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 Sheet 3, Dr.Nafeth, by Manal Dasan 9\2\2012

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Majed Sharayha



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PostSubject: Sheet 3, Dr.Nafeth, by Manal Dasan 922012   Wed Feb 15, 2012 4:50 am

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Oxidative phosphorylation

Oxidative phosphorylation is a terminal process to make ATP.
Oxidative phosphorylation : It's a process of oxidation/reduction rxn & it requires an electron donor [NADH ,FAD[H2]] ,electron acceptor [O2] ,transferring them from a prtn to prtn & finally oxygen can get reduced to water ,
Couple to this process is making ATP from
ADP + phosphate.
Components of the electron transport chain is four complexes [complex 1,2,3&4]. They are named by this way because they are sequential.
Note => The electrons go either from 1 to 3 or 2 to 3 and then 3-4 so the process must go in sequence. If this sequence is interrupted at any place the whole process will be shut down.

Complex 1 =>
Complex 1 is an enzyme
Note =>All enzymes in electron transport chains are oxidoreductase enzymes where they can accept or donate electrons.
In the electron –transport chain ,electrons donated by NADH & FAD[H2] are passed sequentially through a series of electron- carries embedded in the inner mitochondrial membrane of the chain .
The chain start from NADH ….NAD+ is reduced into NADH ( which composed of proton + hydride ion )…then NADH is transferred to NADH Dehydrogenase (complex 1) ….then to Coenzyme Q (co Q or Quinone ) .
Quinone : is a compound made up of 2 oxygen, can accept or release electrons[total of 2 electrons taken from complex1] ,It is a hydrophobic compound so it can travel inside the inner mitochondrial membrane.
then the electrons travel to complex 3 or complex 2 [succinate dehydrogenase]. Quinone takes electrons from FADH and succinate dehydrogenase is using the FAD as a coenzyme. It takes the electrons and travel through membrane until it reaches complex 3. Complex 3 take these electrons and giving it out to cytochrome C [which is a protein that has a heme C in intermembranous space]. Cytochrome C travels to complex 4 [cytochrome C oxidase] where the reduction of oxygen to water takes place.
NOTE:
1.NADH dehydrogenase uses NAD+ as a cofactor.
2.Succinate dehydrogenase takes a hydrogen atom from succinate. It uses FAD as a cofactor.

In complex 2 there are other compounds that can act as enzymes which can act as succinate dehydrogenase and sulfur proteins [it has FAD].
NOTE:
As long as you have a cofactor that has the ability to accept or donate protons inside the protein can act as enzymes.

Sulfur protein that has FAD can act as complex 2 and glycerol-3 phosphate dehydrogenase [which also has FAD] can act as complex 2.
The process goes from complex 1 to complex 3 or from complex 2 to complex 3 but there's no connection between complex 1 and complex 2.
When electrons move from high energy to low energy it loses energy. This lost energy is used in electron transport chains to pump protons in pathways designed for protons movement inside the proteins. Within every step around 16 kilo Calories are released.


ATP synthase
Is enzyme that contains 2 subunits :
inside the mitochondrial membrane [F0].
Contains 2 types of subunits:
C subunit (12 pieces gathered as a circle base [C1-C12]). It's hydrophobic so it can rotate inside the membrane.
A subunit(stationary in the membrane) by binding toa B2 subunit inside the matrix.
Inside matrix [F1] : it contains 3 pairs of alpha & beta. On each beta subunit, there is a site for ATP synthesis .




The relationship between F0 and F1 :
On the base of F1 there are gamma subunits, with every proton movement gamma subunits change hitting alpha or beta subunits inside. With every hit the protein confirmation of the protein causing the synthesis of ATP. There is electron chemical gradient where protons are outside the membrane and these protons will move according to electrochemical gradient through pathways where the entrance is C subunit [hydrophobic so it can move inside the membrane] and the exit is the A subunit.
We have one place on each C subunit that can bind to a protein. As soon as this place is exposed to the periplasmic site it can bind a proton changing to hydrophobic causing conformational changes in the protein then it pushes against the A subunit [stationary] thus it will move, and opens another spacein another C subunit to take up another proton.
So it take 12 proton to complete 1 turn & synthesis of 3 ATP.
this video can help you understand https://www.youtube.com/watch?v=H7P4xOUPYVw )

