Biology  by Bradford
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IB BIOLOGY · THEME C · INTERACTION AND INTERDEPENDENCE

How a cell turns food into ATP

Right now every cell in your body is pumping, building and moving, and every one of those jobs is paid for in ATP. Respiration remakes the ATP, releasing energy from glucose and fat a step at a time. Here is how it works with oxygen and without, and how to measure it in a tube of seeds.

IB Biology C1.2SL and HL2 hours SL, 5 HL12 chaptersdry lab

Start learningRun the dry labTeach it

ribosomesDNAmitochondrionglucoseoxygencarbondioxidewaterpumpingbuildingmovingATPATPATP ribosomesDNAmitochondrionglucoseoxygencarbon dioxidewaterpumpingbuildingmovingATPATPATP
Glucose and oxygen in, carbon dioxide and water out: the mitochondrion makes ATP, and every job in the cell spends it.

01Learn

Twelve chapters, the last seven for higher level. Read one, play its figure, and make each prediction before you open the answer. The film after chapter 4 follows one glucose through a muscle cell; then try keeping a muscle cell running yourself.

  1. 1The cell's small change
  2. 2Spend it, remake it
  3. 3Fuel in, ATP out
  4. 4With oxygen and without
  5. 5A rate you cannot see
  6. 6Taking hydrogen away HL
  7. 7Two ATP in, four out HL
  8. 8Giving NAD back HL
  9. 9The carbon leaves as carbon dioxide HL
  10. 10Down the chain HL
  11. 11Protons through the turbine HL
  12. 12Fat or sugar? HL

C1.2.1 ATP as the molecule that distributes energy within cells

The cell's small change

Every cell is busy all the time: pumping ions across its membrane, building molecules, moving things about. Each of those jobs needs energy, and in every living cell the energy arrives in the same form. It is carried by one molecule, ATP.

ATP stands for adenosine triphosphate. Take the base adenine, join it to the sugar ribose and add one phosphate group, and you have a nucleotide, the same kind of unit that RNA is built from (A1.2). ATP is that nucleotide with two more phosphate groups added in a chain.

Why is this the molecule that does the job? Because of a short list of properties, each with its reason.

  • It dissolves in water, so it moves freely through the cytoplasm to wherever it is needed.
  • It is stable in the watery cytoplasm until an enzyme acts on it, so its energy is not wasted on the way.
  • Taking off one phosphate releases a modest amount of energy, enough for one step of a pump or one step in building a molecule, so little is lost as heat.
  • The phosphate can be passed on to another molecule, making that molecule more reactive.
  • Its charged phosphate groups keep it from leaking out through the membrane.
  • It is remade from ADP and phosphate quickly and endlessly, so a cell needs only a small stock.

That is why ATP is called the cell's energy currency. Like coins, it is one kind of token that every job accepts. The savings are the food molecules: glycogen, starch and fat. ATP is the small change that is actually spent, and a cell holds only enough for seconds to a minute or two of work before it has to make more (chapter 3).

Watch out ATP is not the cell's energy store. A cell keeps only a little and remakes it constantly; the stores are glycogen, starch and fat.

Removing one phosphate from ATP releases only a modest amount of energy. Why does that suit a cell?

OHOHNH2phosphateriboseadeninea nucleotide: adenine, ribose, phosphatetwo phosphates: ADPthree phosphates: ATP, adenosine triphosphateone phosphate off:a useful amount of energycharged: it staysinside the cellstable untilan enzyme actsdissolves in water:it moves anywhere in the cellremade from ADP, again and again OHOHNH2phosphateriboseadeninea nucleotide:adenine, ribose, phosphatetwo phosphates: ADPthree phosphates: ATP,adenosine triphosphateone phosphate off:a useful amountof energycharged: it staysinside the cellstable untilan enzyme actsdissolves in water:it moves anywherein the cellremade from ADP, again and again
  1. A nucleotide: adenine, ribose and one phosphate.
  2. Add a phosphate: ADP.
  3. Add another: ATP, adenosine triphosphate.
  4. What makes it the cell's energy currency.

C1.2.2 C1.2.3 What ATP pays for, and the energy it moves

Spend it, remake it

A cell gets energy out of ATP by splitting it with water. In hydrolysis, a water molecule is used to take the last phosphate group off, and ATP becomes ADP (adenosine diphosphate) and a free phosphate. Energy is released, and the cell spends it.

Where does that energy come from? Not from “breaking a high-energy bond”: breaking any bond takes energy (C1.1). ADP and phosphate together are more stable than ATP and water were, and hold less energy, so the reaction releases the difference. It is the same rule as every other reaction.

Going the other way takes energy. To remake ATP, a phosphate is joined back on to ADP and water is released. In almost every cell the energy comes from respiration (this guide), and in the chloroplasts of a plant it comes from light (C1.3). So the ATP, the ADP and the phosphate go round and round, in the ATP and ADP cycle. Only the energy flows through. No transfer of energy is perfectly efficient, so some of it spreads out as heat each time ATP is spent and each time it is remade, which is part of why you are warm.

The energy pays for three kinds of job.

  • Active transport: a pump in the membrane moves ions against their concentration gradient (B2.1).
  • Building macromolecules, anabolism: a ribosome joins amino acids into a protein, and nucleotides are joined into DNA (C1.1).
  • Movement: of the whole cell, as a sperm’s tail or a muscle fibre moves, or of parts of it, as chromosomes are pulled apart in mitosis.

The guide asks for no number of kilojoules. What matters is that the energy from one ATP is enough for one step of many different tasks, and the cell uses a great many of them every second.

Remember it What ATP pays for

  • BBuildingjoining small molecules into large ones (anabolism)
  • AActive transportpumping against the gradient
  • MMovementof the whole cell or of its parts
Watch out Energy is not “stored in the bond” between phosphates, and breaking that bond does not release energy. Breaking a bond always takes energy; the energy released by hydrolysis is the difference between ATP and water before, and ADP and phosphate after.

Remaking ATP from ADP and phosphate needs energy. Where does a muscle cell get it?

ATPADPphosphate+waterjoinshydrolysisATP splitenergyreleasedactive transportbuildingmoleculesmovementcondensationATP remaderespirationenergyinwaterleavesheatlost both ways ATPADPphosphatewaterjoinshydrolysisATP splitenergy releasedactivetransportbuildingmoleculesmovementcondensationATP remaderespirationenergy inwaterleavesheatheat
  1. ATP, ADP and phosphate: the same molecules, used again and again.
  2. Hydrolysis: water splits off the last phosphate. Energy is released for pumps, building and movement.
  3. Remaking ATP needs energy: from respiration.
  4. Spent and remade, over and over: the energy flows through, and some is lost as heat.

C1.2.4 Cell respiration as a system for producing ATP using energy from carbon compounds

Fuel in, ATP out

Cell respiration is how a cell makes ATP, using energy released from carbon compounds. It happens in every living cell, all the time, because ATP is used all the time and only a little is kept (chapter 1). That includes plants: a leaf cell respires by day and by night.

