Structure of the Digestive System
Note: The focus of the AQA specification is on the mechanisms of digestion and absorption. It doesn’t require knowledge of the structure of the digestive system. However, it’s hard to visualise how digestion and absorption work without a picture of where they occur, so this is included for context.
- Salivary glands: secretions contain amylase, which hydrolyses starch into maltose
- Mouth: physical breakdown of food by teeth, which forms a bolus of food so it can travel down the oesophagus
- Oesophagus: moves food from mouth to stomach by peristalsis
- Stomach: muscular sac with an inner lining containing glands that secrete enzymes (e.g. pepsin) and hydrochloric acid; stores food and digests proteins (protease enzymes)
- Pancreas: produces pancreatic juice containing proteases, lipase and amylase (alkaline).
- The pancreas has both exocrine (digestive enzymes, relevant to this topic) and endocrine functions (see Control of Blood Glucose)
- Small intestine (duodenum and ileum): main site of digestion and absorption.
- Large intestine: absorbs water from undigested food
- Rectum: stores faeces before egestion
What is Digestion?
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
During digestion, large biological molecules are hydrolysed to smaller molecules that can be absorbed across cell membranes.
During digestion, large biological molecules are hydrolysed to smaller molecules that can be absorbed across cell membranes into the bloodstream.
You need to know about the digestion of:
- Carbohydrates: by amylases and membrane-bound disaccharidases
- Lipids: by lipase (with the action of bile)
- Proteins: by endopeptidases, exopeptidases and membrane-bound dipeptidases
All of these reactions are hydrolysis reactions (water is added to break the bond). Each enzyme works at a different optimal pH, which is why digestion happens in different parts of the body (e.g. proteases in the stomach at low pH; lipase in the small intestine at higher pH).
Digestion of Carbohydrates
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
Digestion of carbohydrates by amylases and membrane-bound disaccharidases.
Step 1: Polysaccharides → Disaccharides
Starch is hydrolysed to maltose by amylases, which break the glycosidic bonds.
- Mouth (salivary amylase): hydrolyses starch to maltose
- Small intestine (pancreatic amylase): continues hydrolysing starch to maltose
Do you think starch is broken down in the stomach? Why/why not?
Do you think starch is broken down in the stomach? Why/why not?
No: the stomach is too acidic for salivary amylase, which becomes denatured. So no further hydrolysis of starch happens here. Starch digestion resumes in the small intestine when pancreatic amylase is added.
Step 2: Disaccharides → Monosaccharides
Membrane-bound disaccharidases hydrolyse disaccharides → monosaccharides.
- Disaccharidases are embedded in the cell-surface membrane of epithelial cells
- Each disaccharidase hydrolyses the single glycosidic bond in its disaccharide
- The monosaccharide products are then absorbed into the bloodstream (see Absorption)
| Disaccharide | Disaccharidase | Monosaccharide products |
|---|---|---|
| Maltose | Maltase | Glucose + Glucose |
| Sucrose | Sucrase | Glucose + Fructose |
| Lactose | Lactase | Glucose + Galactose |
Digestion of Lipids
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
Digestion of lipids by lipase, including the action of bile salts.
Lipids are hydrolysed by enzymes called lipases, which are produced in the pancreas.
- Lipase hydrolyses the ester bonds in triglycerides, forming fatty acids and monoglycerides
- A monoglyceride is a molecule of glycerol with one fatty acid attached
Role of Bile Salts
- Bile is produced in the liver and stored in the gallbladder
- Bile is released from the gallbladder via the bile duct into the small intestine
- Bile emulsifies lipids, breaking them up into smaller droplets
- This increases the surface area available for lipase to act on, speeding up the rate of lipid hydrolysis
- Bile is alkaline, so it also neutralises stomach acid, providing the optimum pH for the enzymes
Micelles
After digestion in the duodenum, monoglycerides and fatty acids remain associated with bile salts, forming micelles.
Micelles are important because they:
- Transport the monoglycerides and fatty acids to the epithelial cells of the ileum (where they can be absorbed)
- Are soluble in water, so can move easily through the aqueous environment of the small intestine to the epithelial cells lining the ileum
Digestion of Proteins
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
Digestion of proteins by endopeptidases, exopeptidases and membrane-bound dipeptidases.
Digestion of protein involves breaking long polypeptide chains into amino acids and dipeptides that can be absorbed into the blood.
1. Endopeptidases Hydrolyse peptide bonds between amino acids in the internal region of a polypeptide chain.
2. Exopeptidases Hydrolyse peptide bonds between amino acids at the terminal (ends) of polypeptide chains.
The combined action of endopeptidases (middle of chain) and exopeptidases (ends of chain) increases the rate of protein digestion.
Why does the combined action increase the rate of protein digestion?
Why does the combined action increase the rate of protein digestion?
Endopeptidases cut the polypeptide internally, creating more ends for exopeptidases to work on. This increases the surface area available for exopeptidases, speeding up digestion.
3. Membrane-bound dipeptidases Dipeptidases are embedded in the epithelial cell membrane and hydrolyse dipeptides into single amino acids, which are then absorbed into the bloodstream.