With each movement of C subunit, the stalk (gamma subunit) moves, hitting beta and alpha subunits. The alpha subunits are saving the conformation of the beta subunits.
When the stalk moves, we have 3 beta subunits which have a reaction of ATP. They have the ability to change into 3 conformational changes:
Open (O): where ATP can be released.
Loose (L): can accept ADP and phosphorus.
Tight (T): where reaction can happen.
When the stalk rotates, its hits beta subunit that convert it from L position to T position where reaction can happen then to O position where ATP can be release .
Note : We have 12 c subunit (12proton)and for every 4 proton movement generate one ATP so we make 3 ATP/turn .

oxidoreductase (enzyme input in oxidative phosphorylation ):
NADH dehydrogenase (complex 1): that convert NADH to NAD+ .
always enzyme in oxidoreductase reaction has cofactor can accept and release electron (in general heme is a cofactor can accept or release electron ) we don’t have heme in complex 1 so we use another material like ..
*flavin mononucleotide FMN :flavin is a material can get oxidize and reduce .
* ironsulfer complexes Fe-s : sulfer is transition element that can also reduce and oxidize the NADH .
electrons come from NADH as a hydrate ion and transfer to FMN and Fe-s then to another material which can accept and release electron . the all process happen to transfer electon from one part to another .

We have 4 complexes (1,2,3,4 ) are stable inside the membrane and we have spaces between them so we need hydrophobic material ( can move inside the membrane) and in the same time can get reduce and oxidize … it’s a Quinone : chemical compound characterized by cyclic ring and has 2 oxygen and it transfer electron from complex 1 to complex 3 or from complex 2 to complex 3
If is fully oxidized named Quinone
if is partially oxidized named semiquinone… so according to this Quinone can accept or release 2 electron.
So Quinone can be associated with help problem like uses it to patient with stroke and give it to them like drugs that help in make electron transport chain faster to get more energy ..
Soooo
complex 1 gets energy from NADH and give it to cytochrome bc1 by Quinone OR complex 2 gets energy from FADH2 and give it to cytochrome bc1 by Quinone ..

complex 3 ( cytochrome bc1 ) :
so named because it contains 2 types of heme ( heme c and b ) it can changes its color between oxidation and reduction .
Heme C is not found inside the matrix, it’s situated in the periplasmic place.
When accepting electrons, heme C accepts only 1 electron at a time because it contains iron and iron goes from +2 to +3 and backwards. Electrons will go from cytochrome C to cytochrome C oxidase [it’s called oxidase because it oxides cytochrome C].
Cytochorme C has more than one cofactor which can accept and release protons and has two types of hemes:
Heme A and heme A3
Copper: transitional element which can accept or release protons
The reaction [reduction of oxygen to water] occurs in cytochrome C oxidase where the electrons come from cytochrome C oxidase to copper site then the copper goes to heme A then to heme A3.

Qs: why do we need heme in cytochrome C oxidase?
Because heme has iron and iron can bind to oxygen [oxygen activiating enzymes] so it allows electron movement.
Outside the cytochrome C oxidase affinity for oxygen is higher than myoglobin [transports oxygen inside the tissues] and so it takes the oxygen from the myoglobin and it bonds with heme thus reduction of oxygen to water occurs.
There’s a energy difference in electrons movement from complex 1 to complex 3 and from complex 3 to complex 4 and this energy difference is used to transport protons from complex 1, complex 3 and complex 4.
Outside of complex 1 we can transport 4 protons, from complex 3 we can transport also 4 protons but from complex 4 we can transport 2 protons for every NADH used in the reaction.
So a total of 10 protons for every NADH used in the reaction.
And a total of 6 protons for every FADH, because complex 2 transfers to complex 3 and so complex 1 is excluded from the equation (4 protons are out). The transferring of protons is quite unknown yet.
The energy in complex 2 is approximately equal to the energy of quinine so the movement of electrons form complex 2 to complex 3 doesn’t generate an energy difference so no protons will be transported outside of the membrane. Also complex 2 is not spanning the membrane so no pathway for transferring the protons.


In general, what’s the mechanism of proton pumping?
First there must be an oxidation/ reduction reaction, so you have an enzyme with a negative charge so it can accept a proton [it has an excess of electrons so it can accept protons] it bonds with it so it will be reduced. But when it’s close to the membrane around the intermembraneous space it will lose the electrons to continure the cycle of the oxidation/ reduction reaction so it will have excess protons.

Energy from the electron transport chain:
We used around 30% of the energy we are making.

Forgive me if there are any mistakes & good luck
Done by Manal Dasan & special thanks to sumaya Abuodeh .
Success is to be measured not so much by the position that one hasreached in life as by the obstacles which he has overcome =)
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Sheet 3, Dr.Nafeth, by Manal Dasan 9\2\2012
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