AP General Biology Unit 3 Notes

Chapter 8 An Introduction to Metabolism 8.1 AN ORGANISM’S METABOLISM TRANSFORMS MATTER AND ENERGY, SUBJECT TO THE LAWS OF THERMODYNAMICS 1. Metabolism is the collection of chemical reactions that occur in an organism. 2. Enzymes catalyze reactions in intersecting metabolic pathways, which can be divided into catabolic pathways (the degradative process that releases energy by breaking down complex molecules>simple molecules) or anabolic pathways (consumes energy to synthesize a complex molecule from simpler molecules). 3. Energy is the capacity to cause change/do work. Kinetic energy is associated with motion and includes thermal energy associated with random motion of molecules. Heat is thermal energy in transfer from one substance to another. Potential energy is the energy that matter possesses as a result of its location, including chemical energy possessed by a molecule due to its structure. 4. The First Law of Thermodynamics, or the conservation of energy, states that energy cannot be created or destroyed, only transformed. The Second Law states that spontaneous processes (those requiring no outside input of energy/energetically favorable) increase the entropy (measure of molecular disorder) of the universe. 5. Living organisms are in closed systems; the second law of thermodynamics states that some energy is released as heat, hence the entropy of any closed system increases. 8.2 THE FREE-ENERGY CHANGE OF A REACTION TELLS US WHETHER OR NOT THE REACTION OCCURS SPONTANEOUSLY 1. Free energy, in short terms, is energy that can do work under cellular conditions (uniform temp and pressure). 2. The change in free energy during biological processes (ΔG) is directly related to enthalpy change (ΔH) and the change in entropy temperature in Kelvin (ΔS). ΔG=ΔH−TΔS 3. A spontaneous process occurs with no energy input, in which free energy decreases and the stability of the system increases. At maximum stability, the system is at equilibrium and cannot do work. 4. In an Exergonic spontaneous chemical reaction (net release of free energy), the products have less energy than the reactants (-ΔG). 5. Endergonic nonspontaneous chemical reactions require an input of energy (absorb surrounding free energy). The products have more energy than the reactants. The addition of starting materials and the removal of end products prevent metabolism from reaching equilibrium. 8.3 ATP POWERS CELLULAR WORK BY COUPLING EXERGONIC REACTIONS TO EXERGONIC REACTIONS 1. A cell does 3 kinds of work: a. Chemical Work: endergonic reactions and anabolic pathways b. Transport Work: active transport of substances across cell membranes against gradient w/protein c. Mechanical Work: contraction of muscle cells, movement of chromosomes during cellular reproduction> ATP binds covalently to motor proteins then hydrolyzed, causing shape change to move motor protein forward 2. ATP is the cell’s energy currency. Hydrolysis of its terminal phosphate yields ADP and Phosphate, and releases free energy. This release of energy is used to perform cellular work. 3. Energy Coupling is the use of energy from an exergonic process to drive an endergonic reaction. Moreover, the exergonic process of ATP hydrolysis (yields ADP and inorganic phosphate) drives endergonic reactions by transfer of a phosphate group to specific reactants, forming a phosphorylated intermediate (molecule w/ phosphate group covalently bound; more reactive=less stable than unphosphorylated molecule). 4. ATP Hydrolysis Change in free energy: ATP+ H2O³ADP+Ⓟ1 ΔG=−7.3kcal/mol(−30.5kJ/mol) 5. ATP is able to be regenerated through catabolic pathways. It is a renewable source-- the free energy required to phosphorylate ADP comes from exergonic breakdown reactions/catabolism. 6. ATP Cycle: shuttling of inorganic phosphate and energy; it couples the cell’s exergonic processes to the endergonic ones. Chapter 10 Photosynthesis 10.1 PHOTOSYNTHESIS CONVERTS LIGHT ENERGY TO THE CHEMICAL ENERGY OF FOOD 1. Photosynthetic enzymes and other molecules are grouped together in a biological membrane, enabling the necessary series of chemical reactions to be carried out efficiently. 2. Photosynthesis is summarized as: SG #1: 6 CO2 + 6 H2O + Light Energy > C6H12O6 + 6 O2 SG #2: Reactants= CO2, H2O Light energy; Products= sugar and O2 3. In Eukaryotic Autotrophic cells, photosynthesis occurs in chloroplasts (mostly found in mesophyll--leaf cells specialized for photosynthesis), organelles containing thylakoids (flattened membranous sacs of chlorophyll in membranes). Column stacks of thylakoids form grana. 4. Carbon dioxide enters the leaf and oxygen exits through microscopic pores called stomata. 