9.0 Introduction

1. Life Is Driven by Energy
1. Cells Derive Energy From Organic Molecules
2. Convert Energy into ATP fig 9.1

1. Using Chemical Energy to Drive Metabolism
1. All Living Organisms Require Energy
1. Autotrophs are organisms that convert energy into chemical energy
2. Heterotrophs live on the energy produced by autotrophs

2. All Organisms Must Harvest Chemical Energy to Live fig 9.2
1. Foods contain compounds rich in chemical bonds
2. Extracting this energy is done in stages
3. First stage is digestion
4. Catabolism is the next stage where energy is obtained from C–H bonds

3. Cellular Respiration
1. C–H bond energy is carried by electrons in the covalent bond
2. Electrons used to produce ATP
3. Energy depleted electron donated to another molecule
1. In aerobic respiration oxygen accepts H⁺, water formed
2. In anaerobic respiration a non-oxygen inorganic molecule is the acceptor
3. In fermentation an organic molecule is the H⁺ recipient

4. Basic reaction of carbohydrate catabolism
1. Reactants are carbohydrates and oxygen
2. Products are carbon dioxide, water and energy
3. Change in free energy is –720 kilocalories, energy released
4. Energy used to produce ATP

4. The ATP Molecule
1. ATP molecule transfers energy from respiration to other cellular sites
2. Structure of ATP fig 9.3
1. Ribose sugar bound to adenine base and chain of three phosphate groups
2. Linked phosphates store energy of their electrostatic repulsion
3. Phosphate transfer (phosphorylation) charges that molecule

5. How Cells Use ATP
1. Used to do most activities that require work
1. Movement of cell
2. Movement within cell

2. Used to drive endergonic reactions
1. Building molecules takes energy
2. Chemical bonds of molecules contain more energy than reactants
3. Reaction needs extra energy from ATP to proceed

6. How ATP Drives Endergonic Reactions
1. Enzyme catalyzing reaction has two binding sites
1. Reactant binding site
2. ATP binding site

2. ATP site splits ATP molecule, releases 7 kcal of energy
3. Pushes reactant at other site "uphill" driving reaction
4. Analogy: Belly-flopping in pool of water
5. Two parts of reaction occur in concert
6. Both parts may occur on surface of same enzyme, are physically linked
1. ATP hi-energy phosphate attaches to and activates catalyst fig 9.4

1. An Overview of Glucose Catabolism
1. Cells Make ATP in Two Ways
1. Substrate-level phosphorylation
1. Phosphate from intermediate transferred to ADP making ATP fig 9.5
2. Chemical bonds of glucose shifted around
3. Reactions release more energy than needed to form ATP fig 9.4

2. Aerobic respiration
1. Electrons harvested passed along electron transport chain
2. Forms ATP, electrons ultimately donated to oxygen

3. Most organisms combine two processes, reactions occur in four stages
1. Fist stage is glycolysis, capture by substrate-level phosphorylation
2. Next three stages oxidize end product of glycolysis

2. Glycolysis
1. Stage one: Glycolysis
1. Energy from glucose extracted in 10 reaction biochemical pathway
2. Produces ATP by substrate-level phosphorylation

2. Glycolytic enzymes are present in the cytoplasm of the cell
3. Enzymes are not bound to any membrane or organelle
4. Two ATP formed by substrate-level phosphorylation
1. Two ATP used up early in pathway
2. Four ATP are produced in the phosphorylation

5. Four electrons harvested as NADH, used to make ATP by aerobic respiration
6. Process is not a highly efficient, most energy remains in pyruvate
7. Occurs in all organisms, with or without oxygen
8. In animals process cannot take place indefinitely without oxygen

3. Aerobic Respiration fig 9.6
1. Stage two: Pyruvate oxidation
1. Pyruvate converted to CO₂ and two-carbon acetyl-coA
2. One molecule NADH made per pyruvate (two NADH per glucose)

2. Stage three: Krebs cycle
1. Cycle of nine reactions
2. Alternately called the citric acid cycle or tricarboxylic acid cycle
3. Two more ATP made by substrate-level phosphorylation
4. Large number of electrons removed by NADH

3. Stage four: Electron transport chain
1. Electrons carried by NADH
2. Large number of ATP molecules formed

4. In eukaryotes the second, third and fourth stages occur in mitochondria
5. Photosynthetic plants exhibit oxidative respiration like other organisms

