C1.1Theme C — Interaction and interdependence
Enzymes and metabolism — IB Biology HL Revision Notes & Topical Questions
10 min read 12 parts Lesson 2 of 11 2 quizzes
Curriculum Equation Key قوانين الرقم الهيدروجيني والاتزان الأيوني - pH & Acid-Base Equilibrium FormulasFast Exam Solution
pH = -log[H⁺] | pOH = -log[OH⁻] | pH + pOH = 14 | [H⁺][OH⁻] = 10⁻¹⁴
Word Equation & Conditions: الرقم الهيدروجيني = -لوغاريتم تركيز أيون الهيدروجين | pH + pOH = 14
Location & Specifications: الاتزان الأيوني، كيمياء 3 ثانوي، التحصيلي، و AP Chemistry.
Lesson summary
C1.1 Enzymes and metabolism — IB BIOLOGY HL notes: Explain how enzymes catalyse metabolic reactions, how their activity is affected and measured, and how inhibition controls metabolic pathways.Need for catalysts — most reactions are very slow or do not occur spontaneously at cell…
- Enzyme-substrate specificity
- Collisions
- Enzyme-substrate complex
- Active site
- Lock-and-key model
- Induced-fit hypothesis
Section 1 of 12Enzymes as biological catalysts
1Need for catalysts
- Need for catalysts most reactions are very slow or do not occur spontaneously at cell conditions.
- High temperature, pressure, extreme pH or high reactant concentration speed reactions but would harm cells.
2Enzymes
- Enzymes proteins that act as biological catalysts, allowing reactions at a suitable rate in living organisms.
- They are reusable and unchanged, so only a few are needed.
- They hold substrate molecules in the correct orientation and close together.
- The cell controls which enzymes it makes and so controls its reactions.
3Metabolism
Metabolism all the chemical reactions in cells and organisms, with the molecules involved called metabolites.
- Many reactions have several stages, each with its own enzyme, forming a metabolic pathway.
4Enzyme-substrate specificity
- Enzyme-substrate specificity a globular enzyme has an active site complementary (not identical) in shape and chemistry to its substrate,
- so thousands of enzymes are needed.
Section 2 of 12Anabolism and catabolism
| Feature | Anabolism | Catabolism |
|---|---|---|
| Process | Builds large molecules from small ones | Breaks large molecules into smaller ones |
| Energy | Endergonic, needs energy input | Exergonic, releases energy as free energy or heat |
| Reaction type | Often condensation | Often hydrolysis |
| Substrates | Several substrates make one product | One substrate gives two or more products |
| Purpose | Growth, repair and energy storage | Digestion, excretion and energy supply |
| Examples | Photosynthesis, protein synthesis, glycogen formation | Respiration, deamination releasing urea, digestion |
- Both are enzyme-catalysed and coupled to ATP, the main energy carrier.
Section 3 of 12Enzyme action and the induced-fit model
Collisions
- Collisions substrates collide at random with the active site,
- and the collision must have the correct orientation and speed, otherwise molecules bounce off.
- Some enzymes have two substrates that bind at separate sites at once.
Enzyme-substrate complex
- Enzyme-substrate complex a temporary complex in which the substrate is changed and the products detach, leaving the enzyme free.
Active site
- Active site a few amino acids in the 3-D protein shape bind the substrate, hold it in position and lower the energy needed.
- Catalase binds hydrogen peroxide, but DNA polymerase does not.
Lock-and-key model
- Lock-and-key model the active site is precisely complementary to the substrate.
Induced-fit hypothesis
- Induced-fit hypothesis the current model, in which the enzyme and sometimes the substrate change shape as the substrate enters.
- (conformational changes)
- This gives an ideal binding arrangement and maximises catalysis.
Molecular motion
- Molecular motion greater kinetic energy gives faster movement and more collisions, more complexes and more product.
Section 4 of 12Immobilised enzymes
Methods of immobilising enzymes
- Attachment to an inert substance such as glass.
- Entrapment in a matrix such as alginate gel.
- Entrapment in a partially permeable membrane.
