IB BIOLOGY · THEME C · INTERACTION AND INTERDEPENDENCE

Every reaction, its own enzyme

Most of the reactions in your cells would take years, or millions of years, on their own. Enzymes finish them in a blink, at body temperature, each one only the reaction it was shaped for. Here is how they do it, what stops them, and how a cell keeps the whole web of reactions under control.

IB Biology C1.1SL and HL3 hours SL, 5 HL14 chaptersdry lab

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A chance meetingA close fitBonds brokenFree for the next onereactions by this enzyme01231,000s a second

01Learn

Fourteen chapters, the last six for higher level. Read one, play its figure or move its slider, and make each prediction before you open the answer.

  1. 1Seconds, not millions of years
  2. 2A web of reactions, an enzyme for each
  3. 3A lower hill to climb
  4. 4A pocket held in shape
  5. 5Meeting by chance
  6. 6Lose the shape, lose the fit
  7. 7Three graphs to know
  8. 8Measuring a rate
  9. 9Chains, cycles, inside and out HL
  10. 10Warm from the inside HL
  11. 11A second site HL
  12. 12A look-alike in the active site HL
  13. 13The end product shuts the gate HL
  14. 14A trap that springs once HL

C1.1.1 Enzymes as catalysts

Seconds, not millions of years

A catalyst is a substance that speeds up a chemical reaction without being used up by it. The same molecule works again and again. Enzymes are the catalysts of living things, and nearly all of them are proteins (chapter 4 shows how their shape does the job).

Cells need them because many of the reactions in a cell are possible but hopelessly slow on their own at body temperature. The rate of reaction has to be fast enough for life, and an enzyme raises it enormously.

Speed matters in three places:

  • Digestion. Food spends only a few hours in your gut. Its starch, protein and fat must be broken down in that time, or the food leaves unabsorbed.
  • Growth. A cell has to copy all of its DNA before it divides.
  • Response. A nerve or a muscle has to respond in a fraction of a second.

There is another way to speed up a reaction: heat it. A cell cannot do that, because a temperature high enough to make these reactions fast would unfold the cell's own proteins (chapter 6). Enzymes give the speed at 37 °C instead.

An enzyme is not used up, so a cell needs only a little of each one. A single catalase molecule can deal with millions of hydrogen peroxide molecules every second. Enzymes do not make impossible reactions happen. They make possible ones fast (chapter 3 shows how).

Watch out An enzyme is not used up by the reaction it catalyses. The substrate changes; the enzyme comes out as it went in.

With no enzyme at all, how long would water at room temperature take to break half the bonds between the glucose units in starch?

no enzymewith an enzymeyears ... thousands ...thousands of years ...about 5 million yearshalf the bonds brokenabout a thousandthof a second a bond
  1. The same bond in starch, broken two ways.
  2. With water alone at room temperature, half the bonds take millions of years to break.
  3. Amylase breaks each one in about a thousandth of a second, at body temperature.

C1.1.2 C1.1.3 Role of enzymes in metabolism; anabolic and catabolic reactions

A web of reactions, an enzyme for each

Metabolism is every chemical reaction going on in an organism. There are thousands of them, and they are linked: the product of one reaction is the substrate of the next, and many molecules feed several reactions at once. It is a web, not a list. A metabolic pathway is one thread of it, a series of steps with an enzyme for each.

Each enzyme catalyses one reaction, or one kind of reaction. This enzyme specificity (chapter 6 shows why) is why a cell needs thousands of different enzymes, one for each step. It is also how a cell stays in control: a reaction runs only if its enzyme is there and working. Make more of an enzyme, or less, or switch it off, and that step speeds up, slows or stops.

At higher level, chapters 11 to 13 show how a cell switches enzymes off.

Metabolic reactions fall into two groups. Anabolic reactions build larger molecules from smaller ones and take in energy. Monomers are joined into macromolecules by condensation, as when amino acids become a polypeptide in protein synthesis, or glucose becomes glycogen. Photosynthesis is anabolic too: it builds glucose from carbon dioxide and water.

