BSC 450 Week 15 Notes
BSC 450 Week 15 Notes BSC 450
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This 11 page Class Notes was uploaded by Jordana Baraad on Saturday December 5, 2015. The Class Notes belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 82 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 12/05/15
12/1 Oxidative Phosphorylation: Day 2 Oxidative Phosphorylation (OP) in mitochondria Emphasis: electron transport chain (ETC) very similar to photosynthesis (PS) Plants have mitochondria too Gene production Energy from PS Calvin cycle: low high energy Requires energy input From OP, FADH a2d NADH donate to ETC H+ gradient ATP synthesis Chemiosmotic Theory Electrochemical gradient has 2 components 1. electrical (proton flow) 2. pH (H+ concentration) high [proton] in lumen: pumped out stroma like mitochondrial matrix Structure of Mitochondria ETC on cristae (invagination of inner membrane) Thousands of copies Clustering into “respirisome” Mitochondria reproduce by fission Different number of mitochondria for each organ, based on metabolic needs More ATP more metabolic needs more cristae (mitochondria) All shapes/ sizes ETC … series multibunit proteins Proteins = “big pieces” Proteins house cofactors doing electron transport th 4 complexes (though sometimes, a 5 is counted in with them) 1. NADH dehydrogenase –Complex I 2. Succinate dehydrogenase – Complex II 3. Cytochrome bc –C1mplex III 4. Cytochrome oxidase – Complex IV 5. ATP Synthase – Complex V Part of respiratory chain, not ETC 1-4 are part of ETC: build proton gradient ETC … Series electron carriers Multiple redox centers 1. 2 flavoproteins – FMN & FAD a. FMN = primary electron acceptor from NADH (CI) b. FAD= primary electron acceptfor from FADH (CI2) 2. Cytochromes = heme-containing proteins: Types a, b, c 3. Copper atoms a. Typically occur in pairs; good electron acceptors/ donors 4. Fe-S complexes/ proteins a. All embedded in multisubunit protein complexes 2 mobile carriers 1. ubiquinone: hydrophobic; enzyme CoQ (photosynthetic cousin = plastoquinone) 2. cytochrome C: hydrophilic; peripheral membrane protein both electrons and protons being shuttled Cytochromes Single electron carriers: can only accept from intermediates—not NADH directly Intermediates = flavorproteins, cytochormes, Fe-S Fe-coordinated porphirin ring Top-left pic: Fe @ center Akin to Mg-coordinated porphirin ring in photosynthesis A,b,c differ by ring additions Cytochrome C: protein-bound (covalent bonding); Cys Cytochrome A & B: tightly (but noncovalently) bound Bottom-right pic: isoprenoid tail Can anchor in hydrophobic spaces Graph: each cytochrome seen at distinct wavlengths Ex. cytochrome c @ 556 nm Seen in Cytochrome bc a1d Cytochrome Oxidase Fe-S Cluster Single electron carriers Coordinated by Cys in protiens His Rieske Fe-S proteins Same # Fe and S molecules Moving from matrix intermembrane space Chain electrons accepted / donated to move across membrane CoQ / Ubiquinone Semiquinone: single electron carrier Hangs around to k up 2n electron carrier Picks up protons to balance charge Docks elsewhere Long hydrophobic tail Electron Flow in Respiratory Chain In CIV, O2 = terminal electron acceptor; water released as waste product of OP Opposite of photosynthesis -OH = waste; H20 = essential electron donor ubiquinol docks @ CIII cytochrome c docks @ intermembrane side carriers electrons from CIII-CIV FADH2 doesn’t dissociate Q cycle btwn CIII & CII Every time an electron is passed, it loses some energy Decreased energy as goes through ETC Electrons at CIV are at low-energy state Structure known from x-ray crystallography Sold supplement: ubiquinol v. ubiquinone Ubiquinol = reduced; more costly, but more effective Helps compensate for slowing metabolism All complexes EXCEPT CII pumps protons Different from photosynthesis—NO proton pumps Ubiquinol helps draw prtons form