is a partial degradation of sugars or other organic fuel that occurs without the use of oxygen. - Aerobic respiration is when oxygen is consumed as a reactant along with the organic fuel; the most efficient catabolic pathway. Organic compounds + oxygen -> carbon dioxide + water + energy. - Anaerobic respiration is a process similar to aerobic respiration that harvests chemical energy without oxygen. - Aerobic and anaerobic respiration are both types of cellular respiration. - The breakdown of glucose (C6H12O6) has a free-energy change of -686 kcal per mole of glucose decomposed. - Catabolism is linked to work by a chemical drive shaft: ATP. To keep working, a cell must regenerate its supply of ATP from ADP and inorganic phosphate.

Fermentation

- Consists of glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate. The NAD+ is reused to oxidize sugar by glycolysis, which nets 2 molecules of ATP by substrate-level phosphorylation. - Alchohol fermentation: Pyruvate is converted to ethanol (ethyl alcohol) in two steps- (1) releases CO2 from the pyruvate, which is converted to 2-carbon acetaldehyde; (2) acetaldehyde is reduced by NADH to ethanol, regenerating the supply of NAD+. Carried out in many bacteria, yeast (a fungus). - Lactic acid fermentation: pyruvate is directly reduced by NADH to form lactate (ionized lactic acid), with no release of CO2. Done by certain fungi and bacteria. Used to make cheese and yogurt. Made by human muscle cells when oxygen in scarce and sugar catabolism for ATP production outpaces the muscle's supply of oxygen from the cell, such as during strenuous exercise. May enhance muscle performance. Excess lactate is gradually carried away by the blood to the liver, where it's converted back to pyruvate.

Fermentation v.s. anaerobic respiration

- ETC chain is used in anaerobic respiration but not in fermentation. - Anaerobic respiration occurs in certain prokaryotic organisms that live in oxygen deprived environments. They have an ETC but don't use oxygen as a final electron acceptor; may use sulfate ion. Build up proton-motive force to produce ATP but produce H2S (hydrogen sulfide). - Fermentation harvests chemical energy without oxygen or an ETC. Glycolysis still occurs, producing 2 net ATP by substrate-level phosphorylation. Needs sufficient supply of NAD+ to accept electrons during the oxidation step of glycolysis. So, electrons from NADH are transferred to pyruvate, the end product of glycolysis; this forms NAD+, allowing glycolysis to begin again.

Overview of Cellular Respiration

- Energy flow of cellular respiration: glucose -> NADH -> ETC -> proton-motive force -> ATP - Cellular respiration oxidizes a molecule of glucose to 6 molecules of CO2. - 2 net ATP are formed by substrate-level phosphorylation during glycolysis. 2 net ATP are formed by substrate-level phosphorylation in the citric acid cycle. About 26 or 28 net ATP are forced by oxidative phosphorylation. Glucose can produce a maximum of about 30 or 32 net ATP per glucose. - 3 reasons why we can't state the fact number of ATP generated: (1) the ratio of the number of NADH molecules to ATP isn't a whole number because phosphorylation and the redox reactions aren't directly coupled together; (2) ATP yield varies depending on the type of shuttle used to transport electrons form the cytosol into the mitochnodirion; being passed from NADH to NAD+ generates more ATP than NADH being passed to FAD; (3) The use of proton-motive force generated by the redox reactions of respiration is used for other cellular work. - 34% of the potential chemical energy in glucose is transferred to ATP; percentage varies in different cellular conditions. The rest of the energy stored in glucose is lost as heat. The efficiency of cellular respiration can be regulated, such as in brown fat.