Catabolic reactions break larger molecules into smaller ones and release energy. In digestion, macromolecules are broken into monomers by hydrolysis. In respiration, substrates such as glucose are broken down by oxidation. Drawing on a glycogen store, by breaking it back into glucose, is catabolic too. So not all catabolism is hydrolysis.

Remember it The two halves of metabolism

  • AddAnabolicbuilds bigger molecules from smaller ones, takes in energy
  • CutCatabolicbreaks bigger molecules into smaller ones, releases energy
Watch out In science, metabolism is not how fast you burn food. It is every reaction in the body, building as well as breaking.

A liver cell makes thousands of different enzymes. Why so many?

ABCDGFJKLEHIA, B, C ... are molecules; each arrow has its own enzyme.
  1. One reaction, one enzyme.
  2. The product of one reaction is the substrate of the next.
  3. Thousands of linked reactions make metabolism. Switch off one enzyme and one step stops.
Six reactions to sortAmino acids joined into apolypeptide at a ribosomeGlucose oxidised to carbondioxide and water in respirationGlucose joined into glycogen in aliver cellStarch digested to maltose in themouthCarbon dioxide and water madeinto glucose in a leafProteins digested to amino acidsin the stomach and intestineAnabolic: builds upCatabolic: breaks down

Pick a reaction (tap it, or Tab to it and press Enter), then pick the bin it belongs in.

0 of 6 sorted

Six reactions in a cell or an organism. Is a bigger molecule being made, or a big one being taken apart?
Building glycogen from glucose is anabolic, a condensation at every link; using the store is catabolic. Switch the direction and count the water.

C1.1.10 Effect of enzymes on activation energy

A lower hill to climb

For a substrate to react, some of its bonds must be strained and broken, and breaking bonds takes energy. The energy needed before the reaction can run is the activation energy. On an energy diagram it is a hill that the reaction has to climb: energy up the side, progress of the reaction along the bottom. At the top of the hill the substrate is in an unstable in-between state, part way between substrate and products.

Bond breaking takes in energy. Bond making releases it. When the new bonds of the products form, energy comes out. If more comes out than went in, the reaction releases energy overall and the products sit lower than the substrate. Most catabolic reactions are like this. If less comes out, the reaction takes in energy overall and needs a supply of energy to run, as most anabolic reactions do.

An enzyme lowers the hill. As the substrate binds, the active site strains its bonds and holds it in the right position to react (chapter 4), so less energy is needed to reach the top. At 37 °C many more molecules have that much energy, and the reaction runs faster.

Reading the graph: measure the activation energy from the substrate's level up to the peak, and the energy released or taken in overall from the substrate's level to the products'.

  • Activation energy is the energy needed to strain and break bonds so the reaction can start.
  • Breaking bonds takes in energy; making bonds releases it.
  • On an energy diagram, activation energy is the climb from the substrate up to the peak.
Watch out An enzyme does not give the substrate energy, and it does not change how much energy a reaction releases. It lowers the energy needed to get the reaction started.

An enzyme lowers the activation energy of a reaction that releases energy. What happens to the energy released overall?

EnergyProgress of reactionsubstrateproductsactivationenergybonds strained and breakingenergyreleasedoverallnew bonds forming:energy releasedno enzymeactivation energywith an enzymesame startsame endsubstrateproductsenergytaken inoverallno enzymewith an enzyme
  1. A substrate, before it reacts.
  2. Breaking its bonds needs energy first: the activation energy.
  3. Making new bonds releases energy. Here more comes out than went in.
  4. With an enzyme, the hill is lower. Start and end do not move.
  5. A building reaction ends higher than it starts. An enzyme lowers its hill too.

C1.1.4 C1.1.5 Globular proteins with an active site; induced-fit binding

A pocket held in shape

Enzymes are globular proteins: one or more polypeptide chains folded into a compact, roughly round shape that dissolves in water (B1.2). Their water-loving R groups mostly face outwards and the water-hating ones are tucked inside, which is why they dissolve. Most enzymes are named for their substrate or their job, with the ending -ase: lipase acts on lipids, a protease on proteins and lactase on lactose.

