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Questions and Answers
Which of the following correctly describes a function of ATP?
What occurs during an oxidation reaction?
Which of the following is not a carrier molecule in metabolic reactions?
What is the primary function of phosphoryl-transfer potential?
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What is the primary role of alpha-amylase in carbohydrate digestion?
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Which enzyme is responsible for transferring the phosphate group from 1,3-BPG to ADP during glycolysis?
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Which enzyme is responsible for converting maltose into glucose?
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What structural bond is responsible for linking glucose subunits in glycogen?
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Which of the following statements about substrate-level phosphorylation is false?
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In which pathway does fructokinase act, and what does it produce?
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What type of reaction does the enzyme pyruvate kinase catalyze?
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Which intermediate in the TCA cycle has a high phosphate-transfer potential?
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Which polysaccharide serves as the primary storage form of glucose in animals?
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Which of the following statements describes citrate synthase?
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Which of the following substances is produced from the overall reaction of the TCA cycle?
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What is the primary function of succinyl-CoA synthetase in the TCA cycle?
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What is the primary function of hexokinase in glycolysis?
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What inhibits phosphofructokinase (PFK) activity?
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Which enzyme is considered the rate-limiting step in glycolysis?
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How does pyruvate kinase regulate the glycolytic pathway?
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Which statement is true about the reaction catalyzed by phosphoglycerate kinase?
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What is a major product of the glycolytic breakdown of glucose?
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What is the effect of ATP on phosphofructokinase?
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Which enzyme catalyzes the conversion of G3P and DHAP?
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What is the role of the β subunits in the structure described?
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What occurs during the 'T' conformation of the β subunits?
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In terms of the regulation of ATP synthesis, what effect does a lower mass-action ratio have?
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What is the primary function of the electron transport chain (ETC)?
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What does the concept of proton-motive force (PMF) refer to?
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What does a negative reduction potential (E0) indicate about a molecule?
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During ATP synthesis, where does the proton enter after binding to a glutamate residue on the c-ring subunit?
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Which statement accurately describes the effect of inhibitors on the electron transport chain?
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What is the main function of uncouplers in the electron transport chain?
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Which complex in the electron transport chain directly pumps the most protons per molecule of substrate?
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How do mobile electron carriers contribute to the electron transport chain?
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Which of the following is a characteristic of hydrogen peroxide?
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What is the role of superoxide dismutase within the context of reactive oxygen species?
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Which statement best describes the proton-motive force (PMF)?
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Which of the following is true regarding cytochrome c?
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What distinguishes complex II in the electron transport chain from the other complexes?
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Study Notes
ATP and its functions
- ATP is the cellular currency, derived from fuel or light.
- ATP hydrolysis is highly exergonic due to unstable bonds.
- ATP is used for mechanical work, active transport, macromolecule synthesis and unfavorable reaction coupling.
- ATP consists of adenine, ribose, and three phosphate groups.
Oxidation-reduction reactions
- Oxidation reactions involve losing electrons, hydrogen atoms, or gaining oxygen atoms.
- Reduction reactions involve gaining electrons, hydrogen atoms, or losing oxygen atoms.
Carrier Molecules
- Carrier molecules are used to carry molecular groups or electrons in metabolic reactions.
- ATP carries phosphoryl groups.
- NAD+ and FAD carry electrons.
- Coenzyme A carries acyl groups, like the acetyl group.
Entry of saccharides into the glycolytic pathway
- Alpha-amylase cleaves α1→4 glycosidic bonds in starch.
- Maltase breaks down maltose into glucose.
- Glycogen phosphorylase adds a phosphate group to glycogen, producing glucose 1-phosphate.
- Phosphoglucomutase moves the phosphate group from C-1 to C-6 in glucose 1-phosphate to form glucose 6-phosphate.
- Galactokinase phosphorylates galactose at C-1 using ATP.
- G1P uridyltransferase converts galactose 1-phosphate to glucose 1-phosphate using UDP-glucose.
- Fructokinase phosphorylates fructose at C-1 using ATP.
- Aldolase cleaves fructose 1-phosphate into dihydroxyacetone phosphate (DHAP) and glyceraldehyde.
- Triose kinase phosphorylates glyceraldehyde at C-3, producing glyceraldehyde 3-phosphate.
Polysaccharides
- Starch is a storage form of glucose in plants.
- It is made up of two polymers: amylose and amylopectin.
- Glycogen is the storage form of glucose in animals.
