The Krebs Cycle, the Respiratory Chain and the ATP Total

• Site: the mitochondrial matrix. The one exception is succinate dehydrogenase, which sits in the inner membrane. Other names: citric acid cycle, tricarboxylic acid (TCA) cycle.
• Acetyl CoA (2C) + oxaloacetate (4C) $\rightarrow$ citrate (6C).
• Two oxidative decarboxylations release 2 $\mathrm{CO_2}$ per turn.
• Per turn: 3 NADH, 1 $\mathrm{FADH_2}$, 1 GTP (or ATP) and 2 $\mathrm{CO_2}$.
• One glucose gives two acetyl CoA, so the cycle turns twice per glucose: 6 NADH, 2 $\mathrm{FADH_2}$, 2 ATP, 4 $\mathrm{CO_2}$.
• No oxygen is used in the cycle, but it stops without oxygen, because $\mathrm{NAD^+}$ and FAD are regenerated only by the respiratory chain.

• Site: the inner mitochondrial membrane, folded into cristae to give more area.
• Four complexes (I to IV) are integral membrane proteins. Two mobile carriers shuttle electrons between them: ubiquinone (coenzyme Q, a small lipid-soluble molecule moving within the membrane) and cytochrome c (a small peripheral protein on the outer face of the inner membrane).
• Complex I takes electrons from NADH; complex II (succinate dehydrogenase) takes them from $\mathrm{FADH_2}$. Both pass them to ubiquinone.
• Complex III passes them to cytochrome c, and complex IV (cytochrome c oxidase) passes them to oxygen, which takes up protons to form water.
• Cytochromes are proteins with a haem group whose iron switches between $\mathrm{Fe^{3+}}$ and $\mathrm{Fe^{2+}}$. They carry electrons only, not hydrogen atoms.
• The chain is how reduced coenzymes are reoxidised to $\mathrm{NAD^+}$ and FAD. Without oxygen it stops, the carriers stay reduced, and the Krebs cycle stops too. Cyanide kills by blocking complex IV.

• Complexes I, III and IV pump protons ($\mathrm{H^+}$) from the matrix into the intermembrane space.
• This builds an electrochemical gradient (the proton-motive force): more $\mathrm{H^+}$ (lower pH) and more positive charge in the intermembrane space than in the matrix.
• The inner membrane is impermeable to $\mathrm{H^+}$, so the only way back is through ATP synthase, an enzyme in the inner membrane.
• $\mathrm{H^+}$ flowing back through ATP synthase into the matrix drives $\mathrm{ADP + P_i \rightarrow ATP}$.
• Oxidative phosphorylation = electron transport + chemiosmosis: the energy stored in reduced coenzymes is used to make ATP. It needs both membrane proteins (the complexes, ATP synthase) and mobile molecules (ubiquinone, cytochrome c, the ions themselves).
• Uncouplers let $\mathrm{H^+}$ leak back without passing through ATP synthase: oxygen is still used, but the energy becomes heat. Brown fat uses this on purpose to keep newborns warm.

Per glucose in aerobic respiration:

• Substrate-level: 2 ATP (glycolysis) + 2 ATP or GTP (Krebs cycle) = 4.
• Reduced carriers: 10 NADH (2 glycolysis, 2 link reaction, 6 Krebs cycle) and 2 $\mathrm{FADH_2}$ (Krebs cycle).
• Oxidative phosphorylation: about $10 \times 2.5 + 2 \times 1.5 = 28$ ATP, by far the largest share.
• Total: about 32, or about 30 when the NADH from glycolysis enters the mitochondrion by a shuttle worth only 1.5 each. With the older values of 3 and 2 per carrier the total is 36 to 38.
• Efficiency = energy captured in ATP divided by the energy released by complete oxidation. For glucose it is about 30 to 35%; the rest is lost as heat, which keeps birds and mammals warm.