CHEM 3332 Exam Study Guide: Oxidative Phosphorylation & Photosynthesis

Mitochondria

Site of aerobic metabolism (TCA, β-oxidation, amino acid catabolism).

ETC

Electrons from NADH/FADH₂ go through complexes to O₂, generating a proton gradient.

ATP synthesis

Powered by proton-motive force (chemiosmotic theory).

Proton-motive force

The electrochemical gradient of protons across the mitochondrial inner membrane; drives ATP synthesis.

Chemiosmotic theory

Proposed by Peter Mitchell: proton gradients across membranes power ATP synthesis.

ATP synthase

A multi-subunit enzyme that uses the proton gradient to catalyze ATP formation from ADP and Pi.

Reactive oxygen species (ROS)

Chemically reactive molecules containing oxygen.

ETC components

NADH, FMN, CoQ, Cyt c, Fe-S clusters, heme.

Complex I

NADH → CoQ, pumps 4 H⁺.

Complex II

FADH₂ → CoQ (no H⁺ pumped).

Complex III

QH₂ → Cyt c (4 H⁺ pumped via Q cycle).

Complex IV

Cyt c → O₂ → H₂O (4 H⁺ pumped, 4 e⁻ used).

Ubiquinone (CoQ)

A lipid-soluble mobile electron carrier that transports electrons from Complexes I/II to Complex III.

Cytochrome c

A small, mobile, water-soluble protein that carries electrons from Complex III to Complex IV.

Fe-S Clusters

Prosthetic groups that transfer single electrons; found in Complexes I, II, and III.

Heme

An iron-containing prosthetic group that participates in electron transfer in cytochromes.

Malate-Aspartate Shuttle

Transports NADH equivalents from the cytosol to the mitochondrial matrix efficiently (yields 2.5 ATP per NADH).

Glycerol-3-Phosphate Shuttle

Transfers electrons from cytosolic NADH to FAD in the mitochondrial membrane (yields only 1.5 ATP).

Oligomycin

Inhibitor of ATP synthase; blocks proton flow, halts ATP production.

2,4-Dinitrophenol (DNP)

An uncoupler that dissipates the proton gradient, allowing ETC to continue but stopping ATP synthesis.

IF1 (Inhibitory Factor 1)

Binds to F₁ATPase during low pH (e.g., hypoxia) to prevent it from running in reverse and hydrolyzing ATP.

P/O Ratio

The number of ATP molecules synthesized per atom of oxygen consumed (e.g., 2.5 for NADH, 1.5 for FADH₂).

NADH

A high-energy electron carrier that donates electrons to Complex I in the ETC.

FADH₂

Another electron carrier that donates electrons to Complex II.

FMN

A cofactor in Complex I that accepts electrons from NADH.

Thermogenin (UCP1)

An uncoupling protein in brown fat mitochondria that dissipates the proton gradient to generate heat instead of ATP.

Mitochondrial Matrix

The innermost compartment of the mitochondria; site of the TCA cycle and proton pumping source.

Intermembrane Space

The space between the inner and outer mitochondrial membranes where protons are pumped to build the gradient.

Complex I (NADH:Ubiquinone Oxidoreductase)

Accepts electrons from NADH, passes them through FMN and Fe-S clusters to CoQ. Pumps 4 protons (H+) into the intermembrane space.

Complex II (Succinate Dehydrogenase)

Accepts electrons from FADH2 (generated in the TCA cycle). Transfers electrons to CoQ. Does not pump protons.

Complex III (Cytochrome bc1 Complex)

Uses the Q cycle to transfer electrons from QH2 to cytochrome c and pumps 4 protons.

Complex IV (Cytochrome c Oxidase)

Transfers electrons from cytochrome c to O2 (terminal electron acceptor), forming H2O. Pumps 4 protons.

ATP Synthase (F1F0-ATPase)

Enzyme complex that synthesizes ATP from ADP and Pi using the proton gradient generated by the ETC.

F0

Embedded in the membrane; forms the proton channel.

F1

In the mitochondrial matrix; contains catalytic sites on β-subunits.

γ-subunit

Rotates as protons flow, inducing conformational changes in β-subunits to promote ATP formation.

Malate-Aspartate Shuttle

Transfers NADH electrons from cytosol to mitochondria; electrons enter at Complex I → yields 2.5 ATP per NADH.

Glycerol-3-Phosphate Shuttle

Transfers electrons to FAD (bypassing Complex I), yielding 1.5 ATP per NADH.

Oligomycin

Inhibits ATP synthase by blocking proton channel; halts ATP synthesis.

2,4-Dinitrophenol (DNP)

Uncouples ETC and ATP synthesis by allowing protons to bypass ATP synthase; dissipates gradient as heat.

Light Reactions (Photophosphorylation)

Occur in the thylakoid membranes of chloroplasts. Light energy is used to split water (in PSII), generate ATP, and reduce NADP+ to NADPH.

Photosystem II (PSII)

Absorbs light, splits water to O2, pumps protons across thylakoid membrane.

Cytochrome b6f Complex

Analogous to mitochondrial Complex III; uses Q cycle, pumps protons.

Photosystem I (PSI)

Absorbs light and transfers electrons to reduce NADP+ to NADPH.

ATP Synthase (CF1CF0)

Synthesizes ATP as protons flow from thylakoid lumen to stroma.

Z Scheme of Electron Flow

Describes two light-driven electron lifts (PSII and PSI).

Non-cyclic Electron Flow

Linear path; produces ATP, NADPH, and O2.

Cyclic Electron Flow

Electrons from PSI cycle back to cytochrome b6f; produces ATP only, no O2 or NADPH.

Calvin Cycle (Carbon Fixation)

Occurs in the stroma; uses ATP and NADPH from light reactions to fix CO2 into carbohydrates.

Phase 1 (Carbon Fixation)

RuBisCO adds CO2 to RuBP → 3-PGA.

Phase 2 (Reduction)

3-PGA is reduced to G3P using ATP and NADPH.

Phase 3 (Regeneration)

G3P is converted back into RuBP.

Energy Cost of Calvin Cycle

Fixation of 1 CO2 requires 3 ATP and 2 NADPH.

RuBisCO Regulation

Activated by light (via pH, Mg2+, redox state).

Photorespiration

Occurs when RuBisCO binds O2 → produces 2-phosphoglycolate (toxic).

C4 Plants

Spatial separation; CO2 fixed into oxaloacetate in mesophyll cells, transported to bundle sheath where RuBisCO operates.

CAM Plants

Temporal separation; CO2 captured at night and stored as malate, used during the day.

RuBP

CO2 acceptor in Calvin Cycle.

G3P

Output of Calvin Cycle.

TPP

Cofactor in transketolase.

Plastocyanin / Ferredoxin

Electron carriers in chloroplasts.

Mg2+

Stabilizes RuBisCO active site.

P/O Ratio

NADH = 2.5 ATP, FADH2 = 1.5 ATP.

Photophosphorylation

8 photons → 1 O2 + 2 NADPH + 3 ATP.

RuBisCO

Inefficient enzyme but most abundant protein on Earth.