The fuels are called respiratory substrates. The main two are glucose and fatty acids, but a cell can use a wide range of carbon compounds, amino acids among them when food is short. Glycogen in liver and muscle, and starch in a plant, are broken down to glucose first.

Respiration releases the energy a step at a time, each step helped by its own enzyme at body temperature. Burning glucose is combustion. It starts with glucose and oxygen and ends with carbon dioxide and water, as respiration does, and it releases the same total energy. But combustion releases it all at once, as heat and light, and makes no ATP. One is controlled and useful to a cell, the other is not.

Respiration is not gas exchange. Respiration is chemistry inside cells. Gas exchange is oxygen and carbon dioxide diffusing across a surface, in the lungs, the gills or a leaf, with no reaction and no energy released. The carbon dioxide you breathe out was made in the mitochondria of your cells, and it only leaves through your lungs. Breathing moves the air; that is not respiration either.

The map under this chapter is the whole of respiration on one page: where each stage happens, what goes in, what comes out and where the ATP is made. Come back to it whenever a stage is new.

At higher level, chapters 6 to 12 open up each step, and each stage’s chapter starts with a small copy of the map, marking where you are.

Follow one carbon atom from the air, into a leaf and back out of a mitochondrion: the carbon trail, in C1.3.

Watch out “Respiration” in everyday English means breathing. In biology it is the chemistry that makes ATP in every cell. Breathing moves air; gas exchange moves gases across a surface; neither releases energy.
Watch out Respiration does not “make energy”. Energy is released from the fuel and transferred to ATP; none is created.

A leaf in bright light takes in carbon dioxide and gives out oxygen. Is it respiring?

Burning a fuelglucoseoxygencarbon dioxidewaterheat and lightfood on amounted needleReleased all at once, as heat and light.No ATP is made.Cell respirationa cellglucoseoxygencarbon dioxidewaterATPATPATPan enzymefor each stepenergy, step by stepReleased a step at a time, each step its own enzyme:ATP is made, and some heat.Gas exchangeair in anair sacbloodred bloodcellsoxygencarbon dioxidecarbon dioxidefrom the body's cellsDiffusion across a surface: no reaction,and no energy released. Burning a fuelglucoseoxygencarbondioxidewaterheat and lightfood ona needleReleased all at once,as heat and light.No ATP is made.Cell respirationa cellglucoseoxygencarbondioxidewaterATPATPan enzymeeach stepenergy, stepby stepReleased a step at a time,each step its own enzyme:ATP is made, and some heat.Gas exchangeair in anair sacblood:red blood cellsoxygencarbon dioxidecarbon dioxide fromthe body's cellsDiffusion across a surface:no reaction,and no energy released.

Burning: glucose and oxygen in, carbon dioxide and water out. The energy is released all at once, as heat and light, and no ATP is made.Cell respiration: glucose and oxygen in, carbon dioxide and water out. The energy is released a step at a time, each step with its own enzyme, and ATP is made.Gas exchange: oxygen diffuses from the air in an air sac into the blood, and carbon dioxide the other way. No reaction, and no energy released.

Three different things. What goes in, what comes out, and what is released?
ribosomesDNAcytoplasmmitochondrionits electronsare passed in2 pyruvatematrixinner membranefolded into cristae2 acetyl CoAglucose2 ATPnet: 2 used, 4 made2 reduced NADglycolysisno more ATPlactatein yeast: ethanoland carbon dioxideno oxygen2 carbon dioxide2 reduced NADlink reaction4 carbon dioxide2 ATP6 reduced NAD2 reduced FADKrebscyclepumps protons into theintermembrane spaceoxygenwaterelectron transportchainprotons flow backabout 26 to 28 ATPATP synthaseintermembrane spaceabout 30 to 32 ATPin all, from one glucoseribosomesDNAcytoplasmmitochondrion2 pyruvatefolded innermembraneglucose2 ATPglycolysisno more ATPlactatein yeast: ethanoland carbon dioxideno oxygen6 oxygen6 waterabout 28 to 30 more ATP6 carbon dioxidewith oxygenabout 30 to 32 ATPin all, from one glucose
Where each stage happens, what goes in and what comes out. Tap a stage to read what happens there.

C1.2.5 Differences between anaerobic and aerobic cell respiration in humans

With oxygen and without

cytoplasmmitochondrionglycolysislactateno oxygencarbon dioxidewaterabout 28 to 30 more ATPwith oxygenyou are here

Both kinds of respiration start the same way, in the cytoplasm. A glucose molecule is split into two molecules of pyruvate in a process called glycolysis, which releases enough energy to make a small amount of ATP. After that the routes divide, according to whether there is oxygen, and they differ most in their yield of ATP for each glucose.

Aerobic respiration goes on with oxygen. The pyruvate goes into a mitochondrion and is broken down completely, to carbon dioxide and water, and a large amount of ATP is made. The word equation is glucose + oxygen → carbon dioxide + water. It needs mitochondria and oxygen, and it can use fatty acids and other compounds as well as glucose.

Anaerobic respiration in humans stops early. When there is not enough oxygen, the pyruvate stays in the cytoplasm and is turned into lactate. The word equation is glucose → lactate. It needs no mitochondria, no oxygen, and makes no carbon dioxide, but only glucose can be used: fatty acids cannot be respired without oxygen.

When does a human cell respire anaerobically? When muscles work so hard that the blood cannot bring oxygen fast enough: a short sprint, a heavy lift. Anaerobic respiration gives ATP at once, without waiting for oxygen, but only for a short time. Muscles do not switch from one route to the other. Aerobic respiration goes on, and anaerobic respiration adds to it.

Why make lactate at all, rather than stopping at pyruvate? Chapter 8 explains.

A sprinter’s leg muscles run short of oxygen. Per glucose, how much ATP does anaerobic respiration make compared with aerobic?

Remember it Anaerobic in humans is LOW

  • LLactatethe waste product
  • OOnly 2 ATPper glucose
  • WWithout oxygenin the cytoplasm
Watch out Glycolysis happens in the cytoplasm in both routes; only what follows it happens in the mitochondria.
Watch out The waste product in human muscle is lactate, not carbon dioxide. People often call it lactic acid. Lactate is not what makes muscles ache the next day.
capillarycytoplasm of a muscle cellmitochondrionglucoseglycolysis2 ATP2 pyruvatewith oxygenoxygencarbon dioxidewaterATP made per glucoseabout 30 to 32one tile, one ATP (the last two dashed)2 lactatelactate into the bloodlittle oxygen: the mitochondrion can do littleATP made per glucose2, from glycolysisone tile, one ATPglucose + oxygen → carbon dioxide + waterglucose → lactate capillarymuscle cellglucoseglycolysis2 ATP2 pyruvatemitochondrionwithoxygenoxygencarbon dioxidewaterATP made per glucoseabout 30 to 32one tile, one ATP2 lactatelactate into the bloodlittle oxygen:little done hereATP made per glucose2, from glycolysisone tile, one ATPglucose + oxygen →carbon dioxide + waterglucose → lactate

Plenty of oxygen: glucose is split into two pyruvate in the cytoplasm, and the mitochondrion breaks them down to carbon dioxide and water. About 30 to 32 ATP per glucose.Not enough oxygen: the pyruvate becomes lactate in the cytoplasm and goes out into the blood. 2 ATP per glucose, from glycolysis.

