TCA Cycle and Oxidative Phosphorylation Flashcards
What are the important elements of this case?
What is the diagnosis?
Mitochondrial Encephalopathy
Mutation in Mitochondrial Transfer RNA
Mitochondria has its own ribosomes and its own tRNA and 13 genes of its own.
What is the role of the TCA Cycle?
Mitochondria
Innermembrane Features
Outtermembrane Features
What type of Reaction Occurs in the Mitochondria?
Pyruvate carboxylase is within the Mitochondria.
Invagination increases surface area
Innermembrane transversing needs specific transporters.
Oxidative phosphorylation needs oxygen to make ATP.
Overview of TCA.
Reaction Type?
Products?
Electron Carriers? How Many?
What is the significance of the TCA Cycle?
Fatty Acids produce?
Amino Acid Degredation leads to?
Biosynthesis and TCA?
SIMPLE THERMODYNAMICS
What determines if a reaction is favorable?
Gibbs Free Energy Definitions and Conditions
Standard Gibbs Free Energy
THERMODYNAMICS CONT.
Gibbs Free Energy Eqn for a Reaction.
Condition for the Reaction to Proceed.
Approaching Coupled Reactions.
We are never under standard conditions so this reaction needs to include the [RT ln (C)(D)/(A)(B)]
Coupled reactions Standard Free Energy Changes can be added together.
Being favored thermodynamically doesn’t mean it will occur spontaneously.
Thermodynamically just means in the right conditions it will be favored.
THERMODYNAMICS
Determine the thermodynamics of the First Step of Glycolysis
THERMODYNAMICS
How can reactions with positive Gibbs Free Energy still proceed?
Use Malate conversion to Oxaloacetate as an Example.
If the second expression, which is correcting non-standard conditions, is more negative than 29.7 kJ/mole than the reaction would be overall negative gibbs free energy and the reaction would continue. That means the conc. of the reactants should be small and the products should be larger. But in this case OAA conc. is small not large so we don’t have an over all negative.
2 Methods for Pyruvate to enter Mitochondria
ANtiport is also driven by the proton gradient. Citrate has 3 neg. charges and pyruvate only has one so there is a difference in negative charges.
Pyruvate Dehydrogenase
Once pyruvate is converted to Acetyl CoA you’ve lost the ability to go to gluconeogenesis.
Pyruvate Fates — Alanine, Lactate, Acetyl CoA, and one more…? Go back to glucose via gluconeogenesis.
E3 Subunit will be used by all enzymes that catalyze oxidative decarboxylation reactions.
E3 has an electron acceptor bound to it (FAD).
E1 Subunit
Catalytic Subunit
Pyruvate Decarboxylase
Binds Thiamin Pyrophosphate
E2 Subunit
Catalytic Subunit
Transacetylase
Utilizes Lipoic Acid
E3 Subunit
Catalytic Subunit
Dihydrolipoyl Dehydrogenase
Shared with other enzymes
also has bound FAD
Cofactors required by PDH (Pyruvate Dehydrogenase)
Thiamin Pyrophosphate
Derived from Thiamin, Vitamin B1
What is FAD?
Ribotal is the reduced form of Ribose
Vitamin B2 is riboflavin which is essential for making FAD
How does FAD accept Electrons?
FAD can exist in a radical form.
Better Oxidizing Agent than NAD but not as good as a reducing agent.
Coenzyme A
Lipoic Acid
Importance of Pyruvate Dehydrogenase
Thiamine is in the husk of rice, but not the polished or white rice.
Now days the only patients with BeriBeri are chronic alcoholic because alcohol interferes with absorption.
Any enzymes that use pyruvate as a substrate and becomes defective ends up with a build up of pyruvate which will end up in lactate which causes lactic acidosis.
Thiamin Deficiency
Pyruvate Dehydrogenase Complex Deficiency
Mutations in the E3 Subunit of Pyruvate Dehydrogenase
What is Beriberi
Dry Beriberi — Nervous System effects include Loss of feeling/Speech/Nystagmus.
People don’t usually get both.
Dry BeriBeri develops and can get worse which leads with Wernicke Encephalopathy then -Korsakoff Syndrome.
Dry Beriberi
Wet Beriberi
Wernicke Koraskoff Syndrome?
Wernicke Encephalopathy
Korsakoff Syndrome
How do the TCA cycle enzymes work?
Aconitase and Citrate
Citrate is a symmetrical Molecule. But Aconite treats it as a asymmetrical molecule. so it always uses the same bond and adds OH to the same side every time.
Isocitrate Dehydrogenase
This reaction doesn’t require any other co-factor than NAD which is very different from the other decarboxylation reactions of TCA.
Alpha-KG Dehydrogenase
Succinyl CoA Synthetase
Once we’ve formed Succinate, what is our overall reaction
Half way point.
