IMAT Biology · Free notes
Bioenergetics and Metabolism: ATP, Respiration and Photosynthesis
Bioenergetics and Metabolism has 42 past questions since 2011, and the ministry papers from 2023 on have asked 24 of them. That makes it one of the most tested Biology chapters, and the 2025 paper alone asked eleven items on it. Most items are recall: where a pathway runs, what one stage produces, which carrier is reduced, whether a reaction releases or needs energy. The difficulty sits in the bookkeeping, such as per turn against per glucose, gross against net ATP, NAD⁺ against NADP⁺, and the exact compartment of a mitochondrion or chloroplast. Learn the inputs, outputs and site of each stage as a table, and most items take seconds.
The handout has every subtopic, worked example, formula and trap with answers shown. The formula sheet is the chapter’s formulas and traps alone, on one page.
Subtopic notes
Metabolism, ATP and the Electron Carriers
0 PYQsCatabolism breaks molecules down and releases energy, anabolism builds them and uses it; ATP carries the energy between the two, and NAD⁺, FAD and NADP⁺ carry the electrons.
Glycolysis and the Link Reaction
0 PYQsIn the cytoplasm, glucose is split into two pyruvate for a net 2 ATP and 2 NADH; in the mitochondrial matrix, each pyruvate then loses a CO₂ and becomes acetyl coenzyme A.
The Krebs Cycle, the Respiratory Chain and the ATP Total
0 PYQsIn the mitochondrion the Krebs cycle strips the acetyl group of its electrons, the respiratory chain passes them to oxygen, and the proton gradient this builds drives ATP synthase.
Fermentation: Respiration Without Oxygen
0 PYQsWithout oxygen, cells keep glycolysis running by using pyruvate to reoxidise NADH, making lactate in muscle or ethanol and CO₂ in yeast, for only 2 ATP per glucose.
Photosynthesis: Light Reactions and the Calvin Cycle
0 PYQsIn the chloroplast, light energy splits water and makes ATP and NADPH on the thylakoid membranes; in the stroma, the Calvin cycle uses them to turn CO₂ into sugar.
Fats and Proteins as Fuel, and Where Each Pathway Runs
0 PYQsFatty acids are cut two carbons at a time into acetyl CoA, amino acids lose their nitrogen as urea in the liver, and every pathway has its own place in the cell and the body.
Formula & revision sheet
3 formulas · 15 reference tables · 29 gotchas across all subtopics — the exam-eve cheat-sheet
Formula & revision sheet
3 formulas · 15 reference tables · 29 gotchas across all subtopics — the exam-eve cheat-sheet
Metabolism, ATP and the Electron Carriers
Reference tables (3)
Metabolism: catabolism and anabolism, exergonic and endergonic6 rows
| Feature | Catabolism | Anabolism |
|---|---|---|
| What happens | Large molecules are broken into smaller ones | Small molecules are built into larger ones |
| Energy overall | Released (exergonic) | Required (endergonic) |
| Typical chemistry | Oxidation, hydrolysis | Reduction, condensation |
| Link with ATP | The energy released is used to make ATP from ADP | ATP hydrolysis supplies the energy |
| Electron carriers | NAD⁺ and FAD are reduced | NADPH is oxidised (it gives up its electrons) |
| Examples | Glycolysis, Krebs cycle, β-oxidation of fat, digestion | Protein synthesis, DNA replication, Calvin cycle, glycogen synthesis |
How fast a spontaneous reaction actually goes depends on enzymes, which the Biomolecules and Enzymes chapter covers.
