Pyruvate Dehydrogenation Complex, Citric Acid Cycle and Electron Transport Chain

What is the function of Pyruvate Dehydrogenase (PDH)?

Converts pyruvate → acetyl-CoA, linking glycolysis to the TCA cycle.

Where does PDH (pyruvate dehydrogenase) occur?

Mitochondrial matrix.

Is the PDH (pyruvate dehydrogenase) reaction reversible?

No — irreversible step.

What are the 3 enzymes in PDC (pyruvate dehydrogenase complex) ?

• E1: Pyruvate dehydrogenase

• E2: Dihydrolipoyl transacetylase

• E3: Dihydrolipoyl dehydrogenase

What are the 5 cofactors required for PDC (pyruvate dehydrogenase complex) ?

Mnemonic: TLC FN”

• TPP (B1)

• Lipoic acid

• CoA (B5)

• FAD (B2)

• NAD⁺ (B3)

What activates PDH (pyruvate dehydrogenase)

• ↑ ADP

• ↑ pyruvate

• ↑ NAD⁺

• ↑ Ca²⁺

• PDH phosphatase activates the complex by dephosphorylating it

PDH phosphatase removes the phosphate → PDH becomes active (ON).

What inhibits PDH? (Pyruvate Dehydrogenase)

• ATP

• NADH

• Acetyl-CoA

• PDH kinase inhbits the complex by phosphorylating it

PDH kinase adds a phosphate → PDH becomes inactive (OFF).

What activates PDH kinase?

PDH kinase turns PDH OFF
It is activated when the cell has lots of energy:

• ATP (high energy)

• NADH (high energy)

• Acetyl-CoA (plenty of fuel)

What activates PDH phosphatase?

PDH phosphatase turns PDH ON
It is activated when the cell needs energy:

• Ca²⁺ (muscles working → need ATP)

What is the product of the PDC reaction? (Pyruvate Dehydrogenase Complex)

• Acetyl-CoA

• NADH

• CO₂

What hormone indirectly activates PDH?

Insulin (activates PDH phosphatase → turns PDH ON).

Why does PDH deficiency cause neurological problems?

Brain relies heavily on aerobic metabolism → no acetyl-CoA → low ATP.

What metabolic pathways does PDH feed into?

Citric Acid Cycle + Fatty Acid Synthesis.

The TWO main regulatory enzymes of Pyruvate Dehydrogenase Complex 

1. Pyruvate Dehydrogenase Kinase (PDK) – INACTIVATES PDC

2. Pyruvate Dehydrogenase Phosphatase (PDP) – ACTIVATES PDC

PDK (Pyruvate Dehydrogenase Kinase) is activated by

• ↑ ATP

• ↑ NADH

• ↑ Acetyl-CoA

• ↑ Fatty acids

➡ When the cell has enough energy, it shuts PDC off.

PDK (Pyruvate Dehydrogenase Kinase) is inhibited by (energy is low):

• ADP

• Pyruvate

• NAD+

PDP (Pyruvate Dehydrogenase Phosphatase) is activated by:

• ↑ Calcium (Ca²⁺) → especially in muscle contraction

• ↑ Insulin → especially in fat/adipose tissue

PDP (Pyruvate Dehydrogenase Phosphatase) is inhibited by:

• ATP

• Acetyl-CoA

• Fatty acids

• NADH

What is the purpose of the Citric Acid Cycle?

Oxidize acetyl-CoA to CO₂ and generate high-energy electron carriers (NADH, FADH₂) + GTP for oxidative phosphorylation.

Where does the Citric Acid Cycle occur?

Mitochondrial matrix.

What molecule enters the cycle?

Acetyl-CoA (from pyruvate, via PDH).

what are the products per glucose (2 turns) 

• 6 NADH

• 2 FADH₂

• 2 GTP

• 4 CO₂

What is the RATE-LIMITING step of the TCA cycle?

Isocitrate → α-ketoglutarate (enzyme = Isocitrate dehydrogenase).

What regulates Isocitrate Dehydrogenase?

• ↑ ADP, ↑ Ca²⁺, ↑ NAD⁺ (activate)

• ↓ ATP, ↓ NADH (inhibit)

What regulates α-ketoglutarate dehydrogenase?

• Inhibited by NADH, succinyl-CoA, ATP

• Activated by Ca²⁺

Which steps produce NADH?

• Step 3: Isocitrate → α-KG

• Step 4: α-KG → Succinyl-CoA

• Step 8: Malate → Oxaloacetate

Which step produces FADH₂?