Uses
- Uses food processing, environmental management, pharmaceuticals and manufacturing.
Advantages
- The product is not contaminated, so no filtering or further processing is needed.
- The enzyme can be reused, which is efficient and cheap.
- The enzyme is more tolerant of temperature and pH changes and more stable.
- Substrates meet higher enzyme concentrations, which raises throughput.
- Conditions can be controlled close to the optimum.
Section 5 of 12Denaturation and factors affecting activity
Denaturation
- Denaturation heat or extreme pH breaks hydrogen bonds and other bonds holding the 3-D shape, but not the peptide bonds.
- The active site changes permanently and the substrate cannot bind.
- The enzyme often becomes insoluble and precipitates.
- Few human enzymes work above 50 °C, and temperatures over 40 °C begin to denature enzymes.
Temperature
- Each enzyme has an optimum temperature.
- At low temperatures, molecules have less kinetic energy, so collisions are fewer and less energetic and fewer complexes form.
- As temperature rises, more frequent and more energetic collisions speed the reaction, until the enzyme denatures and the rate drops sharply.
pH
- pH depends on hydrogen ion concentration, and a tenfold increase in H+ lowers pH by 1 unit, so the scale is logarithmic.
- Each enzyme has an optimum pH, such as pH 2 for pepsin and pH 9–10 for some bacterial enzymes.
- Extreme pH alters hydrogen bonding and causes irreversible denaturation.
Substrate concentration
- A higher concentration gives more collisions, but active sites become saturated.
- At saturation, extra substrate has no effect, and raising enzyme concentration adds active sites.
Section 6 of 12Investigating enzyme activity
Design
- Design the independent variable can be temperature, pH or substrate concentration.
- Plan how to measure the dependent variable with units, choose intervals, and control other variables.
Catalase investigation, measuring product formation
Investigating enzyme activity
Catalase in potato pieces breaks down hydrogen peroxide into water and oxygen.
Combine hydrogen peroxide with catalase and measure the volume of oxygen in a set time.
For temperature, hold the flask in a water bath above the level of peroxide, swirling gently.
- Amylase investigation, measuring substrate disappearance
1
Amylase hydrolyses starch to maltose, and works best at pH 7 and 37 °C.
2
Mix amylase and starch and test samples at intervals with iodine in potassium iodide.
3
Blue-black means starch is present and yellow-brown means it has gone.
4
Repeat for different starch concentrations, pH, temperature or enzyme concentration.
- Colorimetry
- absorbance or transmission measures colour change in a reaction.
1
Calibrate the colorimeter using weak iodine solution as the endpoint.
2
Make starch concentrations by serial dilution from a stock solution.
3
Use the red filter and measure percentage absorbance or transmission.
4
Plot a calibration graph of starch concentration against absorbance or transmission.
Section 7 of 12Reaction rates and activation energy
Rate of reaction
- Rate of reaction it is found from product formed or substrate used per unit time, or as 1 ÷ time taken (units s−1).
- A shorter time means a higher rate.
Rate changes during the reaction as substrate falls, so the graph starts linear and then plateaus.
Initial rate
Initial rate change in volume ÷ change in time, the gradient of a tangent at the origin, in cm3 s−1.
Nature of science
- Nature of science describing patterns and trends in graphs and sketching generalised graphs are examples of models.
Enzyme-substrate complex
- Enzyme-substrate complex the substrate is in a transition state before the product forms.
Energy changes
- Exergonic reactions release energy to the surroundings.
- Endergonic reactions absorb energy.
- These differ from exothermic and endothermic, which describe only thermal energy.
Activation energy
Activation energy the energy a substrate needs to become unstable enough to react.
- Enzymes lower it by reducing the stability of bonds in the substrate.
- The energy released by the reaction is unchanged, but the rate is faster.
Section 8 of 12Metabolic pathways
Metabolic pathways
Intracellular enzymes work inside the cell,
- such as those of glycolysis and the Krebs cycle,
- and extracellular enzymes are secreted in vesicles,
- such as digestive enzymes.