One glucose in a muscle cell. Switch the oxygen supply and follow the pyruvate.
Aerobic and anaerobic respiration in humans
AerobicAnaerobic
Substratesglucose, fatty acids and other carbon compoundsglucose (carbohydrate) only
Oxygen needed?yesno
ATP per glucoseabout 30 to 322
Waste productscarbon dioxide and waterlactate
Where in the cellglycolysis in the cytoplasm, the rest in the mitochondriathe cytoplasm
Mitochondria needed?yesno
Word equationglucose + oxygen → carbon dioxide + waterglucose → lactate
Watch one glucose give up its energy in a muscle cell. Then turn the oxygen off.
oxygenwithout oxygenATPa phosphateribosomeglycogenmyofibrilglucosemitochondrionsodiumionsglucosetransporterscapillarylactate42 ATP + lactate33ADP 7about 30 ATPsodium-potassiumpumpglycolysisflow cutlactate02 ATP + lactate0ADP 40about 30 ATPsodium-potassiumpumpcapillarylactate222 ATP + lactate14ADP 26about 30 ATPsodium-potassiumpumpflow cutNADNADNADNADNADNAD= reduced NADmake lactatefree NAD: 0 of 69ADP 31no oxygen: idlesodium-potassiumpump
  1. With oxygen, glycolysis splits each glucose in the cytoplasm and its two pyruvate go into the mitochondrion: about 30 ATP in all. Without oxygen, glycolysis alone: 2 ATP and lactate.
  2. Cut the supply: how long does a working fibre's ATP last?
  3. The sprint: the oxygen cannot keep up. Where does the extra ATP come from?
  4. No oxygen and no lactate made: watch the NAD.

C1.2.6 Variables affecting the rate of cell respiration

A rate you cannot see

Respiration happens inside cells, so you cannot watch it. You measure it from what goes in or comes out: oxygen taken up, carbon dioxide given out, or fuel used. The rate of respiration is the amount changed divided by the time taken, and for living material it is given per gram per minute as well, so that samples of different mass can be compared.

A class can do it three ways.

  • Oxygen uptake in a respirometer: germinating seeds in a sealed tube, with potassium hydroxide to absorb the carbon dioxide they give out, and a drop of coloured liquid in a capillary whose movement shows the change in gas volume.
  • Carbon dioxide output: a gas sensor or data logger in a sealed chamber, or hydrogencarbonate indicator changing colour. With yeast, the rise of a dough or the gas collected over a sugar solution works too (the dry lab's dough mode).
  • Fuel used: the fall in the glucose in a yeast culture, measured with test strips.

The capillary is a long thin cylinder, so the volume of gas is πr² × the distance the drop moved, where r is half the bore. A bore of 1 mm holds 0.785 mm³ for every mm.

A second tube, the same in every way but with glass beads in place of the seeds, is the control. Anything that moves its drop, such as the gas warming or cooling or the air pressure changing, is not respiration, so its movement is taken off the seeds’.

What changes the rate? Temperature: respiration is enzymes at work, so it speeds up as it warms until they begin to denature (C1.1). How far germination has gone: dry seeds hardly respire, and soaked ones respire more each day. The mass of the seeds, and the kind of seed. With yeast: the sugar it is given, the temperature, and how much oxygen there is. The seeds are kept in the dark so that they cannot photosynthesise and hide the gas changes.

In an experiment on any of these, the one thing you change on purpose is the independent variable (the temperature, say), the rate you measure is the dependent variable, and everything else you hold the same is a controlled variable: the mass and age of the seeds, the volume of the tube, the time. You may also be asked to work out a rate from someone else’s numbers: the steps are the same (figure 5.2).

Watch out The drop does not move because the seeds give out carbon dioxide: that is removed. It moves because of what the seeds take up.
Watch out Germinating seeds are not “breathing”. They have no lungs; their cells respire, and the gases cross their surfaces by diffusion.

In the respirometer the seeds respire and the potassium hydroxide absorbs their carbon dioxide. Which way does the drop move?

water baththermometergerminatingseedsglass beads:the controlwire gauzepotassiumhydroxidebung andscrew clipcapillary and coloured drop0100200mmscale thermometerwater bathgerminatingseedsglass beads:the controlwire gauzepotassiumhydroxidebung andscrew clipcapillary and coloured drop0100200scale, mm

Tap a part of the respirometer.

Try it on the bench The dry lab has this respirometer set up and ready: run it, take readings and work out the rate.

germinating seeds, 3.0 g010203040mm24 mmdrop at 0 minat 4 minglass beads: the control010203040mm2 mmcorrected distance = 24 − 2 = 22 mmvolume = π r2 × distance = 3.14 × 0.52 × 22 = 17.3 mm3rate = 17.3 mm3 ÷ 4 min ÷ 3.0 g = 1.44 mm3 g−1 min−1a bore of 1 mm, so r = 0.5 mm germinating seeds, 3.0 g010203040mm24 mmglass beads: the control010203040mm2 mmdrop at 0 minat 4 mincorrected distance = 24 − 2 = 22 mmvolume = π r2 × distance= 3.14 × 0.52 × 22 = 17.3 mm3rate = 17.3 mm3 ÷ 4 min ÷ 3.0 g= 1.44 mm3 g−1 min−1a bore of 1 mm, so r = 0.5 mm
  1. Read both drops at the start and the end.
  2. Take off the control’s movement.
  3. Turn distance into volume with the bore.
  4. Divide by time and by mass.

C1.2.7 Role of NAD as a carrier of hydrogen, and oxidation by removal of hydrogen

Taking hydrogen away

In respiration, energy is released from fuel molecules by taking hydrogen off them. To see why, you need two words. Oxidation is the loss of electrons, and reduction is the gain of electrons. They always happen together: what one molecule loses, another gains. A reaction that does both is a redox reaction.

A hydrogen atom is a proton and an electron. So when hydrogen is removed from a molecule, which is called dehydrogenation, it loses electrons too, and has been oxidised. The enzymes that do it are dehydrogenases.

The hydrogen has to go somewhere. It is accepted by NAD, a molecule built from nucleotides, like ATP. When NAD accepts hydrogen it is reduced, and is then called reduced NAD. Reduced NAD carries the hydrogen, and the energy that comes with it, to where it is used (the electron transport chain, chapters 10 and 11), and is turned back into NAD there. So NAD is a hydrogen carrier.

