Biological catalysts: proteins, the active site and the lock and key
By the end of this lesson you will be able to
- Describe enzymes as biological catalysts that increase the rate of reactions in cells, and explain why life needs them, using the idea of activation energy.
- Outline how an enzyme’s chain of amino acids folds into a specific three-dimensional shape with an active site.
- Describe the formation of the enzyme–substrate complex using the lock-and-key hypothesis, and state that the enzyme is released unaltered and reused.
- Explain why enzymes are substrate-specific, and compare the lock-and-key and induced-fit models.
- Name at least three enzymes with their substrates and products, and calculate the rate of an enzyme-catalysed reaction from measurements.
You met this before
- Digestion breaks large food molecules into small soluble ones: starch → maltose → glucose; protein → amino acids; fat → fatty acids and glycerol (Year 3, Unit 1).
- Salivary amylase starts starch digestion in the mouth; a protease (pepsin) works in the acid of the stomach; the pancreas adds amylase, protease and lipase to the small intestine (Year 3, Unit 1).
- Proteins are long chains of amino acids — about 20 different kinds — joined in an order set by a gene (Year 3, Unit 1; Unit 2 of this course).
- Every cell runs thousands of chemical reactions — respiration, photosynthesis, building proteins — in the cytoplasm and in organelles such as mitochondria (Year 2, Unit 3).
- A reaction goes faster when particles collide more often and with more energy (Year 1 particle model).
Name the enzyme that digests starch and the product it forms, and state where in the gut protein digestion begins.
Reveal
Amylase digests starch into maltose (a sugar made of two glucose units). Protein digestion begins in the stomach, where a protease (pepsin) works in hydrochloric acid at about pH 2.
Revise it in full: Year 3 · Body systems · Lesson 1 — Digestion: from a plate of pap to a molecule in the blood · Year 2 · Cell functions · Lesson 1 — Cells at work: where the energy comes from
The puzzle
Put a spoonful of cooked starch in a jar of water and leave it on a shelf. A year later it is still starch: the reaction starch + water → sugar does happen on its own, but so slowly that you would never notice.
Now hold a mouthful of plain bread or pap in your mouth for two minutes without swallowing. It starts to taste sweet. The same reaction has gone from “a year and nothing” to “two minutes and sugar” — at 37 °C, in water, with no heat, no acid and no pressure.
Something in your saliva does in minutes what a chemist would need boiling acid to do. It is used again and again, it is not changed at the end, and it ignores every other molecule in your mouth. What is it, and how can a molecule be that fast and that choosy?
A chemist can break starch into glucose by boiling it with hydrochloric acid for an hour. Suggest two reasons why a cell cannot use that method, and predict what kind of substance a cell must use instead.
Compare your answer
Boiling would destroy the cell: its proteins would lose their shape and its membranes would break down. Strong acid would do the same, and it would attack every molecule in the cell, not just the starch.
A cell needs something that speeds up one particular reaction at body temperature and near-neutral pH, and that is not used up. That is a catalyst; the catalysts made by living cells are enzymes, and almost all of them are proteins.
The science — structured notes
1.1 Why cells need catalysts: the activation energy barrier
Most reactions that release energy do not start by themselves. The bonds in the reacting molecules must first be stretched and partly broken, and that needs an input of energy called the activation energy. Only particles that collide with at least this energy react.
At 37 °C very few collisions between starch and water carry enough energy, so the reaction is almost too slow to measure. Heating would help, but a cell cannot be heated to 100 °C.
A catalyst is a substance that increases the rate of a chemical reaction without being used up or permanently changed. It works by providing a different route for the reaction, with a lower activation energy, so a much larger fraction of collisions succeed at the same temperature.
Enzymes are biological catalysts: proteins made by living cells that speed up the reactions of life, often by factors of millions, at body temperature. They do not make a reaction happen that could not happen; they make it fast enough to be useful.
“An enzyme is used up in the reaction it catalyses, so the body must keep making new enzyme molecules for every reaction.”
Reveal answer
False. A catalyst is not used up: each enzyme molecule leaves the reaction unaltered and catalyses the next one, thousands or millions of times. Cells do replace enzymes over hours or days, because proteins are slowly damaged and broken down, but that is maintenance, not consumption by the reaction.
