Cellular Energetics

Cellular Respiration (CED Unit 3)

Overview

Cellular respiration is the catabolic process by which cells harvest energy from organic molecules ( glucose). The overall equation:

\mathrm{C_6\mathrm{H_{12}\mathrm{O_6 + 6\mathrm{O_2 \to 6\mathrm{CO_2 + 6\mathrm{H_2\mathrm{O + \mathrm{ATP + \mathrm{heat

$\Delta G^\circ \approx -686 \mathrm{ kcal/mol$ (highly exergonic).

Four Stages

Stage	Location	O $_2$ Required?	ATP Produced (Net)
Glycolysis	Cytoplasm	No	2 ATP (substrate-level)
Pyruvate oxidation	Mitochondrial matrix	No	0
Citric acid cycle	Mitochondrial matrix	No	2 ATP (substrate-level)
Oxidative phosphorylation	Inner mitochondrial membrane	Yes	~26-28 ATP (chemiosmosis)

Glycolysis

Glycolysis (“sugar splitting”) breaks one glucose ( $\mathrm{C_6$ ) into two pyruvate ( $\mathrm{C_3$ ) molecules.

Investment phase (requires 2 ATP):

Hexokinase: glucose $\to$ glucose-6-phosphate (uses 1 ATP)
Phosphoglucose isomerase: glucose-6-phosphate $\to$ fructose-6-phosphate
Phosphofructokinase (PFK): fructose-6-phosphate $\to$ fructose-1,6-bisphosphate (uses 1 ATP)
Aldolase: fructose-1,6-bisphosphate $\to$ DHAP + G3P
DHAP $\to$ G3P (isomerase)

Payoff phase (produces 4 ATP + 2 NADH): 6-10. Each G3P is oxidized to pyruvate, producing 2 ATP (substrate-level phosphorylation) and 1 NADH per G3P.

Net yield per glucose: 2 ATP, 2 NADH, 2 pyruvate.

Regulation: Phosphofructokinase (PFK) is the key regulatory enzyme. It is inhibited by ATP and Citrate (high energy signals) and activated by AMP and fructose-2,6-bisphosphate.

Worked Example: ATP yield from glycolysis alone.

If a cell can only carry out glycolysis (no oxygen available), the net ATP yield per glucose is 2 ATP. The 2 NADH produced cannot enter the electron transport chain without oxygen. In animal cells, These NADH are used to reduce pyruvate to lactate (fermentation). In yeast, NADH are used to reduce Acetaldehyde to ethanol.

Worked Example: Why hexokinase and PFK are different.

Hexokinase catalyses the first step of glycolysis (glucose $\to$ glucose-6-phosphate). It is not the Committed step because glucose-6-phosphate can also enter the pentose phosphate pathway (for NADPH Production). PFK catalyses the committed step (fructose-6-phosphate $\to$ Fructose-1,6-bisphosphate). Once fructose-1,6-bisphosphate is formed, the molecule is committed to Glycolysis. This is why PFK is the key regulatory enzyme — it controls the rate at which glucose Enters glycolysis.

Pyruvate Oxidation (Link Reaction)

Each pyruvate ( $\mathrm{C_3$ ) is transported into the mitochondrial matrix and converted to Acetyl-CoA ( $\mathrm{C_2$ ):

\mathrm{Pyruvate + \mathrm{CoA + \mathrm{NAD^+ \to \mathrm{Acetyl-CoA + \mathrm{CO_2 + \mathrm{NADH

Per glucose: 2 acetyl-CoA, $2 \mathrm{CO_2$ 2 NADH.

The link reaction is catalysed by the pyruvate dehydrogenase complex, a large multi-enzyme complex That requires five coenzymes: CoA, $\mathrm{NAD^+$ FAD, lipoic acid, and thiamine (vitamin B1). This is why thiamine deficiency (beriberi) impairs energy metabolism.

Citric Acid Cycle (Krebs Cycle)

Each acetyl-CoA ( $\mathrm{C_2$ ) enters the cycle and combines with oxaloacetate ( $\mathrm{C_4$ ) to Form citrate ( $\mathrm{C_6$ ). Through a series of redox and decarboxylation reactions:

Per acetyl-CoA:

3 $\mathrm{NADH$
1 $\mathrm{FADH_2$
1 ATP (or GTP)
2 $\mathrm{CO_2$

Per glucose (2 turns):

6 NADH
2 $\mathrm{FADH_2$
2 ATP
4 $\mathrm{CO_2$

Worked Example: Tracking carbon atoms through the Krebs cycle.

The two carbon atoms from one acetyl-CoA enter the cycle as part of citrate. Over the course of one Turn, both carbons are released as $\mathrm{CO_2$ . However, neither $\mathrm{CO_2$ molecule comes Directly from the acetyl-CoA — the carbon atoms are scrambled by the symmetrical nature of some Intermediates (succinate and fumarate). This was demonstrated by Melvin Calvin using radioactive $^{14}\mathrm{C$ -labelled acetyl-CoA. Despite the scrambling, the net result is that the two Carbons from acetyl-CoA are released as $\mathrm{CO_2$ by the end of one turn.

Oxidative Phosphorylation

The electron transport chain (ETC) and chemiosmosis generate the majority of ATP.