A cell has only a little NAD, so it must be unloaded and used again and again, as ATP is. Every stage of respiration that follows either loads NAD or depends on NAD being given back (chapter 8).

Why does it matter? A large part of the energy in a fuel is in its hydrogen and the electrons that go with it. Respiration is, step by step, taking hydrogen off the fuel and passing it to oxygen: that is the role of hydrogen, and of oxygen, in the release of energy.

Remember it Oxidation and reduction

  • OilOxidation Is Lossof electrons
  • RigReduction Is Gainof electrons
Watch out Reduced NAD carries hydrogen, protons and electrons together, and the energy that comes with them. It is not ATP and it is not “energy” itself.

A dehydrogenase takes two hydrogens off a molecule of fuel. What has happened to that molecule?

hydrogen atomprotonelectronsubstrate(fuel)active sitedehydrogenase (an enzyme)NAD:a hydrogen carrierNADNADtwo hydrogens:protons and electronsNADoxidised: lost electronsreduced NAD:gained electronsNADreduced NAD,to the chainNADNAD comes backfor more hydrogen atomprotonelectronsubstrate(fuel)dehydrogenase (an enzyme)its active site holds the fuelNAD:a hydrogencarrierNADNADtwo hydrogens:protons and electronsNADoxidised:lost electronsreduced NAD:gained electronsNADreduced NAD,to the chainNADbackfor more
  1. A substrate, an enzyme, and NAD.
  2. Hydrogen is removed: dehydrogenation. Each hydrogen is a proton and an electron.
  3. The substrate is oxidised; NAD is reduced. A redox reaction.
  4. Reduced NAD carries the hydrogen away, and NAD comes back for more.

C1.2.8 Conversion of glucose to pyruvate in glycolysis, with a net yield of ATP and reduced NAD

Two ATP in, four out

cytoplasmmitochondrionreduced NAD and FADcarried to the chainglycolysislactateno oxygenlink reactionKrebs cycleelectrontransportchainyou are herecytoplasmmitochondrionglycolysislactateno oxygencarbon dioxidewaterabout 28 to 30 more ATPwith oxygenyou are here

Glycolysis turns one glucose into two pyruvate, in the cytoplasm, in about ten steps. Each step has its own enzyme, and the product of one step is the substrate of the next: it is a metabolic pathway (C1.1). The guide groups the steps into four stages, and you do not need to name the molecules in between.

  • Phosphorylation: two ATP each give a phosphate group to the glucose. That costs 2 ATP, but a sugar carrying two charged phosphates is made reactive and ready to split.
  • Lysis: the 6-carbon sugar with its two phosphates splits into two 3-carbon sugars, each with one phosphate.
  • Oxidation: hydrogen is taken off each 3-carbon sugar and accepted by NAD, so two reduced NAD are made for the glucose. The energy released lets each 3-carbon sugar take on a second phosphate, a free one from the cytoplasm, not one from ATP.
  • ATP formation: each 3-carbon sugar passes its two phosphates to ADP, making ATP directly, and ends as pyruvate.

Glycolysis spends 2 ATP at the start. How many does it make by the end, from one glucose?

Remember it The four stages of glycolysis, in order

  • PenguinsPhosphorylation2 ATP spent
  • LoveLysis6 carbons split into 3 and 3
  • OrangeOxidationhydrogen to NAD
  • AnchoviesATP formation4 ATP made
Watch out Glycolysis does not need oxygen, and it does not happen in the mitochondrion.
In the cytoplasmcarbonphosphatehydrogenan enzyme: each step has its own1 Phosphorylation2 Lysis3 Oxidation4 ATP formationglucose6 carbons2 ATP2 ADP6C sugar withtwo phosphates3C sugarphosphateNADreduced NADNADreduced NADfreephosphate3C sugar withtwo phosphates2 ADP2 ATP2 ADP2 ATPpyruvate3 carbons12345667891078910ATP spent2reduced NAD made2ATP made4net gain2 ATP In the cytoplasmcarbonphosphatehydrogenan enzyme: each step has its ownglucose6 carbons1 Phosphorylation2 ATP2 ADP6C sugar withtwo phosphates2 Lysistwo 3C sugarphosphates3 Oxidation2 NAD2 reduced NADfreephosphatetwo 3C sugars,2 phosphates each4 ATP formation4 ADP4 ATPtwo pyruvate3 carbons each12345678910ATP spent2reduced NAD2ATP made4net gain2
  1. One glucose, in the cytoplasm.
  2. Phosphorylation: 2 ATP spent, the sugar made reactive.
  3. Lysis: split into two 3-carbon sugars.
  4. Oxidation: hydrogen to NAD, making 2 reduced NAD.
  5. ATP formation: 4 ATP made, so 2 gained.
  6. Ten steps, each with its own enzyme: two pyruvate, on to the link reaction.

C1.2.9 C1.2.10 Lactate and ethanol as ways of regenerating NAD, and brewing and baking

Giving NAD back

cytoplasmmitochondrionreduced NAD and FADcarried to the chainglycolysislactateno oxygenlink reactionKrebs cycleelectrontransportchainyou are herecytoplasmmitochondrionglycolysislactateno oxygencarbon dioxidewaterabout 28 to 30 more ATPwith oxygenyou are here

Glycolysis needs NAD. Every glucose that goes through it turns two NAD into reduced NAD. A cell has only a little NAD, so if reduced NAD is not turned back into NAD, glycolysis stops very quickly. Giving NAD back is called the regeneration of NAD.

With oxygen, reduced NAD is unloaded at the electron transport chain in the mitochondrion (chapters 10 and 11). Without oxygen it cannot be, so a cell needs another way to give NAD back.

In human muscle, pyruvate takes the hydrogen from reduced NAD and becomes lactate. NAD is given back, so glycolysis can go on, with a net yield of 2 ATP per glucose. Making lactate releases no extra energy: its whole point is to give NAD back.

Yeast follow the same pathway as far as pyruvate. Without oxygen, each pyruvate loses a carbon as carbon dioxide, and what is left takes the hydrogen from reduced NAD to become ethanol. NAD is given back, and the yield is again 2 ATP per glucose. Only the last step differs from humans, and so the final products do.

Bakers and brewers use what yeast make. In baking, yeast respire the sugars in the dough and the carbon dioxide forms bubbles that stretch it, so the dough rises; the ethanol evaporates in the oven. In brewing, yeast in a sugary liquid made from barley or grapes, with little air, make ethanol, which is kept, while the carbon dioxide escapes or is kept in for fizz. Early in a dough or a brew there is oxygen and the yeast respire aerobically, so carbon dioxide is given off from the start; as the oxygen runs out, anaerobic respiration takes over. Anaerobic respiration in yeast is often called fermentation.

Without oxygen, why does a muscle cell turn pyruvate into lactate instead of leaving it as pyruvate?

