# Enzymes and metabolism

> IB Biology SL · IB Diploma Biology Standard Level
> Source: https://www.owlsprep.com/study/ib-biology-sl-u2-enzymes-and-metabolism/

This module covers enzyme structure, mechanisms of action, factors affecting reaction rate, inhibitors, and metabolic pathway regulation aligned to all IB SL Biology assessment objectives.

**Prerequisites:** [Basic globular protein and amino acid structure](https://www.owlsprep.com/study/ib-biology-sl-u2-protein-structure/); [Introduction to cellular respiration and ATP](https://www.owlsprep.com/study/ib-biology-sl-u2-cell-respiration-intro/)

## Learning objectives

- Define enzymes as globular biological catalysts that speed up metabolic reactions without being consumed
- Compare the lock-and-key and induced fit models of enzyme-substrate specificity
- Analyze the effects of temperature, pH, and substrate concentration on enzyme reaction rate
- Describe the role of enzymes in metabolic pathways including end-product inhibition

## Core Properties of Enzymes

**Enzyme** — Globular proteins that act as biological catalysts, lowering the activation energy of chemical reactions without being altered or consumed in the process.

*Example:* Catalase, the enzyme that breaks down toxic hydrogen peroxide in mammalian liver cells.

All enzymes have a unique 3D tertiary structure that forms a pocket called the active site, which is complementary in shape and chemical properties to one specific substrate molecule. This specificity means most enzymes only catalyze one single metabolic reaction, and do not interact with unrelated molecules.

**Worked example:** Identify which of the following statements correctly describes a property of enzymes: A) Enzymes are consumed after 10 reaction cycles, B) Enzymes lower the activation energy of a reaction, C) Enzymes raise the final free energy of product molecules, D) Enzymes work equally well across all pH values.

1. Eliminate option A: Enzymes are not consumed at any point in the reaction, so they can be reused indefinitely for thousands of cycles.
2. Eliminate option C: Enzymes only affect activation energy, not the total free energy of reactants or final products.
3. Eliminate option D: Enzymes have a narrow optimal pH range, and extreme pH values denature their active site permanently.
4. Confirm option B is correct: The core function of all enzymes is to reduce activation energy to speed up reaction rates.

> **tip**
>
> IB mark schemes almost always award 1 mark for stating enzymes are globular proteins, not just 'biological catalysts' — do not skip this detail in extended responses.

## Models of Enzyme Action

**Exam command terms**

IB exam questions often ask you to 'compare' the two enzyme action models, so use the following cues to hit full marks:

- **Lock and key model** — Original 1890s model that assumes the active site is a rigid, perfect match for the substrate at all times *(Used as a simplified analogy for enzyme specificity)*

- **Induced fit model** — Current accepted model that describes the active site changing shape slightly to wrap tightly around the substrate after binding *(Explains why some enzymes can bind multiple closely related substrates)*

> **mnemonic**
>
> Remember: Induced = In motion (the active site moves to fit), Lock and Key = No movement (rigid pre-shaped lock)

**Check your understanding**

Test your understanding of the two models:

1. Which model explains why the active site is not a perfect pre-formed match for the substrate?

   *Why:* The induced fit model accounts for the dynamic, flexible nature of the globular protein structure that forms the active site.

> **Exam tip:** When asked to 'describe the induced fit model' for 3 marks, you must mention: 1) active site is not perfectly complementary pre-binding, 2) substrate triggers conformational change, 3) this change strengthens the enzyme-substrate complex to reduce activation energy.

## Factors Affecting Enzyme Reaction Rate

| Factor | Effect on rate as value increases | Explanation of plateau |
| --- | --- | --- |
| Temperature | Rises to optimum, then drops sharply to zero | Above optimum, hydrogen bonds in tertiary structure break, denaturing the active site |
| pH | Peaks at narrow optimum, drops on either side | H+ or OH- ions alter the charge of amino acid R-groups in the active site |
| Substrate concentration | Rises linearly, then plateaus at maximum Vmax | All available active sites are fully saturated with substrate at any given time |

**Worked example:** Explain the shape of a catalase reaction rate curve as substrate concentration increases from 0 to 1.0 mol dm⁻³.