Electron Transport Chain:

Complexes I—IV are embedded in the inner mitochondrial membrane:

Complex I (NADH dehydrogenase): NADH donates electrons, pumping 4 $\mathrm{H^+$ into the intermembrane space.
Complex II (succinate dehydrogenase): $\mathrm{FADH_2$ donates electrons (no $\mathrm{H^+$ pumped).
Coenzyme Q (ubiquinone): Transfers electrons from Complex I/II to Complex III.
Complex III (cytochrome bc1): Pumps 4 $\mathrm{H^+$ .
Cytochrome c: Transfers electrons to Complex IV.
Complex IV (cytochrome c oxidase): Transfers electrons to $\mathrm{O_2$ (final electron acceptor), forming $\mathrm{H_2\mathrm{O$ . Pumps 2 $\mathrm{H^+$ .

Total $\mathrm{H^+$ pumped per NADH: $\approx 10$ . Total $\mathrm{H^+$ pumped per $\mathrm{FADH_2$ : $\approx 6$ .

Chemiosmosis:

The proton gradient ( $\mathrm{H^+$ concentration and charge difference) stores potential energy (proton-motive force). $\mathrm{H^+$ flows back through ATP synthase, driving the synthesis of ATP:

\mathrm{ADP + \mathrm{P_i + n\mathrm{H^+_{\mathrm{out} \to \mathrm{ATP + \mathrm{H_2\mathrm{O + n\mathrm{H^+_{\mathrm{in}

Approximately 3-4 $\mathrm{H^+$ are needed per ATP synthesized.

The role of ATP synthase: ATP synthase is a molecular motor. The flow of protons through the $F_0$ portion causes the $F_1$ portion to rotate, inducing conformational changes that catalyse the Phosphorylation of ADP to ATP. This mechanism was proposed by Paul Boyer and confirmed by John Walker (Nobel Prize, 1997).

ATP Yield Per Glucose

Source	ATP (Approximate)
Glycolysis	2 ATP (direct)
Glycolysis NADH	3-5 ATP
Pyruvate oxidation	6 ATP
Krebs cycle	2 ATP (direct)
Krebs NADH	15 ATP
Krebs $\mathrm{FADH_2$	3 ATP
Total	30-32 ATP

Worked Example: Calculating total ATP yield.

Using the values of 2.5 ATP per NADH and 1.5 ATP per $\mathrm{FADH_2$ :

Glycolysis: 2 ATP + 2 NADH $\times$ 2.5 = 7 ATP
Pyruvate oxidation: 2 NADH $\times$ 2.5 = 5 ATP
Krebs cycle: 2 ATP + 6 NADH $\times$ 2.5 + 2 $\mathrm{FADH_2 \times$ 1.5 = 2 + 15 + 3 = 20 ATP
Total: 7 + 5 + 20 = 32 ATP

Note: Some textbooks use 3 ATP per NADH and 2 ATP per $\mathrm{FADH_2$ Giving a total of 38 ATP. The actual yield is closer to 30-32 because of proton leak and the cost of transporting molecules Across membranes.

Fermentation (Anaerobic Respiration)

When $\mathrm{O_2$ is unavailable, cells use fermentation to regenerate $\mathrm{NAD^+$ from NADH, Allowing glycolysis to continue.

Alcoholic fermentation (yeast):

\mathrm{Pyruvate \to \mathrm{Acetaldehyde + \mathrm{CO_2 \to \mathrm{Ethanol + \mathrm{NAD^+

Lactic acid fermentation (muscle cells, some bacteria):

\mathrm{Pyruvate + \mathrm{NADH \to \mathrm{Lactate + \mathrm{NAD^+

Worked Example: Why fermentation is necessary.

During glycolysis, NAD+ is reduced to NADH. Without a way to regenerate NAD+, glycolysis would stop After a few seconds because there would be no NAD+ to accept electrons.

In the presence of oxygen, NADH donates its electrons to the ETC, regenerating NAD+. But without Oxygen, the ETC cannot function. Fermentation solves this problem by using NADH to reduce pyruvate (to lactate or ethanol), regenerating NAD+ so glycolysis can continue producing its 2 ATP per Glucose.

Worked Example: Why alcoholic fermentation is important in industry.

Yeast (Saccharomyces cerevisiae) carries out alcoholic fermentation in anaerobic conditions. This is Exploited in brewing (beer), winemaking, and bread-making. In bread-making, the $\mathrm{CO_2$ Produced by fermentation causes the dough to rise, while the ethanol evaporates during baking. In Brewing, ethanol is the desired product, and the $\mathrm{CO_2$ provides carbonation. The yeast Consumes the sugars in the wort or grape juice and produces ethanol and $\mathrm{CO_2$ as waste Products.

Photosynthesis (CED Unit 3)

Overview

Photosynthesis converts light energy into chemical energy stored in glucose:

6\mathrm{CO_2 + 6\mathrm{H_2\mathrm{O + \mathrm{light energy \to \mathrm{C_6\mathrm{H_{12}\mathrm{O_6 + 6\mathrm{O_2

Two Stages

Stage	Location	Inputs	Outputs
Light-dependent	Thylakoid membrane	$\mathrm{H_2\mathrm{O$ Light, $\mathrm{NADP^+$ ADP	$\mathrm{O_2$ ATP, NADPH
Calvin cycle	Stroma	$\mathrm{CO_2$ ATP, NADPH	G3P (sugar), ADP, $\mathrm{NADP^+$

Light-Dependent Reactions

Photosystem II (PS II): Light excites electrons in P680. Water is split (photolysis): $2\mathrm{H_2\mathrm{O \to 4\mathrm{H^+ + 4e^- + \mathrm{O_2$ . Electrons pass through the ETC, pumping $\mathrm{H^+$ into the thylakoid lumen.
Cytochrome b6f complex: Continues the ETC, pumping more $\mathrm{H^+$ .
Photosystem I (PS I): Light excites electrons in P700. Electrons are re-energized and transferred to ferredoxin, then to $\mathrm{NADP^+$ reductase.
$\mathrm{NADP^+$ reductase: $\mathrm{NADP^+ + \mathrm{H^+ + 2e^- \to \mathrm{NADPH$ .
Chemiosmosis: $\mathrm{H^+$ gradient drives ATP synthase, producing ATP.

