IB DP Biology: Enzymes and metabolism: active sites, rates, inhibition (DP Biology)

This study guide covers IB Diploma Programme Biology section C1.1 (Enzymes and metabolism), as set out in the IB Biology guide, first assessment 2025. Statements C1.1.1 to C1.1.10 are for standard level and higher level. Statements C1.1.11 to C1.1.17 are additional higher level, so every part marked HL only below is not needed at SL.

Use it with the revision notes and the practice questions. Course hub: IB DP Biology. Checklist: printable checklist. To find weak spots first, try the free 10-minute diagnostics.

What this unit covers

Section	What you must be able to do	Level
C1.1.1	Explain why speeding up reactions benefits cells	SL and HL
C1.1.2	Describe metabolism as a network and say how enzyme specificity gives control	SL and HL
C1.1.3	Distinguish anabolism and catabolism with the listed examples	SL and HL
C1.1.4	Describe enzymes as globular proteins and explain how the active site gets its properties	SL and HL
C1.1.5	Describe induced fit	SL and HL
C1.1.6	Explain why molecular motion and collisions matter; immobilised substrates and enzymes	SL and HL
C1.1.7	Link active site structure to specificity and denaturation	SL and HL
C1.1.8	Explain and interpret the effects of temperature, pH and substrate concentration	SL and HL
C1.1.9	Measure and calculate reaction rates, including from secondary data	SL and HL
C1.1.10	Explain activation energy and interpret energy profile graphs	SL and HL
C1.1.11 to C1.1.13	Intracellular and extracellular enzymes; metabolic heat; linear and cyclical pathways	HL only
C1.1.14, C1.1.15, C1.1.17	Non-competitive, competitive and mechanism-based inhibition	HL only
C1.1.16	Feedback inhibition	HL only

Catalysts, metabolism and the two directions (C1.1.1 to C1.1.3)

Enzymes are biological catalysts: they raise the rate of a reaction and emerge from it unchanged. Many reactions that cells depend on would be far too slow at body temperature without one, and cells cannot use extreme heat to speed them up.

Metabolism is the whole network of interdependent, interacting chemical reactions in an organism. The products of one reaction are the substrates of the next. Each enzyme is specific to one reaction or one type of reaction, so a cell needs a great many different enzymes. That specificity is also what gives control: if a cell changes how much of one enzyme is active, it changes the rate of that one step.

• Anabolism builds larger molecules from smaller ones, using condensation reactions. Examples: making macromolecules from monomers, protein synthesis at ribosomes, glycogen formation from glucose, and photosynthesis.
• Catabolism breaks larger molecules into smaller ones. Examples: hydrolysis of macromolecules into monomers during digestion, and oxidation of substrates in cell respiration.

The enzyme and its active site (C1.1.4 to C1.1.7)

Enzymes are globular proteins: the polypeptide folds into a compact, roughly spherical three-dimensional shape. The active site is a small region where the substrate binds and the reaction happens. It is built from only a few amino acids. Folding brings these amino acids together even if they are far apart in the primary sequence. Interactions between amino acids elsewhere in the enzyme (hydrogen bonds, ionic bonds, hydrophobic interactions) hold the whole structure in the right shape, so the active site has the right size, shape and chemical properties for catalysis.

Induced fit. The substrate fits the active site closely, but neither is a rigid lock and key. When the substrate binds, both the enzyme and the substrate change shape slightly. This strains bonds in the substrate and makes the reaction easier.

Motion and collisions. Substrate and active site must meet. Molecules in solution move randomly, and a reaction can happen only after a collision with the substrate correctly oriented at the active site. Sometimes the substrate is large and immobilised, for example a structural polymer, so the enzyme moves to it. Sometimes the enzyme is immobilised, for example embedded in a membrane, so the substrate moves to the enzyme.

Specificity and denaturation. The active site shape and charge match only certain substrates, so the enzyme is specific. Anything that changes the three-dimensional structure changes the active site and can stop it binding the substrate. Denaturation is a loss of the enzyme’s three-dimensional structure through disruption of the bonds that hold it. A denatured enzyme usually cannot return to its working shape, so the loss of activity is usually permanent.

Temperature, pH and substrate concentration (C1.1.8)

Explain each effect in terms of collision theory and denaturation.

• Temperature. Below the optimum, a rise in temperature gives molecules more kinetic energy. They move faster, collide more often, and more collisions have enough energy to react, so the rate rises. Above the optimum, the enzyme vibrates enough to break the bonds holding its shape. The active site changes shape, the substrate no longer binds, and the rate falls sharply as more enzyme molecules are denatured.
• pH. Each enzyme has an optimum pH. Away from it, the charges on R groups of amino acids change, which disrupts ionic and hydrogen bonds. The active site distorts and the enzyme may be denatured. Pepsin works best in the acid conditions of the stomach, while enzymes in saliva work best near neutral pH.
• Substrate concentration. More substrate means more collisions with active sites, so the rate rises. At high concentration every active site is occupied nearly all the time. The rate levels off at a maximum, and only more enzyme (or a better temperature or pH) would raise it.

Sketch graphs of these relationships are models, and real data from enzyme experiments can be used to evaluate them.

Worked example: interpreting temperature data

A student mixed a protease with a cloudy milk suspension and recorded the time for the cloudiness to clear. Rate is taken as 1000 divided by time, in arbitrary units per second.

Temperature / °C	Time to clear / s	Rate (1000 / time)
20	240	4.2
30	120	8.3
40	60	16.7
50	90	11.1
60	no clearing in 600 s	about 0

1. From 20 to 40 °C the rate doubles with each 10 °C step (4.2, 8.3, 16.7).
2. From 40 to 50 °C the rate changes by (11.1 − 16.7) / 16.7 × 100 = −33%.
3. The optimum lies between 30 and 50 °C, probably near 40 °C, but no reading lies between 40 and 50.
4. At 60 °C the enzyme was almost certainly denatured, so substrate could not bind.