Watch out Yeast without oxygen make ethanol and carbon dioxide, not lactate; humans make lactate, not ethanol or carbon dioxide.
Watch out Lactate is not a poison that must be got rid of straight away. It is carried in the blood and later used as a fuel, or made back into glucose in the liver.
glucoseglycolysisnet 2 ATP2 pyruvateNAD in the cellNADNADNADNADNADNADreduced NADreduced NAD piles upreduced NADreduced NADreduced NADreduced NADreduced NADreduced NADNothing gives NAD back, so the store runs dryand glycolysis stops: no more ATP.NADNAD back to the store: glycolysis goes on2 lactatebloodMuscle: pyruvate becomes lactate, in the cytoplasm.Lactate is carried away in the blood; no extra ATP.2 CO22 ethanolbaking: carbon dioxidemakes the dough risebrewing: the ethanolis keptYeast: pyruvate loses a carbon as carbon dioxide, and ethanol is left. glucoseglycolysisnet 2 ATP2 pyruvateNAD in the cellNADNADNADNADNADNADreduced NADreduced NAD piles upreduced NADreduced NADreduced NADreduced NADreduced NADreduced NADNothing gives NAD back, so the storeruns dry and glycolysis stops:no more ATP.NADNAD back to the store:glycolysis goes on2 lactatebloodMuscle: pyruvate becomes lactate,in the cytoplasm. Lactate is carriedaway in the blood; no extra ATP.2 ethanol2 CO2baking: carbon dioxidemakes the dough risebrewing: the ethanolis keptYeast: pyruvate loses a carbon ascarbon dioxide, and ethanol is left.

Glycolysis alone: each glucose turns two NAD from the store into reduced NAD. Nothing gives NAD back, so the store runs dry and glycolysis stops.Muscle: pyruvate takes the hydrogen from reduced NAD and becomes lactate. NAD goes back to the store, so glycolysis goes on.Yeast: pyruvate loses a carbon as carbon dioxide, and what is left takes the hydrogen from reduced NAD, becoming ethanol. NAD goes back to the store.

Glycolysis with no oxygen. Watch the NAD in the store, then see what each cell does about it.

C1.2.11 C1.2.12 The link reaction, and the Krebs cycle

The carbon leaves as carbon dioxide

With oxygen, pyruvate is carried from the cytoplasm into the matrix, the fluid inside the inner membrane of the mitochondrion. Two sets of reactions follow, one after the other.

The link reaction links glycolysis to the Krebs cycle. Each pyruvate (3C) is decarboxylated, which takes a carbon off as carbon dioxide, and oxidised: hydrogen is removed and accepted by NAD. The 2-carbon acetyl group that is left is picked up by coenzyme A and carried to the cycle. Fatty acids and other carbohydrates are also broken down to acetyl groups, which join the same route (chapter 12). All of this happens twice for each glucose, once for each pyruvate.

In the Krebs cycle, the acetyl group is transferred to oxaloacetate (4C) to make citrate (6C). Round the cycle the compound is oxidised four times, each a dehydrogenation: three load NAD, and one loads FAD, another hydrogen carrier, as reduced FAD. One ATP is made. Then oxaloacetate is remade, ready for the next acetyl group, and the cycle turns twice for each glucose: 4 carbon dioxide, 6 reduced NAD, 2 reduced FAD and 2 ATP in all.

Each turn of the Krebs cycle takes in a 2-carbon acetyl group. Why does the cycle not fill up with carbon?

Glycolysis and the Krebs cycle sit beside the Calvin cycle on one map in C1.3.

Watch out The Krebs cycle makes little ATP directly, only one a turn. Its main product is reduced NAD, which the chain turns into most of the ATP.
Watch out Citrate is made from oxaloacetate and the acetyl group, not from glucose, and the cycle’s carbon dioxide comes from the fuel’s carbon, not from the oxygen breathed in.
cytoplasmmatrixintermembrane spaceinside a mitochondrionpyruvate3CCO2NADreduced NADCoAacetyl CoA2C acetyl groupLink reactionoxaloacetate4Ccitrate6C5C4C4C4CNADreduced NADNADreduced NADADPATPFADreduced FADNADreduced NADCO2CO2Krebs cycletwo turns a glucosefor one pyruvatefor one glucoselinkKrebscarbon dioxide1224reduced NAD1236reduced FAD0012ATP0012 inside a mitochondrioncytoplasmintermembrane spacematrixpyruvate (3C)Link reactionCO2NADreduced NADCoAacetyl CoA2Coxaloacetate4Ccitrate6CreducedNADreducedNADATPreducedFADreducedNADCO2CO25C4C4C4CKrebscyclefor one pyruvatefor one glucoselinkKrebscarbon dioxide1224reduced NAD1236reduced FAD0012ATP0012
  1. Pyruvate goes into the matrix.
  2. Link reaction: a carbon off as CO2 (decarboxylation), hydrogen to NAD (oxidation). The acetyl group goes on with coenzyme A.
  3. Acetyl (2C) + oxaloacetate (4C) → citrate (6C).
  4. Round the cycle: two decarboxylations, four oxidations (three to NAD, one to FAD), one ATP.
  5. Oxaloacetate is remade: a cycle.
  6. Two turns per glucose: all six carbons gone as CO2.
Eight steps to sortWhich kind of reaction is each step? What is lost or gained?Hydrogen removed from a3-carbon sugar in glycolysisNAD accepts hydrogen andbecomes reduced NADA carbon leaves pyruvate ascarbon dioxideGlucose gains a phosphate fromATPHydrogen removed from acompound in the Krebs cycleOxygen accepts electrons at theend of the chainCitrate loses a carbon ascarbon dioxide, on the wayround the cycleADP gains a phosphate, makingATPOxidationReductionDecarboxylationPhosphorylation

Pick a step (tap it, or Tab to it and press Enter), then pick the bin it belongs in.

0 of 8 sorted

Name the reaction: eight steps of respiration and four kinds of reaction. Which bin does each belong in, and what tells you?

C1.2.13 C1.2.14 Reduced NAD and the electron transport chain; the proton gradient

Down the chain

cytoplasmmitochondrionreduced NAD and FADcarried to the chainglycolysislactateno oxygenlink reactionKrebs cycleelectrontransportchainyou are herecytoplasmmitochondrionglycolysislactateno oxygencarbon dioxidewaterabout 28 to 30 more ATPwith oxygenyou are here

Reduced NAD is made in three places: glycolysis, the link reaction and the Krebs cycle. The electrons they carry all end up at the inner membrane of the mitochondrion, which is folded into cristae to give room for many copies of what happens there.

In that membrane sits the electron transport chain: a series of electron carriers, some of them proton pumps. A pair of electrons is passed from reduced NAD to the first carrier, and the reduced NAD is turned back into NAD, which goes back for more hydrogen. That is the transfer of energy. Reduced FAD from the Krebs cycle hands its electrons on too, one carrier further along, so it pumps fewer protons.