The rest of the cycle captures the remaining 4 electrons (of the 8 total)
TCA supplies intermediates for
Heme Synthesis and Amino Acid Synthesis
A patient has a genetic defect that causes intestinal epithelia cells to produce dissacharidases of much lower activity than normal compared with a normal person, after eating a bowl of milk and oatmeal sweetened with table sugar, this patient will have higher levels of which of the following:
Maltose sucrose and lactose in stool
Starch in the stool
Galactose and Fructose in the Blood
Glycogen in the muscle
Insulin in the blood
Maltose sucrose and lactose in stool
Disaccharides can’t be absorbed only monosaccharides.
A young infant who was nourished by a synthetic formula had a sugar in the blood and urnine tis compound gave a positive sugar reducing test but was negative when measured with glucoses oxidase treat meant of the blood and urin with acid (which cleaves glycosidic bonds did not increase the amount of reducing sugar measured. which one of the following?
Fructose
Type 1 diabetic self injected insulin poor to their evening meal but was then distracted and forgot to eat a few hours later the individual fainted. Paramedics did a STAT blood glucose level and found it to be low. (Question)
Adipose tissue
To fully oxidize the carbons in acetyl coA to carbon dioxide and water, how many electron need to be captured from acetyl coA?
2
4
6
8
10
Explain this question.
8
Succinyl CoA is a high energy bond because…
Thio-ester
Can an enzyme change the favorability of a reaction?
Enzymes don’t change the favorability of a reaction, it only reduces the amount of energy needed to reduce the transition state.
Positive Delta G
Positive Delta G is unfavorable and reverse reaction is favorable.
Why is 1.0 Molar Unreasonable for biological reactions?
Water can never be 1 Molar it’s 55 Molar.
Which Vitamin is NOT required for TCA cycle Reactions?
Niacin
Riboflavin
Pantothenic Acid
Lipoid Acid
Thiamin
Vitamin C
Vitamin C — Needed for Collagen Biosynthesis and Hydroxylation Reactions
Pantothenic Acid — needed for CoA
1 kcal is how many kJ?
4.18 kJ
Succinate Dehydrogenase
Fumarase
Malate Dehydrogenase
Free Energy Changes for the TCA Cycle
Energy Generation in the TCA Cycle
Whats the yield of ATP when one molecule of fructose is completely oxidized to carbon dioxide and water?
28
30
32
34
36
32
Energy Yield from the Total Oxidation of Glucose
Regulation of the TCA Cycle
PDH Kinase Control/Regulation
The same inhibitors of PDH are activators of PDH Kinase which inhibit PDH even further.
Large amounts of Pyruvate will inactivate PDH Kinase which will allow the PDH to be more active and act on pyruvate.
Insulin activates the Phosphatase so we can make our fatty acids.
Ca will activate the phosphatase when muscles contract ca is released
Which other enzymatic activity is inhibited by direct phosphorylation?
Glucokinase
Hexokinase
Liver PFk-1
Liver PFK-2 Phosphatase
Liver Pyruvate Kinase
Glucokinase
Hexokinase
Liver PFk-1
Liver PFK-2 Phosphatase
Liver Pyruvate Kinase
More on PDH Kinase
Regulation of the TCA Cycle
Regulation of the Cycle Pt. II
Disruption of the TCA Cycle
Why can’t acetyl CoA Produce Net Glucose?
Role of Oxaloacetate
Loss of TCA Cycle Intermediates
Anapluerotic Reactions
Anapluerotic Reactions Continued
Summary of TCA Cycle Regulation
Summary of TCA Cycle Regulation Continued
Which TCA Cycle intermediate would be the first intermediate to accumulate in the presence of ARsinite?
citrate
Isocitrate
Alphaketoglutarate
Succinyl coA
Succinate
Fumarate
Malate
Alpha ketoglutarate
Arsenite inhibits enzymes that
Arsenite inhibits enzymes that require lipoid- acid
Which enzyme would be inhibited in the presence of ARSENATE?(Inhibits free phosphate)
citrate
Isocitrate
Alphaketoglutarate
Succinyl coA
Succinate
Fumarate
Malate
Succinate
A full term male infant the only child of unrelated parents was born after normal eat two months of age he was brought to the hospital and got lactic academia which responded to pharmacological levels of biotin:
Pyruvate Carboxylase (All carboxylases require biotin which is vitamin B7)
Role of Oxidative Phosphorylation
How Energy is Captured
A scientist has developed a drug which when added to eukaryotic cells leads to elevated lactate levels. Analysis of mitochondrial contents also demonstrated elevated alpha ketoglutarate levels in drug treated cells. this drug may be interfering with a reaction that requires which vitamin?
