Electron Transport Chain Notes

El ectron ctron Tr anspo ansport rt Chain Intermembrane space: serves to localize & concentrate enzymes enzymes (i.e. Cyt C) Matrix: rich in enzymes & substrates involved in ATP synthesis/receives O2 & fuel delivered by blood flow/ FattyAcid degradation & TCA = primary sources of NADH & FADH2 substrates to ETC Inner Membrane (IM)  Composed of 3 lipids: Phosphatidyl-Choline (PC-3)/Phosphatidyl-Ethanolamine )/Phosphatidyl-Ethanolamine ( PE-2)/Cardiolipin (diphosphatidyl (diphosphatidyl glycerol) ( CL-1)these 3 make up most of the lipids in the IM but it also contains neutral & other phospholipids. phospholipids. Cardiolipin: Unique to inner membrane/not seen in the outer or any other membrane in cell.  IM Extremely high in proteins (65-80%) of membrane  ETC complexes I, II, III, IV are located here! Cristae: folded to increase surface area for enzyme amount/restrict diffusion thru matrix & w/in inter-membrane space/allows localized pH gradients (chemical & electrical) across the inner membrane Outer Membrane (OM)  OM 20% protein  Has mito porin VDAC (Voltage-Dependent Anion Channel) makes OM permeable to molecules <6000 Daporous so has no chemical or electrical gradient ENZYMES in diff Mito Compartments Outer Membrane Intermembrane Space VDAC Cytochrome C  

Inner Membrane ETC enzyme  Complexes  ATP Synthase (Fo Fo Subunit) Subunit)  (transporters for metabolites=AT P, pyruvate & citrate)

 



Matrix ATP synthase (F1 (F1 subunit) TCA enzymes (Citrate Synthase/Isocitrate Dehydrogenase/Fumarase/M alate Dehydrogenase Dehydrogenase Fatty Acid Oxidation enzymes

Know the Chemiosmotic theory Peter Mitchell (1978) proposed that an electrochemical gradient (proton/electrical gradient) is formed across IM by the flow of electrons thru the respiratory chain & in turn ATP molecules are synthesized by the gradient .  The inter-membrane space typically has has more H+ so its pH is lower than the Matrixmatrix side more basic by 1.4 pH units, So So membrane potential potential across IM, IM, (+) outside (-)inside matrix (less protons). protons).  When protons move from cytosolic side to matrix, the free energy will be -21.8 kJ/mol (spontaneous & can be coupled to drive drive other rxns Electrical Potential Diff  Voltage / Proton Concentration Diff  Osmotic Pressure Proton-motive Force (PMF): 1) Is generated by ETC 2) pH gradient & membrane potential used to drive ATP synthesis

Understand the role of the electron transport chain in the cell. ETC:: composed of 4 physically separable units (Complexes) ETC The oxidation/reduction rxns of Complex I, III, IV=result in pumping protons out of the matrix creating a proton potential potential (electrochemical (electrochemical potential=EP) potential=EP) The EP is then used by ATP synthase to drive phosphorylation of ADP to ATP

