Biochemistry - I SPRING Mondays and Wednesdays 9:30-10:45 AM (MR-1307) Lectures Based on Profs. Kevin Gardner & Reza Khayat

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1 Biochemistry - I Mondays and Wednesdays 9:30-10:45 AM (MR-1307) SPRING 2017 Lectures Based on Profs. Kevin Gardner & Reza Khayat 1

2 Outline Anatomy of the mitochondrion Electron transfer Fractionation of the electron transport chain The electron transport chain Proton-motive force Reactive oxygen species (ROS) ATP Synthesis Architecture of ATP synthase (F0F1) complex The proton-motive-force energizes active transport Regulation Why learn about Oxidative Phosphorylation? This is where the majority of ATP is generated, downstream of glycolysis, the TCA cycle and fatty acid oxidation 2

3 Anatomy of the Mitochondrion 3

4 Anatomy of the Mitochondrion The cristae (leaflets, inner membrane) of the mitochondria serves as a platform for many copies of different enzymes to assemble in proximity for substrate shuttling (compartmentalization) These leaflets are home to tens of thousands of proteins responsible for the electron-transfer system, and ATP synthase The mitochondria of heart muscle, a muscle under constant activity, contains >3x the amount of electron-transfer systems than the liver mitochondrion (enzyme regulation) 4

5 Electron Transfer In oxidative phosphorylation, electrons are transferred via three mechanisms: 1. Direct transfer, such as reduction of Fe +3 to Fe +2 (e.g. cytochrome) 2. Transfer as proton H + and electron e - (e.g. flavins, FADH2) 3. Transfer as hydride ion :H (e.g. dehydrogenases, NADH) 5

6 Prosthetic Groups and Ligands involved in Electron Transport: Porphyrin Cytochromes Porphyrin-carrying proteins, similar to Hb and Mb Tightly, sometimes covalently, associated with flavoprotein Fe 3+ converted to Fe 2+ during reduction, as electrons transferred to oxidizing agent 6

7 Prosthetic Groups and Ligands Involved in Electron Transport: Iron-sulfur Centers (a) Cys Cys S S Fe S S Cys Cys (b) Cys S S S Cys Fe Fe S Cys S S Cys (c) Cys Cys S S S Fe Fe Fe S S S S Fe Cys S Cys (d) Protein Iron-sulfur proteins Iron associated with Cys or His AA, and inorganic sulfur different clusters found in different iron-sulfur proteins Clusters vary in complexity Some proteins have multiple clusters, can be of different types The reduction potential of the clusters vary by their environment (number of sulfurs and irons present, the geometry, and the neighbors) Rieske iron-sulfur proteins: One Fe atom is coordinated to 2 His rather than 2 Cys 7

8 Additional Prosthetic Groups and Ligands Involved in Electron Transfer Ubiquinone = coenzyme Q = Q Capable of carrying 2e- and 2H + Remember that H + + e - can also be written as H Water soluble and released into solution by enzyme Carries :H -, H + released into solution FAD <=> FADH2 Either tightly or covalently bound to flavoproteins (e.g. succinate dehydrogenase in TCA) 8

9 Oxidative phosphorylation uses energy released from oxidation of metabolites to produce ATP Electrons flow from more negative reduction potential to more positive electron potential (top to bottom of table) Note how all the cytochromes use Fe +3 Fe +2 oxidation yet have different reduction potentials. The ligand environment of the Fe +3 results in different reduction potential 9

10 Calculating Free Energy Change from Redox Reactions (Sect 13.4) Note free energy related by negative of delta E Remember to pair two half-reactions, and invert sign on oxidation, e.g.: oxidization: NADH + H + -> NAD + + 2H + + 2e - = V reduction: 0.5(O2) + 2H + + 2e - -> H2O = V net: NADH + H + 0.5(O2) -> H2O + NAD = 1.137V : favorable n = number of electrons involved Faraday s constant (F) = 96,500 J / (V mol) Chapter 13 - Bioenergetics 10