ATP: structure, hydrolysis and the cell's energy currency5 rows
| Molecule | What it is | Role |
|---|---|---|
| ATP | Adenine + ribose + 3 phosphates | Universal energy currency: its hydrolysis powers muscle contraction, active transport and biosynthesis |
| ADP | Adenine + ribose + 2 phosphates | Product of ATP hydrolysis; recharged to ATP by phosphorylation |
| AMP | Adenine + ribose + 1 phosphate | Signals that the cell is low on energy; also a nucleotide of RNA |
| Creatine phosphate | Creatine carrying a phosphate group | Muscle reserve that regenerates ATP from ADP for a few seconds |
| NADH, FADH₂ | Reduced electron carriers | Carry energy as electrons to the respiratory chain; not spent directly like ATP |
Redox reactions and the carriers NAD⁺, FAD and NADP⁺4 rows
| Carrier (oxidised → reduced) | Main pathways | Where its electrons go | Vitamin source |
|---|---|---|---|
| NAD⁺ → NADH | Glycolysis, link reaction, Krebs cycle, β-oxidation | Complex I of the respiratory chain | Niacin (vitamin B3) |
| FAD → FADH₂ | Krebs cycle (succinate step), β-oxidation | Complex II, then the rest of the chain | Riboflavin (vitamin B2) |
| NADP⁺ → NADPH | Made in the light-dependent reactions; used in the Calvin cycle and fat synthesis | Onto carbon compounds being built (biosynthesis) | Niacin (vitamin B3) |
| Coenzyme A | Link reaction, Krebs cycle, β-oxidation | Carries acetyl groups, not electrons | Pantothenic acid (vitamin B5) |
Watch out for (6)
- Spontaneous does not mean fast→ Metabolism: catabolism and anabolism, exergonic and endergonic
- Metabolism is both breaking down and building up→ Metabolism: catabolism and anabolism, exergonic and endergonic
- NADH and FADH₂ are not the energy currency→ ATP: structure, hydrolysis and the cell's energy currency
- Creatine phosphate, creatinine and carnitine are different molecules→ ATP: structure, hydrolysis and the cell's energy currency
- Coenzymes are not enzymes→ Redox reactions and the carriers NAD⁺, FAD and NADP⁺
- A redox reaction is defined by moving electrons→ Redox reactions and the carriers NAD⁺, FAD and NADP⁺
Glycolysis and the Link Reaction
Reference tables (2)
Glycolysis: the ten steps from glucose to pyruvate10 rows
| Step | Change | Enzyme | ATP or NADH |
|---|---|---|---|
| 1 | Glucose → glucose 6-phosphate | Hexokinase | 1 ATP used |
| 2 | Glucose 6-phosphate → fructose 6-phosphate | Phosphoglucose isomerase | None |
| 3 | Fructose 6-phosphate → fructose 1,6-bisphosphate | Phosphofructokinase | 1 ATP used |
| 4 | Fructose 1,6-bisphosphate → dihydroxyacetone phosphate + glyceraldehyde 3-phosphate | Aldolase | None |
| 5 | Dihydroxyacetone phosphate → glyceraldehyde 3-phosphate | Triose phosphate isomerase | None |
| 6 | Glyceraldehyde 3-phosphate → 1,3-bisphosphoglycerate | Glyceraldehyde 3-phosphate dehydrogenase | 1 NADH made |
| 7 | 1,3-bisphosphoglycerate → 3-phosphoglycerate | Phosphoglycerate kinase | 1 ATP made |
| 8 | 3-phosphoglycerate → 2-phosphoglycerate | Phosphoglycerate mutase | None |
| 9 | 2-phosphoglycerate → phosphoenolpyruvate (water removed) | Enolase | None |
| 10 | Phosphoenolpyruvate → pyruvate | Pyruvate kinase | 1 ATP made |
Steps 6 to 10 happen twice per glucose, once for each triose phosphate: 2 NADH and 4 ATP made, minus 2 ATP used in steps 1 and 3.