1.2 Enzymes are proteins with a precise shape
An enzyme is built as a chain of amino acids joined in the order coded by one gene; a typical enzyme has a few hundred of them. The chain does not stay a string. It coils and folds into a compact, three-dimensional (globular) shape, like a ball of wool with a definite pattern.
The shape is held by weak bonds between the side chains of amino acids that end up next to each other — hydrogen bonds and ionic bonds — and, in some enzymes, by strong disulfide bridges between sulfur atoms.
Because the order of amino acids decides where the chain folds, the gene decides the shape, and the shape decides the job. Change one amino acid in the wrong place and the enzyme may fold differently and stop working — the link between DNA and enzymes that Unit 2 began.
Somewhere on the surface of the folded enzyme is a small pocket or groove made by just a few of its amino acids: the active site. It is the part of the enzyme that binds the substrate and catalyses the reaction. The rest of the molecule’s job is mainly to hold the active site in exactly the right shape.
| Term | Meaning | Example (amylase) |
|---|---|---|
| Enzyme | A protein that catalyses one kind of reaction | Salivary amylase, about 500 amino acids |
| Substrate | The molecule the enzyme acts on | Starch |
| Active site | The region of the enzyme, shaped to fit the substrate, where the reaction happens | A cleft that holds a few glucose units of the starch chain |
| Enzyme–substrate complex | The enzyme and substrate bound together at the active site | Amylase holding a stretch of starch |
| Product(s) | What the substrate becomes | Maltose |
Two enzymes are made from genes that differ by a single base, so one amino acid in the chain is different. Explain why one enzyme may work normally and the other not at all.
Reveal answer
The order of amino acids decides how the chain folds, because each amino acid’s side chain forms particular hydrogen or ionic bonds. If the changed amino acid is far from the active site and forms similar bonds, the fold and the active site are unchanged and the enzyme works.
If it is in or near the active site, or it breaks a bond that holds the fold, the active site changes shape: the substrate no longer fits and no enzyme–substrate complexes form. That is how one mutation can remove an enzyme’s activity completely.
1.3 The enzyme–substrate complex and the lock and key
The substrate and the enzyme move randomly in the watery cytoplasm or gut contents and collide. When a substrate molecule collides with the active site in the right orientation, it fits into it and is held there by weak bonds: an enzyme–substrate complex forms.
While it is held, the substrate’s bonds are strained, or its atoms are brought close to groups on the enzyme that react with them; the activation energy is lowered and the reaction happens. The products no longer fit the active site so well, and they leave.
The enzyme is released unaltered — the same shape, the same active site — and is free to bind another substrate molecule. One enzyme molecule can repeat the cycle many thousands of times a second; catalase, the enzyme in this lesson’s lab, is among the fastest known, dealing with millions of hydrogen peroxide molecules per second.
In 1894 the German chemist Emil Fischer compared the fit to a key in a lock: only a key of the right shape turns a given lock. This lock-and-key hypothesis says the active site has a fixed shape complementary to the substrate. The substrate is the key, the active site the lock.
Written as a scheme, with E for enzyme, S for substrate and P for products:
E + S → ES (enzyme–substrate complex)
ES → EP (products formed while still held)
EP → E + P (products released; enzyme unaltered)
A diagram shows four shapes left to right: a small shape, a large shape with a notch, the same large shape again after an arrow, and two small pieces. Identify each shape.
Shape 1, small, before the “+”: the substrate — it is what is changed.
Shape 2, large with a notch: the enzyme — the notch is its active site.
Shape 3, the same large shape after the arrow: the enzyme again — it is released unaltered, so it is drawn identical.
Shape 4, two small pieces: the products.
The trap is shape 3: candidates who label it “product” or “enzyme–substrate complex” have missed the key fact that an enzyme is unchanged by the reaction.
Write the three-step scheme (E + S …) for the breakdown of hydrogen peroxide by catalase, naming each species, and state which step the lock-and-key hypothesis describes.
