Respiration

Respiration is the metabolic pathway by which cells release energy from organic molecules (primarily glucose) to synthesise ATP — the universal energy currency of cells. It occurs in all living cells, continuously, and can be aerobic (requiring oxygen) or anaerobic (without oxygen). Respiration is not simply the reverse of photosynthesis — it involves different enzymes, different intermediates, and occurs in different organelles.

Key Definition: Respiration is the enzyme-controlled release of energy from organic molecules (respiratory substrates) to produce ATP. It occurs in every living cell.

Overall equation for aerobic respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP (+ heat)

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Overview of the Four Stages

Stage	Location	Inputs (per glucose)	Outputs (per glucose)	Net ATP yield
Glycolysis	Cytoplasm	1 glucose, 2 ATP, 2 NAD⁺	2 pyruvate, 4 ATP, 2 NADH	2 ATP
Link reaction	Mitochondrial matrix	2 pyruvate, 2 NAD⁺, 2 CoA	2 acetyl CoA, 2 CO₂, 2 NADH	0 ATP
Krebs cycle	Mitochondrial matrix	2 acetyl CoA, 6 NAD⁺, 2 FAD	4 CO₂, 6 NADH, 2 FADH₂, 2 ATP	2 ATP
Oxidative phosphorylation	Inner mitochondrial membrane (cristae)	10 NADH, 2 FADH₂, O₂	H₂O, ATP	~34 ATP

flowchart TD
    G["Glucose (6C)"] -->|"Glycolysis
(Cytoplasm)"| P["2x Pyruvate (3C)
+ 2 ATP + 2 NADH"]
    P -->|"Link Reaction
(Mitochondrial matrix)"| AC["2x Acetyl CoA (2C)
+ 2 CO₂ + 2 NADH"]
    AC -->|"Krebs Cycle
(Mitochondrial matrix)"| KC["4 CO₂ + 6 NADH
+ 2 FADH₂ + 2 ATP"]
    KC -->|"NADH & FADH₂ donate e⁻"| OP["Oxidative Phosphorylation
(Inner mitochondrial membrane)"]
    OP --> ATP["~34 ATP + H₂O"]
    OP -.->|"O₂ = final e⁻ acceptor"| ATP

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Glycolysis

Glycolysis occurs in the cytoplasm and does not require oxygen. It is the most ancient metabolic pathway, occurring in virtually all living organisms.

Key Definition: Glycolysis is the metabolic pathway in which one molecule of glucose (6C) is broken down into two molecules of pyruvate (3C) in the cytoplasm, yielding a net gain of 2 ATP and 2 NADH.

1. Phosphorylation — glucose (6C) is phosphorylated twice using 2 ATP to form fructose-1,6-bisphosphate (6C). This "investment" of ATP makes the molecule more reactive and lowers the activation energy of subsequent reactions. Phosphorylation also prevents the sugar from leaving the cell, as the charged phosphate groups cannot pass through the membrane.
2. Lysis — fructose-1,6-bisphosphate is split into two molecules of triose phosphate (TP) (3C each).
3. Oxidation and substrate-level phosphorylation — each TP is oxidised: hydrogen atoms are removed and transferred to NAD⁺, forming 2 NADH in total. Simultaneously, substrate-level phosphorylation produces 4 ATP (2 per TP).
4. Net yield per glucose: 2 pyruvate, 2 ATP (net: 4 produced minus 2 invested), 2 NADH.

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The Link Reaction

Pyruvate is actively transported from the cytoplasm into the mitochondrial matrix via specific carrier proteins in the mitochondrial membranes.

• Each pyruvate (3C) is oxidatively decarboxylated:
  • A carboxyl group is removed as CO₂ (decarboxylation).
  • Hydrogen is removed and transferred to NAD⁺, which is reduced to NADH (oxidation).
  • The remaining 2C acetyl group combines with coenzyme A (CoA) to form acetyl CoA.
• Per glucose: 2 CO₂ released, 2 NADH produced, 2 acetyl CoA formed.

Exam Tip: The link reaction is sometimes overlooked in ATP yield calculations. Remember it produces 2 NADH per glucose, which later generate ATP via oxidative phosphorylation.

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The Krebs Cycle (Citric Acid Cycle)

The Krebs cycle takes place in the mitochondrial matrix, which contains all the necessary enzymes in solution.

