BIOL 3510 1st EditionExam # 3 Study Guide Lectures: 15 - 21Lecture 15 (October 21)Chloroplasts contain light-capturing pigments called chlorophylls and perform photosynthesis. Photosynthesis creates organic molecules from CO2 using energy derived from light. Parts of theChloroplast - Outer membrane: highly permeable, Intermembrane space: composition similar to the cytosol, Inner membrane: less permable, Stroma: space enclosed by the inner membrane, contains metabolic enzymes, chloroplast genomes and ribosomes, Thylakoid: third membrane (contains photosystems, ETC, and ATP synthase) and the space it encloses.The outer membrane, intermembrane space, and the inner membrane are part of the chloroplast envelope. Chloroplast genomes are larger than mitochondrial genomes. The equation for photosynthesis is light + CO2 + H2O  sugars + O2 + heat. Interaction with photons of light energy raises the energy of chlorophyll electrons. Chlorophyll associates with proteins in photosystems in the thylakoid membrane.Photosystems have two parts: Antenna complex: chlorophyll molecules capture light energy (in high energy e-) and funnels the energy to a reaction center, and the Reaction center: contains a special pair of chlorophyll molecules that accepts energy from the atenna complex and transfersone high energy e- to an e- acceptor.Charge Separation: 1) The special pair donates an e- to an electron carrier and it enters the e- transport chain, 2) The special pair accepts an e- from a nearby donor. Noncyclic Photophosphorylation: 1) The special pair in photosystem II donates e- to an e- transport chain, lost e- replaces by the splitting of water, 2) The special pair in photosystem I donates e- to an e- transport chain, lost e- is replaced by the e- donated by photosystem II, 3) E- are added to NADP+ by ferrodoxin NADP-reductase to make NADPH.Electron flow generates an H+ gradient (which is used to make ATP) and NADPH. H2O is the source of electrons moving through the chloroplast electron transport chain. ATP synthase generates ATP using energy derived from the flow of H+ down its electrochemical gradient into the stroma. Chloroplasts can generate ATP only. Cyclic phosphorylation: electrons from photosystem I are transferred to the cytochrome b6-f complex instead of NADP+Carbon Fixation in the Stroma: ATP and NADPH generated by the light reactions are used to convert CO2 into sugar, Addition of CO2 to ribulose 1, 5 biphosphate is catalyzed by rubisco, Thenet gain of the carbon fixation cycle is 1 moleculee of glyceraldehydes 3-phosphate.Uses of glyceradehyde 3-phosphate: 1) Converted to starch in the stroma (energy storage for later), 2) Transported to the cytoplasm and converted to other metabolites (including sucrose – energy transport), 3) Transported to the cytoplasm and converted to pyruvate via glycolysis (energy consumption). Pyruvate enters the citric acid cycle in the plant mito. Endosymbiont hypothesis: origin of mitochondria, and origin of chloroplastsLecture 16 (October 23)Cells contain many membrane-enclosed organelles. Organelles perform diverse functions. Cytosol: metabolic pathways, protein synthesis. Nucleus: contains nuclear genome, DNA and RNA synthesis. Mitochondria: ATP synthesis by oxidative phosphorylation. Chloroplasts: ATP synthesis and carbon fixation by photosynthesis. Endoplasmic reticulum (ER): membrane synthesis, protein distribution. Rough ER: ribosomes attached. Smooth ER: Ca 2+ sequestration etc. Golgi apparatus: proteins and lipid modification and sorting. Lysosomes: intracellular degradation. Endosomes: sorting of endocytosed material. Peroxisomes: oxidation of toxic moleculesThree Mechanisms of Protein Transport into Organelles: 1) Transport through nuclear pore: folded proteins enter through nuclear pores, 2) Transport across membrane: unfolded proteins enter organells via protein translocators, 3) Transport by vesicles: folded proteins move via transport vesicles that fuse with destination membranes. Folded proteins with nuclear localization signals (NLS) are bound by import receptors. Nuclear import receptors and cargo cross the nuclear envelope via the nuclear pore. Ran-GTP binds to the nuclear import receptor in the nucleus and returns it to the cytoplasm. Ran-GAP (GTPase activating protein) and RAN-GEF (guanine exchange factor) mediate the activity of Ran. Unfolded proteins enter mitochondria (and chloroplasts) via protein translocators. Chaparones that bind unfolded proteins and hydrolyze ATP drive import into the mitochondria.Peroxisomes contain oxidative enzymes, use O2 and H2O2 to remove protons, break down fatty acids, are involved in the formation of plasmalogen, a phopholipid needed for neuron function, import proteins via the action of peroxins that use ATP as n energy source, exact mechanism is unclear. Rough ER contains bound ribosomes. When translating proteins with ER signal sequences, ribosomes are targeted to the ER. ER protein targeting depends on the interaction between the signal recognition particle (SRP) and the SRP receptor. ER proteins are threaded through a protein translocator. After signalsequence cleavage, soluble proteins are released into the ER lumen. The arrangement of ER membrane proteins is determined by hydrophobic start transfer and stop transfer sequences. The location of positively charged amino acids determines the orientation of protein insertion. Before the start-transfer: N terminus is cytosolic. After the start-transfer: N terminus is luminal.Lecture 17 (October 28)Transport by vesicles moves proteins and lipids between membrane compartments. Coated vesicles bud from membrane surfaces. Cargo receptors recognize transport signals on cargo molecules and bind. Adaptins mediate the connection between coat proteins and cargo receptors. Dynamin (binds GTP) pinches off the vesicle. Protein-protein interactions mediate fusion of transport vesicles with appropriate membranes. Proteins are modified by enzymes in the ER. Pre-formed oligosaccharides are transferred to asparagines by oligosaccharide protein transferase. Oligosaccharides are further modified in both the ER and Golgi apparatus. Exit from the ER is selective. Proteins remain in the ER if they: have an ER retention signal (4 aa),are incorrectly folded which are retained by chaperones, or are incorrectly assembled multimeric proteins retained by chaperones. Osteogensis imperfecta – “brittle bones disease”. Defects in type 1 collagen; collection of