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Ch. 8 and 9 (Chemiosmosis (ATP Production by Cellular Respiration…
Ch. 8 and 9
Chemiosmosis
Populating the inner membrane of the mitochondrion or the prokaryotic plasma membrane are many copies of a protein complex called ATP synthase, the enzyme that makes ATP from ADP and inorganic phosphate.
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Enzymes can catalyze a reaction in either direction, depending on the delta G for the reaction, which is affected by the local concentrations of reactants and products.
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The power source for ATP synthase is a difference in the concentration of H+ on the opposite sides of the inner mitochondrial membrane.
This process in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP is called chemiosmosis.
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This chain is an anergy converter that uses exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane, from the mitochondrial matrix into the intermembrane space.
The H+ moves back across the membrane, diffusing down its gradient.
Energy stored in an H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis.
At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution.
In eukaryotic cell, the electron carriers are arranged n the inner mitochondrial matrix and deposited in the intermembrane space.
The H+ gradient that results is referred to as a proton-motive force, emphasizing the capacity of the gradient to perform work.
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In mitochondria, the energy for gradient formation comes form exergonic redox reactions along the electron transport chain and ATP synthesis is the work performed.
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Metabolism and Pathways
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A metabolic pathway begins with a specific molecule, which is then altered into defined steps, resulting in a certain product.
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A major pathway of catabolism is cellular respiration, where sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water.
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Forms of Energy
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In everyday life, energy is important because some forms of energy can be used to do work.
Energy exists in various forms and the work of life depends on the ability of cells to transform energy from one form to another.
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Thermal energy is kinetic energy associated with the random movement of atoms or molecules through the transfer from one object to another by heat.
Energy that is not kinetic is potential energy, or energy that matter possesses because of its location or structure.
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Laws of Thermodynamic
The study of energy transformations that occur in a collection of matter is known as thermodynamics.
The first law of thermodynamics states that energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. The law is also known as the principle of conservative energy.
Scientists use a quantity called entropy as a measure of molecular disorder, or randomness.
The more randomly arranged a collection of matter is, the greater its entropy.
The second law of thermodynamics states: Every energy transfer or transformation increases the entropy of the universe.
The concept of entropy helps to understand why certain processes are energetically favorable and occur on their own. If a given process leads to an increase in entropy, the process can proceed without requiring an input of energy. The process is called spontaneous.
Free-Energy Change
J. Willard Gibbs, a professor in Yale, defined a function called Gibbs free energy of a system.
Free energy is the portion of a systems energy that can perform work when temperature and pressure are uniform throughout the system.
The change in free energy can be calculated for a chemical reaction by applying the following equation:
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H symbolizes the change in the system's enthalpy, S is the change in the system's entropy and Tis the absolute temperature in Kelvin (K) units.
Using chemical methods, we can measure G for any reaction.
Once the value of G is known, it can be used to predict whether the process will be spontaneous.
Only processes with a negative G are spontaneous. For G to be negative, H must be negative or T/S must be positive. Every spontaneous process decreases the systems free energy and processes that have a positive or zero G are never spontaneous.
Free Energy, Stability and Equilibrium
Another way to think of G is to realize that it represents the difference between the free energy of the final state and the free energy of the initial state: delta G= G final state - G initial state :
G can be negative only when the process involves a loss of free energy during the change from initial state to final state. The system in its final state is less likely to change and is more stable than it was previously.
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There is an important relationship between free energy and equilibrium, including chemical equilibrium.
Most chemical reactions are reversible and proceed to a point which they move forward and backward occurring at the same rate. The reaction is a chemical equilibrium and there is no further net change in relative concentration of products and reactants.
As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases. Free energy increases when it is pushed away from equilibrium.
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Regeneration of ATP
An organism at work uses ATP continuously, but ATP is a renewable source that can be regenerated by the addition of phosphate to ADP.
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This is known as the ATP cycle, and it couples the cell's energy-yielding processes to the energy consuming ones.
Since ATP formation from ADP and Pi is not spontaneous, free energy must be spent to make it occur.
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All About Enzymes
An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction.
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Changing one molecule into another involves contorting the staring molecule into a highly unstable state before the reaction can proceed.
To reach the contorted state where bonds change, reactant molecules must absorb energy from their surroundings.
When new bonds of the product molecules form, energy is released as heat, and molecules return to stable shapes with lower energy than contorted state.
The energy required to contort the reactant molecules so the bonds can break is known as activation energy.
Activation energy is often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings.
The absorption of thermal energy accelerates the reactant molecules, so they collide more often and forcefully.
When the molecules have absorbed enough energy for the bonds to break, the reactant are in an unstable condition known as transition state.
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Proteins, DNA and other complex cellular molecules are rich in free energy and have the potential to decompose spontaneously.
