Ch. 8 and 9
Metabolism and Pathways
Metabolism is an emergent property of life that arises from orderly interactions between molecules.
A metabolic pathway begins with a specific molecule, which is then altered into defined steps, resulting in a certain product.
Metabolism manages the material and energy resources from the cell.
Catabolic pathways break down complex molecules to simpler compounds.
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.
Energy that was stored in the organic molecules do the work of the cell.
Anabolic pathways consume energy to build complicated molecules from simpler ones.
Bioenergetics is the study of how energy flows through living organisms.
Forms of Energy
Energy is the capacity to cause change.
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.
Kinetic energy can be associated with the relative motion of objects.
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.
Chemical energy is potential energy available for release in chemical reaction.
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:
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.
Another term that describes a state of maximum stability is equilibrium.
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.
Exergonic and Endergonic Reactions
Based on their free-energy changes, chemical reactions can be classified as exergonic and endergonic.
Exergonic reaction proceeds with a net release of free energy.
The chemical mixture loses free energy (G decreases), delta G is negative for an exergonic reaction. Using delta G as a standard for spontaneity, exergonic reactions occur spontaneously.
The magnitude of delta G for an exergonic reaction represents the maximum amount of work the reaction can perform. The greater the decrease in free energy, the greater amount of work that can be done.
An endergonic reaction is one that absorbs free energy from its surroundings.
This reaction stored free energy in molecules (G increases), delta G is positive and the reactions are nonspontaneous.
If a chemical process is exergonic (downhill), releasing energy in one direction, then the reverse process must be endergonic (uphill) using energy.
Equilibrium and Metabolism
Reactions in an isolated system eventually reach equilibrium and can do no work.
The chemical reactions of metabolism are reversible and they would reach equilibrium if they occurred in the isolation of a test tube.
Systems at equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead.
The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium and the cel continues to do work throughout its life.
A catabolic pathway in a cell releases free energy in a series of reactions.
Some of the reversible reactions of respiration are "pulled" in one direction and are kept our of equilibrium.
The key to maintaining the lack of equilibrium is that the product of a reaction doe not accumulate but becomes a reactant in the next step; waste products are expelled from the cell.
The overall sequence of reactions is kept going by free energy difference between glucose and oxygen at the top of the energy and carbon dioxide and water at the end.
As long as our cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life.
Hydrolysis of ATP
ATP (adenosine triphosphate) contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups bonded to it.
ATP is also one of the nucleoside triphosphate used to make RNA.
The bonds between the phosphate groups of ATP can be broken by hydrolysis.
When the terminal phosphate bond is broken by addition of a water molecule, a molecule of inorganic phosphate leaves the ATP, which becomes adenosine diphosphate or ADP.
The reaction is exergonic and releases 7.3 kcal of energy per mole of ATP hydrolyzed:
ATP + H2O --> ADP + Pi
delta G= -7.3 kcal/mol (-30.5 kj/mol)
Because their hydrolysis releases energy, the phosphate bonds of ATP are sometimes referred to as high energy phosphate bonds.
The phosphate bonds of ATP are not unusually strong bonds, rather the reactants themselves have high energy relative to the energy of the products (ADP and Pi).
The release of energy during the hydrolysis of ATP comes fro the chemical change of the system to a state of power free energy.
With the help of enzymes, the cell is able to use the energy released by ATP hydrolysis directly to drive chemical reactions that are endergonic.
If the delta G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so the coupled reactions are exergonic.
This involves phosphorylation, the transfer of a phosphate group from ATP to some other molecule such as a reactant.
The recipient molecule with the phosphate group covalently bonded to it is called a phosphorylated intermediate.
The key to coupling exergonic and endergonic reactions is the formation of the phosphorylated intermediate, which is more reactive than the original unphosphorylated molecule.
Transport and mechanical work in the cell are also powered by the hydrolysis of ATP.
ATP hydrolysis leads to a change in a proteins shape and often its ability to bind another molecule.
Mechanical work involving motor proteins "walking" along cytoskeleton elements, a cycle occurs in which ATP is first bound noncovalently to the motor protein.
Next, ATP is hydrolyzed, releasing ADP and Pi. Another ATP molecule can then bind.
The motor protein changes its shape and ability to bind the cytoskeleton, resulting in the movement of protein.
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.
The free energy required to phosphorylate ADP comes from exergonic breakdown reactions in the cell.
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.
Catabolic pathways provide the energy for the endergonic process of making ATP.
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.
Every chemical reaction between molecules involves both bind breaking and bond forming.
