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Bioenergetics and oxidative
Phosphorylation
Objectives
-To understand the general concepts of Bioenergetics; Enthalpy,
entropy and free energy change and standard free energy and the
mathematical relation between them
-To understand the concepts of high energy compounds and know
the most important examples, like ATP
- To know the general concept of oxidative phosphorylation and
the general mechanism of ATP production.
Bioenergetics
-Enthalpy, entropy and free energy
- Free energy change and standard free energy change and relationship
between them and the equilibrium constant
- ATP is the universal energy carrier in the biological systems
-Structural basis of the high phosphate group transfer potential
-Phosphorylated compound with high phosphate group transfer potential,
PEP, phosphocreatine
-ATP has an intermediate group-transfer potential
Oxidative Phosphorylation
-Electron carriers, NADH and FADH2
-Mitochondria are the respiratory organelles in the cell
-NADH dehydrogenase has two prosthetic groups FMN and iron-sulfur cluster
-QH2 is the entry for electrons from FADH2
-Cytochrome Reductase
-Cytochrome oxidase catalyses the transfer of electrons from CytC to O2
-Chemiosmaotic hypothesis in the phosphorylation of ADP
Bioenergetics & Thermodynamics
Bioenergetics: is the quantitative study of energy transduction in the living cells
and nature and the chemical process underlying these transductions .
•Bioenergetics concerns only with the initial and final energy states of reaction components, NOT the mechanism of the reaction, Not, the time needed for the reaction to occur. It allows to predict the spontaneousity of the reaction, wither a reaction will take place or not
Factors that determine the direction of a reaction
The direction and extent to which a chemical reaction proceeds is determined by two factors
- Enthalpy- Entropy- Temp
- Enthalpy: DH, a measure of the change in heat reaction content of the reactant and product. DH= H2(product)- H1(reactant) DH +ve Endothermic DH -ve Exothermic
-systems tend to go forward to a lowest-energy statee.g: fall goes downhill, oxidation of fatty acids produce a lot of
energy, these are spontaneous reactions and ∆H is negative, but
the melting of Ice is a spontaneous reaction even it is
endothermic reaction and ∆H is positive
∆H alone is not sufficient to predict the direction of a
reaction
-Entropy (∆S): a measure of randomness or disorder of the
reactants and products.
-systems have a natural tendency to randomize and the
degree of randomness of a system is defined as S which is
the entropy.
∆S= S2(product)-S1(reactant)
∆S +ve Increased entropy
∆S -ve Decreased entropy
Entropy (∆S): a measure of randomness or
disorder of the reactants and products.
-Systems tend to increase the entropy (∆S +ve),
e.g. Homogenization of sucrose solution with water. Entropy of ordered
state is lower than that of the disordered state of the same system.
Neither the entropy nor the enthalpy alone can predict the
direction of the reaction.
•Free Energy: Gibbs free energy that correlates the entropy and the enthalpy
mathematically which allow to predict in which direction a reaction proceeds spontaneously.
•Free Energy change, DG, Predicts the change in the free energy and thus
direction of reaction at any specified concentration of products and reactants DG = D H - T D SIf DG is –ve, the reaction proceeds spontaneously.
•Standard Free energy change: DGº: Free energy change under standard
conditions; that when reactant and product concentration are kept at 1M conc. •The sign of the DG predicts the direction of the reaction.
DG is –ve exergonic reaction.DG is +ve endergonic reaction.DG is zero equilibrium.