These molecules only persist because at temperatures typical for cells, few molecules can make it over the activation energy.
Heat can increase the rate of reaction by allowing reactants to attain the transition state more often.
First, high temperature denatures proteins and kills cells and second, heat would speed up all reactions.
Instead of heat, organisms carry out catalysis, a process by which a catalyst speeds up a reaction without itself being consumed.
An enzyme catalyzes a reaction by lowering the EA barrier enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.
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Its important to now that an enzyme cannot change the delta G for a reaction; it cannot make an endergonic reaction exergonic.
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While enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product of the reaction.
Only a restricted region of the enzyme molecule actually binds to the substrate and the region is called active site which is a pocket or groove on the surface of the enzyme where catalysis occurs.
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Active site is formed by only a few of the enzymes amino acids, with the rest of the protein molecule providing framework that determines the shape of the active site.
The specificity of an enzyme is attributed to a complementary fit between the shape of its active site and shape of the substrate.
The shape that best fits the substrate isn't necessarily the one with the lowest energy, but during the very short time the enzyme takes on this shape, its active site can bind to the substrate.
As the substrate enters the active site, the enzyme changes shape due to interactions between the substrates chemical groups and chemical groups on the side of the amino acid that form the active site.
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In most enzymatic reactions, the substrate is held in the active site by weak interactions such as hydrogen and ionic bonds.
R groups of amino acids that make up the active site catalyze the conversion of substrate to product and the product departs from the active site.
The enzyme is then free to take another substrate molecule into its active site and the cycle happens so fat that a single enzyme molecule acts on about 1,000 substrate molecules per second and sometimes faster.
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Most metabolic reactions are reversible and an enzyme can catalyze either the forward or the reverse reaction, depending on which direction has a negative delta G.
The rate at which a particular amount of enzyme converts substrate to product is a function of the initial concentration of the substrate: the more substrate molecules are available, the more frequently they access the active sites of the enzyme molecules.
At some point the concentration of substrate will be high enough that all enzyme molecules will have their active sites engaged.
Each enzyme works better under some conditions because these optimal conditions favor the most active shape for the enzyme.
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The rate of the enzymatic reaction increases with increasing temperatures because substrates collide with active sites more frequently when molecules move rapidly.
The thermal agitation of the enzyme molecule disrupts weak interactions that stabilize the active shape of the enzyme and the protein molecule eventually denatures.
without denaturing the enzyme, this temperature allows the greater number of molecular collisions and the fastest conversion of the reactants to product molecules.
Each enzyme has an optimal temperature, it also has a pH at which it's the most active.
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Cofactors are bound to enzymes as permanent residents, or they may be bind loosely and reversibly along with the substrate.
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If the cofactor is an organic molecule, its referred to as a coenzyme.
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Sometimes the inhibitor attaches to the enzyme by covalent bonds. Many enzyme inhibitors bind to the enzyme by weak interactions and when this occurs the inhibition is reversible.
Competitive inhibitors reduce the productivity of enzymes by blocking substrates from entering the active sites.
Noncompetitive inhibitors do not directly compete with the substrate to bind to the enzyme at the active site.
This inhibitor increases the concentration of substrate so that as active sites become available, more substrate molecules that inhibitors are around to gain entry to sites.
This inhibitor causes the enzyme molecule to change its shapes that the active site becomes much less effective to catalyzing the conversion of substrate to product.
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The molecules that naturally regulate enzyme activity in a cell behave like reversible noncompetitive inhibitors: These regulatory molecules change an enzymes shape and the functioning of its active site by binding to a site elsewhere on the molecule.
Allosteric regulation describes any case in which a proteins function at one site is affected by the binding of a regulatory molecule to a separate site.
Most enzymes known to be allosteric are constructed by two or more subunits, each composed of a polypeptide chain with its own active site.
The entire complex oscillates between two different shapes, one catalytically active and the other inactive.
An activating or inhibiting regulatory molecule binds to a regulatory site often located where subunits join.
The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme.
The subunits of an allosteric enzyme fit together that a shape change in one subunit is transmitted to all others.
Through this interaction of subunits, a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits.
In another kind of allosteric activation a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, increasing catalytic activity at the other active sites.
Cooperativity is a mechanism that amplifies the response of enzymes to substrates: one substrate molecule primes an enzyme to act on additional substrate molecules more readily.
Cooperativity is allosteric regulation because even though substrate is binding to an active site, its binding affects catalysis in another actives site.
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Feedback inhibition occurs when a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that its early in the pathway.
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The arrangement facilitates the sequence of reactions with the product from the first enzyme becoming the substrate for an adjacent enzyme in the complex until the end product is released.
Some enzymes and enzyme complexes have fixed locations within the cell and act as structural components of particular membranes.
Others are in solution within particular membrane enclosed eukaryotic organelles, each with its own internal chemical environment.
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