Reveal answer
catalase + hydrogen peroxide → catalase–peroxide complex
catalase–peroxide complex → catalase + water + oxygen
Overall: 2H₂O₂ → 2H₂O + O₂, with catalase unchanged. The lock-and-key hypothesis describes the first step: the substrate binding to an active site of complementary shape to form the enzyme–substrate complex.
1.4 Specificity: one enzyme, one kind of substrate
Because the active site has one particular shape and pattern of charges, only substrate molecules with a complementary shape bind to it. Each enzyme therefore catalyses one reaction, or a small group of very similar reactions: enzymes are substrate-specific.
Amylase breaks the bonds between glucose units in starch, but not the bonds between amino acids in protein. Protease does the reverse. Lactase splits lactose but not sucrose, although both are sugars made of two units.
Specificity is why the body needs thousands of different enzymes — a human cell makes several thousand — and why a missing enzyme causes a specific disease. People without enough lactase cannot digest milk sugar; every other part of their digestion works.
Most enzyme names end in -ase and are built from the substrate: maltase breaks maltose, lactase lactose, lipase lipids (fats), protease protein. A few older names, such as pepsin and trypsin, break the rule.
| Enzyme | Substrate | Product(s) | Where it works |
|---|---|---|---|
| Amylase | Starch | Maltose | Mouth (saliva); small intestine (from the pancreas); germinating seeds |
| Maltase | Maltose | Glucose | Lining of the small intestine |
| Protease (e.g. pepsin, trypsin) | Protein | Peptides, then amino acids | Stomach (pepsin); small intestine (trypsin from the pancreas) |
| Lipase | Lipids (fats and oils) | Fatty acids and glycerol | Small intestine (from the pancreas) |
| Lactase | Lactose (milk sugar) | Glucose and galactose | Lining of the small intestine |
| Catalase | Hydrogen peroxide | Water and oxygen | Inside almost all cells, especially liver; potato, yeast |
| DNA polymerase | Nucleotides | A new DNA strand | Nucleus, before cell division (building up, not breaking down) |
A student writes: “Amylase is specific because it only works at pH 7. It digests all carbohydrates, including starch and cellulose. After the reaction the amylase is broken down into maltose.” Find three errors.
Reveal answer
(1) Specificity is about the shape of the active site matching one substrate, not about pH; pH changes the rate but does not make an enzyme specific.
(2) Amylase acts on starch, not on all carbohydrates. Cellulose is also made of glucose, but the units are linked differently and do not fit amylase’s active site, which is why humans cannot digest cellulose.
(3) Amylase is not broken down; it is released unaltered. The starch is broken down into maltose.
1.5 A better model: induced fit
The lock-and-key hypothesis explains specificity well, but it pictures the enzyme as rigid. In 1958 the American biochemist Daniel Koshland proposed the induced-fit model: the active site is flexible, and binding the substrate makes it change shape slightly so that it grips the substrate tightly.
That grip strains the bonds of the substrate and lowers the activation energy; when the products leave, the enzyme springs back to its original shape. Induced fit explains observations the rigid lock cannot.
Some enzymes act on several similar substrates. Some molecules bind to the active site but are not changed, and X-ray pictures of enzymes such as hexokinase show the protein visibly closing round its substrate, like a hand closing on a ball.
Both models are useful. At MYP level the examiners ask for lock and key by name — “describe this attachment as the Lock and Key Hypothesis” is in the course content — and credit induced fit as a refinement. A good answer knows that a model is a simplification that can be improved when new evidence arrives.
A drug molecule has almost the same shape as an enzyme’s substrate. It binds to the active site but is not changed and does not leave quickly. Predict the effect on the rate of the enzyme’s reaction, and explain it with the lock-and-key idea.
Reveal answer
The rate falls. The drug is complementary enough to bind to the active site, like a key that enters the lock but does not turn. While it occupies the active site, substrate molecules cannot bind, so fewer enzyme–substrate complexes form per second.
This is exactly how statins lower cholesterol: they block the active site of an enzyme in the liver that is needed to make cholesterol. The November 2021 Biology paper asked for it, and the markscheme wanted “blocks the active site”, not “affects the active site”.
