Oxidative Phosphorylation and Glucose Metabolism Flashcards
What are the purposes of catabolic pathways
Breakdown of larger molecules into smaller building units. Release and (temporary) storage of energy in high-energy molecules through ATPS/NTPs and Reduced cofactors (NADH/FADH2)
How are catabolic pathways oxidative
Metabolites are oxidized as cofactors are reduced. Re-oxidization of cofactors is used to generate ATP.
What is the overview of Oxidative Phosphorylation
Reduced cofactors (NADH, FADH2) from glycolysis and CAC (oxidative catabolism). Which leads to electron transport chain (reoxidation of NADH/FADH2) (reduction of O2 to H2O). Which leads to proton gradient (inner mitochondrial membrane). Which leads to ATP synthesis.
Where does Oxidative Phosphorylation occur
Inner mitochondria membrane
What are the components of the electron transport chain
Complexes 1-4
Coenzyme Q
Cytochrome C
What are the cofactors in oxidative phosphorylation
Flavin mononucleotide (Prosthetic groups), Iron-sulfur clusters (Prosthetic groups), Copper (Cu2+) (Prosthetic groups), Cytochrome heme groups (Prosthetic groups), Coenzyme Q (Lipid-soluble cofactor). Each cofactor has a characteristic reduction potential or affinity for electrons. Electrons move from cofactors will lower reduction potential to those with higher reduction potentials.
What are cytochromes
Cytochromes are hemoproteins that carry out electron transport.
What is Coenzyme Q
Lipid-soluble molecule. It transports electrons to Complex 3 from Complexes 1 and 2 in the inner mitochondrial membrane (Cosubstrate for all three complexes).
What is the Electron Transport Chain
Redox reactions have a free energy change related to reduction potential. Reduction potential is “affinity for electrons.” Higher reduction potential leads to a more negative free energy. Electrons move from compounds with lower reduction potentials to those with higher reduction potentials. Free energy changes from redox reactions can be used to transport protons across the membrane (primary active transport)
What is the number of protons reoxidized by every NADH
Every NADH reoxidized results in 10 protons being move out of the matrix
What is the number of protons reoxidized by every FADH2
Every FADH2 reoxidized results in 6 protons being moved out of the matrix
What is the overall potential energy converted to
Overall, the potential energy of the H+ gradient is converted to the chemical energy in the phosphoanhydride bonds of ATP.
What is FO of ATP Synthase
FO: Oligomycin. Transmembrane portion, Protons pass through and Triggers conformational change in F1.
What is F1 of ATP Synthase
Catalytic portion and Synthesis of ATP from ADP and Pi.
What is the adenine nucleotide translocase and the Pi H+ support
Newly synthesized ATP is export from the mitochondrial matrix into the cytosol where it can be used to “drive” the many energy-requiring processes in the cell. The ADP and Pi produced in the cytosol are then transported back into the mitochondrial matrix.
What is the P:O Ratio
P:O Ratio is the amount of ATP made (P) per oxygen atom reduced to water (O): 1 water made for each NADH or FADH2 reoxidized (each 2 electrons)
Non-stoichiometric: P:O ratio is ~2.5 ATP/NADH reoxidized, P:O ration is ~1.5 ATP/FADH2 reoxidized
P:O ratio may vary with uncoupling.
What is the rate of oxidative phosphorylation determined by
O2 consumption (via electron transport) is connected to ATP production at the ATP Synthase. Oxygen consumption increases when ADP concentration rises. ADP concentration reflects the energy-consumption of the cell.
What is the coupling of ATP synthesis to electron transport
Oxygen consumption increases in isolated mitochondria when ATP synthesis is stimulated (addition of ADP)
What does oxygen consumption increase
The presence of an uncoupler. This refers to situations when electron transport occurs without ATP synthesis (and thus, also, when catabolism of fuel molecules occurs without ATP synthesis). The proton gradient is then dissipated faster, and the rate of electron transport increases (O2 consumption goes up). The rate of re-oxidation of reduced electron carriers increases, and the rate of reactions in the citric acid cycle increases.
What is the uncoupling of ATP synthesis to electron transport
Oxygen consumption with uncouplers, even in the absence of ATP synthesis.