membrane Electron carriers from glycolysis did their job CIII accepts electrons 1 at a time from ubiquinone CIII does Q cycle (complex process) Recycle both ubiquinones (need multiple docking sites) Cytochrome c (inner membrane space side) undocks cytochrome b CIV ATP in matrix—mobile carriers must distribute 2 arms Multiple Complexes Association = Respirasome Repeated throughout cristae PIC 3? Chemiosmotic Model ATP Synthesis Electron ransport -- Proton motive force energy ATP synthesis IMS matrix ATP Synthase (proton ATP-ase) F1head + F b0se + proton channel Key Asp resiue coordinates Gamma “ stick” btwn channel and head Turns w/ proton movement—transmits movement Alpha-beta pair forms enzyme active site Nucleotide active site on beta ADP + P iATP Gamma-subunit turning Alpha helices interact w/ alpha-beta pairs Each helix has different face Face contact interaction: several configurations--cyclical Open loose tight open Empty ADP +P biund ATP formed ATP released F1catalysis 3 alpha-beta dimers pic: alpha = gray; beta= purple gamma @ center turning – rotation through all 3 dimers pic: left: yellow: ADP-bound right: red: ATP bound Binding-Change Model Counter-clockwise roation In each Q3 wheel Binding affinities altered 12/3/15 Photosynthesis Photosynthesis (PS)—big picture Left ½: “photo” Reverse of OP Requires light & water Water = electron donor Donor, but not good donor Main difference btwn OP and photosynthesis NADH = good donor Water turned to electron donor by H2O-splitting enzyme Large proton complexes in thylakoid grana Make energy: NADPH & proton gradient Mn complex = electron acceptor Very specific transporters (like in mitochondria) Synthesis CO2 Calvin Cycle Sugars Carboxylation G3P (sugar precursor) ATP = product of Part I Dumped stroma Used for Calvin Cycle CO2 + RuBP sugar precursor (G3P) Sugars: Sucrose: synthesized in cytoplasm Starch: stored and produced in chloroplasts (never leave) Leaves are plant organs that have evolved to maximize photosynthesis Palidsade parenchyma: powerhouses—filled w/ chloroplasts Spongey mesophyll: only site of gas exchange & water loss Rest of plant has waterproof wax coating Maximize # light photons captured General Features of Photosynthesis 2 membranes (inner and outer) a) “stacks” = grana linker membranes connecting grana = (stroma) lamellae chlorophyll (embedded in membrane) green color pigment absorbs blue and red; reflects green (Energy from) Light Drives Photosynthesis light energy CREATION of electron acceptor / donor chlorophyll only 1 of light-absorbing pigments complex excites electrons higher levels so can be picked off by ETC shorter wavelength = higher energy; longer wavelength = lower energy w/o electron acceptor, lost—radiated as heat and light Various Pigments Harvest the Light Energy Porin head group like heme (w/ 1 more ring) Absorbs visible light energy w/ double bond system Chlorophyll a & b have different absorption capabilities A: slightly better Other pigments always found in light—harvesting complex Help chloroplasts Protect plant from excess light destructive radicals Particularly lutein (xanthophyll): radiate out extra light/energy Absorb energy, but not as well as chlorophyll Beta-carotene: yellow/orange Lutein (xanthophyll): yellow Photopigments absorb different wavelengths of light The energy is transferred to the PS reaction center Full sunlight is higher energy on spectrum “sun plants” absorb at higher wavelength “shade plants” @ lower wavelength some—not all—plants can adapt requires rearrangement of the thylakoid membrane 4 main plant photopigments: chlorophyll a chlorophyll b lutein beta-cartone phycoerythrin: found more in bacteria/ algeae, lower plants absorbs lower light Organization of Light-Absorbing Molecules in Chloroplasts Photosystems= huge protein complexes: PSI & PSII PSI: P700 rxn center; PSII: P680 rxn center # describes