1. Start at 0 reaction rate when there is no substrate present to bind to active sites.
2. At low substrate concentrations, rate increases proportionally with substrate, as more active sites have molecules to bind.
3. At ~0.4 mol dm⁻³, the curve levels off to a flat horizontal line at Vmax.
4. Explain the plateau: every enzyme active site is occupied at all times, so adding more substrate cannot increase the rate further.

## Inhibitors and Metabolic Pathway Regulation

**End-product inhibition** — A regulatory mechanism for metabolic pathways where the final product of the reaction sequence binds to an allosteric site on the first enzyme in the pathway to stop over-production of the product.

*Example:* ATP inhibiting phosphofructokinase in the glycolysis pathway.

- Competitive inhibitors bind to the active site directly, and can be overcome by increasing substrate concentration
- Non-competitive inhibitors bind to an allosteric site separate from the active site, and cannot be overcome by adding more substrate

> **warning**
>
> IB examiners will deduct marks if you state competitive inhibitors 'block the substrate' — the correct phrasing is that they 'compete with the substrate for access to the active site'.

## Common pitfalls

- **Wrong:** Stating that enzymes are denatured at temperatures below their optimum
  - Why it fails: Low temperature only reduces molecular kinetic energy, it does not break the bonds that maintain the active site shape
  - Correct: Write that low temperature reduces reaction rate due to fewer successful collisions between substrate and active site, with no permanent denaturation.
- **Wrong:** Describing the induced fit model as 'the substrate changes shape to fit the active site'
  - Why it fails: The substrate is usually a small, rigid molecule — the enzyme's active site is the part that undergoes conformational change
  - Correct: Explicitly state that the active site of the enzyme alters its shape to form a tight, complementary fit around the bound substrate.
- **Wrong:** Claiming that increasing enzyme concentration will never increase reaction rate
  - Why it fails: If substrate is in excess, adding more enzyme will increase the number of available active sites, raising Vmax
  - Correct: Note that Vmax only plateaus when all active sites are saturated, so extra enzyme will raise the maximum rate if substrate is abundant.
- **Wrong:** Classifying end-product inhibition as a form of competitive inhibition
  - Why it fails: The end product binds to a separate allosteric site, not the active site of the first enzyme in the pathway
  - Correct: Label end-product inhibition as an example of allosteric non-competitive inhibition, as required by IB mark schemes.
- **Wrong:** Writing that enzymes 'raise the activation energy' of a reaction
  - Why it fails: This is the exact opposite of their core function, and is one of the most common mark scheme penalties
  - Correct: Always confirm you write that enzymes lower activation energy to speed up the conversion of substrates to products.

## Cheatsheet

| Key term | IB mark scheme definition |
| --- | --- |
| Enzyme | Globular biological catalyst that lowers activation energy, not consumed in reaction |
| Active site | Region of enzyme complementary to substrate shape and chemical properties |
| Induced fit | Active site changes shape to tightly bind substrate after initial contact |
| Vmax | Maximum reaction rate when all enzyme active sites are fully saturated |
| End-product inhibition | Allosteric regulation of metabolic pathways by final product binding to first enzyme |

## What's next

Mastering enzymes and metabolism is critical for scoring well on both Paper 1 multiple choice and Paper 2 extended response questions, as this topic frequently overlaps with content on cellular respiration, photosynthesis, and molecular biology lab practicals. The concepts you have learned here will also directly support your work on the required enzyme catalase IA investigation, where you will design and execute your own experiment to test the effect of a variable on reaction rate. This foundational knowledge of biological catalysts will help you contextualize all metabolic processes covered later in the syllabus.

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