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Cell Metabolism

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Organisms live at the expense of free energyThe maximum amount of usable energy that can be harvested from a particular reaction is the system’s free energy change from the initial to the final state.

This change in free energy (ΔG) is given by the Gibbs-Helmholtz equation at constant temperature and pressure:

ΔG = ΔH – TΔSWhere:

ΔG = change in free energyΔH = change in total energy (enthalpy)ΔS = change in entropyT = absolute temperature in K (C+273)

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Free energy and metabolismExergonic reactionChemical products have less free energy than the reactant molecules.

Reaction is energetically downhill.

Spontaneous reaction.

ΔG is negative.

-ΔG is the maximum amount of work the reaction can perform

Endergonic reactionProducts store more free energy than reactants

Reaction is energetically uphill.

Non-spontaneous reaction (requires energy input)ΔG is positive.

+ΔG is the minimum amount of work required to drive the reaction.

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An energy profile of a reaction

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Comparison of passive and active transportIn passive transport, a substance diffuses spontaneously down its concentration gradient with no need for the cell to expend energy.

Hydrophobic molecules and very small uncharged polar molecules diffuse directly across the membrane.

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Comparison of passive and active transport

Hydrophilic substances diffuse through transport proteins in a process called facilitated diffusion.

In active transport, a transport protein moves substances across the membrane "uphill" against their concentration gradients.

Active transport requires an expenditure of energy, usually supplied by ATP.

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An electrogenic pump. Proton pumps are examples of membrane proteins that store energy by generating voltage (charge separation) across membranes.

Using ATP for power, a proton pump translocates positive charge in the form of hydrogen ions.

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An electrogenic pump.

Proton pumps are the main electrogenic pumps of plants, fungi, and bacteria.

The voltage and H+ gradient represent a dual energy source that can be tapped by the cell to drive other processes, such as the uptake of sugar and other nutrients.

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Cotransport.

As the substance leaks back across the membrane through specific transport proteins,

it escorts other substances into the cell.

An ATP-driven pump stores energy by concentrating a substance (H+, in this case) on one side of the membrane.

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Cotransport.The proton pump of the membrane is indirectly driving sucrose accumulation by a plant cell,

with the help of a protein that cotransports the two solutes.

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Energy flow and chemical recycling in

ecosystems

The mitochondria of eukaryotes (including plants) use the organic products of photosynthesis as fuel for cellular respiration, which also consumes the oxygen produced by photosynthesis.

Respiration harvests the energy stored in organic molecules to generate ATP, which powers most cellular work.

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Energy flow and chemical recycling in

ecosystemsThe waste products of respiration, carbon dioxide and water, are the very substances that chloroplasts use as raw materials for photosynthesis.

Thus, the chemical elements essential to life are recycled. But energy is not: It flows into an ecosystem as sunlight and leaves it as heat.

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How ATP drives cellular work

Enzymes shift a phosphate group (P) from ATP to some other molecule, and this phosphorylated molecule undergoes a change that performs work.

Phosphate-group transfer is the mechanism responsible for most types of cellular work.

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How ATP drives cellular work

and drives chemical work by phosphorylating key reactants.

For example, ATP drives active transport by phosphorylating specialized proteins built into membranes;

drives mechanical work by phosphorylating motor proteins, such as the ones that move organelles along cytoskeletal "tracks" in the cell;

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How ATP drives cellular work

The phosphorylated molecules lose the phosphate groups as work is performed, leaving ADP and inorganic phosphate as products.

Cellular respiration replenishes the ATP supply by powering the phosphorylation of ADP.

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Cellular respiration and fermentation are catabolic

Fermentation – an ATP-producing catabolic pathway in which both electron donors and acceptors are organic compounds.

Can be an anaerobic process

Results in partial degradation of sugars

Cellular respiration – an ATP-producing catabolic process in which the ultimate electron acceptor is an inorganic molecule, such as oxygen.

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Cellular respiration

Most prevalent and efficient catabolic pathwayIs an exergonic process (ΔG = -2870 kJ/mol or -686 kcal/mol)

Can be summarized as:

Organic compounds + Oxygen Carbon dioxide + Water + Energy

Carbohydrates, proteins, and fats can all be metabolized as fuel, but cellular respiration is most often described as the oxidation of glucose:

C6H12O6 +6O2 6CO2 + 6 H2O + Energy (ATP + Heat)

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Cellular respiration An introduction to redox reactions

Oxidation-reduction reactions – chemical reactions which involve a partial or complete transfer of electrons from one reactant to another; called redox reactions for short.

