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84 Cards in this Set
- Front
- Back
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What is the driving step behind the tenth step of glycolysis?
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Tautomerization of Pyruvate from enol --> keto form
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Why bother converting Glu-6-P into Fru-6-P?
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-Move carbonyl to C2
-Frees up C1 hydroxyl --> easier to phosphorylate in Fru-1,6-Bisphosphate -Without C2 carbonyl, no reverse aldol cleavage between C3+4 |
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What is the catalytic mechanism of Phosphoglycerate Mutase?
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His at active site is already phosphorylated.
His donates P to C2 --> 2,3-Bisphosphoglycerate intermediate His takes P away from C3, releases 2-phosphoglycerate. |
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What is the catalytic mechanism of aldolase?
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Lys in active site forms Schiff base/imine with C2 carbonyl of F6P
Asp acts as base to catalyze aldol cleavage G3P leaves Asp deprotonates DHAP imine, DHAP leaves upon imine hydrolysis |
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What is the catalytic mechanism of GAPDH (Glyceraldehyde-3-P Dehydrogenase)?
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Active site Cys attacks carbonyl C1 --> tetrahedral intermediate; NAD+ acts as base and deprotonates to allow reformation of carbonyl (acyl thioester)
SN2 rxn: Phosphate attacks C1 and displaces Cys's S -->1,3BPG |
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What enzyme catalyzes the conversion of DHAP to GAP?
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Triose Isomerase
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What is the catalytic mechanism of Phosphoglycerate Kinase (PGK)?
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Metal ion catalysis with Mg2+
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What enzyme catalyzes conversion of 3PG to 2PG?
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Phosphoglycerate Mutase (PGM)
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What enzyme makes the first ATP in glycolysis?
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PGK
Phosphoglycerate Kinase |
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What enzyme makes the second ATP in glycolysis?
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Pyruvate Kinase
Facilitates an SN2 attack on PEP's Phosphate by O- on ADP. Displaces Pyruvate and steals its Phosphate. |
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What is the function of TPP?
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Facilitates the decarboxylation (-CO2 lost) of pyruvate to form acetaldehyde by stabilizing the carbanion intermediate.
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What structural characteristic is shared by most allosterically regulated enzymes?
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They are multimers: multi-subunit proteins.
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Which steps are regulated in glycolysis?
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Step 1, 3, 10
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How is hexokinase regulated?
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Inhibited by G6P: product negative feedback loop.
PFK also talks to Hexokinase: if it stops it causes G6P to accumulate and slow Hexokinase too. |
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How is PFK regulated?
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Allosteric activators: AMP, Fru-2,6-Bisphosphate (R state)
Allosteric Inhibitors: citrate, ATP (T state) Active site Arg 162 in R state attracts F6P Changes to Glu 161 in T state --> repels F6P. |
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What happens to enzyme activity curves upon addition of allosteric activators?
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They become more hyperbolic as enzyme activity increases.
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What happens to enzyme activity curves upon addition of allosteric inhibitors?
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They become more sigmoidal in shape.
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What is the advantage to regulating enzymes in both the forward and reverse reactions in a pathway?
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Activating forward + inhibiting reverse = larger effect than altering the rate of just one.
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What is the principle behind global regulation?
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Tissues have isozymes (different enzyme but same reaction) with different affinities and speeds --> different rates of flux.
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What is the principle behind allosteric modification?
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Enzyme in T/R state equilibrium.
Effector molecules bind away from active site. Inhibitor --> T state equilibrium shift Activator --> R state |
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What enzyme cofactor is involved in ALL a-keto acid decarboxylation reactions?
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Thiamine Pyrophosphate, TPP.
Thiazolium ring --> carbanion upon deprotonation; nucleophilic attack on alpha-carbonyl to allow decarboxylation. |
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What are the major regulatory enzymes in the TCA cycle?
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Step 1: Citrate Synthase
Step 3: Isocitrate Dehydrogenase Step 4: alpha-ketoglutarate Dehydrogenase |
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What is the net yield of
NADH FADH2 CO2 GTP per mole of pyruvate? |
3 NADH
2 CO2 1 FADH 1 GTP |
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What enzyme catalyzes the "linking step" reaction?
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Pyruvate Dehydrogenase Complex
pyruvate + coA + NAD+ --> acetyl-coA + CO2 + NADH + H+ |
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What reaction does pyruvate dehydrogenase catalyze?
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TPP-mediated decarboxylation of Pyruvate, transfer to Lipoic Acid tail of E2
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What reaction does Transacetylase catalyze?
