Glycolysis, Citric Acid Cycle, Oxidative Phosphorylation

Phase 1, Reaction 1:

Phosphorylation of D-Glucose

List in the following form:

Reactants:

Products:

Enzyme:

Cofactor:

Delta G:

Reversibility:

Reactants: Glucose + ATP

Products: Glucose 6-Phosphate + ADP

Enzyme: Hexokinase

Cofactor: Mg2+

delta G: -16.7 kJ/mol

Reversibility: Irreversible

Phase 1, Reaction 2:

Isomerization of Glucose 6-phosphate

List in following form:

Reactants:

products:

Enzyme:

Reversibility:

Reactant: Glucose 6-phosphate

Product: Fructose-6-phosphate

Enzyme: Phosphohexose Isomerase

Reversibility: Reversible

Phase 1, Reaction 3:

Phosphorylation of Fructose-6-phosphate

Rate Limiting step!!!

List in following form:

Reactants:

products:

Enzyme:

Reversibility:

Reactants: Fructose-6-phosphate + ATP

Products: Fructose-1,6- biphosphate + ADP

Enzyme: Phosphofructokinase

Cofactor: Mg2+

Reversibility: Irreversible

How do high concentrations of AMP and ATP allosterically control PFK?

ATP Inhibits

AMP Promotes

Phase 1, Reaction 4:

Asymmetric Cleavage of C3-C4 bond to produce 2 triose phosphates

List in following form:

Reactants:

Products:

Enzyme:

Reversibility:

Delta G:

in vivo delta g and why:

Reactants: Fructose-1,6-biphosphate

Product: Dihydroxyacetone phosphate (DHAP) + Glyceraldehyde-3-phosphate (G-3-P)

Enzyme: Fructose biphosphate aldolase

Reversibility: Reversible

Delta G: 23.9

in vivo delta g and why: -0.23 because product concentrations are kept low

Phase 2, Reaction 1, overall (5):

Conversion of DHAP into G-3-P

List in the following form:

Reactants:

Products:

Enzyme:

Reversibility:

Reactants: Dihydroxyacetone Phosphate (DHAP)

Products: Glyceraldehyde-3-phosphate (G-3-P)

Enzyme: Triose Phosphate Isomerase

Reversibility: Reversible

Phase 2, Reaction 2, Overall (6):

Oxidation of G-3-P

List in the following form:

Reactants:

Products:

Enzyme

Delta G:

Reversibility:

Reactants: G-3-P + NAD+ + H(PO4)2-

Products: 1,3-Bisphosphoglycerate + NADH + H+

Enzyme: G-3-P dehydrogenase

Delta G: +6.3 kj/mol

Reversibility: Reversible

Phase 2, Reaction 3, Overall (7):

Phosphoryl transfer to ADP

List in the following form:

Reactants:

Products:

Enzyme:

Cofactor:

Delta G:

Reversibility:

Reactants: 1,3-bisphosphoglycerate (1,3-BPG) + ADP

Products: 3-Phosphoglycerate (3-PG) + ATP

Enzyme: Phosphoglycerate Kinase

Cofactor: Mg2+

Delta G: -18.9 kJ/mol

Reversibility: Reversible

Phase 2, Reaction 4, Overall (8):

Convert 3-PG to 2-PG to set up next substrate level phosphorylation

List in the following form:

Reactants:

Products:

Intermediate:

Enzyme:

Reversibility:

Reactants: 3-Phosphoglycerate (3-PG)

Products: 2-Phosphoglycerate (2-PG)

Intermediate: 2,3-biphosphoglycerate

Enzyme: Phosphoglycerate mutase

Reversibility: Reversible

Phase 2, Reaction 4, Overall (9):

Dehydration of 2-PG into phosphoenolpyruvate

List in the following form:

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: 2-PG

Products: Phosphoenolpyruvate (PEP) + H2O

Enzyme: Pyruvate Kinase

Delta G: 7.5 kJ/mol

Reversibility: Reversible

Phase 2, Reaction 5, Overall (10):

Second Substrate-level Phosphorylation

List in the following form:

Reactants:

Products:

Enzyme:

Cofactors:

Delta G:

Reversibility:

Reactants: Phosphoenolpyruvate (PEP) + H+ + ADP

Products: Pyruvate + ATP

Enzyme: Pyruvate Kinase

Cofactors: Mg2+, K+

Delta G: -31.7 kJ/mol

Reversibility: Reversible

Anaerobic Conditions in muscle

Reactants:

Products:

Reactants: 2 Pyruvate + 2 NADH

Products: 2 lactate + 2 NAD+

Anaerobic Conditions Alcoholic Fermentation in Yeast

Reactants:

Products:

Reactants: 2 Pyruvate + 2 NADH

Products: 2 Ethanol + 2 CO2 + 2 NAD+

Investment in Glycolysis: ____

Payoff in glycolysis: ____

2 ATP, 4 ATP (Net 2 ATP) + 2 NADH + 2 Pyruvate

Where is pyruvate imported to for aerobic respiration in cells

Mitochondrial Matrix

Conversion of Pyruvate into Acetyl-CoA

Reactants:

Products:

Enzyme:

Coenzymes:

Delta G:

Reversibility:

Reactants: Pyruvate + CoA-SH + NAD+

Products: Acetyl-CoA + CO2 + NADH

Enzyme: Pyruvate Dehydrogenase complex (E1 + E2 + E3)

Coenzymes: TPP, Lipoate, FAD

Delta G: -33.4 kJ/mol

Reversibility: Irreversible

TCA Reaction 1: Claisen Condensation to generate Citrate

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: Acetyl-CoA + Oxaloacetate + H2O

Products: Citrate + CoA-SH

Enzyme: Citrate synthase

Delta G: -32.2 kJ/mol

Reversibility: Irreversible

TCA Reaction 2a: Dehydration/Rehydration of Citrate

Reactants:

Products:

Enzyme:

Overall Delta G:

Reversibility:

Reactants: Citrate

Products: Cis-Aconitate + H2O

Enzyme: Aconitase

Overall Delta G: 13.3 kJ/mol

Reversibility: Reversible

TCA Reaction 2b: Dehydration/Rehydration of Citrate

Reactants:

Products:

Enzyme:

Overall Delta G:

Reversibility:

Reactants: cis-aconitate + H2O

Products: Isocitrate

Enzyme: aconitase

Overall Delta G: 13.3 kJ/mol

Reversibility: Reversible

TCA Reaction 3: Oxidative decarboxylation

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: Isocitrate + NAD(P)+

Products: alpha-ketoglutarate + NADH + H+ + CO2

Enzyme: isocitrate dehydrogenase

Delta G: -20.9 kJ/mol

Reversibility: Reversible

TCA Reaction 4: Oxidative decarboxylation

Reactants:

Products:

Enzyme:

Coenzyme:

Delta G:

Reversibility:

Reactants: Alpha-ketoglutarate + NAD+ + CoASH

Products: Succinyl-CoA + NADH + CO2

Enzyme: Alpha-Ketoglutarate dehydrogenase

Coenzyme: TPP, Lipoate, FAD

Delta G: -33.5 kJ/mol

Reversibility: Irreversible

TCA Reaction 5: Substrate level phosphorylation

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: Succinyl-CoA + GDP (ADP) + P

Products: Succinate + GTP (ATP) + CoA-SH

Enzyme: Succinyl-CoA Synthetase

Delta G: -2.9 kJ/mol

Reversibility: Reversible

TCA Reaction 6: Succinate Dehydrogenase

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: Succinate + FAD

Products: Fumarate + FADH2

Enzyme: Succinate Dehydrogenase

Delta G: 0 kJ/mol

Reversibility: Reversible

How is FAD linked to proteins?

Covalently linked to protein; Limited mobility

What is the redox potential of FAD compared to NAD+?

Carries a lower redox potential than NAD+

Is FAD easier or harder to reduce compared to NAD+?

Easier to reduce (Source is not as easily oxidized)

Is NAD+ water soluble?

Yes

Does NAD+ have a higher or lower redox potential than FAD?

Higher

What type of reaction is needed to reduce NAD+?

A highly exergonic reaction

TCA Reaction 7: Hydration of Fumarate

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: Fumarate + H2O

Products: L-Malate

Enzyme: Fumarase

Delta G: 0 kJ/mol

Reversibility: Reversible

TCA Reaction 8: Malate Dehydrogenase catalyzes the final oxidation and produces oxaloacetate

Reactants:

Products:

Enzyme:

Delta G:

Reversibility:

Reactants: L-Malate + NAD+

Products: Oxaloacetate + NADH + H+

Enzyme: malate Dehydrogenase

Delta G: 29.7 kJ/mol

Reversibility: Reversible

Is the concentration of Oxaloacetate from step 8 of TCA high or low

Low

Products of 1 Trip around TCA

3 NADH

1 FADH2

1 GTP (ATP)

2 CO2

How many trips around TCA occurs per molecule of glucose

2

Where does Oxidative Phosphorylation Occur?

mitochondria

Coenzyme Q (CoQ)

-Ubiquinone (UQ or Q)

-Quinone head group with long hydrocarbon tail

-Transfer one of two electrons

What enters Complex I of the oxidation process?

NADH + H+

What is formed when 2 electrons are transferred to Q in Complex I?

QH2

What happens during the electron transfer in Complex I?

A conformation change occurs, releasing 4 H+ into the intermembrane space

What is generated as a result of the reactions in Complex I and pumped into the IMS?

