Educerie
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Educerie · IB Diploma · Biology

Theme C Interaction and interdependence · C1.1 Enzymes and metabolism

Level
SL and HL. Sections 9, 10 and 11 are HL only. If you are SL, skip them; nothing in your papers tests them.
Themes (key concepts)
interaction and interdependence, at the level of molecules. Metabolism is a system of thousands of reactions, each run by its own enzyme and each depending on the products of others; this subtopic is how those molecules meet, how fast they react, and how the network is kept under control.
The question this unit answers
in what ways do enzymes interact with other molecules, and what makes the reactions of metabolism depend on one another?
Where it is examined
Paper 1A multiple choice; Paper 1B, where an unfamiliar enzyme experiment arrives as a graph or table and you calculate a rate and judge the method; Paper 2 Section A short answers of 2 to 4 marks; Paper 2 Section B, where enzymes are one of the commonest parts of an extended response. HL adds inhibition and pathway control in all three.

What you must be able to do

You must be able toLevelWhat it looks like in the exam
Explain why cells need catalysts, define metabolism and say why so many enzymes are neededSL, HL"Outline the role of enzymes in metabolism" (2 marks)
Distinguish anabolic from catabolic reactions, with the guide's examplesSL, HL"Distinguish between anabolism and catabolism" (3 marks)
Explain the active site, induced fit, specificity and denaturationSL, HL"Explain how an enzyme catalyses a reaction" (4 marks)
Explain why molecular motion and collisions are needed, including immobilised enzymes and substratesSL, HLPaper 2 short answer, or Paper 1A
Explain and interpret graphs of the effect of temperature, pH and substrate concentrationSL, HLPaper 1B graph, or a Section B "explain" worth 5 to 7 marks
Determine rates from your own data and from secondary dataSL, HLPaper 1B: "Calculate the initial rate" (2 marks), with units
Interpret an energy diagram showing lowered activation energySL, HLLabel or annotate a graph (2 to 3 marks)
Compare intracellular and extracellular reactions; explain metabolic heat; distinguish linear and cyclic pathwaysHL onlyPaper 1A, or 2 to 3-mark short answers
Explain competitive and non-competitive inhibition and read their rate curvesHL onlyPaper 1B: "Deduce the type of inhibition" (3 marks)
Explain feedback inhibition (isoleucine) and mechanism-based inhibition (penicillin)HL only"Outline feedback inhibition" (3 to 4 marks)

Before you start

You need protein structure from B1.2: a polypeptide folds into a precise three-dimensional tertiary structure, held by hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between the R groups of its amino acids. You also need condensation and hydrolysis from B1.1, because most reactions below are one or the other.


1The idea in one paragraph

A cell runs thousands of chemical reactions at once, at a low temperature and in water, and almost none would run fast enough on their own to keep it alive. Enzymes are protein catalysts that make each reaction fast, and because each enzyme fits only one kind of substrate, the cell decides which reactions run by deciding which enzymes it makes and switches on. The substrate must collide with a pocket on the enzyme called the active site; when it binds, both change shape, bonds in the substrate are strained, and less energy is needed to break them. Anything that changes how often those collisions happen, or the shape of the active site, changes the rate. Fit, collision, shape and control: that is the subtopic.

2Enzymes as catalysts, and why metabolism needs so many

A catalyst speeds up a chemical reaction without being used up by it. An enzyme is a biological catalyst, and almost every enzyme is a protein.

Why does a cell need one? The hydrolysis of a protein into amino acids, in water at 37 °C, would take years. In your small intestine it takes minutes. A cell cannot heat itself to speed reactions up without destroying its own proteins, so it lowers the barrier instead, and reactions then run fast enough for the cell to grow, divide, move and respond on a timescale that matters.

Metabolism is the complex network of interdependent and interacting chemical reactions in a living organism. The product of one reaction is the substrate of the next, so a change at one point is felt everywhere downstream.