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Proton pumping=ETC ATP synthesis=uses Proton Motive Force Oxidative Phosphorylation=Process for making ATPresponsible for 34 of the 36 ATP molecules formed by the oxidation of one glucose molecule. Cell obtains energy from foodenergy from oxidation of Fatty acids & sugars coupled to reduction of NAD & FAD to form NADH & FADH2which are then Oxidized by mito ETCenergy from these oxidative-reductive oxidative-reductive events is utilized to make ATP which is used by the cell for biosynthetic rxns, rxns, active transport systems & other energy requiring processes! 1) Glycolsis in cytosol 2) Pyruvatemito matrix by Pyruvate Carrier 3) PDH complex converts Pyruvate Acetyl CoA 4) TCA takes Acetyl CoA to produce NADH & FADH2 5) ETC uses these for electrochemical potential potential 6) ADP  ATP via ATP Synthase Summary: Energy from oxidation rxns converted into EP, & then the energy of EP is used for phosphorylation of ADP to ATP= entire process is Oxidative Phosphorylation Phosphorylation Know the names (and alternative names) of the components of the electron transport chain: Complex I, Complex II, Complex III and Complex IV. ETC complexes are enzymes for oxidation/reduction of substrates Alternate Names Sub Prosthetic Oxidant/Reductant # Protons Inhibitors/ units Group Pumped Diseases FMN: 2e45 Matrix: NADH 4 I NADH Dehydrogenase Amytal NADH-Q Oxidoreductase Oxidoreductase acceptor/ Membrane core: Q Rotenone Hydride) Myxothiazol NADH-Coenzyme Q Reductase Fe-S: 1e NADH: Ubiquinone Ubiquinone Piericidin A LHON/MELAS Oxidoreductase carrier Leigh Syndrome Dehydrogenase 4 Matrix: Succinate 0 II Succinate Dehydrogenase FAD Malonate Membrane core: Q Succinate-Q Reductase Fe-S Leigh Syndrome Complex Certain Tumors 11 Membrane core: Q 4 Stigmatellin Stigmatellin (P) III Q-cytochrome c Heme bH Cytoplasm: Myxothiazol Myxothiazol (P) oxidoreductase Heme bL Antimycin A (N) Ubiquinone: Cyto c Cytochrome c Heme c1 Oxidoreductase Ilicicolin (N) Fe-S Cyto b-c1 Reductase Encephalomyop Cyto bc1 Complex athy IV Cytochrome c Oxidase 13 Cytoplasm: 2 Heme a Cyanide/Azide Cytochrome Oxidase Cytochrome c Heme a3 CO CuA & Encephalomyop CuB athy/Myopathy Oxidases: catalyze the removal of Hydrogen from a substrate using O2 as hydrogen acceptor They form H20 or H2O2 as rxn product AH2(red) + 1/2O2  A(ox) + H2O AH2(red) + O2  A(ox) + H2O2 Oxidation-Reduction rxn w/o using Dehydrogenases: transfer hydrogen from 1 substrate to another in coupled Oxidation-Reduction molecular O2  AH(red) + B(ox)  A(ox) + BH(red) **Reductase = reduct(ion)ase = oxidoreductase oxidoreductase







Complex oxidizes NADH & reduces Q (Ubiquinone/Coenzyme)  QH2 (Ubiquinol) = favorable rxn & complex uses some of this energy to pump 4 protons out of matrix into inter-membrane space generating EP across inner membrane. 3 Steps: Step1: Oxidation of NADH NADH NAD + H+ (matrix) + 2eStep2: Reduction of Coenzyme Q Q + 2e- + 2H+ (matrix)  QH2 (contains stoichiometric stoichiometric protons) Step3: Proton pumping 4H (matrix)  4H+ (cytosol) Net equation: NADH + Q + 5H+ (matrix)  NAD + QH2 + 4H+ (cytosol) # of cofactors participate in Complex I: simultaneously sly from NADH & transfers them 1 at a time to 1e- carriers Fe-S clusters. FMN accepts 2e- (Hydride) simultaneou These electrons reduce membrane-embedded membrane-embedded Q(oxidized) to QH2(reduced) in two 1electron steps/ CoQ is freely diffusible in the lipid bilayer & can shuttle 2 reducing equivalents equivalents (electrons). The electrons in quinols will be shuttled to Complex III & eventually to O2 via complex 4. Dinucleotide made from vitamin Niacin) NADH = carries 2 electrons (Nicotinamide Adenine Dinucleotide FMN = accepts 2 electrons (but can transfer 1 at a time) (Flavin Mononucleotide) Mononucleotide) Clusters:: can only accept 1e- at a time/ (ferric) Fe 3+ Clusters Fe 2+ (ferrous) Fe = cluster of single iron bound to 4 Cys residues 2Fe-2S = 2 clusters w/ ions bridged by sulfide ions 4Fe-4S = 4 clusters bridged by 4 sulfide ions Protons pumped per pumped per NADH: the electron flow results in pumping 4 protons to inter-membrane space and uptake of 2 protons from mito matrix to QH2 Inhibitors Amytal (barbiturate drug/sleeping pill): Non-selective Non-selective CNS depressants that are primarily used as sedative hypnotics. Binds to Quinone site of Complex I stops H+ pump↓ ATP synthesis↓ energygo to sleep Rotenone (insecticide from plant): isolated from plant roots & people catch fish by releasing root extracts to H2O Myxothiazol (antibtiotic)/ (antibtiotic)/Piericidin A (antibiotic) All inhibit e- transfer rxns from Fe-S Fe -S clusters to Q blocking the the overall process of oxidative oxidative phoshorylation phoshorylation Diseases Encephalomyopathy w/ Lactic Acid&Stroke-like Episodes/Leigh Syndrome Leber Hereditary Optic Neuro /Mito Encephalomyopathy 