DG of the forward and back reactions
A B DG= -500 cal/mol, spontaneous in this directionThe back reaction B A DG= 500 cal/mol non-spontaneous at this direction
DG depends on the concentration of both reactants and products.For a reaction A ↔ BA: the reactants B: the product
[A]
[B]RTlnΔGΔG o
The sign of DG and DGº can be different
DGº gives prediction of the direction of the reaction only at the standard conditions:
At standard conditions the [A]=[B]=1
DG = DGº + RTln1 DG = DGº at standard conditions
Relation between equilibrium constant (Keq) and DGº
at equilibrium DG=0
A ↔ B at equilibrium
eq[A]
eq[B]
eqK
eq
eqo
[A]
[B]RTlnΔGΔG
eq
eqo
[A]
[B]RTlnΔG0
eqo RTlnkΔG
If Keq=1 DGº=0
If Keq>1 DGº < 0 (-ve)
If Keq<1 DGº > 0 (+ve)
DG is –ve exergonic reaction spontaneous from A to B
DG is +ve endergonic reaction non-spontaneous from B to A
Free Energy change profile
Glucose 6-PO4 ↔ Fructose 6-PO4
The reaction of Glucose 6-PO4 into Fructose 6-PO4 under different conditions
Glucose 6-PO4 Fructose 6-PO4
Fructose 6-PO4 Glucose 6-PO4
Glucose 6-PO4 ↔ Fructose 6-PO4
DGº of two consecutive reactions are
additives and also DG of pathways are
additives
Reactions or processes with a large +ve DGº as
moving against electrochemical gradient are
made possible by coupling the endergonic
process with a large –ve process as hydrolysis of
ATP
Favorable and unfavorable reactions are
coupled through common intermediates
A + B C + D DGº1 (non-spontaneous)
D F DGº2 (spontaneous)
A + B + DC+ D+ F
A + B C + F DGº3= DGº1 + DGº2
(spontaneous)
D is a common intermediate and can serve as
energy carriers for this reaction
•ATP is the universal energy carrier in biological systemsATP: nucleotide consists of adenine, ribose and triphosphate unit, the active
form of ATP is complex with Mg+2 or Mn+2
ATP is energy rich molecule because of its triphosphate unit that contain 2 phosphanhydrid bonds, large free energy is released when
ATP is hydrolyzed to ADP + Pi or to AMP and PPi
ATP + H2O ↔ ADP + Pi + H+ DGº= -7.3kcal/mol
ATP + H2O ↔ AMP + PPi + H+ DGº= -7.3kcal/mol
ATP-ADP cycle: the energy exchange in biological system
ATP ADP
Motion Biosynthesis
Active transportSignal amplification
PhotosynthesisOxidation of Fuel molecules
-Some biosynthesis reactions are driven by nucleotide analogous to ATP and these are:
Gaunosine triphosphate: GTP
Cytidine triphosphate: CTP
Uridine triphosphate: UTP
ATP + GDP ADP + GTP
The free energy liberated in the hydrolysis of ATP is used to drive reactions that requires an input of free energy ATP is form from ADP and Pi when fuel molecules are oxidized
ATP is continuously formed and consumed
Structural basis of the high P group transfer potential of ATP
ATP + H2O↔ ADP + Pi + H+ DGº = -7.3 kcal/mol
Glycerol 3-phosphate + H2O ↔ Glycerol + Pi DGº= -2.2 kcal/mol
ATP has a stronger
tendency to transfer its
terminal phosphoryl
group to water than
dose the glycerol 3-
phosphate ATP has high
phosphate group
transfer potentials
Why?
1- Electrostatic
repulsion
2- Resonance
stabilization
Other compounds have high phosphate group transfer potential
-Phosphoenol pyruvate (PEP), phosphocreatine have a higher group transfer potential
than dose ATP.PEP can donate P to ADP to produce ATP
PEP ↔ pyruvate + Pi DGº = -62 kj/mol
ADP + Pi ↔ ATP DGº = +13 kj/mol
PEP + ADP ↔ Pyrovate +ATP DGº = -49 kj/mol ??????