Why water is the source of electrons: The electrons from water replace those lost by P680. Without water, the photosystems would run out of electrons and photosynthesis would stop. This was Demonstrated using $^{18}\mathrm{O$ -labelled water: the labelled oxygen appeared in $\mathrm{O_2$ Gas, not in glucose, confirming that water (not $\mathrm{CO_2$ ) is the source of oxygen released During photosynthesis.

The Calvin Cycle (Light-Independent Reactions)

Also called the C3 pathway. Three phases:

Carbon fixation: RuBisCO catalyzes $\mathrm{CO_2$ + RuBP (5C) $\to$ 2 molecules of 3-PGA (3C).

RuBisCO is the most abundant protein on Earth.
It can also catalyze photorespiration (RuBP + $\mathrm{O_2$ $\to$ 3-PGA + 2-phosphoglycolate), which wastes energy.

Reduction: 3-PGA + ATP + NADPH $\to$ G3P. For every 3 $\mathrm{CO_2$ fixed, 6 G3P are produced (5 are recycled, 1 is net gain).
Regeneration of RuBP: 5 G3P (15C) + 3 ATP $\to$ 3 RuBP (15C).

Net: 3 $\mathrm{CO_2$ + 9 ATP + 6 NADPH $\to$ 1 G3P + 9 ADP + 8 $\mathrm{P_i$ + 6 $\mathrm{NADP^+$

To make one glucose: 2 G3P needed, so the cycle must turn 6 times, fixing 6 $\mathrm{CO_2$ : 6 $\mathrm{CO_2$ + 18 ATP + 12 NADPH $\to$ glucose + 18 ADP + 16 $\mathrm{P_i$ + 12 $\mathrm{NADP^+$ .

Photorespiration

When stomata close on hot, dry days, $\mathrm{CO_2$ levels drop and $\mathrm{O_2$ levels rise. RuBisCO binds $\mathrm{O_2$ instead of $\mathrm{CO_2$ Producing 2-phosphoglycolate (a 2-carbon Compound) and 3-PGA. This consumes energy without producing sugar.

C4 and CAM Photosynthesis

C4 plants (corn, sugarcane):

$\mathrm{CO_2$ is initially fixed into a 4-carbon compound (oxaloacetate) by PEP carboxylase in mesophyll cells.
The 4-carbon compound is transported to bundle-sheath cells, where $\mathrm{CO_2$ is released for the Calvin cycle.
PEP carboxylase has a much higher affinity for $\mathrm{CO_2$ than RuBisCO and does not bind $\mathrm{O_2$ .
Minimizes photorespiration.

CAM plants (cacti, pineapples):

Open stomata at night to fix $\mathrm{CO_2$ into organic acids.
Close stomata during the day to conserve water.
Release $\mathrm{CO_2$ from organic acids during the day for the Calvin cycle.
Temporal separation of $\mathrm{CO_2$ fixation and the Calvin cycle.

Comparison table: C3, C4, and CAM plants.

Feature	C3 Plants	C4 Plants	CAM Plants
Carbon fixation	RuBisCO (mesophyll)	PEP carboxylase (mesophyll), RuBisCO (bundle-sheath)	PEP carboxylase (night), RuBisCO (day)
Photorespiration	Significant	Minimal	Minimal
Water use	Moderate	Moderate	Very efficient
Habitat	Temperate, cool	Tropical, hot	Arid, desert
Examples	Wheat, rice, soybeans	Corn, sugarcane	Cacti, pineapples, orchids

Worked Example: Comparing C4 and CAM strategies.

Both C4 and CAM plants minimise photorespiration by concentrating $\mathrm{CO_2$ around RuBisCO. C4 Plants achieve this through spatial separation: PEP carboxylase fixes $\mathrm{CO_2$ in mesophyll Cells, and the resulting 4-carbon acid is transported to bundle-sheath cells where $\mathrm{CO_2$ Is released. CAM plants achieve the same result through temporal separation: $\mathrm{CO_2$ is Fixed at night (when stomata can open without excessive water loss) and stored as organic acids. During the day, the organic acids release $\mathrm{CO_2$ for the Calvin cycle. The key difference Is that C4 plants fix $\mathrm{CO_2$ and run the Calvin cycle simultaneously in different cells, While CAM plants separate them in time within the same cell.