best-absorbed wavelength P700 – hihgher energy Rxn center = 2 chlorophyll a molecules (dimers) Light harvesting complex = flat disk in pic Huge array of pigments Funnel down light --? Rxn center The ETC Contains a series of multisubunit proteins Large protein complexes embedded in thylakoid membrane 1. PSI a. PSI + FD + FNR + NADPH 2. PSII a. Associates w/ water-splitting enzyme b. Proton gradient built btwn (outside) stroma and lumen i. Want all energy left in stroma (for Calvin Cycle) 3. Cytochrome b 6f Mobile carriers 4. plastoquinone (PQ)—hydrophobic (2-electron carrier) 5. plastocyanin (PC)—hydrophilic (1-electron carrier) 6. proton-ATPase ATP (from gradient) peripheral membrane proteins attached to stromal side of PSI 7. ferrodoxin (FD) 8. ferrodoxin NAD reductase (FNR) 9. Fe-S protens, Cu proteins/ ions help perform electron transport (similar to OP) Overview of the Light Rxns 1000 x more acidic in lumen—strong pH gradient stroma: pH = 8; lumen: pH = 5 NONE of the complexes are proton pumps Proton pumps supplied by PQ Begins w/ PSII Cytochrome b = 6ftermediate PC btwn cytochrome b & P6f Both PS’s absorb light @ same time Funneled rxn centers (pair of chlorophyll a’s) Electrons excited higher energy state, picked off by acceptor Higher-energy state = higher level orbital Fed to PQ (2 electrons( PQ picks up protons on stromal side reduced plastoquinol cytochrome b 6f protonsdropped of on lumen side PC carriers 1 electron at a time t PSI Resets rxn center ATP synthesis in stroma almost identical to OP Membrane btwn stroma & lumen Can only donate 1 electron at a time to cytochrome b 6f 2 branches of electron direction (bc of cytochromes) lower energy electrons accepted by b 6 cytochrome b d6nates electron --? PC (single electron carrier) PC donates electron PSI to reset Higher energy electrons move through cytochrome f Redonated to PQ (Q cycle) Picks up more protons and redocks on lumen side continuation of cycle (building proton gradient) PC = electron donor From Light Energy to Charge Separation SKIPPED Z-Scheme of Photosynthesis SKIPPED PSII evolves oxygen Water-splitting enzyme has 2 parts 1. Mn cluster w/ calcium ion—splits water 2. Tyr residue—KEY a. Intermediate btwn enzyme complex & P680 P680 resets self by immediately “stealing” electron from Tyr Tyr radical; not favorable Tyr stabilizes by stealing electron from Mn Mn stable from 2+ - 4+ so OK Electron-stealing process happens 4 times Each time, Mn becomes stronger oxidizer Capable f splitting 2 H20 molecules Takes back 4 electrons to reset itself Water-Splitting Complex of PSII PSI results in reduced NADPH SKIPPED Structure of PSI SKIPPED Cytochrome b f Complex links PSII and PSI and translocates protons 6 into the lumen SKIPPED Organization of photosynthetic machinery in the thylakoid membrane Known crystalline structure Location of photosynthetic machinery in the thylakoid membrane PSII on thylakoid stacks PSI in lamellae Cytochromeb mostly in lumen (some in lamellae) b Light-induced redox rxn cause acidification of lumen Proton-motive force across the thylakoid membrane drives the synthesis of ATP Flow of Protons: Mitochondria, Chloroplasts, Bacteria According to endosymbiotic theory, mitochondria and chloroplasts arose from entrapped bacteria Bacterial cytosol became mitochondrial matrix and chloroplast stroma The Evolution of Oxygenic Photosynthesis SKIPPED The Carbon Fixation Reactions (Calvin – not in txt) The Calvin Cycle Melvin Calvin, Nobel Prize in 1961 Rubisco 5C acceptor = ribulose 1,5 bisphosphate 2-part sugar production pathway 1/2 path G3P other ½: rgenerate RuBP (original 5C acceptor molecule) energy-demanding step—needs lots ATP input The Calvin Cycle Carboxylation Rubisco 3 PGA Reduction 3 PGA G3P and DHAP Regeneration RuBP Sucrose and Starch Synthesis Sucrose synthesis Cytoplasm G3P Transport Starch synthesis Chloroplast G3P storage