L5: TCA cycle & oxidative phosphorylation

STAGE I: Digestion where large molecules in food are broken down into smaller molecules.
STAGE II: Breakdown of smaller molecules from stage I to acetyl CoA.
STAGE III: TCA cycle (citric acid cycle) and oxidative phosphorylation.
- Processes that produce ATP by oxidation of the acetyl group from acetyl CoA.

The TCA cycle is also known as the Krebs cycle, named after Hans Kreb.
Function of the TCA Cycle:
- Substrate-level phosphorylation occurs here, leading to the complete breakdown of carbon, producing CO2 and energy intermediates.
Net Reaction of the TCA Cycle:
$\text{Acetyl CoA} + 3\text{NAD}^+ + \text{FAD} + \text{GDP} + \text{Pi} + 2\text{H}<em>2\text{O} \rightarrow 2\text{CO}</em>2 + 3\text{NADH} + \text{FADH}_2 + \text{GTP} + 2\text{H}^+ + \text{CoA}$

LO3: Explaining the role of NADH and FADH2
- Oxidation of NADH and FADH2 produces a proton motive force in the intermembrane space, which powers ATP synthase for ATP production.

LO4: Explain why the cycle functions only in aerobic conditions.
- The fate of carbon would be different in absence of oxygen, as the TCA cycle depends on oxygen to proceed.

Goals of Regulation:
- To completely breakdown carbon and produce energy intermediates.
- Regulation is necessary when there is excess energy (ATP, NADH).
Key Regulatory Points:
1. Pyruvate Dehydrogenase - Stops the formation of Acetyl CoA.
2. Isocitrate dehydrogenase - Involves substrate-level phosphorylation and requires NAD+, producing CO2.
3. α-Ketoglutarate dehydrogenase - Involves substrate-level phosphorylation and requires NAD+, producing CO2.

Mitochondria are known as the powerhouse of the cell due to their role in ATP production through oxidative phosphorylation.
The outer membrane contains porins allowing small molecules <10 kDa to enter.
The inner membrane is selectively impermeable, permeable only to O2, CO2, and H2O.

Overview of the Process:
- The ETC consists of four complexes and ATP Synthase, reoxidizing NADH and FADH2 to generate a proton gradient in the intermembrane space.
- Complexes in the electron transport chain function as follows:
- Complex I: Receives electrons from NADH and pumps 4 H+.
- Complex II: Receives electrons from FADH2.
- Complex III: Pumps 2 H+.
- Complex IV: Receives electrons and uses oxygen as an acceptor, producing water.

LO3: Describe the chemiosmotic theory where:
- The free energy of electron transport is conserved by pumping H+ from the mitochondrial matrix to the intermembrane space, creating an electrochemical potential responsible for ATP synthesis.
Disruption of membrane permeability could impede ATP production despite electron transport continuing.

ATP Synthase:
- Comprised of multi-subunit proteins, F1 and F0.
- The influx of H+ through F0 drives F1 to synthesize ATP from ADP + Pi, powered by the rotation of F1's $ ext{ϒ}$ subunit with respect to $ ext{α}3 ext{β}3$.
- Approximately four protons are needed to produce one ATP molecule, along with the cost of one proton for transporting ATP from the matrix to the cytosol.
- $ ext{1 NADH} = 10 ext{H}^+ = 2.5 ext{ATP}$; $ ext{1 FADH}_2 = 6 ext{H}^+ = 1.5 ext{ATP}$.

Definition of Uncoupling:
- An uncoupler increases the permeability of the inner mitochondrial membrane to H+. This dissipates the proton gradient.
- Example: 2,4-dinitrophenol (DNP) was historically used as a diet pill, causing energy from the H+ gradient to be lost as heat, requiring the body to metabolize more carbohydrate and fat reserves to yield ATP.
Natural Uncoupling:
- Non-shivering thermogenesis, such as in brown adipose tissue, utilizes uncoupling proteins (thermogenin/UCP-1) to allow protons to flow to the matrix, generating heat instead of ATP.