A pool of UQH2

What is the function of Complex II in the electron transport chain?

Complex II produces enough energy to reduce UQ into UQH2.

What does FADH2 donate in the process of fumarate formation in the TCA cycle?

FADH2 donates H2 for QH2.

Does Complex II pump protons into the intermembrane space (IMS)?

No, Complex II does not pump H+ into IMS.

What does Complex II generate in terms of ubiquinone in the IMS?

Complex II generates a pool of UQH2.

What is the function of Complex III in the electron transport chain?

Oxidizes UQH2, transferring 1 electron at a time via cytochrome c

How many subunits does Complex III have?

9-10 subunits.

What mechanism does Complex III use to drive proton transport?

The Q cycle.

Q Cycle Step 1:

- Oxidation of the first UQH2 to UQ

- 1 electron goes to cytochrome C

- 1 electron goes back to UQ to form UQdot (semiquinone intermediate)

- 2 H+ released

Q Cycle Step 2:

- Oxidation of the second UQH2 to UQ

- 1 electron goes to cytochrome c

- 1 electron goes to UQdot (semiquinone intermediate) to regenerate UQH2

- 2 H+ released

How many H+ Released by compelex III?

4 H+

What is Complex IV also known as?

Cytochrome C oxidase

What does Complex IV accept electrons from?

Cytochrome c

What is the result of the 4 electron reduction of O2 in Complex IV?

Formation of 2 H2O

What has the highest affinity for electrons in the electron transport chain?

Oxygen

How many protons are pumped across the inner membrane per 4 electrons transferred from cytochrome c to O2?

4 H+

Which metal ions are involved in transferring electrons to stabilize oxygen in Complex IV?

Copper (Cu) and Iron (Fe)

What does Complex IV minimize the formation of?

Reactive oxygen species (H2O2, O2-)

How many H+ are pumped from NADH Oxidation?

10 H+

How many H+ are pumped from FADH2 Oxidation?

6 H+

Chemiosmosis

The movement of protons down its concentration gradient is coupled with ATP Synthesis

What is the result of uncoupling O2 consumption and ATP Synthesis?

O2 consumption skyrockets

ATP Synthesis decreases

What drives the rotation of the F0 rotor in ATP Synthase?

Proton gradient

What happens when the F0 rotor and rotor shaft rotate in ATP Synthase?

It causes a conformational change in the F1 subunit.

What do conformational changes in the F1 subunit of ATP Synthase drive?

ATP synthesis

What is the structure of the F0 subunit in ATP synthase?

It has a hydrophobic core embedded within the mitochondria inner membrane

What is the function of the stator (b2) in the F0 subunit?

It is the stationary component that anchors the entire enzyme.

What is the role of the rotor in the F0 subunit?

It consists of 8-15 c subunits that rotate as H+ flow into subunit a.

What is the function of the rotor shaft or stalk (gamma) in ATP synthase?

It translates rotational movement in F0 to cause conformational changes in F1.

What causes F0 rotation in ATP synthase?

The flow of H+ ions

What happens when a proton enters from the IMS in ATP synthase?

It protonates an Aspartate

What occurs after the Aspartate is protonated in ATP synthase?

The c-subunit becomes neutral and can rotate into the hydrophobic membrane

What effect does the rotation of the c-subunit have on the entire ring in ATP synthase?

It pushes the entire ring forward by one subunit.

What happens when a c-subunit completes the circle and hits the Matrix channel?

The proton dissociates

Where does the changed Aspartate stay until it is protonated again?

At the aqueous interface.

What is the structure of the F1 subunit?

Hexamer of alpha and beta subunits

Which subunits of the F1 subunit catalyze ATP synthesis?

Only beta subunits

What type of change do the beta subunits undergo?

Significant conformational change

How many states are the beta subunits found in?

3 states

What is the shape of the rotor shaft in the F1 subunit?

Asymmetrical

What effect does the asymmetrical rotor shaft have on the beta subunits?

Causes each beta subunit to be in different conformations

What causes the Beta-subunit conformational change?

Rotor Shaft Rotation

Which subunit interacts strongly with the Open beta subunit form?

Gamma subunit

How often does the gamma subunit come into contact with a different ATP-containing beta subunit?

Every 120 degrees

What state is the beta subunit forced into when the gamma subunit interacts with it?

Beta-empty state

What is required to move the gamma subunit from the empty beta subunit to the next ATP-containing beta subunit?

Energy

What is the affinity of the Open (O) state?

Lowest Affinity

What is the affinity of the Loose (L) state?

Affinity for ADP + Pi

What is the affinity of the Tight (T) state?

High affinity for ATP

How much ATP is produced from NADH Pumps?

2.5 ATP

How much ATP is produced from FADH2 Pumps?

1.5 ATP