Common Pitfalls

Confusing the inputs and outputs of cellular respiration and photosynthesis. They are essentially reverse processes (respiration: glucose + $\mathrm{O_2$ $\to$ $\mathrm{CO_2$ + $\mathrm{H_2\mathrm{O$ ; photosynthesis: $\mathrm{CO_2$ + $\mathrm{H_2\mathrm{O$ $\to$ glucose + $\mathrm{O_2$ ).
Misidentifying the final electron acceptor. In respiration, it is $\mathrm{O_2$ . In the light reactions, it is $\mathrm{NADP^+$ .
Confusing NADH and $\mathrm{FADH_2$ ATP yields. NADH yields more ATP because electrons enter the ETC at Complex I (pumping more protons), while $\mathrm{FADH_2$ enters at Complex II.
Forgetting that the Calvin cycle must turn 6 times to produce one glucose molecule.
Confusing C4 and CAM plants. C4 plants have spatial separation (mesophyll vs bundle-sheath); CAM plants have temporal separation (night vs day).
Thinking fermentation produces ATP. Fermentation only regenerates $\mathrm{NAD^+$ to allow glycolysis to continue; the ATP comes from glycolysis alone.
Confusing the roles of photosystems I and II. PS II comes first (P680), splits water, and produces ATP. PS I comes second (P700) and produces NADPH.
Forgetting that $\mathrm{CO_2$ is released in both pyruvate oxidation and the Krebs cycle. A total of 6 $\mathrm{CO_2$ are released per glucose (2 from link reaction, 4 from Krebs cycle).
Thinking that the Krebs cycle directly produces a lot of ATP. It only produces 2 ATP per glucose by substrate-level phosphorylation; most ATP comes from oxidative phosphorylation.
Confusing photophosphorylation and oxidative phosphorylation. Photophosphorylation occurs in chloroplasts and uses light energy; oxidative phosphorylation occurs in mitochondria and uses energy from the electron transport chain.
Thinking glycolysis requires oxygen. Glycolysis is anaerobic and occurs in the cytoplasm. Oxygen is only required for oxidative phosphorylation.
Confusing the source of oxygen released in photosynthesis. Oxygen comes from the splitting of water (photolysis), not from $\mathrm{CO_2$ .
Forgetting the role of PEP carboxylase in C4 plants. PEP carboxylase has no oxygenase activity, unlike RuBisCO, so it does not catalyse photorespiration.

Practice Questions

Trace the complete path of a carbon atom from $\mathrm{CO_2$ to glucose through the Calvin cycle, including the number of turns needed.
Explain why poisons like cyanide (which blocks Complex IV of the ETC) are lethal.
Compare the ATP yield of aerobic respiration with fermentation. Why does aerobic respiration produce so much more ATP?
A researcher adds a proton ionophore (a chemical that makes the thylakoid membrane permeable to $\mathrm{H^+$ ) to chloroplasts. Predict the effect on ATP synthesis and explain why.
Explain how C4 plants minimize photorespiration and why this is advantageous in hot, dry climates.
Describe the role of RuBisCO in both the Calvin cycle and photorespiration.
During intense exercise, muscle cells switch to lactic acid fermentation. Explain why this is necessary and how it affects ATP production.
Calculate the total ATP yield from one molecule of glucose, assuming 2.5 ATP per NADH and 1.5 ATP per $\mathrm{FADH_2$ in the electron transport chain.
Explain the chemiosmotic theory of ATP production. How is it similar in mitochondria and chloroplasts, and how does it differ?
A plant is grown in an atmosphere with radioactive $^{14}\mathrm{CO_2$ . Describe the path of the radioactive carbon from the atmosphere to glucose, naming the molecules it passes through.
Compare the light-dependent reactions and the Calvin cycle in terms of location, inputs, outputs, and dependence on light.
Explain why the proton gradient is necessary for ATP synthase to function.
Describe the role of PEP carboxylase in C4 photosynthesis and explain why it has a higher affinity for $\mathrm{CO_2$ than RuBisCO.
A researcher measures the rate of oxygen production by isolated chloroplasts under different light intensities. Sketch the expected graph and explain its shape.
Explain why uncoupling proteins (which make the inner mitochondrial membrane permeable to protons) cause increased oxygen consumption but decreased ATP production.
Describe how the products of the light-dependent reactions (ATP and NADPH) are used in the Calvin cycle.
Explain why fermentation is less efficient than aerobic respiration in terms of ATP yield per glucose.
Compare the electron transport chains in mitochondria and chloroplasts. What are the key similarities and differences?
Explain the effect of increasing temperature on the rate of photosynthesis, including why very high temperatures reduce the rate.
A student claims that “plants release oxygen during photosynthesis and absorb oxygen during respiration.” Evaluate this claim for a plant in (a) bright sunlight and (b) complete darkness.
Explain why the glycerol-3-phosphate shuttle reduces the total ATP yield from glycolysis compared to the malate-aspartate shuttle.
Describe the mechanism of brown fat thermogenesis and explain how it differs from normal oxidative phosphorylation.
A researcher isolates mitochondria and measures oxygen consumption and ATP production in the presence and absence of DNP (dinitrophenol). Explain the expected results.
Explain how the enzyme RuBisCO can be both essential for photosynthesis and wasteful (through photorespiration). Why has evolution not produced a better enzyme?
Compare the structure and function of ATP synthase in mitochondria and chloroplasts.

Review: Detailed Comparison of Respiration and Photosynthesis

Understanding the similarities and differences between these two processes is essential for the AP Exam.

Feature	Cellular Respiration	Photosynthesis
Location	Cytoplasm and mitochondria	Chloroplasts
Organisms	All living organisms	Plants, algae, some bacteria
Overall equation	$\mathrm{C_6\mathrm{H_{12}\mathrm{O_6 + 6\mathrm{O_2 \to 6\mathrm{CO_2 + 6\mathrm{H_2\mathrm{O$	$6\mathrm{CO_2 + 6\mathrm{H_2\mathrm{O \to \mathrm{C_6\mathrm{H_{12}\mathrm{O_6 + 6\mathrm{O_2$
Energy change	Exergonic ( $\Delta G \lt 0$ )	Endergonic ( $\Delta G \gt 0$ )
Electron donor	Glucose (organic molecule)	Water ( $\mathrm{H_2\mathrm{O$ )
Electron acceptor	$\mathrm{O_2$ (final)	$\mathrm{NADP^+$ (final)
ATP production	Substrate-level + oxidative	Photophosphorylation
$\mathrm{CO_2$	Released	Consumed
$\mathrm{O_2$	Consumed	Released

The two processes are essentially reverse reactions in terms of overall chemical equation, but they Differ fundamentally in their mechanisms: respiration catabolises glucose to harvest energy, while Photosynthesis uses light energy to build glucose.

