Enzymes and the Induced Fit Model — AQA A-level Biology

SPEC 3.1.4.2 - ENZYMES

Enzymes

Induced fit, active site specificity, factors affecting rate, competitive and non-competitive inhibition, and Required Practical 1

What is an Enzyme?

AQA SPEC (3.1.4.2)

Each enzyme lowers the activation energy of the reaction it catalyses. 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.

Key Properties

Globular proteins — specific 3D tertiary structure

Biological catalysts — speed up reactions without being consumed or permanently altered

Lower the activation energy (Ea) of the reaction

Highly specific — each enzyme catalyses one reaction or type of reaction

Work both intracellularly (inside cells) and extracellularly (outside cells, e.g. digestive enzymes)

Activation Energy

Activation energy is the minimum energy needed for reactants to reach the transition state so a reaction can proceed. Enzymes lower Ea by:

Orienting substrates correctly

Straining bonds in the substrate (induced fit)

Providing a microenvironment that stabilises the transition state

A lower Ea means a greater proportion of molecules have sufficient energy → faster reaction rate.

The Active Site and Enzyme Specificity

DEFINITION

The active site is the region of the enzyme with a specific three-dimensional shape that is complementary to the shape of its substrate(s).

Enzyme specificity arises directly from the tertiary structure of the active site:

1

The specific sequence of amino acids (primary structure) → determines which R-group interactions occur → determines tertiary structure → creates a precise active site shape

2

The active site is complementary in shape and charge to one specific substrate (or class of substrate) only

3

Substrate binds to form an enzyme-substrate complex → reaction proceeds → products released → active site is free for the next substrate molecule

Complementary ≠ Identical

The active site is complementary to the substrate — not the same shape. Just as a lock is complementary to a key (not identical to it). The shapes fit together — they are not the same shape. This distinction is tested directly in AQA mark schemes.

The Induced Fit Model

AQA SPEC (3.1.4.2)

The induced-fit model of enzyme action. Students should be able to appreciate how models of enzyme action have changed over time.

Lock-and-Key Model (Historical)

Proposed by Emil Fischer (1894) — contextual enrichment only, not required for AQA exams

Active site has a fixed, rigid shape

Substrate fits exactly — like a key into a lock

Now superseded — does not explain all enzyme behaviour

Induced Fit Model (Current)

Proposed by Daniel Koshland (1958) — contextual enrichment only, not required for AQA exams

Active site is flexible — not rigid

When substrate binds, the active site changes shape slightly to mould around the substrate more precisely

This conformational change strains the substrate's bonds → lowers activation energy → catalysis occurs

Products are released; active site returns to original shape

Use the Correct Model

AQA mark schemes award marks for the induced fit model. Do not describe the lock-and-key model as current — it is historical. In induced fit, the active site changes shape as substrate binds. Saying "the active site is exactly the right shape for the substrate" (lock-and-key language) loses marks.

Effect of Temperature on Enzyme Activity

RangeEffect on rateExplanation

Below optimumRate increases with temperatureGreater kinetic energy → enzyme and substrate molecules move faster → more frequent enzyme-substrate collisions per second → higher rate

Above optimumRate decreases sharply, eventually = 0Heat disrupts hydrogen bonds and ionic bonds maintaining tertiary structure → active site changes shape → no longer complementary to substrate → enzyme denatured

Effect of pH on Enzyme Activity

Mechanism

Each enzyme has an optimum pH — the pH at which its active site shape is most complementary to its substrate. Changes in pH away from optimum disrupt the tertiary structure of the enzyme:

H⁺ and OH⁻ ions interact with charged R-groups (e.g. protonating –COO⁻ or deprotonating –NH₃⁺)

This disrupts ionic bonds between oppositely charged R-groups maintaining tertiary structure

May also disrupt hydrogen bonds between R-groups

Active site changes shape → no longer complementary to substrate → enzyme activity reduced or abolished → denaturation

EnzymeLocationOptimum pHReason for optimum

PepsinStomach~pH 2Evolved for the highly acidic stomach environment; R-groups optimised for acidic ionic bond pattern

AmylaseMouth / small intestine~pH 7–8Salivary amylase works near neutral; pancreatic amylase works in slightly alkaline duodenum

TrypsinSmall intestine~pH 7.5–8Produced by pancreas into alkaline duodenum

pH and Denaturation Language

Do not say "pH change breaks peptide bonds." pH disrupts ionic bonds and hydrogen bonds between R-groups → changes active site shape → denaturation. Peptide bonds are not affected by physiological pH changes.

Effect of Substrate Concentration

Explanation

Low [S]: Not all active sites occupied → rate increases as [S] increases (more enzyme-substrate complexes form per second)

At Vmax: All active sites are occupied (saturated) — adding more substrate has no effect because there are no free active sites. Rate is limited by the number of enzyme molecules present.