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.
Two reactant molecules: AB+CD (Reactants) --> AC+BD (Products)
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.
Its important to now that an enzyme cannot change the delta G for a reaction; it cannot make an endergonic reaction exergonic.
The reactant an enzyme acts on is referred to as the enzyme's substrate.
The enzyme binds to its substrate forming an enzyme-substrate complex.
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.
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.
The tightening of the bidding after initial contact called induced fit.
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.
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.
Temperature and pH are environmental factors important in the activity of an enzyme.
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.
The optimal pH values for most enzymes fall in the range of pH 6 to 8 but there are exceptions.
An acidic environment denatures most enzymes.
Cofactors are bound to enzymes as permanent residents, or they may be bind loosely and reversibly along with the substrate.
Catabolic Pathways and Production of ATP
The cofactors of some enzymes are inorganic.
If the cofactor is an organic molecule, its referred to as a coenzyme.
Certain chemicals inhibit the action of specific enzymes.
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.
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.
Allosteric inhibition of an enzyme in an ATP-generating pathway by ATP itself.
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.
The cell is compartmentalized and cellular structures help bring order to metabolic pathways
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.
One catabolic process, fermentation, is a partial degradation of sugars or other organic fuel that occurs without the use of oxygen.
Chemiosmosis
The most efficient catabolic pathway is aerobic respiration, in which oxygen is consumed as a reactant along with the organic fuel.
The cells of most eukaryotic and many prokaryotic organisms can carry out aerobic respiration.
Some prokaryotes use substances other than oxygen as reactants in a similar process that harvests chemical energy without oxygen; the process is called anaerobic respiration.
Cellular respiration includes aerobic and anaerobic processes.
The process of aerobic respiration can be summarized as: Organic compounds + Oxygen --> Carbon dioxide + Water + Energy
Cellular respiration by tracking the degradation of the sugar glucose: C6H12O6 + 6O2 --> 6CO2 + 6H2O + Energy (ATP+heat)
Catabolic pathways do not directly move flagella, pump solutes across membranes, polymerize monomers, or perform other cellular work.
Catabolism is linked to work by a chemical drive shaft - ATP.
To keep working, the cell must regenerate its supply of ATP from ADP and Pi.
The Principle of Redox
In many chemical reactions, there is transfer of one or more electrons (e-) from one reactant to another.
These electron transfers are called oxidation-reduction reactions, or redox reactions.
In a redox reaction, the loss of electrons from one substance is called oxidation and the addition of electrons to another substance is known as reduction.
In the equation Xe- + Y --> X + Ye-, Xe becomes oxidized (loses electrons) while Y becomes reduced (gains electrons).
In the reaction, Xe- is the electron donor which is called the reducing agent; it reduces Y which accepts the donated electron.
Substance Y, the electron acceptor, is the oxidizing agent; it oxidizes Xe- by removing its electron.
Because an electron transfer requires both an electron donor and an acceptor, oxidation and reduction go hand in hand.
Not all redox reactions involve the complete transfer of electrons from one substance to another; some change the degree of electron sharing in covalent bonds.
NAD+ and the Electron Transport Chain
In oxidation reactions, each electron travels with a proton as a hydrogen atom.
The hydrogen atoms are not transferred directly to oxygen, but are assed first to an electron carrier, a coenzyme called nicotinamide adenine dinucleotide, a derivative of the vitamin niacin.
The coenzyme is suited as an electron carrier because it can cycle easily between its oxidized form, NAD+, and its reduced form, NADH.
As an electron acceptor, NAD+ functions as an oxidizing agent during respiration.
NAD+ trap electrons from glucose and other organic molecules by enzymes called dehydrogenases.
The enzyme delivers the 2 electrons along with 1 proton to its coenzyme, NAD+, forming NADH.
The other proton is released as a hydrogen ion (H+) into the surrounding solution: H-C-OH + NAD+ ----Dehydrogenase---> C=O + NADH + H+
By receiving 2 negative electrons but only 1 positive proton, the nicotinamide portion of NAD+ has its charge neutralized when NAD+ is reduced to NADH.
Electrons lose very little of their potential energy when they are transferred from glucose to NAD+.
NAD+ is the most versatile electron acceptor in cellular respiration and functions in several of the redox steps during the breakdown of glucose.
Each NADH molecule formed during respiration represents stored energy and can make ATP.
Cellular respiration bring hydrogen and oxygen together to form water but there are two differences.
First, in cellular respiration, the hydrogen that reacts with oxygen is derived from organic molecules rather than H2.