5. Chloroplasts split water into hydrogen and oxygen, incorporating the electrons of hydrogen into sugar molecules. Photosynthesis is a redox process: H2O is oxidized, and CO2 is reduced. The light reactions in the thylakoid membranes split water, releasing O2, producing ATP, and forming NADPH. 6. The Calvin Cycle in the stroma forms sugar from CO2, using ATP for energy and NADPH for reducing power. 3 CO2 + 6 NADPH + 5 H2O + 9 ATP ³ glyceraldehyde-3-phosphate (G3P) + 2 H+ + 6 NADP+ + 9 ADP + 8 Pi SG#3: Reactants= CO2, NADPH, H2O, ATP; Products= G3P, H+, NADP+, ADP, Pi 10.2 THE LIGHT REACTIONS CONVERT SOLAR ENERGY TO THE CHEMICAL ENERGY OF ATP AND NADPH 1. Light is a form of electromagnetic energy. Visible light includes the wavelengths that drive photosynthesis. A pigment absorbs light of specific wavelengths-- chlorophyll a being the main photosynthetic pigment in plants. Alternative pigments absorb different wavelengths of light and pass the energy on to chlorophyll a. 2. SG #4: The wavelengths that are most effective for photosynthesis are violet-blue and red light, while green light is the least effective because its energy level is not precise enough. 3. A pigment goes from a ground state to an excited state (unstable) when a photon of light boosts one of the pigment’s electrons to a higher-energy orbital. Electrons from isolated pigments tend to fall back to the ground state, giving off heat and/or light. 4. A photosystem is composed of a reaction-center complex surrounded by light-harvesting complexes that funnel the energy of photons to the reaction-center complex. When a special pair of reaction-center chlorophyll molecules absorbs energy, one of its electrons is boosted to a higher energy level and transferred to the primary electron acceptor. Photosystem II contains P680 chlorophyll a molecules in the reaction-center complex; photosystem I contains P700 molecules. Linear electron flow during the light reactions uses both photosystems and produces NADPH, ATP, and oxygen. 5. SG #5: Electrons pass from photosystem II to photosystem I in an electron transport chain. Light strikes antenna pigments in photosystem I; these pigments transfer the energy to the reaction center chlorophyll molecule of photosystem I. The reaction center chlorophyll releases two energized electrons, which are replaced by the electrons from photosystem II. In photosystem I, energy from sunlight energizes a pair of electrons in the reaction center (replaced by a pair of electrons from photosystem II) and these are passed to molecules of NADP+ to reduce them to NADPH. This molecule carries the electrons (and potential energy) to the carbon reactions of photosynthesis. 6. Cyclic electron flow employs only one photosystem, producing ATP but no NADPH or oxygen. 7. During chemiosmosis in mitochondria/chloro, electron transport chains generate an H+ gradient across a membrane. ATP synthase uses this proton-motive force to make ATP. 10.3 THE CALVIN CYCLE USES THE CHEMICAL ENERGY OF ATP AND NADPH TO REDUCE CO2 TO SUGAR 1. Calvin cycle is anabolic, building carbohydrates from smaller molecules and consuming energy. It spends ATP as an energy source, and consumes NADPH as a reducing power. 2. Calvin cycle occurs at the stroma using electrons from NADPH and energy from ATP. One molecule of G3P ( glyceraldehyde 3-phosphate) exits the cycle per three CO2 molecules fixed (cycle takes place 3 times for one G3P) and is converted to glucose and other organic molecules. 3. Calvin Cycle Phases: a. Carbon fixation: a CO2 molecule combines with a five carbon acceptor molecule, ribulose-1,5-bisphosphate, creates a six carbon compound that splits into two molecules of 3-PGA b. Reduction: ATP and NADPH are used to convert the 3-PGA molecules into molecules of three carbon sugar called G3P c. Regeneration of CO2 acceptor: G3P recycled to regenerate the RuBP receptor 4. SG #6: Phase 1 of the Carbon Cycle is called Carbon Fixation because 3 molecules of CO2 are "fixed" to 3 molecules of ribulose-1, while 5-bisphosphate is broken down to create two 3-carbon molecules of 3-phosphoglycerate (6 total) 10.4 ALTERNATIVE METHODS OF CARBON FIXATION HAVE EVOLVED IN HOT, ARID CLIMATES 1. In plants living in extreme environments there must be a compromise between Photosynthesis and the prevention of excess water loss from the plant, 2. On a hot day, most plants would close their stomata to prevent loss of water due to evaporation-- limiting the Photosynthetic yield by limiting access to Co2. 3. On hot, dry days, C3 plants close their stomata, conserving water-- but keeping CO2 out and O2 in. Photorespiration can occur under these conditions: rubisco binds to O2 instead of CO2, consuming ATP and releasing CO2 without producing ATP or carbohydrate. 