What is ATP, and what are its three parts?

Adenosine triphosphate, a nucleotide. It is made of the base adenine, the pentose sugar ribose and a chain of three phosphate groups.

Give four properties that make ATP suitable as the energy currency of cells.

Soluble, so it moves easily through the cytoplasm; stable at cell pH; cannot diffuse through membranes, so it stays where it is needed; releases a useful amount of energy when one phosphate is removed; easily regenerated from ADP.

Name three types of cell process that use energy from ATP.

Active transport across membranes; synthesis of macromolecules (anabolism), such as proteins and DNA; movement of the whole cell or of parts of it, such as chromosomes.

ATP ⇌ ADP + Pi — which direction releases energy?

Hydrolysis of ATP to ADP + Pi releases energy (water is used). Making ATP from ADP + Pi is a condensation reaction that phosphorylates ADP; it requires energy, from respiration.

How is cell respiration different from gas exchange?

Cell respiration is the release of energy from organic compounds by reactions inside cells, to make ATP. Gas exchange is the diffusion of O₂ and CO₂ across an exchange surface.

Word equations for aerobic and anaerobic respiration in humans

Aerobic — glucose + oxygen → carbon dioxide + water. Anaerobic — glucose → lactate. Both release energy used to make ATP.

Compare aerobic and anaerobic respiration in humans (four differences).

Oxygen used / not used; mitochondria needed / cytoplasm only; large / small (2) ATP yield per glucose; CO₂ and water / lactate as waste; carbohydrates or lipids / glucose only.

Why does a respirometer contain KOH or soda lime?

To absorb CO₂ released by the organisms, so any decrease in gas volume — shown by the drop moving — is due only to the oxygen used.

How do you calculate a rate of oxygen uptake from a respirometer reading?

Distance moved = start − end reading; volume = πr² × distance (r = capillary radius); rate = volume ÷ time (and ÷ mass of organisms if comparing samples). Give units such as mm³ min⁻¹.

Why is removing hydrogen from a substrate an oxidation?

A hydrogen atom contains an electron, so dehydrogenation removes electrons — and loss of electrons is oxidation. The hydrogen is accepted by NAD, which is reduced (a redox reaction).

Four stages of glycolysis and its net yield

Phosphorylation (2 ATP used), lysis (6C → two 3C), oxidation (2 NAD reduced), ATP formation (4 ATP made). Net per glucose — 2 ATP, 2 reduced NAD, 2 pyruvate. In the cytoplasm; no O₂ needed.

Why do humans convert pyruvate to lactate when oxygen is short?

To regenerate NAD. Pyruvate accepts hydrogen from reduced NAD, so NAD is available again and glycolysis can continue producing a net 2 ATP per glucose.

Anaerobic respiration in yeast and its uses

Pyruvate is decarboxylated to ethanal (releasing CO₂), then reduced to ethanol by reduced NAD, regenerating NAD. Baking uses the CO₂ to make dough rise; brewing uses the ethanol (beer, wine).

What happens in the link reaction?

In the matrix, pyruvate (3C) is decarboxylated (CO₂ removed) and oxidized (NAD reduced). The acetyl group (2C) left is attached to coenzyme A, forming acetyl CoA.

Summarize one turn of the Krebs cycle.

Acetyl (2C) + oxaloacetate (4C) → citrate (6C). Two decarboxylations (2 CO₂) and four oxidations (3 reduced NAD, 1 reduced FAD), plus 1 ATP, regenerate oxaloacetate. Two turns per glucose.

How is the proton gradient made and used in mitochondria?

Electrons from reduced NAD flow along carriers in the inner membrane, and the energy pumps protons from the matrix into the intermembrane space. Protons diffuse back through ATP synthase, which uses the energy to phosphorylate ADP (chemiosmosis).

What is the role of oxygen in aerobic respiration?

Terminal electron acceptor — it accepts electrons from the end of the chain and protons from the matrix, forming water. This keeps electrons flowing; without it the chain, link reaction and Krebs cycle stop.

Lipids vs carbohydrates as respiratory substrates

Lipids release about twice the energy per gram (less oxygen, more oxidizable C and H). Fatty acids enter as acetyl CoA, so only aerobically; carbohydrates go through glycolysis, so aerobically or anaerobically.

C1.2 Cell respiration – Interactive IB Biology

ATP: the molecule that distributes energy

SL & HLSyllabus understandings: C1.2.1 · C1.2.3

ATP and the mitochondrion in 3D

Text description of this visual

The first model is a molecule of ATP built from atoms. Adenine, a base made of a five-membered ring fused to a six-membered ring, is bonded to the ribose sugar ring. From carbon 5′ of the ribose runs a chain of three phosphate groups linked through oxygen atoms. In the hydrolysis step a water molecule splits off the third (terminal) phosphate, leaving ADP and inorganic phosphate (Pi), and energy is released. In the condensation step energy from respiration is used to join Pi back onto ADP, re-forming ATP and releasing water. The second model (AHL) is a mitochondrion cut lengthways, with an outer membrane, an inner membrane folded into cristae, an intermembrane space and a matrix. One crista is enlarged to show electron carriers and ATP synthase. Six steps show glycolysis in the cytoplasm, the link reaction and the Krebs cycle in the matrix, the electron transport chain pumping protons into the intermembrane space, chemiosmosis through a rotating ATP synthase, and oxygen accepting electrons and protons to form water.