Step 6: Succinate → Fumarate (Succinate dehydrogenase).

Which step produces GTP?

Step 5: Succinyl-CoA → Succinate (Succinyl-CoA synthetase).

What enzyme is embedded in the inner mitochondrial membrane?

Succinate dehydrogenase (also Complex II of ETC).

What are the irreversible steps of the TCA cycle?

• Step 1: Citrate synthase

• Step 3: Isocitrate dehydrogenase

• Step 4: α-KG dehydrogenase

What inhibits Citrate Synthase?

ATP, NADH, citrate, succinyl-CoA.

Step 1: Acetyl-CoA + OAA → Citrate

Enzyme: Citrate synthase
Type: Condensation (irreversible)
What to know: inhibited by citrate & succinyl-CoA, atp and nadh

Step 2: Citrate → Isocitrate

Enzyme: Aconitase
Type: Isomerization
What to know: Rearranges citrate to make it oxidizable.

Step 3: Isocitrate → α-Ketoglutarate

Enzyme: Isocitrate dehydrogenase
Type: Oxidative decarboxylation
Produces: NADH + CO₂
What to know: RATE-LIMITING step; activated by ADP & Ca²⁺; inhibited by ATP & NADH.

Step 4: α-Ketoglutarate → Succinyl-CoA

Enzyme: α-Ketoglutarate dehydrogenase
Type: Oxidative decarboxylation
Produces: NADH + CO₂
What to know: Similar to PDH; requires TPP, lipoic acid, CoA, FAD, NAD⁺; inhibited by NADH & succinyl-CoA.

Step 5: Succinyl-CoA → Succinate

Enzyme: Succinyl-CoA synthetase
Type: Substrate-level phosphorylation
Produces: GTP
What to know: Only step producing GTP.

Step 6: Succinate → Fumarate

Enzyme: Succinate dehydrogenase (Complex II)
Type: Oxidation
Produces: FADH₂
What to know: Only CAC (CITRIC ACID CYCLE) enzyme in the inner mitochondrial membrane.

Step 7: Fumarate → Malate

Enzyme: Fumarase
Type: Hydration
What to know: Adds water across double bond.

Step 8: Malate → Oxaloacetate (OAA)

Enzyme: Malate dehydrogenase
Type: Oxidation
Produces: NADH
What to know: Strongly inhibited by NADH (needs low NADH to proceed).

Which steps produce NADH, FADH₂, GTP, and CO₂ in the Citric Acid Cycle?

NADH: Steps 3, 4, 8
FADH₂: Step 6
GTP: Step 5
CO₂: Steps 3, 4

Which steps of the CAC are irreversible?

• Citrate synthase

• Isocitrate dehydrogenase

• α-KG dehydrogenase

what is the purpose of the electron transport chain?

Generate a proton gradient (H⁺) across the inner mitochondrial membrane to drive ATP synthesis via ATP synthase.

Where does the ETC occur?

Inner mitochondrial membrane

IMPORTANT: What are the 4 ETC Complexes + their roles?

• Complex I (NADH dehydrogenase): Accepts electrons from NADH, pumps 4 H⁺, passes e⁻ to CoQ.

• Complex II (Succinate dehydrogenase): Accepts electrons from FADH₂, NO H⁺ pumped, sends e⁻ to CoQ.

• Complex III (Cytochrome bc1): Pumps 4 H⁺, sends electrons to cytochrome c.

• Complex IV (Cytochrome c oxidase): Pumps 2 H⁺, transfers e⁻ to O₂ → H₂O (final e⁻ acceptor).

Which electron carriers donate to ETC?

• NADH → Complex I

• FADH₂ → Complex II

what is the Final electron acceptor?

Oxygen (O₂) → reduced to H₂O

Total proton pumping per NADH vs FADH₂?

• NADH: 10 H⁺

• FADH₂: 6 H⁺
  (This is why NADH gives more ATP.)

ATP yield per NADH / FADH₂?

• NADH: ~2.5 ATP

• FADH₂: ~1.5 ATP

What does ATP synthase do?

Uses H⁺ gradient → ADP + Pi → ATP
(chemiosmosis)

What is chemiosmosis?

Flow of H⁺ back into matrix through ATP synthase that drives ATP production.

What inhibits ETC? (need to know!)

• Rotenone → Complex I

• Antimycin A → Complex III

• Cyanide & CO → Complex IV

• Oligomycin → ATP synthase (Complex V)

What are uncouplers?