Oxidation – partial or complete loss of electrons

Reduction – partial or complete gain of electrons

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Cellular respiration and fermentation are catabolic

Generalized redox reaction:

Electron transfer requires both a donor and acceptor, so when one reactant is oxidized the other is reduced.

Xe- + Y X + Ye- X = substance being oxidized, acts as reducing agent because it reduces Y Y = substance being reduced; acts as an oxidizing agent because it oxidizes X.

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Methane combustion as an energy-yielding redox reaction

During the reaction, covalently shared electrons move away from carbon and hydrogen atoms and closer to oxygen, which is very electronegative.The reaction releases energy to the surroundings, because the electrons lose potential energy as they move closer to electronegative atoms.

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NAD+ as an electron shuttle.Nicotinamide adenine dinucleotide molecule consists of two nucleotides joined together.

The enzymatic transfer of two electrons and one proton from some organic substrate to NAD+ reduces the NAD+ to NADH. Most of the electrons removed from food are transferred initially to NAD+.

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NAD+ as an electron shuttle.During the oxidation of glucose, NAD+ functions as an oxidizing agent by trapping energy-rich electrons from glucose or food.

These reactions are catalyzed by enzymes called dehydrogenases, which:

Remove a pair of hydrogen atoms (two electrons and two protons) from substrate

Deliver the two electrons and one proton to NAD+

Release the remaining proton into the surrounding solution

The high energy electrons transferred from substrate to NAD+ are then passed down the electron transport chain to oxygen, powering ATP synthesis (oxidative phosphorylation).

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Electron transport chains

Electron transport chains convert some of the chemical energy extracted from food to a form that can be used to make ATP.

Are composed of electron-carrier molecules built into the inner mitochondrial membrane.

Structure of this membrane correlates with its functional role.

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Electron transport chainsAccept energy-rich electrons from reduced coenzymes (NADH and FADH2); and pass these electrons down the chain to oxygen, the final electron acceptor.

The electronegative oxygen accepts these electrons, along with hydrogen nuclei, to form water.

Release energy from energy-rich electrons in a controlled stepwise fashion

Since electrons lose potential energy when they shift toward a more electronegative atom, this series of redox reactions releases energy.

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An introduction to electron transport chains.(a) The exergonic reaction of hydrogen with oxygen to form water releases a large amount of energy in the form of heat and light: an explosion.

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Electron transport chains.

It stores some of the released energy in a form that can be used to make ATP (the rest of the energy is released as heat).

(b) In cellular respiration, an electron transport chain breaks the "fall" of electrons in this reaction into a series of smaller steps

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Cellular Respiration

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Respiration is a cumulative function of three metabolic

stages:1. Glycolysis2. The Krebs cycle3. The electron transport chain and

oxidative phosphorylation

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Respiration is a cumulative function of three metabolic

stages:

Glycolysis is a catabolic pathway that:

Occurs in the cytosolPartially oxidizes glucose (6C) into two pyruvate (3C) molecules.

The Krebs cycle is a catabolic pathway that:

Occurs in the mitochondrial matrixCompletes glucose oxidation by breaking down a pyruvate derivative (acetyl CoA) into carbon dioxide

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Respiration is a cumulative function of three metabolic stages:

Glycolysis and the Krebs cycle produce:A small amount of ATP by substrate-level phosphorylationNADH by transferring electrons from substrate to NAD+ (Krebs cycle also produces FADH2 by transferring electrons to FAD+)

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Respiration is a cumulative function of three metabolic stages:

The electron transport chain:Is located at the inner membrane of the mitochondrion

Accepts energized electrons from reduced coenzymes (NADH and FADH2) that are harvested during glycolysis and Krebs cycle.

Couples this exergonic slide of electrons to ATP synthesis or oxidative phosphorylation. This process produces most (90%) of the ATP.