ATP and ADP

Adenine (base): A nitrogenous base made of a six-membered ring fused to a five-membered ring. It is bonded to carbon 1′ of ribose; adenine plus ribose is called adenosine.
Ribose (pentose sugar): A five-carbon sugar whose ring contains four carbon atoms and one oxygen. Base, sugar and phosphate make ATP a nucleotide, like the monomers of RNA.
Three phosphate groups: A chain of three phosphate groups attached to carbon 5′ of ribose, linked to each other through oxygen atoms. Their negative charges make ATP soluble in water.
Terminal (third) phosphate: Only this phosphate is removed when ATP is used. Hydrolysis of the bond linking it to the rest of the molecule releases a useful amount of energy.
ADP (adenosine diphosphate): What remains when the terminal phosphate has been removed. It is recycled — respiration turns it back into ATP many times a day.
Inorganic phosphate (Pi): The phosphate released by hydrolysis. One of its oxygen atoms came from the water molecule that was split. In condensation it is joined back onto ADP.
Water: Hydrolysis uses one water molecule to split off the phosphate; condensation (making ATP) releases one water molecule.
Energy: Hydrolysis of ATP releases energy that the cell uses for work; making ATP from ADP and Pi needs an input of energy, which comes from cell respiration.

Structure of ATP. ATP (adenosine triphosphate) is a nucleotide — adenine, the five-carbon sugar ribose and a chain of three phosphate groups. It is small and soluble, so it moves easily through the cytoplasm, but it cannot cross membranes.
Hydrolysis releases energy. A water molecule is used to split off the terminal phosphate. ATP becomes ADP (adenosine diphosphate) and inorganic phosphate (Pi), and energy is released — enough for many tasks such as active transport, synthesis and movement, with little wasted.
Making ATP needs energy. Energy released by cell respiration is used to join Pi back onto ADP. This condensation reaction phosphorylates ADP, re-forming ATP, and releases a molecule of water. ATP and ADP are converted back and forth continuously.

Stages in a mitochondrion

Outer mitochondrial membrane: The outer of the two membranes. Pyruvate and fatty acids cross both membranes through transport proteins to reach the matrix.
Inner mitochondrial membrane: Contains the electron transport chain and ATP synthase. It is almost impermeable to protons except through ATP synthase, so a proton gradient can build up across it.
Crista (fold of inner membrane): Cristae are folds of the inner membrane. They give a large surface area for electron carriers and ATP synthase. This one is drawn far larger than life.
Intermembrane space: The narrow space between the two membranes, continuous with the inside of each crista. Protons are pumped into it, so its proton concentration becomes high.
Matrix: The fluid inside the inner membrane. It contains the enzymes of the link reaction and the Krebs cycle, and its own DNA and 70S ribosomes.
Cytoplasm (outside): Glycolysis happens here, outside the mitochondrion, and needs no oxygen.
Pyruvate (3C): Glycolysis converts each glucose (6C) into two pyruvate (3C). If oxygen is available, pyruvate is taken into the mitochondrial matrix.
Acetyl CoA: A two-carbon acetyl group attached to coenzyme A. Coenzyme A carries the acetyl group into the Krebs cycle and is then released to be reused.
Krebs cycle: Acetyl (2C) joins oxaloacetate (4C) to form citrate (6C). Two decarboxylations and four oxidations regenerate oxaloacetate. Two turns happen for each glucose.
Reduced NAD: NAD that has accepted hydrogen removed from a substrate (an oxidation). It carries the hydrogen and its electrons, with their energy, to the electron transport chain.
Reduced FAD: In one of the four Krebs cycle oxidations the hydrogen is accepted by FAD instead of NAD. Reduced FAD also passes electrons to the electron transport chain.
Carbon dioxide: Released by decarboxylation — once per pyruvate in the link reaction and twice per turn of the Krebs cycle, six per glucose in total. It diffuses out as a waste product.
ATP: A little ATP is made directly in glycolysis and the Krebs cycle; most is made by ATP synthase using the proton gradient (chemiosmosis).
Electron transport chain: A series of electron carriers (proteins) in the inner membrane. Electrons pass from carrier to carrier, releasing energy that is used to pump protons.
Protons (H⁺): Pumped from the matrix into the intermembrane space by the electron carriers. Their high concentration there is a store of potential energy.
ATP synthase: Protons diffuse back into the matrix through it, making part of it rotate. The rotation causes conformational changes in the head, which phosphorylates ADP to ATP.
Oxygen (O₂): The final (terminal) electron acceptor. It accepts electrons from the last carrier and protons from the matrix.
Water: Metabolic water formed when oxygen accepts electrons and protons. Removing protons from the matrix also helps keep the proton gradient steep.

