Bioenergetics and Oxidation Notes

Bioenergetics and Oxidation

Bioenergetics

  • Transfer and utilization of energy in biological systems.

  • ΔG\Delta G (Change in Free Energy):

    • Provides a measure of energetic feasibility of a chemical reaction.

    • Allows prediction of whether a reaction or process can take place.

Free Energy Change, ΔG\Delta G

  • Predicts the direction in which a reaction will proceed: A⇌BA \rightleftharpoons B

  • Negative ΔG\Delta G:

    • Net loss of energy.

    • The reaction proceeds as written.

  • Positive ΔG\Delta G:

    • Net gain of energy.

    • Reaction does not go spontaneously from B to A.

  • Zero ΔG\Delta G:

    • Reactants are in equilibrium.

  • ΔG\Delta G of 2 consecutive reactions are additive.

  • Free energy changes are additive in any sequence of consecutive reactions.

  • ΔG\Delta Gs of a pathway are additive.

  • Very important in biochemical pathways.

  • As long as the sum of the ΔG\Delta G s of an individual pathway is negative, the pathway can potentially proceed even if some parts have a positive ΔG\Delta G.

ATP as an Energy Carrier

  • ATP acts as an energy carrier to decrease the ΔG\Delta G of reactions or processes that have a large positive ΔG\Delta G.

  • Hydrolysis of ATP = large NEGATIVE ΔG\Delta G.

  • ENERGY COUPLING: Decreasing the ΔG\Delta G of a highly (+) reaction by coupling it to another reaction with a very large (-) ΔG\Delta G.

  • ATP is a high-energy phosphate compound.

  • Consists of a molecule of adenosine (adenine + ribose) + 3 phosphate groups attached.

  • ADP = ATP – 1 Phosphate group.

  • AMP = ADP – 1 Phosphate group.

  • ΔG\Delta G of hydrolysis of 1 phosphate group ~ 7.3kcal/mol7.3 kcal/mol

The Mitochondria

  • Outer Membrane

  • Inner Membrane

    • ETC located.

    • Impermeable to most small ions.

    • Specialized carriers or transport systems are needed to move ions and molecules.

    • Cristae = convolutions of the membrane to increase surface area.

  • Matrix

    • Gel-like solution.

    • 50% protein.

    • Enzymes for oxidation of pyruvate, amino acids, fatty acids, and the TCA cycle.

    • Contains coenzymes and several other metabolites.

Electron Transport Chain (ETC)

  • After glycolysis, a lot of electrons are being lost but transferred to electron carriers (NAD+ and FAD) to form energy-reduced coenzymes NADH and FADH2:

    • C<em>6H</em>12O<em>6+6H</em>2O→6CO2+24H++24e−C<em>6H</em>{12}O<em>6 + 6 H</em>2O \rightarrow 6 CO_2 + 24 H^+ + 24 e^−

  • NADH and FADH2 → ETC to produce energy.

  • The energy is stored as ATP (OXIDATIVE PHOSPHORYLATION).

  • The energy is used to drive reactions in the mitochondria and to generate heat:

    • 6O<em>2+24H++24e−→12H</em>2O6 O<em>2 + 24 H^+ + 24 e^− \rightarrow 12 H</em>2O

  • Occurs inside the mitochondria.

  • NADH cannot readily pass through from the cytosol to the mitochondrial matrix.

  • Only the ELECTRONS from cytosolic NADH are transported into the mitochondrion using different SHUTTLE SYSTEMS.

Electron Shuttles

  • Malate Aspartate Shuttle

    • Location: liver, kidney, and heart

    • OXALOACETATE – impermeable to mitochondrial membrane

    • MALATE, ASPARTATE, GLUTAMATE, & α-KETOGLUTARATE – permeable to the mitochondrial membrane

    • 2.5 ATPs per 1 NADH

  • Glycerophosphate Shuttle

    • Location: Skeletal muscle, and brain

    • Delivers NADH through FAD

    • Uses glycerol 3 phosphate and DHAP

    • 1. 5 ATP per 1 NADH

  • GLYCOLYSIS and TCA/Krebs Cycle

    • Produces a lot of electrons ferried by reduced electron carriers (NADH)

    • Electrons – eventually carried to O2O_2 through the RESPIRATORY CHAIN/ELECTRON TRANSPORT CHAIN

Electron Transport Chain Components

  • Inner mitochondrial membrane

  • Composed of several electron carriers (Complexes)

  • Free energy transport from NADH to O2O_2

Formation of NADH

  • NAD+NAD^+ is reduced to NADH

  • Dehydrogenases in the TCA/Glycolysis

Formation of FADH2

  • SEVERAL SOURCES

    • Succinate Dehydrogenase (COMPLEX II)