4. Anaerobic Respiration
1. Other organisms may use other compounds as final electron acceptors
2. Methanogens
1. Are primitive archaebacteria, including thermophiles
2. Use CO₂ as electron acceptor
3. Reduce CO₂ to CH₄ (methane)

3. Sulfur bacteria
1. Bacteria present in and the source of rocks enriched in sulfur ³²S
2. Electron acceptor is inorganic sulfates (SO₄) reduced to H₂S
3. High quantities of H₂S helped evolve first form of photosynthesis

2. Stage One: Glycolysis
1. Glycolysis Synthesizes ATP
1. Occurs in cytoplasm
2. Involves 10 reactions that convert glucose to two 3-C pyruvates fig 9.7
3. Energy yield of 2 ATP by substrate-level phosphorylation

2. Priming
1. Five reactions convert glucose to 2 molecules of 3-C glyceraldehyde-3-phosphate
2. Reactions require energy
3. Step A: Glucose priming
1. Change glucose into a compound that is readily cleaved in half
2. Cell uses 2 ATP

4. Step B: Cleavage and rearrangement
1. Six-C product of step A split into 2 3-C molecules
2. One molecule of G3P, other molecule is converted into G3P

3. Substrate-Level Phosphorylation
1. Five more reactions convert G3P into pyruvate
2. Yields production of ATP
3. Step C: Oxidation
1. Two electrons and one proton transferred from G3P to NAD⁺
2. Forms NADH, one per G3P, two per glucose
3. Both electrons in new covalent bond from G3P

4. Step D: ATP generation
1. G3P converted into pyruvate (two per glucose)
2. Two ATP made per G3P (four ATP per glucose) fig 9.5
3. Complete yield of 2 ATP, 2 NADH, 2 pyruvate

5. Net energy is 24 k/cal per mole of glucose (3.5% of what's available)
6. Even though amount is small, life survived on it for a billion years
7. Evolution of glycolysis was backwards like most biochemical reactions
1. ATP-producing breakdown of G3P evolved first
2. Synthesis of G3P developed later when original G3P used up

4. All Cells Use Glycolysis
1. Glycolysis was among the earliest pathways to evolve
2. Does not require oxygen, occurs readily in anaerobic environment
3. Reactions occur freely in the cytoplasm
4. Most organisms extract additional energy through aerobic respiration
5. Glycolysis has been added to, but not replaced by other processes
1. Evolution is an incremental process
2. Change occurs by improving upon past success

5. Closing the Metabolic Circle: The Regeneration of NAD⁺
1. Three changes occur during glycolysis
2. Glucose is converted to two pyruvates
3. Two ADPs are converted to ATPs
4. Two NAD⁺ molecules are converted to NADHs

6. The Need to Recycle NADH
1. Glycolytic processes cannot continue ad infinitum
1. Cell will ultimately accumulate NADH and run out of NAD⁺
2. NADH must be recycled back to NAD⁺ for glycolysis to continue

2. Recycling occurs in one of two ways fig 9.8
1. Aerobic respiration
1. Oxygen is the final electron acceptor, water is final product
2. This process also called aerobic metabolism

2. Fermentation
1. Organic molecules serve as the final electron acceptor
2. Occurs in many organisms, even those capable of aerobic respiration fig 9.9

3. Pyruvate molecule from glycolysis changed in one of two ways
1. Anaerobic respiration path changes it to acetyl-co A and into the Krebs cycle
2. Fermentation reduces all or part of the pyruvate

3. Stage Two: The Oxidation of Pyruvate
1. Oxidation of Pyruvate Occurs in Two Stages
1. In eukaryotes, occurs only in mitochondria
2. Oxidation of pyruvate into acetyl-CoA
3. Oxidation of acetyl-CoA in Krebs cycle

2. Producing Acetyl-CoA fig 9.10a
1. One carbon of the three-carbon pyruvate is cleaved, leaves as CO₂
2. This is a decarboxylation reaction that leaves
1. A two-carbon fragment called an acetyl group
2. A pair of electrons and associated H⁺ reduces NAD⁺ to NADH

3. Complex reaction involves three intermediate steps
1. Catalyzed within the mitochondria by a multienzyme complex
2. Pyruvate dehydrogenase: Enzyme that removes a CO₂ from pyruvate
3. Acetyl group added to cofactor (co-enzyme A) makes acetyl-CoA
4. Reaction produces one molecule of NADH
5. Remaining acetyl-CoA is a more important consequence fig 9.10b
1. Formed by many metabolic processes
2. Most molecules catabolized for energy converted to acetyl-CoA
3. Most acetyl-CoA is directed toward energy storage