Glycolysis (cytoplasm). In the cytoplasm, glucose (6C) is phosphorylated using 2 ATP and split into two 3C molecules. These are oxidized, reducing 2 NAD, and 4 ATP are made, giving two pyruvate (3C) and a net gain of 2 ATP. No oxygen is needed.
Link reaction (matrix). Each pyruvate is taken into the matrix. It is decarboxylated (CO₂ removed) and oxidized (hydrogen removed, reducing NAD), leaving a 2C acetyl group that joins coenzyme A to form acetyl CoA. This happens twice per glucose.
Krebs cycle (matrix). The acetyl group (2C) is transferred to oxaloacetate (4C), forming citrate (6C), and CoA is released. Each turn releases 2 CO₂ (two decarboxylations), reduces 3 NAD and 1 FAD (four oxidations) and makes 1 ATP. Oxaloacetate is regenerated; the second acetyl CoA waits for a second turn.
Electron transport chain (inner membrane). Reduced NAD passes a pair of electrons to the first carrier in the chain and becomes NAD again. As the electrons pass from carrier to carrier, energy is released and used to pump protons from the matrix into the intermembrane space (here, inside the crista), building a proton gradient.
Chemiosmosis (ATP synthase). Protons diffuse back down their concentration gradient into the matrix through ATP synthase, their main route across the inner membrane. Their flow turns the rotor and central stalk, and the resulting shape changes in the head join ADP and Pi to make ATP.
Oxygen accepts electrons. At the end of the chain, oxygen accepts the electrons and combines with protons from the matrix to form water (O₂ + 4e⁻ + 4H⁺ → 2H₂O). Without oxygen the chain would stop, reduced NAD could not be reoxidized and the link reaction and Krebs cycle would stop too.

Every cell needs a supply of energy for its activities, and it uses one molecule to deliver it: ATP (adenosine triphosphate). ATP is a nucleotide, made of:

the base adenine;
the five-carbon sugar ribose (adenine + ribose = adenosine);
a chain of three phosphate groups, attached to carbon 5′ of the ribose.

Why ATP suits its job

ATP works like a currency: it is made in one place and spent in many others. Its properties fit this role.

It is soluble in water, so it moves quickly through the cytoplasm to wherever it is needed.
It is stable at the pH of the cytoplasm and does not break down unless an enzyme hydrolyses it, so energy is not lost by accident.
It cannot diffuse through the phospholipid bilayer, because it is charged, so it stays in the cell, and its movement between compartments is controlled by transport proteins.
Removing one phosphate releases an amount of energy that is enough for many cell tasks, but not so much that most is wasted as heat.
It is easily regenerated from ADP. Each ATP is used and remade many times a day.

Energy transfers between ATP and ADP

Hydrolysis of ATP uses a water molecule to remove the terminal phosphate. The products are ADP (adenosine diphosphate) and inorganic phosphate (Pi), and energy is released:

ATP + H₂O → ADP + Pi (energy released)

The reverse, joining Pi to ADP, is a condensation reaction that phosphorylates ADP. It releases water and requires energy, which comes mainly from cell respiration (and in plants, also from photosynthesis):

ADP + Pi → ATP + H₂O (energy required)

You do not need to know the amount of energy in kilojoules, only that it is enough for many of the tasks a cell carries out.

What ATP is used for

SL & HLSyllabus understandings: C1.2.2

ATP supplies energy to almost every energy-requiring process in a cell. Usually an enzyme or other protein hydrolyses the ATP and uses the energy released directly, often by a conformational change (change in shape) of the protein. Three main groups of processes depend on it.

Active transport

Pump proteins in membranes use ATP to move particles against their concentration gradient. For example, the sodium–potassium pump moves three Na⁺ out of a cell and two K⁺ in for each ATP hydrolysed (see B2.1 Membranes and membrane transport).

Synthesis of macromolecules (anabolism)

Building large molecules from smaller ones by condensation reactions needs energy. ATP provides it for:

linking amino acids into proteins during translation;
making DNA and RNA from nucleotides;
building polysaccharides such as glycogen and starch from sugars.

Movement

Movement of the whole cell, such as the beating of a sperm cell’s flagellum or the crawling of a white blood cell.
Movement within cells, such as the movement of chromosomes towards the poles during mitosis and meiosis, which is done by motor proteins and microtubules of the spindle, and the transport of vesicles.
In multicellular animals, muscle contraction depends on ATP-powered movement of protein filaments.

Cells keep only a small store of ATP (in a contracting muscle, enough for just a few seconds), so respiration has to make it continuously. A resting human recycles roughly their own body mass of ATP each day.