What is Complex 2
Succinate Dehydrogenase (part of the citric acid cycle). An integral membrane protein, Complex II contains FAD as a prosthetic group. Catalyzes oxidation of succinate to fumarate as part of the citric acid cycle. Electrons from succinate are ultimately transferred to coenzyme Q in the membrane. No protons are moved across the membrane at Complex II
What do uncoupled systems allow
Uncoupled systems allow protons to enter the matrix without ATP synthesis. Protons may enter matrix through a separate process, generating heat instead of ATP
How does oxygen consumption increase in the presence of an uncoupler.
This refers to situations when electron transport
occurs without ATP synthesis (and thus, also, when
catabolism of fuel molecules occurs without ATP
synthesis). The proton gradient is then dissipated faster, and the rate of electron transport increases (O2 consumption goes up). The rate of re-oxidation of reduced electron carriers increases, and the rate of reactions in the citric acid cycle increases.
How does affect uncoupling of ATP synthesis to electron
Oxygen consumption with uncouplers, even in the absence of ATP synthesis
What is glycolysis
Catabolic pathway. Conversion of 1 molecule of glucose into two molecules of pyruvate. Generates ATP directly and NADH from oxidation of metabolites
What are the major pathways of Glucose Metabolism
Glucose to Glycogen is glycogen synthesis
Glycogen to the main pathway is glycogenolysis
Glucose to pyruvate is glycolysis
Pyruvate to glucose is gluconeogenesis
What are the structures of glucose
Glucose is a six-carbon compound with one aldehyde group and five hydroxyl groups, aldose, hexose and aldohexose, which cyclizes to form a 6-membered ring.
What is Glycolysis
Anaerobic pathway for ATP generation. It is ancient. It is conserve. It can operate aerobically in a manner of NADH reoxidation. 10 enzyme-catalyzed reactions occur in the cytosol. One glucose is broken down to 2 pyruvate.
What are the Stages of Glycolysis
Stage 1: Energy Investment
Stage 2: Energy Payout
What is Stage 1 of Glycolysis
Energy Investment. Glucose needs to be activated. Energy (ATP) is consumed. Involved “hexose” (6 carbons) sugars
What is Stage 2 of Glycolysis
Energy Payout. Energy is harvested in the form of ATP. NADH also generated. Involves “triose” (3 carbon) sugars.
What are the energy investment steps of glycolysis
Glucose to Glucose-6-phosphate to Fructose-6-phosphate to Fructose-1,6-biphosphate to Dihydroxyacetone phosphate
What are the energy payout steps of glycolysis
Glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate to 3-phosphoglycerate to 2-phosphoglycerate to phosphoenolpyruvate to pyruvate
What are the important enzymes involved in glycolysis
Hexokinase, Phosphofructokinase-1, Glyceraldehyde 3-phosphate dehydrogenase, and Pyruvate kinase
What step is Hexokinase involved in
Glucose to Glucose-6-phosphate
What step is Phosphofructokinase-1 involved in
Fructose-6-phosphate to Fructose-1,6-biphosphate
What step is glyceraldehyde-3-phosphate dehydrogenase
Glyceraldehyde-3-phosphate to 1,3-biphosphateglycerate
What step is pyruvate kinase
Phosphoenolpyruvate to pyruvate
How much ATP is consumed for glucose to glyceraldehyde-3-phosphate (GAP) x2
2 ATP are consumed for every glucose
What occurs during the Glucose to Glucose-6-phosphate reaction
Irreversible, Exergonic, Coupled reaction (ATP used), Phosphate transfer reaction, Catalyzed by hexokinase. It is regulated but not rate limiting
What occurs during the fructose-6-phosphate to fructose-1,6-biphosphate reaction
Irreversible. Exergonic. Coupled reaction (ATP used). Phosphate transfer reaction. Catalyzed by phosphofructokinase-1. Regulated. Rate limiting step.
What is the production of two molecules of glyceraldehyde-3-phosphate
Via two separate reactions, two molecules of glyceraldehyde-3-phosphate are produced from one molecule of fructose-1,6-biphosphate. Every reaction described from GAP to pyruvate happens twice per glucose.
How much ATP are produced from Glyceraldehyde-3-phosphate x2 to pyruvate x2
4 ATP are generated for every glucose
What is the Glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate reaction
Oxidation. Reversible. “Energy capture” step. Catalyzed by GAPDH
What is 1,3-bisphosphoglycerate (1,3-BPG)
1,3-BPG is a “high-energy” intermediate because it is an acyl phosphate (phosphates attached to carboxylates). This chemical group has a large, negative delta G of hydrolysis (both products are stabilized by resonance). 1,3-BPG has a large phosphate transfer potential.
