BioMetabolism PDF

Metabolism Catabolism Cellular Respiration Fermentation Alcohol Fermentation Lactic Acid Fermentation Anabolism Photosynthesis Thermodynamics in Biological Processes 1. The First Law of Thermodynamics: Energy can be transferred and transformed, but it cannot be created or destr...

Metabolism Catabolism Cellular Respiration Fermentation Alcohol Fermentation Lactic Acid Fermentation Anabolism Photosynthesis Thermodynamics in Biological Processes 1. The First Law of Thermodynamics: Energy can be transferred and transformed, but it cannot be created or destroyed. Ex. Light energy from the sun is transformed by the plants into chemical energy in organic molecules 2. The Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe. During every energy transformation, some energy is converted to thermal energy and is released as heat. Metabolism all the chemical reactions that tranform energy inside the body totality of an organism’s chemical reactions an emergent property of life that arises from orderly interactions between molecules manages the material and energy resources of the cell Metabolic Pathway  a series of defined steps that alters a specific molecule, resulting in a certain product each step is catalyzed by an enzyme the product of one reaction become the substrate (reactant an enzyme acts on) of another reaction Enzyme a macromolecule that speeds up a chemical reaction (protein) acts as a catalyst that speeds up the reaction without being consumed by the reaction lowers the activation energy barrier A. Catabolic Pathway breaking down of large molecules to form smaller molecules energy stored in the organic molecules becomes available to do cellular work stored energy is released Ex. cellular respiration B. Anabolic Pathway (Biosynthetic Pathway) building of large complicated molecules from simpler ones energy is consumed Ex. photosynthesis, protein synthesis Energy capacity to cause change can be used to do work the ability to rearrange a collection of matter Chemical Energy the potential energy available for release in a chemical reaction Plants act as energy transformer by converting light energy into chemical energy The chemical energy of the organic molecules in the food is converted into kinetic energy and other forms of energy as it carries out biological processes. a. Exergonic energy released spontaneous (without energy input) lose free energy, more stable state than previous Glucose is less stable (more likely to break down) than the simpler molecules into which it can be split. Therefore, The glucose molecule is broken down into smaller molecules to have greater stability. b. Endergonic energy required absorbs free energy from surroundings stores free energy nonspontaneous The chemical reactions of metabolism are reversible. Reactions in an isolated system will try to reach equilibrium. Metabolism is never at equilibrium because an organism is an open system (materials flow in and out) otherwise the organism is dead because there would be insufficient free energy left to perform the necessary work to maintain life. The key to maintaining this lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step. Energy coupling the use of an exergonic process to drive an endergonic one mediated by ATP (adenosine triphosphate) In coupled reactions, an energetically favorable reaction (exergonic) releases energy, which is then used to drive an energetically unfavorable reaction (endergonic). The energy that is released by the exergonic reactions is channeled down to the endergonic reactions to make them energetically favorable too. ATP acts as the immediate source of energy that powers cellular work contains the sugar ribose, the nitrogenous base, and a chain of three phosphate groups bonded together (nucleic acid) energy currency of the cell powers all the metabolic activities of the cell  bonds between phosphate groups can be broken by hydrolysis (addition of H₂O causes the inorganic phosphate to leave ATP then it becomes ADP, exergonic), the energy is then used for anabolism To synthesize ATP, ADP and one phosphate group is bonded together which uses energy from catabolism The hydrolysis of ATP is an exergonic reaction, meaning it releases energy, and this energy is transferred to endergonic processes through a mechanism called energy coupling. Phosphorylation the transfer of a phosphate group from ATP to some other molecule, such as the reactant Receipient molecule that has the phosphate group is called phosphorylated intermediate. (less stable, with more free energy) Activation Energy (Free energy of activation) energy required to contort the reactant molecules so the bonds can break initial investment of energy for starting a reaction often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings Transition State when the reactancts absorbs enough energy for the bonds to break When the molecules bond, energy is released to the surroundings, becoming less reactive. In most cases, the activation energy is so high that the transition state is reached so rarely that the reaction will hardly proceed at all. Heat increases the temperature but high temperature denatures proteins and kills cells. It also speeds up all reactions rather than those that are needed. An enzyme catalyzes a reaction by lowering the activation energy barrier for reactant molecules to absorb enough energy to reach the transition state. Energy flows into an ecosystem as sunlight and exits as heat. Cells harvest the chemical energy stored in organic molecules and use it to generate