BIOL 408 Ch. 12 PDF

Chapter 12 -​ Aerobic vs Anaerobic respiration -​ Aerobic: O2 final e- acceptor -​ Anaerobic: SO4^2- or NO3- final e- acceptor -​ Complete aerobic oxidation of one molecule of glucose -​ Yield 30-32 ATP -​ Overall reaction: 1 Glucose + 6 O2 + 30 Pi + 30 ADP...

Chapter 12 -​ Aerobic vs Anaerobic respiration -​ Aerobic: O2 final e- acceptor -​ Anaerobic: SO4^2- or NO3- final e- acceptor -​ Complete aerobic oxidation of one molecule of glucose -​ Yield 30-32 ATP -​ Overall reaction: 1 Glucose + 6 O2 + 30 Pi + 30 ADP + 30 H+ -> 6 CO2 + 30-32 ATP + 36 H2O -​ Glycolysis -​ Takes place in cytoplasm -​ Yields 2 NADH, 2 Pyruvate, 4 ATP (2 ATP Net) -​ Pyruvate to Acetyl CoA -​ Takes place in mitochondrial matrix -​ Pyruvate Dehydrogenase -​ Yields 1 NADH and 1 CO2 -​ TCA Cycle -​ Rate limiting step: Isocitrate Dehydrogenase -​ Produces 3 NADH, 1 FADH2, 1 GTP, 2 CO2 -​ Yield of ATP from NADH and FADH2 -​ 1 NADH = 2.5 ATP -​ 1 FADH2 = 1.5 ATP -​ Beta Oxidation of Fatty Acids -​ Acyl groups are transferred via carnitine transporter -​ Acyl-CoA is degraded into acetyl-coA -​ Important Steps -​ Cytosolic acyltransferase transfers an acyl group from acyl-CoA to carnitine -​ Carnitine transporter allows acyl carnitine to enter mitochondrial matrix -​ Mitochondrial carnitine acyltransferase (CAT) transfers the acyl group to a mitochondrial CoA molecule -​ Free carnitine returns to the cytosol via the CAT protein -​ Once inside, Acyl CoA undergoes the following reactions -​ Oxidation -​ Hydration -​ Oxidation -​ Thiolysis -​ Final Products include -​ 1 Acyl CoA with n-2  -​ 1 Acetyl CoA -​ 1 FADH2 -​ 1 NADH -​ ODD NUMBER FA YIELDS 1 MOL OF PROPINYL-COA PER MOL OF FA -​ Propinyl-CoA can be turned to Succinyl-CoA to enter TCA cycle -​ Coenzyme Q -​ Ubiquinone (Oxidized form) -​ Semiquinone (Free radical form) -​ Dihydroquinone/Ubiquinol (Fully reduced form) -​ ETC -​ Complex 1 -​ NADH Dehydrogenase -​ Complex 2 -​ Succinate Dehydrogenase -​ Complex 3 -​ Cytochrome C reductase -​ Complex 4 -​ Cytochrome C oxidase -​ Cytochrome C: hydrophilic e- carrier -​ Ubiquinone: hydrophobic e- carrier -​ Q cycle takes place between C2 and C3 -​ Complex 1 movement of e- -​ E- start at NADH -​ From NADH, e- flow first to FMN -​ E- flow from FMN to seven of the nine Fe-S clusters -​ From Fe-S clusters to CoQz -​ Two H+ from matrix bind to CoQz to produce CoQH2 -​ Complex 2 movement of e- -​ Electron flow from succinate to complex 2 via FAD/FADH2 and Fe-S clusters -​ Like complex 1, two matrix H+ bind to CoQ to produce CoQH2 -​ NO PROTON PUMPING IN C2 -​ Q Cycle (CYCLE 1) -​ QH2 binds to Qo of cyt b -​ QH2 -> Q + 2H+ + 2e- -​ Oxidized QH2 (Q) binds to Qi site of cyt b -​ The free 2 H+ are pumped into intermembrane space of mitochondria -​ One of the e- of QH2 moves to Fe-S center while the second e- moves to heme bL.  -​ e- bound to Fe-S moves to C1 heme of cyt c1 -​ The other e- from Qo moves through bL to bH and finally to Q at Qi, creating a radical. -​ Q Cycle (CYCLE 2) -​ Cycle 1 repeats where Q radical gains another electron and 2 H+ to reform QH2. -​ This replaces the QH2 borrowed from the pool at the beginning of the cycle Steps of the Q Cycle: ​ 1.​ Oxidation of Ubiquinol (QH₂) ​ ​ A molecule of QH₂ binds to Complex III and donates two electrons: ​ ​ One electron is transferred to an iron-sulfur (Fe-S) center, then to cytochrome c₁, and finally to cytochrome c (which carries it to Complex IV). ​ ​ The other electron is transferred to cytochrome b, which passes it to a partially oxidized ubiquinone (Q) at the Q₀ site, reducing it to a semiquinone (Q ⁻). ​ ​ Two protons (H⁺) from QH₂ are released into the intermembrane space. ​ 2.​ Second Oxidation of Ubiquinol ​ ​ Another QH₂ molecule binds to Complex III and undergoes the same process: ​ ​ One electron goes to cytochrome c. ​ ​ The second electron reduces the semiquinone (Q ⁻) from the first step into fully reduced ubiquinol (QH₂) at the Qi site by picking up two protons from the mitochondrial matrix. ​ 3.