What is the reaction of 1,3-biphosphoglycerate to 3-phosphoglycerate
Reversible. Couple (ATP synthesis). “Energy capture” step (ATP). Substrate-level phosphorylation. This reaction is a coupled reaction, a phosphate-transfer reaction, and specifically, a substrate-level phosphorylation reaction.
What is the reaction of 3-phosphoglycerate to 2-phosphoglycerate
Isomerization. Reversible.
What is the reaction of 2-phosphoglycerate to phosphoenolpyruvate
This is a dehydration reaction. Reversible. Phosphoenolpyruvate (PEP) is a high-energy intermediate.
What the reaction that creates pyruvate
Phosphoenolpyruvate to enolpyruvate to pyruvate. In this reaction, large amounts of free energy are released during the conversion of enolpyruvate to pyruvate
What is the reaction of phosphoenolpyruvate to pyruvate
Irreversible. Coupled (ATP synthesis). Substrate-level phosphorylation. Catalyzed by pyruvate kinase (regulated). 2 ATP made per glucose (Net yield: 2 ATP)
Why is glycolysis regulated
Ensures energy needs are met. Glucose is not wasted when ATP is abundant. Intermediate may be used in other processes and reactions.
How is the rate of metabolic pathways regulated
Substrate availability
Alteration of enzyme activity
Alteration of amount of enzyme
Compartmentation
How does substrate availability regulated in glycolysis
Glucose import (transporters)
How does enzyme regulation regulated in glycolysis
Hexokinase, Phosphofructosekinase-1 and Pyruvate kinase
What is Hexokinase regulation
Glucose-6-phosphate (G6P) is an inhibitor. G6P acts as a negative allosteric effector for hexokinase. Product inhibition
What phosphofructokinase-1 regulation
PFK-1 is allosterically regulated buy ADP/AMP and PEP. The concentration of ADP/AMP in a cell is a good indicator of the need for ATP. Elevated PEP levels signal that the products of glycolysis are not being consumed.
What is pyruvate kinase regulation
Allosteric enzyme. Inhibited by ATP (product inhibition). Pyruvate kinase is part of the reciprocal of regulation (glycolysis and gluconeogenesis). Activated by fructose-1,6-biphosphate. Occurs in yeast. Feed forward activation
What is the effect of F-1,6-BP on Pyruvate Kinase
In some tissues, and in yeast, pyruvate kinase is activated by fructose-1,6-biphosphate. “Heteroallosteric activator” “Feed forward activation”
What are PFK-1 and PK both inhibited by
Both inhibited by ATP. Most enzymes catalyze reversible reactions. Synchronous regulation of irreversible reactions.
What are the ATP investment reactions in glycolysis
Glucose to Glucose-6-phosphate
Fructose-6-phosphate to Fructose-1,6-biphosphate
What are the isomerization reactions in glycolysis
Glucose-6-phosphate to Fructose-6-phosphate
DHAP to GAP
3-phosphglycerate to 2-phosphoglycerate
What is the lysis reaction in glycolysis
Fructose-1,6-biphosphate to GAP + DHAP
What is the oxidation followed by phosphorylation reaction in glycolysis
GAP to 1,3-biphosphoglycerate
What are the substrate level phosphorylation (SLP) reactions in glycolysis
1,3-biphosphoglycerate to 3-phosphoglycerate
Phosphoenolpyruvate to Pyruvate
What is the dehydration reaction in glycolysis
2-phosphoglycerate to phosphoenolpyruvate
What is glycogen metabolism
Glycogen is synthesized from glucose-6-phosphate. Breakdown of glycogen uses inorganic phosphate to break glycosidic bonds. No ATP is used to generate glucose-6-phosphate from glycogen. Increases NET yield of ATP (1 more unit)
Why is an anaerobic fate for pyruvate required?
To generate NAD+ for the oxidation reaction in glycolysis under anaerobic conditions
What is pyruvate metabolism
Glycolysis produces: 2 pyruvate, 2 NADH, Net of 2 ATP. NADH needs to reoxidized to NAD+ for glycolysis to continue. Oxidative phosphorylation (aerobic). Pyruvate (anaerobic)
What is the production of lactate
Lactate is not an acid. Lactate is a “dead-end” product in skeletal muscle during anaerobic activity.
What does lactate do
Hydrolysis of ATP by myosin during vigorous muscle contraction can cause acidotic damage to muscle fibers. Lactate is a metabolic fuel for cardiac tissue.