Review: Factors Affecting the Rate of Photosynthesis

Light intensity: At low light intensity, the rate of photosynthesis increases linearly because More photons are available to excite electrons in the photosystems. As light intensity increases, The rate plateaus because another factor ( $\mathrm{CO_2$ concentration or temperature) Becomes limiting.

$\mathrm{CO_2$ concentration: At low $\mathrm{CO_2$ The rate increases because RuBisCO has More substrate to fix. At high $\mathrm{CO_2$ The rate plateaus because light or temperature is Limiting. Commercial greenhouses often enrich the atmosphere with $\mathrm{CO_2$ to increase crop Yields.

Temperature: Affects enzyme activity (particularly RuBisCO). The rate increases with temperature Up to an optimum ( $25$ — $35\degree$ C for most plants) and then decreases sharply as Enzymes denature. The effect of temperature is most pronounced at high light intensities where light Is not the limiting factor.

Water availability: Water is a reactant in the light-dependent reactions, but it is rarely a Limiting factor in practice because plants use relatively little water for photosynthesis compared To the amount lost through transpiration. However, severe drought causes stomata to close, reducing $\mathrm{CO_2$ uptake and therefore limiting photosynthesis.

Worked Example: Interpreting a photosynthesis rate graph.

A graph shows the rate of photosynthesis plotted against light intensity at two temperatures, $15\degree$ C and $30\degree$ C.

At low light intensity, both curves rise at the same rate. Light is the limiting factor at both temperatures.
The $15\degree$ C curve plateaus at a lower maximum rate than the $30\degree$ C curve. At $15\degree$ C, temperature limits the rate of enzyme-catalysed reactions (particularly RuBisCO activity).
At $30\degree$ C, the higher enzyme activity allows a higher maximum rate of photosynthesis.
If a third curve at $40\degree$ C were added, it might plateau at a similar or lower level than the $30\degree$ C curve if $40\degree$ C is close to the optimum, or it might show a lower rate if enzymes are beginning to denature.

Review: The Role of the Electron Transport Chain in Respiration

The ETC is a series of membrane-bound protein complexes and mobile electron carriers that transfer Electrons from NADH and $\mathrm{FADH_2$ to $\mathrm{O_2$ The final electron acceptor. The energy Released by electron transfer is used to pump protons across the inner mitochondrial membrane, Creating the electrochemical gradient that drives ATP synthesis.

Key points:

Electrons move through the complexes in order of increasingly positive reduction potential (each successive complex has a greater affinity for electrons).
$\mathrm{O_2$ is essential because it is the only molecule with a positive enough reduction potential to accept electrons at the end of the chain. Without $\mathrm{O_2$ Electrons back up through the chain, NADH and $\mathrm{FADH_2$ cannot be oxidised, and the Krebs cycle stops.
Some compounds that block the ETC are poisons: cyanide blocks Complex IV, rotenone blocks Complex I, and antimycin A blocks Complex III. DNP (dinitrophenol) is an uncoupler that makes the membrane permeable to protons, dissipating the gradient without producing ATP. Energy is released as heat instead.

Worked Example: Effect of cyanide on cellular respiration.

Cyanide blocks Complex IV (cytochrome c oxidase) of the ETC. When Complex IV is blocked:

Electrons cannot be passed to $\mathrm{O_2$ So the entire ETC backs up.
NADH and $\mathrm{FADH_2$ cannot be oxidised because there is no electron acceptor available.
Without NAD $^+$ regeneration, glycolysis, the link reaction, and the Krebs cycle all stop.
The proton gradient is not maintained, so ATP synthase cannot produce ATP.
The cell cannot produce ATP aerobically and must rely on fermentation (if possible), which produces only 2 ATP per glucose.
Cells with high energy demands (brain cells, heart muscle) are particularly affected, which is why cyanide is lethal even in small doses.

Worked Example: DNP as an uncoupler.

DNP (2,4-dinitrophenol) makes the inner mitochondrial membrane permeable to protons. The proton Gradient is dissipated because $\mathrm{H^+$ can flow back across the membrane without passing Through ATP synthase. The ETC continues to operate (electrons are still passed to $\mathrm{O_2$ ), And oxygen consumption increases as the cell tries to maintain the gradient, but no ATP is produced. All the energy from electron transfer is released as heat. This is the mechanism behind brown fat Thermogenesis in newborns and hibernating animals, where uncoupling proteins (UCP1) perform a Similar function. DNP was used as a weight-loss drug in the 1930s (it “burned” calories as heat) but Was banned due to dangerous side effects including fatal hyperthermia.

Review: The Compensation Point

The compensation point is the light intensity at which the rate of photosynthesis exactly equals The rate of respiration. At this point, there is no net gas exchange: all $\mathrm{CO_2$ produced By respiration is used for photosynthesis, and all $\mathrm{O_2$ produced by photosynthesis is used For respiration.

Below the compensation point: respiration exceeds photosynthesis; the plant has a net consumption of $\mathrm{CO_2$ and net release of $\mathrm{O_2$ (or more precisely, the plant takes in more $\mathrm{O_2$ than it releases).
Above the compensation point: photosynthesis exceeds respiration; the plant has a net uptake of $\mathrm{CO_2$ and net release of $\mathrm{O_2$ .