It is significant that ATP has a group-transfer potential that is intermediate among the biological important phosphorylated molecules. This intermediate position enable ATP to function efficiently as a carrier of phosphoryl groups. NO enzyme in cells that transfer P from high-P donor to low energy acceptor should first transfer first to ATP to form ADP
ATP is continuously formed and consumedATP is intermediate donor of free energy in biological systems rather than as long-term storage form of energy
ATP molecule is consumed after 1 min of its formation and the turnover of ATP is high, human consumes about 40 kgs of ATPs in 24 hr
ATP hydrolysis is coupled to reaction to shift the reaction toward product A B (non-spontaneous) DGº = +4 kcal/molATP + H2O ADP + Pi DGº = -7.4 kcal/molA + ATP + H2O B + ADP + Pi + H+DGº = -3.4 kcal/molSpontaneous
* NAD+ is the oxidized form of nicotinamide adenine dinucleotide, NADH is the reduced form* NAD+ is the major e- acceptor in oxidation of fuel molecules.
* electron donor= reducing agent (reductant) electron acceptor= oxidizing agent (oxidant)
NADH: generation of ATPNADPH: reductive biosynthesis
NAD+ + 2e- + H+ NADHOxidizing agent reducing agent
Oxidized form reduced form
NAD+ is strong oxidizing agent that can oxidize secondary alcohol into keton
* Flavin adenine dinucleotide (electron carrier molecule)FAD: Oxidized FormFADH2: Reduced Form
FAD + 2e- + 2H+ FADH2
Oxidizing agent reducing agentOxidant reductant
FAD is strong oxidizing agent it can oxidize the alkain into alkene
Oxidative Phosphorylation
Oxidative phosphorylation: is the process in which ATP is formed as a result of
transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers
NADH, FADH2 formed glycolysis, Fatty acid oxidation and citric acid cycle. They
have a pair of electrons with high transfer potential when these electrons are
transferred to O2, a large free energy is librated
The flow of electrons from NADH or FADH2 to O2 through protein complexes in the
inner membrane of the mitochondria leads to pumping of protons out the
mitochondrial matrix, this makes pH and Transmembrane electrical gradient
ATP is synthesized when proton flow to the mitochondrial matrix
H+
-- - - - + + + +
ADP + Pi
H+
ATPO2
H2O
•The Respiratory chain consists of three proton pumps, linked by two mobile electron carriers.• electrons are transferred from NADH to O2 through a chain of three large protein complexes Complex I:NADH dehydrogenase, NADH-Q reductase.Complex III: Cytochrome reductase.Complex IV: Cytochrome oxidase.The above protein complexes are pump protons
Ubiquinone (Q): carries electrons from NADH dehydrogenase (I) to cytochrome reductase (III) Cytochrome C: carries electrons from cyt-reductase (III) to cytochrome oxidase (IV).
Complex II: succinate dehydrogenase, (succinate- Q reductase), doesn't pump protons, production of FADH2 from succinate
NADH dehydrogenase
NADH
Q
Cytochrome reductase.
Cytochrome C
Cytochrome oxidase.