What is the production of ethanol
Anaerobic fate of pyruvate. Does not occur in vertebrates. Occurs in yeast. Two steps: decarboxylation and reduction. Final products include CO2, ethanol and NAD+
What is the pyruvate dehydrogenase reaction
Catalyzed by pyruvate dehydrogenase complex. Links glycolysis to the citric acid cycle. Occurs inside mitochondria, in the matrix
How is pyruvate transported into the mitochondria
Glycolysis generates pyruvate in the cytosol. Pyruvate is converted to acetyl-CoA in the mitochondrial matrix. Transport across the inner mitochondrial membrane requires the transporter protein pyruvate translocase. A proton is transported with the pyruvate
What is acetyl-coA
Acetyl group attached via thioester bond. Coenzyme A is a derivative of vitamin B5 linked to an adenosine nucleotide. The “functional” portion of the molecule is the terminal, reaction sulfhydryl group (thiol), which forms a thioester bond with acetyl groups.
What is the formation of acetyl-CoA
The formation of acetyl-CoA is a key irreversible step in carbohydrate metabolism
What is the pyruvate dehydrogenase reaction
Oxidative decarboxylation. Transacetylation. Irreversible. Catalyzed by Pyruvate Dehydrogenase Complex (PDH) which requires 5 cofactors including: NAD+, FAD, and CoA
What is the pyruvate dehydrogenase complex
Multienzyme complex that contains: multiple copies of three catalytic enzymes: decarboxylate, transfer to CoA and oxidation. 5 cofactors including NAD+, FAD and CoA. Regulated by kinases and phosphatases.
What are the advantages of multienzyme complexes
Speeds up reaction times, limits number of side reactions, and enzymes controlled as a single unit.
How is the pyruvate dehydrogenase complex regulate
Highly regulated. Irreversible. Acetyl-CoA cannot be used to make glucose in mammals. Sensitive to ATP requirements. Regulated by: NAD+/NADH ratio, Ca2+ concentration and Acetyl-CoA
How does NAD+/NADH regulation occur in PDH
Substrate/Product effect. NADH inhibits (regulates) PDH. Allostery. Protein kinase activator (phosphorylation of PDH)
How does Acetyl-CoA regulation occur in PDH
Inhibitor. Protein kinase activation (phosphorylation of PDH)
How does Ca2+ regulation occur in PDH
Activator. Protein phosphatase activation. Dephosphorylation of PDH
How is PDH regulated in reversible phosphorylation
Switched off when energy levels are high. Phosphorylation (via a kinase) switches off the activity of the complex. Dephosphorylation (via a phosphatase) activates the complex.
What is the result of the inhibition of the pyruvate dehydrogenase complex
NADH and acetyl-CoA
What is the result of activation of the pyruvate dehydrogenase complex
NAD+ and HS-CoA
What are the sources of Acetyl-CoA
Acetyl-CoA comes from many sources like carbohydrates, fatty acid, and amino acid catabolism
What are the products of the reactions of the citric acid cycle
Acetyl-CoA (2 C) condenses with oxaloacetate (4 C) to make citrate (6 C)
Two carbons are oxidized to CO2
Oxaloacetate is regenerated
3 NADH, 1 FADH2/QH2 and 1 GTP are made (high-energy products) for each acetyl-CoA
What is the Citric Acid Cycle
Occurs in mitochondrial matrix (eukaryotes). Oxidizes acetyl-CoA to CO2. Generates high-energy products: NADH, FADH2/QH2, GTP (NTP). Aerobic (O2 reduction to reoxidize NADH, FADH2). Cyclic. Acetyl-CoA generated by metabolism of many compounds: carbohydrates, fats and protein. Amphibolic: intermediates can be used in anabolic reactions
What is the reaction of citrate synthase
Acetyl-CoA and oxaloacetate to create citrate. Irreversible reaction. Catalyzed by citrate synthase. Not regulated (physiologically)
What is the reaction of aconitase
Citrate to Isocitrate. Isomerization. Reversible.