Each enzyme catalyses one reaction, or a small group of very similar ones. This specificity (section 4) has two consequences. Many different enzymes are needed: thousands, for thousands of reactions. And enzymes are where metabolism is controlled: stop making one enzyme, or switch it off, and its one reaction stops. A cell steers its chemistry by adjusting its enzymes.

3Anabolic and catabolic reactions

Anabolism builds larger, more complex molecules from smaller ones. It needs an input of energy, usually from ATP, and many of its reactions are condensations, which join two molecules and release water.

Catabolism breaks larger molecules into smaller ones and releases energy. Many of its reactions are hydrolyses, which break a bond by adding water; others are oxidations.

AnabolicCatabolic
What happenssmall molecules → large moleculeslarge molecules → small molecules
Energyneeded (usually from ATP)released
Typical reactioncondensationhydrolysis, or oxidation
Guide's examplesprotein synthesis; glycogen formation from glucose; photosynthesisdigestion (starch → maltose, protein → amino acids); oxidation of glucose in respiration

Use the guide's examples, because the mark scheme is written around them. Anabolism adds on; catabolism cuts apart.

4The active site, induced fit and specificity

An enzyme is a globular protein: its chain is folded into a compact, roughly spherical shape. On its surface is a small pocket, the active site, where the substrate binds and the reaction happens.

The active site is made of only a few amino acids. Of hundreds in the chain, perhaps a handful have R groups that touch the substrate. The rest of the protein holds those few in exactly the right positions, at the right distances, with the right charges facing the right way. Change the fold anywhere and the active site can be pulled out of shape, even though the amino acids lining it are unchanged.

It has chemistry as well as a shape. The R groups lining the site may be charged, polar or hydrophobic, and they form temporary bonds with the substrate. A substrate binds because both its shape and its chemistry match.

Induced fit is the model of what happens when they meet. When the substrate binds, the enzyme changes shape slightly and so does the substrate, so the two fit more closely than either did before. Figure 1 draws the sequence.

Figure 1 · Induced fit: both molecules change shape when they bind Figure 1 · Induced fit: both molecules change shape when they bind substrate enzyme active site products 1 Substrate collides with the active site 2 Enzyme–substrate complex: site and substrate both bend 3 Bonds in the substrate are strained and broken 4 Products released, enzyme unchanged The enzyme comes out of the reaction unchanged and can catalyse the next one.
Figure 1 · Induced fit: both molecules change shape when they bind

The change of shape does the work. As the enzyme closes around the substrate it strains particular bonds, making them easier to break, or holds two substrates in the exact position to bond. The products are released and the enzyme returns to its original shape, ready for the next molecule. Write "both the enzyme and the substrate change shape": the guide asks for exactly that.

Specificity follows. Only a molecule whose shape and chemistry match the active site can bind and be induced to fit, so each enzyme catalyses one reaction or type of reaction. Amylase hydrolyses starch and leaves proteins alone; a protease does the reverse.

Denaturation is a permanent change in a protein's three-dimensional structure, caused by breaking the bonds that hold its tertiary structure. For an enzyme it means the active site loses its shape and chemistry, the substrate can no longer bind, and catalysis stops. The amino acid sequence is still there; the fold is not. That is the chain the guide wants: active-site structure → specificity → loss of structure → loss of function.

5Molecules have to collide

An enzyme can only act if a substrate molecule reaches its active site. Molecules in solution are in constant random motion, and every so often a substrate collides with an active site in the right orientation and binds. Most collisions fail: wrong angle, wrong part of the enzyme. The rate depends on the number of successful collisions per second.

Usually both partners move, but the smaller one moves faster, so it is mostly the substrate that travels. The guide names two cases where one partner is held still.