Complex II (aka ( aka Succinate Dehydrogenase/Succinate Dehydrogenase/Succinate CoQ Reductase=SQR ): ): SMALLEST  4 subunits 2 Reactions: Rxn1: Succinate + FAD(enzyme-bound) FAD(enzyme-bound)fumarate + FADH2(enzyme-bound) FADH2(enzyme-bound) Rxn2: FADH2 + QFAD + QH2 Net Rxn: Succinate + Q  fumarate + QH2 FAD (covalently bound) and non-heme 2Fe-2S & 4Fe-4S are the cofactors for Succinate Dehydrogenase. FADH2 synthesized from the oxidation of succinate & still bound to enzyme (SDH), undergoes further oxidation/reduction oxidation/reduction rxns to pass e - to Q NO proton pumping: so the favorable energy of rxn is not conserved for ATP synthesis. But the energy passed down to Q will be used by Complexes III & IV to pump protons out of the matrix, contributing to ATP synthesis Inhibitor: Malonate Inhibitor: Malonate Diseases: Leigh Syndrome & Syndrome & certain tumors result from defects in Complex II due to mutations coding the protein

Reductase/CoQ-cytochorme c Oxidoreductase) Oxidoreductase) Complex III (aka Cytochrome b-c1 Reductase/CoQ-cytochorme







QH2 + 2Cyt c(oxidized) + 2H+ (matrix) Q + 2Cyt c(reduced) + 4H+ (cytosol)  The energy of oxidation of QH2 is converted into EP by pumping 2 protons from matrix to intermembrane space=less than half of what Complex I does so ATP amount made from this energy is half too  Cyt c(oxidized) = Fe3+ & Cyt c(reduced) = Fe2+ Protons pumped per NADH: each half of the Q cycle pumps 2 protons out of the matrix = total of 4H+ Inhibitors: Stigmatellin & Myxothiazol bind to Psite, blocking ETC rxns btw QH2 & Cyt c. (PMS) Streptomyces bacteria/used bacteria/used in fish fish poison (piscicide) (piscicide) & Ilicicolin bind to Nsite blocking Antimycin A: A: produced by Streptomyces the enzyme too. (NIA) Disease: Encephalomyopathymuscle & nervous system dysfunction dysfunction Complex IV (aka Cytochrome c Oxidase= COX)  13 subunits (integral membrane protein w/ distinct polypeptides)  Prosthetic groups: CuA/CuA center, CuB center, Heme a, Heme a3 (all are 1e- acceptors & participate in electron transfer rxn). Heme a-CuB site=site of reduction of molecular O2 to H2O (where O2 binds). Cyt c is 1e- carrier  e- carried by Cyt c (from reduction of QH2 by complex III) are shuttled to Cyt c Oxidase (Complex IV). The e- are then used to pump protons out of matrixconsumed by O2 resulting in H2O (reduction of O2) 2 Reactions Rxn1: Reduction of O2 to H2O 4 Cyt c(reduced) + O2 + 4H+ (matrix)  4 Cyt c(oxidized) + 2H2O Rxn2: Pumping of 4 protons out of Matrix 4 H+ (matrix)  4 H+ (cytosol) Net Rxn: 4 Cyt c(reduced) + O2 + 8H+ (matrix)4 Cyt c(oxidized) + 2H2O + 4H+ (cytosol) Overall rxn results in loss of 8 protons from matrix creating a pH gradient. 4 protons are protons are stoichiometric and the other 4 result from cytochrome oxidase acting a proton pump Cytochrome c Oxidase Rxn Cycle  Rxn mechanism of 4 e- reduction of O2 to H2O in cytochrome oxidase  Cycle begins & ends w/ all prosthetic pro sthetic groups in their oxidized forms  Cytochrome C is in the Inter-membrane space, space, so the active site for this rxn this rxn w/ Cytochrome C is on the cytosolic side of the inner membrane  4 cyt c molecules donate 4e-, which, in allowing binding & cleavage of an O2 molecule, also makes possible the import of 4 protons from matrix to form 2 molecules of H2Owhich are released from the enzyme to generate the initial state. 1) 2 molecules of cyt c sequentially transfer e- to CuA/CuA to Heme a Heme a3 then to CuB (both reduced) (Heme a3 has a high affinity for molecular O2 & binds it) 2) Reduced CuB & Fe in Heme a3 bind O2 (reducing it), which forms a Peroxide Bridge 3) 2 more Cyt c molecules add 2 more e- reducing O2 resulting in cleavage of Peroxide Bridge & uptake of 2 protons 4) The addition of 2 more protons leads to H2O release (from rxn btw Hs & OHs bound to Heme a3 & CuB) Protons pumped per NADH: 2 total because only use ½ O2. Inhibitors: Cyanide (CN-), Azide (N3-) & Carbon Monoxide (CO) inhibit Cyt c oxidase by binding to Heme a3/CuBthey block O2 from binding to these prosthetic groups! (CoCA) Diseases: Encephalomyopathy & Myopathy