4. C4 plants minimize the cost of photorespiration by incorporating CO2 into four-carbon compounds in mesophyll cells. These compounds are exported to bundle-sheath cells (Arranged into tightly packed sheaths around leaf veins; btwn bundle sheath cells and leaf surface are mesophyll cells), where they release CO2 for use in the Calvin Cycle. 5. The C4 leaf anatomy and pathway/steps (right hand-side): 6. CAM plants use a mode of carbon fixation called crassulacean acid metabolism. In this process, the plants open their stomata at night, incorporating CO2 into organic acids that are stored in mesophyll cells. During the day, their stomata close, and the CO2 is released from the organic acids for use in the Calvin Cycle. 7. SG #7: Photorespiration decreases photosynthetic output by adding oxygen, instead of carbon dioxide, to the Calvin cycle. As a result, no sugar is generated (no fixed carbon), and the cell adapts to this process by using O2 rather than generating it. Chapter 9 Cellular Respiration and Fermentation 9.1 CATABOLIC PATHWAYS YIELD ENERGY BY OXIDIZING ORGANIC FUELS 1. Catabolic Processes don’t directly do work, just provide the ATP for work to be done: a. Fermentation: a partial degradation of sugars that occurs without the use of oxygen; makes a limited amount of ATP b. Aerobic Respiration: oxygen is consumed as a reactant with an organic fuel c. Anaerobic Respiration: a substance rather than oxygen is consumed as a reactant along with the organic fuel d. Cellular Respiration: includes both aerobic and anaerobic respiration, which break down organic molecules and use an electron transport chain for the production of ATP 2. Redox reaction: a reaction in which one or more electrons are transferred from one reactant to another a. The loss of electrons from one substance is called oxidation, and the addition of electrons to another substance is known as reduction. b. The reducing agent is the electron donor and the oxidizing agent is the electron acceptor c. During aerobic respiration, glucose C6H12O6 is oxidized to CO2, and O2 is reduced to H2O. 3. Electrons lose potential energy during the transfer from glucose/ organic compounds to oxygen. Electrons are usually passed first from NAD+, reducing it to NADH, and are passed from NADH to an electron transport chain, which conducts the electrons to O2 in energy-releasing steps. The energy that is released is used to make ATP. 4. NAD+: electrons are first transferred to an electron acceptor/oxidizing agent NAD+ 5. Dehydrogenase: enzyme that removes 2 electrons and 2 H+ protons from a substrate (glucose), however only 2 electrons and 1 proton is delivered to the NAD+ and the other proton is released to the surrounding solution 6. NADH represents temporary stored energy in electron form, in the electron transport chain it actas an electron donor in which the electrons go to oxygen 7. Electron transport chain: sequence of electron carrier molecules (membrane proteins) that shuttle electrons down a series of redox reactions that release energy used to make ATP. 8. Three stages of cellular respiration: a. Glycolysis: Begins cellular respiration by breaking glucose into two molecules of a three-carbon compound called pyruvate. (occurs in cytosol) i. Reactants: 1 glucose molecule + 2 ATP ii. Products: 2 pyruvate + 2 ATP + 2 NADH b. Pyruvate Oxidation and the Citric acid cycle/Krebs Cycle: Oxidation of glucose by taking the pyruvates from glycolysis (occurs in mitochondria, mitochondrial matrix) i. Reactants: 2 pyruvate ii. Products: CO2 + 1 ATP + 2 NADH + 1 Acetyl CoA c. Oxidative phosphorylation (electron transport and chemiosmosis): The production of ATP using energy derived from the redox reactions of an electron transport chain (occurs in the mitochondria’s cristae, surrounded by mitochondrial matrix) i. Reactants: 6 O2, 2 FADH2, 10 NADH ii. Products: 6 H2O, 34 ATP iii. Produces the majority of ATP in cellular respiration 9. The chemical formula of cellular respiration is: C6H12O6 + 6O2 ³ 6CO2 + 6H2O + ATP 10. Substrate-level phosphorylation: enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism (during glycolysis and citric acid cycle 11. (SG #4) The mitochondrial intermembrane space and the thylakoid space are both involved in the process of chemiosmosis. 9.2 GLYCOLYSIS HARVESTS CHEMICAL ENERGY BY OXIDIZING GLUCOSE TO PYRUVATE 1. Glucose split into three-carbon sugars, which are oxidized and their remaining atoms are rearranged to form two pyruvate molecules. 2. Glycolysis (breakdown of glucose) is a series of reactions that breaks down glucose into two pyruvate molecules, which may go on to enter the citric acid cycle, and nets 2 ATP and NADH per glucose molecule. 