Second, instead of occurring in one explosive reaction, respiration uses an electron transport chain to break the fall of electrons to oxygen into several energy-releasing steps.
An electron transport chain consists of a number of molecules built into the inner membrane of the mitochondria of eukaryotic cells.
Electrons removed from glucose are shuttled by NADH to the top and at the bottom end O2 captures the electrons along with hydrogen nuclei (H+) forming water.
Electron transfer from NADH to oxygen is an exergonic reaction with a free-energy change of -53 kcal/mol.
Electrons transferred from glucose to NAD+, is reduced to NADH, fall down an energy gradient in the electron transport chain to a more stable location in the electronegative oxygen atom.
The Stages of Cellular Respiration
Glycolysis occurs in the cytosol, begins the degradation process by breaking glucose glucose into two molecules of a compound called pyruvate.
In eukaryotes, pyruvate enters the mitochondria and is oxidized to a compound called acetyl CoA, which enters the citric acid cycle.
The breakdown of glucose to carbon dioxide is completed there.
Some of the steps of glycolysis and the citric acid cycle are redox reactions in which dehydrogenases transfer electrons from substrates to NAD+ or the related electron carrier FAD, forming NADH or FADH2.
In the third state of respiration, the electron transport chain accepts electrons from NADH or FADH2 generated during the first two stages and passes these electrons down the chain.
At the end of the chain, the electrons are combined with molecular oxygen and hydrogen ions, forming water.
The energy released at each step of the chain is stored in a form the mitochondrion can use to make ATP from ADP. The mode of ATP synthesis is called oxidative phosphorylation because its powered by the redox reactions of the electron transport chain.
In eukaryote cells, the inner membrane of the mitochondrion is the site of electron transport and another process called chemiosmosis making up oxidative phosphorylation.
Oxidative phosphorylation accounts for about 90% of the ATP generated by respiration.
A smaller amount of ATP is formed directly in a few reactions of glycolysis and the citric acid cycle by a mechanism called substrate-level phosphorylation.
Glycolysis
Glycolysis means "sugar splitting" and that is what occurs.
Glucose is a six-carbon sugar, is split into two three-carbon sugars.
The smaller sugars are oxidized and their remaining atoms rearranged to form two molecules of pyruvate.
Glycolysis can be divided into two phases: the energy investment and energy payoff phase.
In the energy investment phase, the cell spends ATP.
The investment is repaid with interest during the energy payoff phase, when ATP is produced by substrate level phosphorylation and NAD+ is reduced to NADH by electrons released from oxidation of glucose.
The net energy yield from glycolysis, per glucose molecule, is 2 ATP plus 2 NADH.
No carbon is released as CO2 during glycolysis and glycolysis occurs whether or not O2 is present.
If O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, citric cycle and oxidative phosphorylation.
Oxidation of Pyruvate to Acetyl CoA
Upon entering the mitochondrion via active transport, pyruvate is first converted to a compound called acetyl coenzyme A or acetyl CoA.
The linking glycolysis and the citric acid cycle, is carried out by a multienzyme complex that catalyzes three reactions.
First, pyruvate carboxyl groupie somewhat oxidized and thus carrying little chemical energy, is now fully oxidized and given off as a molecule of CO2.
Second, the remaining two-carbon fragment is oxidized and the electrons transferred to NAD+ soaring energy in the form of NADH.
Third, coenzyme A is a sulfur-containing compound derived from a B vitamin, is attached via sulfur atom to the two-carbon intermediate, forming acetyl CoA. Acetyl CoA has a hight potential energy and is used to transfer the acetyl group to a molecule in the citric acid cycle.
Citric Acid Cycle
The cycle has 8 steps each catalyzed by a specific enzyme.
For each turn of the cycle, two carbons ever in the reduced form of an acetyl group (step 1) and two different carbons leave in the oxidized form of CO2 molecules (steps 3 and 4).
The acetyl group of acetyl CoA joins the cycle by combining to form citrate.
For each acetyl group entering the cycle, 3 NAD+ are reduced to NADH (steps 3,4 and 8).
In step 6, electrons are transferred to FAD which accepts 2 electrons and 2 protons to become FADH2.
The output from step 5 represents only ATP generated during the citric acid cycle.
The total yield per glucose from the cycle turns out to be 6 NADH, 2 FADH2 and the equivalent of 2 ATP.
Pathway of Electron Transport
The electron transport chain is a collection of molecules embedded in the inner membrane of the mitochondrion in eukaryotic cells.