Summary of ETC: NADH oxidation via Complex I, III and IV: Complex I:

NADH + Q + 5H + (m)

NAD+ + QH2 + 4H+ (c)

Complex III: QH2 + 2 Cyt c (ox) + 2H+ (m)

Q + 2Cyt c (red) + 4H+ (c)

Complex IV: 2 Cyt c (red) + 4H+ (m) + ½ O2 2 Cyt c (ox) + H2O + 2H+ (c) --------------------------------------------------------------------------------------------------------NADH + 11 H +(m) + ½ O2 NAD+ + H2O + 10 H+ (c)

FADH2 oxidation Complex II: FADH2 + Q

via Complex II, III and IV: FAD + QH 2

Complex III: QH2 + 2 Cyt c (ox) + 2H+ (m)

Q + 2Cyt c (red) + 4H+ (c)

Complex IV: 2 Cyt c (red) + 4H+ (m) + ½ O2 2 Cyt c (ox) + H2O + 2H+ (c) --------------------------------------------------------------------------------------------------------FADH2 + 6 H+(m) + ½ O2 FAD FAD + H2O + 6 H+ (c) where m= matrix, c= cytosol

Know how the energy from the oxidation-reduction reactions in the electron transport chain is saved for the synthesis of ATP (formation of a proton gradient across the membrane). Some of the energy released from the oxidation of NADH & reduction of O2 is conserved as a form of electrochemical gradient by proton pumping actions of Complexes I, III, & IV the energy conserved @ these 3 steps is utilized by mitochondrial ATP synthase to make ATPs Understand the Thermodynamics of the ETC. Know how the standard free-energy change (ΔG°’) and change in standard reduction potential (ΔE°’) are related in oxidation reduction reactions.

Half-rxns

Standard Reduction Potential

½ O2 + 2H + 2e  H2O

ΔE°’ = +0.82 V

NAD + H + 2e  NADH

ΔE°’ = -0.32 V

Full rxn is (a)-(b) = (c)

ΔE°’ = +1.14V

NADH + H + ½ O2 O2  H2O + NAD

If rxn is exothermic (energy released)= +∆E. ΔG°’ = nF ΔE°’ (n = # of electrons & F = Faraday’s constant = 96, 485 C/mol) ÷ 4.185 J/cal ÷1000 = kcal/mol The ∆E of rxn for NADH oxidation & O2 reduction is 1.14volts or ∆G=∆G=-52.6 kcal/mol (this kcal/mol (this energy drives the etransport & proton pumping)

NADH has a negative negative reduction potential (strong (strong reducing agent agent wants to donate donate e-) O2 has a positive reduction potential potential (strong oxidizing agent wants to accept e-) The flow of Electrons proceed down a thermodynamically favorable pathway (NADFMNCoQCytbCytc1CytcCytaCyta3O2)







L ectur e 17 ATP Synthase Structure: Fo:: integral membrane component a/b/c subunits Fo  Proton turbine  ‘O’= oligomycin oligomycin-sensitive  a proton channel/c channel/c subunits form a concentric concentric c-ring in membrane F1:: peripheral membrane protein α/β/γ/δ/ε F1  ATPase (enzyme activity)  γsubunit inserted into α3β3 hexamer ring (catalytic (catalytic unit) which is fixed to the a subunit via subunit b (stator) γ breaks symmetry in the α3β3 hexamer  hexamer ring Stationary part (stator): (stator): α, b2, δ, & α3β3 Moving part (rotor): (rotor):c-ring & γε stalk (tightly attached to c-ring)  rotation of this is propelled by the proton gradient proton enters from the the intermembrane intermembrane space into the cytoplasmic half-channel half-channel to neutralize neutralize the charge on Asp61 Asp61 in csubunit (the proton is attracted to the negative charge of the carboxylate) with the charge neutralized the c ring can rotate clockwise by 1 c subunit moving the Asp residue out of membrane into matrix half-channel  this proton can move into the matrix, resetting the system to its initial state. 10protons/revolution (10 subunits). Understand the binding-change mechanism of mechanism of ATP synthesis Rotation of the γε stalk interconverts the 3β subunits btw 3 diff conformations. Rotates CW from top & CWW from bottom 360◦ rotation of the γsubunit will lead to synthesis and release of ATP from each subunit 1) O pen form: form: ATP release/ADP + P bind loosely 2) Loose form: form: ADP + Pi are bound tightly. ATP in T form can not be released until site is filled by ADP & Pi 3) Tight form: form: ATP present in equilibrium w/ ADP + Pi. Exchange occurs btw H2O & Pi. Energy (from proton gradient) is required to change its conformation to O form so ATP can be released. OLTOLT Know Common Inhibitors of ATP Synthase 1) F1 Inhibitor Protein: naturally occurring protein in the mitofunction is to prevent ATP hydrolysis by ATP Synthase under conditions that the mito is ATP rich & not synthesizing ATP