What is the reaction of isocitrate dehydrogenase
Isocitrate to alpha-ketoglutarate. Oxidative decarboxylation. Irreversible. Energy capture step (NADH). Catalyzed by isocitrate dehydrogenase. Regulated
What is the reaction of alpha-ketoglutarate dehydrogenase complex
Alpha-Ketoglutarate to Succinyl CoA. Oxidative decarboxylation. Irreversible. Energy capture step (NADH). Catalyzed by alpha-ketoglutarate dehydrogenase. Similar to PDH reaction. Regulated. Succinyl CoA is a high-energy intermediation (thioester)
What is the reaction of the Succinyl CoA synthetase
Succinyl CoA to Succinate. Reversible reaction. Energy capture (NTP). Substrate-level phosphorylation
What is the reaction of the Succinate dehydrogenase complex
Succinate to Fumarate. Oxidation. Reversible. Catalyzed by succinate dehydrogenase. FAD/FADH2 oxidation of C-C single bond. Integral membrane protein (Complex 2)
Explain the details of the reversible reaction of succinate and fumarate
FADH2 is reoxidized by donating electrons to coenzyme Q (ubiquinone reduced to ubiquinol). QH2 is reoxidized in the electron transport chain. Succinate dehydrogenase is a membrane-bound enzyme and is part of Complex 2 in the electron transport chain
What is the reaction of fumarase
Fumarate to L-Malate. Reversible. Hydration
What is the reaction of malate dehydrogenase
L-Malate to Oxaloacetate. Oxidation. Reversible. Energy capture step (NADH). Regenerates oxaloacetate
What is the regulation of the citric acid cycle
No rate-limiting reactions per se because it is cycle. It is affected by NAD+/NADH ratio (product/substrate). Regulated enzymes. Affected by concentrations of intermediates.
What are the regulated enzymes of the citric acid cycle
Isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase
What are the inhibitors of the Citric Acid Cycle
NADH and ATP
What are the activators of the Citric Acid Cycle
ADP and Ca2+
How can we slow down the pyruvate dehydrogenase complex and the Citric Acid Cycle
Lower ADP in the matrix Lower activity of ATP synthase Increase H+ gradient across IMM Lower the rate of electron transport Lower the oxidation of NADH Lower the NAD+/NADH ratio
How can we speed up the pyruvate dehydrogenase complex and the Citric Acid Cycle
Increase the ADP in the matrix Increase the activity of ATP synthase Decrease the H+ gradient across IMM Increase the rate of electron transport Increase the oxidation of NADH Increase the NAD+/NADH ratio
Is the citric acid cycle catabolic or anabolic
It is both catabolic and anabolic so it makes it amphibolic. Citric acid cycle intermediates can be used in synthesis of amino acids, carbohydrates, fats, nucleotides and other compounds
What are the anaplerotic reactions in the Citric Acid Cycle
Replenish citric acid cycle intermediates. Intermediates may be consumed in other processes. Must be adequate intermediates to continue the citric acid cycle. Many reactions may be anaplerotic: amino acid breakdown and pyruvate carboxylase
What are the functions of the Citric Acid Cycle
Provide biosynthetic precursors. An important step in the generation of ATP for cellular needs.
How much ATP does the Citric Acid Cycle generate for each acetyl-CoA
Approximately 10
How much ATP do 3 NADH produce in the Citric Acid Cycle
7.5 ATP
How much ATP does 1 FADH2 produce in the Citric Acid Cycle
1.5 ATP
How much ATP does 1 GTP produce in the Citric Acid Cycle
1 ATP
How much ATP does a complete aerobic oxidation of glucose yield
32 ATP
How much ATP does anaerobic glycolysis generate
2 ATP
What reaction links glycolysis to the citric acid cycle
Pyruvate to Acetyl-CoA
What reactions in glycolysis and the citric acid cycle are decarboxylation reactions
Pyruvate to Acetyl-CoA
Isocitrate to Alpha-ketoglutarate
Alpha-ketoglutarate to Succinyl-CoA
What reactions in glycolysis and the citric acid cycle are energy capture steps (NADH, FADH2, GTP)
Pyruvate to Acetyl-CoA Isocitrate to Alpha-ketoglutarate Alpha-ketoglutarate to Succinyl-CoA Succinyl-CoA to Succinate Succinate to Fumarate Malate to Oxaloacetate
What reactions in glycolysis and the citric acid cycle are oxidation (redox) reactions
Pyruvate to Acetyl-CoA Isocitrate to Alpha-ketoglutarate Alpha-ketoglutarate to Succinyl-CoA Succinate to Fumarate Malate to Oxaloacetate
What reaction in glycolysis and the citric acid cycle are regulated reactions
Pyruvate to Acetyl-CoA
Isocitrate to Alpha-ketoglutarate
Alpha-ketoglutarate to Succinyl-CoA
(Possibly Acetyl-CoA to Citrate if we include citrate inhibition; rather ambiguous)