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GLYCOLYSIS

During glycolysis, each glucose molecule is broken down into two molecules of the compound pyruvate. The pyruvate crosses the double membrane of the mitochondrion to enter the matrix, where the Krebs cycle decomposes it to carbon dioxide.

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Respiration is a cumulative function of three metabolic stages:

The electron transport chain converts the chemical energy to a form that can be used to drive oxidative phosphorylation, which accounts for most of the ATP generated by cellular respiration.

A smaller amount of ATP is formed directly during glycolysis and the Krebs cycle by substrate-level phosphorylation.

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Substrate-level phosphorylation

O-

C

C

CH2

O

O

=

=

O-

C

C

CH3

O

O

=

=

P P P

P P

Adenosine

Adenosine

ADPSubstrate(PEP)

Product(pyruvate)

+ P

ATP

Some ATP is made by direct enzymatic transfer of P group from a substrate to ADP.

Phosphoenolpyruvate (PEP) is formed from breakdown of sugar during glycolysis

Enzyme

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GlycolysisHarvests chemical energy by oxidizing glucose to pyruvate

Glycolysis – catabolic pathway during which six-carbon glucose is split into two three-carbon sugars, which are then oxidized and rearranged by a step-wise process that produces two pyruvate molecules.

Each reaction is catalyzed by specific enzymes dissolved in the cytosol.

No CO2 is released as glucose is oxidized to pyruvate; all carbon in glucose can be accounted for in the two molecules of pyruvate.

Occurs whether or not oxygen is present.

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The energy input and output of glycolysisKrebs

cycle

GLYCOLYSISElectron transport

chain and oxidative phosphorylation

ATP ATPATP

Electrons carriedvia NADH

And FADH2

Energy-investment phaseGlucose

2 ADP 2ATP

4ADP 4ATP

2NAD+ 2NADH

NETGlucose

2ADP +2 iP

2NAD+ 2NADH +2H+

2ATP

2Pyruvate + 2H2O

2Pyruvate

Energy-payoff phase

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Glycolisis: steps 1-5

The orientation diagram at the right relates glycolysis to the whole process of respiration.

Steps 1-5 are the energy-investment phase of glycolysis.

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Steps 6-10 are the energy-payoff phase of glycolysis.

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GlycolisisTen reactions, each catalyzed by a specific enzyme, makeup the process we call glycolysis.

ALL organisms have glycolysis occurring in their cytoplasm.

At steps 1 and 3 ATP is converted into ADP, inputting energy into the reaction as well as attaching a phosphate to the glucose.

At steps 7 and 10 ADP is converted into the higher energy ATP. At step 6 NAD+ is converted into NADH + H+.

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GlycolisisThe process works on glucose, a 6-C, until step 4 splits the 6-C into two 3-C compounds.

The end of the glycolysis process yields two pyruvic acid (3-C) molecules, and a net gain of 2 ATP and two NADH per glucose.

The process is exergonic (ΔG = -140 kcal/mol or -586 kJ/mol); most of the energy harnessed is conserved in the high-energy electrons of NADH and in the phosphate bonds of ATP.

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Glycolisis

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Krebs Cycle (Citric Acid Cycle)Most of the chemical energy originally stored in glucose still resides in the two pyruvate molecules produced by glycolysis.

The fate of pyruvate depends upon the presence or absence of oxygen.

If oxygen is present, pyruvate enters the mitochondrion where it is completely oxidized by a series of enzyme-controlled reactions.

The junction between glycolysis and the Krebs cycle is the oxidation of pyruvate to acetyl CoA.

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Acetyl Co-A: The Transition Reaction from glycolysis and the Krebs cycle

Pyruvic acid is first altered in the transition reaction by removal of a carbon and two oxygens (which form CO2).

When the carbon dioxide is removed, energy is given off, and NAD+ is converted into the higher energy form NADH.

S

C

CH3

O=

=

CoAO-

C

C

CH3

O

O

=

=

CO2

NADH + H+NAD+

Coenzyme A1 3

2

Cytosol Mitochondrion

Transport protein

Acetyl CoA

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Acetyl Co-A: The Transition Reaction from glycolysis and the Krebs cycle

Coenzyme A attaches to the remaining 2-C (acetyl) unit, forming acetyl Co-A. This process is a prelude to the Krebs Cycle.