Stepwise energy harvest

- Glucose is broken down in a series of steps (in order to harvest energy more efficiently), each one catalyzed by an enzyme. At key steps, electrons are stripped from the glucose. Each electron travels with a proton, thus as a hydrogen atom; the hydrogen atoms aren't transferred directly to oxygen, but instead are passed first to an electron carrier, a coenzyme called NAD+ (nicotinamide adenine dinucleotide). NAD+ can easily cycle between oxidized and reduced (NADH) states. NAD+ functions as an oxidizing agent during respiration. - Dehydrogenases remove a pair of hydrogen atoms from the substrate (such as glucose), thereby oxidizing it. This enzyme then delivers the 2 electrons with 1 proton to its coenzyme, NAD+; the other proton is released as H+. The 2 electrons reduce NAD+ to NADH. NAD+ is the most versatile electron acceptor in cellular respiration. - H-C-OH + NAD+ ->(dehydrogenase)-> C=O + NADH + H+ - NADH has stored energy that can be tapped to make ATP when the electrons "fall" (closer to the electronegative atoms) in a series of steps down an energy gradient from NADH to oxygen. - An electron transport chain is used to break the fall of electrons to oxygen in several energy-releasing steps. Electron transport chain: consists of a number of molecules, mostly proteins, built into the inner membrane of the mitochondria of eukaryotic cells (and the plasma membrane of respiring prokaryotes). Oxygen captures electrons at the end of this chain along with H+ to form water. (Anaerobic prokaryotes have a final electron acceptor different from O2.) - Electron transfer from NADH to oxygen results in -53 kcal/mol (-222 kJ/mol). Instead of the energy all being released at once, electrons move down the chain from one carrier molecule to the next in a series of redo reactions, losing a small amount of energy with each step until they reach oxygen, the terminal electron acceptor. Each downhill carrier is more electronegative than before. The electrons become more stable as they move down the chain. - Glucose -> NADH -> electron transport chain -> O2.

Redox reactions in cellular respiration

- Glucose is oxidized to carbon dioxide. Oxygen is reduced to water. As electrons lose potential energy along the way, energy is released. - Molecules with hydrogen are usually excellent fuels because their bonds are a source of "hilltop" electrons, whose energy may be released as these electrons "fall" down an energy gradient when transferred to oxygen. - The oxidation of glucose transfers electrons to a lower energy state, liberating energy that becomes available for ATP synthesis. - Carbohydrates and fats are the main energy-yielding foods; they have lots of hydrogen. - The barrier of activation energy holds back the flood of electrons to a lower energy state; otherwise, food molecules would almost instantaneously combine with O2.

Glycolysis

- Glucose, a 6-carbon sugar, is split into two 3-carbon sugars. These smaller sugars are then oxidized and their remaining atoms are rearranged to form two molecules of pyruvate (the ionized form of pyruvic acid). - Can be divided into 2 phases: (1) the energy investment phase, where the cell spends ATP; and (2) the energy payoff phase, where ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose. - Net energy yield is 2 ATP + 2 NADH per glucose molecule. Overall process has 10 steps. Requires investment of 2 ATP to form 2 ADP and 2 phosphates (will be attached to glucose to make it more chemically reactive). Results in formation of 4 ATP, 2 NADH, 2 H+, 2 pyruvate, and 2 H2O. - All carbon originally present in glucose is accounted for in the 2 molecules of pyruvate; no carbon is released as CO2 during glycolysis. Glycolysis occurs with or without O2, but if O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation. - Enzymes: hexokinase, phosphoglucoisomerase, phosphofructokinase, aldolase, isomerase, triose phosphate dehydrogenase, phosphoglycerokinase, phosphoglyceromutase, enolase, and pyruvate kinase.