The link reaction: pyruvate to acetyl coenzyme A4 rows
| Product | Per pyruvate | Per glucose | What happens to it |
|---|---|---|---|
| Acetyl CoA | 1 | 2 | Enters the Krebs cycle |
| CO₂ | 1 | 2 | Diffuses out; the first CO₂ of aerobic respiration |
| NADH | 1 | 2 | Reoxidised by the respiratory chain |
| ATP | 0 | 0 | No ATP is made in this step |
Watch out for (4)
- Gross is not net→ Glycolysis: the ten steps from glucose to pyruvate
- Glycolysis releases no CO₂→ Glycolysis: the ten steps from glucose to pyruvate
- Isomerases rearrange; kinases phosphorylate→ Glycolysis: the ten steps from glucose to pyruvate
- Decarboxylation releases CO₂ but uses no oxygen→ The link reaction: pyruvate to acetyl coenzyme A
The Krebs Cycle, the Respiratory Chain and the ATP Total
Formulas (1)
Reference tables (3)
The Krebs cycle: products per turn and per glucose8 rows
| Step | Carbon atoms | Product made |
|---|---|---|
| Acetyl CoA + oxaloacetate → citrate | 2 + 4 → 6 | Coenzyme A released |
| Citrate → isocitrate | 6 → 6 | Rearrangement only |
| Isocitrate → α-ketoglutarate | 6 → 5 | 1 CO₂ and 1 NADH |
| α-ketoglutarate → succinyl CoA | 5 → 4 | 1 CO₂ and 1 NADH |
| Succinyl CoA → succinate | 4 → 4 | 1 GTP (or ATP), by substrate-level phosphorylation |
| Succinate → fumarate | 4 → 4 | 1 FADH₂ (succinate dehydrogenase) |
| Fumarate → malate | 4 → 4 | Water added |
| Malate → oxaloacetate | 4 → 4 | 1 NADH; the acceptor is ready again |
The respiratory chain: complexes, mobile carriers and oxygen6 rows
| Component | Type | Takes electrons from | Passes them to | Pumps protons? |
|---|---|---|---|---|
| Complex I | Integral membrane protein | NADH | Ubiquinone | Yes |
| Complex II | Integral membrane protein (also a Krebs enzyme) | FADH₂ (from succinate) | Ubiquinone | No |
| Ubiquinone (coenzyme Q) | Mobile, lipid-soluble | Complexes I and II | Complex III | No |
| Complex III | Integral membrane protein | Ubiquinone | Cytochrome c | Yes |
| Cytochrome c | Mobile peripheral protein | Complex III | Complex IV | No |
| Complex IV | Integral membrane protein | Cytochrome c | Oxygen, which forms water | Yes |
Chemiosmosis: the proton gradient drives ATP synthase5 rows
| Part of the mitochondrion | Location | Role |
|---|---|---|
| Complexes I, III and IV | Inner membrane | Pump H⁺ from the matrix into the intermembrane space |
| Intermembrane space | Between the outer and inner membranes | Holds the high H⁺ concentration (low pH) |
| Inner membrane | Folded into cristae | Impermeable to H⁺, so the gradient is kept |
| ATP synthase | Inner membrane, its head facing the matrix | Lets H⁺ flow back and uses the flow to make ATP |
| Matrix | Inside the inner membrane | Low H⁺ concentration; ATP is made here, and the Krebs cycle runs here |
Watch out for (5)
- Per turn or per glucose?→ The Krebs cycle: products per turn and per glucose
- Oxygen does not oxidise NADH directly→ The respiratory chain: complexes, mobile carriers and oxygen
- FADH₂ enters the chain later than NADH→ The respiratory chain: complexes, mobile carriers and oxygen
- ATP synthase is driven by protons, not by electrons→ Chemiosmosis: the proton gradient drives ATP synthase
- ATP totals are approximate→ Counting the ATP from one glucose, and the efficiency of respiration
Fermentation: Respiration Without Oxygen
Formulas (1)
Reference tables (1)
Lactic and alcoholic fermentation compared7 rows
| Feature | Lactic fermentation | Alcoholic fermentation |
|---|---|---|
| Where it occurs | Animal muscle, red blood cells, lactic acid bacteria | Yeast, some plant cells |
| Site in the cell | Cytoplasm | Cytoplasm |
| End products | Lactate | Ethanol and CO₂ |
| CO₂ released | No | Yes, one per pyruvate |
| What happens to pyruvate | Reduced directly to lactate | Decarboxylated to ethanal, which is then reduced |
| ATP per glucose | 2 | 2 |
| Everyday use | Yoghurt and cheese making | Bread rising, beer and wine |