3. Phases of Glycolysis: a. Energy Investment Phase: cell spends ATP b. Energy Payoff Phase: ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose. 10 steps of the glycolytic pathway: Energy Investment Phase Energy Payoff Phase 9.3 AFTER PYRUVATE IS OXIDIZED, THE CITRIC ACID CYCLE COMPLETES THE ENERGY-YIELDING OXIDATION OF ORGANIC MOLECULES 1. Most energy after glycolysis remains in the two molecules of pyruvate 2. In eukaryotic cells, pyruvate enters the mitochondria via an active transport protein because it is charged, and its oxidized acetyl CoA product (high potential energy) is used to transfer the acetyl group to a molecule in the citric acid cycle, a reaction that is highly exergonic 3. Oxidation of pyruvate to acetyl CoA (step before citric acid cycle): 4. The Citric Acid Cycle generates 1 ATP per turn by substrate-level phosphorylation, but most of the chemical energy is transferred to NAD+ and FAD during the redox reactions. The reduced coenzymes, NADH and FADH2, shuttle their cargo of high-energy electrons into the electron transport chain. 9.4 DURING OXIDATIVE PHOSPHORYLATION, CHEMIOSMOSIS COUPLES ELECTRON TRANSPORT TO ATP SYNTHESIS 1. The electron transport chain is a collection of molecules embedded into the inner membrane of the mitochondria in eukaryotic cells, innerfoldign of the cristae provide surface area 2. Prosthetic groups are essential for the catalytic functions of certain enzymes. 3. NADH and FADH2 transfer electrons to the electron transport chain. Electrons move down the chain, losing energy in several energy-releasing steps. Finally, electrons are passed to O2, reducing it to H2O ⇽ 4. Along the electron transport chain, electron transfer causes protein complexes to move H+ from the mitochondrial matrix to the intermembrane space, storing energy as a proton-motive force (H+ gradient). As H+ diffuses back into the matrix through ATP synthase, its passage drives the phosphorylation of ADP to form ATP, called chemiosmosis ´ (Figure 15) 5. Around 34% of the energy stored in C2H12O6 is transferred to ATP during cellular respiration, producing a maximum of approx 32 ATP. 9.5 FERMENTATION AND ANAEROBIC RESPIRATION ENABLE CELLS TO PRODUCE ATP WITHOUT THE USE OF OXYGEN 1. Glycolysis nets 2 ATP by substrate-level phosphorylation, regardless if oxygen is present. 2. Under anaerobic conditions, anaerobic respiration or fermentation can take place. In fermentation, the electrons from NADH are passed to pyruvate or a derivative of pyruvate, regenerating the NAD+ required to oxidize more glucose. 2 types of fermentation are alcohol fermentation and lactic acid fermentation. 3. In anaerobic respiration, an electron transport chain is present with a final electron acceptor other than oxygen. Cells use fermentation in the absence of oxygen to produce ATP by substrate-level phosphorylation. 4. Fermentation, anaerobic, and aerobic respiration use glycolysis to oxidize glucose, but they differ in the final electron acceptor and whether an electron transport chain is used. Respiration yields more ATP; aerobic w/O2 as the final electron acceptor yields 16x as much ATP as fermentation. 5. The electron transport chain is used in anaerobic respiration, but not in fermentation. 6. Glycolysis occurs in nearly all organisms and evolved in prokaryotes before there was O2 in the atmosphere 9.6 GLYCOLYSIS AND THE CITRIC ACID CYCLE CONNECT TO MANY OTHER METABOLIC PATHWAYS 1. Catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration. a) Carbohydrates can enter glycolysis, most often after conversion to glucose. b) Amino acids of proteins must be deaminated before being oxidized. c) The fatty acids of fats undergo beta oxidation to two-carbon fragments and then enter the citric acid cycle as acetyl CoA. d) Anabolic pathways can use small molecules from food directly or build other substances using intermediates of glycolysis or the citric acid cycle. 2. Cellular respiration is controlled by allosteric enzymes at key points in glycolysis and the citric acid cycle. The mitochondrial intermembrane space and the thylakoid space both functionally perform chemiosmosis, or the movement of H+ ions across a semipermeable membrane using special channels that perform down the gradient. Chemiosmosis in photosynthesis occurs in chloroplasts, whereas in mitochondria it is incorporated in cellular respiration. Structurally, the cristae, or folds, in the mitochondrial intermembrane space and the stacked granum inside thylakoids both create more surface area for the electron transport chain components. Thylakoid membrane and Mitochondrial membrane Similarities: + Both contain ATP synthase proteins + Both undergo chemiosmosis + Both contain the Electron transport chain Differences: + Mitochondrial membrane transduces energy through oxidative phosphorylation production of ATP + The light-dependent reaction, or the calvin cycle, occurs in the thylakoid membrane, using light energy to produce ATP and NADH.