The compensation point varies among plants. Shade-tolerant plants have a lower compensation point (their rate of respiration is lower, so they need less light to compensate). Sun-loving plants have A higher compensation point.

Review: Detailed ATP Yield Calculations

Understanding the precise ATP yield from aerobic respiration requires tracking every NADH and $\mathrm{FADH_2$ molecule through the electron transport chain.

Per NADH: Approximately 10 protons are pumped into the intermembrane space. Approximately 4 Protons are needed per ATP (3 for ATP synthase + 1 for phosphate transport). So each NADH yields Approximately 2.5 ATP.

Per $\mathrm{FADH_2$ : Approximately 6 protons are pumped (electrons enter at Complex II, Bypassing Complex I). So each $\mathrm{FADH_2$ yields approximately 1.5 ATP.

Detailed accounting per glucose:

Source	NADH	$\mathrm{FADH_2$	Direct ATP	ATP from NADH	ATP from $\mathrm{FADH_2$	Total
Glycolysis	2	0	2	5	0	7
Pyruvate oxidation	2	0	0	5	0	5
Krebs cycle (2 turns)	6	2	2	15	3	20
Total	10	2	4	25	3	32

Why the actual yield may be lower:

Proton leak: Some protons leak back across the inner mitochondrial membrane without passing through ATP synthase, reducing the proton-motive force.
Cost of transport: Cytoplasmic NADH must be shuttled into the mitochondrion. The glycerol-3- phosphate shuttle produces $\mathrm{FADH_2$ (1.5 ATP) instead of NADH (2.5 ATP) in the mitochondrion, reducing the yield by 2 ATP per glucose.
Variation in proton/ATP ratio: The actual number of protons per ATP varies between organisms and tissues.

Review: Regulation of Cellular Respiration

Respiration is regulated at several key control points to match ATP production to the cell’s energy Demands.

Phosphofructokinase (PFK): The most important regulatory enzyme of glycolysis. It catalyses the Phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate (the committed step of Glycolysis).

Inhibited by: ATP (high energy signal — when ATP is abundant, glycolysis should slow down), citrate (intermediate of the Krebs cycle — signals that the cell already has sufficient intermediates for energy production).
Activated by: AMP (low energy signal — when ATP is being depleted, glycolysis should speed up), fructose-2,6-bisphosphate (a potent allosteric activator whose concentration increases when glucose is abundant).

Pyruvate dehydrogenase (link reaction): Converts pyruvate to acetyl-CoA. Inhibited by high Levels of ATP, NADH, and acetyl-CoA. Activated by high levels of ADP and pyruvate.

Isocitrate dehydrogenase and $\alpha$ -ketoglutarate dehydrogenase (Krebs cycle): Both are Inhibited by ATP, NADH, and succinyl-CoA. Both are activated by ADP and $\mathrm{Ca^{2+}$ (which Signals increased energy demand in muscle cells).

Worked Example: How a sprinter’s cells regulate respiration.

During a sprint, the muscle cells’ demand for ATP increases dramatically. ATP levels drop, AMP Levels rise, and ADP levels increase. These changes activate PFK and other regulatory enzymes, Speeding up glycolysis and the Krebs cycle. However, oxygen delivery cannot keep up with demand, so The electron transport chain cannot process all the NADH produced. The cell switches to anaerobic Respiration (fermentation) to regenerate NAD $^+$ and maintain glycolysis. Lactate accumulates, and The oxygen debt builds up.

Review: Anaerobic Respiration in Various Organisms

While most eukaryotic organisms use lactic acid fermentation or alcoholic fermentation, some Prokaryotes carry out anaerobic respiration using electron acceptors other than oxygen.

Nitrate respiration: Some bacteria use nitrate ( $\mathrm{NO_3^-$ ) as the final electron Acceptor instead of oxygen. This is denitrification, which converts nitrate to nitrogen gas ( $\mathrm{N_2$ ). Denitrifying bacteria are important in the nitrogen cycle and are found in Waterlogged, anaerobic soils.

Sulphate respiration: Sulphate-reducing bacteria use sulphate ( $\mathrm{SO_4^{2-}$ ) as the Final electron acceptor, producing hydrogen sulphide ( $\mathrm{H_2\mathrm{S$ ), which has a Characteristic “rotten egg” smell. These bacteria are found in anaerobic sediments and hot springs.

Methanogenesis: Archaea in anaerobic environments (e.g., swamps, landfill sites, the guts of Ruminants) use $\mathrm{CO_2$ as the final electron acceptor, producing methane ( $\mathrm{CH_4$ ). Methane is a potent greenhouse gas.

Review: Photophosphorylation — Linear and Cyclic

Linear (non-cyclic) photophosphorylation: The standard pathway involving both photosystems. Produces both ATP and NADPH. Water is split, and oxygen is released.

Cyclic photophosphorylation: Uses only photosystem I. Electrons from ferredoxin are returned to The cytochrome b6f complex (rather than being passed to $\mathrm{NADP^+$ ), creating a proton Gradient that drives ATP synthesis. No NADPH is produced, and no water is split (no oxygen Released).

Why cyclic photophosphorylation is important: The Calvin cycle uses more ATP than NADPH (18 ATP And 12 NADPH per glucose). Linear photophosphorylation produces ATP and NADPH in approximately equal Amounts. Cyclic photophosphorylation allows the plant to produce extra ATP without producing excess NADPH, balancing the supply to meet the Calvin cycle’s demands.