Chemical Inhibitors: both natural and syntheticinhibit both synthesis & hydrolysis of ATP 2) Aurovertin Bsite of action F1a poisonous mushroom binds to βsubunit inhibiting ATP synthase 3) Dicyclohexyl-carbodiimide (DCCD) site of action Foreacts to free caboxylate groups that are in hydrophobic environments environments forming a covalent bond 4) Oligomycinsite of action Fobinds to δ subunit. Both (D&O) prevent the influx of protons by ATP synthase

Carrier systems of the inner mitochondrial membrane 5 Types 1. ATP/ADP Translocase:  Function: shuttle ATP of out (export) & bring ADP in (import) to mito when ADP is brought in it is phosphorylated then exported out









Electroneutral but alters the proton gradient by bringing a proton into the matrix  Combining the ADP & Phosphate carrier together, Phosphate & ADP (substrates for ATP synthesis) are brought into the mito, which effectively brings along a single H+ 3. Other Carriers  Include those of Pyruvate (Pyruvate/OH-), Dicarboxcyclic Dicarboxcyclic Acid (Phosphate/Malate), (Phosphate/Malate), Tricarboxycyclic Tricarboxycyclic Acid (Malate/Citrate+H) (Malate/Citrate+H) & Amino Acid Carriers 4. Malate-Aspartate Shuttle (liver & heart)  Function: shuttles reducing equivalents from NADH, via OXA reduction to Malate things to know listed below:  Aspartate is involved in transamination rxn w/ α-KG α -KG to form OXA & Glu both in matrix & cytosol  OXA is reduced by NADH to form Malate  Malate transverses the membrane  NAD+ is reduced to NADH w/ oxidation oxidation of Malate Malate back to OXA  NADH is effectively, effectively, but not actually, actually, transferred across the the membranethe reducing equivalents are transferred across the membrane 5. Glycerol Phosphate Shuttle (present in brain)  Function: shuttle reducing equivalents for FADH2  Glycerol-Phosphate Glycerol-Phosphate is formed from the reduction of Dihydroxyacetone Phosphate by NADHwhich is able to transverse the mito membrane  Once inside the mito it is converted to DHAP via FAD+ linked enzyme (G3PDH) forming FADH2  Net loss of 1 ATP per NADH because FADH2 FADH2 is @ a lower potential potential than FMN FMN from NADH dehydrogenase dehydrogenase & only provides enough enrgy for 2 ATPs via ETC So the NADH made in the cytoplasm during glycolysis go into the matrix by shuttles (not by carriers) 

Know how many ATP molecules can be synthesized from the complete oxidation of a glucose molecule 30 (glycerol phosphate) 32 (malate-aspartate) Note: Anaerobic metabolism yields only 2 molecules of ATP one of the effects of endurance exercise is to increase the num of mito & blood vessels in muscle  thus increasing the extent of ATP generation by Ox/Phos P/O Ratio: Number of Pi consumed consumed per oxygen oxygen atom in ATP synthesis by mito mito aPi + aADP + ½ O2 + H + NADH (or FADH2) aATP + NAD (or FAD + H) + H2O ~2.5 (10/4) & for FADH = ~1.5 (6/4) a = P/O ratio for NADH = ~2.5 (10/4) Summary of yield of ATP by OxPhos of Various Reducing Equivalents Glycerol 3-Phosphate (NADHFADH2) 1.5 ATP   Malate-Aspartate (NADH) 2.5 ATP