Cell respiration produces ATP

SL & HLSyllabus understandings: C1.2.4

Cell respiration is the controlled release of energy from organic (carbon) compounds inside cells, used to make ATP. It happens in every living cell, all the time, as a series of enzyme-catalysed steps, so energy is released gradually rather than all at once as in burning.

The principal substrates are glucose (and other carbohydrates) and fatty acids (from lipids).
A wide range of other carbon compounds can also be used, including amino acids when proteins are broken down.
Only part of the energy released is captured in ATP; the rest is lost as heat, which helps keep birds and mammals warm.

Respiration is not gas exchange

Students often mix up three processes that are linked but different:

	What it is	Where
Cell respiration	Chemical reactions that release energy from organic compounds to make ATP	Inside every cell (cytoplasm and mitochondria)
Gas exchange	Diffusion of O₂ into, and CO₂ out of, an organism across a surface	Exchange surfaces, such as alveoli, gills or leaves
Ventilation	Movement of air or water over a gas exchange surface, for example breathing	Lungs, gills

Gas exchange supplies the oxygen that aerobic respiration uses and removes the CO₂ it produces (see B3.1 Gas exchange). A single-celled organism carries out respiration and gas exchange, but it does not breathe.

Aerobic and anaerobic respiration in humans

SL & HLSyllabus understandings: C1.2.5

Human cells can respire with or without oxygen. Both start in the same way, by breaking glucose down to a three-carbon compound in the cytoplasm; what happens next depends on whether oxygen is available.

	Aerobic	Anaerobic
Oxygen needed?	Yes	No
Substrates	Carbohydrates (glucose) or lipids (fatty acids)	Glucose (carbohydrate) only
Yield of ATP per glucose	Large — about 30–32	Small — 2
Waste products	Carbon dioxide and water	Lactate
Where in the cell	Cytoplasm and mitochondria	Cytoplasm only

The word equations, with glucose as the substrate, are:

Aerobic: glucose + oxygen → carbon dioxide + water
Anaerobic (humans): glucose → lactate

In both cases energy is released and used to make ATP. Mitochondria are needed for aerobic respiration but not for anaerobic respiration, so red blood cells, which have no mitochondria, rely on anaerobic respiration.

Glucose is first broken down to pyruvate in the cytoplasm. Without oxygen it is converted to lactate, still in the cytoplasm. With oxygen, pyruvate is broken down completely to carbon dioxide and water in the mitochondria, giving far more ATP.

When humans use anaerobic respiration

Anaerobic respiration produces ATP more quickly than oxygen can be delivered to the muscles, so it is used for short, intense bursts of activity such as sprinting or lifting a heavy weight. Its disadvantages are the small yield of ATP per glucose and the build-up of lactate, which lowers the pH. After the exercise, extra oxygen is needed to deal with the lactate, much of which is converted back to glucose in the liver.

Measuring the rate of respiration

SL & HLSyllabus understandings: C1.2.6

The rate of cell respiration can be measured from how fast a substrate is used or a product forms, for example:

oxygen uptake, using a respirometer (below);
carbon dioxide production, using a CO₂ sensor and data logger, or a pH indicator (CO₂ forms an acid in solution);
with yeast, the volume of gas released, or the loss in mass as CO₂ escapes.

A simple respirometer

Small organisms, such as germinating seeds or invertebrates, are sealed in a tube with a CO₂ absorber, such as potassium hydroxide (KOH) solution or soda lime. As the organisms take in oxygen and release CO₂, the CO₂ is absorbed, so the volume of gas in the tube falls by the volume of oxygen used. A drop of coloured fluid in an attached capillary tube moves towards the organisms.

Simulation Measuring the rate of respiration with a respirometer

Your tube Control tube (glass beads)

In the tube Germinating seeds Boiled (dead) seeds Glass beads only

CO₂ absorber (KOH) in the tubeTemperature: 20 °CMass of seeds: 5 gTime since the start: 5 min

Distance moved = start − end reading = 90 − 80.5 = 9.5 mm

Volume of O₂ used = πr²d = 3.14 × 0.5² × 9.5 = 7.5 mm³

Rate = 7.5 ÷ 5 min = 1.50 mm³ min⁻¹, or 0.30 mm³ g⁻¹ min⁻¹ for 5 g of seeds

The capillary has an internal radius of 0.5 mm. Move the time slider to read the scale at different times.

Show data table

Time (min)	Scale reading (mm)	Distance moved (mm)
0	90.0	0.0
1	88.1	1.9
2	86.2	3.8
3	84.3	5.7
4	82.4	7.6
5	80.5	9.5
6	78.5	11.5
7	76.6	13.4
8	74.7	15.3
9	72.8	17.2
10	70.9	19.1

Qualitative model with illustrative values: the rate roughly doubles for every 10 °C rise until enzymes begin to denature above about 40 °C. Real seeds vary, and in a real experiment a control tube is also needed to correct for changes in temperature and air pressure.

