Chapter 20: The Electron Transport Chain

oxidative phosphorylation

ATP formation from electron transfer from NADH or FADH2 to O2 by a series of electron carriers

are the redox rxns of oxidative phosphorylation endo/exo

very exergonic

electron transport chain

aka respiratory chain → 4 protein complexes embedded in inner mitochondrial membrane; allos redox of oxidative phosphorylations

what makes up cellular respiration

citric acid cycle and oxidative phosphorylation collectively

2 compartments of the mitochondria

intermembrane space and matrix

why do mitochondria have cristae

increases surface area of the inner mitochondrial membrane → more sites for oxidative phosphorylation

mitchochondria outer membrane

lots of mitochondrial porin protein (aka VDAC) → permeable to most small molecules/ions

VDAC

voltage dependent anion channel → pore-forming protein found on the outer membrane of mitochondria

mitchochondria inner membrane

• impermeable to most ions and polar molecules → ATP, pyruvate, citrate and other metabolites shuttled via transporters

• high protein and cardiolipin content

• matrix side (faces matrix) and cytoplasmic side (faces IM space)

why is the mitochondria considered semi-autonomous

has its own DNA (maternally inherited) and has a endosymbiotic relationship with the host cell

measure of phosphoryl transfer potential

ΔG° ′ for the hydrolysis of the activated phosphoryl compound

measure of electron transfer potential

reduction potential (aka redox potential or oxidation-reduction potential) → E₀’

reductant or reducing agent

species in a redox rxn that gets oxidized → has a negative reduction potential

oxidant or oxidizing agent

species in a redox rxn that gets reduced → has a positive reduction potential

conditions of standard reduction potential tables

1 M oxidant, 1M reductant, 1 M H+, 1 atm H2

standard reference half cell

1 M H+ and 1 atm H2 → reduction potential of 0 volts

negative E₀’

reducing agent; donates electrons

positive E₀’

oxidizing agent; accepts electrons

electron affinity arrangement of ETC components

electrons go from low E₀’ to high E₀’ (lower electrong affinity to higher electron affinity)

common electron carrier components of ETC

• flavin mononucleotide (FMN)

• iron-sulfur proteins (aka nonheme iron proteins) → iron associated with sulfur

• cytochromes (iron incorperated into heme)

• coenzyme Q₁₀ (ubiquinone)

how does iron facillitate redox rxns in iron-sulfur proteins and cytochromes

iron shuttles between its reduced ferrous (Fe²⁺) form and oxidized ferric state (Fe³⁺)

how is does NADH pass its electrongs to O2

passes its electrons to flavin mononucleotide (FMN) → similat to FAD but lacks nucleotide component

complexes of the ETC

• NADH-Q oxidoreductase → complex 1

• succinate Q-reductase → complex 2

  • not a proton pump

• Q-cytochrom c oxidoreductase → complex 3

• Cytochrome c oxidase → complex 4

why does FADH2 enter downstream for NADH?

FADH2 has a lower reduction potential; gets reduced at complex II instead of complex I

• complex 2 doesnt pump protons → FADH2 yields less ATP

heme prosthetic group of cytochromes

iron-protoporphyrin IX → same heme of hemoglobin and myoglobin, except the Fe intentionally cycles oxidation states

how can iron be present as an electron carrier in multiple spots of the ETC (how can iron have several different reduction potentials)

oxidation–reduction potential of iron can be altered by its environment

copper in the ETC

member of complex IV (cytochrome c oxidase) → gets alternately oxidized and reduced (Cu⁺ and Cu²⁺)

coenzyme Q

• aka ubiquinone → prominent electron carrier of ETC

• quinone derivitaive with long hydrophobic isoprenoid tail → shuttles quick within the inner mitochondrial membrane

• takes electrons from complex I and II → complex III

most common coenzyme Q in mammals

has 10 isoprene units → coenzyme Q₁₀

• subscript commonly omitted bcz they all function the same

quinone oxidation states

• ubiquinone; fully oxidized (Q) → coQ has 2 keto groups

• semiquinone radical ion (Q^_.-) → addition of 1 e^-

• semiquinone intermediate (QH_^.) → addition of 1 e^- and 1 H⁺

• ubiquinol; fully reduced (QH₂) → addition of 2 e^- and 2 H⁺

cytochrome C

small soluable protein loosely associated with the inner mitochondrial membrane → shuttles electrons from complex III to complex IV

arrangement of the ETC

supracomplex called a respirasome → mainly complex I, III, and IV

• complex 2 and other proteins feed e^- to the respirasome via Q

alternate names for complex 1

• NADH-coenzyme Q oxidoreductase

• NADH-Q oxidoreductase

• NADH dehydrogenase

where do NADH electrons enter the ETC

• NADH-Q oxidoreductase (complex I)

• electrons flow from NADH → FMN (flavin mononucleotide) → 7 iron-sulfur clusters → Q (forms QH₂)

what happens to complex 1’s coQ once its reduced

the ubiquinol (QH₂) dissociates from the enzyme to allow for another rxn cycle to occur

prothetic groups of NADH-coenzyme Q oxidoreductase (complex 1)

FMN and iron-sulfur clusters

how many protons get pumped at complex 1

transfer of 2 e^- from NADH to coQ lead to pumping of 4 H⁺ out of the matrix → contrubutes to the proton-motive force

complex 2

succinate-Q reductase → its enzyme succinate dehydrogenase is shared with CAC (succinate → fumerate)

complex 2 structure

• integral membrane protein of inner mitochondrial membrane

• 2 prosthetic groups

  • FAD, Fe-s

FADH2 in CAC electrons to ETC

after FADH2 is made, it doesnt leave the succinate dehydrogenase → its electrons tranfer to Fe-S centers of complex 2 and then to Q → forms QH₂

do electrons from complex 1 interact with complex 2

no → already get encapsulated within QH2, so they skip complex 2

NADH vs FADH2 path in ETC

NADH electrons skip C2, FADH2 electrons skip C1

structure of complex 3

22 subunits (2 are cytochrom subunits); 4 prothetic groups (Fe-s and 3 heme)

structure of complex 3: 3 heme groups

contained within 2 cytochrome subunits

• cytochrome b subunit has 2 hemes

  • heme b_L (low affinity)