ATP. Catabolism Through the activity of enzymes, a cell systematically degrades complex organic molecules that are rich in potential energy to simpler waste products that have less energy. Fermentation partial degradation of sugars or other organic fuel that occurs without the use of oxygen Cellular Respiration A. Aerobic Respiration oxygen is consumed as a reactant along with the organic fuel occur in most eukaryotic and many prokaryotic organisms B. Anaerobic Respiration use substances other than oxygen as reactants in a similar process that harvests chemical energy without oxygen Cellular respiration is similar to combustion: Food provides the fuel for respiration, and the exhaust is carbon dioxide and water. Carbohydrates, fats, and proteins from food can all be processed and consumed as fuel. glucose is oxidized oxygen is reduced Major source of carbohydrates in animals: starch, a storage polysaccharide that can be broken down into glucose (C6H12O6) subunits. Catabolic pathways yield energy through the transfer of electrons during the chemical reactions. (Redox Reactions) Oxidation Reduction Lose Gain Electrons Electrons Oxidized Reduced Reducing Oxidizing Agent Agent In respiration, the oxidation of glucose transfers electrons to a lower energy state, liberating energy that becomes available for ATP synthesis. This coenzyme is well suited as an electron carrier because it can cycle easily between its oxidized form, NAD+ (nicotinamide adenine dinucleotide), and its reduced form, NADH. As an electron acceptor, NAD+ functions as an oxidizing agent during respiration. Each NADH stores energy that is tapped to synthesize ATP. Enzymes called dehydrogenases remove a pair of hydrogen atoms (2 electrons and 2 protons) from the substrate thereby oxidizing it. The enzyme delivers the 2 electrons along with 1 proton to its coenzyme, NAD+, forming NADH. The other proton is released as a hydrogen ion (H+) into the surrounding. NAD+ + (2e-) + (2H+) -> NADH + (H+) 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) breaks the fall of electrons to oxygen into several energy-releasing steps instead of one explosive reaction O2 pulls electrons down the chain in an energy-yielding tumble The energy yielded is used to regenerate ATP. Electrons removed from glucose are shuttled by NADH to the “top,” higher energy end of the chain. At the “bottom,” lower-energy end, O2 captures these electrons along with hydrogen nuclei (H+), forming water. glucose -> NADH -> ETC -> oxygen substrate-level phosphorylation - enzyme transfers a phosphate group from a substrate molecule to ADP (occurs in glycolysis and krebs cycle) 1. Glycolysis “sugar splitting” occurs in the cytosol occurs whether or not O2 is present breaking glucose (six-carbon ocmpound) into two molecules of a compound called pyruvate (three-carbon sugars, ionized form of pyruvic acid) Phases: Energy investment phase the cell spends 2 ATP to split the glucose by adding a phosphate group Energy payoff phase the cell gains 4 ATP ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation (lose electrons) of glucose Oxidation of Pyruvate to Acetyl CoA after the pyruvate is oxidized, it enters the mitochondria via active transport where the oxidation of glucose is completed pyruvate must be converted to acetyl CoA, linking glycolysis and the citric acid cycle Reactants: C6H12O6 + 2ATP Products: 2 pyruvate + 2 NADH + 2H+ 2. Citric Acid Cycle (Krebs Cycle) occurs in the matrix of the mitochondrion breakdown of glucose to carbon dioxide acetyl CoA is oxidized to CO2 two-carbon acetyl group of acetyl CoA combines with four-carbon oxaloacetate, forming six-carbon citrate citrate is converted to isocitrate and is oxidized to five-carbon alpha-ketoglutarate, NAD+ is reduced to NADH, CO2 is released (decarboxylation) five-carbon alpha-ketoglutarate is oxidized to four-carbon succinyl-CoA, NAD+ is reduced to NADH, CO2 is released (decarboxylation) succinyl-CoA is converted to succinate and is oxidized to fumarate, FAD is reduced to FADH2 fumarate is hydrated to malate and is oxidized to oxaloacetate, NAD+ is reduced to NADH Reactant: (1 acetyl coA) x 2 (from 2 pyruvate) Product: (3 NADH, 1 FADH2, 1 ATP, 2 CO2) x 2 (for 2 acetyl coA) 3. Electron Transport Chain occurs in the inner membrane of the mitochondrion accounts for almost 90% of the ATP generated by respiration oxidative phosphorylation - adding an inorganic phosphate from redox reactions of the ETC to ADP (generates most ATP) The folding of the inner membrane to form cristae increases its surface area, providing space for thousands of copies of each component of the electron transport chain (mostly protein) in a mitochondrion. NAD+ and FAD are two electron carriers that donate electrons to the electron transport chain, which powers ATP synthesis throught oxidative phosphorylation Electrons - drop in free energy (less reactive, release energy gradually) as they travel down the chain that is finally received by O2 - move from an electron carrier with a lower affinity for electrons to an electron carrier down the chain with a greater affinity for electrons, releasing free energy Electrons transfer in the ETC causes proteins to pump H+ from the mitochondrial matrix to intermembrane space During chemiosmosis, the protons flow back down their gradient via ATP synthase ATP synthase uses the flow of H+ to drive phosphorylation of ATP greater affinity for electrons - more tendency for accepting electrons Oxygen has a high degree of electronegativity O2 is reduced to form H2O O2 + (4e-) + (4H+) -> 