  • The substrate is immobilised. Very large substrates, such as a starch grain or a strand of cellulose, stay put while enzyme molecules move to them and work at their surface.
  • The enzyme is immobilised. Some enzymes are embedded in membranes: the enzymes that finish digesting disaccharides are fixed in the membranes of cells lining the small intestine, and ATP synthase sits in the inner mitochondrial membrane. The substrate must reach them, and the enzyme is always where the cell needs it.

Everything in the next section follows: whatever raises the number of successful collisions per second raises the rate.

6Temperature, pH and substrate concentration

The guide wants each effect explained with reference to collision theory and denaturation. Use one or both in every answer about rate.

Temperature. Figure 2(a) is the shape to know.

Figure 2 · The effect of temperature and of pH on the rate of an enzyme reaction Figure 2 · The effect of temperature and of pH on the rate of an enzyme reaction (a) Temperature Rate of reaction (arbitrary units) Temperature (°C) optimum more collisions, more with enough energy denaturation: active site loses its shape 0 20 40 60 (b) pH Rate of reaction (arbitrary units) pH optimum charges in the active site altered charges in the active site altered 3 5 7 9 11 Both curves are sketch models, not data. Their exact positions differ from enzyme to enzyme.
Figure 2 · The effect of temperature and of pH on the rate of an enzyme reaction

As temperature rises, molecules move faster, collide more often, and more collisions have enough energy to react, so the rate rises; for many enzymes it roughly doubles with each 10 °C rise here. At the optimum the rate is highest. Above it, extra vibration breaks the hydrogen bonds and other weak bonds holding the tertiary structure, the active site loses its shape, fewer substrates bind, and the rate falls steeply as more molecules are denatured. The curve is asymmetric: a gentle rise, a steep fall.

Two details decide marks. At low temperature an enzyme is not denatured; it is slow because collisions are few and weak, and warming restores it. At high temperature denaturation is permanent; cooling does not bring it back. And the optimum is not always 37 °C: enzymes from bacteria in hot springs can have optima above 70 °C.

pH. Figure 2(b). At the optimum pH the charges on the R groups in the active site, and on the substrate, are right for binding. Away from it, the change in hydrogen ion concentration alters those charges; the substrate binds less well, the ionic and hydrogen bonds of the tertiary structure are disrupted, and at extremes the enzyme is denatured. The curve falls on both sides. The optimum depends on where the enzyme works: about pH 2 for pepsin in the stomach, about 7 for salivary amylase, about 8 for trypsin in the small intestine.

Substrate concentration. Figure 3.

Figure 3 · The effect of substrate concentration on the rate Figure 3 · The effect of substrate concentration on the rate Initial rate of reaction (arbitrary units) Substrate concentration (mmol dm⁻³) maximum rate: all active sites occupied rate limited by substrate: more collisions per second as [S] rises rate limited by the number of enzyme molecules Past a point, every active site is busy all the time. Adding substrate cannot help.
Figure 3 · The effect of substrate concentration on the rate

At low concentration most active sites are empty most of the time, so more substrate means more collisions per second and the rate rises almost in proportion. As concentration rises further, more sites are already occupied, so each extra substrate molecule adds less. Eventually every active site is busy all the time, the enzyme is saturated, and the curve levels off. The rate is now limited by the number of enzyme molecules, and only more enzyme would raise it.

These graphs are models. Figures 2 and 3 are sketch graphs: generalised shapes drawn without real numbers, which makes them models, and a model can be tested. If your catalase results fall steeply at 40 °C rather than 50 °C, the model still holds; the optimum is just different for your enzyme. If they kept rising to 90 °C, the model would not describe that enzyme at all. Faced with data in Paper 1B, describe the relationship in words (which variable, which direction, where it changes) and say whether it fits the sketch.

7Measuring the rate of an enzyme reaction

Rate is change per unit time: product made, or substrate used, divided by the time taken. Its unit is always "per time": cm³ s⁻¹, mg min⁻¹, or s⁻¹ when you have only a time.