Text description of this simulation

A sealed boiling tube in a water bath contains germinating seeds resting on wire gauze above potassium hydroxide solution, which absorbs carbon dioxide. A capillary tube with a millimetre scale leads from the bung, and a drop of coloured fluid in it starts at the 90 mm mark. As the seeds take in oxygen the gas volume falls and the drop moves towards the tube. Sliders set the water-bath temperature, the mass of seeds and the time since the start; the scale reading, a graph of distance moved against time and a worked calculation update. The rate is found from distance moved, converted to a volume using πr²d, divided by time and by mass. The rate roughly doubles for each 10 °C rise up to the mid-30s °C and falls above about 40 °C. Controls with boiled seeds or glass beads show no movement, and without potassium hydroxide the drop hardly moves.

Calculating the rate

Find the distance moved by the drop: start reading − end reading.
Convert it to a volume of oxygen: volume = π r² × distance, where r is the internal radius of the capillary.
Divide by the time taken, and by the mass of organisms if you want to compare samples of different sizes.

For example, a drop that moves from 90 mm to 62 mm in 8 minutes in a capillary of radius 0.5 mm has moved 28 mm. Volume = 3.14 × 0.5² × 28 ≈ 22.0 mm³, so the rate is 22.0 ÷ 8 ≈ 2.75 mm³ O₂ min⁻¹. For 5 g of seeds this is about 0.55 mm³ g⁻¹ min⁻¹. Repeat the measurement and calculate a mean.

Variables and controls

Independent variables that can be investigated include temperature, the type or stage of organism (germinating or dormant seeds), and, with yeast, the concentration of glucose or other sugars.
Controlled variables: temperature (a water bath), mass of organisms, volume of the tube and amount of KOH.
Control: an identical tube with glass beads or boiled seeds instead of living ones. Gas volume changes with temperature and air pressure, so any movement in the control tube is used to correct the readings.
Temperature affects respiration because its steps are catalysed by enzymes: the rate rises with temperature up to an optimum and then falls as enzymes denature (see C1.1 Enzymes and metabolism).

If animals are used, choose invertebrates, keep them away from the KOH, handle them gently and return them to their habitat afterwards. KOH is corrosive, so wear eye protection.

Oxidation, reduction and NAD

AHLSyllabus understandings: C1.2.7

The energy released in respiration comes from oxidizing the substrate. Most of the oxidations in respiration do not involve oxygen at all: they remove hydrogen.

Oxidation is the loss of electrons (it can also be seen as adding oxygen or removing hydrogen).
Reduction is the gain of electrons (or removing oxygen, or adding hydrogen).

A hydrogen atom is a proton with one electron. So when hydrogen atoms are removed from a substrate — a dehydrogenation reaction — the substrate loses electrons and has been oxidized.

The electrons cannot just float free: whatever accepts them is reduced. Oxidation and reduction therefore always happen together, as redox reactions. In respiration the main acceptor is NAD (nicotinamide adenine dinucleotide), a coenzyme that carries hydrogen.

NAD + 2H → reduced NAD

(More precisely, NAD⁺ accepts two electrons and one proton, giving NADH, and the other proton is released as H⁺. At IB level you can write “reduced NAD”.)

Energy released by oxidizing the substrate is transferred to the reduced NAD. Reduced NAD carries the hydrogen, and its energy, to the electron transport chain, where it is oxidized back to NAD and can be used again. A smaller amount of hydrogen is carried by a second carrier, FAD, in the Krebs cycle.

Glycolysis

AHLSyllabus understandings: C1.2.8

Glycolysis (“sugar splitting”) is the first stage of respiration of glucose, both aerobic and anaerobic. It takes place in the cytoplasm, needs no oxygen, and turns one glucose (6C) into two pyruvate (3C) in a series of about ten small steps, each catalysed by a different enzyme. You need to know four stages but not the names of the intermediates.

Phosphorylation: two phosphate groups from 2 ATP are added to glucose, forming hexose bisphosphate. This makes the sugar less stable, so it can be split.
Lysis: the 6C hexose bisphosphate splits into two triose phosphates (3C).
Oxidation: two hydrogen atoms are removed from each triose phosphate and accepted by NAD, giving 2 reduced NAD per glucose.
ATP formation: the energy released by oxidation is used to make 4 ATP (2 from each triose phosphate) by transferring phosphate groups to ADP, and pyruvate is formed.

Net yield per glucose: 2 ATP (4 made − 2 used) and 2 reduced NAD, plus 2 pyruvate.

Aerobic respiration of one glucose, stage by stageAHL

Phosphorylation. Two ATP are used to add two phosphate groups to glucose, forming hexose bisphosphate. This makes the sugar less stable and ready to split. Each step of glycolysis is catalysed by a different enzyme.

Lysis. Hexose bisphosphate (6C) is split into two triose phosphates (3C), each with one phosphate group.

Oxidation. Two hydrogen atoms are removed from each triose phosphate (dehydrogenation). This is an oxidation, so NAD, which accepts the hydrogen, is reduced — 2 reduced NAD per glucose.