2H2O Reactants: 8 NADH, 2FADH2 Products: 26 or 28 ATP Net Gain: 30 or 32 ATP, 4 CO2 Fermentation harvesting chemical energy without using either O2 or any electron transport chain glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate produces 2 ATP per glucose molecule Alcohol Fermentation pyruvate is convered to ethanol in two steps CO2 is released from pyruvate and acetaldehyde is reduced by NADH to ethanol requires regeneration of NAD+ yeast carries out alcohol fermentation used in brewing, winemaking, baking Lactic Acid Fermentation pyruvate is reduced to NADH, forming lactate used by some fungi and bacteria to make cheese and yogurt human muscle cells use lactic acid to generate ATP when O2 is scarce Anabolism Autotrophs “self-feeders” sustain themselves without eating anything derived from other living beings producers of the biosphere Photoautotrophs organisms that use light as a source of energy to synthesize organic substances plants, algae, some protists, prokaryotes, cyanobacteria Heterotrophs unable to make their own food biosphere’s consumer obtain organic material from other organisms Chloroplasts similar to and likely evolved from photosynthetic bacteria allows for the chemical reactions of photosynthesis found mainly in the cells of the mesophyll, the tissue in the interior of the leaf green color is from chlorophyll a, green pigment that reflects green light and absorb red andviolet-blue wavelengths chlorophyll b - absorbs orange, violet and blue light cartenoid - absoubs blue-green light Stomata microscopic pores where the CO2 enters the leaf and O2 exits Stroma a dense interior fluid Thylakoid where chlorophyll is located connected sacs in the chloroplast that are stacked in columns called grana suspended within the stroma Photosynthesis process that transforms the energy of sunlight into chemical energy stored in sugars and other organic molecules reverses the direction of electron flow compared to cellular respiration endergonic process (uses energy), the energy boost is provided by light H2O is oxidized CO2 is reduced 1. Light Reaction (photo part) occurs in the thylakoids chloroplasts split H2O into hydrogen and oxygen the electrons of hydrogen is incorporated into sugar molecules and releasing oxygen as byproduct NADP+ is an electron acceptor and is first cousin of NAD+ NADP+ is reduced to NADPH by adding a pair of electrons along with an H+ Photophosphorylation - generate ATP from ADP Components of Photosystem A photosystem consists of a reaction-center complex (a type of protein complex) surrounded by light-harvesting complexes Light-harvesting complexes (pigment molecules bound to proteins) transfer the energy of photons to the reaction center A primary electron acceptor in the reaction center accepts excited electrons and is reduced as a result. Types of Photosystem Photosystem II (PS II) functions first reaction-center chlorophyll a is called P680 (absorption peak of 680nm) Photosystem I (PS I) first discovered reaction-center chlorophyll a is called P700 (absorption peak of 700nm) 1. Light strikes on PS II 2. Electrons becomes excited from light energy and travel across the thylakoid membrane to photosystem I (PS I) through the electron transport chain (ETC) 3. Water splits (photolysis) to release an electron and replace the one donated “-lysis” - splitting Photolysis - splitting water using light H₂O -> (2H+) + ½O₂ + (2e-) H+ is located inside the thylakoid membrane O₂ is the byproduct 4. ETC transports the electrons 5. The energy in the electrons are used to pump in H+ ion across the thylakoid membrane into the inner thylakoid space (higher concentration of H+ ions inside the thylakoid) 6. ATP synthase allows H+ ions to diffuse from high to low concentration 7. The flow of H+ ions (chemiosmosis) causes ATP synthase to spin, creating ATP 8. Adenosine diphosphate (ADP) fuses with inorganic phosphate (Pi) to produce adenosine triphosphate (ATP) (phosphorylation) ADP + Pi -> ATP ATP is the byproduct 9. (after 4.) Light excites the electrons as it reaches PS I and travels through another ETC 10. NADP+ accepts the electrons and reduced to NADPH (reduction) (NADP+) + (H+) + (2e-) -> NADPH NADPH is the byproduct ATP and NADPH will be used in the Calvin Cycle 2. Calvin Cycle (synthesis part) Dark Reaction - no light needed - uses ATP and NADPH from LR ATP - provides the energy NADPH - provides the electrons and the hydrogens to build sugar RuBisCO (crackers) - an enzyme G3P (glyceraldehyde 3-phosphate) - a three-carbon sugar - used to make glucose Carbon fixation - CO₂ is “fixed” from inorganic form to its organic molecules Phase 1: Carbon Fixation 1. RuBisCO catalyzes (causes) reaction between CO₂ and ribulose bisphosphate (RuBP) to form a six-carbon compound (occurs three times) 3CO₂ + RuBisCO + 3RuBP 2. Six-carbon compound splits into two molecules of 3-phosphoglycerate (3-PGA) Total: 6 3-PGA Phase 2: Reduction 1. 6ATP provides energy to 6 3-PGA and receives a phosphate group to form an intermediate compound ADP is the byproduct 2. The intermediate compound gains electrons from NADPH and loses one of its phosphate group to form glyceraldehyde 3-phosphate (G3P) NADPH donates electrons (2e-) and hydrogen, so it is reduced 3CO₂ in = 1G3P out (three carbons and one phosphate) G3P, NADP+ and Pi are the byproducts Phase 3: Regeneration 1. Five carbons are required to form RuBP 5G3P (15 carbons) forms 3RuBP with the use of 3ATP Since G3P contains three carbons, it takes 2G3P or two full cycles to form a six-carbon glucose molecule 1G3P = ½C₆H₁₂O₆