The electrons are passed from carrier to carrier, each holding them a little more tightly than the one before, so they always move on and never go back. A little energy is released at each step, like a ball dropping down a staircase. Oxygen, at the very end, holds them most tightly of all (chapter 11). You do not need to name the carriers: “the chain” and “proton pumps” are enough.

The pumps use that energy to move protons (hydrogen ions) from the matrix, across the inner membrane, into the narrow intermembrane space. They pile up there, so there are far more protons in the space than in the matrix: a proton gradient. The membrane does not let them leak back, so the gradient is a store of energy, like water held behind a dam. Chapter 11 lets it out.

Watch out The chain does not make ATP; it makes a proton gradient. And “proton” here means a hydrogen ion, not a hydrogen atom.

Electrons pass along the chain of carriers, releasing a little energy at each step. What is that energy used for?

proton (a hydrogen ion)electrona small electron carrierouter membraneintermembrane spaceinner membranematrixreduced NADfrom glycolysisNADunloaded: NAD againreduced NADfrom the link reactionreduced NADfrom the Krebs cycleto oxygen(chapter 11)reduced FADfrom the Krebs cycleproton pumpsmany protons: a proton gradientfew protons in the matrix proton (a hydrogen ion)electrona small electron carrierouter membraneintermembrane spaceinnermembranematrixreducedNADfromglycolysisNADunloaded:NAD againreducedNADfrom thelink reactionreducedNADfrom theKrebs cycletooxygenreducedFADfrom the Krebs cycleproton pumpsmany protons:a proton gradientfew protonsin the matrix
  1. Reduced NAD from all three stages arrives at the inner membrane.
  2. It hands a pair of electrons to the first carrier, and becomes NAD again.
  3. Each step down releases a little energy, used to pump protons. Reduced FAD hands its electrons on one carrier later.
  4. Protons pile up in the intermembrane space: a proton gradient.

C1.2.15 C1.2.16 Chemiosmosis and ATP synthesis; oxygen as the terminal electron acceptor

Protons through the turbine

Protons can return to the matrix through one protein only: ATP synthase. It spans the inner membrane, with a channel through it, a part that turns, and a head in the matrix where ATP is made.

As protons flow down their gradient through the channel, they turn the rotor. The turning changes the shape of the head, which joins ADP and phosphate into ATP. ATP synthase couples the energy released by the flow of protons to the phosphorylation of ADP. Making ATP with the energy of a proton gradient across a membrane is called chemiosmosis. (Biochemists call the chain and the synthase together oxidative phosphorylation.)

The chain needs one more thing at its end. Oxygen is the terminal electron acceptor: it takes the electrons from the last carrier, and protons from the matrix, and becomes water, called metabolic water. That empties the chain so that electrons keep flowing, and taking protons from the matrix helps to keep the gradient steep. About 26 to 28 of the 30 to 32 ATP from one glucose are made here, by ATP synthase.

So ATP is made in two ways. A little is made directly, in glycolysis and the Krebs cycle, when a phosphate is passed from a substrate to ADP: substrate-level phosphorylation. The rest is made by ATP synthase, with energy brought to the chain by the carriers: about 2.5 ATP for each reduced NAD and 1.5 for each reduced FAD. The ledger after the film adds it up, stage by stage.

How we know (beyond the guide) In 1961 Peter Mitchell suggested that the chain and the making of ATP were linked by a gradient of protons, not by some unknown high-energy chemical. Most biochemists doubted it for years. Experiments in the 1960s and 1970s, in which membranes given an artificial proton gradient made ATP, won them over, and he received the Nobel Prize in Chemistry in 1978.
Watch out ATP synthase is not a pump: protons flow through it, down their gradient, and that flow drives it. The pumps are in the chain.
Watch out Oxygen does not become carbon dioxide. It ends up in water. The carbon dioxide came from the fuel’s carbon, in the link reaction and the Krebs cycle.

A cell’s mitochondria run out of oxygen. What happens to the electron transport chain?

proton (a hydrogen ion)electronintermembrane spaceouter membranematrixATP synthaseADPphosphateATPoxygenwaterreduced NADchemiosmosisthe gradient drives ATP synthase:about 26 to 28 ATP a glucose proton (a hydrogen ion)electronouter membraneintermembrane spaceATP synthasematrixADPphosphateATPoxygenwaterreducedNADchemiosmosisthe gradient drivesATP synthaseabout 26 to 28ATP a glucose
  1. One way back for the protons: ATP synthase.
  2. Protons flowing down the gradient turn it, and their energy joins ADP and phosphate: ATP.
  3. Oxygen takes the electrons and protons at the end, making water.
  4. Chemiosmosis: the gradient makes ATP, and oxygen keeps the chain flowing.
Watch the protons pile up, then turn the oxygen off and see what stops first.
substrate-levelphosphorylationATP made directlycarried tothe chainoxidativephosphorylationthrough ATP synthasein all4 ATP10 reduced NAD2 reduced FADabout 26 to 28 ATPabout 30 to 32 ATPfrom one glucose, with oxygencytoplasm2 ATPnet: 4 made, 2 used2 reduced NADabout 3 to 5 ATP1.5 to 2.5 eachglycolysismatrixnone2 reduced NADabout 5 ATPabout 2.5 eachlink reactionmatrix2 ATP6 reduced NADabout 15 ATPabout 2.5 each2 reduced FADabout 3 ATPabout 1.5 eachKrebs cycleGlycolysis makes its reduced NAD in the cytoplasm, and passing its electrons into themitochondrion can cost some of their worth. Older books say 36 to 38 ATP: they count 3a reduced NAD and 2 a reduced FAD.
Every stage against the ATP it makes, directly or through the chain. Tap a stage to see it on the map.

C1.2.17 Differences between lipids and carbohydrates as respiratory substrates

Fat or sugar?

Glucose and fatty acids are the two main fuels, and they are not equal. Lipids release about twice as much energy per gram as carbohydrates when they are respired: about 37 kJ in each gram against about 17.

They also take different routes. Carbohydrate goes through glycolysis, so it can be respired with oxygen or without. A fatty acid is cut into 2-carbon acetyl groups, which enter the Krebs cycle at once as acetyl CoA (acetyl coenzyme A). Glycolysis is the one stage that works without oxygen, and a fatty acid never goes through it: no oxygen, no use for fat.

In practice, muscles use fat for long, steady work, such as walking, a gentle jog or a migrating bird in flight, and carbohydrate for hard, fast work, when oxygen is short. That is why fat is the long-term store and glycogen the quick one (B1.1).

Gram for gram, fat releases about twice the energy of carbohydrate when respired. Why?