Enzyme and substrateWhat you measureRate
Catalase (yeast, potato, liver) breaking hydrogen peroxide into water and oxygenVolume of oxygen in a gas syringe or upturned measuring cylindervolume ÷ time, cm³ s⁻¹
Amylase hydrolysing starchTime until a sample no longer turns iodine blue-black1 ÷ time, s⁻¹
A reaction with a coloured substrate or productAbsorbance in a colorimeterchange in absorbance ÷ time

Figure 4 shows invented results from the first: yeast suspension added to hydrogen peroxide, the oxygen read off every few seconds.

Figure 4 · Oxygen released by catalase in yeast (invented data) Figure 4 · Oxygen released by catalase in yeast (invented data) Volume of oxygen collected (cm³) Time (s) tangent at t = 0 0 20 40 60 80 100 120 0 10 20 30 36 rate slows as substrate is used up The initial rate is the gradient of the tangent at time zero: 36 cm³ ÷ 40 s = 0.9 cm³ s⁻¹.
Figure 4 · Oxygen released by catalase in yeast (invented data)

The curve flattens because hydrogen peroxide is being used up, so collisions become rarer. That is why enzyme experiments compare initial rates, measured at the very start before the substrate runs down.

mean rate over first 10 s = 8.0 cm3 ÷ 10 s = 0.80 cm3 s-1quick, slightly low
tangent at t = 0: rise ÷ run = 36 cm3 ÷ 40 s = 0.90 cm3 s-1the initial rate
mean rate over 120 s = 34.2 cm3 ÷ 120 s = 0.29 cm3 s-1useless for comparison

To draw the tangent, lay a ruler against the curve at the origin so it touches without cutting across, and read the gradient from two points far apart on the line. The mean over the whole run mixes the fast start with the slow end, so it says almost nothing about the enzyme.

In the experiment itself, change one independent variable (temperature, say), measure the dependent variable (rate), and control everything else that affects rate: enzyme volume and concentration, substrate volume and concentration, pH (with a buffer), and temperature unless it is the variable you are testing. Repeat each condition at least three times and take a mean.

8Enzymes lower the activation energy

Before new bonds can form in the products, bonds in the substrate must break, and breaking bonds takes energy. The activation energy is the energy that must be put in to break those bonds and start the reaction. When new bonds form in the products, energy is released; in a reaction such as protein hydrolysis more comes out than went in, so there is an overall yield of energy.

An enzyme lowers the activation energy, as Figure 5 shows.

Figure 5 · An enzyme lowers the activation energy of a reaction Figure 5 · An enzyme lowers the activation energy of a reaction Energy in the molecules Progress of the reaction without enzyme with enzyme Each vertical arrow is an activation energy: the energy needed to break bonds in the substrate substrate products overall energy released The enzyme changes the height of the hill, not the start or the finish.
Figure 5 · An enzyme lowers the activation energy of a reaction

The start (energy in the substrate) and the finish (energy in the products) are the same with or without the enzyme, so the overall energy released is the same. Only the hill between them changes. With the enzyme it is lower, because the strain of induced fit has already weakened the bonds that must break, and at cell temperature far more substrate molecules can get over a low hill than a high one. An enzyme supplies no energy and does not change the products; it changes only the route.

9HLWhere enzymes work, heat, and the shape of pathways

SL students can skip to section 12.

Intracellular and extracellular reactions. Most enzymes work inside the cell that made them: intracellular reactions, such as glycolysis in the cytoplasm and the Krebs cycle in the mitochondrial matrix (both in C1.2). Some are secreted and work outside: extracellular reactions, of which chemical digestion is the guide's example. Amylase, proteases and lipase are made in gland cells, released into the lumen of the gut, and hydrolyse food there, because starch and protein molecules are too large to enter a cell until they are broken into monomers.