Vmax is not changed by competitive inhibitors (eventually) — but is reduced by non-competitive inhibitors

Competitive Inhibition

DEFINITION

A competitive inhibitor has a molecular shape complementary to the active site. It competes with the substrate for the active site, occupying it and preventing substrate binding.

Mechanism

Competitive inhibitor has a shape similar to the substrate → binds to the active site

When inhibitor is bound, substrate cannot bind → no enzyme-substrate complex → no product

Binding is reversible — the inhibitor dissociates from the active site

Effect can be reduced by increasing [substrate] — more substrate molecules outcompete the inhibitor for active sites

Effect on Rate–Substrate Graph

Vmax is unchanged — at high enough [S], substrate outcompetes the inhibitor completely

A higher [S] is needed to reach Vmax — the curve shifts to the right

Example: malonate (similar shape to succinate) competitively inhibits succinate dehydrogenase

Non-Competitive Inhibition

DEFINITION

A non-competitive inhibitor binds to an allosteric site on the enzyme (not the active site). This causes a conformational change in the active site shape, so the substrate can no longer bind effectively.

Mechanism

Non-competitive inhibitor binds to the allosteric site — a site separate from the active site

Binding changes the shape of the active site (conformational change) — active site is no longer complementary to the substrate

Binding may be reversible or irreversible depending on the inhibitor

Effect CANNOT be overcome by increasing [substrate] — the active site is permanently misshapen regardless of how much substrate is present

Effect on Rate–Substrate Graph

Vmax is reduced — even at very high [S], the rate cannot reach the original Vmax

Example: cyanide non-competitively inhibits cytochrome oxidase (in the electron transport chain)

Key Distinction on Graphs

Competitive: same Vmax, curve shifts right (higher [S] needed). Non-competitive: reduced Vmax, curve flattens at a lower maximum. This graph interpretation is a consistent AQA exam question.

Inhibition — Side by Side

FeatureCompetitiveNon-Competitive

Binding siteActive siteAllosteric site (not active site)

Effect on active siteBlocks substrate access (active site shape unchanged)Changes active site shape (via conformational change)

ReversibilityReversible — inhibitor competes with substrateUsually irreversible (sometimes reversible)

Effect of ↑[substrate]Reduces inhibition — substrate outcompetes inhibitorNo effect — active site is misshapen regardless

VmaxUnchanged (at high enough [S])Reduced

ExampleMalonate inhibiting succinate dehydrogenaseCyanide inhibiting cytochrome oxidase; heavy metal ions

Required Practical 1 — Enzyme Activity

RP1: Investigating Factors Affecting Enzyme Activity (e.g. Amylase/Starch with Iodine Clock, or Catalase/H₂O₂)

Variables

IV (examples): temperature, pH, substrate concentration, inhibitor concentration, enzyme concentration

DV: time for colour change (iodine clock), volume of O₂ produced (catalase), change in absorbance (colorimeter)

Control variables: temperature (water bath), pH (buffer), enzyme concentration (if not IV), substrate concentration (if not IV)

Calculating Rate

Rate (iodine clock) = 1 ÷ time (for colour change to occur)

Rate (O₂ production) = volume O₂ ÷ time (cm³ min⁻¹)

Initial rate: draw tangent to the curve at time = 0; calculate gradient

Control Variable Justification

AQA mark schemes require you to state why each variable is controlled — not just what is controlled. Example: "I used a buffer solution of pH 7 to maintain constant pH because a change in pH would disrupt the ionic bonds in the enzyme's tertiary structure, altering the active site shape and changing the rate independently of the variable being investigated."

Effect of Enzyme Concentration

Effect

Increasing enzyme concentration increases the rate of reaction — provided substrate concentration is not limiting. More enzyme molecules → more active sites available → more enzyme-substrate complexes form per second → greater rate.

If substrate concentration is limiting (fixed, low [S]), increasing enzyme concentration beyond a certain point has no further effect — all substrate molecules are already being processed; active sites are empty waiting for substrate.

Synoptic Link — Proteins

Enzyme concentration affects rate because each enzyme molecule has a specific active site (tertiary structure). More enzyme = more active sites = more simultaneous enzyme-substrate complexes. This links enzyme action directly back to protein structure from Lesson 1.04.

Exam Alert — Limiting Factors

Always state the condition under which an increase in enzyme concentration will increase rate: "...provided substrate concentration is not the limiting factor." If substrate is limiting, increasing enzyme concentration has no effect regardless of how many more active sites are present.

DEEP Framework: Extended Answer

Question: "Using the induced fit model, explain how a competitive inhibitor reduces the rate of an enzyme-catalysed reaction and explain why increasing substrate concentration reduces this inhibition." [5 marks]

D

Define: A competitive inhibitor has a molecular shape complementary to the active site of the enzyme. It competes with the substrate for the active site. The active site is the specific region of the enzyme with a shape complementary to its substrate (induced fit model — the site changes shape slightly as substrate/inhibitor binds).