1.6 Building up and breaking down, inside and outside cells
The digestive enzymes you met in Year 3 break large molecules into small ones. Many more enzymes build molecules: DNA polymerase joins nucleotides into DNA, enzymes in chloroplasts build glucose from carbon dioxide, and enzymes in the liver join glucose into glycogen for storage.
The May 2023 Biology paper’s markscheme for “outline the importance of enzymes” gave one mark for “speed up reactions / biological catalysts” and one for “build up or break down molecules”.
Most enzymes work inside the cell that made them (intracellular): respiration alone needs dozens, in the cytoplasm and mitochondria. Digestive enzymes are secreted to work outside the cells (extracellular), in the gut.
Fungi and bacteria also secrete enzymes into their surroundings and absorb the products — the reason bread goes mouldy and the reason industry grows fungi to make enzymes (Lesson 5).
For each process, state whether an enzyme builds up or breaks down molecules, and whether it works inside or outside cells: (i) lipase in the small intestine; (ii) the enzyme that joins amino acids at a ribosome; (iii) catalase in a liver cell.
Reveal answer
(i) Breaks down fats into fatty acids and glycerol; extracellular (secreted by the pancreas into the gut).
(ii) Builds up a protein from amino acids; intracellular.
(iii) Breaks down hydrogen peroxide, a toxic by-product of metabolism, into water and oxygen; intracellular.
1.7 Measuring how fast an enzyme works
You cannot watch one enzyme molecule, so you measure the whole reaction. The rate of an enzyme-catalysed reaction is the amount of product formed, or of substrate used, per unit time.
rate = amount of product formed ÷ time taken
rate = amount of substrate used ÷ time taken
With catalase, the product oxygen can be collected in a gas syringe or measured as the height of foam in a tube. With amylase, the substrate starch can be followed with iodine (Lesson 3). The unit is always “amount per unit time”: cm³ s⁻¹, mm min⁻¹, g s⁻¹.
A rate measured over a long time is an average; the rate just after mixing, the initial rate, is the one that reflects the conditions you set, because later the substrate is being used up. Lesson 4 shows how to find it from a graph.
1.0 g of liver is added to 10 cm³ of hydrogen peroxide. The gas syringe reads 24 cm³ of oxygen after 60 s. Calculate the mean rate of oxygen production.
rate = volume of oxygen ÷ time
rate = 24 cm³ ÷ 60 s
rate = 0.40 cm³ s⁻¹
Two significant figures, matching the 24 cm³ reading. Per minute it is 24 cm³ min⁻¹ — say which unit you are using.
Hydrogen peroxide left on its own at 25 °C released 0.20 cm³ of oxygen in 5.0 minutes. With 1.0 g of liver it released 45 cm³ in 30 s. How many times faster is the catalysed reaction?
Convert to the same time unit: 5.0 min = 300 s
uncatalysed rate = 0.20 cm³ ÷ 300 s
uncatalysed rate = 6.67 × 10⁻⁴ cm³ s⁻¹ (keep the extra figure until the end)
catalysed rate = 45 cm³ ÷ 30 s
catalysed rate = 1.5 cm³ s⁻¹
ratio = 1.5 cm³ s⁻¹ ÷ (6.67 × 10⁻⁴ cm³ s⁻¹)
ratio = 2.3 × 10³ — the enzyme makes the reaction more than 2 000 times faster
Converting both rates to the same unit before dividing is where marks are won; 45 ÷ 0.20 = 225 is wrong because the times differ.
One catalase molecule breaks down about 5 × 10⁶ molecules of hydrogen peroxide per second. How many molecules of peroxide can one catalase molecule break down in one hour? A cell makes 3 × 10⁹ peroxide molecules per second; estimate the minimum number of catalase molecules it needs to keep up, and suggest why real cells have many more than this.
Reveal answer
1 hour = 3 600 s
molecules per hour = 5 × 10⁶ s⁻¹ × 3 600 s
molecules per hour = 1.8 × 10¹⁰
minimum catalase molecules = (3 × 10⁹ s⁻¹) ÷ (5 × 10⁶ s⁻¹)
minimum catalase molecules = 6 × 10²
About 600 molecules would be enough only if every one worked at its maximum rate all the time. In a real cell the peroxide concentration is kept very low, so most active sites are empty at any instant and each enzyme works far below its maximum; peroxide also appears unevenly in different places. Many more enzyme molecules keep the peroxide concentration low everywhere — Lesson 4 explains why rate depends on substrate concentration.
