Many proteins are enzymes — AQA A-Level Biology
Verified courseTeaching note checked against the official specification.
Many proteins are enzymes explained
Many proteins are enzymes covers 6 specification points, including Each enzyme lowers the activation energy of… and The induced-fit model of enzyme action..
Read the full explanation
Open a point below for its explanation and revision guidance.
Each enzyme lowers the activation energy of the reaction it catalyses.
Reactions require an initial energy input, the activation energy, to break bonds and reach the transition state. Enzymes provide an alternative pathway with a lower activation energy. When a substrate binds to the active site, an enzyme-substrate complex forms. Interactions with specific R groups (charged, polar, or hydrophobic) lining the active site can strain bonds in the substrate. Alternatively, the active site holds multiple substrates close together in the correct orientation. Consequently, less energy is needed. At a given temperature, a greater proportion of molecules possesses kinetic energy greater than or equal to this lowered activation energy, increasing the frequency of successful collisions and raising the reaction rate without needing extra heat.
The induced-fit model of enzyme action.
In the older lock-and-key model the active site is a rigid shape that exactly matches the substrate. The induced-fit model replaces that rigidity with flexibility: before binding, the substrate is only approximately complementary to the active site. As it enters, the tertiary structure of the enzyme changes so the active site moulds itself around the substrate, becoming fully complementary. This conformational change puts strain on bonds in the substrate, which lowers the activation energy. It also explains observations a rigid model cannot: why some enzymes accept a small range of similar substrates, and why a non-competitive inhibitor binding away from the active site can still alter the active site's shape.
The properties of an enzyme relate to the tertiary structure of its active site and its ability to combine with complementary substrate(s) to form an enzyme-substrate complex.
An enzyme is a globular protein, and its active site is a small depression formed when the polypeptide folds. The sequence of amino acids, the primary structure, determines which R groups face each other and therefore which hydrogen bonds, ionic bonds and disulfide bridges form. This determines the tertiary structure and the precise arrangement of the active site. Only a substrate with a complementary shape and complementary charges can bind there, forming an enzyme-substrate complex. The R groups then catalyse the reaction and the products leave. Because it is the tertiary structure of the site that matters, two enzymes with completely different amino acid sequences elsewhere can theoretically catalyse the same reaction if their active sites share a similar tertiary structure.
The specificity of enzymes The effects of the following factors on the rate of enzyme- controlled reactions – enzyme concentration, substrate concentration, concentration of competitive and of non- competitive inhibitors, pH and temperature.
Enzyme specificity arises from the complementary fit between a substrate and the active site. Rate depends on collision frequency and enzyme-substrate complex formation. Increasing enzyme or substrate concentration increases rate until the other becomes a limiting factor, causing a plateau. Temperature increases kinetic energy and collision rate up to an optimum; above this, or at extreme pH, hydrogen and ionic bonds break. This alters the tertiary structure, denaturing the active site so it is no longer complementary. Competitive inhibitors bind the active site, which is overcome by adding substrate. Non-competitive inhibitors bind allosteric sites, changing the active site shape so fewer enzyme-substrate complexes form; this inhibition is typically reversible, though some inhibitors can bind irreversibly.
Students should be able to: appreciate how models of enzyme action have changed over time appreciate that enzymes catalyse a wide range of intracellular and extracellular reactions that determine structures and functions from cellular to whole-organism level.
Enzyme models have evolved with new evidence. The lock-and-key model proposed a rigid active site perfectly complementary to the substrate. Later evidence supported the induced fit model, where the active site is flexible and moulds around the substrate, straining bonds to lower activation energy. Enzymes catalyse diverse reactions determining structure and function across all levels. Intracellularly, enzymes like DNA polymerase determine cellular structure and function by synthesising DNA. Extracellularly, amylase hydrolyses starch into maltose in the gut, aiding whole-organism digestive function. Other enzymes determine whole-organism structure, such as those synthesising structural proteins like collagen.
Required practical 1: Investigation into the effect of a named variable on the rate of an enzyme-controlled reaction.
You choose one named independent variable, temperature, pH, substrate concentration, enzyme concentration or inhibitor concentration, and measure a rate. The common systems are catalase from potato, celery or yeast acting on hydrogen peroxide, with the volume of oxygen collected in a gas syringe per unit time; amylase acting on starch, taking samples into iodine in potassium iodide solution at fixed intervals and timing how long the blue-black colour takes to disappear; and trypsin clearing a milk suspension, timed or followed with a colorimeter. Enzyme and substrate must be brought separately to the test temperature in a water bath before mixing, the pH held with a buffer, and every other volume and concentration kept the same, so that only the chosen variable changes. Timing starts at mixing.
