BIOL 408 Exam Study Guide PDF

Chapter 10: Biomembrane Structure I. The Fluid Mosaic Model of Biomembranes ​ Plasma Membrane (PM): ○​ Composed of lipid bilayer, proteins, and carbohydrates. ○​ Functions as a semi-permeable barrier, regulating the movement of substances. ○​ Exhibits fluidity due...

Chapter 10: Biomembrane Structure I. The Fluid Mosaic Model of Biomembranes ​ Plasma Membrane (PM): ○​ Composed of lipid bilayer, proteins, and carbohydrates. ○​ Functions as a semi-permeable barrier, regulating the movement of substances. ○​ Exhibits fluidity due to lateral movement of lipids and proteins. ​ Types of Membrane Proteins: ○​ Integral (Transmembrane) Proteins: Span the bilayer. ○​ Peripheral Proteins: Attach via non-covalent interactions. ○​ Lipid-Anchored Proteins: Covalently bonded to lipids (e.g., GPI anchors). II. Composition of Biomembranes ​ Lipid Bilayer: ○​ Hydrophilic head groups face outward, hydrophobic tails face inward. ○​ Cholesterol modulates fluidity and stability. ​ Membrane Lipids: ○​ Phospholipids: Glycerophospholipids (e.g., phosphatidylcholine, phosphatidylserine). ○​ Sphingolipids: Sphingomyelin, glycolipids, ceramides. ○​ Sterols: Cholesterol in animals, phytosterols in plants. ​ Membrane Asymmetry: ○​ Different lipid compositions in cytosolic vs. extracellular leaflets. ○​ Flipases, Floppases, and Scramblases regulate lipid distribution. III. Membrane Properties and Dynamics ​ Self-sealing and fusion properties: Enables vesicle formation, endocytosis, and exocytosis. ​ Lateral diffusion: Movement of lipids/proteins within the membrane. ​ Phase transition (gel → fluid state): Temperature-dependent changes in membrane fluidity. ​ Lipid Rafts: ○​ Rich in cholesterol and sphingolipids. ○​ Specialized for signaling and trafficking. IV. Transport Across the Membrane ​ Passive Transport: ○​ Simple diffusion (O₂, CO₂, small lipophilic molecules). ○​ Facilitated diffusion (via channels or transporters). ​ Active Transport: ○​ Requires ATP (e.g., Na+/K+ ATPase, Ca²+ ATPase). ​ Endocytosis & Exocytosis:  ○​ Endocytosis: Phagocytosis (large particles), pinocytosis (fluids), receptor-mediated. ○​ Exocytosis: Secretion of substances (e.g., neurotransmitters). Chapter 11: Transmembrane Transport of Ions and Small Molecules I. Overview of Membrane Transport Mechanisms ​ Pumps (Primary Active Transport): ATP-powered, move molecules against gradients. ​ Channels: Allow specific ion passage down electrochemical gradients. ​ Transporters (Carriers): Conformational change-mediated transport. II. Types of Transporters ​ Uniporters: Transport a single molecule down its gradient (e.g., GLUT1 for glucose). ​ Symporters: Move two molecules in the same direction (e.g., Na+/glucose symporter). ​ Antiporters: Move two molecules in opposite directions (e.g., Na+/H+ exchanger). III. ATP-Powered Transport Proteins ​ P-Class Pumps: ○​ Na+/K+ ATPase (pumps 3 Na+ out and 2 K+ in per cycle). ○​ Ca²+ ATPase (sarcoplasmic reticulum, muscle contraction). ​ V-Class Pumps: ○​ Acidify organelles (lysosomes, endosomes) by pumping H+ inside. Opposite of F-Class. ​ F-Class Pumps: ○​ ATP synthase in mitochondria and chloroplasts (proton gradient-driven ATP production). ​ ABC Transporters: ○​ Multiple ATP binding domains to open channel ○​ Multidrug resistance (MDR1), CFTR (cystic fibrosis chloride channel). IV. Ion Channels & Action Potentials ​ Resting membrane potential (~ -70 mV): Set by Na+/K+ ATPase and K+ leak channels. ​ Voltage-Gated Ion Channels: 1.​ Open/close in response to voltage changes (e.g., Na+, K+, Ca²+ channels). ​ Action Potential:  1.​ Depolarization: Na+ channels open, Na+ influx. 2.​ Repolarization: K+ channels open, K+ efflux. 3.