TCA Cycle and Oxidative Phosphorylation Flashcards by Omar Saqr

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.

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What is the role of the TCA Cycle?

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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.

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Overview of TCA.

Reaction Type?

Products?

Electron Carriers? How Many?

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What is the significance of the TCA Cycle?

Fatty Acids produce?

Amino Acid Degredation leads to?

Biosynthesis and TCA?

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SIMPLE THERMODYNAMICS

What determines if a reaction is favorable?

Gibbs Free Energy Definitions and Conditions

Standard Gibbs Free Energy

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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.

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THERMODYNAMICS

Determine the thermodynamics of the First Step of Glycolysis

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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.

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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.

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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).

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E1 Subunit

Catalytic Subunit

Pyruvate Decarboxylase

Binds Thiamin Pyrophosphate

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E2 Subunit

Catalytic Subunit

Transacetylase

Utilizes Lipoic Acid

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E3 Subunit

Catalytic Subunit

Dihydrolipoyl Dehydrogenase

Shared with other enzymes

also has bound FAD

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Cofactors required by PDH (Pyruvate Dehydrogenase)

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Thiamin Pyrophosphate

Derived from Thiamin, Vitamin B1

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What is FAD?

Ribotal is the reduced form of Ribose

Vitamin B2 is riboflavin which is essential for making FAD

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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.

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Coenzyme A

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Lipoic Acid

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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.

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Thiamin Deficiency

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Pyruvate Dehydrogenase Complex Deficiency

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Mutations in the E3 Subunit of Pyruvate Dehydrogenase

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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: ## Footnote 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.

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? ## Footnote 28 30 32 34 36

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? ## Footnote 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? ## Footnote 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) ## Footnote 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? ## Footnote 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?