ATP formation. Energy released by the oxidation is used to make 4 ATP from ADP and phosphate (2 per triose phosphate), and pyruvate (3C) is formed. With 2 ATP used at the start, glycolysis gives a net gain of 2 ATP per glucose.

Link reaction. In the matrix, pyruvate is decarboxylated — one carbon leaves as CO₂ — and oxidized, reducing NAD. The remaining acetyl group (2C) is attached to coenzyme A, forming acetyl CoA. Per glucose this happens twice — 2 CO₂ and 2 reduced NAD.

Krebs cycle. Acetyl (2C) is transferred from CoA to oxaloacetate (4C), forming citrate (6C). Two decarboxylations release 2 CO₂, four oxidations reduce 3 NAD and 1 FAD, and 1 ATP is made, regenerating oxaloacetate. Two turns per glucose double these numbers.

Electron transport and chemiosmosis. Reduced NAD and reduced FAD give electrons to the chain and are regenerated as NAD and FAD. Energy from the electrons pumps protons into the intermembrane space; protons flow back through ATP synthase, making most of the ATP. Oxygen accepts the electrons with protons, forming water. Total yield is about 30–32 ATP per glucose (an estimate).

Text description of this animation

A step-through diagram of aerobic respiration of one glucose molecule, with gold beads showing carbon atoms. A bar at the top shows where each stage happens: cytoplasm, mitochondrial matrix or inner mitochondrial membrane. A ledger on the right keeps a running total, per glucose, of net ATP, reduced NAD, reduced FAD and carbon dioxide. By the end of the Krebs cycle the totals are 4 ATP, 10 reduced NAD, 2 reduced FAD and 6 CO₂. The electron transport chain and chemiosmosis then regenerate NAD and FAD and make most of the ATP, about 30–32 in total; the exact number is uncertain and varies between cells.

Phosphorylation. Two ATP are used to add two phosphate groups to glucose, forming hexose bisphosphate. This makes the sugar less stable and ready to split. Each step of glycolysis is catalysed by a different enzyme.
Lysis. Hexose bisphosphate (6C) is split into two triose phosphates (3C), each with one phosphate group.
Oxidation. Two hydrogen atoms are removed from each triose phosphate (dehydrogenation). This is an oxidation, so NAD, which accepts the hydrogen, is reduced — 2 reduced NAD per glucose.
ATP formation. Energy released by the oxidation is used to make 4 ATP from ADP and phosphate (2 per triose phosphate), and pyruvate (3C) is formed. With 2 ATP used at the start, glycolysis gives a net gain of 2 ATP per glucose.
Link reaction. In the matrix, pyruvate is decarboxylated — one carbon leaves as CO₂ — and oxidized, reducing NAD. The remaining acetyl group (2C) is attached to coenzyme A, forming acetyl CoA. Per glucose this happens twice — 2 CO₂ and 2 reduced NAD.
Krebs cycle. Acetyl (2C) is transferred from CoA to oxaloacetate (4C), forming citrate (6C). Two decarboxylations release 2 CO₂, four oxidations reduce 3 NAD and 1 FAD, and 1 ATP is made, regenerating oxaloacetate. Two turns per glucose double these numbers.
Electron transport and chemiosmosis. Reduced NAD and reduced FAD give electrons to the chain and are regenerated as NAD and FAD. Energy from the electrons pumps protons into the intermembrane space; protons flow back through ATP synthase, making most of the ATP. Oxygen accepts the electrons with protons, forming water. Total yield is about 30–32 ATP per glucose (an estimate).

The animation follows one glucose all the way through aerobic respiration, keeping a running total. The link reaction, Krebs cycle and electron transport chain are explained in the sections below.

Anaerobic respiration: regenerating NAD

AHLSyllabus understandings: C1.2.9 · C1.2.10

Glycolysis reduces NAD. A cell has only a small amount of NAD, so if reduced NAD is not oxidized back to NAD, glycolysis soon stops. In aerobic conditions the electron transport chain regenerates NAD. Without oxygen, cells must use pyruvate to accept the hydrogen instead.

Lactate in humans

In human cells, pyruvate accepts hydrogen from reduced NAD and is reduced to lactate (3C). This regenerates NAD, so glycolysis can continue and keep producing ATP. The net yield is 2 ATP per glucose, all from glycolysis; the lactate step itself makes no ATP.

Ethanol and CO₂ in yeast

Yeasts are single-celled fungi that can respire aerobically or anaerobically. The anaerobic pathway in yeast is the same as in humans except for how NAD is regenerated:

pyruvate (3C) is decarboxylated to ethanal (2C), releasing CO₂;
ethanal accepts hydrogen from reduced NAD and is reduced to ethanol (2C), regenerating NAD.

The net yield is again 2 ATP per glucose, but the final products differ: lactate in humans, ethanol and CO₂ in yeast.

