this chapter was a short introduction to free energy and oxidative phosphorylation. it probably oversimplified the process and left out some details but was good to read just to get an overview of the main ideas. free energy is introduced as a measure of the driving force or "energetic feasibility" of reactions, concerned with the bond energies and entropies of only the reactants and products (and contrasted this with kinetics, which is concerned with the pathway and rate of reaction). if the change in free energy from reactants to products is negative, then the reaction is energetically favorable, "exergonic", and occurs spontaneously - and the opposite case for a positive change in free energy.
standard free energy is just the free energy of a reaction at standard conditions: 1M concentration for products and reactants, pH 7. free energy change can then be related to actual concentration of reactants / products via the equation G=Gº+RTln(B/A) where B=products and A=reactants. the equation implies that if the concentration of the products is greater than reactants, then B/A will be greater than 1, making the second term in the equation negative, allowing the free energy change to be negative (spontaneous) even if the standard free energy change is positive (non spontaneous). at equilibrium, the change in free energy = 0, making the equation Gº=-RTln(B/A), and B/A represent the static equilibrium concentrations... equivalent to Keq. thus Gº=-RTln(Keq) and this yields another set of predictions: if Keq is greater than 1, then Gº is negative. if Keq is less than 1, then Gº is positive. if Keq is 1, then Gº = 0.
the idea of energetic "coupling" is introduced: a endergonic reaction can proceed by being coupled with an exergonic one via a common intermediate. we then turn to the production of ATP via the electron transport chain, which can be summarized as the synthesis of ATP in the matrix of the mitochondria, powered by a H+ gradient across the inner membrane, which is created by a chain of membrane complexes that pump H+ into the mitochondrial matrix in response to electron transfers from high energy metabolic intermediates. electrons are transferred between "complexes" which are groupings of membrane proteins that work in tandem to either accept and donate electrons.
the first step in the chain is the reduction of NAD+ to NADH plus H+, via donation of a hydride ion from random dehydrogenases. NADH plus H+ can then donate its electrons to complex 1, also named NADH dehydrogenase, which then transfers the electrons to FMN to make FMNH2. FMNH2 can then donate its electrons to coenzyme Q, which is a "quinone derivative" with a long hydrophobic tail, which then transfers them to complex III. complexes III through V are cytochromes, which have a heme group made up of a porphyrin ring with a Fe atom in the middle (which is reduced from ferric Fe3+ to ferrous Fe2+ during electron transfers). electrons are passed from coenzyme Q to cytochrome "b+c1" to "c" to "a+a3".
the mitchell hypothesis is introduced as an explanation of the actual mechanism for the powering of the ATP synthesis. it explains that during transfer of electrons between each complex, H+ ions are pumped into the intermembrane space of the mitochondria and the resulting pH, electrical, concentration gradient is what powers the ATP synthase protein embedded in the inner mitochondrial membrane. this happens when H+ ions flow in through the "F0" domain of the ATP synthase protein, which causes conformational changes in the "F1" domain which activates its catalytic activity and allows it to phosphorylate ADP, resulting in synthesis of ATP in the matrix. oligomycin is a drug that blocks the H+ from entering the F0 domain, which prevents dissipation of the H+ complex, making it energetically unfavorable for the electron transport reactions to occur (since they have to work against a higher concentration gradient) and thereby blocking ATP synthesis.
"uncoupling" is then introduced in reference to uncoupling the H+ gradient from ATP synthesis activity. uncoupling proteins are sometimes present in the inner mitochondrial membrane, especially in the brown adipose cells of hibernating animals or babies, which allow H+ to leak back into the mitochondrial matrix without powering the ATP synthase, instead producing heat. synthetic uncouplers have the same effect by generally increasing the permeability of the membrane to protons by way of molecular "proton carriers" than can traverse the inner mitochondrial membrane and dissipate the H+ gradient.
questions
how do the studies of bioenergetics and kinetics differ?
what is the free energy formula? what is enthalpy? what is entropy?
what is Gº?
what is indicated by a negative, positive, and zero value for change in free energy?
how does G relate to the concentration of the reactants?
how does Gº relate to Keq?
what is reaction coupling and how does it relate to ATP?
what is the bond energy for the first two phosphate bonds of ATP?
describe the electron transport chain.
where does electron transport take place?
where do the electrons in the electron transport chain ultimately flow to?
describe the inner mitochondrial membrane.
what is inside the matrix of the mitochondrion?
what are the "complexes" in the electron transport chain?
describe the formation of NADH
describe the next step involving complex 1
describe complex 2's role in the electron transport chain
what is coenzyme Q's role in the electron transport chain
what are the basic structure of cytochromes?
how do cytochromes accept and donate electrons?
describe the pathway of the electrons from coenzyme Q through the cytochromes.
what are site specific inhibitors and what do they result in?
what are the two specific molecular methods of electron transport in the electron transport chain?
what are standard reduction potentials and how are they related to the electron transport chain?
how is G related to E?
what is the mitchell hypothesis?
according to the mitchell hypothesis, what drives ATP synthase activity?
describe the action of H+ on ATP synthase
describe the actions of oligomycin
what are uncoupling proteins and what are their ultimate effect in mitochondria?
what are the actions of synthetic uncouplers and what is one example?
how is ADP replenished in the mitochondria?
answers
bioenergetics is the study of the energetic feasibility of reactions that is concerned with the free energy of only the reactants and products, while kinetics is more concerned about the rates of reaction as well as the pathways between reactants and products.
change in free energy = change in enthalpy - (temperature) * (change in entropy). change in enthalpy is a measure of the difference of total bond energies between the reactants and products. change in entropy represents the change of order of randomness between reactants and products.