    • glycerophosphate dehydrogenase (shuttle system)

    • Acyl CoA dehydrogenase (lipid metabolism)

Coenzyme Q (CoQ)

  • AKA Ubiquinone

  • Mobile carrier and accepts H from FMNH<em>2FMNH<em>2 and FADH</em>2FADH</em>2

  • Transfers electrons to Complex III

Cytochromes

  • They contain heme groups (porphyrin ring + Fe)

  • Electrons are passed along the cytochromes with reversible conversion of Fe from ferric to ferrous states

    • Complex III (Cytochrome bc1)

    • Cytochrome c

    • Complex IV (Cytochrome a+a3)

Cytochrome a + a3 (COMPLEX IV)

  • Only complex that can react directly with O2O_2 = Cytochrome c oxidase

  • O2O_2 is reduced to WATER

Oxidative Phosphorylation

  • Transfer of electrons down the ETC = energetically favored

  • Flow of electors does not directly result in ATP synthesis

Chemiosmotic Theory (Peter Mitchell, 1961)

  • Mitchell hypothesis

  • Explains how free energy is generated by the transport of e by the ETC to produce ATP

Proton Pump

  • electron transport is coupled to the phosphorylation of ADP by the transport (“pumping”) of protons (H+H^+) across the inner mitochondrial membrane from the matrix to the intermembrane space at Complexes I, III, and IV.