E

Explain mechanism: The inhibitor binds to the active site, preventing substrate from binding. No enzyme-substrate complex forms. The activation energy cannot be lowered. No product is formed. Therefore the rate of reaction decreases. As [inhibitor] increases, more active sites are occupied by inhibitor at any one time → fewer enzyme-substrate complexes per second → lower rate.

E

Evidence/Example: Malonate competitively inhibits succinate dehydrogenase (in Krebs cycle). Malonate is structurally similar to succinate (the substrate) and occupies the active site. When more succinate is added, it outcompetes malonate → rate increases. This is reversible competitive inhibition.

P

Practical/Graph: On a rate-vs-substrate concentration graph: with competitive inhibitor, the curve shifts to the right — a higher [S] is needed to reach Vmax. At very high [S], the curve reaches the same Vmax as without inhibitor — because substrate molecules outcompete the inhibitor. Vmax unchanged.

Practice Question

(a) Describe the induced fit model of enzyme action and explain how it lowers the activation energy of a reaction. [3 marks]

(b) A student adds a non-competitive inhibitor to an enzyme-catalysed reaction. Explain, using the concept of the allosteric site, why increasing substrate concentration does not restore the original rate. [3 marks]

(c) Sketch the expected shape of a rate-vs-substrate concentration graph for: (i) no inhibitor, (ii) competitive inhibitor, (iii) non-competitive inhibitor. State which property of each curve — Vmax or shape — distinguishes the inhibitor type. [3 marks]

D:

(a) The active site is not rigid — when the substrate binds, the active site changes shape slightly to mould more closely around the substrate (1). This conformational change strains the bonds in the substrate, lowering the activation energy needed for the reaction to proceed (1). Products are released and the active site returns to its original shape (1).

E:

(b) The non-competitive inhibitor binds to the allosteric site — a site on the enzyme separate from the active site (1). This causes a conformational change in the shape of the active site (1). The active site is no longer complementary to the substrate, so enzyme-substrate complexes cannot form regardless of how much substrate is present — increasing [S] cannot restore the rate because the active site itself is misshapen, not merely occupied (1).

E:

(c) (i) No inhibitor: curve rises then plateaus at Vmax. (ii) Competitive inhibitor: curve rises but needs higher [S] to reach the same Vmax — curve shifts right; Vmax unchanged (1). (iii) Non-competitive inhibitor: curve plateaus at a lower Vmax; the shape of the early rise may be similar but the maximum is reduced (1). Distinguishing property: competitive = same Vmax, shifted right; non-competitive = reduced Vmax (1).

Common Exam Errors

Alert 1 — Lock-and-Key vs Induced Fit

Never describe the lock-and-key model as current AQA theory. Always use induced fit: "as the substrate binds, the active site changes shape slightly around it." Lock-and-key language (rigid, pre-formed, perfect fit from the start) will not score full marks.

Alert 2 — Non-competitive inhibitor binding site

Non-competitive inhibitors bind to the allosteric site — not the active site. Students who write "binds to a different part of the active site" or "changes the shape of the substrate" both lose marks. The inhibitor binds at the allosteric site → changes the active site shape.

Alert 3 — Denaturation language for temperature/pH

Always name the specific bonds disrupted: "increased temperature disrupts hydrogen bonds and ionic bonds maintaining the tertiary structure → active site changes shape → substrate can no longer bind." "The enzyme changes shape" alone scores 1 mark. The mechanism is required for full marks.

Alert 4 — Vmax and inhibitor type

Competitive inhibitor: Vmax unchanged (substrate can outcompete). Non-competitive: Vmax reduced (cannot be overcome by substrate). Confusing these on graph questions loses marks in every sitting.

Summary

Key Points

TopicKey Fact

EnzymeGlobular protein; biological catalyst; lowers activation energy; highly specific (one active site = one substrate type)

Induced fitActive site is flexible; changes shape slightly as substrate binds; strains substrate bonds → lowers Ea

Temperature ↑Below optimum: more collisions → rate↑. Above optimum: H-bonds/ionic bonds broken → denaturation → rate↓

pH changeH⁺/OH⁻ disrupt ionic bonds/H-bonds → active site shape changes → denaturation

[Substrate] ↑Rate↑ until Vmax (all active sites saturated)

Competitive inhibitorBinds active site; blocks substrate; reversed by ↑[S]; Vmax unchanged

Non-competitive inhibitorBinds allosteric site; changes active site shape; NOT reversed by ↑[S]; Vmax reduced

RP1Rate = 1/time (iodine clock) or volume/time (O₂). State control variables WITH justification.

Exam Tip

Enzyme questions always reward: (1) naming the model (induced fit), (2) naming bonds disrupted in denaturation (H-bonds, ionic bonds), (3) stating the consequence (active site changes shape/substrate cannot bind), and (4) linking inhibitor type to graph behaviour (Vmax changed or unchanged).