Why do dipeptides and disaccharides need to be broken down into amino acids and monosaccharides?
Why do dipeptides and disaccharides need to be broken down into amino acids and monosaccharides?
Smaller molecules (amino acids and monosaccharides) can cross the cell membranes of the epithelial cells lining the ileum. Larger molecules like dipeptides and disaccharides cannot.
Absorption
Absorption allows smaller molecules to pass across cell membranes and into the bloodstream, where they can be transported around the body. It’s important that larger molecules are first broken down into smaller molecules so they can pass across the cell membranes.
Ileum Structure & Adaptations for Absorption
Absorption takes place in the epithelial cells lining the ileum (in the small intestine).
- Folded with finger-like projections (villi)
- Each epithelial cell has a further folded surface (microvilli), sometimes called a “highly folded cell membrane”
- Microvilli increase surface area to accelerate the rate of absorption
- Single layer of epithelial cells: short diffusion pathway to the blood capillaries
- Rich network of blood capillaries: maintains a steep concentration gradient
- Co-transport / carrier proteins: required for co-transport of glucose and sodium ions (see mechanism below)
- High number of mitochondria: produce ATP used in active transport
Monosaccharides & Amino Acids
Epithelial cells of the ileum absorb glucose (and other monosaccharides and amino acids) via active transport and co-transport.
1. Active transport (Na⁺ ions)
The sodium–potassium pump actively transports Na⁺ ions out of the ileum epithelial cells into the blood.
This creates a concentration gradient:
- Low Na⁺ concentration in the epithelial cells
- High Na⁺ concentration in the lumen of the ileum (the space inside the ileum, where the digested food is)
What is needed for the sodium–potassium pump?
What is needed for the sodium–potassium pump?
ATP: active transport requires energy from ATP hydrolysis.
2. Co-transport
Sodium ions diffuse from the lumen of the ileum into the epithelial cell down their concentration gradient, via a co-transport protein. This carrier carries glucose (or amino acids) along with it.
3. Facilitated diffusion
Now the concentration of glucose/amino acids is higher inside the epithelial cells than in the blood, so they diffuse into the bloodstream down their concentration gradient by facilitated diffusion.
What is the difference between facilitated diffusion and simple diffusion?
What is the difference between facilitated diffusion and simple diffusion?
- Simple diffusion: molecules diffuse directly across the phospholipid bilayer (no protein needed). Only works for small, non-polar molecules (e.g. O₂, CO₂).
- Facilitated diffusion: molecules diffuse through a channel or carrier protein in the membrane. Used for larger or polar molecules (e.g. glucose, amino acids) that can’t cross the bilayer directly.
Both are passive (no ATP required) and move molecules down their concentration gradient.
Water follows by osmosis
As glucose, amino acids and ions are absorbed into the epithelial cells, the water potential inside the cells falls (this is below the water potential in the lumen). Water then moves from the lumen into the cells by osmosis.
This is how most water is absorbed in the small intestine. If fewer products of digestion are absorbed (e.g. when the microvilli are damaged), less water is absorbed too, which can cause diarrhoea.
Try the exam-style question Rotavirus and absorption in the ileum in Exam Question Practice below.
Monoglycerides & Fatty Acids
- Micelle formation: monoglycerides and fatty acids combine with bile salts, making them soluble in water
- Micelles travel through the aqueous environment to the epithelial cells lining the villi of the ileum
- Micelles break down close to the epithelial cells, releasing monoglycerides and fatty acids
- Monoglycerides and fatty acids diffuse through the membrane into the epithelial cells
Why are monoglycerides and fatty acids able to move through the membrane?
Why are monoglycerides and fatty acids able to move through the membrane?
They are non-polar (lipid-soluble), so they can diffuse directly through the phospholipid bilayer by simple diffusion. No protein is needed.
Once inside the epithelial cells:
- Transported to the smooth ER → reassembled into triglycerides
- Triglycerides + cholesterol + proteins → packaged into chylomicrons (in the Golgi apparatus)
- Chylomicrons leave by exocytosis → enter lacteals (lymphatic capillaries in villi) → lymphatic system → bloodstream
Important: read the question carefully
Read questions carefully when they ask about lipid absorption. If a question asks about the role of micelles in lipid absorption, it’s asking about transporting fatty acids/monoglycerides to the epithelial cells (steps before they enter the cell), not what happens inside the cell (smooth ER, chylomicrons, lacteals).
Summary Table
Test yourself: click any button to reveal that column.
| Substance | Enzyme(s) | Bond broken | Final products |
|---|---|---|---|
| Carbohydrates (starch) | Amylase, then membrane-bound disaccharidases | Glycosidic | Monosaccharides (e.g. glucose) |
| Proteins | Endopeptidases, exopeptidases, membrane-bound dipeptidases | Peptide | Amino acids |
| Lipids (triglycerides) | Lipase (with bile salts) | Ester | Fatty acids + monoglycerides |
How this topic is tested
This analysis is based on past paper data from 2017 to 2025. It is intended for interest only and is not predictive of what will appear in future papers.