Understand the actions of uncoupling proteins and chemical uncouplers Heat generation by mito: Nonshivering Thermogensis by uncoupling Proteins. In animals, brown fat is a specialized tissue that generates heat uncoupling proteins dissipate the proton gradient, generating heat w/o ATP synthesis. UCP1 (aka thermogenin): present in the inner inner mito membrane membrane forms a pathway for the flow of protons from the Cytoplasm to Matrix energy of proton gradient is released as heat. This dissipative proton pathway is activated when the core body temp begins to fall, the release of hormones triggered by the temp drop leads to liberation of free fatty acids from triacylglycerols that in turn activate UCP1. 2,4-dinitrophenol (DNP): uncouples the tight coupling of electron transport & phosphorylation in mito. It is able to cross the membrane as a charged species & has a proton w/ a pka around 7.0 ETC keeps running w/ uncoupler because it is t rying to make up for ATP deficit the loss of respiratory control leads to increased O2 consumption and oxidation of NADH. Reactive oxygen species (ROS) generation and their roles are in tissue aging and apoptosis. In hypoxic cells (stroke/heart attack) there is an imbalance btw the input of electrons from fuel oxidation in mito Species. matrix & transfer of electrons to molecular O2 this leads to formation of Reactive Oxygen Species. Complex I & III are the primary sites of ROS generation: in Complex I, superoxide is produced in the bound flavin facing the matrix side. In Complex III, superoxide is formed @ the ubiquinol oxidation site (Qo site, center P) facing the intermembrane space. Superoxide: is produced when there is a transfer of 1 electron to molecular O2 Peroxide: produced when there is a transefer of 2electrons to O2 Hydroxyl Radical (Fenton rxn): Fe2 + H2O2  Fe3 + OH + OH produced when peroxide peroxide reacts w/ w/ reduced iron. This This radical is very reactive can damage DNAexample: guanine base reacts w/ 2 hydroxyl hydroxyl radicals to forms H2O & 8-oxoguanine 8-oxoguanine which can incorrectly base pair w/ adenine during DNA replication resulting in a G-C to T-A base pair substitution=mutation in amino acid in protein Oxidative damage by ROS has been implicated in apoptosis (programmed cell death)/ cellular injury during ischemia & reperfusion/ aging process / pathophysiology of neurodegenerative diseases including Parkinson, Huntington & Alzheimer’s/ cellular signaling Defense Mechanisms against the ROS 1) Superoxide Dimutase (SOD): catalyzes the degradation of superoxide radicals into hydrogen peroxide (H2O2) & O2. 2 forms: manganese-containing manganese-containing in mito (MnSOD) & copper-zinc dependent in cytoplasm (Cu/ZnSOD). Amyotropic Lateral Sclerosis (ALS) or Lou Gehrig’s Disease : is caused by a mutation in gene coding for cytosolic SOD it is a rapidly progressive, invariably fatal neurological disease that attacks nerve cells responsible for controlling voluntary muscles.







2) Integration Phase: Pro & anti-apoptotic metabolic cascades converge on mito & if legal signals predominate, mito membranes are permeabilized (MMP)  when MMP is permanent & affects mito significantly, cells are irreversibly committed to death 3) Post-mito Execution Phase: MMP leads to mito transmembrane potential dissapiation (no proton concentration gradient across the inner-membrane), respiratory chain uncoupling, uncoupling, ROS overproduction, ATP synthesis arrest & release of protein in the intermembrane space into cytoplasmcell death MOMP (Mitochondrial Outer Membrane Permeabilization): Cell death signals: ROS/Ca2+ ↑/Lack of survival signals/death ligands/various ligands/various stresses. Bcl-2 family forms a pore on outermembrane only permeabilizing itit spills out Cytochrome C & other factors that bind to other proteins forming proteasesactivating caspases cell death. PTPC (Permeability Transition Pore Complex): Opening in the inner-membraneoccurs under hypoxic conditions (ischemia due to heart attack/stroke) attack/stroke) followed by reperfusionwhen blood is supplied again it triggers PTPC H2O & small solutes rush into mito rupture occurs due to osmosiscell death/necrosis death/necrosis (circulation) to a local area due to blockage of the blood vessels to the area. Ischemia: Inadequate blood supply (circulation) Hypoxic: deficiency in the amount of O2 reaching r eaching body tissues