11 Determining Order of Electron Transfer Method 1 - Spectroscopic: 1. This requires that you know and can spectroscopically characterize all the players 2. Remove O2 and reduce the entire system by providing reducing agents (NADH + H + ) 3. Add O2 and spectroscopically identify which component is oxidized first, second, third The species that gets oxidized first is the species that is closest to O2 in the electron transport chain. rotenone NADH Q Cyt b Cyt c 1 Cyt c Cyt (a a 3 ) O 2 Method 2 Chemical inhibitors: 1. Identify inhibitors that kill the electron transport chain 2. Add inhibitor to electron transport chain and identify which components are oxidized and which components are reduced 3. Oxidized components are to the right of the inhibitor and reduced components are to the left of the inhibitor 4. Use many inhibitors to identify the order of components 11

12 Fractionation of the Electron Transport Chain Outer membrane dissolved and washed away with detergent Inner membrane fragmented by osmotic pressure (i.e. water leaking in) Inner membrane fragments solubilized with detergents Fractionation done by ion-exchange chromatography 12

13 The Electron Transport Chain I) NADH dehydrogenase II) Succinate dehydrogenase (TCA, Rx 6) III) Ubiquinone:Cytochrome c oxidoreductase IV) Cytochrome oxidase Electron transport chain serves to: oxidize the reducing agents (NADH and FADH2) generated during glycolysis, TCA, and FA oxidation generate a proton gradient across the mitochondrion membrane Proton gradient stores energy that is used to condense ADP and Pi to ATP by ATP synthase 13

14 The Role of Ubiquinone/Coenzyme Q/Q Electrons from a variety of sources are passed to Q Complex 1 uses electrons from NADH+H + Complex 2 uses the FADH2 generated in the oxidation of succinate to fumarate (TCA Rx 6) Glycerol 3-phosphate dehydrogenase uses FADH2 generated during glycerol oxidation Electrons from FADH2 generated in the first step of fatty acid oxidation is passed to Q Role of Q is to transport electrons Q remains in and travels across membrane bilayer 14

15 Coenzyme Q Structure - Membrane association, Redox Sites 15

16 Complex I NADH dehydrogenase 42 different polypeptide chains six Fe-S clusters/centers FMN is the prosthetic group (+) (-) similar to FAD Coupled processes carried out by Complex I: Exergonic transfer 2e - from NADH to Q, and two proton from matrix to Q Endergonic transfer of 4 protons from matrix to intermembrane space NADH 5H N Q NAD QH 2 4H P 16

17 Complex II Succinate dehydrogenase (enzyme 6 in TCA) Four polypeptide chains 5 prosthetic groups FAD is tightly bound to enzyme Transmembrane domains with cytoplasmic extensions Transfers electrons to FAD from oxidation of succinate fumarate Heme b acts to protect against formation of reactive oxygen species by electrons that interact with O2 Purpose is to generate QH2 No H + are transported 17

18 Fatty Acid Oxidation First step in β-oxidation involves generation of FADH2 FADH2 needs to be oxidized to FAD + FAD + cannot be released into solution Electrons are passed from one flavoprotein to another The final protein ETF:Q passes the electrons to Q to make QH2. 18

19 Complex III (+) (-) Cytochrome bc1 has 11 polypeptide chains (subunits) Complex is a homo-dimer of two cytochrome bc1 Hemes bh, bl, c1, and Q shuttle electrons Rieske iron-sulfur protein swivels between Heme bl and c1 2Fe-2S receives electrons from Qp when it s close to Qp 2Fe-2S donates electrons when it s closer to Heme c1 Transfer of H + out of matrix, next slide 19