​ Refractory period: Na+ channels temporarily inactivated. Chapter 12: Cellular Energetics I. Overview of Cellular Respiration ​ Aerobic Respiration: O₂ is final electron acceptor in the electron transport chain. ​ Anaerobic Respiration: Alternative electron acceptors (e.g., sulfate, nitrate). ​ Overall Equation:​ C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + 30-32 ATP II. Stages of Glucose Oxidation 1.​ Glycolysis (Cytoplasm): ○​ Glucose → 2 Pyruvate + 2 ATP + 2 NADH 2.​ Pyruvate Oxidation (Mitochondrial Matrix): ○​ Pyruvate → Acetyl-CoA + NADH + CO₂ 3.​ Citric Acid Cycle (TCA Cycle): ○​ Produces NADH, FADH₂, and ATP/GTP. 4.​ Electron Transport Chain & Oxidative Phosphorylation: ○​ Generates proton gradient, driving ATP synthesis via ATP Synthase. III. Lipid and Protein Metabolism ​ Fatty Acid Oxidation (Beta-Oxidation): ○​ Acyl-CoA → Acetyl-CoA + NADH + FADH₂ ​ Protein Catabolism: ○​ Amino acids are deaminated, entering TCA cycle. IV. Photosynthesis 1.​ Light-Dependent Reactions (Thylakoid Membrane): ○​ Photosystem II (P680) splits H₂O, producing O₂ and protons. ○​ Photosystem I (P700) reduces NADP+ to NADPH. 2.​ Calvin Cycle (Stroma of Chloroplasts):  ○​ Fixes CO₂ and Ribulose 1,5-bisphosphate into glyceraldehyde-3-phosphate (G3P). i.​ Ribulose 1,5-bisphosphate to 3-phosphoglycerate 1.​ Enzyme: Rubisco ii.​ 3-phosphoglycerate to 1,3-bisphosphoglycerate iii.​ 1,3-bisphosphoglycerate to G3P ○​ G3P can exit the chloroplast and enter the cytoplasm to make i.​ 1 molecule of glucose/fructose ○​ 6 CO2 = 1 SIX CARBON SUGAR ○​ REGENERATION OF 6 RIBULOSE 1,5-BISPHOSPHATE ○​ USES 12 NADPH AND 18 ATP Chlorophyll a Structure & Function ​ Core Structure: Porphyrin ring with a Mg²⁺ ion (instead of Fe²⁺ in heme) + hydrocarbon phytol tail for membrane anchoring. ​ Chlorophyll a vs. b: Chl b has a –CHO (formyl) group instead of a –CH₃ group. ​ Function: Major light-absorbing pigment in thylakoid membrane, bound to proteins in photosystems. Photosynthetic Pigments & Light Absorption ​ Chlorophyll a (Chl a) absorbs red (680 nm) & blue light, driving photosynthesis. ​ Chlorophyll b (Chl b) absorbs 650 nm light, extending the range. ​ Carotenoids absorb shorter wavelengths & protect chlorophyll from damage. ​ Phytochromes detect far-red light (705–740 nm) for photoreception. Photoelectron Transport (Primary Event in Photosynthesis) ​ Light excites Chl a in the reaction center, donating an electron to a quinone (Q/PQ). ​ Creates an irreversible charge separation across the thylakoid membrane. ​ Plastoquinol (PQH₂) = reduced form, passes electrons to cytochrome b₆f complex. ​ Chlorophyll a⁺ is neutralized by: ○​ PSII: Water oxidation (H₂O → O₂ + 4H⁺ + 4e⁻). ○​ PSI: Electron transfer from plastocyanin (PC). Light-Harvesting Complex (LHC) in Cyanobacteria  ​ Contains 90 chlorophyll molecules in an optimal geometric arrangement. ​ Resonance energy transfer funnels absorbed light to special-pair Chl a in the reaction center. Redox Potential in Photosynthesis ​ H₂O oxidation (O₂ evolution) requires 1.14 V but cells use >2 V due to non-standard conditions. ​ Photon energy at 680 nm = 1.8 V, enough to reduce NADP⁺ to NADPH via electron transport. PSII & Water Splitting (Photolysis) ​ P680 (reaction center of PSII) is the strongest biological oxidant. ​ Splitting H₂O (O₂ evolution): ○​ 2 H₂O → O₂ + 4H⁺ (lumen) + 4e⁻ (P680 oxidizes H₂O). ○​ Requires 4 photons (one per electron). ○​ Mn/Ca cluster in PSII accumulates 4 "+" charges before O₂ release. Electron Transport Pathway & Proton Gradient ​ Electrons flow: H₂O → PSII → PQ → Cyt b₆f → PC → PSI → NADP⁺ → NADPH. ​ Proton gradient (ΔpH): ○​ H⁺ released in lumen during photolysis. ○​ Cytochrome b₆f pumps protons, increasing proton-motive force (PMF) for ATP synthesis. ​ PSI: Accepts electrons from PC & transfers to ferredoxin (Fd) → FNR → NADPH. Emerson Effect & Photosystems I & II ​ Emerson Effect: Photosynthesis is more efficient when plants absorb light at two different wavelengths (PSI = 700 nm, PSII = 680 nm). ​ Z-Scheme: Linear electron flow from H₂O to NADP⁺, involving PSII & PSI.