Bio notes #2

Metabolism & Bioenergetics Content: Spontaneous Process: A process in which it happens on its own, without input of external energy. Important Concept: Every spontaneous process is capable of doing work. -G.N. Lewis (1875-1946) Hydroelectric Dam Analogy: Water flowing down the dam is spontaneous. This water can spin turbines to create electricity. If water moving from bottom to top would consume energy, non-spontaneous. Also Covering in Sections: Anabolism: Building up processes. Complex molecules are produced. Link monomers to polymers. Catabolism: Breaking down complex molecules. Breaks down into simpler products. Reasons for a Cell to do Catabolism: Remove complex molecules that are no longer useful to the cell: Release monomers that can be used to produce other complex molecules.   Provides some of the basic building blocks for producing molecules: Example: Ribosome is produced by a respiratory pathway.   Provides energy: Makes existing potential energy available. Catabolism provides energy. Anabolism & any other cellular work require input/provision of energy. Energy coupling is the coupling/pairing/linking of catabolic processes (release energy) to anabolism (or any other form of work) which require energy. Metabolism: Anabolism + Catabolism; the sum of biochemical/metabolic/cellular reactions of an organism or cell. Energy Coupling Concept of Biochemical/Metabolic Pathway: A series of linked, sequential biochemical reactions, where the product of one reaction becomes the reactant for the next reaction. Example: A → B → C → D → E → F Important biochemical/metabolic pathways include: Glycolysis Citric acid cycle (Krebs cycle, TCA cycle) Calvin cycle (photosynthesis) Principles of Energy Transformation Each reaction is catalyzed by a unique enzyme. System: Collection of matter under study (e.g., organism or cell) Surroundings: Everything outside of the system. Isolated System: A system that does NOT exchange energy or matter with its environment. Open System: A system that does exchange energy/matter 1 with its environment.   First Law of Thermodynamics (Conservation of Energy): Energy cannot be created or destroyed, but can be converted from one form to another. Example: Potential energy in the form of chemical bonds (glucose) can be converted into kinetic energy (electricity/ATP). Analogy: Water at the top of a dam = glucose or other high-energy molecule (carbs or fats). Chemical potential energy (not energy of position). Electricity/ATP = performing cellular work. Making toast = performing cellular work. Water falling down dam = turning the turbine to produce electricity = aerobic cellular respiration (ACR). ACR catabolizes glucose to regenerate ATP. ATP powers cellular work. Second Law of Thermodynamics: In every energy transfer or transformation, increases the entropy of the universe. Entropy (S): A measure of disorder or randomness. Low S = A highly ordered state High S = A disordered state. Increasing Disorder can be seen in various ways: Polymers → Monomers Mixing molecules in a solution Production of heat Respiratory Electron Transport Chain (RS ETC) Location: Inner mitochondrial membrane Electrons: LEES = Low energy electrons HEES = High energy electrons NADH & FADH2: Represent HEES. O2: Is garbage can for LEES. HEES enter the RS ETC, LEES leave the RS ETC. Job of the RS ETC: To convert CPE of NADH & FADH2 into the CPE of H+ ΔμH+ Respiratory Electron Transport Chain Diagram: A visual representation of the electron transport chain with labeled components like NADH, FADH2, O2, H+, and ATP synthase. Activity of the chain creates a ΔμH+ Meaning: There is lower [H+] in the matrix and higher [H+] in the intermembrane space. Ox Phos The combination of the RS ETC and ATP synthase. ATP SYNTHASE Same location as RS ETC (inner membrane) - NOT PART of RS ETC! Merging the two pathways = Oxidative phosphorylation (Ox Phos) Responsible for majority of ATP regen Overall ATP production in OCR CPE of NADH & FADH2 - CPE of H+ = CPE of ATP CPE of H+ = CPE of ATP + Ox Phos CPE of NADH & FADH2 = CPE of ATP + Ox Phos + Ox Phos Overall ATP production in OCR = 28 ATP/glucose (Sub: Real phosphorylation = 4 ATP/glucose) = 32 ATP What Happens if O2 is not available for ACR? Can happen in muscles During intense physical exercise Happens to yeast during wine-making Water-logged plant roots in soil No O2 = no ETC activity No H+ pumping No ΔμH+ No ATP synthase activity Oxid. phos. also shuts down Entire Process of ACR shuts down Glucose → 2 pyruvate → Linker Reaction → Citric Acid Cycle Lack of Oxygen All that left is glycolysis via SLP. But glycolysis needs NAD+, just like CAC. Fermentation Running glycolysis w/ no O2 Regenerates NAD+ Sub-level phosphorylation provides ATP during fermentation. Energy Transformation during ACR Glycolysis: CPE of 2 Glucose (Sub-level phosphorylation) = 2 ATP CPE of 2 NADH = 4 ATP Linker Reaction & Citric Acid Cycle: CPE of 2 pyruvate = 2 GTP CPE of 8 NADH (6 from CAC oxidation + 2 from glycolysis) = 24 ATP CPE of 2 FADH2 = 4 ATP Respiratory Electron Transport Chain: CPE of 10 NADH (8 from previous oxidation + 2 from glycolysis) = 28 ATP CPE of 2 FADH2 = 4 ATP CPE of H+ = CPE of ATP + Ox Phos CPE of NADH & FADH2 = CPE of ATP + Ox Phos + Ox Phos Overall ATP production in OCR = 28 ATP/glucose (Sub: Real phosphorylation = 4 ATP/glucose) = 32 ATP