Try it — meet catalase: an enzyme you can watch working
Potato cells, like yours, contain catalase to destroy hydrogen peroxide, a poisonous by-product of their reactions. Drop a piece of potato into hydrogen peroxide and the foam that rises is oxygen. The lab lets you set the temperature, the pH and the mass of potato. In this lesson use it to see a catalyst at work; in Lesson 2 you will use it for a full temperature investigation.
Mean foam heights at 30 °C: 1 g → 18 mm; 2 g → 37 mm; 3 g → 55 mm; 4 g → 74 mm; 5 g → 92 mm. Calculate the foam height per gram at 1 g and at 5 g, and state whether foam height is directly proportional to mass. Explain in terms of active sites.
Reveal answer
1 g: 18 mm ÷ 1 g = 18 mm g⁻¹
5 g: 92 mm ÷ 5 g = 18.4 mm g⁻¹
The ratio is the same (about 18 mm per gram) and a graph would be a straight line through the origin, so foam height is directly proportional to the mass of potato in this range.
Each gram contains about the same number of catalase molecules; with peroxide in excess, every extra active site forms complexes at the same rate, so the amount of oxygen produced in 60 s rises in proportion. If the peroxide ran short, the line would level off — the idea behind Lesson 4’s lab.
Common mistakes to avoid
- “Enzymes are alive” or “enzymes are killed” — enzymes are protein molecules, not organisms. They are denatured, never killed.
- “The enzyme is used up” or “the enzyme changes into the product” — the enzyme is released unaltered; the substrate becomes the product.
- “The substrate and active site are the same shape” — they are complementary, like a lock and its key.
- “Enzymes give the energy for reactions” — they lower the activation energy; they add no energy and do not change the energy released.
- Labelling the enzyme after the reaction as “product” — it is drawn identical because it is identical.
- Writing “affects the active site” — examiners want the precise action: “binds to”, “blocks” or “changes the shape of” the active site.
- Confusing specificity with optimum conditions — specific means one substrate; optimum means the best temperature or pH.
Study smart: how this is examined
Study routine. Today: draw the three-frame lock-and-key diagram from memory and label every part; write the enzyme table (enzyme, substrate, products) for five enzymes without looking.
In two days: explain the statin question and the “labelled enzyme” trap aloud to someone, then do the two rate calculations again with new numbers. In a week: run the catalase lab, take the quiz, and write a 2-mark answer to “Outline the importance of enzymes” in under a minute.
How we found out — from “ferments” to folded proteins
In 1833 the French chemists Anselme Payen and Jean-François Persoz extracted a substance from germinating barley (malt) that turned starch into sugar; they called it diastase. It was the first enzyme to be isolated, and it is the amylase of this unit.
In 1836 Theodor Schwann found pepsin in the stomach lining. But for most of the century a great argument ran: was fermentation — yeast turning sugar into alcohol — a chemical process, or did it need a living cell?
Louis Pasteur held that fermentation needed living yeast. Justus von Liebig thought it was ordinary chemistry. In 1877 Wilhelm Kühne coined the word “enzyme” (Greek, “in leaven”) for the substances that did the work.
In 1897 Eduard Buchner ground yeast with sand, pressed out a juice containing no living cells, and showed that the juice still fermented sugar. The chemistry of life was chemistry; he received the 1907 Nobel Prize in Chemistry.
In 1894 Emil Fischer, studying why an enzyme from yeast broke down one form of a sugar compound but not a very closely related form, proposed the lock and key — a model built to explain specificity, thirty years before anyone knew what an enzyme was made of.
That changed in 1926, when James Sumner crystallised the enzyme urease from jack beans and showed the crystals were pure protein. Many chemists refused to believe it until John Northrop crystallised pepsin and trypsin in the early 1930s. Sumner and Northrop shared the 1946 Nobel Prize in Chemistry (with Wendell Stanley, who crystallised a virus).