Anaerobic respiration in humans and yeastAHL

Glycolysis needs NAD. Glycolysis turns glucose into two pyruvate, giving a net 2 ATP, but it also reduces 2 NAD. Without oxygen, reduced NAD cannot be reoxidized by the electron transport chain, so the cell's small supply of NAD would run out and glycolysis would stop.

Humans — lactate. In human cells (for example in muscles during a sprint), pyruvate is reduced to lactate (3C) by accepting hydrogen from reduced NAD. NAD is regenerated, so glycolysis can continue, with a net yield of 2 ATP per glucose. No CO₂ is produced.

Yeast — ethanol and CO₂. In yeast, pyruvate is decarboxylated to ethanal (2C), releasing CO₂. Ethanal is then reduced to ethanol (2C) by reduced NAD, regenerating NAD. The pathway is the same as in humans except for this final stage, so the products differ.

Baking and brewing. In baking, yeast in bread dough respires anaerobically; CO₂ bubbles make the dough rise and the ethanol evaporates during baking. In brewing, yeast ferments sugars, such as those from malted barley (beer) or grape juice (wine), producing ethanol; the CO₂ escapes or is kept to make the drink fizzy.

Text description of this animation

The top band shows glycolysis, which is the same in humans and yeast: glucose (6C) is converted to two pyruvate (3C), two NAD are reduced and there is a net gain of 2 ATP. A meter shows that NAD would soon run out. In human cells, such as muscle during a sprint, pyruvate accepts hydrogen from reduced NAD and becomes lactate (3C), regenerating NAD. In yeast, pyruvate is decarboxylated to ethanal (2C) and carbon dioxide, and ethanal accepts hydrogen from reduced NAD, becoming ethanol (2C) and regenerating NAD. Both give a net 2 ATP per glucose. The last step shows uses of yeast: carbon dioxide makes bread dough rise, and ethanol accumulates in beer and wine.

Glycolysis needs NAD. Glycolysis turns glucose into two pyruvate, giving a net 2 ATP, but it also reduces 2 NAD. Without oxygen, reduced NAD cannot be reoxidized by the electron transport chain, so the cell's small supply of NAD would run out and glycolysis would stop.
Humans — lactate. In human cells (for example in muscles during a sprint), pyruvate is reduced to lactate (3C) by accepting hydrogen from reduced NAD. NAD is regenerated, so glycolysis can continue, with a net yield of 2 ATP per glucose. No CO₂ is produced.
Yeast — ethanol and CO₂. In yeast, pyruvate is decarboxylated to ethanal (2C), releasing CO₂. Ethanal is then reduced to ethanol (2C) by reduced NAD, regenerating NAD. The pathway is the same as in humans except for this final stage, so the products differ.
Baking and brewing. In baking, yeast in bread dough respires anaerobically; CO₂ bubbles make the dough rise and the ethanol evaporates during baking. In brewing, yeast ferments sugars, such as those from malted barley (beer) or grape juice (wine), producing ethanol; the CO₂ escapes or is kept to make the drink fizzy.

Uses in baking and brewing

Baking: yeast (Saccharomyces cerevisiae) is mixed into bread dough. It quickly uses up the oxygen, then respires anaerobically. The CO₂ forms bubbles that make the dough rise; the small amount of ethanol evaporates during baking.
Brewing: yeast is grown in a sugary liquid without oxygen, such as grape juice for wine or a solution of sugars from malted barley for beer. The useful product is ethanol; CO₂ escapes through an airlock or is kept to make the drink fizzy. Fermentation stops when the sugar runs out or the ethanol concentration becomes toxic to the yeast (about 15% for most wine yeasts).

The link reaction and the Krebs cycle

AHLSyllabus understandings: C1.2.11 · C1.2.12

If oxygen is available, pyruvate is taken into the matrix of the mitochondrion by a transport protein.

The link reaction

Each pyruvate (3C) is changed in two ways:

decarboxylation: one carbon is removed as CO₂;
oxidation: hydrogen is removed and accepted by NAD, giving reduced NAD.

This leaves a two-carbon acetyl group, which is attached to coenzyme A (CoA), forming acetyl CoA. Lipids are broken down to acetyl groups in the matrix too, so both carbohydrates and lipids reach the Krebs cycle as acetyl CoA, and CoA transfers the acetyl group into the cycle. Per glucose, the link reaction happens twice.

The Krebs cycle

The acetyl group (2C) is transferred from CoA to oxaloacetate (4C), forming citrate (6C). CoA is released and reused.
Citrate is converted back to oxaloacetate through several intermediates (whose names you do not need). On the way there are:
- two decarboxylations, releasing 2 CO₂;
- four oxidations, all dehydrogenations: three reduce NAD and one reduces FAD;
- one reaction that makes ATP directly.
Oxaloacetate is regenerated, ready to accept another acetyl group.

Each glucose produces two acetyl groups, so the cycle turns twice per glucose.

Per glucose	Glycolysis	Link reaction	Krebs cycle	Total
CO₂	0	2	4	6
Reduced NAD	2	2	6	10
Reduced FAD	0	0	2	2
ATP (net)	2	0	2	4

So far only 4 ATP have been made, but all six carbons of glucose have left as CO₂. Most of the energy is now held by the reduced NAD and reduced FAD.