20 Heme a Complex III Intermembrane space (P side) Cyt c Cyt c electrons transported to complex IV QH2 Heme b L Heme b H Q Matrix (N side) Heme c 1 Cyt c 1 e e QH 2 e e e Q Cytochrome b e 2Fe-2S Q Q 2H + Q QH2 e e QH 2 e e e 2H + e Q Q Q 2H + Q QH 2 QH 2 (+) (-) QH 2 Q cyt c 1 (oxidized) Q Q 2H P cyt c 1 (reduced) QH 2 2H N cyt c 1 (oxidized) QH 2 Q 2H P Q cyt c 1 (reduced) Net equation: QH 2 2 cyt c 1 (oxidized) 2H N Q 2 cyt c 1 (reduced) 4H P FIGURE The Q cycle, shown in two stages. The path of electrons through Complex III is shown by blue arrows. In the first stage (left), Q protons per Q molecule (four protons in all) into the intermembrane space. Each QH 2 donates one electron (via the Rieske Fe-S center) to QH2 (on top) on the N side passes is reduced to the one semiquinone electron radical, which in to the second stage (right) is converted to QH 2Fe-2S cytochrome and c another to Heme bl QH2 passes its two H + 1, and one electron (via cytochrome b) to a molecule of to 2. Meanwhile, on the P side of the Q near the N side, reducing it two steps to QH the intermem. space to increase electro. 2. This reduction also pot. membrane, two molecules of QH 2 are oxidized to Q, releasing two uses two protons per Q, which are taken up from the matrix. 2Fe-2S passes electron to Heme c1 which passes it to Cyt c The Heme bl electron is passed to bh then to a Q to generate Q (a) The same reaction happens again, except that Q picks up two protons Intermembrane from the mitochondrial space matrix (b) (P side) Thus, 2QH2 pass 4H + to intermem. space and pull 2H + from matrix space Heme a Met Cys His Cys 20

21 Complex IV electrons transported from complex III (+) (-) Uses binuclear Fe-Cu center (Heme a3 and CuB) Has 13 subunits and the 3 shown in right image are most important Needs 4 electrons from complex III (each Cyt c carries only 1 e-) 2e - from 2Cyt c are passed to Heme a3 to reduce O2 to O H + are shuttled from matrix to balance charge at Heme a3 This is repeated to make 2H2O molecules 4H + are also pumped into the inter membrane space Thus 8H + from the matrix are needed to generate 2H2O 21

22 (b) molecule of Complex III (red; from yeast) and two of Complex IV The Electron Transport Chain mposed of Complexes III ing Complexes III and IV, copy after staining with dreds of images were ave x-ray structures of one (green; from bovine heart) could be fitted to the electron-density map to suggest one possible mode of interaction of these complexes in a respirasome. This view is in the plane of the bilayer (yellow). Much of this energy is used to pump protons out of ondria, the actions of the matrix. For each pair of electrons transferred to O2, tual [NADH]/[NAD!] four protons are pumped out by Complex I, four by ee-energy change for Complex III, and two by Complex IV (Fig ). The is therefore substanvectorial equation for the process is therefore "220 kj/mol. A simisuccinate shows that! NADH! 11HN! 12O2 NAD!! 10HP!! H2O (19 7) $ for fumarate/succier, but still negative, The electrochemical energy inherent in this difference The electron transport chain serves to oxidize the reducing agents (NADH and ut "150 kj/mol. in glycolysis, proton concentration and Oseparation of charge FADH ) generated during TCA, and FA with. 2 2 These are highly exergonic reactions and the released energies are used to generate a proton gradient across the mitochondrion membrane CytADP c This energy is used to condense and Pi to ATP + II III 4H IV + 2H22

23 Reactive Oxygen Species (ROS) Flow of e - results in oxide O2 - formation (superoxide free radical) Under normal conditions 0.1-4% of O2 is converted to O2 - (lethal levels) Superoxide dismutase gets rid of the superoxides 2 O 2 2H H 2 O 2 O 2 NAD + Nicotinamide nucleotide transhydrogenase NADPH I NADH NADP + Q NAD + glutathione reductase Inner mitochondrial membrane O 2 OH. Q O 2. GSSG 2 GSH III superoxide dismutase H 2 O 2 glutathione peroxidase H 2 O Cyt c IV Hydrogen peroxide is reduced to water with use of GSH (GSSG is formed, previously discussed) oxidative stress inactive S Enz S SH SH active 2 GSH protein thiol reduction GSSG 23