Metabolism generates heat. No energy transfer in a cell is 100% efficient; in every reaction some energy ends up as heat rather than in the bonds of a product such as ATP. So heat production is inevitable while metabolism runs. Mammals, birds and some other animals depend on this heat to keep their body temperature constant, usually well above their surroundings, and raise their metabolic rate in the cold to make more. That is why an endotherm needs far more food than an ectotherm of the same mass.

Linear and cyclic pathways. A metabolic pathway is a sequence of enzyme-catalysed reactions in which each product is the substrate of the next step. Figure 6 shows the two shapes.

Figure 6 · Linear and cyclic pathways (HL) Figure 6 · Linear and cyclic pathways (HL) (a) Linear: glycolysis glucose (6C) enzyme 1 intermediate enzyme 2 intermediate enzyme 3 … enzyme n pyruvate (3C) (b) Cyclic: the Krebs cycle oxaloacetate (4C) citrate (6C) 5C and 4C compounds acetyl (2C) in CO₂ and reduced NAD out (c) Cyclic: the Calvin cycle RuBP (5C) GP (3C) TP (3C) CO₂ in some TP out to make sugars In a linear pathway the start is used up. In a cycle the start is made again at the end.
Figure 6 · Linear and cyclic pathways (HL)

In a linear pathway the starting substrate is converted step by step into an end product and is used up. Glycolysis is linear: glucose to pyruvate in about ten steps, each with its own enzyme. In a cyclic pathway the last step regenerates the molecule the cycle began with. In the Krebs cycle a 2-carbon acetyl group joins 4-carbon oxaloacetate to make 6-carbon citrate, and the rest of the cycle turns citrate back into oxaloacetate. In the Calvin cycle carbon dioxide joins 5-carbon RuBP, and most of the product rebuilds RuBP. The advantage of a cycle is economy: a small pool of the carrier molecule processes a large amount of incoming substrate, because it is turned over, never used up.

10HLInhibitors: competitive and non-competitive

An enzyme inhibitor binds to an enzyme and reduces its activity. The two kinds in Figure 7 bind reversibly, by weak bonds, and can leave again.

Figure 7 · Competitive and non-competitive inhibition (HL) Figure 7 · Competitive and non-competitive inhibition (HL) (a) Competitive (b) Non-competitive (allosteric) ✕ substrate inhibitor in the active site Similar shape to the substrate. More substrate wins the site back. substrate no longer fits inhibitor on the allosteric site active site changed shape Different shape from the substrate. More substrate does not help. A competitive inhibitor takes the active site. A non-competitive one changes its shape from elsewhere.
Figure 7 · Competitive and non-competitive inhibition (HL)

Competitive inhibition. A competitive inhibitor resembles the substrate in shape and chemistry, so it binds to the active site itself, and while it is there no substrate can bind. Inhibitor and substrate compete for the same sites, and whichever is more concentrated wins more collisions. So adding substrate reduces the inhibition, and at very high substrate concentration the rate approaches the uninhibited maximum.

The guide's example is statins, drugs that lower blood cholesterol. They competitively inhibit an enzyme in liver cells that catalyses an early step in cholesterol synthesis, so the liver makes less cholesterol.

Non-competitive inhibition. A non-competitive inhibitor binds elsewhere, at an allosteric site. Only specific substances can bind there, because the allosteric site has its own shape and chemistry. Binding causes interactions within the enzyme that change its shape (a conformational change), and the change alters the active site enough to prevent catalysis. Binding is reversible: when the inhibitor concentration falls, it leaves and the enzyme works again.

Because the substrate is not competing with the inhibitor, adding substrate does nothing for the inhibited molecules; it is as though some enzyme had been removed, so the maximum rate is lower. Figure 8 puts both on one graph, the graph a Paper 1B question will expect you to read.