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Oxidation of hydroxyethyl group to acetyl group; transfer to coA
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What reaction does Dihydrolipoyl Dehydrogenase catalyze?
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Reoxidation of lipoic acid by FAD, reduction of NAD+ to NADH2. Restores E2 so it can begin another catalytic cycle.
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How is PDH regulated?
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Kinase Phosphorylates PDH --> inactivates
Phosphatase dephos. PDH --> activates PDH inhibited by NADH, Acetyl-CoA |
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How is PDH Kinase regulated?
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HIF-1 (upregulated due to hypoxia)
PDH Substrates inhibit: ADP, Ca2+, NAD+, CoA-SH PDH products activate: ATP, NADH, Acetyl-CoA |
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How is PDH Phosphatase regulated?
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Activated by Ca2+, Mg2+ which indicate muscle contraction and need for ATP.
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What is purpose of TCA cycle?
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Make reducing power for Electron Transport Chain
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Oxaloacetate + Acetyl-CoA = ?
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Citrate Synthase --> Citrate
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Citrate --> ?
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Aconitase --> Isocitrate
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Isocitrate --> ?
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Isocitrate Dehydrogenase --> CO2 + NADH + a-ketoglutarate
decarboxylation at C3 |
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a-ketoglutarate --> ?
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+ NAD+ + CoA-SH --(a-ketoglutarate dehydrogenase)--> NADH + CO2 + Succinyl-CoA
Decarboxylation at C5 CoA-SH reduces NADH |
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Succinyl-CoA --> ?
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+ GDP + P --(Succinyl-CoA Synthetase)--> GTP + Succinate + CoA-SH
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Succinate --> ?
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Succinate Dehydrogenase + FAD+ --> FADH2 + Fumarate
Oxidation: Succinate loses 2 H's and forms C2-C3 double bond |
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Fumarate --> ?
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Fumarase + H2O --> Malate
hydration of double bond |
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Malate --> ?
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Malate Dehydrogenase + NAD+ --> Oxaloacetate + NADH
oxidation of hydroxyl |
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Glycolysis
Glucose --> ? |
Hexokinase +ATP --> Glucose-6-Phosphate + ADP
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Glycolysis
Glucose-6-P --> ? |
Posphoglucose Isomerase --> Fructose-6-P
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Glycolysis
Fructose-6-P --> ? |
Phosphofructokinase + ATP--> Fructose-1,6-Bisphosphate + ADP
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Glycolysis
Fructose-1,6-BP --> ? |
Aldolase --> Dihydroxyacetone Phosphate/DHAP + Glyceraldehyde-3-Phosphate/GAP
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Glycolysis
DHAP --> ? |
Triose Isomerase --> GAP
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Glycolysis
GAP --> ? |
Glyceraldehyde-3-Phosphate Dehydrogenase + P + NAD+ --> 1,3-Bisphosphoglycerate + NADH
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Glycolysis
1,3-Bisphosphoglycerate --> ? |
Phosphoglycerate Kinase + ADP --> 3-PG + ATP
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Glycolysis
3-Phosphoglycerate --> ? |
Phosphoglycerate Mutase --> 2-Phosphoglycerate
2,3-PG intermediate, His-mediated P transfer |
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Glycolysis
2-Phosphoglycerate --> ? |
Enolase --> Phosphoenol Pyruvate + H2O
dehydration |
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Glycolysis
PEP --> ? |
Pyruvate Kinase + ADP --> Pyruvate + ATP
Pyruvate: enol --> --> KETO form |
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What molecule controls the overall balance of the TCA cycle?
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NADH
Controls both citrate synthase and a-ketoglutarate dehydrogenase |
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Why does HIF-1 respond to hypoxic conditions by upregulating PDH Kinase?
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PDH Kinase shuts off PDH, which is the "gateway" to the AEROBIC metabolic pathways, which are useless in low oxygen conditions.
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What is the structure of lactose?
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B-1,4 Galactose + Glucose
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What is the structure of sucrose?
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A-1, B-4 Glucose + Sucrose
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What is the structure of amylose?
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Long A-1,4 Glucose chains
Forms helical structure |
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What is the structure of amylopectin?
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Amylose with branches
Long A-1,4 glucose chains occasional A-1,6 glucose branches every 24-30 glucoses |
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What is the structure of cellulose?
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Long B-1,4 glucose chains
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What is the structure of glycogen?
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Amylopectin with MORE branches
Long A-1,4 glucose chains occasional A-1,6 glucose branches every 12 glucoses |
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What is the structure of NAD?
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2 x ribose 5-phosphate
joined by phosphpdiester bond one ribose: adenine residue other one: nicotinamide residue, e- acceptor |
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What is the structure of FAD?