Review: Photorespiration and Its Impact

What is photorespiration? When $\mathrm{CO_2$ levels inside the leaf are low and $\mathrm{O_2$ Levels are high (e.g., on hot, dry days when stomata close to conserve water), RuBisCO binds $\mathrm{O_2$ instead of $\mathrm{CO_2$ . This produces one molecule of 3-PGA (3 carbons) and one Molecule of 2-phosphoglycolate (2 carbons). The 2-phosphoglycolate enters a salvage pathway in the Peroxisome and mitochondrion, ultimately releasing $\mathrm{CO_2$ and consuming ATP without Producing any sugar.

Impact: Photorespiration can reduce the efficiency of photosynthesis by 25—50% in C3 plants Under hot, dry conditions. It is estimated to consume approximately 25% of the carbon fixed by Photosynthesis globally.

Why RuBisCO is not more specific: RuBisCO evolved in an atmosphere with very little $\mathrm{O_2$ (and abundant $\mathrm{CO_2$ ). As photosynthesis produced $\mathrm{O_2$ over Billions of years, the $\mathrm{O_2$ concentration increased, making photorespiration inevitable. Evolution has not produced a more $\mathrm{CO_2$ -specific form of RuBisCO, possibly because any Mutation that increases specificity also decreases catalytic rate.

C4 and CAM adaptations: C4 and CAM plants have evolved mechanisms to concentrate $\mathrm{CO_2$ At the site of RuBisCO, reducing photorespiration. C4 plants use a spatial separation (mesophyll and Bundle-sheath cells); CAM plants use a temporal separation (fixing $\mathrm{CO_2$ at night).

Review: Summary Comparison Table

Process	Cellular Respiration	Photosynthesis
Purpose	Harvest energy from glucose	Build glucose from light
ETC location	Inner mitochondrial membrane	Thylakoid membrane
ETC final acceptor	$\mathrm{O_2$	$\mathrm{NADP^+$
Proton gradient site	Intermembrane space	Thylakoid lumen
ATP synthase location	Inner mitochondrial membrane	Thylakoid membrane
ATP yield per glucose	~30-32 ATP	~18 ATP consumed per glucose
Water role	Final product ( $\mathrm{H_2\mathrm{O$ )	Reactant (split for electrons)
Carbon dioxide role	Waste product	Reactant (fixed by RuBisCO)

Review: Brown Fat and Uncoupling Proteins

Brown adipose tissue (brown fat) is specialised for thermogenesis (heat production). It contains Mitochondria with uncoupling protein 1 (UCP1, also called thermogenin), which forms a channel in the Inner mitochondrial membrane that allows protons to flow back into the matrix without passing Through ATP synthase.

Mechanism:

Brown fat cells oxidise fatty acids, generating NADH and $\mathrm{FADH_2$ .
The ETC pumps protons into the intermembrane space, creating a gradient.
Instead of flowing through ATP synthase, protons flow through UCP1, dissipating the gradient as heat.
No ATP is produced; all the energy from electron transfer is released as heat.

Physiological significance: Brown fat is abundant in newborns (who have a large surface Area-to-volume ratio and cannot shiver effectively) and in hibernating animals. It helps maintain Body temperature. Adults also have small amounts of brown fat, and there is research interest in Activating brown fat as a treatment for obesity (burning calories as heat).

Review: The Role of Alternative Oxidases

Some plants and fungi possess an alternative oxidase (AOX) in their mitochondrial ETC. AOX transfers Electrons directly from ubiquinol to $\mathrm{O_2$ Bypassing Complexes III and IV. This pathway Does not pump protons, so no ATP is produced, but it does allow the ETC to continue operating when The cytochrome pathway is saturated. AOX also reduces the production of reactive oxygen species (ROS) by preventing over-reduction of the ETC.

Review: Metabolic Disorders of Energy Metabolism

Several inherited disorders affect cellular energy metabolism:

Leigh syndrome: A severe neurological disorder caused by defects in mitochondrial ETC complexes (especially Complex I or IV). Symptoms include developmental delay, muscle weakness, and respiratory Failure. Cells cannot produce sufficient ATP, particularly affecting high-energy-demand tissues like The brain.

Pyruvate dehydrogenase deficiency: Caused by mutations in the pyruvate dehydrogenase complex. Pyruvate cannot be converted to acetyl-CoA, so it accumulates and is converted to lactate (lactic Acidosis). Treatment includes a ketogenic diet (high in fats, which produce acetyl-CoA directly Through beta-oxidation, bypassing the link reaction).

Phosphofructokinase deficiency (Tarui disease): A glycogen storage disease caused by a Deficiency of muscle PFK. Affected individuals experience muscle pain and cramping during exercise Because glycolysis cannot proceed past the PFK step.

Practice Problems

Question 1: ATP yield with a mitochondrial inhibitor

A researcher adds rotenone, which blocks Complex I of the electron transport chain, to isolated Mitochondria. Pyruvate and ADP are supplied. Calculate the maximum ATP yield per glucose molecule Under these conditions, assuming 2.5 ATP per NADH and 1.5 ATP per $\mathrm{FADH_2$ . Explain which Electrons can still reach the ETC.

Answer

With Complex I blocked, NADH from glycolysis, pyruvate oxidation, and the Krebs cycle cannot donate Electrons to the ETC. However, $\mathrm{FADH_2$ from the Krebs cycle donates electrons at Complex II, which is downstream of the block. So only the $\mathrm{FADH_2$ pathway is functional.

ATP sources:

Glycolysis: 2 ATP (substrate-level). The 2 NADH from glycolysis cannot enter the ETC.
Pyruvate oxidation: 0 ATP. The 2 NADH cannot enter the ETC.
Krebs cycle: 2 ATP (substrate-level) + 2 $\mathrm{FADH_2 \times 1.5 = 3$ ATP.