Electron transport

- Glycolysis and the citric acid cycle yield 4 ATP molecules (2 from glycolysis, 2 from citric acid cycle) per glucose molecule, all by substrate-level phosphorylation. - FADH2 and NADH are electron escorts that link glycolysis and the citric acid cycle to oxidative phosphorylation, which uses energy released by the electron transport chain to power ATP synthesis. - The electron transport chain (ETC) is a collection of molecules embedded in the inner membrane of the mitochondrion in eukaryotic cells (in the plasma membrane of prokaryotic cells). - The inner membrane foldings that form cristae increase surface area and provide space for thousands of copies of the ETC in each mitochondrion. - Electron carrier molecules are placed in row for the series of sequential redox reactions that occur along the ETC. Most components of the chain are proteins, which exist in multiprotein complexes numbered I though IV. Prosthetic groups (nonprotein components essential for the catalytic functions of certain enzymes) are bound tightly to these proteins. - There is a drop in free energy as electrons travel down the ETC. Electron carriers alternate between reduced and oxidized states during ETC as they accept and donate electrons. - Accepting electrons from uphill neighbors with lower affinity for electrons (i.e. less electronegative) = reduction. Passing electrons downhill to more electronegative neighbor = oxidation. - Complex I: Electrons gained from glucose by NAD+ during glycolysis and the critic acid cycle are transferred from NADH to this complex. Flavoprotein. After a redox reaction, flavoprotein returns to its oxidized form as it passes electrons to an iron-sulfur protein, which then passes its electrons to a small hydrophobic nonprotein electron carrier called ubiquinone (Q). Q doesn't reside in a particular complex and is mobile; also called CoQ; only nonprotein in ETC. - Complex II: FADH2 adds its electrons to the ETC from within this complex; done at a lower energy level than for NADH. ETC provides about 1/3 less energy for ATP synthesis for FADH2 then NADH. - Complex III: Made up of cytochromes. Cytochromes have a prosthetic group called a heme group, which has an iron atom that accepts and donates electrons. The ETC has several cytochromes, each a different protein with different electron-carrying heme groups. - Complex IV: Also made up of cytochromes. Cyt a3 is the last cytochrome in ETC, and it passes its electrons to oxygen, which is VERY electronegative. Each O atom also picks up a part of hydrogen ions (protons) from the aqueous solution, neutralizing the -2 charge of the added electrons and forming water. - Overall energy drop (∆G) from NADH to oxygen in 53 kcal/mol. - ETC makes no ATP directly, just eases fall of electrons from food to oxygen, breaking a large free-energy drop into a series of smaller steps that release energy in manageable amounts.

Additional information

- Humans obtain most of their calories in the form of fats, proteins, sucrose and other disaccharides, and starch, a polysaccharide. Many of these compounds can be hydrolyzed to glucose or, in the case of proteins, digested to amino acids. Amino acids can be converted by enzymes into intermediates of glycolysis and the citric acid cycle, but they must undergo deamination (amino groups are removed, and nitrogenous refuse is excreted as ammonia, urea, or other waste products) first. Fats are digested to glycerol and fatty acids (where most of the energy is stored). Glycerol is coveted to an intermediate of glycolysis. Beta oxidation breaks fatty acids into 2-carbon fragments that enter the citric acid cycle as acetyl CoA; FADH2 and NADH are also generated during this process and can enter the ETC. A gram of fat produces more than twice as much ATP as a gram of carbohydrate. - Anabolic, or biosynthetic, pathways don't generate ATP, but consume it. Used to make specific molecules a cell requires that aren't present in food. - Glycolysis and the citric acid cycle function as metabolic interchanges that allow cells stop convert some kinds of molecules to others as a body needs them. - Feedback inhibition (the end product of an anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway) is the most common mechanism for ensuring a cell don'ts waste energy making more of a particular substance than it needs. Control is based mainly on regulating enzyme activity at strategic points in anabolic and catabolic pathways. Allosteric enzymes at certain points in the respiratory pathway respond dot inhibitors and activators that help set the pace of glycolysis and the citric acid cycle (e.g. phosphofructokinase, which is stimulated by AMP and inhibited by ATP and citrate; catalyzes step 3 of glycolysis).

The citric acid cycle

- Oxidizes organic fuel from pyruvate. Pyruvate is broken down to 3 CO2 molecules, which includes the 1 CO2 released during the conversion of pyruvate to acetyl CoA. - Generates 1 ATP per turn via substrate-level phosphorylation, but most chemical energy is transferred to NAD+ and FAD (another coenzyme electron career, flaming adenine dinucleotide, derived from B vitamin Riboflavin) during the redox reactions. The reduced coenzymes, NADH and FADH2, shuttle their cargo of high-energy electrons into the electron transport chain. - Also called tricarboxylic acid cycle or Krebs Cycle. - Most of the ATP produced by respiration results from oxidative phosphorylation, when the NADH and FADH2 produced by the cycle relay the electrons extracted from food to the electron transport chain. This process supplies the necessary energy for the phosphorylation of ADP to ATP. - Has 8 steps, each catalyzed by a different enzyme. 2 carbons enter the cycle in the first step; 2 carbons leave as CO2 in steps 2 and 4. - The oxaloacetate that's regenerated at step 8 is made up of different carbon atoms each time around. - In eukaryotic cells, all the enzymes are located in the mitochondria enzyme, except for the enzyme that catalyzes step 6, which is in the inner mitochondria membrane. - The last 7 steps of the cycle decompose citrate back to oxaloacetate. Citrate is the ionized form of citric acid. - For each acetyl group entering the cycle, 2 NAD+ are reduced to NADH (steps 3, 4, and 8). Electrons are transferred to FAD, which accepts 2 electrons and 2 protons to become FADH2 (step 6). GTP (made in step 5) is similar in structure and function to ATP, and can be used to make ATP or directly power the work in a cell. Some plants, bacteria, and animal cells form an ATP molecule directly by substrate-level phosphorylation in step 5; this is the only step of the cycle where ATP is generated. - Total yield per glucose form the citric acid cycle: 6 NADHs, 2 FADH2s, and the equivalent of 2 ATPs.

