biochem electron transport chain

flow of protons across membrane

• inside the matrix is negative and outside is positive

• electrochemical gradient powers ATP synthase

  • protons flowing inside (down the gradient)

end goal of ETC

to make oxygen that will later be reduced to H2O and power proton pumps

T or F: the intermembrane space of the mitochondria has a low concentration of protons

F: high concentration of protons (low pH); the matrix has a low concentration of protons and a higher pH

Role of cristae in ETC

allow multiple proteins to be embedded

T or F: the outer membrane of the mitochondria is freely permeable to small molecules and ion

True!

Overall role of inner membrane of mitochondria in ETC

• impermeable to most molecules, including protons

• contains complexes 1 to 4 and the ATP translocase and ATP synthase

  • ATP translocase: transports ATP out and ADP in

  • ATP synthase: ADP to ATP using proton electrochemical gradient

overall role of matrix in ETC

site of PDC, CAC, and fatty acid oxidation

Reduction potential

• will oxidation reduction pair pass electrons or accept

  • negative V: passes electrons to SHE

  • Positive V: accepts electrons from SHE

• Oxygen has the highest V value, so it is the final acceptor of electrons

  • electrons flow from low to high reduction potential (exergonic)

standard reduction potential

• measure of affinity for electrons in volts using a half cell (equimolar solution of redox pair) vs standard hydrogen electrode (SHE)

  • negative V: passes electrons to SHE

  • Positive V: accepts electrons from SHE

• change of G = -nFchange in E

  • n = electrons transferred

T or F: NADH has a lower reduction potential than FADH2

F: FADH2 has a lower reduction potential than NADH and releases less energy (gives 1.5 ATP compared to NADH’s 2.5)

overview of ETC complexes and carriers

1. NADH Q oxireductase

   • NADH passes to coenzyme Q

2. Succinate Q reductase

   • Succinate to coenzyme Q (powered by FAD)

3. Q cytochrome c oxidoreductase

   • QH2 to cytochrome C

4. Cytochrome c oxidase

   • cytochrome c to oxygen (then to water)

electron affinity increases as you go down the chain

what are the two mobile carriers of the ETC

• coenzyme Q (between 1 / 2 and 3)

• cytochrome c (between 3 and 4)

T or F: the citric acid cycle is a culmination of anabolic pathways

F: catabolic pathways; dehydrogenases collect electrons and funnel to NAD+ and FAD to deliver to ETC

Differences between NAD+ and FAD

• NAD+ passes 2 electrons and passes them at the same time

• FAD can accept 2 electrons and can pass 1 or 2 (doesn’t have to be at the same time)

  • more flexibility

membrane bound electron carriers

• cytochromes

  • 1 electron carriers

  • iron/pophyrin ring derivatives

  • type a: Heme A with hydrophobic tail

  • tybe b: alkenes

  • type c: heme C with cys-S (can form disulfide bonds)

• electrons are transferred to the iron molecule in the center

  • shift electron flow named based on the alpha band

Iron sulfur clusters as electron carriers

• one electron carriers

  • only one iron changes oxidation state during electron transfer

• coordinate by cys in the protein

  • equal number of iron and sulfur atoms

• increasing complexity means the reduction potential varies more

  • enviormental factors

Coenzyme Q/Ubiquinone

• accepts 2 electrons and 2 protons at benzoquinone head group

• accepts from complex 1 and 2 and transfers to complex 3

  • intermediate structure can have a ROS (QH radical)

complex 1 overview

• NADH-Q oxioreductase

• largest

• prosthetic groups: FMN and Fe-S

• matrix side: NADH, membrane core: Q

Complex 2 overview

• succinate-Q reductase

• prostethic groups: FAD and Fe-S

• matrix side: succinate

• membrane core: Q

complex 3 overview

• Q-cytochrome c oxidoreductase

• prosthetic groups: Heme bs, heme c, and Fe-S

• membrane core: Q

• cytoplasmic side: cyto c

complex 4 overview

• cytochrome c oxidase

• prosthetic groups: heme as, coppers

• cytoplasmic side: cyto c

Complex 1 reactions

• complex 1 accepts 2 electrons from NADH on the matrix side at the matrix arm

  • NADH is reduced

• in the arm, FMN accepts 2 electrons and passes them one at a time through 7 Fe-S clusters