Collapse H⁺ gradient → ETC runs but no ATP made
Example: DNP, thermogenin

Why does Complex II not pump protons?

Because the oxidation of FADH₂ isn’t energy-rich enough to drive H⁺ pumping.

What is the proton gradient used for?

ATP synthesis + transport of pyruvate, ATP/ADP exchange.

How do CAC and ETC connect?

CAC produces NADH & FADH₂, which carry high-energy electrons to the ETC. ETC uses these electrons to pump H⁺ and make ATP.

What does CAC supply to the ETC?

• 3 NADH per cycle → Complex I

• 1 FADH₂ per cycle → Complex II

• These provide electrons for oxidative phosphorylation

Why does CAC stop without ETC?

If ETC stops → NADH & FADH₂ accumulate → CAC can’t regenerate NAD⁺/FAD → CAC stops.
O₂ is needed to keep ETC running and regenerate NAD⁺/FAD.

Why does ETC depend on CAC?

ETC needs constant NADH/FADH₂ input.
Without CAC → no electron donors → ETC stops → no proton gradient → no ATP.

How much ATP does CAC indirectly generate through ETC?

From 1 CAC turn:

• 3 NADH × 2.5 = 7.5 ATP

• 1 FADH₂ × 1.5 = 1.5 ATP

• TOTAL from ETC = 9 ATP
  Plus 1 GTP from CAC.

(Per glucose = double.)

Role of oxidative phosphorylation in this connection?

ETC → pumps H⁺
ATP synthase → uses gradient to make ATP
This ATP production depends on CAC supplying electron donors.

What happens with low oxygen?

Low O₂ → ETC backs up → NADH increases → NAD⁺ drops → CAC slows/stops → ATP drops.

Key relationship summary between CAC and ETC

CAC = makes NADH/FADH₂
ETC = uses NADH/FADH₂
Together = oxidative phosphorylation → ATP

What is the main purpose of the electron transport chain?

To transfer electrons from NADH and FADH₂ to oxygen, pump protons to create a proton gradient, and use that gradient to synthesize ATP.

What is the name of Complex I and its main reaction?

Complex I is NADH dehydrogenase. It transfers electrons from NADH to coenzyme Q (CoQ), forming CoQH₂, and pumps 4 protons into the intermembrane space.

What is the name of Complex II and its main reaction?

Complex II is succinate dehydrogenase. It transfers electrons from FADH₂ to coenzyme Q (CoQ), forming CoQH₂.

What is the name and main function of Complex III?

Complex III is cytochrome bc₁ complex. It transfers electrons from CoQH₂ to cytochrome c and pumps 4 protons via the Q cycle.

What is the name and main function of Complex IV?

Complex IV is cytochrome c oxidase. It uses electrons to reduce oxygen to water and pumps 2 protons.

What is the reaction catalyzed by ATP synthase (Complex V)? (ATP SYNTHASE)

ADP + inorganic phosphate → ATP, using proton flow.

How many protons are required to synthesize one ATP?

Approximately 3–4 protons per ATP.

What is the electron flow for NADH?

NADH → Complex I → CoQ → Complex III → cytochrome c → Complex IV → oxygen.

What is the electron flow for FADH₂?

FADH₂ → Complex II → CoQ → Complex III → cytochrome c → Complex IV → oxygen.

How much ATP does NADH generate in the electron transport chain?

2.5 ATP.

How much ATP does FADH₂ generate in the electron transport chain?

1.5 ATP.

What is the main regulator of the electron transport chain?

ADP availability (called respiratory control).

What happens to ETC when ADP is high?

ETC speeds up.

What happens when oxygen is low?

ETC stops because oxygen is the final electron acceptor.

What does it mean that the ETC and ATP synthase are “coupled”?

Proton pumping by ETC generates a gradient that ATP synthase uses to make ATP; if ATP synthase stops, ETC slows due to gradient buildup.

What do uncoupling proteins or chemicals do?

They allow protons to leak back into the matrix without making ATP, collapsing the gradient.

What is the effect of uncoupling on oxygen consumption?

Oxygen consumption increases because electron flow accelerates.

What is the effect of uncoupling on ATP production?

ATP production decreases or stops.

Name a chemical uncoupler.

DNP (2,4-dinitrophenol) or aspirin overdose.

What inhibits Complex I?

Rotenone and amytal.

What inhibits Complex III?

Antimycin A.

What inhibits Complex IV?

Cyanide, carbon monoxide, and azide.

What inhibits ATP synthase?

Oligomycin.