Biotin
Vitamin K
Pantothenate
Ascorbate
Pyridoxine
Pantothenate
The conversion of fructose to pyruvate under aerobic conditions, results in the generation of which of the following?
2 ATP 4 NADH
2 ATP 2 NADH
4 ATP 4 NADH
4ATP 2NADH
3ATP 3 NADH
2 ATP 2 NADH
WHAT TYPE OF GRADIENT WILL BE CREATED BY PROTONS ?
ELECTRICAL GRADIENT
PH GRADIENT
BOTH ARE CORRECT
NEITHER ARE CORRECT
WHAT TYPE OF GRADIENT WILL BE CREATED BY PROTONS ?
ELECTRICAL GRADIENT
PH GRADIENT
BOTH ARE CORRECT
NEITHER ARE CORRECT
How is Energy Yield Caclulated for a Proton Gradient?
What determines the sign of E’0
An Example in Standard Change in Electrical Energy
Related Delta E to Delta G
Explain the improtant features of this table
Higher == Better Oxidizing Agents
Lower = Better Reducing Agents
Better reducing agents give out less ATP
An organism has a 4-component electron transfer chain, with the following redox potential in volts
A = 0.45
B = -.13
C = +0.77
D = -.32
What is their order in terms of reducing agents:
D to B to A to C
A to b to c to d
D to c to b to A
C to a to b to d
An organism has a 4-component electron transfer chain, with the following redox potential in volts
A = 0.45
B = -.13
C = +0.77
D = -.32
What is their order in terms of reducing agents:
D to B to A to C
A to b to c to d
D to c to b to A
C to a to b to d
Overview of the Electron Transport Chain
Which one of the following enzymes will synthesize a high energy bond only in the presence of oxygen?
Phosphoglycerate kinase
Pyruvate Kinase
Succinate Thiokinase
All require oxygen to synthesize ATP
None require oxygen to synthesize ATP
Which one of the following enzymes will synthesize a high energy bond only in the presence of oxygen?
Phosphoglycerate kinase
Pyruvate Kinase
Succinate Thiokinase
All require oxygen to synthesize ATP
None require oxygen to synthesize ATP
Complex I
What other enzymes requires FAD?
g3P dehydrogenase
Isocitrate dehydragenase
pyruvate dehydrogenase
succinate thiokinase
malate— dehydrogenase
What other enzymes requires FAD?
g3P dehydrogenase
Isocitrate dehydragenase
pyruvate dehydrogenase
succinate thiokinase
malate— dehydrogenase
Structure of FMN and FAD
CoQ is stable as a radical or with 2 e-
Complex IV
Complex II
Summary of the Electron Transport Chain
The Proton Motive Force
Calculation of the PMF
Why does a lack of oxygen inhibit the TCA cycle?
Citrate synthase is inhibited
Fumaraseis inhibited
aconitase is inhibited
Succinyl coA thiiokinase is inhibited
Isocitrate dehydrogenase is inhibited
Why does a lack of oxygen inhibit the TCA cycle?
Citrate synthase is inhibited
Fumaraseis inhibited
aconitase is inhibited
Succinyl coA thiiokinase is inhibited
Isocitrate dehydrogenase is inhibited
The ATP Synthase
How does the Synthase Work?
Principles of the Chemiosmotic Hypothesis
If you add a small amount of dilute hydrochloric acid to a suspension of mitochondria which of the following will occur?
Atp will be hydrolyzed
ATP will be synthesized
phosphate will leave the mitochondria
nothing
If you add a small amount of dilute hydrochloric acid to a suspension of mitochondria which of the following will occur?
Atp will be hydrolyzed
ATP will be synthesized — artificial proton gradient lead to the synthesis of the ATP
phosphate will leave the mitochondria
nothing
What is the P:O Ratio and What is uncoupling?
What happens to Cytosolic NADH?
Malate Aspartate Shuttle
Coupling of Oxidative Phosphorylation
How can one Inhibit Ox. Phos.
Why does blocking ATP synthase block oxidation?
Reduced protons gradient
Enhanced proton gradient
Lack of ADP
Inhibition by High ATP
Enhanced proton gradient
Inhibitors of Oxidative Phosphorylation
Classes of ETC Inhibitors
Oxygen Consumption Graph
ADP Entry into the Mitochondria
Regulation of Oxidative Phosphorylation
Energy Yield From Glucose
Energy Yield from Glucose cont.
Ox. Phos. Diseases
TCA Cycle and Cancer
What is Alpha Keto Glutarate Needed for?
Inhibition of N-Methyl Lysine Hydroxylase
Inhibition of Methylcytosine Dioxygenase
Hypoxida Inducibe Factor
TCA Cycle Enzymes and Tumors
MELAS— tRNA leu is mutated in the mitochondria