S

C

CH3

O=

=

CoAO-

C

C

CH3

O

O

=

=

CO2

NADH + H+NAD+

Coenzyme A1 3

2

Cytosol Mitochondrion

Transport protein

Acetyl CoA

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Krebs Cycle (Citric Acid Cycle)

The Krebs cycle reactions oxidize the remaining acetyl fragments of acetyl CoA to CO2.

Energy released from this exergonic process is used to reduce coenzyme (NAD+ and FAD) and to convert ADP to ATP (substrate-level phosphorylation).

A German-British scientist, Hans Krebs, elucidated this catabolic pathway in the 1930s.

The Krebs cycle, which is also known as the citric acid cycle, has eight enzyme-controlled steps that occur in the mitochondrial matrix.

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Summary of the Krebs cycle.

The cycle functions as a metabolic "furnace" that oxidizes organic fuel derived from pyruvate, the product of glycolysis.

The cycle generates 1 ATP per turn by substrate phosphorylation, but most of the chemical energy is transferred during the redox reactions to NAD+ and FAD.

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Summary of the Krebs cycle.

The reduced coenzymes, NADH and FADH2, shuttle high-energy electrons to the electron transport chain, which uses the energy to synthesize ATP by oxidative phosphorylation.

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The inner mitochondrial membrane couples electron transport to ATP synthesis

Only few molecules of ATP are produced by substrate-level phosphorylation:

2ATPs per glucose from glycolysis2ATPs per glucose from the Krebs cycle

Most molecules of ATP are produced by oxidative phosphorylation.

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The inner mitochondrial membrane couples electron transport to ATP synthesis

At the end of the Krebs cycle, most of the energy extracted from glucose is in molecules of NADH and FADH2.

These reduced coenzymes link glycolysis and the Krebs cycle to oxidative phosphorylation by passing their electrons transport chain to oxygen.

The exergonic transfer of electrons down the ETC to oxygen is coupled to ATP synthesis.

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Cell metabolism, Part II

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Mitochondriaouter membrane

inner membrane

Cristae

Matrix

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Cellular respiration and fermentation are catabolic

Oxidation-reduction reactions – chemical reactions which involve a partial or complete transfer of electrons from one reactant to another; called redox reactions for short.

Oxidation – partial or complete loss of electronsReduction – partial or complete gain of electrons

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Electron Transport Phosphorylation

The electron transport chain is made of electron carrier molecules embedded in the inner mitochondrial membrane.

Each successive carrier in the chain has a higher electronegativity than the carrier before it, so the electrons are pulled downhill towards oxygen, the final electron acceptor and the molecule with the highest electronegativity.

Except for ubiquinone (Q), most of the carrier molecules are proteins and are tightly bound to prosthetic groups (non-protein cofactors).

Prosthetic groups alternate between reduced and oxidized states as they accept and donate electrons.

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Electron transport chains.

It stores some of the released energy in a form that can be used to make ATP (the rest of the energy is released as heat).

In cellular respiration, an electron transport chain breaks the "fall" of electrons in this reaction into a series of smaller steps

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Electron Transport Phosphorylation

Protein Electron Carriers Prosthetic GroupFlavoproteins flavin mononucleotide (FMN)Iron-sulfur proteins iron and sulfurCytochromes heme group

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Electron Transport Phosphorylation

Heme group – prosthetic group composed of four organic rings surrounding a single iron atom.

Cytochrome – type of protein molecule that contains a heme prosthetic group and functions as an electron carrier in the electron transport chains of mitochondria and chloroplasts

There are several cytochromes, each a slightly different protein with heme group.It is the iron of cytochromes that transfers electrons.

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Electron Transport Chain

Each member of the chain oscillates between a reduced state and an oxidized state.

A component of the chain becomes reduced when it accepts electrons from its "uphill" neighbor (which has a lower affinity for the electrons).

Each member of the chain returns to its oxidized form as it passes electrons to its "downhill" neighbor (which has a greater affinity for the electrons).

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Electron Transport ChainAt the bottom of the chain is oxygen, which is very electronegative.

The overall energy drop for electrons traveling from NADH to oxygen is 53 kcal/mol, but this fall is broken up into a series of smaller steps by the electron transport chain.