- It is a polymer of α1→4 linked glucose subunits with α1→6 linked branch points every 8-12 residues.
- Cellulose is a linear, unbranched polysaccharide found only in plants.
- It is linked by β1→4 glycosidic bonds.
- Chitin is a polysaccharide composed of N-acetyl glucosamine residues in β1→4 linkage.
- It is the second most abundant polysaccharide.
Overall Reaction Equation for Glycolysis
- Glucose + 2 NAD+ + 2 ADP + 2Pi → 2 pyruvate + 2NADH + 2H+ + 2 ATP + 2H2O
- Free energy change: -85 kJ/mol (irreversible)
Enzymes of Glycolysis
-
Hexokinase:
- Phosphorylates glucose at C-6, forming glucose 6-phosphate (G6P).
- Inhibited by G6P.
- Traps glucose in the cell.
- Largely irreversible.
-
Phosphoglucose isomerase:
- Converts G6P to fructose 6-phosphate (F6P).
- Reversible reaction.
-
Phosphofructokinase (PFK):
- Phosphorylates F6P at C1, yielding fructose 1,6-bisphosphate (F16P).
- Traps sugar as fructose.
- Irreversible.
- Allosterically regulated.
- Inhibited by ATP and citrate
- Activated by AMP
- Rate-limiting step of glycolysis.
-
Aldolase:
- Cleaves F16P into G3P and DHAP.
- Reversible reaction.
-
Triose phosphate isomerase:
- Interconverts G3P and DHAP.
- Reversible.
-
Glyceraldehyde 3-phosphate dehydrogenase (G3PDH):
- Oxidizes G3P and adds phosphate, forming 1,3-bisphosphoglycerate (1,3-BPG).
- Reversible.
- Occurs in two steps:
- Exergonic oxidation and reduction of NAD+ to NADH.
- Endergonic addition of phosphate.
-
Phosphoglycerate kinase:
- Transfers phosphate group from 1,3-BPG to ADP, forming ATP and 3-phosphoglycerate (3-PG).
- Reversible.
-
Phosphoglycerate mutase:
- Shifts the phosphate group from C-2 to C-3 in glycerate, forming 2-phosphoglycerate (2-PG).
- Reversible.
-
Enolase:
- Removes H2O from 2-PG, producing phosphoenolpyruvate (PEP).
- Reversible.
- PEP has a high phosphate-transfer potential.
-
Pyruvate kinase:
- Transfers the phosphate group from PEP to ADP, yielding ATP and pyruvate.
- Irreversible.
- Highly exergonic.
Regulation of Glycolysis
- Hexokinase is allosterically inhibited by G6P.
-
Phosphofructokinase (PFK) is allosterically inhibited by ATP and allosterically activated by AMP.
- ATP lowers PFK's affinity for F6P.
- AMP competes with ATP for the allosteric site.
- Pyruvate kinase is allosterically inhibited by ATP and alanine, but stimulated by F16P.
Phosphoryl-Transfer Potential
- The phosphoryl-transfer potential is the standard free energy change involved in the hydrolysis of a phosphoryl-containing compound.
- It is used to compare the tendency of organic molecules to transfer a phosphate group to an acceptor molecule.
- ATP has an intermediate phosphate-transfer potential among important phosphate molecules.
Substrate-Level Phosphorylation
- Substrate-level phosphorylation is the formation of ATP via the transfer of a phosphate group from a substrate to ADP.
- It does not require oxygen.
- Substrate-level phosphorylation is the only source of ATP production in anaerobic conditions or organisms.
Substrate-Level Phosphorylation Enzymes in Glycolysis
- Phosphoglycerate kinase transfers the phosphate group from 1,3-BPG to ADP, forming ATP and 3- phosphoglycerate (3-PG).
- Pyruvate kinase transfers the phosphate group from PEP to ADP, yielding ATP and pyruvate.
Substrate-Level Phosphorylation Enzymes in the TCA Cycle
-
Succinyl-CoA synthetase (ligase) cleaves the thioester bond of succinyl-CoA, forming succinate.
- It regenerates CoA.
- The intermediate, succinyl phosphate, has a high phosphate-transfer potential and donates the phosphate group to ADP forming ATP.
TCA Cycle
- The TCA cycle harvests electrons from carbon fuels.
- It occurs in the mitochondrial matrix.