- Tested in 7 of 9 years (2017–2025): 16 question parts worth 41 marks.
- 26th most-examined topic overall by marks, 4th in Unit 3.
Marks by year
Most-tested spec points
- Absorption in the Ileum: tested in 9 parts (23 marks)
- Digestion of Large Biological Molecules: tested in 7 parts (20 marks)
Also links to: Osmosis, Triglycerides & Ester Bonds, Adaptations & Factors Affecting Rate of Transport.
Tips from examiner reports
What students commonly get wrong
- Emulsification is not micelle formationWatch out: emulsification and micelles are different. Emulsification by bile salts breaks fat into small droplets, giving a larger surface area for lipase; it isn't hydrolysis. Micelles form after digestion, when fatty acids and monoglycerides associate with bile salts. They carry them to the epithelial cells, where they're absorbed by diffusion. 2024 P1 Q2.3 · 2020 P1 Q2.3 · 2025 P1 Q1.1
- Microvilli vs villiWatch out: microvilli are folds of an epithelial cell's membrane. Villi are folds of the whole gut wall, made of many cells. "Increased surface area" is what microvilli do, not what they are. 2024 P1 Q2.2 · 2020 P1 Q1.3
- Starch digestion has two stagesWhen describing starch digestion, give both stages: amylase hydrolyses starch to maltose (say maltose, not just "disaccharide"), then membrane-bound maltase (a disaccharidase) hydrolyses maltose to glucose. Don't go straight to glucose. 2022 P1 Q9.3
- Endopeptidases vs exopeptidasesWatch out: endopeptidases hydrolyse peptide bonds inside the chain, and exopeptidases hydrolyse bonds at the ends. Together they're faster because endopeptidases create more ends for exopeptidases to act on. 2023 P1 Q4.3 · 2021 P3 Q5.1
Exam Question Practice
Bread contains a lot of starch.
Describe how starch is completely digested in a mammal.
(4 marks)
Hint
Digestion happens in two stages. Which enzyme acts first and what does it make? Which enzyme completes the digestion, and where is it?
Mark Scheme
Max 4 marks
- Hydrolysis (1 mark)
- Of glycosidic bonds (1 mark)
- Amylase breaks starch down to maltose (1 mark)
- Maltase breaks maltose down to glucose (1 mark)
- Maltase is membrane-bound (on the epithelial cells of the ileum) (1 mark)
Also accepted / rejected
Tips
- Describe two stages: amylase hydrolyses starch to maltose (name it, not just “disaccharide”), then membrane-bound maltase hydrolyses maltose to glucose
- Say hydrolysis of glycosidic bonds, not “breakdown” into “sugar”
- Bile salts and co-transport aren’t part of starch digestion
Vitamin D is a fat-soluble substance. Micelles are involved in its absorption.
Describe how vitamin D is absorbed into the cells lining the ileum.
(3 marks)
Hint
The vitamin is absorbed whole; it isn’t digested. How do micelles help it reach the cells, and how does it get in?
Mark Scheme
Max 3 marks
- Vitamin D combines with bile salts (forming micelles) (1 mark)
- This makes it more soluble in water (1 mark)
- Micelles carry vitamin D to the cells lining the ileum, keeping its concentration high next to the membrane (1 mark)
- Vitamin D diffuses into the cells (1 mark)
Also accepted / rejected
Not accepted
- Describing vitamin D being digested into fatty acids or monoglycerides (max 2 marks)
- Saying the micelles themselves are absorbed
Tips
- Describe how the whole vitamin is absorbed; describing lipid digestion limits you to 2 marks
- Micelles form when vitamin D combines with bile salts; this is not emulsification
- The micelle carries vitamin D to the cells; the vitamin D, not the micelle, diffuses across the membrane
- Vitamin D enters by simple diffusion, not by co-transport
Rotavirus infects the epithelial cells lining the ileum of young children. The infected cells lose their microvilli. As a result, the children absorb fewer products of digestion and less water, and they develop diarrhoea.
Explain why losing microvilli reduces the absorption of the products of digestion, and why this then reduces the absorption of water.
(3 marks)
Hint
What do microvilli provide for absorption? If more products of digestion stay in the ileum, what happens to the water potential there?
Mark Scheme
Products of digestion
- A smaller surface area, or fewer carrier (co-transport) proteins (1 mark)
Water
Normally, water follows the absorbed products of digestion into the cells by osmosis.
- More products of digestion stay in the lumen, so the water potential in the lumen stays lower than normal (1 mark)
- So there is a smaller water potential gradient, and less water moves from the lumen into the cells by osmosis (1 mark)
Also accepted / rejected
Also accepted
- Fewer channel proteins (point 1)
- The water potential in the cells is higher, or the water potential gradient is smaller (point 2)
- Water moves out of the cells into the ileum by osmosis (point 3)
Not accepted
- “SA” or “WP” written as abbreviations
Tips
- Losing microvilli means a smaller surface area and fewer carrier proteins, so fewer products of digestion are absorbed
- Water moves by osmosis, not diffusion; the unabsorbed products lower the water potential in the ileum
- Give the direction: less water moves out of the ileum into the cells
Also accepted