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Electron Transport ChainAs molecular oxygen is reduced it also picks up two protons from the medium to form water. For every two NADHs, one O2 is reduced to two H2O molecules.

FADH2 also donates electrons to the electron transport chain, but those electrons are added at a lower energy level than NADH.

The electron transport chain does not make ATP directly.

It generates a proton gradient across the inner mitochondrial membrane, which stores potential energy that can be used to phosphorylate ADP.

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Chemiosmosis: the energy-coupling mechanism

Cytochromes are molecules that pass the "hot potatoes" (electrons) along the ETC.

Energy released by the "downhill" passage of electrons.

The ADP is reduced by the gain of electrons.

ATP formed in this way is made by the process of oxidative phosphorylation.

The mechanism for the oxidative phosphorylation process is the gradient of H+ ions discovered across the inner mitochondrial membrane.

This mechanism is known as chemiosmotic coupling.This involves both chemical and transport processes.

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Chemiosmosis: the energy-coupling

This protein complex, which uses the energy of an H+ gradient to drive ATP synthesis,

resides in mitochondrial and chloroplast membranes and in the plasma membranes of prokaryotes.

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Chemiosmosis: the energy-coupling

ATP synthase has three main parts: a cylindrical component within the membrane,

a protruding knob (which, in mitochondria, is in the matrix), and

a rod (or "stalk") connecting the other two parts.

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Chemiosmosis: the energy-couplingThe cylinder is a rotor that spins clockwise when H+ flows through it down a gradient.

The attached rod also spins, activating catalytic sites in the knob,

the component that joins inorganic phosphate to ADP to make ATP.

The chemiosmosis hypothesis was proposed by Peter Mitchell in 1961, later he would win the Nobel Prize for his work.

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Electron transport chain ATP synthase

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Chemiosmosis: the energy-coupling mechanism

The mechanism for coupling exergonic electron flow from the oxidation of food to the endergonic process of oxidative phosphorylation is chemiosmosis.

Chemiosmosis – the coupling of exergonic electron flow down an electron transport chain to endergonic ATP production by the creation of a protein gradient across membrane.

The proton gradient drives ATP synthesis as protons diffuse back across the membrane.

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Chemiosmosis: the energy-coupling mechanismThe term chemiosmosis emphasizes a coupling between

(1) chemical reactions (phosphorylation) and (2) transport processes (proton transport).

Process involved in oxidative phosphorylation and photophosphorylation.

Potential energy is captured by ADP and stored in the pyrophosphate bond.

NADH enters the ETS chain at the beginning, yielding 3 ATP per NADH.

FADH2 enters at Co-Q, producing only 2 ATP per FADH2.

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Chemiosmosis: the energy-coupling mechanism

How does the electron transport chain pump hydrogen ions from the matrix to the intermembrane space?

The process is based on spatial organization of the ETC in the membrane:

Some electron carriers accept and release protons along with electrons. These carriers are spatially arranged so that protons are picked up from the matrix and are released into the intermembrane space.

As complexes transport electrons, they also harness energy from this exergonic process to pump protons across the inner mitochondrial membrane.

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Chemiosmosis: the energy-coupling mechanism

When the transport chain is operating: the pH in the intermembrane space is one or two pH units lower than in the matrix.

The H+ gradient that results is called a proton-motive force – to emphasize that the gradient represents potential energy.

Proton-motive force – potential energy stored in the proton gradient created across biological membranes that are involved in chemiosmosis.

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Chemiosmosis: the energy-coupling mechanism

This force is an electrochemical gradient with two components:

1. Concentration gradient of protons (chemical gradient)

2. Voltage across the membrane because of a higher concentration of positively charged protons on one side (electrical gradient)

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Chemiosmosis: the energy-coupling

Cristae, or infoldings of the inner mitochondrial membrane, increase the surface area available for chemiosmosis to occur.

Membrane structure correlates with the prominent functional role membranes play in chemiosmosis:

Using energy from exergonic electron flow, the electron transport chain creates the proton gradient by pumping H+s from the mitochondrial matrix, across the inner membrane to the intermembrane space.

This proton gradient is maintained, because the membrane’s phospholipid bilayer is impermeable to H+s and prevents them from leaking back across the membrane by diffusion.