3. Using Acetyl-CoA
1. Limited number of processes use acetyl-coA
1. Directed toward energy storage (lipid synthesis)
2. Oxidized in Krebs cycle to produce ATP

2. Choice of option dependent on cell's ATP level
1. If high, oxidative pathway inhibited, fat synthesis occurs
2. If low oxidative pathway stimulated to produce energy

4. Stage Three: The Krebs Cycle
1. The Oxidation of Acetyl-CoA fig 9.11
1. Acetyl-CoA is oxidized by binding it to four-carbon oxaloacetate
2. The resulting six-carbon molecule passes through series of reactions
1. Electron-yielding reactions split off two molecules of CO₂
2. The four-carbon molecule is regenerated

2. Overview of the Krebs Cycle
1. Consists of nine reactions in two stages
2. Step A: Priming
1. Acetyl-CoA first joins the cycle
2. Chemical groups are rearranged

3. Step B: Energy extraction
1. Four of the six reactions are oxidations, electrons are removed
2. One reaction generates an ATP equivalent via substrate-level phosphorylation

3. The Reactions of the Krebs Cycle
1. Reaction 1: Condensation
1. 2-C acetyl-coA + 4-C oxaloacetate = 6-C citrate + coA
2. Irreversible reaction
3. Reaction inhibited in presence of large amounts of ATP
4. Reaction stimulated when ATP is low

2. Reactions 2 and 3: Isomerization
1. Hydroxyl group repositioned
2. Water removed from one carbon, then added to different carbon
3. Result is change in position of an -H and an -OH
4. Molecule is now called isocitrate

3. Reaction 4: The first oxidation
1. Isocitrate undergoes oxidative decarboxylation reaction
2. Oxidation produces pair of electrons that reduce NAD⁺ to NADH
3. Oxidized intermediate is decarboxylated, CO₂ is removed
4. Product is a 5-C molecule of ða-ketoglutarate

4. Reaction 5: The second oxidation
1. 5-C ða-ketoglutarate decarboxylated by multienzyme complex
2. 4-C Succinyl group + coA = succinyl-coA
3. Two electrons extracted reducing another NAD⁺ to NADH

5. Reaction 6: Substrate-level phosphorylation
1. Bond between succinyl group and coA is high energy
2. Gives a phosphorylation reaction of GDP to GTP
3. GTP converted to ATP
4. Remaining molecule is 4-C succinate

6. Reaction 7: The third oxidation
1. Succinate oxidized to fumarate
2. Free energy can't drive NAD⁺ reaction, but can make FAD⁺ into FADH₂
3. FAD⁺ is an integral part of inner mitochondrial membrane
4. FADH₂ can contributes electrons to electron transport chain

7. Reactions 8 and 9: Regeneration of oxaloacetate
1. Water molecule added to 4-C fumarate, forms 4-C malate
2. Malate oxidized to 4-C oxaloacetate and two electrons
3. Electrons drive reaction NAD⁺ to NADH
4. Oxaloacetate can combine with a new molecule of acetyl-coA

4. The Products of the Krebs Cycle
1. Glucose totally consumed
2. 6-C --> 2(3-C) --> 2(2-C-coA + CO₂) --> 2(2CO₂)
3. Products are six CO₂, four ATPs and 12 electron carriers (10 NADH, 2 FADH₂)

5. Harvesting Energy by Extracting Electrons
1. Transfer of Electron's Energy of Position
1. Is sometimes all-or-none, a complete transfer from one molecule to another
2. Reduction sometimes just changes the degree of sharing in the covalent bond
3. Consider what happens when transfer of electrons is incomplete

2. A Closer Look at Oxidation Reduction
1. In glucose covalent bonds in C-Hs shared equally
2. C and H have same affinity for valance electrons (similar electronegativity)
3. Electrons in new bonds of CO2 are not shared equally
1. Shift far towards oxygen which is very electronegative
2. Thus carbon atoms are oxidized (lose electrons) oxygens are reduced (gain electrons)

4. Same thing happens when Hs of glucose combine with oxygen to form water
1. Oxygen atoms draw shared electrons towards themselves
2. Oxygen reduced, glucose oxidized
3. Oxygen is an oxidizing (electron-attracting) agent