Measuring rates (C1.1.9)

Rate is the amount of product formed, or substrate used, per unit time, found from your own experiment or from secondary data. Typical measures: volume of gas collected, absorbance of a coloured product measured in a colorimeter, mass of substrate remaining, or the time for a visible change (rate is then proportional to 1 / time).

Reaction rate is highest at the start, when substrate is most concentrated. Use the initial rate: the gradient of the curve at the start, or the change over the first few readings.

Worked example: initial rate from absorbance

An enzyme converts a colourless substrate to a coloured product.

Time / min	0	1	2	3	4	5	6	7
Absorbance	0	0.12	0.23	0.33	0.41	0.47	0.51	0.53

1. Initial rate over the first 3 minutes = (0.33 − 0) / 3 = 0.11 absorbance units per minute.
2. Rate between 5 and 7 minutes = (0.53 − 0.47) / 2 = 0.03 absorbance units per minute.
3. The rate has fallen to about 27% of the initial rate (0.03 / 0.11). Substrate has been consumed, so collisions with active sites are rarer.

Activation energy (C1.1.10)

Activation energy is the energy needed to start a reaction. In an enzyme-catalysed reaction, energy is needed to break bonds in the substrate, and energy is released when bonds form in the products. An enzyme lowers the activation energy by holding the substrate in a strained position in the active site. It does not change the energy of reactants or products, so the overall energy change is the same.

Worked example: reading an energy profile

Data: reactants at 40 kJ mol⁻¹, products at 15 kJ mol⁻¹, peak of the uncatalysed path at 85 kJ mol⁻¹, peak of the catalysed path at 50 kJ mol⁻¹.

1. Activation energy without enzyme = 85 − 40 = 45 kJ mol⁻¹.
2. Activation energy with enzyme = 50 − 40 = 10 kJ mol⁻¹.
3. The enzyme lowers it by 35 kJ mol⁻¹.
4. Overall change = 15 − 40 = −25 kJ mol⁻¹ in both cases, so energy is released.

Where enzymes work, and metabolic heat (C1.1.11, C1.1.12) – HL only

Intracellular enzymes work inside cells. Examples: glycolysis in the cytoplasm and the Krebs cycle in the mitochondrial matrix. Extracellular enzymes are made in cells, secreted, and work outside them. Chemical digestion in the gut is the example: pancreatic and salivary amylase act on starch in the lumen.

Metabolic reactions are not 100% efficient at transferring energy, so some energy always appears as heat. Mammals, birds and some other animals rely on this heat to keep a constant body temperature.

Pathways (C1.1.13) – HL only

A linear pathway runs from start to end product in a line. Glycolysis is the example: glucose is converted step by step to pyruvate. A cyclical pathway regenerates a starting molecule, so the cycle can run again. The Krebs cycle and the Calvin cycle are the examples.

Inhibition (C1.1.14, C1.1.15, C1.1.17) – HL only

An inhibitor reduces enzyme activity.

• Competitive inhibitor. It resembles the substrate and binds reversibly to the active site, so substrate and inhibitor compete. Raising substrate concentration makes the inhibitor less effective, because the substrate wins more often. Statins are an example: they compete with the substrate of an enzyme in cholesterol synthesis in the liver, so less cholesterol is made.
• Non-competitive inhibitor. It binds reversibly to an allosteric site, a site other than the active site. Only specific substances fit it. Binding causes a conformational change that alters the active site enough to prevent catalysis. The inhibitor does not resemble the substrate and does not compete with it, so extra substrate does not overcome the inhibition.
• Mechanism-based inhibition. The inhibitor binds irreversibly and chemically changes the active site. Penicillin is the example. It binds permanently to the active site of transpeptidase, the bacterial enzyme that forms cross-links in the cell wall, so the wall is weakened. Resistant bacteria have a changed transpeptidase that penicillin cannot bind, and these bacteria survive and reproduce.

Worked example: which inhibitor?

Rates (arbitrary units) at different substrate concentrations:

Substrate / mM	1	2	4	8	16	32
No inhibitor	20	33	50	67	80	89
Inhibitor P	8	14	25	40	57	73
Inhibitor R	10	17	25	33	40	44

1. P at 1 mM: (20 − 8) / 20 × 100 = 60% reduction. At 32 mM: (89 − 73) / 89 × 100 = 18% reduction.
2. R at 1 mM: (20 − 10) / 20 × 100 = 50% reduction. At 32 mM: (89 − 44) / 89 × 100 = 51% reduction.
3. The effect of P shrinks as substrate rises, so P is competitive. The effect of R stays about the same, so R is non-competitive.

Feedback inhibition (C1.1.16) – HL only

In feedback inhibition the end product of a pathway inhibits an enzyme near the start. In the pathway that makes isoleucine, the end product isoleucine inhibits the first enzyme, threonine deaminase, which acts on threonine. When isoleucine is plentiful the pathway slows, saving resources. When it falls, the inhibition lifts and the pathway speeds up.

Common errors

• Saying heat “kills” an enzyme. A protein molecule was never alive, so call it denatured.
• Saying the substrate “no longer fits” without naming the cause: the active site has changed shape.
• Saying a competitive inhibitor “blocks” the enzyme at all substrate concentrations.
• Giving rate as “time taken” without converting to 1 / time.

Official syllabus

IB Diploma Programme Biology guide, first assessment 2025, published by the International Baccalaureate Organization. This page is a paraphrase aligned to section C1.1.