The active site is the small region where the substrate binds and the reaction happens. It is made of only a few amino acids, often from far-apart places in the chain, brought together by the fold. In lysozyme from egg white, a protein of 129 amino acids, a handful line a groove in its surface and two of them do the chemistry.

The rest of the protein matters as much. Interactions between amino acids all through the folded chain hold the active site in shape and give it the right charges and chemical groups for catalysis.

When the substrate binds, the two form an enzyme-substrate complex. Both change shape as it forms: the active site closes in around the substrate, and the substrate is pulled and bent, straining the bonds that are about to break. This is induced fit. The substrate is converted into products, which no longer fit and leave, and the enzyme returns to its starting shape, ready for another substrate.

Remember it What happens at the active site

  • BindBindingthe substrate binds the active site
  • BendInduced fitboth change shape; the substrate's bonds are strained
  • BreakReactionbonds break and new ones form: products
  • ByeReleasethe products leave; the enzyme is free again
Built as a model Two models, a century apart. Emil Fischer's lock and key (1894) pictured a rigid site that the substrate fits like a key. Daniel Koshland's induced fit (1958) pictured a site that changes shape as the substrate binds. Both are models. Lock and key cannot explain how binding can improve the fit, or how bonds get strained; induced fit explains both, and matches what is seen in hexokinase, whose two lobes close like jaws round glucose.
Watch out The active site is not the whole enzyme, and not a fixed, rigid hole. It is a few amino acids that move as the substrate binds.

An enzyme has 300 amino acids, and only about six touch the substrate. A mutation changes one amino acid far from the active site, and the enzyme stops working. How?

a chain of amino acids, not yet foldedactive siteenzyme-substratecomplexinduced fit:both change shapeproducts leavesame shape as at the start
  1. Only a few amino acids will form the site, far apart in the chain.
  2. Folding brings them together: the active site.
  3. The substrate binds: an enzyme-substrate complex.
  4. Both change shape: induced fit strains the substrate's bonds.
  5. Products leave; the enzyme is unchanged.

C1.1.6 Molecular motion and substrate-active site collisions

Meeting by chance

Enzymes and substrates are dissolved in water: in the cytoplasm, in the contents of the gut, in blood plasma. Their molecules move all the time and at random, jostled by the water molecules around them. This molecular motion is what brings them together.

A reaction can happen only when a substrate and an active site meet in a collision, and only if the substrate arrives the right way round (its orientation) and close enough to bind. Most collisions miss the site, or arrive the wrong way round, and the molecules bounce apart.

More collisions a second means a faster rate. Warmer molecules move faster and collide more often; more substrate or more enzyme in the same volume means more meetings. Chapter 7 puts numbers on both, and the film that follows it lets you watch these meetings and change them.

Movement is needed, but not both partners have to move. Sometimes an immobilised enzyme is held still, embedded in a membrane. Sometimes it is a large substrate that is held still, such as a cellulose fibre in a plant cell wall, and the enzyme moves to it: cellulase released by a fungus reaches the fibre and digests it where it lies. Tap the three states to compare them.

Fixing an enzyme in place also keeps it where its products are wanted. Lactase sits in the membrane of the cells that line the small intestine, so the glucose and galactose it makes appear right at the surface of the cells that absorb them.

On purpose Industry fixes enzymes on purpose too: lactase held on beads makes lactose-free milk as the milk flows past.

Lactase sits fixed in the membrane of cells lining your small intestine. It cannot move. How does lactose reach its active site?

collision at an active sitemembrane of the cells lining the small intestinecollisiongut contentslactase(fixed)plant cell wallcellulose fibre, held in the wallboundcellulase

Both move at random. Water molecules jostle them, and now and then a substrate meets an active site.

C1.1.7 Active site structure, specificity and denaturation

Lose the shape, lose the fit

The active site's shape and charges match its substrate's, so few other molecules bind. This is enzyme-substrate specificity. Some enzymes act on one substrate, or very nearly: urease on urea. Others act on a family of similar substrates: lipase on many lipids, a protease on many peptide bonds. The rule is the same: what binds is what fits.

