Term
| citric acid cycle key features |
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Definition
1. occurs in the matrix of the mitochondria
2. Before cycle pyruvate is converted to acetyl CoA
3. TCA cycle generates 1 GTP which is converted to ATP
4. generates 8 electrons that are used in the ETC chain and oxidative phosphorylation
5. Harvests 3 NADH and 1 FADH2 |
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Term
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Definition
1. generate ATP
2. All the food you eat, fatty acids, glucose, and amino acids enter glycolysis and become pyruvate |
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Term
| what shuttles pyruvate to the mitochondria |
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Definition
| monocarboxylate transporter 2 |
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Term
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Definition
1. Fuel for citric acid cycle
2. generated from pyruvate |
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Term
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Definition
oxidation--loss of electrons in the form of hydrogen atoms
reduction--gain of electrons in the form of hydrogen atoms |
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Term
| what is the enzyme that converts acetyl CoA to pyruvate? |
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Definition
| pyruvate dehydrogenase complex 1. large complex of enzymes (ball of proteins) in the mitochondrial matrix, consisting of sub-units E1, E2, and E3 |
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Term
| E1 sub-unit of pyruvate dehydrogenase complex |
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Definition
| 1. pyruvate dehydrogenase, Has prosthetic group TPP, decarboxylates and oxidizes pyruvate |
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Term
| E2 subunit of pyruvate dehydrogenase |
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Definition
| dihydrolipoyl transacetylase, has lipoamide prosthetic group, transfers CoA to acetyl group |
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Term
| E3 subunit of pyruvate dehydrogenase |
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Definition
| Dihydrolipoyl dehydrogenase, has FAD co-enzyme, regenerates lipoamide in oxidized form |
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Term
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Definition
1. tightly bound, specific non-polypeptide unit required for the biological function of some proteins
2. usually found at the active site |
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Term
| Advantageous structural features of pyruvate dehydrogenase |
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Definition
| flexible linkages between E1, E2, and E3 that allows the prosthetic group lipoamide to move between active sites |
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Term
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Definition
1. Occurs in E1
2. pyruvate is decarboxylated and attaches to TPP
3. CO2 leaves |
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Term
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Definition
| lipoamide arm, attached to a lysine, moves from the E@ sub-unit into E1. |
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Term
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Definition
| E1 catalyzes the transfer of the acetyl group to lipoamide; and lipoamide moves to the 2nd E2 active site |
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Term
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Definition
| the acetyl moeity is transferred to acetyl CoA, and leaves as Acetyl CoA. The reduced lipoamide arm swings into the E3 active site |
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Term
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Definition
| two SH groups need to be oxidized to regenerate their original state. In E3 FAD takes the two electrons becoming FADH2. Lipoamide is regenerated. |
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Term
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Definition
| FADH2 trasnfers 2 electrons and one proton to NAD+, generating NADH. (This whole reaction took place in the mitochondrial matrix.) |
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Term
| what type of catalysis does pyruvate dehydrogenase perform? |
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Definition
| coordinated catalysis--the proximity of the enzymes |
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Term
| what are the advantages of coordinated catalysis? |
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Definition
the proximity of the enzymes allows for
1. increase in the overall reaction rate, you're not waiting for the different enzymes to randomly run into their substrate
2. minimizes side reactions, due to super-fast rate
3. the intermediates remain bound to the enzyme complex and can be efficiently transferred from one active site to another |
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Term
| overall products harvested from the citric acid cycle |
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Definition
1. 3 NADHs, 1 FADH2, 1 GTP, 2 CO2's (decarboxylating twice)
2. We're harvesting 6 electrons |
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Term
| why does the citric acid cycle only operate under aerobic conditions? |
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Definition
| Under anaerobic conditions NAD+ runs out because you stop consuming NADH in oxidative phosphorylation which means NAD+ can't be regenerated, the whole cycle stops. |
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Term
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Definition
| Was studying the TCA cycle and got stuck on understanding the transition from oxaloacetate to malate back to pyruvate. Couldn't determine how CoA is made from pyruvate when malate seemed like the final product. |
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Term
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Definition
| discovered that the entry point into the TCA cycle was citrate generated by citrate synthase |
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Term
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Definition
substrate-acetyl CoA and oxaloacetate
product-Citrate (Citryl CoA is an intermediate)
enzyme-citrate synthase
reaction type-aldol condensation
notes-hydrolysis of Citryl CoA is the driving force in the reaction, Citryl CoA is an energy rich molecule because of the thioester bond of Acetyl CoA |
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Term
| What type of kinetics does citrate synthase exhibit? |
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Definition
1. sequential ordered kinetics
2. oxaloacetate binds first causing a conformational shift on the enzyme
3. The conformational shift creates the binding site for Acetyl CoA
4. Acetyl CoA binds and the reaction proceeds |
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Term
| why is sequential ordered kinetics important for citrate sythesis? |
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Definition