The shape itself was first seen in 1965, when David Phillips and his team in London used X-ray crystallography to solve the structure of lysozyme, an enzyme in tears and egg white: a folded chain of 129 amino acids with a deep cleft — the active site — exactly where the substrate bound.
By then Daniel Koshland (1958) had argued from evidence about flexible enzymes that the lock is not rigid, and the induced-fit model joined the lock and key. Each step changed minds because it came with evidence nobody could explain away: a cell-free juice that fermented, a crystal that was protein, a photograph of a cleft.
Explain why Buchner’s cell-free yeast juice was more convincing evidence against the idea that fermentation needed living cells than any number of experiments on whole yeast.
Reveal answer
Every experiment on whole yeast has living cells present, so any result can be explained either by chemistry or by “life”. Buchner removed the variable: grinding and pressing destroyed the cells, and the juice contained no living cells, yet sugar was still fermented.
The only explanation left was that substances in the juice — enzymes — catalysed the reactions. A good experiment is one whose result the rival explanation cannot accommodate.
Where it is used now
- Malting sorghum. Traditional sorghum beer (bojalwa) and sorghum porridge in Botswana and across southern Africa start with malting: grain is soaked and allowed to germinate, and the young seedling makes amylases that turn its starch store into sugars. Brewers then use those sugars — the same enzyme Payen and Persoz found in barley malt in 1833.
- Tenderising meat with pawpaw. Cooks in many parts of Africa, Asia and the Caribbean wrap tough meat in pawpaw (papaya) leaves or rub it with green pawpaw. The fruit and leaves contain papain, a protease that breaks down some of the proteins of the meat; commercial meat tenderisers contain the same enzyme.
- Blood tests. When liver or pancreas cells are damaged, their enzymes leak into the blood. Clinics measure enzymes such as ALT (liver) and amylase and lipase (pancreas) to diagnose disease — reading illness from enzyme activity.
- Snakebite. Much of the damage from puff adder and other adder bites is done by enzymes in the venom, such as proteases and phospholipases, which break down tissue and blood-vessel walls. Antivenoms work partly by binding these enzymes.
- Medicines that block active sites. Statins (cholesterol), many HIV drugs (protease inhibitors) and aspirin-like painkillers act by binding to the active site of a specific enzyme — the lock-and-key idea turned into medicine.
Science now — and the scientist you need to be
What is happening in 2026
For a century, finding an enzyme’s shape took years of crystallography. In 2020–2021 the AI system AlphaFold, from Google DeepMind, began predicting the folded shape of proteins from their amino acid sequence alone, and its database now holds predicted structures for over 200 million proteins — essentially every protein known to science.
The 2024 Nobel Prize in Chemistry went to Demis Hassabis and John Jumper for AlphaFold and to David Baker for designing new proteins by computer. The newest versions, released from 2024, also predict how a protein binds small molecules such as substrates and drugs — a computer picture of the enzyme–substrate complex.
Baker’s group and others have gone further: they now design new enzymes on a computer, choosing an active site first and building a protein around it, then making and testing it in the laboratory. Early designs are far slower than natural enzymes, and most still need improving by laboratory evolution.
The goal for the next decade is enzymes made to order — to break down plastics, capture carbon or make medicines without toxic solvents. Careers here are called protein engineer, computational biologist, structural biologist and enzymologist.
The mindshift
What you need to be able to do
Define an enzyme in one sentence; label substrate, enzyme, complex and products on any diagram; explain specificity from the shape of the active site; name enzymes with their substrates and products; and calculate a rate with its unit. Examiners’ reports have described enzymes as an area where many candidates do well — so marks are lost mainly on precise wording such as “die”, “used up” and “affects”.
See an example
One assistant wrote: “Enzymes are special proteins that speed up reactions. The substrate fits into the enzyme like a key in a lock. The enzyme then breaks the substrate apart and is ready to work again.”
It is mostly right, but “fits into the enzyme” should be “binds to the active site”, it never names the enzyme–substrate complex, and “breaks apart” leaves out building-up reactions. A better third sentence: “The products are released and the enzyme, unchanged, binds another substrate molecule.”