Proton Gradient

  • Created by the chain

  • Drives the synthesis of ATP

  • Oxidative phosphorylation

The ATP Synthase

  • Functions as a rotatory motor to form ATP

F1

  • protein subunits froming a ball like shape arranged around an axis

  • Projects into the matrix

  • Contains the phosphorylation mechanism

F0

  • Attached to F1

  • Spans the membrane and forms a proton channel

  • Flow of protons causes it to rotate driving ATP production by F1

  • 1 mol NADH oxidized

    • Complex I & III = 4 H+H^+ each = 8 H

    • Complex IV = 2 H+</p></li></ul></li></ul><h4id="f62b95d8−91e1−4cf0−9ed9−21774b570a91"data−toc−id="f62b95d8−91e1−4cf0−9ed9−21774b570a91"collapsed="false"seolevelmigrated="true">PhosphorylationReactionsandEnergyGeneration</h4><h5id="b0753c6b−0bf4−4c17−938c−fa8569b8f674"data−toc−id="b0753c6b−0bf4−4c17−938c−fa8569b8f674"collapsed="false"seolevelmigrated="true">SubstrateLevelPhosphorylation</h5><ul><li><p>Highenergyphosphategroups(ATP)generatedwithinthecycles</p><ul><li><p>Glycolysis=2</p></li><li><p>TCA=2</p></li></ul></li></ul><h5id="88dd87b2−146e−4a31−8252−c39de955be9e"data−toc−id="88dd87b2−146e−4a31−8252−c39de955be9e"collapsed="false"seolevelmigrated="true">OxidativePhosphorylation</h5><ul><li><p>Respiratorychainlevel</p><ul><li><p>NADH=2.5ATP/0.5H^+</p></li></ul></li></ul><h4 id="f62b95d8-91e1-4cf0-9ed9-21774b570a91" data-toc-id="f62b95d8-91e1-4cf0-9ed9-21774b570a91" collapsed="false" seolevelmigrated="true">Phosphorylation Reactions and Energy Generation</h4><h5 id="b0753c6b-0bf4-4c17-938c-fa8569b8f674" data-toc-id="b0753c6b-0bf4-4c17-938c-fa8569b8f674" collapsed="false" seolevelmigrated="true">Substrate Level Phosphorylation</h5><ul><li><p>High energy phosphate groups (ATP) generated within the cycles</p><ul><li><p>Glycolysis = 2</p></li><li><p>TCA = 2</p></li></ul></li></ul><h5 id="88dd87b2-146e-4a31-8252-c39de955be9e" data-toc-id="88dd87b2-146e-4a31-8252-c39de955be9e" collapsed="false" seolevelmigrated="true">Oxidative Phosphorylation</h5><ul><li><p>Respiratory chain level</p><ul><li><p>NADH = 2.5 ATP / 0.5O_2</p></li><li><p></p></li><li><p>FADH_2(Substratesuccinateor3phosphogycerateoxidized)=1.5molATP</p></li></ul></li></ul><h4id="fce8ce12−43f2−4b1f−8212−18d77574de0a"data−toc−id="fce8ce12−43f2−4b1f−8212−18d77574de0a"collapsed="false"seolevelmigrated="true">PoisonsthatInhibittheRespiratoryChain</h4><ul><li><p>BARBITURATES:InhibitviaComplexI</p></li><li><p>ANTIMYCINAandDIMERCAPROL:InhibitviaComplexIII</p></li><li><p>(Substrate succinate or 3 phosphogycerate oxidized) = 1.5 mol ATP</p></li></ul></li></ul><h4 id="fce8ce12-43f2-4b1f-8212-18d77574de0a" data-toc-id="fce8ce12-43f2-4b1f-8212-18d77574de0a" collapsed="false" seolevelmigrated="true">Poisons that Inhibit the Respiratory Chain</h4><ul><li><p>BARBITURATES: Inhibit via Complex I</p></li><li><p>ANTIMYCIN A and DIMERCAPROL: Inhibit via Complex III</p></li><li><p>H_2S,CO,andCyanide:InhibitviaComplexIV</p></li><li><p>Malonate:</p><ul><li><p>CompetitiveinhibitorofComplexII</p></li></ul></li><li><p>Atractyloside:</p><ul><li><p>InhibittransporterofADPintoandATPoutofthemitochondrion</p></li></ul></li><li><p>Oligomycin:</p><ul><li><p>CompleteblockageofoxidativephosphorylationbyblockingprotonflowthroughATPsynthase</p></li></ul></li></ul><h4id="3c77a47b−fc14−4ec0−a878−199ca4008ce9"data−toc−id="3c77a47b−fc14−4ec0−a878−199ca4008ce9"collapsed="false"seolevelmigrated="true">Uncouplers</h4><ul><li><p>Dissociateoxidationintherespiratorychainfromphosphorylation</p></li></ul><h5id="ea770dbf−5f3d−47a4−8964−f11cde62bd8d"data−toc−id="ea770dbf−5f3d−47a4−8964−f11cde62bd8d"collapsed="false"seolevelmigrated="true">Thermogenin(UCP)</h5><ul><li><p>Physiologicuncoupler</p></li><li><p>Foundinbrownadiposetissue</p></li><li><p>Usedtogeneratebodyheat</p></li><li><p>Newbornbabies</p></li><li><p>“BrownFat”</p></li></ul><h4id="3e607157−1fd6−43bc−87f5−222414026b86"data−toc−id="3e607157−1fd6−43bc−87f5−222414026b86"collapsed="false"seolevelmigrated="true">KrebsCycleTCAEnzymes(Mnemonic)</h4><ul><li><p>Corrupt:CitrateSynthase</p></li><li><p>Anti:Aconitase</p></li><li><p>Intelligence:Isocitratedehydrogenase</p></li><li><p>Agent:Alpha−ketoglutaratedehydrogenasecomplex</p></li><li><p>Spoke:Succinatethiokinase/Succinyl−CoAsynthetase</p></li><li><p>Slander:Succinatedehydrogenase</p></li><li><p>For:Fumarase</p></li><li><p>Money:Malatedehydrogenase</p></li></ul><h4id="6351ebad−4098−4226−a470−996f17ea3023"data−toc−id="6351ebad−4098−4226−a470−996f17ea3023"collapsed="false"seolevelmigrated="true">TricarboxylicAcidCycleSummary(for1cycleofKrebsenzyme)</h4><tablestyle="min−width:75px"><colgroup><colstyle="min−width:25px"><colstyle="min−width:25px"><colstyle="min−width:25px"></colgroup><tbody><tr><thcolspan="1"rowspan="1"style="text−align:left;"><p>PRODUCTFORMED</p></th><thcolspan="1"rowspan="1"style="text−align:left;"><p>PHOSPHORYLATION</p></th><thcolspan="1"rowspan="1"style="text−align:left;"><p>ATPsGenerated</p></th></tr><tr><tdcolspan="1"rowspan="1"style="text−align:left;"><p>IsocitrateDehydrogenase</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>NADH</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>Oxidative</p></td></tr><tr><tdcolspan="1"rowspan="1"style="text−align:left;"><p>AlphaKetoglutarateDH</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>NADH</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>Oxidative</p></td></tr><tr><tdcolspan="1"rowspan="1"style="text−align:left;"><p>SuccinateThiokinase</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>ATP</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>Substratelevel</p></td></tr><tr><tdcolspan="1"rowspan="1"style="text−align:left;"><p>SuccinateDehydrogenase</p></td><tdcolspan="1"rowspan="1"style="text−align:left;"><p>, CO, and Cyanide: Inhibit via Complex IV</p></li><li><p>Malonate:</p><ul><li><p>Competitive inhibitor of Complex II</p></li></ul></li><li><p>Atractyloside:</p><ul><li><p>Inhibit transporter of ADP into and ATP out of the mitochondrion</p></li></ul></li><li><p>Oligomycin:</p><ul><li><p>Complete blockage of oxidative phosphorylation by blocking proton flow through ATP synthase</p></li></ul></li></ul><h4 id="3c77a47b-fc14-4ec0-a878-199ca4008ce9" data-toc-id="3c77a47b-fc14-4ec0-a878-199ca4008ce9" collapsed="false" seolevelmigrated="true">Uncouplers</h4><ul><li><p>Dissociate oxidation in the respiratory chain from phosphorylation</p></li></ul><h5 id="ea770dbf-5f3d-47a4-8964-f11cde62bd8d" data-toc-id="ea770dbf-5f3d-47a4-8964-f11cde62bd8d" collapsed="false" seolevelmigrated="true">Thermogenin (UCP)</h5><ul><li><p>Physiologic uncoupler</p></li><li><p>Found in brown adipose tissue</p></li><li><p>Used to generate body heat</p></li><li><p>Newborn babies</p></li><li><p>“Brown Fat”</p></li></ul><h4 id="3e607157-1fd6-43bc-87f5-222414026b86" data-toc-id="3e607157-1fd6-43bc-87f5-222414026b86" collapsed="false" seolevelmigrated="true">Krebs Cycle TCA Enzymes (Mnemonic)</h4><ul><li><p>Corrupt: Citrate Synthase</p></li><li><p>Anti: Aconitase</p></li><li><p>Intelligence: Isocitrate dehydrogenase</p></li><li><p>Agent: Alpha-ketoglutarate dehydrogenase complex</p></li><li><p>Spoke: Succinate thiokinase/Succinyl-CoA synthetase</p></li><li><p>Slander: Succinate dehydrogenase</p></li><li><p>For: Fumarase</p></li><li><p>Money: Malate dehydrogenase</p></li></ul><h4 id="6351ebad-4098-4226-a470-996f17ea3023" data-toc-id="6351ebad-4098-4226-a470-996f17ea3023" collapsed="false" seolevelmigrated="true">Tricarboxylic Acid Cycle Summary (for 1 cycle of Krebs enzyme)</h4><table style="min-width: 75px"><colgroup><col style="min-width: 25px"><col style="min-width: 25px"><col style="min-width: 25px"></colgroup><tbody><tr><th colspan="1" rowspan="1" style="text-align:left;"><p>PRODUCT FORMED</p></th><th colspan="1" rowspan="1" style="text-align:left;"><p>PHOSPHORYLATION</p></th><th colspan="1" rowspan="1" style="text-align:left;"><p>ATPs Generated</p></th></tr><tr><td colspan="1" rowspan="1" style="text-align:left;"><p>Isocitrate Dehydrogenase</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>NADH</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>Oxidative</p></td></tr><tr><td colspan="1" rowspan="1" style="text-align:left;"><p>Alpha Ketoglutarate DH</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>NADH</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>Oxidative</p></td></tr><tr><td colspan="1" rowspan="1" style="text-align:left;"><p>Succinate Thiokinase</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>ATP</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>Substrate level</p></td></tr><tr><td colspan="1" rowspan="1" style="text-align:left;"><p>Succinate Dehydrogenase</p></td><td colspan="1" rowspan="1" style="text-align:left;"><p>FADH_2$$