O2
FADH2 FAD
Ubiquinone (Q), Cytochrome C are mobile e-carriers
Complex II
Complex I
Complex III
Complex IV
NADH dehydrogenase.Complex I
Complex IIsuccinate dehydrogenase (Succinate-Q
oxireductase)
Cytochrome reductase.Complex III
Cytochrome Oxidase.Complex IV
Oxidative Phosphorylation
NADH dehydrogenase.(Complex I)The electrons of NADH enter the chain at the NADH dehydrogenase, the initial step is
the binding of NADH and then the transfer the two electrons to the flavin mono
nucleotide (FMN) prosthetic group of this protein to give the reduced form FMNH2
NADH + H+ + FMN FMNH2 +NAD+
Electrons transfer from the Fe-S cluster of complex I are shuttled to Coenzyme Q
NADH FMN reduced Fe-S QNAD+ FMNH2 oxidized Fe-S QH2
The flow of two electrons from NADH to QH2 leads to pumping of four H+ from the matrix to intermembrane space
Oxidized form of Q
Intermediate
Reduced form
QH2 shuttle electrons from complex I to cytochrome reductase (complex III)It is hydrophobic quinone diffuse rapidly within the inner membrane of mitochondria
Electrons flow from Ubiqinol to cyto. C through Cytochrome reductaseCytochrome is an electron-transferring proteins that contain a heme prosthetic group. Their iron atoms alternate between a educed ferrous(+2) state and an oxidized ferric(+3) state during electron transport.Cyt. Reductase catalyzes the transfer of 2 e- from QH2 to Cyt. C (water soluble protein) and this is coupled to pumping of 4 H+ to the inter-membrane space* Cyt. Reductase has two types of cytochromes; b and C1
Cyt. C1 and Cyt. C have iron-protoporphyrine1X the same as heme of myoglobin, hemoglobin and these hemes are covalently linked to protein
Cytochrome reductase.Complex III
QH2 transfer one of its electrons to Fe-S cluster in the reductase. Then this electron is shuttled to Cyt. C1 then to Cyt. C which carries it away from the complex
Complex IV: Cytochrome Oxidase.Cytochrome Oxidase catalyses the transfer of electrons from Cyt C to O2In this reaction
2Cyt C(+2) + 2H+ +1/2 O2 2Cyt C(+3) +H2O This process accomplished by pumping 2 protons from matrix to intermembrane space
O2 is reduced into water
Cytochrome Oxidase contains two heme A groups called heme a and heme a3 , they are different because they differ in their location in the location.
Cyt. Oxidase contains also two copper ions called CuA and CuB as prosthetic group
FADH2 doesn't leave the complex, but its electrons are transferred to Fe-S cluster then to Q for the entry to the electron transport chain, the same thing for the FADH2 moieties of glycerol dehydrogenase, and Fatty acyl Co dehydrogenase transfer their high potential electrons to Q to from QH2, these enzymes are not proton pumps
Complex II: succinate dehydrogenase (Succinate-Q oxireductase) QH2 is the entry for electrons from FADH2 of FlavoproteinsFADH2 is formed in citric acid cycle by the oxidation of the succinate to fumarate by succinate dehydrogenase (complex II) which is integral protein in the mitochondrial inner membrane,
* Oxidation and Phosphorylation are coupled by a proton-motive force
NADH + ½ O2 + H+ H2O + NAD+ DG0= -52.6 kcal/mol
ADP + Pi + H+ ATP + H2O DG0= +7.3 kcal/mol
* ATP synthesis is mediated by mitochondrial ATPase (ATP synthase in the
inner membrane of mitochondria)
* Oxidation of NADH is coupled to Phosphorylation of ADP into ATP
The chemiosmotic hypothesis
The transfer of electrons through the respiratory chain leads to pumping of
protons from the matrix to the other side of the inner mitochondrial
membrane. The H+ concentration becomes higher on the systolic side and
the electrical potential is generated and this proton motive force drives the
synthesis of ATP by the ATP-synthase complex
* Oxidation of 1 NADH 3ATP 1 FADH2 2ATP
Oxidative Phosphorylation
* Electrons transfer in the respiratory chain can be blocked by specific
inhibitors
* Oligomycin: drug bind to ATP synthase that prevents the rentry of H+
prevents ATP synthesis prevent electron transport so electron transport
and phosphorylation are coupled
The End
iron-sulfur cluster (Fe-S) in iron-sulfur proteins (non-hem proteins) play a critical role in a wide range of reduction reactions in biological systems, three types of Fe-S cluster:
The simplest one is consisting of one iron atom coordinated to 4 sulfhydryl group of four cysteine molecules A second type [2Fe-2S]Third type [4Fe-4S]NADH Dehydrogenase contain the [2Fe-2S] and [4Fe-4S]
Iron atoms in these clusters cycle between Fe (reduced ) and Fe (oxidized )
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