The electron transport chain and the proton gradient

AHLSyllabus understandings: C1.2.13 · C1.2.14

The electron transport chain is a series of electron carriers, mostly proteins, in the inner mitochondrial membrane. The inner membrane is folded into cristae, which give a large area for many chains and ATP synthase molecules.

Reduced NAD hands over its energy

Reduced NAD comes from glycolysis, the link reaction and the Krebs cycle. It transfers a pair of electrons (as part of its hydrogen) to the first carrier in the chain. This transfers energy to the chain and converts reduced NAD back to NAD, which returns to accept more hydrogen. Reduced FAD passes its electrons to the chain at a later point.

Pumping protons

The electrons pass from one carrier to the next. At each transfer they lose some energy, and some carriers use it to pump protons (H⁺) from the matrix into the intermembrane space.

The intermembrane space is small, so the proton concentration there rises quickly.
The inner membrane is almost impermeable to protons, so they cannot simply leak back.

The result is a proton gradient: a high H⁺ concentration in the intermembrane space and a low concentration in the matrix, with the intermembrane side also positively charged. This gradient is a store of potential energy. You do not need to know the names of the protein complexes.

Switch the 3D model to Stages in a mitochondrion to see where each stage happens; one crista is enlarged so the carriers and ATP synthase can be seen.

Chemiosmosis and the role of oxygen

AHLSyllabus understandings: C1.2.15 · C1.2.16

ATP synthase

Protons can only diffuse back into the matrix in significant numbers through ATP synthase, an enzyme that spans the inner membrane. As they flow down their concentration gradient, ATP synthase couples the energy they release to the phosphorylation of ADP:

Protons pass through the part of ATP synthase in the membrane, making it rotate, together with a central stalk.
The rotating stalk turns inside the head of the enzyme, which projects into the matrix and does not rotate.
This causes conformational changes in the active sites in the head, which bind ADP and Pi, join them to form ATP, and release it.

Making ATP using the energy of a proton gradient is called chemiosmosis. It was proposed by Peter Mitchell in 1961, against strong opposition, and became accepted as evidence built up; he was awarded the Nobel Prize in 1978. The same mechanism makes ATP in chloroplasts (see C1.3 Photosynthesis).

Oxygen as the terminal electron acceptor

At the end of the chain, the electrons, now with little energy, are passed to oxygen, the final (terminal) electron acceptor. Oxygen also accepts protons from the matrix, forming water:

O₂ + 4e⁻ + 4H⁺ → 2H₂O

Removing electrons from the end of the chain keeps them flowing, so protons keep being pumped.
Taking protons from the matrix also helps to keep the gradient steep.
The water produced is called metabolic water.

Without oxygen, electrons cannot leave the chain, so it stops. Reduced NAD can no longer be oxidized, NAD runs out and the link reaction and Krebs cycle stop too. Only glycolysis can continue, with anaerobic regeneration of NAD. This is why oxygen increases the ATP yield so much: in total, aerobic respiration gives about 30–32 ATP per glucose (the exact figure is uncertain and varies), compared with 2 ATP anaerobically.

Lipids and carbohydrates as respiratory substrates

AHLSyllabus understandings: C1.2.17

Both carbohydrates and lipids are respired, but they differ in the amount of energy they release and in the pathways they can use.

Energy per gram

Lipids release about twice as much energy per gram as carbohydrates (about 37 kJ g⁻¹ compared with about 17 kJ g⁻¹). This is because:

lipids contain much less oxygen in proportion to carbon and hydrogen (for example, a typical fatty acid such as palmitic acid, C₁₆H₃₂O₂, compared with glucose, C₆H₁₂O₆), so they are less oxidized to begin with;
they contain more oxidizable hydrogen and carbon per gram, so more hydrogen can be removed and passed to the electron transport chain.

Pathways

Carbohydrates: glucose is respired through glycolysis, so it can be used aerobically or anaerobically.
Lipids: triglycerides are first hydrolysed to glycerol and fatty acids. Fatty acids are broken into two-carbon fragments in the mitochondrial matrix, which enter as acetyl CoA, bypassing glycolysis and the link reaction. They can therefore be respired only aerobically. Glycerol, a small part of each triglyceride, can be converted into an intermediate of glycolysis.

Glucose enters respiration through glycolysis, so it can be respired with or without oxygen. Fatty acids are cut into two-carbon acetyl groups in the mitochondrion and enter as acetyl CoA, so they can only be respired aerobically. Glycerol from lipids can join glycolysis.

This explains why muscles use mainly glucose and stored glycogen during intense exercise, when oxygen is in short supply, but use more fat during long periods of steady, aerobic activity. See B1.1 Carbohydrates and lipids for lipids as energy stores and C4.2 Transfers of energy and matter for energy flow through ecosystems.