Enzymes and Biochemical Reactions

🟢 Lite — Quick Review (1h–1d)

Rapid summary for last-minute revision before your NECO exam.

What are Enzymes? Enzymes are biological catalysts — proteins that speed up chemical reactions in living organisms without being consumed. They are not used up in the reaction.

Key Properties:

• Specific: Each enzyme acts on one specific substrate (lock and key model)
• Reusable: An enzyme molecule can catalyse thousands of reactions per second
• Efficient: Can increase reaction rate by millions of times
• Sensitive: Affected by temperature, pH, and substrate concentration

The Lock and Key Model: The substrate (key) fits into the enzyme’s active site (lock). The enzyme-substrate complex forms, the reaction occurs, and products are released.

Induced Fit Model (more accurate): The active site is not rigid — it adjusts shape to fit the substrate more precisely, like a glove moulding around a hand.

Factors Affecting Enzyme Activity:

Factor	Effect
Temperature	Increases to optimum (~37–40°C in humans), then denatures
pH	Each enzyme has optimum pH (e.g., pepsin: pH 2, amylase: pH 7)
Substrate concentration	Rate increases until enzyme saturation
Enzyme concentration	Rate proportional to enzyme concentration (if substrate is excess)
Inhibitors	Competitive (binds active site) or non-competitive (binds elsewhere)

⚡ NECO Tip: Remember the optimum pH values: pepsin (stomach, pH 1.5–2), amylase (saliva/pancreas, pH 7), trypsin (duodenum, pH 8). Below pH 2 or above pH 10, enzymes denature permanently.

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🟡 Standard — Regular Study (2d–2mo)

Standard content for NECO Biology students with a few days to months.

Mechanism of Enzyme Action:

1. Substrate binds to active site of enzyme
2. Enzyme-substrate complex forms
3. Reaction occurs (bonds broken/formed)
4. Products are released
5. Enzyme is free to catalyse another reaction

Enzyme Classification:

Type	Reaction Catalysed	Example
Oxidoreductases	Oxidation-reduction	Dehydrogenase
Transferases	Transfer of groups	Transaminase
Hydrolases	Bond breaking with water	Amylase, lipase, protease
Lyases	Bond breaking without water	Decarboxylase
Isomerases	Structural rearrangement	Phosphohexose isomerase
Ligases	Bond formation	DNA ligase

Enzyme Cofactors:

• Metal ions: Fe²⁺, Mg²⁺, Zn²⁺, Mn²⁺ — essential for enzyme function
• Coenzymes: Non-protein organic molecules (e.g., NAD⁺, FAD, coenzyme A) — act as electron carriers
• Prosthetic groups: Tightly bound cofactors (e.g., haem in catalase)

Competitive Inhibition: The inhibitor competes with the substrate for the active site. Effect can be overcome by increasing substrate concentration. Example: sulfa drugs inhibit bacterial folic acid synthesis.

Non-competitive Inhibition: The inhibitor binds to a site other than the active site (allosteric site), changing the enzyme’s shape. Effect cannot be overcome by adding more substrate. Example: cyanide inhibits cytochrome oxidase.

Reversible vs Irreversible Inhibition:

• Reversible: inhibitor binds weakly (electrostatic/hydrogen bonds)
• Irreversible: inhibitor forms covalent bonds with enzyme (e.g., organophosphate pesticides)

⚡ NECO Common Mistakes:

• Thinking enzymes are used up in reactions — they are not
• Forgetting that high temperatures denature enzymes (permanent loss of function)
• Confusing competitive and non-competitive inhibition
• Not knowing that enzymes work best within a specific pH range

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🔴 Extended — Deep Study (3mo+)

Comprehensive coverage for NECO and JAMB Biology preparation.

Enzyme Kinetics — Michaelis-Menten Model:

$$v = \frac{V_{\max}[S]}{K_m + [S]}$$

Where:

• $v$ = initial reaction rate
• $V_{\max}$ = maximum rate (when all enzyme molecules are saturated)
• $[S]$ = substrate concentration
• $K_m$ = Michaelis constant (substrate concentration at which $v = V_{\max}/2$)

When $[S] \ll K_m$: reaction is first-order with respect to substrate. When $[S] \gg K_m$: reaction is zero-order with respect to substrate.

Lineweaver-Burk Plot (Double Reciprocal): $$\frac{1}{v} = \frac{K_m}{V_{\max}} \cdot \frac{1}{[S]} + \frac{1}{V_{\max}}$$

A straight line is obtained. The y-intercept = $1/V_{\max}$, x-intercept = $-1/K_m$. Useful for determining inhibition type:

• Competitive inhibition: same $V_{\max}$, increased $K_m$
• Non-competitive inhibition: same $K_m$, decreased $V_{\max}$

Denaturation:

Enzyme structure (3D shape) is maintained by:

• Hydrogen bonds
• Ionic bonds
• Hydrophobic interactions
• Disulfide bridges

Denaturation occurs when these bonds are broken:

• Heat: Vibration disrupts bonds above optimum temperature
• pH: Changes ionisation state of amino acids
• Organic solvents: Disrupt hydrophobic interactions

Allosteric Regulation:

Allosteric enzymes have multiple binding sites. Binding of a molecule at one site affects binding at another. Allosteric inhibitors bind to the allosteric site, changing the active site shape. This is how feedback inhibition works: the end product of a metabolic pathway inhibits an enzyme earlier in the pathway.

Specific Enzymes — Detailed:

Catalase: Found in liver and blood. Catalyses decomposition of hydrogen peroxide (a toxic byproduct of metabolism): $$2\text{H}_2\text{O}_2 \rightarrow 2\text{H}_2\text{O} + \text{O}_2$$

Carbonic Anhydrase: In red blood cells. Catalyses: $\text{CO}_2 + \text{H}_2\text{O} \rightleftharpoons \text{H}_2\text{CO}_3$ This reaction is 10,000× faster with the enzyme.

DNA Polymerase: Replicates DNA during cell division. Adds nucleotides to the 3’-OH end of a growing strand. Requires a primer.

Photosynthetic Enzymes: Rubisco (ribulose bisphosphate carboxylase/oxygenase): The most abundant enzyme on Earth. Catalyses carbon fixation in the Calvin cycle. Can also act as an oxygenase (photorespiration) when $O_2$ concentration is high relative to $CO_2$.

NECO/JAMB Patterns:

• NECO frequently asks: explain the lock and key model; describe the effect of temperature and pH on enzyme activity; distinguish between competitive and non-competitive inhibition; describe the induced fit model; state the role of coenzymes

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