3. Releasing Energy
1. Focus on energy of shared electrons
2. Energy added to remove electron from its atom in a covalent bond
3. Energy is released when
1. Electron shifted away from less electronegative atom
2. And towards a more electronegative atom

4. Energy released when glucose oxidized, electrons relocated closer to oxygen fig 9.12
5. Glucose has many electrons held far from atoms, all can potentially move to oxygen
6. Some energy released by shifting H atoms from glucose to oxygen
7. Energy also released because of shift of positions of valence electrons, use to make ATP

4. Harvesting the Energy in Stages
1. With large release of energy, most is wasted as heat, less available for work
2. Same amount of energy released if gas explodes or powers car
1. With explosion all energy released at once
2. With smaller release, very small explosions push pistons, move car
3. Energy better utilized when released in small increments

3. Same principle with oxidation of glucose in cell
1. H transferred to oxygen in one step, explosive waste of energy
2. Used a little at a time is valuable
3. Reactions occur in series of stages, NAD⁺ is primary electron acceptor fig 9.13

5. Following the Electrons
1. Enzymes extract two hydrogens (two electrons and two protons) from glucose
1. Both electrons and one proton transferred to NAD⁺ forming NADH
2. Other proton released as hydrogen ion (H⁺)

2. Energy captured by NADH not harvested at one time
3. Two electrons pass along electron transport chain in presence of oxygen
4. Structure of chain
1. Series of molecules (proteins) embedded in inner membranes of mitochondria
2. Electrons delivered by NADH to top of chain
3. Captured by oxygen at bottom
4. Oxygen then combines with hydrogen forming water

5. Position of electrons shift as each moves to a more electronegative carrier
6. Electrons move down an energy gradient, releasing 53 kcal/mole of energy

6. Stage Four: The Electron Transport Chain
1. NADH and FADH₂ Contain Electrons Gathered from Glucose Breakdown
1. NADH molecules carry their electrons to mitochondrial membrane
2. Transfer electrons to membrane-associated electron transport chain

2. Moving Electrons Through the Electron Transport Chain
1. Transfer electrons to NADH dehydrogenase, membrane-embedded protein
2. Ubiquinone carries electrons to bc1 protein-cytochrome complex
1. Complex acts as proton pump, drives proton outside of membrane
2. Cytochromes contain heme groups

3. Cytochrome c carries electron to cytochrome oxidase complex fig 9.14
1. Four electrons used to reduce one oxygen
2. Combines with two hydrogens to form water

4. Series of carrier called electron transport chain fig 9.15
5. Slight difference between NADH and FAHDH₂
1. NADH carries electrons to first position in chain
2. FADH₂ carries electrons to ubiquinone, later down the chain

6. The plentiful electron acceptor makes oxidative respiration possible
1. Process cannot occur in the absence of the molecule
2. Electron transport chain is similar to the one in aerobic photosynthesis

3. Building an Electrochemical Gradient
1. Inner compartment (matrix) of mitochondrion contains Krebs cycle enzymes
2. Electrons passed along electron transport chain
1. Energy transports protons to outer compartment (intermembrane space)
2. Transport accomplished by proton pumps, transmembrane proteins

3. Electrons from NADH activate three pumps
4. Electrons from FADH₂ activate two pumps

4. Producing ATP: Chemiosmosis
1. Concentration of protons in outer compartment increases over matrix
1. Matrix becomes slightly negative in charge
2. The protons attracted back inward through special channels
3. ATP is synthesized when protons diffuse through them
4. ATP leaves the mitochondrion via facilitated diffusion

2. Force driving reaction is similar to osmosis, reaction called chemiosmosis fig 9.16
3. Summarization of ATP production fig 9.17

7. Summarizing Aerobic Respiration
1. Theoretical Yield
1. Each NADH activates three pumps, FADH₂ activates two
1. ATP generation expected to be 3ATP and 2ATP respectively
2. NADH from glycolysis transport into mitochondrion costs energy of 1 ATP
3. Net ATP production is therefore decreased by two

2. Net theoretical yield = 36 ATP fig 9.18
1. 4 ATP from substrate-level phosphorylation
2. 30 ATP from 3 each of 10 molecules of NADH
3. 4 ATP from 2 each of 2 molecules of FADH₂
4. -2 ATP needed to transport NADH from glycolysis