Figure 8 · What each inhibitor does to the rate (HL) Figure 8 · What each inhibitor does to the rate (HL) Initial rate of reaction (arbitrary units) Substrate concentration (mmol dm⁻³) no inhibitor competitive non-competitive maximum: no inhibitor, or competitive at very high [S] lower maximum The competitive curve catches up at high [S]. The non-competitive curve never does.
Figure 8 · What each inhibitor does to the rate (HL)
CompetitiveNon-competitive
Binds toactive siteallosteric site
Shape compared with substratesimilardifferent
Adding more substratereduces inhibition; rate approaches the uninhibited maximumno effect; maximum rate stays lower
Guide's examplestatinsisoleucine on threonine deaminase (section 11)

To tell them apart from data, look at high substrate concentration. If the inhibited rate catches up with the uninhibited rate, the inhibitor is competitive. If it stays proportionately lower, it is non-competitive.

11HLFeedback inhibition and mechanism-based inhibition

Feedback inhibition is control of a pathway by its own end product, which acts as a non-competitive inhibitor of the enzyme for the pathway's first step. The guide's example is the synthesis of the amino acid isoleucine from threonine in bacteria and plants (Figure 9).

Figure 9 · Isoleucine switches off its own production (HL) Figure 9 · Isoleucine switches off its own production (HL) threonine threonine deaminase intermediate enzyme 2 intermediate enzyme 3 intermediate enzyme 4 intermediate enzyme 5 isoleucine isoleucine binds the allosteric site of threonine deaminase and inhibits it a chain of five enzyme-catalysed steps The end product inhibits the first enzyme, so supply follows demand without any waste.
Figure 9 · Isoleucine switches off its own production (HL)

Threonine becomes isoleucine through five enzyme-catalysed steps, the first catalysed by threonine deaminase. Isoleucine binds to an allosteric site on threonine deaminase and inhibits it.

  1. When isoleucine is plentiful, more of it binds, the first step slows, and less isoleucine is made.
  2. As the cell uses isoleucine to make proteins, its concentration falls; binding is reversible, so it leaves the allosteric sites.
  3. The enzyme becomes active again and isoleucine production resumes.

Supply follows demand. Inhibiting the first enzyme matters: no intermediates pile up uselessly and no threonine is spent on isoleucine that is not needed. This is negative feedback at the level of molecules.

Mechanism-based inhibition is different in kind: the inhibitor binds irreversibly. It enters the active site, the enzyme starts to act on it as if it were substrate, and the inhibitor becomes covalently bonded to the active site. That enzyme molecule never works again.

The guide's example is penicillin. An enzyme called transpeptidase forms the cross-links between chains of peptidoglycan that make a bacterial cell wall strong. Penicillin binds to its active site and becomes permanently attached. Without new cross-links the wall of a growing bacterium is weak; water enters by osmosis and the cell bursts. Human cells have no cell wall and no transpeptidase, which is why penicillin harms bacteria and not us.

Resistance. A mutation in the transpeptidase gene can change the active site so that penicillin no longer binds, while the enzyme still binds its normal substrate and still makes cross-links. A bacterium with that version survives penicillin, and repeated use of the antibiotic selects for it. (Some bacteria resist by making an enzyme that breaks penicillin down instead, but the altered transpeptidase is the route the guide asks for.)

12Where marks are lost

"The enzyme is killed." Enzymes are molecules, not organisms. Write denatured and give the reason: the active site has changed shape, so the substrate no longer binds.

Saying enzymes are denatured at low temperature. At low temperature the enzyme is intact but slow, because collisions are fewer and less energetic.

Explaining the plateau in Figure 3 as "the substrate has run out". Substrate is in excess there. The rate levels off because every active site is occupied, so enzyme is now limiting.

Saying the enzyme "provides energy". It lowers the activation energy, supplies none, and leaves the overall energy released unchanged.

Saying only the substrate changes shape. Induced fit means the enzyme and the substrate both change shape.

Describing an effect with no mechanism. "Rate rises to the optimum and then falls" is description. The marks are for the reasons: more frequent, more energetic collisions on the way up; denaturation of the active site on the way down.