Your focus
- Explain, using an energy level diagram, why a catalysed reaction proceeds quickly at 37 degrees Celsius when the uncatalysed reaction needs far more heat.
- Describe how binding of the substrate in the active site strains its bonds so that less energy is needed to reach the transition state.
- State two quantities an enzyme does not change, the overall energy change of the reaction and the final amount of product, and justify each.
Show all 18 objectives
- Describe what happens to the active site as a substrate enters, and name the change as a change in tertiary structure.
- Compare the induced-fit and lock-and-key models, giving one observation that induced fit explains and lock and key does not.
- Explain why an enzyme can catalyse many reactions one after another, referring to the active site returning to its original shape.
- Explain how two enzymes with different amino acid sequences can catalyse the same reaction, referring to the tertiary structure of their active sites.
- Describe the formation of an enzyme-substrate complex, naming the property of the substrate that allows it to bind.
- Predict the effect on the rate of reaction of a mutation that changes one amino acid within the active site, and justify the prediction.
- Explain the shape of a rate against substrate concentration curve by naming the limiting factor for each region of the graph.
- Distinguish competitive from non-competitive inhibition from data showing what happens when substrate concentration is raised.
- Describe, in terms of bonds and tertiary structure, why activity falls either side of the optimum pH and above the optimum temperature.
- Explain how the induced fit model developed from the lock-and-key model due to new evidence.
- Distinguish between intracellular and extracellular enzyme reactions with named examples.
- Describe how enzymes determine both structures and functions from the cellular to the whole-organism level.
- Plan an investigation into one named variable affecting enzyme activity, stating the range of values, the measure of rate and three controlled variables.
- Calculate an initial rate of reaction from a product against time curve by drawing a tangent at the origin.
- Evaluate a given enzyme method, identifying one variable that has not been controlled and explaining how it would affect the results.
Many proteins are enzymes exam tips
Marking Points
- State that the enzyme lowers the activation energy of the reaction.
- Describe the substrate binding to the active site to form an enzyme-substrate complex.
- Explain that bonds in the substrate are strained or distorted, or substrates are held in the correct orientation, so bonds break or form more readily.
- Note the consequence that a greater proportion of molecules now has enough energy to react, so the rate increases at a lower temperature.
- Note that the enzyme is unchanged and reused, and that the energy difference between substrate and product is unaltered.
- stating that the active site, not the substrate, changes shape as the substrate binds
- explaining that the substrate is only partly complementary at first and becomes fully complementary as the enzyme moulds around it
- describing this process as a change in the tertiary structure of the enzyme or active site
- linking the shape change to strain on bonds in the substrate and the subsequent lowering of activation energy
- noting that the active site returns to its original shape after the products leave
- stating that the active site has a specific tertiary structure, determined by the sequence of amino acids
- explaining that the substrate is complementary to the active site, allowing it to bind
- describing the successful binding as the formation of an enzyme-substrate complex
- explaining that two enzymes with different amino acid sequences can bind the same substrate if their active sites share a similar tertiary structure
- noting that a change in tertiary structure leaves the active site no longer complementary, preventing enzyme-substrate complexes from forming
- Enzyme specificity is determined by the tertiary structure of the active site being complementary to the substrate.
- At high temperatures or extreme pH, hydrogen and ionic bonds break, altering the tertiary structure and denaturing the enzyme.
- A competitive inhibitor has a similar shape to the substrate and binds to the active site, but its effect is reduced by increasing substrate concentration.
- A non-competitive inhibitor binds to an allosteric site, changing the active site shape so fewer enzyme-substrate complexes form; this inhibition is typically reversible, not necessarily permanent.
- On a rate against substrate concentration graph, the plateau indicates that all active sites are occupied, making enzyme concentration the limiting factor; on a rate against enzyme concentration graph, the plateau indicates that substrate concentration is limiting.
- Describe the lock-and-key model as featuring a rigid active site that is already complementary to the substrate.
- Describe the induced fit model as the active site changing shape to mould around the substrate, straining bonds to lower activation energy.
- Explain that models changed because later evidence showed the active site is flexible rather than rigid.
- Provide an example of an enzyme determining function, such as extracellular amylase hydrolysing starch to maltose for digestion.
- Provide an example of an enzyme determining structure, such as intracellular enzymes synthesising structural molecules like cellulose or collagen.
- one mark for naming the independent variable and stating a suitable range and interval of values
- one mark for a valid measure of rate, such as volume of oxygen collected per minute or one divided by the time for the colour to disappear
- one mark for two relevant controlled variables, such as volume and concentration of substrate, enzyme concentration, pH held with a buffer, or temperature held in a water bath
- one mark for equilibrating enzyme and substrate separately to the set temperature before mixing, and starting timing at the moment of mixing
- one mark for repeating at each value, discarding anomalies and calculating a mean
Examiner Tips
- 💡On an energy level diagram, draw a lower peak for the catalysed route but keep the substrate and product levels exactly where they were.