The folding of the inner membrane to form cristae increases its surface area, providing space for thousands of copies of each component of the electron transport chain in a mitochondrion.
The infolded membrane with its concentration of electron carrier molecules is suited for the series of sequential redox reactions that take place along the electron transport chain.
Most components of the chain are proteins and bound to the proteins are prothetic groups, nonprotein components such as cofactors and coenzymes essential for the catalytic functions of certain enzymes.
The figure above shows the sequence of electron carriers in the electron transport chain and the drop in free energy as electrons travel down the chain.
During this electron transport, electron carriers alternate between reduced and oxidized states as they accept and then donate electrons.
Each component of the chain becomes reduces when it accepts electrons from its "uphill" neighbor, which has lower affinity for electrons and then it returns to its oxidized form as it passes electrons to its "downhill" more electronegative neighbor.
Electrons acquired from glucose by NAD+ during glycolysis and the citric acid cycle are transferred from NADH o the first molecule of the electron transport chain in complex I.
The molecule is flavoprotein and returns to its oxidized form as it passes electrons to an iron-sulfur protein.
Most of the remaining electron carriers between ubiquinone and oxygen are protein called cytochromes.
The electron transport chain has several types of cytochromes, each named "cat" with a letter and number to distinguish it as a different protein with a different electron carrying heme group.
Each oxygen atom also picks up a pair of hydrogen ions from aqueous solution, neutralizing the -2 charge of the added electrons and forming water.
Another spruce of electrons for the electron transport chain is FADH2, the other recited product of the citric acid cycle.
Although NADH and FADH2 each donate an equivalent number of electrons (2) for oxygen reduction, the electron transport chain provides about 1/3 less energy for ATP synthesis when the electron donor is FADH2 than NADH.
The electron transport chain makes no ATP directly.
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.
ATP synthase works like an ion pup running in reverse.
Ion pumps use ATP as energy to transport ions agains their gradients.
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.
ATP synthase uses the energy of an existing ion gradient to power ATP synthesis.
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.
Establishing the H+ gradient is a major function of the electron transport chain.
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.
The force drives H+ back across the membrane through the H+ channels provided by ATP synthases.
In mitochondria, the energy for gradient formation comes form exergonic redox reactions along the electron transport chain and ATP synthesis is the work performed.
ATP Production by Cellular Respiration
During respiration, most energy flows in this sequence: glucose --> NADH --> electron transport chain --> proton motive force --> ATP.
In the figure above, gives details of ATP yield for each glucose molecule that is oxidized.
It adds to 4 ATP produced directly by substrate-level phosphorylation during glycolysis and the citric acid cycle to the many more molecules of ATP generated by oxidative phosphorylation.
Each NADH that transfers a pair of electrons from glucose to the electron transport chain contributes enough to the proton-motive force tp generate a maximum of 3 ATP.
There are three reasons there is not an exact number of ATP molecules generated by the breakdown of one molecules of glucose.
First, phosphorylation and the redox reaction are not coupled to each other, so the ration of the number of NADH molecules to the number of ATP is not a whole number.
A single molecule of NADH generates enough proton-motive force for the synthesis of 2.5 ATP.
The citric acid cycle supplies electrons to the electron transport chain via FADH2, but since its electrons enter later in the chain, each molecule of this electron carrier is responsible for transport of only enough H+ for the synthesis of 1.5 ATP.
Second, the ATP yield varies depending on the type of shuttle used to transport electrons from the cytosol into the mitochondrion.
The mitochondrial inner membrane is impermeable to NADH, so NADH in the cytosol is segregated form the machinery of oxidative phosphorylation.
Only about 1.5 ATP can result form each NADH that was originally generated in the cytosol.
If the electrons are passed to mitochondrial NAD+ the yield is about 2.5 ATP per NADH.
Third, the use of the proton-motive force generated by the redox reactions of respiration to drive other kinds or work.
If all the proton-motive force generated by the electron transport chain were sed to drive ATP synthesis, one glucose molecule could generate a maximum of 28 ATP produced by oxidative phosphorylation plus 4 ATP from substrate-level phosphorylation to vie a total yield of about 32 ATP.
Fermentation and Anaerobic Respiration
There are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP without he use of oxygen: anaerobic respiration and fermentation.
The distinction between these two is that an electron transit chain is used in anaerobic respiration but not in fermentation.
As mentioned before, anaerobic respiration takes place in certain prokaryotic organisms that live in environments without oxygen.
The organisms have an electron transport chain but do not use oxygen as a final electron acceptor at the end of the chain.