Quoting a rate without units, or the mean over the whole run. A rate is per unit time, and the fair comparison is the initial rate.

HL · Mixing up the inhibitors. A competitive inhibitor competes with the substrate for the active site, reversibly; a non-competitive one binds an allosteric site. Penicillin is neither: it is a mechanism-based, irreversible inhibitor.

13Draw it right

  1. Axes labelled with variable and unit: temperature in °C, pH (no unit), substrate concentration in mmol dm⁻³ or %, rate per unit time or "arbitrary units".
  2. Temperature: gradual, accelerating rise to the optimum, then a steep fall. Not a symmetrical hump.
  3. pH: roughly symmetrical about the optimum, falling on both sides, optimum marked on the x-axis.
  4. Substrate concentration: from the origin, rising steeply, levelling off, never turning down.
  5. Initial rate: a ruled tangent at time zero, touching not cutting, with the rise and run shown.
  6. Activation energy: substrate above products, two humps from the same start to the same finish, the enzyme's lower, each activation energy an arrow from the substrate level to the top of its hump.
  7. HL inhibition: three curves from the origin; the competitive curve approaches the uninhibited maximum; the non-competitive curve levels off lower.

14Try it

Marks in brackets. Answers and marker's notes are at the end.

Q1. Which statement describes induced-fit binding? 1 mark

A. The active site has a fixed shape that exactly matches the substrate.

B. The substrate changes shape but the enzyme does not.

C. Both the enzyme and the substrate change shape when the substrate binds.

D. The enzyme changes shape permanently after catalysing each reaction.

Q2. Distinguish between anabolic and catabolic reactions, giving one example of each. 3 marks

Q3. A student timed how long amylase took to hydrolyse all the starch in a sample at six temperatures, testing a drop with iodine every 5 seconds, and calculated rate as 1 ÷ time. (Invented data.)

Temperature (°C)102030405060
Time for starch to disappear (s)48026015095120600
Rate (s⁻¹)0.00210.00380.00670.00830.0017

(a) Calculate the rate at 40 °C. 1 mark

(b) Estimate the optimum temperature and state how the method could locate it more precisely. 2 marks

(c) Explain the change in rate between 50 °C and 60 °C. 2 marks

(d) State two variables that should have been controlled. 1 mark

Q4. Explain the effect of increasing substrate concentration on the rate of an enzyme-catalysed reaction. 4 marks

Q5 (HL). The initial rate of an enzyme reaction was measured at six substrate concentrations, without and with a fixed concentration of substance X. (Invented data.)

Substrate concentration (mmol dm⁻³)125102040
Rate, no inhibitor (µmol min⁻¹)3.35.07.18.39.19.5
Rate, with X (µmol min⁻¹)1.42.54.56.37.78.7

(a) Calculate the rate with X as a percentage of the uninhibited rate at 1 mmol dm⁻³ and at 40 mmol dm⁻³. 2 marks

(b) Deduce, with a reason, the type of inhibition caused by X. 2 marks

Q6 (HL). Outline how the synthesis of isoleucine is controlled by feedback inhibition, and suggest one advantage of inhibiting the first enzyme in the pathway. 4 marks

15In one breath

Enzymes are globular proteins that catalyse the reactions of metabolism, a network of interdependent reactions; because each is specific, a cell needs thousands and controls its chemistry through them. Anabolism builds by condensation and needs energy (protein synthesis, glycogen, photosynthesis); catabolism breaks down by hydrolysis or oxidation and releases it (digestion, respiration). The active site is a few amino acids held in place by the whole fold; the substrate must collide with it, and on binding both change shape, straining bonds and lowering the activation energy. Warmer means more frequent, more energetic collisions up to the optimum, then denaturation; pH away from the optimum alters the active site's charges; more substrate means more collisions until every site is saturated. Compare initial rates, from a tangent, with units. HL: glycolysis and Krebs are intracellular, digestion extracellular; inefficient metabolism makes the heat endotherms rely on; glycolysis is linear, Krebs and Calvin are cycles. Competitive inhibitors (statins) take the active site and are beaten by more substrate; non-competitive ones bind an allosteric site and lower the maximum; isoleucine inhibits the first enzyme of its own pathway; penicillin binds transpeptidase irreversibly, and an altered transpeptidase gives resistance.