1. Acetyl CoA (2C) combines with oxaloacetate (4C) to form citrate (6C). CoA is released and recycled.
2. Citrate is gradually converted back to oxaloacetate through a series of enzyme-catalysed reactions involving:
   • Decarboxylation reactions that release 2 CO₂ per turn (at the 6C → 5C and 5C → 4C steps).
   • Oxidation reactions that reduce 3 NAD⁺ to 3 NADH and 1 FAD to 1 FADH₂ per turn.
   • 1 ATP is produced by substrate-level phosphorylation per turn (technically GTP in some organisms, which is readily converted to ATP).
3. Oxaloacetate is regenerated and can accept another acetyl CoA — the cycle continues.

flowchart TD
    ACoA["Acetyl CoA (2C)"] --> Citrate["Citrate (6C)"]
    OAA["Oxaloacetate (4C)"] --> Citrate
    Citrate -->|"Decarboxylation
→ CO₂ + NADH"| C5["5C intermediate"]
    C5 -->|"Decarboxylation
→ CO₂ + NADH"| C4["4C intermediate"]
    C4 -->|"Oxidation → FADH₂
Substrate-level → 1 ATP"| C4b["4C intermediate"]
    C4b -->|"Oxidation → NADH"| OAA

Per glucose (2 turns): 4 CO₂, 6 NADH, 2 FADH₂, 2 ATP.

Key Definition: Decarboxylation is the removal of a carboxyl group from a molecule, releasing CO₂. Oxidation in this context refers to the removal of hydrogen atoms (dehydrogenation), which are accepted by NAD⁺ or FAD.

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Oxidative Phosphorylation

This is the final and most productive stage, occurring on the inner mitochondrial membrane (cristae). The cristae are highly folded, providing a very large surface area for the electron transport chain and ATP synthase complexes.

1. NADH and FADH₂ donate electrons (and hydrogen atoms) to the electron transport chain (ETC) — a series of protein complexes (Complexes I–IV) and mobile carriers (ubiquinone, cytochrome c).
2. As electrons pass along the chain, they lose energy at each carrier. This energy is used to actively pump H⁺ ions from the matrix into the intermembrane space, creating a proton motive force (electrochemical gradient — a difference in both H⁺ concentration and charge).
3. The intermembrane space is small, so even a modest number of H⁺ ions creates a steep gradient.
4. H⁺ ions flow back into the matrix through ATP synthase (chemiosmosis), driving the rotation of ATP synthase and the synthesis of ATP from ADP + Pi.
5. Oxygen is the final electron acceptor: it combines with electrons and H⁺ ions to form water (H₂O). Without oxygen, electrons cannot leave the chain, the ETC stops, NADH and FADH₂ cannot be reoxidised, and the Krebs cycle and link reaction also halt.

Approximate yield: Each NADH yields ~2.5 ATP; each FADH₂ yields ~1.5 ATP (FADH₂ enters the chain at Complex II, bypassing Complex I, so fewer H⁺ are pumped).

Exam Tip: Students often ask "why is the yield approximate?" The answer is that the H⁺ gradient is also used for other processes (e.g., transporting pyruvate into the matrix), and the exact H⁺-to-ATP ratio may vary. Always write "approximately" or use the tilde (~) symbol.

Worked Example 1 — Total ATP Yield from Aerobic Respiration of One Glucose

Source	Coenzymes produced	ATP equivalent
Glycolysis	2 NADH	2 × 2.5 = 5 ATP
Glycolysis (substrate-level)	—	2 ATP
Link reaction	2 NADH	2 × 2.5 = 5 ATP
Krebs cycle	6 NADH	6 × 2.5 = 15 ATP
Krebs cycle	2 FADH₂	2 × 1.5 = 3 ATP
Krebs cycle (substrate-level)	—	2 ATP
Total	10 NADH + 2 FADH₂	~32 ATP

Note: Some textbooks quote ~38 ATP, assuming each NADH yields 3 ATP and each FADH₂ yields 2 ATP. The more accepted modern figure is ~30–32 ATP per glucose, because the actual yield per NADH is closer to 2.5 ATP. Either figure is acceptable in A-Level exams provided you show your reasoning.

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Anaerobic Respiration

When oxygen is unavailable, oxidative phosphorylation and the Krebs cycle cannot proceed (because NAD⁺ and FAD cannot be regenerated). Only glycolysis continues, but it requires a mechanism to reoxidise NADH back to NAD⁺.