Gº is the standard free energy which is just the free energy at standard conditions: pH 7, [1M].
negative delta G indicates an exergonic, spontaneous reaction where the products are at a lower energy than the reactants. positive delta G indicates an endergonic, non-spontaneous reaction in which the products are at a higher energy than the reactants. zero delta G represents an equilibrium state, where the rate of formation of product is equal to the rate of backreaction for formation of reactant.
the concentrations of the reactants vs the products is related to the free energy change via this equation: G=Gº+2.303RTlog(B/A) where B=products and A=reactants
@ equilibrium, G=0, and thus the G=Gº+RTln(B/A) equation becomes: Gª=-RTln(Keq). this equation allows for some simple predictions: if Keq=1, then Gº=0. if Keq is greater than 1, then Gº > 0.
highly endergonic reactions harness the energy of highly exergonic reactions through coupling via common intermediates. ATP is the most common example of this, providing copious amounts of energy by the breaking of its high energy phosphate bonds.
7.3 kcal/mol of energy is released when the phosphate groups in ATP are released.
the electron transport chain is the the series of reactions in which the high energy reduced intermediate coenzymes NADH2 and FADH2 (reduced by the oxidation of glucose) donate their electrons to a "specialized set of electron carriers" which then produce ATP from ADP. it takes place inside the inner mitochondrial membrane and the ultimate receptor is O2.
the inner mitochondrial membrane is rich with proteins, most of which participate in the electron transport chain. it is also impermeable to small ions and molecules which are important in metabolism; they need specialized carriers to be transported into the inner space. the inner membrane is also folded with cristae which increase the inner surface area. proteins transport cristae.
inside the mitochondrial matrix is: a gel like solution made up of 50% protein, including enzymes related to oxidation of pyruvate, krebs cycle, amino acids, fatty acids, NAD, FAD, ADP, pi.
the "complexes" 1-5 are functional subdivisions of the proteins involved in the electron transport chain based on the coordinated action of donating or accepting electrons to and from "mobile electron carriers" such as coenzyme Q or cytochrome c.
the first step in the chain is the reduction of NAD to NADH plus free proton via a dehydrogenase that donates a hydride ion.
the free proton plus the hydride ion of NADH are donated to NAD hydrogenase, complex 1, which has a tightly bound coenzyme FMN which accepts the 2 hydrogen atoms and becomes FMN2.
complex II is succinate dehydrogenase, transferring two electrons, from the formation of fumarate from succinate, to FAD to form FADH2.
coenzyme Q is the next electron acceptor, taking FMNH2's two hydrogen atoms, as well as FADH2's two hydrogen atoms, from complex 1 and 2, respectively.
cytochromes are made up of a heme group made of a porphyrin ring containing an atom of iron.
the Fe3+ (ferric) ion in the porphyrin ring is reduced to Fe2+ (ferrous) form when it accepts electrons.
electrons passed from Coenzyme Q to cytochromes b+c1 (complex III), c, and a+a3 (complex iv)
site specific inhibitors are molecules that bind to certain components of the electron transport chain and block electron flow by preventing the oxidation/reduction reaction to occur. this causes all components upstream to be fully reduced and the downstream components to be fully oxidized.
the two ways that electrons are transferred in the chain: as hydride ions, in the case of FADH2 and FMNH2, and as free electrons, in the case of cytochromes.
standard reduction potentials are a measure of the potential for a reduction reaction to take place, ie a measure of the tendency of the reductant to lose electrons. it is related to the electron transport chain because each reduction (transfer, or donation of electrons) is always accompanied by an oxidation reaction (loss of electrons)
G = -nFE, where n = number of electrons transferred, F = faraday constant, and E = standard reduction potential.
the mitchell hypothesis (also known as the chemiosmotic hypothesis) is a theory of how the free energy released during electron transport powers the formation of ATP from ADP and pi.
the mitchell hypothesis says that the proton gradient produced by electron transport (where more H+ ions in the intermembrane space than in the matrix) powers the ATP synthase.
H+ proton reenters the F0 domain of the ATP synthase and causes rotation, which causes conformational change in the F1 domain which catalyzes synthesis of ATP.
oligomycin binds to the F0 domain of ATP synthase and prevents any H+ ion to enter, preventing dissipation of the H+ gradient, which stops electron transport, which stops ATP synthase activity.
uncoupling proteins are proteins on the inner mitochondrial wall that allow H+ to enter back into the matrix without production of ATP. UCP1 is one uncoupling protein that is responsible for fatty acid oxidation and heat production in the brown adipocyte cells of hibernating mammals.
synthetic uncouplers produce the same effect, allowing electron transport to transpire without establishing the proton gradient necessary for ATP synthesis, by way of increasing the membrane permeability to protons. aspirin can have this effect in high doses.
ADP + Pi are transported actively back into the mitochondria via an "adenine nucleotide carrier", which also exports ATP into the cytosol of the cell.
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