Watch out Fat cannot be used anaerobically: fatty acids enter at the Krebs cycle, which needs the chain, which needs oxygen. A sprint runs on carbohydrate.
OHOHHOHOHHHHOHCH2OHOHOglucosepalmitic acid, a fatty acidBy massC 40%H 7%O 53%C 75%H 13%O 12%carbonhydrogenoxygenEnergy released when a gram is respiredcarbohydrateabout 17 kJ g−1lipidabout 37 kJ g−1mitochondrioncytoplasmglucoseglycolysispyruvateno oxygen: lactate2 ATPlinkCoAacetyl CoAfatty acidno oxygen: no routefat never enters glycolysiscut into 2Cacetyl groups8 from palmitic acidKrebs cycleand the chainoxygenneededOxygen used to respire a gramcarbohydratelipidabout 2.7 times as much OHOHHOHOHHHHOHCH2OHOHOglucoseBy massC 40%H 7%O 53%palmitic acid, a fatty acidC 75%H 13%O 12%carbonhydrogenoxygenEnergy released when a gram is respiredcarbohydrate: about 17 kJ g−1lipid: about 37 kJ g−1cytoplasmglucoseglycolysispyruvateno oxygen:lactate, 2 ATPfatty acidno oxygen:no route: itnever entersglycolysismitochondrionlinkCoAacetyl CoAcut into 2Cacetyl groups8 from palmitic acidKrebs cycleand the chainoxygen neededOxygen used to respire a gramcarbohydratelipidabout 2.7 times as much

What is in them: glucose is about half oxygen by mass, palmitic acid about one eighth. A gram of lipid releases about 37 kJ, a gram of carbohydrate about 17.How they are respired: glucose goes through glycolysis in the cytoplasm, so it has a route without oxygen. A fatty acid is cut into acetyl groups in the mitochondrion, which needs oxygen. A gram of lipid uses about 2.7 times as much oxygen.

Glucose and a fatty acid, side by side: what they are made of, and how each is respired.
Every stage in one film. Switch the fuel to a fatty acid, or the cell to yeast, then cut the oxygen.
ribosomesDNAcytoplasmmitochondrionits electronsare passed in2 pyruvatematrixinner membranefolded into cristae2 acetyl CoAglucose2 ATPnet: 2 used, 4 made2 reduced NADglycolysisno more ATPlactatein yeast: ethanoland carbon dioxideno oxygen2 carbon dioxide2 reduced NADlink reaction4 carbon dioxide2 ATP6 reduced NAD2 reduced FADKrebscyclepumps protons into theintermembrane spaceoxygenwaterelectron transportchainprotons flow backabout 26 to 28 ATPATP synthaseintermembrane spaceIn all, from one glucoseglucose + oxygencarbon dioxide + wateraerobic respirationabout 30 to 32 ATPglucoselactateanaerobic, in humans2 ATPglucoseethanol + carbon dioxideanaerobic, in yeast2 ATPribosomesDNAcytoplasmmitochondrion2 pyruvatefolded innermembraneglucose2 ATPglycolysisno more ATPlactatein yeast: ethanoland carbon dioxideno oxygen6 oxygen6 waterabout 28 to 30 more ATP6 carbon dioxidewith oxygenIn all, from one glucoseglucose + oxygencarbon dioxide + wateraerobic respirationabout 30 to 32 ATPglucoselactateanaerobic, in humans2 ATP
The whole map again, with the word equations and the totals. Tap a stage to go over it.

02Dry lab: Respirometer: seeds and dough

Germinating seeds in a sealed tube use oxygen, and a coloured drop creeps along a scale as they do. Change one thing, read the drop each minute, and work out how fast the seeds respire. Or switch to dough and race five sugars.

Your questionHow does one factor change the rate at which germinating seeds take up oxygen? Start with temperature. Then try the dough: which sugar makes yeast respire fastest?
What you can changeOne independent variable at a time: the water bath's temperature, how long ago the seeds were soaked, the mass of seeds, or whether the potassium hydroxide is in. In dough mode, the sugar. Everything else stays fixed unless you change it on purpose.
What to recordThe drop's position on the scale every minute, in mm, for the seeds and for the glass-bead tube beside them. Then the rate in mm³ of oxygen per gram per minute, three or more trials at each value, a mean and a standard deviation, and a graph. The coach under the bench helps you plan, process and evaluate.
glucosefructosesucrosestarch050100150none30 °C0:00min : s050100150200050100150200coloured dropstart25 °C2.03 g0:00min : sbalanceclockseedsglass beadsseedsglass beads12341capillary2screw clip3potassium hydroxide4wire gauzepotassium hydroxide is corrosivethe bath is under a dark cover
  1. Yeast dough: five tubes, one sugar in each, read against a ruler every 5 minutes.
  2. Germinating seeds over potassium hydroxide, with a glass-bead tube beside them as the control. Both drops sit at the start mark: read each one every minute.
Run it on the page: set it up, press Start, read the drops each minute, and the table and graph fill in.

IA coach

Write it up as an investigation

Your results from this dry lab can be written up the way an IB scientific investigation is: four criteria, each worth 6 marks. Tick each line as your write-up does it. The coach on the page checks these as you go; it never gives a mark.

1 Research design

A focused question set in its biology; your choices of what to measure, how, over what range and how often, explained rather than listed; what you kept the same and how; safety, ethics and the environment; a method someone else could follow and repeat.

  • My question names what I changed.
  • It gives the range I used, with units.
  • It names what I measured and how.
  • It names the organism or system.
  • My background explains, with the biology, why the two should be linked.
  • I cite my sources, and each reference can be traced.
  • If I give a hypothesis, it predicts and explains.
  • Every variable has its How, Why and Units.
  • For each thing kept the same, I say how I kept it so.
  • I list at least three things I kept the same.
  • I name the apparatus that set what I changed, and the instrument that measured.
  • I test enough values.
  • My values spread wide enough.
  • I run at least three trials at every value.
  • I run a control.
  • I explain why these values, this many and this often.
  • Someone else could repeat my method.
  • I deal with safety, ethics and the environment.

2 Data analysis

Raw data recorded clearly, with titles, units, uncertainties and the same decimal places down a column; what you saw as well as what you measured; processing that suits the question, shown with a worked example; the spread shown; a graph a reader can trust.

  • Each table has a numbered title that says what it shows.
  • Every heading has its quantity and its unit.
  • Every raw data heading has its uncertainty.
  • Each uncertainty is realistic for the instrument.
  • Each uncertainty has the same decimal places as its readings.
  • I record what I saw as well as what I measured.
  • I show one worked example of my processing, and it is right.
  • I say why I left out any trial.
  • My error bars show a spread my repeats can support.
  • My graph has a numbered title and labelled axes with units.
  • I say what the error bars show.
  • A straight line, if I draw one, has its R².
  • A statistical test, if I run one, has its hypotheses and suits the data.

3 Conclusion

Your question answered from the processed data, with numbers quoted and the spread taken into account; the biology that explains the pattern; a comparison with published work; no claim bigger than the data.

  • I answer my question in a sentence, naming both variables.
  • I quote my processed numbers.
  • I say how sure the spread lets me be.
  • I say whether my hypothesis is supported.
  • I explain the pattern with biology.
  • I compare my result with published work, and cite it.
  • I claim no more than my data show.