  • heme b_H (high affinity)

• cytochrome c₁ subunit has 3rd heme

structure of complex 3: Fe-s

complex 3 contains an iron-sulfur protein with a 2Fe-2S center (rieske center)

• unqiue because one of the 2 Fe coordinated by 2 histidine instead of 2 cysteine → more stability for reduced form (increased reduction postential)

what happens to thr QH2 carrying electrons from complex 1 and 2

QH2 passes its electrons to cytochrome c at complex 3 (Q-cytochrome c oxidoreductase) → 2 e^- flowing through C3 moves 2 H⁺ into the IM space

problem with QH2 tranfering electrons to cytochrome c at complex 3

QH₂ (ubiquinol) passes 2 e^- but cyt c can only accpet one e^- at a time → uses the Q cyle

Q-cycle

2 QH₂ (each gives up 2 e^- and 2 H⁺) and a Q used to pass 2 e^- to 2 cytochrome C

first half of the Q-cycle

the first QH₂ binds to Q_o binding site

• 2 protons release to IM space

• 1 e^- travels rieske center → heme at cyt c₁ → cytochrome c (was oxidized, now reduced)

• other e^- travels to the 2 heme of cytochrome b → ubiquinone in Q_i binding site (forms semiquinone Q⋅−)

• the oxidized Q in binding site 1 releases

second half of the Q-cycle

second molecule of QH₂ binds and reacts in the same way:

• 2 protons to IM space

• 1 e^- travels rieske center → cyt c₁ → cytochrome c (was oxidized, now reduced)

• other e^- travels to the 2 heme of cytochrome b → semiquinone in Q_i binding site (consumed 2 H⁺ from matrix and forms QH₂)

• the oxidized Q in binding site 1 and reduced QH₂ release

summarized rxn of the Q cycle

2 QH₂ + Q + 2 cyt c_ox + 2 H⁺ _matrix → 2 Q + QH₂ + 2 cyc c_red + 4 H⁺_{IM space}

• 4 H+ pumped into the IM space

• 2 H+ pulled out of the matrix

what at complex III contribute to the [H+] gradient

• QH₂ formation at Q_i takes 2 H from the matrix

• QH₂ oxidation at Q_o releases 2 H+ to IM space

what happens to the reduced cytochrome c and QH₂ from complex III

• cytochrome C travels from complex III to complex IV to get transfered to final acceptor, O₂

• QH₂ re-enters the Q pool

how does cytochrome c carry its electron

on iron

• Fe²⁺ (ferrous) is reduced

• Fe³⁺ (ferric) is oxidized

complex IV

• cytochrome c oxidase

• catalyzes the transfer of overall 4 electrons from 4 reduced cytochrom c to O2 → generates 2 H₂O

structure of cytochrome C oxidase

• 13 subunits, 4 prosthetic groups (heme a, heme a3, Cu_A, Cu_B)

• 3 Cu ions

  • Cu_A center has 2 Cu

  • Cu_B center has 3rd Cu

steps of water generation at cytochrome C oxidase: first 2 electrons

• 2 Cyt c_red pass 2 e^- (flow Cu_A → heme a → heme a₃/Cu_B center) → 1 e reduces Cu_B and one reduces Fe at heme a₃

• O₂ binds and removed electrons from the heme a₃/Cu_B active center → forms peroxide bridge

steps of water generation at cytochrome C oxidase: second 2 electrons

• 2 more Cyt c_red pass 2 e^- (Cu_A → heme a → heme a₃/Cu_B center) → 1e^- & 1H⁺ added to each O atom, cleving peroxide bridge into Cu_B²⁺-OH and Fe³⁺-OH

• 2 more H⁺ react with 2 OH^- in active site → relases 2 H₂O

where do the protons used to make water at complex 4 come from

exclusively come from the matrix → contributes to the proton gradient

how many H+ does complex 4 pump into the IM space

• uses redox energy to pump 4H⁺ from matrix to the IM space

• 8 protons get removed from the matrix in total per 4 cyt c oxidized (or 1 O₂ reduced) but only 4 directly go to the IM space

overall cataylzzed rxn of complex IV

4 cyt c_red + 8H⁺_matrix + O₂ → 4 cyt c_ox + 2H₂O + 4H⁺_{IM soace}

dead zones

when some organisms undergo so much cellular respiration they hog O2 → not enough O2 for other orgnaisms (like fish) to survive

how many H+ pumped into the IM space per NADH and FADH2

• 10 H+ pumped per NADH (4 at c1, 4 at c3, 2 at c4)

• 6 H⁺ pumped per FADH₂ (4 at c3, 2 at c4)

after the ETC, whats the proton gradien

• lots of H in the IM space (more acidic pH)

• little H in the matrix

why is O2 the ideal final acceptor; caveat

high electron affinity BUT partial reduction forms dangerous side reactions

full vs partial reduction of O2

• full → H₂O

• partial (1e^-) → superoxide ion (O₂^{. -})

• partial (2e^-) → peroxide ion (O₂^2-)

ROS

reactive oxygen species → partially reduced O₂ radicals and species they generate (like OH^. radical)

harm of ROS

reacts with all macromolecules → cause oxidative damage