Key terms
| Catalyst | A substance that increases the rate of a reaction without being used up or permanently changed. |
| Enzyme | A biological catalyst: a protein made by living cells that speeds up a specific reaction. |
| Activation energy | The minimum energy that colliding particles need for a reaction to happen; enzymes lower it. |
| Substrate | The molecule an enzyme acts on. |
| Product | The substance formed from the substrate in the reaction. |
| Active site | The region of an enzyme, with a shape complementary to its substrate, where the substrate binds and the reaction is catalysed. |
| Enzyme–substrate complex | The temporary structure formed when a substrate binds to the active site. |
| Lock-and-key hypothesis | The model in which the active site has a fixed shape complementary to the substrate, like a lock and its key (Fischer, 1894). |
| Induced-fit model | The model in which the active site changes shape slightly as the substrate binds, gripping it (Koshland, 1958). |
| Specificity | The property of an enzyme of catalysing only one reaction, or one kind of substrate, because of the shape of its active site. |
| Rate of reaction | The amount of product formed, or substrate used, per unit time. |
Think like a scientist
Criterion A Sucrase is an enzyme in the lining of the small intestine. It breaks down sucrose (table sugar) into glucose and fructose. A student is given this information and a diagram with five shapes: a large shape with a notch (P), a small two-part shape that fits the notch (Q), the large shape holding the small shape (R), the large shape with the notch empty (S), and two separate small shapes (T).
(a) Identify P, Q, R, S and T, using the names of the real molecules where you can. [3]
(b) Describe what happens between R and S, using the lock-and-key hypothesis. [3]
(c) Lactose is also made of two sugar units. Explain why sucrase does not break down lactose. [2]
(d) Outline one observation that the lock-and-key hypothesis cannot explain and that the induced-fit model can. [2]
(e) In a test, 2.0 cm³ of sucrase solution produced 0.36 g of glucose in 4.0 minutes. Calculate the mean rate of glucose production in g min⁻¹ and in mg s⁻¹. [2]
Model answer
(a) P: sucrase (the enzyme), with its active site. Q: sucrose (the substrate). R: the enzyme–substrate complex. S: sucrase again, released unaltered. T: the products, glucose and fructose. [All five 3; four 2; two or three 1.]
(b) The sucrose is held in the active site, whose shape is complementary to it [1]; the bond joining the two sugar units is broken — the enzyme lowers the activation energy for this reaction [1]; glucose and fructose no longer fit the active site and are released, leaving the enzyme unchanged and free to bind another sucrose molecule [1].
(c) Lactose has a different shape from sucrose (different sugar units, joined differently), so it is not complementary to sucrase’s active site [1]; it cannot bind, so no enzyme–substrate complex forms and the reaction is not catalysed — sucrase is specific to sucrose [1].
(d) Any one, with the reason: some enzymes act on several substrates of slightly different shape [1], which a rigid lock could not accept but a flexible active site that moulds itself round each can [1]; or X-ray structures show the enzyme changing shape as the substrate binds [1], which contradicts a fixed lock [1].
(e)
rate = 0.36 g ÷ 4.0 min
rate = 0.090 g min⁻¹ [1]
0.36 g = 360 mg; 4.0 min = 240 s
rate = 360 mg ÷ 240 s
rate = 1.5 mg s⁻¹ [1]
Probe deeper — exam-style questions
Attempt every question before opening the answer. Marks in brackets show what a full answer is worth.
Outline the importance of enzymes in the body.
Reveal answer
Enzymes are biological catalysts that speed up the reactions of the body at body temperature, without being used up [1]; they build up molecules (e.g. DNA polymerase making DNA) or break them down (e.g. lactase breaking down lactose, amylase breaking down starch) [1].
State the name given to the region of an enzyme where the substrate binds.
Reveal answer
The active site [1].
Complete a table naming the substrate and the product(s) of amylase, protease and lipase.
Reveal answer
| enzyme | substrate | product(s) |
|---|---|---|
| amylase | starch | maltose |
| protease | protein | amino acids |
| lipase | lipids (fats and oils) | fatty acids and glycerol |
Amylase: starch → maltose [1]. Protease: protein → amino acids (accept peptides) [1]. Lipase: lipids / fats → fatty acids and glycerol (both needed) [1].