24 Proton-motive Force Electron passing/transporting and proton pumping generate an electrochemical gradient The gradient is between the mitochondrion matrix and intermembrane space (NOT cytosol!) Composed of chemical and electrical potential energy Energy can be converted to ATP 24

25 ATP Synthesis 25

26 ATP Synthase (F0F1) Complex F1 hydrolyzes ATP F0 destroys electrochemical gradient F1 and F0 together synthesize ATP ATP synthase binds ATP (Kd=10-12 ) stronger than ADP+Pi (10-5 ) Binding energy of ATP responsible for condensation (endergonic) reaction Protons responsible for releasing ATP from ATP synthase ATP (in solution) G (kj/mol) ES P ADP P i E ADP P i [E ATP] 0 E S Typical enzyme Reaction coordinate ATP synthase 26

27 Architecture of ATP Synthase (F0F1) Complex Determined using biochemical, biophysical, and structural (X-Ray and cryo-em) studies F1 (alpha, beta, gamma, epsilon) F0 (c10, a, b2, δ) The C10, epsilon and gamma rotate as protons flow from P side to N side With each incremental turn, the gamma subunit associates with different alpha-beta pair This interaction results in conformational change in beta Beta converts ADP+Pi to ATP Reversible! F1 F0 27

28 Linkage Between Motion & Catalysis: ATP Synthase 3 non-equivalent binding sites ATP ADP+Pi empty Proton flow causes gamma shaft to turn (arrow) ATP is released from beta facing the gamma shaft ADP+Pi condenses to generate ATP ADP+Pi occupy new empty space ~3 H + are needed per turn 28

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30 Artist s Rendition of ATP Synthase in Action URL: 30

31 The Proton-motive Force Energizes Active The proton force also used to move molecules into and out of the matrix Antiporter transports driven by concentration gradient ATP (higher negative charge) moves into the intermembrane space (plus charge) ADP (lower negative charge) moves into the matrix Net change of (-)-charge in the inter-membrane space Pi is H2PO4 - at physiological ph Symporter transports driven by H + H2PO4 - and H + (0 net charge) Transport 31

32 Re-oxidizing the NADH Generated via Glycolysis Oxidize the NADH generated during glycolysis NADH/NAD+ cannot be transported across mitochondria inner membrane In liver, kidney and heart: Malate-aspartate shuttle 32

33 (e - c e - m) In skeletal muscle and brain: glycerol 3-phosphate shuttle GPDH isozymes:cytosolic, mitochondrial intermembrane space, and mitochondrial, associated with intermembrane NADH+H + diffuse through outer membrane (<5000 Da) GPDHc reduces DHAP to G3P with NADH GPDHm oxidizes G3P to DHAP to create FADH2 FADH2 passes electrons to Q Intermembrane space (P side) CH 2 OH CHOH NAD + Glycerol 3- phosphate CH 2 O P Matrix (N side) cytosolic glycerol 3-phosphate dehydrogenase FAD FADH 2 QH 2 Glycolysis NADH + H + Dihydroxyacetone phosphate CH 2 OH C O mitochondrial glycerol 3-phosphate dehydrogenase CH 2 O P III 33

34 The NAD+/NADH Pool The pool of NAD+/NADH in the mitochondria is distinct from the cytoplasm Mitochondria responsible for oxidizing both pools of NADH to NAD+ NAD+ and NADH can cross the outer but not inner mitochondrial membrane Shuttle systems act to oxidize cytoplasmic NADH using oxygen present in mitochondria Mitochondria can synthesize its own NAD+ NAD+ precursors can be transported into and out of mitochondria 34

35 Regulation Oxidative phosphorylation works best with O2 +O2 = 32ATP/glucose -O2 = 2ATP/glucose O2 consumption also regulated by [ADP+Pi] Under low O2 (hypoxia) proton-motive force collapses, leading to drop of ph. ATP synthase runs in reverse IF1 dimerizes at ph 6.5 Dimer of IF1 inhibits reverse ATP synthase --why does the ph drop? 35