Watch out for (4)
- Fermentation regenerates NAD⁺; it makes no extra ATP→ Lactic and alcoholic fermentation compared
- Only alcoholic fermentation releases CO₂→ Lactic and alcoholic fermentation compared
- Both fermentations happen in the cytoplasm→ Lactic and alcoholic fermentation compared
- Compare totals, not yields per glucose→ Comparing ATP yields: fermentation against aerobic respiration
Photosynthesis: Light Reactions and the Calvin Cycle
Reference tables (4)
Photosynthesis: the overall equation and the chloroplast5 rows
| Part | Structure | What happens there |
|---|---|---|
| Envelope | Two membranes, outer and inner | Controls exchange with the cytoplasm; holds no chlorophyll |
| Thylakoid membrane | Membrane of the flattened sacs | Light absorbed by chlorophyll, water split, electron transport, ATP synthase |
| Granum | A stack of thylakoids | Gives a large membrane area for the light-dependent reactions |
| Thylakoid lumen | The space inside each thylakoid | Protons collect here; oxygen from water is released here |
| Stroma | Fluid around the thylakoids | Calvin cycle: CO₂ fixed by RuBisCO and sugar made; starch stored |
The light-dependent reactions: photolysis, NADPH and ATP6 rows
| Feature | Mitochondrion | Chloroplast |
|---|---|---|
| Membrane holding the chain and ATP synthase | Inner membrane (cristae) | Thylakoid membrane |
| Source of the electrons | NADH and FADH₂ from food | Water, split using light energy |
| Protons pumped into | Intermembrane space | Thylakoid lumen |
| ATP made in | Matrix | Stroma |
| Final electron acceptor | Oxygen, forming water | NADP⁺, forming NADPH |
| Name of the ATP synthesis | Oxidative phosphorylation | Photophosphorylation |
Both organelles make ATP by chemiosmosis, so ATP is made in both photosynthesis and respiration.
The Calvin cycle: fixing carbon dioxide in the stroma4 rows
| Stage | What happens | Uses | Carbon atoms |
|---|---|---|---|
| Fixation | CO₂ joins RuBP, catalysed by RuBisCO | No ATP or NADPH | 1 + 5 → 6, which splits into 2 × 3 |
| Reduction | GP is reduced to triose phosphate | ATP and NADPH | 3 → 3 |
| Regeneration | Five triose phosphates are rearranged into three RuBP | ATP | 5 × 3 → 3 × 5 |
| Export | One triose phosphate in six leaves the cycle | Nothing more | 2 × 3 → 6 (two make one glucose) |
Limiting factors, the compensation point and respiration in plants4 rows
| Condition | Photosynthesis | Respiration | Net gas exchange with the air |
|---|---|---|---|
| Darkness | Stopped | Running | CO₂ released, O₂ taken in |
| Dim light, below the compensation point | Slower than respiration | Running | Small net release of CO₂ |
| At the compensation point | Equal to respiration | Running | None |
| Bright light | Faster than respiration | Running | O₂ released, CO₂ taken in |
Watch out for (6)
- The oxygen comes from water→ Photosynthesis: the overall equation and the chloroplast
- Proton pumps are in membranes, not in spaces→ The light-dependent reactions: photolysis, NADPH and ATP
- Photosynthesis reduces NADP⁺, not NAD⁺→ The light-dependent reactions: photolysis, NADPH and ATP
- Light-independent does not mean it runs at night→ The Calvin cycle: fixing carbon dioxide in the stroma
- Light splits water, not carbon dioxide→ The Calvin cycle: fixing carbon dioxide in the stroma
- Plants respire all the time→ Limiting factors, the compensation point and respiration in plants
Fats and Proteins as Fuel, and Where Each Pathway Runs
Formulas (1)
Reference tables (2)
Protein breakdown: transamination, deamination and the urea cycle6 rows
| Process | What happens | Where |
|---|---|---|
| Proteolysis | Proteins hydrolysed to amino acids | Gut (digestion) and inside cells |
| Transamination | Amino group moved from an amino acid to a keto acid | Many tissues, especially liver and muscle |