Total: 2 + 2 + 3 = 7 ATP per glucose.

The 6 NADH from pyruvate oxidation (2) and the Krebs cycle (4) are unable to donate electrons Because Complex I is blocked. Only the 2 $\mathrm{FADH_2$ from the Krebs cycle can feed electrons Through Complex II to Complex III, cytochrome c, and Complex IV.

Question 2: Calvin cycle stoichiometry

How many molecules of ATP and NADPH are required to synthesise one molecule of sucrose ( $\mathrm{C_{12}\mathrm{H_{22}\mathrm{O_{11}$ ) from $\mathrm{CO_2$ ? Show your working.

Answer

Sucrose is a disaccharide of glucose + fructose, each with 6 carbons, so 12 carbons total. Each G3P Has 3 carbons, so 12/3 = 4 G3P molecules are needed. However, 3 $\mathrm{CO_2$ produce 6 G3P (5 Recycled, 1 net), so 1 net G3P requires 3 $\mathrm{CO_2$ 9 ATP, and 6 NADPH.

For 4 net G3P: 4 $\times$ 3 = 12 $\mathrm{CO_2$ 4 $\times$ 9 = 36 ATP, and 4 $\times$ 6 = 24 NADPH.

Since the cycle turns 6 times per glucose (2 G3P), for sucrose (4 G3P) it turns 12 times: 12 $\mathrm{CO_2$ 36 ATP, 24 NADPH.

Question 3: DNP and oxygen consumption

Isolated mitochondria are supplied with pyruvate, ADP, and $\mathrm{P_i$ . The rate of oxygen Consumption is measured. DNP is then added. Predict and explain the change in oxygen consumption and ATP production after adding DNP.

Answer

Oxygen consumption will increase after DNP is added. DNP is an uncoupler that makes the inner Mitochondrial membrane permeable to protons. The proton gradient is dissipated because $\mathrm{H^+$ flows back across the membrane without passing through ATP synthase. The ETC Continues to operate (electrons are still passed to $\mathrm{O_2$ ), and oxygen consumption Increases as the cell tries to maintain the gradient by pumping more protons. However, no ATP is Produced because the gradient is destroyed. All the energy from electron transfer is released as Heat. This is similar to the mechanism of brown fat thermogenesis, where uncoupling protein 1 (UCP1) Performs the same function.

Question 4: Fermentation and lactate accumulation

A runner sprints for 30 seconds. During this time, the muscle cells produce lactate at a rate of $0.5 \mathrm{ mmol/(g\cdot min)$ . If the muscle weighs $25 \mathrm{ kg$ Calculate the total moles Of lactate produced and the number of glucose molecules consumed by fermentation during the sprint.

Answer

Lactate production rate: $0.5 \mathrm{ mmol/(g\cdot min) = 0.5 \times 10^{-3} \mathrm{ mol/(g\cdot min)$ .

Muscle mass: $25 \mathrm{ kg = 25,000 \mathrm{ g$ .

Time: $0.5 \mathrm{ min$ .

Total lactate: $0.5 \times 10^{-3} \times 25,000 \times 0.5 = 6.25 \mathrm{ mol$ .

Each glucose produces 2 lactate molecules (via fermentation: 1 glucose $\to$ 2 pyruvate $\to$ 2 Lactate).

Moles of glucose consumed: $6.25 / 2 = 3.125 \mathrm{ mol$ .

Number of glucose molecules: $3.125 \times 6.022 \times 10^{23} = 1.88 \times 10^{24}$ molecules.

Question 5: Photorespiration calculation

In a C3 plant on a hot dry day, RuBisCO fixes $\mathrm{O_2$ for 20% of its reactions instead of $\mathrm{CO_2$ . If the plant fixes $1000 \mathrm{ molecules$ of $\mathrm{CO_2$ per minute, how Many molecules of $\mathrm{CO_2$ are released by photorespiration per minute? What is the net Carbon gain per minute?

Answer

If RuBisCO fixes $\mathrm{O_2$ for 20% of its reactions, then 20% of the RuBP molecules undergo Photorespiration and 80% undergo normal carbon fixation.

Total RuBisCO reactions per minute: Let this be $R$ .

Carbon-fixing reactions: $0.8R = 1000$ So $R = 1250$ .

Photorespiration reactions: $0.2R = 0.2 \times 1250 = 250$ .

For every photorespiration event, approximately 0.5 molecules of $\mathrm{CO_2$ are released (2-phosphoglycolate is partially salvaged, with a net loss of about 0.5 $\mathrm{CO_2$ per Oxygenation event).

$\mathrm{CO_2$ released by photorespiration: $250 \times 0.5 = 125$ molecules per minute.

Net carbon gain per minute: $1000 - 125 = 875$ molecules of $\mathrm{CO_2$ fixed.

Photorespiration reduces the net carbon gain by approximately 12.5% in this scenario.

Worked Examples

Example 1: Light-dependent reactions

Describe the roles of photosystems I and II in the light-dependent reactions of photosynthesis.

Solution:

Photosystem II (PSII): Absorbs light at $680\,\text{nm}$ (P680). Light energy excites electrons, which are passed to the electron transport chain. Photolysis of water replaces the lost electrons, releasing $\text{O}_2$ as a by-product.
Photosystem I (PSI): Absorbs light at $700\,\text{nm}$ (P700). Electrons from PSII (via the electron transport chain) are re-energised. These electrons are passed to NADP $^+$ along with $\text{H}^+$ ions to form NADPH.

Mark this page as reviewed