Respiration Flashcards
Substrate-level phosphorylation
ATP is being made by phosphorylation of ADP and it’s happening as part of an enzyme-catalysed reaction (‘at substrate level’).
This is the only source of ATP in organisms that are fermentative in their metabolism. Not really efficient/sufficient enough for complex organisms.
ATP biosynthesis (proton gradient)
Electron-transport-coupled phosphorylation – (“oxidative phosphorylation”) this is catalysed by a membrane bound enzyme that phosphorylates ADP at the expense of a flow of protons down a proton gradient across the membrane.
H+ -translocating two-sector ATPase (EC 7.1.2.2) in all
taxa.
Structure of ATP synthase
FO sector- Hydrophobic, sits inside membrane.
[“O” for oligomycin]
F1 sector-Hydrophilic, hangs into cytoplasm or
mitochondrial matrix (depending what it’s in).
Binds ADP and Pi and catalyses their
reaction when inner grey ‘axle’ rotates
(which is dependent on proton-flow).
The respiratory chain (the electron transport chain) and how proton motive force is generated
- in the aerobic respiration of Eukarya, takes electrons from NADH(glycolysis and Krebs’ cycle) and electron flow through three proteins causes proton translocation into the intermembrane space/invagination: this generates proton-motive force (PMF or Δp).
- the latter is consumed by ATP synthase to make ATP.
What do the major enzyme complexes in respiration do? Name the two key electron carriers?
There are four and three of them translocate protons from one side of the membrane to the other to build Δp.
*the translocating proteins are referred to as ‘coupling sites’ as they ‘couple’ the respiratory chain to ATP biosynthesis by generating Δp.
*electron carriers:
-quinones, Q (oxidised form) → quinols, QH2 (reduced form)
* each molecule carries 2 electrons
* lipid-soluble electron carrier dissolved in the membrane.
* Eukarya all use ubiquinone-10, UQ-10 (thus ubiquinol-10, UQH2-10)
* Some Bacteria use other ubiquinones (e.g. ubiquinone-8), some use menaquinones (vitamin K2)- numbers
are how many isoprenoid repeats in tail.
- cytochrome c
* each molecule carries 1 electron
* water-soluble electron carrier (a small protein) in the intermembrane space.
* contains heme c.
* oxidised/reduced forms can either be written as cyt c(ox)/cyt c(red)
In space between mitochondrial membrane Respiratory chain. Name all the complexes
NADH dehydrogenase= (Complex I)
succinate dehydrogenase=(Complex II)
bc1 complex=(Complex III)
cytochrome c/cytochrome c oxidase=(Complex IV)
Quinone pool
Explain the process that occurs in the electron transport chain
NADH dehydrogenase (Complex I)= NADH –>NAD+
succinate dehydrogenase=(Complex II)= succinate –>fumarate
These occur simultaneously and/or
Electrons from both reactions get deposited into the quinone pool so quinones become quinols
When this set of reaction happens and electrons go from NADH to quinone pool it opens a gate from the NADH dehydrogenase and lets a number of protons cross the membrane.
Electron then carry on and get to bc1 complex where another gate opens and lets more protons cross the membrane.
Two electron need 2 cytochrome c’s. electrons then go to cyt c (ox) and then on molecular oxygen which binds with protons and makes water and then we exhale it. Different protons (red) go into mitochondrial space.
What happens if too much NADH and not much bc1?
- QH2 would be formed but could not be reverted back to Q and before long, NADH will build up to levels in the matrix that inhibit glycolysis completely.
- in the Eukarya alternative oxidase (AOX) would rectify this – a
quinol oxidase. - in the Bacteria or Archaea, quinol oxidase (non-translocating) [EC 1.10.3.11] does same reaction as AOX in the Eukarya:
2QH2 + O2 → 2H2O + 2Q - allows oxidation of the quinone pool to stop NADH build-up but does not translocate any protons. As such, the O2
and electrons are “wasted” (no ATP made) but the cell does not die (in short).
Variations of the respiratory chains
- outside of the Eukarya, respiratory chains are extremely diverse.
- some are shorter e.g. in Escherichia coli:
NADH → UQ-8 → bo3 ubiquinol oxidase (H+
-translocating) - terminal oxidases vary – many isoenzymes [structure is different but same reaction]:
- translocating quinol oxidases (bo3 some of bd-I and bd-II)
- translocating cytochrome c oxidases (aa3, cbb3 , baa3…)
Uncoupling agents: synthetic
- respiratory chain builds Δp, ATP synthase consumes Δp.
- if we allow Δp to build as normal but then destroy it, we
have uncoupled the respiratory chain from ATP biosynthesis. - in vitro we use many uncoupling agents (aka proton
ionophores) to allow study of these systems – e.g. 2,4-
dinitrophenol (DNP), FCCP, CCCP. All are lipid-soluble
proton carriers that carry protons back over the
membrane so that the ATP synthase can’t use them.
Energy from Δp is lost as heat.
Uncoupling agents: natural (produce heat)
- natural uncoupling agents like thermogenin generate heat
during non-shivering thermogenesis in brown
adipose tissue in the Mammalia – specifically in
neonates, in hibernators and in e.g. adult
Primates around the spine and aorta - also used to heat various non-animals e.g.
fruiting bodies.
Reversing the chain
- in chemolithoautotrophic Bacteria and Archaea there is no glycolysis, thus no NADH is made (these organisms can’t use any C compounds other than CO2)
- inorganic electron donors provide energy for growth (e.g. thiosulfate (S2O3 2-), molecular hydrogen (H2), Fe2+) – these donate electrons to cytochrome c or quinone pool via
enzymes that oxidise the electron donors. - that allows Δp to be built and ATP to be made.
- NADPH is needed for biosynthesis (anabolism) and is made from NADH.
- cells thus need NADH and make it by reverse electron transport – sending electrons
‘backwards’ from cyt c/quinone pool to NADH dehydrogenase which then operates in
reverse, generating NADH from NAD+, H+ and the electrons. - for that to happen, NADH dehydrogenase and the bc1
complex must translocate in reverse, bringing electrons out of the periplasmic space and into the cytoplasm, reducing
Δp.
what structure of the photosynthesis electron transport chain is the bc1 complex analogous to?
The b6f complex
give one isoenzyme of cytochrome c oxidase not found in the Eukarya?
cbb3, ba3, baa3
how does fermentation generate ATP in humans?
ATP is made during substrate-level phosphorylation steps during glycolysis.