- 💡For 'explain', write the chain in order: substrate binds to active site, enzyme-substrate complex forms, bonds strained, activation energy lowered, rate increases.
- 💡Never use the word 'energy' on its own in an enzyme answer; say activation energy, and say whether it goes up or down.
- 💡When describing the induced-fit model, use terms like 'moulds' or 'changes shape as the substrate binds' to clearly distinguish it from the lock-and-key model.
- 💡Say 'complementary to', never 'the same shape as', when describing substrate and active site.
- 💡When comparing the two models, write both halves of each comparison in the same sentence to make the contrast explicit.
- 💡Trace the chain in this order every time: gene, base sequence, amino acid sequence, tertiary structure, active site, complementary substrate.
- 💡Write enzyme-substrate complex in full at least once before using any abbreviations.
- 💡If a question says two enzymes catalyse the same reaction, focus your answer on the active site's tertiary structure, not the rest of the molecule.
- 💡When describing a plateau on a graph, explicitly name the limiting factor at that point rather than just describing the shape of the curve.
- 💡Use the term 'denatured' only for high temperatures or extreme pH, and always specify that hydrogen and ionic bonds break to alter the tertiary structure.
- 💡For non-competitive inhibition, say the inhibitor binds an allosteric site and changes the active site shape; avoid claiming the change is permanent unless the question specifies an irreversible inhibitor.
- 💡When comparing enzyme models, explicitly contrast the rigid active site of lock-and-key with the flexible active site of induced fit.
- 💡Ensure you can provide specific examples of enzymes determining both structure (e.g., cellulose synthase) and function (e.g., amylase producing maltose).
- 💡Give rate with correct units: a volume of oxygen collected per second has units cm³ s⁻¹, while s⁻¹ applies only to a rate expressed as 1/time.
- 💡Name the buffer and the water bath explicitly; 'kept pH the same' without saying how does not earn the control mark.
- 💡If asked to improve the method, change one thing that reduces uncertainty, such as smaller intervals near the optimum or a data logger instead of a stopwatch.
Common Mistakes
- Writing that the enzyme gives energy to the reaction or supplies the activation energy, instead of lowering it.
- Saying the enzyme lowers 'its own' activation energy rather than that of the reaction it catalyses.
- Claiming the enzyme produces more product, when it only changes how quickly the same amount of product forms.
- Labelling the active site on the substrate rather than on the enzyme.
- Stating that the enzyme is used up, so more must be added as the reaction proceeds.
- describing the substrate as changing shape to fit the active site, when it is the enzyme that changes
- writing that the substrate has an active site, which is a fundamental misunderstanding of enzyme action
- using lock-and-key wording such as 'exact fit' or 'rigid' while claiming to describe induced fit
- saying the enzyme changes shape and is therefore denatured, confusing a reversible conformational change with denaturation
- relying solely on 'shape' rather than specifying 'tertiary structure' when explaining active site conformation
- saying the substrate is 'the same shape as' the active site rather than complementary to it
- assuming that two enzymes with different primary structures must always catalyse different reactions
- using abbreviations like ESC without first defining them as enzyme-substrate complex
- carrying active site language into antibody, receptor or transport protein answers, where binding site is the correct term
- Stating that low temperatures denature enzymes; correction: low temperatures only reduce kinetic energy and collision frequency, whereas high temperatures cause denaturation.
- Claiming that increasing substrate concentration overcomes a non-competitive inhibitor; correction: non-competitive inhibitors alter the active site shape, so adding more substrate has no effect.
- Saying a non-competitive inhibitor binds to the active site; correction: they bind to an allosteric site elsewhere on the enzyme.
- Describing non-competitive inhibition as always permanent; correction: non-competitive inhibition is typically reversible, so the active site shape change is not necessarily permanent.
- Stating amylase breaks starch directly into glucose; correction: amylase hydrolyses starch into the disaccharide maltose.
- Describing the induced fit model as the substrate changing shape to fit the enzyme; correction: it is the enzyme's active site that changes shape to mould around the substrate.
- Overlooking the 'structure' aspect of enzyme function; correction: remember enzymes also synthesise structural components, such as cellulose for plant cell walls or collagen in animals.
- quoting the total volume of gas collected as the rate, instead of volume per unit time
- reading rates from the flattening part of a product against time curve rather than using initial rate from a tangent at the origin
- mixing enzyme and substrate before either has reached the water bath temperature, so the first readings are at the wrong temperature
- writing 'the same amount of enzyme' rather than the same volume and the same concentration
- saying repeats make the results accurate, when repeats improve repeatability and do nothing about a systematic error