Energy and heat
- Aerobic respiration oxidises glucose to carbon dioxide and water, releasing free energy, some as heat because transfers are not 100% efficient.
- Endotherms (birds, mammals) use metabolic heat to keep body temperature constant, and ectotherms cannot.
- Endergonic reactions such as protein synthesis are linked to exergonic reactions by ATP.
Pathway types
- Linear pathways have a distinct start and end, such as glycolysis.
- Cyclic pathways have an end product that restarts the cycle, such as the Calvin cycle and Krebs cycle.
- Intermediates are metabolites that form new molecules or break down molecules with energy transfer.
Section 9 of 12Competitive and non-competitive inhibition
Competitive and non-competitive inhibition
Inhibitor
Inhibitor a chemical that binds an enzyme and reduces its activity, either formed in the cell or from outside.
Competitive inhibitors
- Competitive inhibitors they resemble the substrate, bind reversibly to the active site and compete with it.
- Statins resemble the substrate of the enzyme that makes cholesterol,
- so LDL cholesterol falls, reducing the risk of atherosclerosis and coronary heart disease.
Non-competitive inhibitors
- Non-competitive inhibitors they bind reversibly to an allosteric site away from the active site.
- Binding causes a conformational change that alters the active site while the effector stays bound.
| Feature | Competitive | Non-competitive |
|---|---|---|
| Binding site | Active site | Allosteric site |
| Resemblance to substrate | Similar | Unlike |
| Effect | Blocks the active site | Changes the shape of the active site |
| Raising substrate concentration | Overcomes inhibition | Cannot overcome it |
| Maximum rate | Unchanged | Lowered |
- Both types lower the initial rate, and a high enough inhibitor concentration stops the reaction.
Section 10 of 12End-product and mechanism-based inhibition
1End-product (feedback) inhibition
- End-product (feedback) inhibition an excess end product acts as an allosteric, non-competitive inhibitor of the first enzyme.
- It stops intermediates building up.
- When product falls, the inhibitor detaches and the enzyme restarts, forming a feedback loop.
2Isoleucine example
- Isoleucine example isoleucine inhibits threonine deaminase, the first enzyme of its own pathway in bacteria.
- Use of isoleucine in protein synthesis lowers its level, so more enzymes are free and production resumes.
3Mechanism-based inhibition
- Mechanism-based inhibition a substrate analogue forms covalent bonds with the active site and is changed into a reactive group.
- A stable inhibitor-enzyme complex forms and inhibition is irreversible.
4
Penicillin example
1
Growing bacterial walls of cross-linked peptidoglycan are opened by autolysins so new peptidoglycan can be added.
2
Penicillin resembles part of the peptide chain, so DD-transpeptidase binds it and forms a stable complex.
3
Cross-links can no longer form while autolysins keep making holes.
4
The weakened wall bursts by osmosis, which is death by lysis.
5
It works only on growing bacteria.
- Resistance
- mutations change the active site of DD-transpeptidase, and plasmid genes spread by conjugation, even between species.
Section 11 of 12Key terms
| Term | Meaning |
|---|---|
| Active site | the region of an enzyme where the substrate binds. |
| Activation energy | the energy needed for a reaction to start. |
| Induced fit | the active site changing shape as the substrate binds. |
| Allosteric site | a site away from the active site where effectors bind. |
| Competitive inhibitor | an inhibitor that binds the active site in place of the substrate. |
| End-product inhibition | control of a pathway by its product inhibiting an early enzyme. |
| Anabolism | building large molecules from small ones using energy. |
| Catabolism | breaking down large molecules and releasing energy. |
| Immobilised enzyme | an enzyme fixed to or trapped in a support. |
Section 12 of 12Exam technique
1
Enzymes are used up — they are reusable and unchanged.
2
The active site and substrate have the same shape — their shapes are complementary.
3
Denaturation breaks peptide bonds — it breaks bonds holding the 3-D shape only.
4
Raising substrate concentration overcomes all inhibition — it works for competitive but not non-competitive inhibitors.
Marked practiceQuizzes for this lesson
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