| Deamination | Amino group removed as ammonia | Mainly the liver |
| Urea cycle | Ammonia and CO₂ combined into urea, using ATP | Liver cells only |
| Excretion of urea | Urea filtered from the blood into urine | Kidneys |
| Use of the carbon skeleton | Burned in the Krebs cycle, or made into glucose or fat | Mainly the liver |
Where each metabolic pathway takes place: organelle and organ10 rows
| Pathway | Site in the cell | Main tissues |
|---|---|---|
| Glycolysis | Cytoplasm | Every cell, including red blood cells |
| Lactic fermentation | Cytoplasm | Working muscle, red blood cells |
| Link reaction and Krebs cycle | Mitochondrial matrix | Every cell with mitochondria |
| Respiratory chain and ATP synthase | Inner mitochondrial membrane | Every cell with mitochondria |
| β-oxidation | Mitochondrial matrix | Muscle, heart and liver (the brain uses little fat) |
| Fatty acid synthesis | Cytoplasm | Liver and adipose tissue |
| Urea cycle | Mitochondrial matrix and cytoplasm | Liver only |
| Gluconeogenesis | Mostly cytoplasm (starts in mitochondria) | Liver, and kidney in long fasting |
| Light-dependent reactions | Thylakoid membranes | Green plant cells and algae |
| Calvin cycle | Chloroplast stroma | Green plant cells and algae |
Watch out for (4)
- Fat beats protein as a store on two counts→ Fat as fuel: lipolysis and β-oxidation
- β-oxidation is not oxidative phosphorylation→ Fat as fuel: lipolysis and β-oxidation
- Transamination moves the amino group; deamination removes it→ Protein breakdown: transamination, deamination and the urea cycle
- Respiration starts outside the mitochondrion→ Where each metabolic pathway takes place: organelle and organ
PYQ weightage by concept
18 concepts · 0 PYQs — where the marks actually sit, so you know what to drill first
PYQ weightage by concept
18 concepts · 0 PYQs — where the marks actually sit, so you know what to drill first
Metabolism, ATP and the Electron Carriers0 PYQs · 0%
| Concept | PYQs | Share |
|---|---|---|
| Metabolism: catabolism and anabolism, exergonic and endergonicfoundation | — | — |
| ATP: structure, hydrolysis and the cell's energy currencyfoundation | — | — |
| Redox reactions and the carriers NAD⁺, FAD and NADP⁺foundation | — | — |
Glycolysis and the Link Reaction0 PYQs · 0%
| Concept | PYQs | Share |
|---|---|---|
| Glycolysis: the ten steps from glucose to pyruvatefoundation | — | — |
| The link reaction: pyruvate to acetyl coenzyme Afoundation | — | — |
The Krebs Cycle, the Respiratory Chain and the ATP Total0 PYQs · 0%
| Concept | PYQs | Share |
|---|---|---|
| The Krebs cycle: products per turn and per glucosefoundation | — | — |
| The respiratory chain: complexes, mobile carriers and oxygenfoundation | — | — |
| Chemiosmosis: the proton gradient drives ATP synthasefoundation | — | — |
| Counting the ATP from one glucose, and the efficiency of respirationfoundation | — | — |
Fermentation: Respiration Without Oxygen0 PYQs · 0%
| Concept | PYQs | Share |
|---|---|---|
| Lactic and alcoholic fermentation comparedfoundation | — | — |
| Comparing ATP yields: fermentation against aerobic respirationfoundation | — | — |
Photosynthesis: Light Reactions and the Calvin Cycle0 PYQs · 0%
| Concept | PYQs | Share |
|---|---|---|
| Photosynthesis: the overall equation and the chloroplastfoundation | — | — |
| The light-dependent reactions: photolysis, NADPH and ATPfoundation | — | — |
| The Calvin cycle: fixing carbon dioxide in the stromafoundation | — | — |
| Limiting factors, the compensation point and respiration in plantsfoundation | — | — |
Fats and Proteins as Fuel, and Where Each Pathway Runs0 PYQs · 0%
| Concept | PYQs | Share |
|---|---|---|
| Fat as fuel: lipolysis and β-oxidationfoundation | — | — |
| Protein breakdown: transamination, deamination and the urea cyclefoundation | — | — |
| Where each metabolic pathway takes place: organelle and organfoundation | — | — |