L ectur e 18 Understand what the mitochondrial genomes are made of .  For the function of mito ~1500 genes are predicted to code for various factors:  Among them, 37 genes are encoded by mito DNA (mtDNA) exists as circular double-stranded DNA. 2-rRNAs 22-tRNs 13-polypeptides 13-polypeptides for OxPhos Gene for complex II not present in mito (7 for I=ND1,2,3,4,4L,5,6)(1 for III=Cytochrome b)(3 for IV=COI,II,III)(2 for ATP Synthase=ATPase6 & 8)  Remaining 99% of genes are encoded by nuclear DNA  Each mito has 2-10 copies of its own DNA, separate from the nuclear DNA Types of Mutations: 1) DNA insertion or deletion mutations: frameshift mutations/chain termination termination total or partial loss of genes 2) DNA base substation mutations A) In protein-coding genes: amino-acid substitution, or polypeptide chain termination B) In tRNAs or rRNAs: protein synthesis compromised compromised globally Genetics of Mito Dysfunction  By mtDNAsmaternal pattern inheritance in phenotypes phenotypes (w/ large variability)  By nuclear DNA mutations Mendelian pattern  If both are mutated then it will be hard to predict which way it will work Know how mitochondrial DNAs are replicated and how they are inherited. Mito are inherited maternally: maternally: Oocyte has 100,000/sperm has 50-75 mtDNA are prone to mutations can be exposed to ROS produced by the respiratory chain defects in mito DNA accumulate over time during the lifetime of each individual one theory of aging is that the gradual accumulation of defects w/ increasing age is the primary cause of many symptoms of aging. Female germ-line filter is : maternally inherited mito DNA has a high mutation rate & mito DNA base substitution or deletions have been reported in a variety of inherited degenerative degenerative diseases including Myopathy, Cardiomyopathy & Neurological & Endocrine disorders -Studies suggest that oocytes containing mito w/ severe mutations in their mito DNA are selectively eliminated by apoptosis during oogenis, however the filter is not perfect it will select healthy oocytes too. Heteroplasmy







Representative syndromes/diseases caused by the pathogenic mitochondrial DNAs. Disease Mutation DEAF: deafness

rRNA

NARP: Neurogenic muscle weakness Ataxia (failure of muscular coordination) Retinis Pigmentosum (slow retinal deterioration)

ATPase low 10-20% low 10-20% (T8,9993G leu to Arg change in subunit 6 marked instability in ATPsynthase, ↓ ATP synthesis, ↑ROS production)

      

Leigh Syndrome Lethal childhood disease

ATPase high 70% high 70%



details same as NARP Caused by nuclear or mtDNA mutations

  

LHON Leber Hereditary Optic Neuropathy

Complex I genes ND4 G11778A ND4 G11778A (69% of cases) His to Arg replacement @ residue 340 in subunit 4 in Complex I



 



MERRF Myoclonic Epilepsy & Ragged Red Fiber

Type II Diabetes MELAS Mito Encephalomyopathy Lactic Acidosis Stroke-like Episodes

tRNA & rRNA tRNA Lys A8344G mutation results in defective tRNA Lysoverall decrease in mito protein synthesisOxPhos compromised (Complex I & IV have the greatest num of mito encoded subunits so are the most affected) Low level 10-30% tRNA Leu A3243G High level 70% tRNA Leu (generally associated w/ complex I defects)



 

Symptoms

↓muscle strength & coordination regional brain degeneration retinal degeneration seizures dementia sensory neuropathy developmental delays Degenerative neurological condition lesions in basal ganglia, thalamus & brainstemresulting in developmental delay seizures uncontrolled eye movements breathing abnormalities Mid-life (27yrs), sudden onset blindnessmaternally inherited. Caused by death of optic nerves More common in males than females May also have cardiac problems & behavior abnormalities Uncontrollable muscular jerking (myoclonic epilepsy) Muscles less effective Mito Myopathy (RRF) overaccumulation of mito makes them look ragged

Non-insulin dependent diabetes     

Worsen w/ age (degenerative) Short stature Cardiomyopathy Mito encephalomyopathy Lactic acidosis









L ectur e 19 Monooxygenases (Mixed Function Oxidases/Oxgenases): incorporate 1 oxygen atom into substrate & one to H2O

R-H (substrate) + O2 + ZH2 (co-substrate)  R-OH + H2O + Z Co-substrates: NADH / NADPH / FMNH2 / FADH2 Reactions involved:

1) 2) 3) 4) 5)

Drug metabolism by Cytochrome P450 Synthesis of Tyrosine/Serotonin/Catechol Tyrosine/Serotonin/Catecholamines-DOPA amines-DOPAepinephrine & norepinephrine norepinephrine Cholesterol Vitamin D Nitric Oxide