2. Actual Yield
1. Actual total in eukaryotes is lower than 36
1. Inner membrane is leaky, some protons reenter without generating ATP
2. Mitochondria use proton gradient for other purposes
3. Truer values are 2.5 ATP per NADH and 1.5 ATP per NADH₂
4. Net total closer to 30 ATP (4 + 25 + 3 – 2)

2. Energy efficiency
3. (12 x 30)/686 = 52% efficiency of aerobic oxidation of glucose
4. Efficiency of car engine is 25%
5. High efficiency fostered evolution of heterotrophs

8. Regulating Aerobic Respiration
1. ATP Levels Determine Whether More ATP Is Produced
1. ATP high, glycolysis, Krebs cycle and fatty acid breakdown inhibited
1. Regulation by ATP is example of feedback inhibition
2. When ATP is low ADP is high, ADP activates enzymes of carbohydrate catabolism

2. Control occurs at two key points of catabolic pathway fig 9.19
1. In glycolysis control is at phosphofructokinase
1. Catalyzes conversion of fructose phosphate to fructose bisphosphate
2. First reaction that is not readily reversible
3. High ADP stimulate same enzyme, as do low levels of citrate

2. Control in oxidation of pyruvate at pyruvate decarboxylase step
1. Inhibited by high levels of NADH
2. Thus no more NADH needed

3. Another control point in Krebs cycle is citrate synthetase
1. Catalyzes oxaloacetate + acetyl – coA to citrate
2. High ATP inhibit this enzyme
3. Also inhibits pyruvate decarboxylase and two other Krebs cycle enzymes

1. Glucose Is Not the Only Food
1. Proteins and Fats Are Also Important Sources of Energy fig 9.20
2. Cellular Respiration of Protein
1. Must first break proteins into constituent amino acids
2. Nitrogen-containing amino group removed from each amino acid: Deamination
3. Remaining carbon chain converted to substance in glycolysis or Krebs cycle
1. Alanine to pyruvate
2. Glutamate to ða-ketoglutarate
3. Aspartate to oxaloacetate

3. Cellular Respiration of Fat
1. Fats first degraded to individual fatty acids and glycerol
2. Long carbon chains with many hydrogens hold much energy
3. Fats oxidized in the matrix of the mitochondrion
1. Enzymes attack the long fatty acid chains
2. Remove carbons in chunks of 2C acetyl groups
3. Entire chain converted into acetyl-CoA
4. Process called b-oxidation

4. Efficiency of metabolizing fats
1. Each b-oxidation cycle uses one ATP to prime the process
2. Produces 1 acetyl-CoA + 1 NADH + 1 FADH₂
3. NADH produces 2.5 ATPs
4. FADH₂ produces 1.5 ATPs
5. Acetyl-CoA produces 10 ATPs
6. Total number of ATPs from a six carbon fatty acid
1. Two cuts = 2 NADH + 2 FADH₂= 2(2.5+1.5) –2 = 6 ATPs
2. Three acetyl-CoA molecules = 3(10) = 30 ATPs
3. Total = 36 ATPs

7. Overall actual yield is 20% more than glucose
8. Fatty acid of same size weighs less than glucose
1. One gram of fatty acid contains more than twice as many kcal as glucose
2. Animal bodies would be bulkier if they stored carbohydrates instead of fat

1. Fermentation
1. Bacteria Carry Out Many Different Types of Fermentations
1. An organic molecule serves as the electron acceptor
1. NADH is returned to NAD⁺
2. The organic molecule is reduced

2. Bacteria produce acetic, butyric, propionic, lactic acids, alcohol

2. Ethanol Fermentation
1. Eukaryotes exhibit only a few types of fermentations
2. Yeasts decarboxylate pyruvate to produce acetaldehyde and CO₂
1. NADH and acetaldehyde are converted to ethyl alcohol and NAD⁺
2. Ethanol is another name for ethyl alcohol
3. This is a commercially important process that makes wine and beer fig 9.21
4. Ethanol is toxic to cells, kills at 12%, the maximum for natural brewing

3. Lactic Acid Fermentation
1. Most multicellular animals regenerate NAD⁺ without decarboxylation
2. Utilizes the enzyme lactate dehydrogenase
3. Muscle cells convert NADH ⁺ pyruvate to NAD⁺ + lactic acid
4. Blood circulation removes lactate from muscle cells
1. With great exertion lactic acid is not removed fast enough
2. Contributes to muscle fatigue