4 Evaluation

Weaknesses and limitations of this method (not slips in carrying it out), with evidence from your own data, the effect each had on the results, which mattered most and why, and a realistic improvement for each.

  • I give at least three weaknesses or limitations.
  • Every row is filled in.
  • No slips in carrying it out: weaknesses of the method itself.
  • Each improvement is specific: which instrument, how many, what changes.
  • Each effect says what it did to my data.
  • At least two rows point to evidence in my own data.
  • At least one limitation: what this experiment cannot tell me.
  • I say which mattered most, and why.
  • I deal with what stands out in my data.
  • My improvements improve this investigation, not a new one.

Variables

VariableHow?Why?Units
Independent: temperature
Dependent: rate of oxygen uptake
Kept the same: days since soaking
Kept the same: mass of seeds
Kept the same: capillary bore
Kept the same: volume and strength of potassium hydroxide
Kept the same: time with the clip open before starting
Kept the same: volume of glass beads
Kept the same: kind of seed
Kept the same: length of the run

Evaluation

Weakness or limitationWhich?Evidence in my dataEffect on my resultsImprovement

Data generated with the respirometer dry lab, biologybybradford.com (a simulation). These checks catch what is missing. They cannot judge how good it is: that is what your teacher does.

Open the bench full screen: the apparatus, its controls, your readings and the graph then fit on one screen.

Find out

  • Temperature. Run 5 to 40 °C in 5 °C steps, with 3-day seeds and 2.0 g, three trials at each. Then try 45 °C: what happens to the drop as the run goes on?
  • Waking up. At 25 °C, run dry seeds, then 1 to 5 days since soaking, then boiled seeds.
  • Per gram. At 25 °C, run 1 to 6 g of seeds. The table gives the rate for the whole tube: work out the rate per gram for each mass too, and plot both.
  • No potassium hydroxide. Run 3-day mung beans with it in, then with water in its place.
  • HL Fat or starch? Switch the seeds to sunflower, run them with the potassium hydroxide in and out, and work out the respiratory quotient: 1 − (rate without ÷ rate with).
  • Which apparatus? At 25 °C, run 3-day seeds with the capillary and its drop, then with the U-tube manometer and its control tube. Which reads more precisely, and why? (A third, an insect over soda lime with a bubble in a pipette, is in the check questions.)
  • The clip. At 25 °C, leave the clip open for 0, 5 and 10 minutes before starting. Watch the bead tube's drop.
  • Five sugars. Switch to yeast dough at 30 °C and run the rack three times, so you have three tubes of each sugar, over 30 minutes.

Record

  • Every run's settings: what you changed, and everything you kept the same.
  • Both tubes' readings every minute, the seeds' and the glass-bead tube's, in the units your apparatus reads. For the dough, each top every 5 minutes.
  • Change one thing at a time.
  • Three or more trials at each value, then a mean and its standard deviation.
  • The bench’s graph plots each reading as it is taken. Work out each rate yourself, then press Calculate to check it.
  • For the means and their spread, use Graph your results under the lab, or download the CSV and plot it yourself.
  • The bench keeps each variable's results: choose it again to see them.
  • When you are done, choose one investigation and write it up with the IA coach under the bench.

With the potassium hydroxide taken out, the drop beside the mung beans hardly moves. Why?

In the first two minutes the drop beside the glass beads moved 10 mm away from its tube, then stopped. What does that tell you?

Sucrose dough rose almost as fast as glucose dough, but starch dough barely beat dough with no sugar. Why?

With the potassium hydroxide out, the drop beside germinating sunflower seeds still creeps towards them. Why?

03Check

A fresh paper from the exam bank on this guide's topics each time: past-paper style questions, marked as you go, and saved to your Exam practice progress when you are signed in.

Exam practice

Exam questions on C1.2, marked

Start 15 marks of exam questionsYour exam practice

C1.2 revision mapC1.2 exam questionsC1.2 multiple choice quizC1.2 higher level quizC1.2 lessonC1.2 higher level lessonBack: C1.1 enzymes and metabolismNext: C1.3 photosynthesis

04Downloads

Take the guide with you, or into a classroom with no internet.

DOCXNote templateFor students to fill in alongside the guide: a page per chapter with cues, gaps for the key terms and a summary box. Edit it in Word or Google Docs (A4). 2.3 MB PDFNote template, to printThe same note template, ready to print (A4). 3.4 MB PDFRevision guideThis guide as a printed book: every chapter, every step of every figure, the key terms, the predictions with answers at the back, and a link to the Check. 7.2 MB HTMLThe guide, offlineOne file that opens in any browser with no internet: the figures, the animations and the dry lab all work. 2.3 MB

The whole IB Biology revision guide, every guide written so far in one PDF.

05Teacher resources

The guide as two one-hour lessons, and three more at higher level. Each has a plan to print (the timings, what to project and where to stop, the activities with what they need, what students get wrong) and slides to teach it from, in the same order, with the teacher's moves in the notes.

LessonCoversFocusChaptersLesson planSlides
1ATP, and two ways to make it C1.2.1 to C1.2.560 min ATP as the cell’s energy currency, what it pays for, respiration against gas exchange, and aerobic against anaerobic respiration 1, 2, 3, 4 Lesson planPDF 811 KB SlidesPPTX 5.4 MB
2Measuring a rate you cannot see C1.2.660 min Measuring respiration rate: the dough lab, the respirometer, the control, and the rate per gram per minute 5, dry lab Lesson planPDF 709 KB SlidesPPTX 453 KB
3Hydrogen off, and glycolysis HL C1.2.7 to C1.2.1060 min Oxidation as hydrogen removal and NAD as its carrier, the four stages of glycolysis, and lactate and ethanol as ways to give NAD back 6, 7, 8 Lesson planPDF 703 KB SlidesPPTX 1.1 MB
4Inside the matrix, and which fuel HL C1.2.11, C1.2.12 and C1.2.1760 min The link reaction and the Krebs cycle, counting carbons and carriers, and fat against sugar as fuels 9, 12 Lesson planPDF 738 KB SlidesPPTX 4.6 MB
5The chain, the turbine and the whole journey HL C1.2.13 to C1.2.1660 min Reduced NAD and the electron transport chain, the proton gradient, ATP synthase and oxygen as the last acceptor 10, 11 Lesson planPDF 731 KB SlidesPPTX 4.7 MB
PDFEvery lesson planAll five plans in one PDF, with this overview at the front. 1.5 MB KEYNote template, filled inThe class’s note template with every gap filled. 2.3 MB

The note template, the revision guide and the offline copy are in Downloads, for you and the class.

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How this was made. The course structure, the activities and the teaching choices come from my own classroom, my presentations and my years of teaching IB and AP Biology. I use Claude, an AI, to help write and build the interactive guides, lesson plans, slides and practice questions, and to draw the diagrams and code the interactives. I direct the work and review it against the IB and AP specifications before it goes live.