| 1. prevents the wasteful hydrolysis of acetyl CoA, if you bind the CoA first you risk the possibility that water will unnecessarily hydrolyze it. It ensures that oxaloacetate is in close proximity to Acetyl CoA to form the deisred product, citrate, which can be used in the TCA cycle. |
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Term
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Definition
Substrate-citrate
Product-isocitrate
enzyme-aconitrase
reaction type-isomerization
notes-occurs via a dehydration followed by a hydration step; facilitates the upcoming decarboxylation |
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Term
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Definition
substrate-isocitrate
product-alpha-ketoglutarate (oxalosuccinate intermediate)
enzyme-isocitrate dehydrogenase
reaction type-oxidation and decarboxylation
notes-First time NADH is produced; rate of aalpha-ketoglutarate is important in the overall rate of the krebs cycle |
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Term
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Definition
substrate-alpha-ketoglutarate
product-succinyl CoA
enzyme-alpha-ketoglutarate dehydrogenase complex
reaction type-oxidation and decarboxylation
notes-2nd oxidation step generates CO2 and NADH, homologous to pyruvate dehydrogenase comples with TPP, lipoamide, and FAD as catalytic cofactors; performs an analogous reaction |
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Term
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Definition
substrate-Succinyl CoA
product-Succinate
enzyme-Succinyl CoA synthetase
reaction type-Phosphoryl transfer
notes-Only reaction that will generate GTP upon cleavage of the thioester bond and convert it to ATP |
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Term
| What's converts GTP to ATP? |
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Definition
| nucleoside diphosphokinase |
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Term
| What is the purpose of the final three steps of the Krebs cycle? |
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Definition
| regenerate oxaloacetate for another round of TCA cycle |
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Term
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Definition
substrate-succinate
product-fumarate
enzyme-succinate dehydrogenase
reaction type-oxidation
notes-Reaction generates FADH2 |
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Term
| What is significant about generating FADH2? |
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Definition
1. FAD accepts two hydrogens from succinate
2. FAD is attached to the enzyme, and the reaction is typically drawn as E-FAD + succinate ---> E-FADH2 + Fumarate
3. FADH2 becomes stuck in the membrane
4. The harvest electrons do not dissociate away, but are instead transferred to iron-sulfur clusters in the enzyme
5. the iron-sulfur clusters transfer them directly to Coenzyme Q in the oxidative P process |
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Term
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Definition
substrate-fumarate
product-malate
enzyme-fumarase
reaction type-hydration
notes--notice loss of the double bond and the addition of an H and OH group |
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Term
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Definition
substrate-malate
product-oxaloacetate
enzyme-malate dehydrogenase
reaction type-oxidation
notes-delta G of this reaction is very high, unfavorable reaction that would never happen. Reaction is driven by the consumption of the products oxaloacetate (citrate synthase) and NADH by electron transport chain. |
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Term
| Net reaction of TCA cycle and net gains |
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Definition
Acetyl COA+3NAD(+) + FAD +ADP + Pi + 2H2O--->2 CO2+ 3NADH + FADH2 +ATP+2H(+)+CoA
Net gain: 2.5 ATP per NADH and 1.5 ATP per FADH2
1 acetyl group generates 10 ATP vs. 2 ATP from glucose during glycolysis
Cycle only operates when oxygen is available vs glucose which can occur anaerobically |
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Term
| regulation of citric acid cycle |
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Definition
1. Generation of Acetyl CoA is an irreversible step for glucose
2. Once Acetyl CoA is formed the carbon molecule will end up as CO2 or incorporated into lipids
3. This places regulatory control on pyruvate dehydrogenase |
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Term
| eukaryotic method of regulating pyruvate dehydrogenase |
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Definition
1. covalent modification via phosphorylation
2. Phosphorylation inactivates PDH and occurs when there are high amounts of energy (muscle at rest)
3. Dephosphorylation activates PDH and occurs when energy is needed |
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Term
| what drives phosphorylation of PDH (what shuts it off in high energy conditions) |
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Definition
| 1. high concentrations of its product--Acetyl CoA, NADH, ATP. These up-regulate the kinase, which will phosphorylate PDH, turning it off |
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Term
| what drive dephosphorylation of PDH? (What turns it on in low energy conditions?) |
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Definition
1. ADP and a build-up of substrates, Pyruvate and NADH, turn the kinase off, so that it won't phosphorylate PDH. PDH stays active
2. Simultaneously, increase Ca2+ signalling activates a phosphatase that will de-phosphorylate PDH, making it active
3. Remember Ca2+ is a signal of muscle contraction |
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Term
| where else is the krebs cycle controlled? |
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Definition
1. isocitrate and alpha-ketoglutarate steps
2. These are the first two enzymes that harvest electrons in the form of NADH |
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Term
| isocitrate dehydrogenase regulation |
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Definition
1. up-regulated: stimulated by ADP, enhancing its affinity for substrate (essentially up-regulated by low energy circumstances)
2. down-regulated: ATP and NADH have inhibitory effects |
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Term
| alpha-ketoglutarate dehydrogenase regulation |
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Definition
1. down-regulated: inhibited by succinyl CoA and NADH, and ATP
2. similar to PDH |
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Term
| how does a build-up of alpha-ketoglutarate shut down glycolysis? |
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Definition
1. succinyl CoA in high amounts shuts down alpha-ketoglutarate dehydrogenase
2. alpha-ketoglutarate builds up
3. isocitrate dehydrogenase shuts down
4. isocitrate builds up
5. Citrate builds up, due to isomerable reaction
6. a build-up of citrate indicates a backed up TCA cycle, shuts down glycolysis |
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