​ Recycling of Ubiquinone ​ ​ The newly formed QH₂ can now re-enter the cycle and donate electrons again. ​ ​ The electron transfer contributes to the proton gradient, as each full cycle results in four protons (H⁺) being pumped into the intermembrane space. Importance of the Q Cycle: ​ ​ Helps maintain efficiency by splitting electrons from QH₂, directing them to different pathways. ​ ​ Contributes to the proton motive force, which drives ATP synthesis in Complex V (ATP synthase). ​ ​ Ensures that ubiquinone/ubiquinol is continuously recycled, sustaining electron flow through the ETC. -​ Path of e- through Complex IV -​ Complex IV has 13 subunits but 3 shown -​ Subunit 1 -​ Two heme groups near a single copper ion -​ Subunit 2 -​ Contains 2 copper ions complexed with the -SH groups of two Cys residues -​ Oxygen binds to heme a3 and is reduced to its peroxy -​ Subunit 3 -​ Essential for rapid proton movement through subunit 2 -​ Transfer of two e- from NADH to O2 is accompanied by outward pumping of 10 H+ -​ C1: 4 H+ -​ C3: 4 H+ -​ C4: 2 H+ -​ Generation and inactivation of toxic reactive oxygen species -​ Reactive radical ion superoxide (O2 -) -​ Converted to H2O2 by SOD -​ Reactive peroxide (H2O2) -​ Hydroxyl radicals (OH ) -​ H2O2 can be converted by metal ions such as Fe2+ to hydroxyl radicals -​ Synthesis of ATP by ATP synthase depends on pH gradient across the membrane -​ Thylakoid experiment -​ Thylakoid vesicle buffered in pH 4 -​ When lumen = pH of 4, vesicles were rapidly mixed with solution at pH 8 containing ADP and Pi -​ ATP synthesized accompanied H+ movement -​ Synthesis of ATP synthase in bacterial plasma membrane -​ F0: 1a +2b +10c -​ F1: (3a+3b) resting on y subunit + d subunit + e subunit -​ 10 C subunits = 10X 36º -​ 36º rotation per H+ -​ 1 full rotation = 3 ATP -​ 1 full rotation = 3 shaft rotations (1 shaft rotation = 120º) -​ 1 full rotation requires 10 H+ -​ Number of H+ needed to produce 1 ATP = 4 -​ Photosynthesis -​ Products of photosynthesis are starch and sucrose -​ Photosynthesis can be divided into four stages -​ 1. Absorption of light -​ 2. Electron transport leading to reduction of NADP+ to NADPH -​ 3. Generation of ATP -​ 4. C fixation -​ Structure of chlorophyll -​ Porphyrin ring with Mg2+ + phytol tail -​ Most important pigment for photosynthesis is chl. a -​ Multiprotein light harvesting complex (LHC) contains 90 chlorophyll molecules -​ Study Notes: Evolution of Oxygenic Photosynthesis -​ Evolutionary Changes in Photosynthesis -​ ​ Oxygenic photosynthesis required modifications to the photosynthetic machinery. -​ ​ ​ H₂O as an electron donor posed new energetic challenges. -​ 2. Energetics of Oxygenic Photosynthesis -​ ​ ​ Redox potential differences: -​ ​ ​ O₂/H₂O = +0.82 V -​ ​ ​ NADP⁺/NADPH = –0.32 V -​ ​ ​ Total difference = 1.14 V (minimum energy required for electron transfer). -​ ​ ​ Actual chloroplast function: Requires >2 V for electron transfer (more than theoretical minimum). -​ 3. Light Energy and Electron Transfer -​ ​ ​ 1 mole of 680 nm photons = 1.8 V energy change. -​ ​ ​ 1 photon (theoretically) enough to drive NADP⁺ reduction (1.14 V) under standard conditions. -​ ​ ​ In reality: Two separate light reactions are used to achieve electron transfer. -​ Photosystem 2 reaction center -​ Contains two molecules of chlorophyll a, two accessory chlorophylls, two pheophytins, two quinones, and one non heme Fe -​ Pheophytin is a chlorophyll molecule lacking a central Mg2+ ion -​ P680 is the strongest biological oxidant known. It can oxidize water to generate O2 and H+ -​ Purple bacteria use H2S and H2 as electron donors to reduce chlorophyll a -​ Mn/Ca Cluster -​ Closely associated with PS2 D1 protein at its luminal surface is a cluster of 5 metal ions (4 Mn2+ and 1 Ca2+)  -​ The Mn/Ca cluster is stabilized and protected by a number of peripheral proteins that form oxygen-evolving complex -​ Accumulates 4 successive “+” charges by passing electrons one at a time to the nearby P680 -​ Accomplished by passing e- through Tyr167 -​ Driven by the successive absorption of 4 photons of light -​ Cytochrome b6f -​ Equivalent to cytochrome c reductase in mitochondria -​ Receives electrons from quinone and engages in Q cycle -​ Hands electrons off to plastocyanin (pC) -​ Plastocyanin diffuses along membrane surface to PS1 and transfers electrons via ferredoxin to ferredoxin-NADP+ reductase (FNR), where they are used to produce NADPH -​ Stage IV photosynthesis (dark reactions) -​ CO2 + Ribulose 1,5-bisphosphate -​ Ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) then generates 3-phosphoglycerate -​ 3PG -> 1,3-bisphosphoglycerate -​ 1,3BPG -> G3P -​ G3P regenerates R-1,5-BP and a sugar which can be used to generate glucose, fructose, and sucrose. -​ Redox control of the Calvin Cycle -​ Thioredoxin reduces S=S groups of certain calvin-cycle enzymes, making them ACTIVE -​ In the dark, electron flow to thioredoxin ceases, sulfhydryl groups become oxidized, and become inactivated -​ C4 plants -​ Bundle sheath cells contain chloroplasts and are the site of the Calvin cycle