  • electrons hop from one to another until they reach Q

• Q takes 2 protons (from matrix) and 2 electrons (from arm) to make QH2

• four protons are pumped to the intermembrane space

T or F: all carriers in complex 1 are located in the matrix arm

T: carriers are arranged in the matrix arm until they reach QH2

more on the proton pumping of complex 1

• electrons from NADH reduce Q to QH radical near hydrophilic patch

• negative patch of QH radical interacts with negatively charged residues in arm and initiate conformational change

• helix HL and Beta hairpin helix shift, causing the pka of key amino acids to change

  • makes it more favorable for protons to enter IMS

• protons hop until 4 protons are pumped into the IMS

• QH radical takes 2 protons from matrix and becomes QH2

• QH2 enters Q pool

order or proton hopping to to be pumped to IMS in complex 1

matrix half channels, water channel, IMS half channels, IMS

role of helix HL and beta hairpin helix

• helix HL: keeps protons from going into IMS

  • comes first

• Beta: keeps half channels into IMS closes

complex 2 reactions

• succinate converts to fumarate using FAD and FADH2 stays bound to complex 2 (a chain)

• FADH2 gives electrons to Fe-S centers (3) (b to c chain)

• Fe-S centers pass electrons to upiquinone (QH2) which detaches and moves to complex 3

• d chain holds heme b which does not transfer electrons

T or F: complex 2 pumps electrons

FALSE: does not generate enough energy

heme b role

• doesn’t transfer electrons

• may prevent electrons from escaping complex 2 and thus the reaction

  • not directly involved in the reaction

complex 3 reactions

• transfers electrons from QH2 (ubiquinol) to cyt c

• Q cycle is here

• Q moves through cavern in dimer

heme bL/H of complex 3

• heme bL: closer to IMS side

  • lower affinity for electrons

• heme bH: closeer to matrix side

  • higher affinity for electrons

Q cycle part 1

• QH2 binds to the positive side (IMS)

• 1 electron goes to cyt c1 1with Fe-S and heme

  • then moves to cyt c (can carry one electron)

  • once it gets the electron, detaches and goes to complex 4

• other electron goes to cyt b with 2 hemes (bL to bH)

  • then passed to oxidized Q at the Q negative side and a radical is generated and electron is held

• 2 protons are pumped to the IMS once second QH2 binds pos side again

Q cycle part 2

• QH2 binds again to complex 3 at Q pos

• 1 electron moves through cyt c1 to cyt c again

  • different cyt c that will move to complex 4 again

• 1 electron moves through cyt b to Q radical

  • makes QH2 that can re-enter Q pool and be recycled

  • 2 protons are taken from the matrix side and given to Q to make QH2

• 2 protons pumped to IMS

Complex 4 reactions

• carries electrons from cyt c to oxygen one at a time

• includes heme A3-CuB binuclear center and CuA (2) binuclear center

Complex 4 full reaction

• 2 cyt c bind one at a time to complex 4

• release electron to CuA/CuA center

• then goes to heme a

• then heme a3

• then cuB

  • heme a3 (fe) and copper are reduced (the binuclear center)

• oxygen comes in and forms a peroxide bridge

  • 2 protons from matrix and 2 electrons cleaves peroxide bridge and leaves OHs bound to fe and Cu

• 2 more protons from the matrix releases water

• 4 protons are pumped to IMS (proton motive force)

respirasome

• two complex 1s, 2 complex 3s, 2 complex 4s, and 2 cyt c that stay bound

• substrate channeling, efficient, stable

• proposed model of ETC

Reactive Oxygen Species

• superoxide, hydrogen peroxide, hydroxyl radical

• need to be made safe

• superoxide dismutase and catalase

Superoxide dismutase

• 2 superoxide plus two protons

  • 1 oxidized to oxygen

  • 1 reduced to hydrogen peroxide (still unsafe)

catalase

two hydrogen peroxide made into oxygen and water

diseases from ROSs

• they build up over time in the mito

  • older people have problems

• parkinsons, cancer, liver disease, diabetes, atherogenesis, bronchitis , etc.