Midterm 2: TCA cycle and PPP

Name the 5 cofactors used in Pyruvate Dehydrogenase Complex(PDC). How many enzymes r involved?

CoA, NAD+, thiamine (TPP), lipoate, FAD.

3 enzymes are used

Where do the PDC and TCA cycles occur? Do they need O2?

Occurs in mitochondria, needs O2

What are the outputs of the PDC?

acetyl-CoA + CO2 + NADH

Which PDC step is the committed/regulated step?

E1: the decarboxylation step is irreversible since CO2 is lost

Thiamine deficiency leads to :

Neuromuscular deficiency like beriberi

If the body does not need energy, will E1 be turned on?

No, PDC won’t run

Which specific enzyme of the TCA cycle is located in the inner mitochondrial membrane rather than the matrix?

Succinate dehydrogenase

For every molecule of glucose, how many times does the PDC and TCA cycles occur?

twice

How do mercury and arsenite inhibit the pyruvate dehydrogenase complex?

They bind to the sulfurs of lipoic acid, inactivating the cofactor.

In Step 1 of the TCA cycle, which two molecules condense to form citrate? What enzyme is used?

Acetyl-CoA and oxaloacetate; citrate synthase

Draw citrate

Draw oxaloacetate

The formation of citrate is driven by the hydrolysis of what high-energy bond?

The thioester bond of acetyl-CoA.(O=C-CH3)

What enzyme catalyzes citrate—>isocitrate?

aconitase

Draw isocitrate

What enzyme catalyzes the oxidative decarboxylation of isocitrate to alpha-ketoglutarate?

Isocitrate dehydrogenase

What does the isocitrate dehydrogenase step produce?

1NADH, CO2

Draw alpha-ketoglutarate

What are the reactants and products in the reaction catalyzed by α-ketoglutarate dehydrogenase complex (α-KG DC)?

alpha-ketoglutarate + NAD+ + CoA—>succinyl CoA, NADH, CO2

Draw succinyl CoA

Draw succinate

What enzyme catalyzes the reaction turning succinyl CoA to succinate

Succinyl-CoA-synthetase

What are the reactants and products of the reaction catalyzed by succinyl-CoA-synthetase?

Succinyl-CoA+GDP—>Succinate + GTP + CoA

Difference between Synthase vs. Synthetase?

Synthases catalyze synthesis without direct energy input from nucleoside triphosphates, while synthetases require energy (e.g., ATP or GTP).

Succinate is oxidized into _______ using what enzyme and what e- carrier?

Fumarate, uses succinate dehydrogenase; FAD—>FADH2

The enzyme _____ catalyzes the hydration of fumarate to malate.

Fumerase

Draw fumerate

Draw malate

Malate is turned into oxaloacetate using which enzyme? What else is produced?

Malate dehydrogenase; NAD+—>NADH

Dehydrogenases are involved in _____ reactions.

Redox

Per turn, the TCA cycle produces ___NADH, ___FADH2, and ___GTP?

3 NADH, 1 FADH2, 1GTP

Which step(s) produce NADH(give the enzyme name)?

Isocitrate dehydrogenase. alpha KG dehydrogenase, malate dehydrogenase

Which step(s) produce FADH2(give the enzyme name)?

Succinate dehydrogenase

Which step(s) produce GTP(give the enzyme name)?

Succinyl-CoA synthetase

Identify the four steps in the PDC/TCA sequence that are highly thermodynamically favorable and irreversible.

PDC, citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase.

What two metabolic molecules act as general inhibitors for all regulated enzymes in the TCA cycle?

NADH and ATP

What two molecules generally act as activators for the regulated enzymes of the TCA cycle?

NAD+ and AMP (or ADP).

A metabolic pathway that is involved in both catabolism (oxidative breakdown) and anabolism (reductive synthesis).

Amphibolic

Which intermediate of the TCA cycle can be converted to glucose via gluconeogenesis?

Oxaloacetate

A metabolic process that "fills up" or replenishes depleted intermediates in the Citric Acid Cycle

anaplerotic reaction

Explain the reciprocal control by acetyl-CoA

High acetyl-CoA activates pyruvate carboxylase activated to make oxaloacetate—>TCA cycle

Low acetyl CoA activates PDC to generate more AcCoA

What is NADPH used for?

Biosynthesis(fatty acids, cholesterol, neurotransmitters, etc.) as well as detoxification in the liver.

What is ribose 5-phosphate(R5P) used for?

used to make nucleotides and coenzymes

What are the 2 phases of the Pentose Phosphate Pathway (PPP)? Are are reversible or irreversible?

Oxidative(irreversible) and nonoxidative(reversible)

In which part of the cell does the Pentose Phosphate Pathway occur?

The cytosol

What are the inputs and outputs of the oxidative phase?

Inputs: Glucose 6 phosphate, 2 NADP+, H2O

Outputs: NADPH + 2H, ribulose 5-phosphate, CO2

What is the net production of NADPH per one molecule of glucose 6-phosphate entering the PPP?

2 NADPH

What is the relationship between ribulose 5 phosphate and ribose 5 phosphate?

Isomers; ribulose is the ketose form while ribose is the aldose form

What enzyme interconverts ribulose and ribose 5 phosphate?

Phosphopentose isomerase

What occurs in the non oxidative phase?

Ribose 5 phosphate is carbo shuffled into F6P and G3P.

Suppose you need more ribose 5 phosphate than NADPH. What pathway will your body run?

G6P—>F6P via glycolysis

F6P—>ribose 5 phosphate via nonoxidative phase

Suppose you need BOTH ribose 5 phosphate and NADPH. What pathway will your body run?

The oxidative phase

Suppose you need more NADPH than ribose 5 phosphate. What pathway will your body run?

Oxidative phase

R5P—>F6P via nonoxidative phase

F6P—>G6P via gluconeogenesis

Repeat to produce more NADPH

Suppose you need more NADPH and ATP. What pathway will your body run?

Oxidative phase

Nonoxidative phase

F6P and G3P—>ATP via glycolysis