Oxidation of pyruvate to acetyl CoA

- When O2 is present, the two pyruvate molecules enter the mitochondria via active transport (because they're charged), where glucose oxidation is completed (process occurs in the cytosol of aerobic prokaryotes). - Pyruvate is converted to acetyl coenzyme A (acetyl CoA) upon entering the mitochondria. This process is carried out by a multienzyme complex called the pyruvate dehydrogenase complex that catalyzes 3 reactions: (1) pyruvate's carboxyl group (--COO-), which is already fully oxidized and just has little chemical energy, is removed and given off as one CO2; (2) the remaining 2-carbon fragment is oxidized, forming acetate (CH3COO-), and the extracted electrons are transferred to NAD+, storing energy in the form of NADH; (3) CoA, a sulfur-containing compound derived from vitamin B, is attached via its sulfur atom to the acetate, forming acetyl CoA, which has high potential energy, is highly exergonic, and is able to yield lower-energy products. - The acetyl group of acetyl CoA enters the citric acid cycle for further oxidation. The CO2 molecule produced will diffuse out of the cell.

The stages of cellular respiration

1. Glycolysis: Produces the starting material for the citric acid cycle. Occurs in the cytosol. Begins the degradation process by breaking glucose into two molecules of pyruvate. 2. Pyruvate oxidation and the citric acid cycle: Pyruvate enters the mitochondrion and is oxidized to acetyl CoA, which enters the citric acid cycle, where glucose is broken down to carbon dioxide. 3. Oxidative phosphorylation: The electron transport chain accepts electrons (typically via NADH) from the breakdown of the first 2 stages, passing these electrons from one molecule to another. Energy released at each step is stored in a form the mitochondria can use to make ATP from ADP; this mode of ATP synthesis is called oxidative phosphorylation because it's powered by the redox reactions of the electron transport chain. Accounts for 90% of ATP generated by respiration. Cellular respiration usually encompasses steps 2 and 3. Inner membrane of the mitochondria is the site of electron transport and chemiosmosis, which together constitute oxidative phosphorylation. A small amount of ATP is formed directly in a few reactions of glycolysis and the citric acid cycle by substrate-level phosphorylation, a mode of ATP synthesis when an enzyme transfer a phosphate group from a substrate molecule to ADP, rather than adding an inorganic phosphate to ADP as in oxidative phosphorylation. For each molecule of glucose, a cel makes up to 32 molecules of ATP, each with 7.3 kcal/mol of free energy.

Steps of the citric acid cycle

1.) Acetyl CoA adds its two-carbon acetyl group (carbon bonded to CH3 and double-bonded to O) to oxaloacetate, producing citrate. CoA-SH is produced as a waste product. The two carbons are relatively reduced in the acetyl CoA form. 2.) Citrate is converted to its isomer, isocitrate, by removal of one water molecule and the addition of another. 3.) Isocitrate is oxidized, reducing NAD+ to NADH. Then the resulting compound loses a CO2 molecule. 4.) Another CO2 is lost, and the resulting compound is oxidized, reducing NAD+ to NADH. The remaining molecule is then attached to coenzyme A by an unstable bond. 5.) CoA is displaced by a phosphate group, which is transferred to GDP, forming GTP, a molecule with functions similar to ATP. GTP can be used to generate ATP. 6.) Two hydrogens are transferred to FAD, forming FADH2 and oxidizing succinate. 7.) Addition of a water molecule rearranges the bonds in the substrate. 8.) The substrate is oxidized, reducing NAD+ to NADH and regenerating oxaloacetate.