      Oxidative

      Malate Dehydrogenase

      NADH

      TOTAL

      ATP Computation

      How many mol of ATP is formed from 1 mol of Glucose? (Assume Malate Aspartate Shuttle for cytosolic NADH)

      STEP

      Total ATP

      Glycolysis

      Investment Phase

      -2 mol ATP

      Pay off Phase

      2 mol NADH = 5 mol ATP

      4 mol ATP

      NET ATP GAIN

      7 mol ATP

      PDH (x2)

      5 mol ATP

      TCA (x2)

      20 mol ATP

      TOTAL ATP GAINED

      32 mol of ATP

      How many mol of ATP is formed from 1 mol of Glucose? (Assume glycerophosphate shuttle for cytosolic NADH)

      STEP

      Total ATP

      Glycolysis

      Investment Phase

      -2 mol ATP

      Pay off Phase

      2 mol NADH = 3 mol ATP

      4 mol ATP

      NET ATP GAIN

      7 mol ATP

      PDH (x2)

      5 mol ATP

      TCA (x2)

      20 mol ATP

      TOTAL ATP GAINED

      30 mol of ATP

      How many mol of ATP is formed from 1 mol of pyruvate? Assume glycerophosphate shuttle for cytosolic NADH

      STEP

      Total ATP

      PDH

      2.5 mol ATP

      TCA

      10 mol ATP

      TOTAL ATP GAINED

      15 mol of ATP

      How many mol of ATP is formed from 1 mol of Acetyl-CoA. Assume glycerophosphate shuttle for cytosolic NADH

      STEP

      Total ATP

      TCA

      10 mol ATP

      TOTAL ATP GAINED

      10 mol of ATP