Oxygen performs this function well because its electronegative, but other, less electronegative substances can also serve as final electron acceptors.
Fermentation is a way of harvesting chemical energy without using either oxygen or any electron transport chain.
Types of Fermentation
In alcohol fermentation, pyruvate is converted to ethanol in two steps.
First, carbon dioxide from the pyruvate with is converted to the two carbon compound acetaldehyde.
Second, acetaldehyde is reduced by NADH to ethanol.
This regenerates the supplies of NAD+ needed for the continuation of glycolysis.
Bacteria carry out alcohol fermentation under anaerobic conditions and yeast also carries out alcohol fermentation.
In lactic acid fermentation, pyruvate is reduced by NADH to form lactate as an end product, regenerating NAD+ with no release of CO2.
Lactic acid fermentation by certain fungi and bacteria is used in the dairy industry to make cheese and yogurt.
Human muscle cells make ATP by lactic acid fermentation when oxygen is scarce.
This occurs during strenuous exercise, when sugar catabolism for ATP production outpaces the muscle's supply of oxygen from the blood.
The cells switch from aerobic respiration to fermentation.
Comparing Fermentation with Anaerobic and Aerobic Respiration
All three are alternative cellular pathways for producing ATP by harvesting the chemical energy of food.
All three use glycolysis to oxidize glucose and other organic fuels to pyruvate, with a net production of 2 ATP by substrate level phosphorylation.
In all three, NAD+ is the oxidizing agent that accepts electrons from food during glycolysis.
One difference is the contrasting mechanism for oxidizing NADH back to NAD+, which is require to sustain glycolysis.
In fermentation, the final electron acceptors is an organic molecule such as a pyruvate or acetaldehyde.
In cellular respiration, electrons carried by NADH are transferred to an electron transport chain, which generates the NAD+ required for glycolysis.
One major difference is the amount of ATP produced.
Fermentation yields two molecules of ATP, produced by substrate-level phosphorylation.
In cellular respiration, pyruvate is oxidized in the mitochondrion. Most of the chemical energy is shuttled by NADH and FADH2 in forms of electrons to the electron transport chain.
Aerobic respiration yields up to 32 molecules of ATP per glucose molecule- up to 16 times as much as fermentation.
Some organisms, obligate anaerobes, carry out only fermentation or anaerobic respiration.
Those organisms cannot survive in the presence of oxygen, some forms of which can actually be toxic if protective systems are not present in the cell.
Other organisms, including yeasts and many bacteria, can make enough ATP to survive using either fermentation or respiration are known as facultative anaerobes.
The Versatility of Catabolism
We obtain most of our calories from fats, proteins and carbohydrates.
All these organic molecules in food can be used by cellular respiration to make ATP.
Glycolysis can accept a wide range of carbohydrates for catabolism.
Proteins can also be used for fuel but first they must be digested to their constituent amino acids.
Many amino acids are used by the organism to build new proteins. Amino acids present in excess are converted by enzymes to intermediates of glycolysis and the citric acid cycle.
Catabolism can also harvest energy stored in fasts obtained from four or from fat cells in the body.
After fats are digested to glycerol and fatty acids, the glycerol is converted to glyceraldehyde 3-phosphate an intermediate of glycolysis.
Most of the energy of a fat is stored in the fatty acids by a metabolic sequence called beta oxidation that breaks down fatty acids down to tow-carbon fragments, which enter the citric acid cycle as acetyl coA.
NAHD and FADH2 are also generated during beta oxidation.
Fats make excellent fuels, in large part due to their chemical structure and the high energy level of their electrons.
Regulation of Cellular Respiration via Feedback Mechanisms
The most common mechanism for this control is feedback inhibition: the end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway.
If the cell is working hard and its ATP concentration begins to drop, respiration speeds up.
When there is plenty of ATP to meet demand, respiration slows down, sparing organic molecules for other functions.
One switch from the figure above is phosphofructokinase, the enzyme that catalyzes step 3 of glycolysis.
That is the first step that commits the substrate irreversibly to the glycolytic pathway.
By controlling the rate of this step, the cell can speed up or slow down the entire catabolic process. Phosphofructokinase can be considered the pacemaker of respiration.
Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors and activators.
It is inhabited by ATP and stimulated by adenosine monophosphate.
Phosphofructokinase is sensitive to citrate, the first product of the citric acid cycle.
If citrate accumulates in mitochondria, some of it passes into the cytosol and inhibits phosphofructokinase.
The mechanism helps synchronize the rates if glycolysis and the citric acid cycle.