Describe how an enzyme catalyses a reaction, using the lock-and-key hypothesis.
Reveal answer
The substrate collides with and binds to the active site, which has a shape complementary to the substrate, forming an enzyme–substrate complex [1]; the reaction takes place, lowering the activation energy / the substrate is broken down or joined [1]; the products are released and the enzyme is unaltered and can be reused [1].
Explain why an enzyme is described as substrate-specific.
Reveal answer
The active site has a particular shape (and pattern of charges) [1]; only a substrate with a complementary shape can bind to it and form an enzyme–substrate complex, so each enzyme catalyses only one reaction or type of reaction [1].
Statins block the action of an enzyme that catalyses a step in making cholesterol in the liver. Suggest how statins reduce cholesterol levels.
Reveal answer
The statin molecule binds to / blocks the enzyme’s active site, so the substrate cannot bind [1]; the reaction that produces cholesterol is prevented or slowed, so less cholesterol is made [1]. (Not “affects the active site”.)
7. People with the inherited disease phenylketonuria (PKU) lack a working enzyme that converts the amino acid phenylalanine into another amino acid, tyrosine. Untreated, phenylalanine builds up in the blood and damages the developing brain. Explain, from DNA to enzyme, how one faulty gene can cause this, and suggest why treatment is a diet low in protein rather than a tablet of the enzyme.
Reveal answer
The gene for the enzyme has a mutation that changes the order of amino acids in the protein [1]; the chain folds differently, so the active site no longer has a shape complementary to phenylalanine, which cannot bind; no enzyme–substrate complexes form and phenylalanine is not converted, so it accumulates [1].
The enzyme is a protein: swallowed as a tablet it would be digested by proteases in the stomach and small intestine into amino acids, and even if some survived, it is needed inside liver cells, not in the gut [1]; a low-protein diet (with a special protein substitute lacking phenylalanine) reduces the substrate entering the body so it cannot build up [1].
8. Two tubes of hydrogen peroxide are prepared. To tube A a student adds 1 g of raw liver; to tube B 1 g of manganese(IV) oxide, an inorganic catalyst. Both foam. The student then boils fresh samples of both catalysts for five minutes, cools them, and repeats.
Predict and explain the results, and use them to explain one way in which an enzyme differs from an inorganic catalyst and one way in which it is the same.
Reveal answer
Unboiled: both foam, because both catalysts lower the activation energy of 2H₂O₂ → 2H₂O + O₂ [1]. Boiled liver: little or no foam, because catalase is a protein and heating breaks the bonds holding its shape, so the active site changes shape and peroxide no longer binds — it is denatured [1].
Boiled manganese(IV) oxide: still foams, because it is not a protein and has no folded shape to lose [1]. Difference: an enzyme is a protein whose activity depends on its three-dimensional shape and is destroyed by heat (and extreme pH). Same: both speed up the reaction without being used up, and both give the same products [1].
Summary
- Enzymes are biological catalysts — proteins that increase the rate of reactions in living things by lowering the activation energy, without being used up.
- An enzyme is a chain of amino acids folded into a specific three-dimensional shape, held by hydrogen and ionic bonds; the active site is a small region complementary in shape to the substrate.
- The substrate binds to the active site to form an enzyme–substrate complex; the reaction is catalysed; the products are released and the enzyme is unaltered and reused. Fischer described this attachment as the lock-and-key hypothesis (1894); Koshland’s induced-fit model (1958) adds that the active site is flexible.
- Enzymes are substrate-specific. Amylase: starch → maltose. Protease: protein → amino acids. Lipase: fats → fatty acids and glycerol. Lactase: lactose → glucose and galactose. Catalase: hydrogen peroxide → water and oxygen.
- Rate = amount of product formed (or substrate used) ÷ time, with its unit; convert to the same units before comparing rates.
Next time → Temperature: why your enzymes work best at 37 °C, why a fever of 42 °C is dangerous, why bacteria in a hot spring can live at 80 °C — and what “denatured” really means.