- The overall reaction equation is: 2 acetyl CoA + 6 NAD+ + 2 FAD + 2ADP + 2Pi → 4 CO2 + 6 NADH + 6 H+ + 2 FADH2 + 2 ATP
TCA Cycle Enzymes
-
Citrate synthase (ligase):
- Joins acetyl CoA with oxaloacetate, forming citrate.
- Irreversible.
- CoA is regenerated.
- Exhibits induced fit.
-
Aconitase (isomerase):
- Rearranges citrate, forming isocitrate.
- Reversible.
- Endergonic.
-
Isocitrate dehydrogenase:
- Converts isocitrate to α-ketoglutarate via oxidative decarboxylation, releasing CO2.
- Irreversible.
- Reduces NAD+ to NADH.
-
α-ketoglutarate dehydrogenase complex:
- Converts α-ketoglutarate to succinyl-CoA via oxidative decarboxylation, releasing CO2.
- Composed of 3 alpha subunits and 3 beta subunits.
-
Succinyl-CoA synthetase:
- Cleaves the thioester bond of succinyl-CoA, forming succinate and regenerating CoA.
- The intermediate, succinyl phosphate, has high phosphate-transfer potential and donates the phosphate group to ADP forming ATP.
-
Succinate dehydrogenase:
- Oxidizes succinate to fumarate.
- Reduces FAD to FADH2.
-
Fumarase:
- Adds H2O to fumarate, forming malate.
- Reversible.
-
Malate dehydrogenase:
- Oxidizes malate to oxaloacetate.
- Reduces NAD+ to NADH.
Mechanism of ATP Synthesis
- Proton enters the intermembrane space.
- Proton enters the half-channel facing the intermembrane space.
- Proton binds to glutamate residue on a c-ring subunit.
- After a full rotation of the c-ring, the proton enters the half-channel facing the matrix.
- Proton moves into the matrix, down the proton gradient.
Regulation of ATP Synthesis
- The [ATP]/([ADP][P]1) ratio regulates respiration:
- A low energy charge ratio increases the rate of respiration.
- ADP regulates oxidative phosphorylation:
- Low ADP levels decrease the rate of oxidative phosphorylation.
Uncouplers and Inhibitors of ETC and ATP Synthesis
-
Uncouplers:
- Increase IMM permeability to protons, dissipating the proton gradient.
- Decrease ATP synthesis.
-
Inhibitors:
- Block electron flow through the ETC.
- Interfere with ATP synthesis.
Chemiosmotic Theory
- The ETC and ATP synthesis are coupled by a proton gradient across the inner mitochondrial membrane (IMM).
- The energy stored in the electrochemical gradient created by the ETC is used to produce ATP.
- Protons are pumped from the matrix into the intermembrane space, creating higher [H+] in the intermembrane space and lower [H+] in the matrix.
- The potential difference between the two compartments is called the proton-motive force (PMF).
Free Energy Change, Reduction Potential, and Redox Reactions
- The free energy change (ΔG´°) indicates the likelihood of a redox reaction occurring.
- The reduction potential (E0) measures a molecule's electron-transfer potential.
- Negative E0: Strong reducing agent.
- Positive E0: Strong oxidizing agent.
- Electrons transfer from positive to negative reduction potentials.
Electron Transport Chain (ETC)
- The ETC is a series of oxidation-reduction reactions that generate a proton gradient used to power ATP synthesis.
- It consists of four large complexes within the IMM:
- Complex I (NADH- Q oxidoreductase): pumps 4 protons per NADH.
- Complex II (Succinate-Q reductase): does not pump protons.
- Complex III (Q-cytochrome c oxidoreductase): pumps 4 protons per QH2.
- Complex IV (cytochrome c oxidase): pumps 2 protons per 2 cyt c.
-
Mobile Electron Carriers:
- Ubiquinone (Coenzyme Q10): transfers two electrons at a time and moves between the four complexes.
- Cytochrome c: carries one electron at a time.
Reactive Oxygen Species (ROS)
- ROS are oxygen-containing compounds that damage cellular biomolecules.
- Common ROS include:
- Superoxide (O2−)
- Hydrogen peroxide (H2O2)
- Hydroxyl radical (OH·)
-
Protective Enzymes:
- Superoxide dismutase: converts superoxide into H2O2.
- Catalase: cleaves H2O2.
ATP Synthesis
- The energy stored in the electrochemical gradient across the IMM drives ATP synthesis.
- The PMF is created by the ETC as protons are pumped from the matrix into the intermembrane space.
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