Answers

Q1. C. A is the old lock-and-key model; B leaves out the enzyme's change; D is wrong because the enzyme returns to its original shape. C only.

Q2. Anabolic reactions build larger molecules from smaller ones and need energy, whereas catabolic reactions break larger molecules into smaller ones and release energy. Anabolic: condensation of glucose into glycogen (or amino acids into a polypeptide, or photosynthesis). Catabolic: hydrolysis of starch into maltose in digestion (or oxidation of glucose in respiration). 1 for build-up versus break-down as a comparison, 1 for the energy difference or condensation versus hydrolysis, 1 for a correct example of each. An example on the wrong side scores 0 for that mark.

Q3. (a) 1 ÷ 95 = 0.011 s⁻¹ (0.0105), the highest rate in the table. value with unit. (b) Between 30 °C and 50 °C, most likely about 40 to 45 °C, since 40 °C gave the highest rate and 50 °C the next. Repeat with smaller intervals, such as every 2 °C from 36 °C to 50 °C, with repeats at each. 1 for an estimate consistent with the data, 1 for narrower intervals in that region. (c) The rate falls from 0.0083 s⁻¹ to 0.0017 s⁻¹ because more of the amylase is denatured: vibration breaks the bonds holding its tertiary structure, the active site changes shape, and starch can no longer bind. 1 for denaturation, 1 for the active site changing shape so the substrate cannot bind. "The enzyme is killed" scores 0. (d) Any two of: amylase volume or concentration; starch volume or concentration; pH, using a buffer. both needed. Temperature scores 0; it is the independent variable.

Q4. At low substrate concentration many active sites are empty. Raising the concentration increases the number of collisions between substrate and active sites per unit time, so more enzyme–substrate complexes form and the rate rises. As concentration rises further the rate increases by less and less, because more active sites are already occupied. At high concentration all active sites are occupied (the enzyme is saturated), so the rate reaches a maximum; enzyme concentration is now limiting. 1 for more frequent collisions, 1 for more enzyme–substrate complexes, 1 for smaller increases as sites fill, 1 for saturation or enzyme becoming limiting. "The substrate runs out" scores 0.

Q5 (HL). (a) At 1 mmol dm⁻³: 1.4 ÷ 3.3 × 100 = 42%. At 40 mmol dm⁻³: 8.7 ÷ 9.5 × 100 = 92%. 1 for each. (b) Competitive. Inhibition is large at low substrate concentration and small at high, where the rate approaches the uninhibited rate, because substrate molecules out-compete X for the active site. 1 for competitive, 1 for a reason using the change with substrate concentration, ideally quoting the percentages.

Q6 (HL). Isoleucine is the end product of a pathway beginning with threonine. When its concentration is high, isoleucine binds to the allosteric site of the first enzyme, threonine deaminase, changing the active site so threonine is not converted; the pathway slows and less isoleucine is made. When isoleucine is used up and its concentration falls, it detaches, because binding is reversible, and production resumes. Advantage: no intermediates accumulate and no threonine is wasted. 1 for end product inhibiting the first enzyme, 1 for allosteric binding changing the active site, 1 for reversibility so production resumes, 1 for a plausible advantage. Isoleucine binding to the active site loses the second mark.


Educerie · written from the published IB Diploma Programme Biology guide, first assessment 2025, section C1.1 Enzymes and metabolism. Original text, examples and questions. Diagrams drawn by Educerie. Last reviewed 25 September 2026.

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