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One molecule of glucose – 38 ATP

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Anaerobic versus aerobic

- lactic acid fermentation;- alcohol fermentation;- cellular (anaerobic) respiration.

Pyruvic acid O2O2

- Krebs cycle; - electron transport.

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Fermentation enables some cells to produce ATP without the help of oxygen

Food can be oxidized under anaerobic conditions

Aerobic – existing in the presence of oxygen

Anaerobic – existing in the absence of free oxygen

Fermentation – anaerobic catabolism of organic nutrients

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FermentationPyruvate, the end-product of glycolysis, serves as an electron acceptor for oxidizing NADH back to NAD+.

The NAD+ can then be reused to oxidize sugar during glycolysis, which yields two net molecules of ATP by substrate-level phosphorylation.

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FermentationTwo of the common waste

products formed from fermentation are

(a) Ethanol

(b) lactate, the ionized form of lactic acid.

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Pyruvate as key juncture in catabolism

Glycolysis is common to fermentation and respiration.

The end-product of glycolysis, pyruvate, represents a fork in the catabolic pathways of glucose oxidation.

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Pyruvate as key juncture in catabolism

In a cell capable of both respiration and fermentation,

pyruvate is committed to one of those two pathways,

depending on oxygen presence.

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Anaerobic pathways

Humans cannot ferment alcohol in their own bodies, we lack the genetic information to do so.

Many organisms will also ferment pyruvic acid into other chemicals, such as lactic acid.

Humans ferment lactic acid in muscles where oxygen becomes depleted, resulting in localized anaerobic conditions.

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Anaerobic pathwaysThis lactic acid causes the muscle stiffness couch-potatoes feel after beginning exercise programs.

The stiffness goes away after a few days since the cessation of the physical activity allows aerobic conditions to return to the muscle,

and the lactic acid can be converted into ATP via the normal aerobic respiration pathways.

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Fermentation/respirationSimilarity:

Use glycolysis to oxidize glucose and other substrates to pyruvate, producing a net of two ATPs by substrate level of P

Use NAD+ as the oxidizing agent that accepts electrons from food during glycolysis

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Fermentation/respirationDifferences:

How NADH is oxidized back to NAD+ (necessary for glycolysis to continue)

During fermentation, NADH passes electrons to pyruvate. As pyruvate is reduced, NADH is oxidized to NAD+.

Electrons transferred from NADH to pyruvate or other substrates are not used to power ATP production.

ETC not only drives oxidative P, but regenerates NAD+

Final electron acceptor: pyruvate, acetaldehyde; in cellular respiration: oxygen

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Fermentation/respirationDifferences:

Amount of energy harvestedCellular respiration yields 18 times more ATP per glucose

Requirement for oxygenFermentation does not requireCellular respiration does

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The evolutionary significance of glycolysis

The first prokaryotes probably produced ATP by glycolysis:

The oldest known bacterial fossils date back to 3.5 billion years ago when oxygen was not present

Glycolysis is the most widespread metabolic pathway, so it probably evolved early

Glycolysis occur in cytosol and does not require membrane-bound organelles.

Eukaryotic cell with organelles probably evolved about two billion years after prokaryotes.

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The catabolism of various food molecules.

Carbohydrates, fats, and proteins can all be used as fuel for cellular respiration.

Monomers of these food molecules enter glycolysis or the Krebs cycle at various points.

Glycolysis and the Krebs cycle are catabolic funnels through which electrons from all kinds of food molecules flow on their exergonic fall to oxygen.

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The catabolism of various food molecules.

Catabolism can harvest energy stored in fats obtained either from food or from storage cell in the body.

Most of the energy of a fat is stored in the fatty acids.

A metabolic sequence called beta oxidation breaks the fatty acids down to two-carbon fragments.

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The control of cellular respiration

Allosteric enzymes at certain points in the respiratory pathway respond to inhibitors and activators that help set the pace of glycolysis and the Krebs cycle.

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The control of cellular respiration

Phosphofructokinase, the enzyme that catalyzes step 3 of glycolysis, is one such enzyme. It is stimulated by AMP that is derived from ADP, but it is inhibited by ATP and by citrate.

This feedback regulation adjusts the rate of respiration as the cell's catabolic and anabolic demands change.

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ReadingCh. 9 pp. 162-184