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Ribose-5-PP + adenine residue
Riboflavin ring attached to PP via phosphoester bond. |
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http://wps.prenhall.com/esm_horton_biochemistry_4/37/9594/2456230.cw/content/index.html
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great tca cycle quiz
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What is the reaction mechanism of succinyl-coA synthetase?
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removal of S-CoA from succinyl coA through His-mediated attack on carbonyl by Pi
Pi displaces S-CoA; succinate and S-CoA both released; PO3- attached to His His-mediated phosphorylation of GDP |
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Which reactions in the TCA cycle generate CO2?
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isocitrate + NAD+ --(isocitrate dehydrogenase)--> a-ketoglutarate + CO2 + NADH
a-ketoglutarate + NAD+ + CoA-SH --(a-ketoglutarate dehydrogenase)--> succinyl CoA + CO2 + NADH |
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Which reactions in the TCA cycle generate FADH2?
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Succinate + FAD+ --(Succinate Dehydrogenase)--> Fumarate + FADH2
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Which reactions in the TCA cycle generate NADH?
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isocitrate + NAD+ --(isocitrate dehydrogenase)--> a-ketoglutarate + CO2 + NADH
a-ketoglutarate + NAD+ + CoA-SH --(a-ketoglutarate dehydrogenase)--> succinyl CoA + CO2 + NADH malate + NAD+ --(malate dehydrogenase)--> oxaloacetate + NADH |
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What is an anapleurotic pathway?
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rxn that feeds intermediates into a system.
replenishes |
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What is a catapleurotic pathway?
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rxn that siphons intermediates away from the system.
depletes |
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What is an amphibolic pathway?
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A pathway that both builds larger molecules and breaks others down
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What is the purpose of the Malate-Aspartate shuttle? What steps are involved?
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Transfer reducing power from mitochondrial intermembrane space to the inner matrix.
Malate + cMDH --> oxaloacetate --> aspartate aspartate passes into matrix aspartate --> oxaloacetate --> mMDH --> malate malate passes back into cytoplasm. |
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What does antimycin A block in the ETchain?
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Transfer of e- from cytochrome b to cytochrome c1 within the Complex III protein.
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Which complexes pump protons out of the mitochondrial matrix?
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Complexes I, III, IV
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What is the second source of electrons for the ETchain, aside from NADH?
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Succinate --> Fumarate + 2e- + 2H+ in Complex II.
These electrons are carried by FADH2 to Ubiquinone. |
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Where does amytal block in the ETChain?
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First step: NADH donating e- to complex I
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Where does rotenone block in the ETChain?
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First step: NADH donating e- to Complex I
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Where does cyanide block in the ETChain?
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Very last step: passing of e- from Complex IV to O2
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How can you circumvent addition of amytal or rotenone to the ETChain?
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Add succinate. This bypasses the block and supplies e- through Complex II.
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What is the effect of adding 2,4 Dinitrophenol to the cell?
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It dissipates the H+ gradient
e- transport continues, O2 consumption continues no ATP synthesis occurs. |
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How does Triose Phosphate Isomerase (TIM) drive the DHAP --> GAP reaction forward?
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Binds intermediate 150x better than it binds DHAP --> rxn goes forward.
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What is the anaerobic fate of pyruvate in muscle cells?
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Pyruvate + NADH --(lactate dehydrogenase)--> lactate + NAD+ + H+
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What is the anaerobic fate of pyruvate in yeast cells?
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pyruvate --(pyruvate decarboxylase/TPP)--> acetataldehyde + CO2
acetaldehyde + NADH --> etOH + NAD+ |
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Why does alanine inhibit Pyruvate Kinase?
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Ala can easily be turned into pyruvate --> no need to make pyruvate from PEP.
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How is pyruvate kinase regulated?
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Phosphorylate to deactivate
inhibited by ATP, alanine STRONGLY activated by Fructose2,6-bisphosphate, AMP |
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How do oligomycin and venturicidin affect the electron transport chain?
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They stop it because they prevent H+ gradient dissipation.
Eventually no more e- can flow because gradient is too high. |
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What causes the conformational change in the a/b subunits of F1 ATPase?
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Gamma subunit rotates with F0 intermembrane domain "proton turbine."
Which a/b dimer the gamma subunit contacts determines conformation. |
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Describe the reactions in the glycerophosphate shuttle.
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DHAP + NADH --> glycerol-3-phosphate
glycerol 3-phosphate + FAD+ --> DHAP + FADH2 in membrane FADH2 feeds e- to Complex II in ETChain. |