A1) Cytochrome P450  Monooxygenase Monooxygenase ~50kd  Contains Heme that absorbs light maximally @ 450nm (when reduced & CO -bound)  Family of enzymes (57 genes in human)  Present in mito & ER of liver and other tissues  Catalyzes hydroxylation, hydroxylation, epoxidation & other modification of hydrophobic (aromatic) compounds (drugs) for their detoxification & excretion  Catalyzes synthesis of steroid hormones & bile salts  Causes drug interactions

Mechanism of Action: In order to hydroxylate the substrate P450 activates oxy molecule using its iron containing heme. For it to function it also requires NADPH which transfers 2 high potential electrons to flavoproteinwhich







Phenylketonuria (PKU) Most common disease due to loss of phenylalanine hydroxylase. 97% due to recessive mutation in gene encoding phenylalanine phenylalanine hydroxylase hydroxylase & 3% due to recessive recessive mutation in genes whose products products are required for for synthesis or reduction of biopterin. High concentration of phenylalanine phenylalanine in blood leads mental retardation (1%)/therarpy=low phenylalanine phenylalanine diet(casein from milk). Phenylpyruvate (aka phenylketone) is produced by deamidation of phenylalanine & removed by urine when phenylalanine builds up. A3 Serotonin Synthesis Tryptophan is hydroxylated to 5-hydroxytryptophan 5-hydroxytryptophana precursor for neurotransmitter neurotransmitter serotonin. Low level of serotonin or compromise d signaling by compound can influence mood, leading to depression. Tryptophan hydrolase uses tetrahydrobiopterin same as phenylalanine phenylalanine hydrolase. A4) Catecholamine Synthesis (hormones that mediate stress response). Tyrosine hydrolase converts Tyrosine to DOPA  precursor for norepinephrine/epinephrine. norepinephrine/epinephrine. Parkinson’s disease is caused by insufficient formation & action of dopamine in the brain. A5) Cholesterol & Vitamin D Squalene monooxygenase catalyzes the hydroxylation of squalene to cholesterol using NADPH & O2

In Vit D3 (calcitriol) ( calcitriol) synthesis, 2 hydroxylation reactions occur. 1) in the liver microsome & 2) In kidney mitochondria by monooxygenases A6) Nitric Oxide Synthesis Nitric oxide (NO is a free radical gas @ room room temp) is an important important messenger messenger in signaling signaling pathways pathways in vertebrate animal cells. For example, NO stimulates mito biogensis the free radical gas is produced from arginine in a







for housekeeping prostaglandins, like E2 E2,, which is used for kidney function, & I2 I2 which which is used for stomach protection. Specific drugs made for COX-2 did not effect kidney/stomach but did result in increased heart attack/stroke (Celebrex{Celecoxib} (Celebrex{Celecoxib} & Vioxx B2) Dioxygenases in Phenyl Alanine/Tyrosine catabolism In synthesis & degradation of Tyrosine T yrosine1 monooxygenase monooxygenase & 2 dioxygenases are required. 1 st for formation of homogentisate from p-hydroxyphenylpyruvate & 2 nd for the formation of 4-maleylacetoacetate 4-maleylacetoacetate from homogentisate. In Last rxnthe result is a cleavage of aromatic ringnearly all cleavages of aromatic rings involve dioxygenases. Alcaptonuria is due to a defect in Homogentisate Oxidase resulting in excretion of homogentisate in urine  this autooxidizes the quinine which polymerizes forming a deep black color in urine of patients w/ the disease (no other symptoms). B3) Prolyl Hydroxylase in collage Synthesis & Scurvy In synthesis of Collagen (structural support that helps bind cells together), both hydroxyl proline & lysine are required. Hydroxylation Hydroxylation rxns occur by dioxygenases that utilize ascorbate (Vit C) as the reducing agent rxn results in hydroxylation of proline & decarboxylation of α-KG α -KG forming succinate. Scurvy results from a deficiency in Vit C  people w/ this have internal hemorrhages (which result in black & white marks on the skin)/bleeding skin)/bleeding gums/weakness & joint pain. In the absence of hydroxylproline, hydroxylproline, the blood capillaries break down & hemorrhaging occurs throughout the body B4) Dioxygenase in Retinal Synthesis Dioxygenase is needed for formation of Retinal & Vitamin A from β -carotene. In Vit A1 synthesis, β-carotene β -carotene is hydroxylated & reduced to form vit A1  the rxn breaks C=C bond resulting in 2 molecules of trans-retinal Retinal is very important for vision while Vit A has many other roles in the cell.

Electron Transport Chain Notes

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