The shape is held by weak interactions between amino acids: hydrogen bonds, ionic bonds and interactions between non-polar R groups (B1.2), with a few strong ones. That is why the shape can be lost. You watched a protein unfold in B1.2.

Heat makes the chain vibrate harder. Above a certain temperature the weak bonds break, the chain unfolds and the active site loses its shape. A pH far from the enzyme's normal one changes the charges on R groups in and around the site, because they gain or lose hydrogen ions, so ionic bonds break and the site's charges no longer match the substrate. Either way the substrate no longer binds, or binds and does not react. This is denaturation.

A denatured enzyme is not killed: it was never alive. Heat denaturation is usually permanent, and cooling does not refold the chain. A small, brief change in pH can sometimes be undone when the pH returns, but an extreme one usually cannot. Cold does not denature an enzyme at all. It slows the enzyme, because there are fewer collisions (chapter 7), and the enzyme works again when it is warmed.

Watch out Enzymes are not killed by heat, and cold does not denature them. Heat denatures; cold only slows.

Pepsin digests protein in the stomach at about pH 2. Carried on into the small intestine at about pH 8, what happens to it?

−+−+−+−+The shapes fit and thecharges match: oppositesigns sit side by side.−+−+−−−A different molecule:wrong shape and charges,so it does not bind.Heated: the chain loosens,the groove is gone, and thesubstrate drifts by.H+H+H+−Wrong pH: the site's chargeschange, a bond in the foldbreaks, and the substrate nolonger matches.

It fits. The substrate's shape matches the site, and its charges are opposite to the site's, so it binds.

C1.1.8 Effects of temperature, pH and substrate concentration

Three graphs to know

Sketch it first. On paper or a whiteboard, sketch rate of reaction against temperature, against pH and against substrate concentration before you play the figure. Then check yourself against it.

Temperature. Below the optimum, warming the solution makes enzyme and substrate move faster, so they collide more often and more collisions have enough energy to react. The rate rises, roughly doubling for every 10 °C. Above the optimum the enzyme denatures faster than the extra collisions can help, and the rate falls steeply. So the curve is not symmetrical: a gentle rise, a steep fall. Optima differ. Many human enzymes work best at about 37 to 40 °C; the DNA polymerase of a bacterium from hot springs works best at about 75 °C.

pH. Each enzyme works fastest at its own optimum pH, and the rate falls either side as the charges in the active site change and, further out, the enzyme denatures. Pepsin in the stomach prefers about pH 2, salivary amylase about pH 7 and trypsin in the small intestine about pH 8.

Substrate concentration. At low concentration, more substrate means more collisions with free active sites, so the rate rises almost in step. Then the curve bends over and levels off at a maximum. More enzyme would raise that maximum. All three effects follow from collision theory and denaturation.

Describe a graph in parts, with numbers from its axes: "rises steadily to an optimum near 40 °C, then falls steeply". These smooth curves are sketch graphs: models of the general pattern, not the data of one enzyme. Real results scatter and have their own optimum, and a model is tested against results from experiments such as the dry lab's.

Inhibitors change these graphs too: chapters 11 and 12.

Remember it The three factors you must explain

  • TigersTemperaturecollisions, then denaturation
  • PreferpHcharges in the active site
  • SteakSubstrate concentrationcollisions, then saturation
Watch out The optimum is not always 37 °C. That is roughly where many human enzymes peak; enzymes from other organisms peak far higher or lower.

On a graph of rate against substrate concentration, the curve levels off. Why?

Rate of reactionTemperature / °C0204060TemperaturemorecollisionsoptimumdenaturesRate of reactionpH0714pHpepsinamylasetrypsinRate of reactionSubstrate concentrationSubstratemaximum ratemore enzyme
  1. Temperature: faster collisions, then denaturation.
  2. pH: each enzyme has its own optimum.
  3. Substrate: the rate rises, then levels off.
  4. More enzyme raises the maximum.
Turn the substrate up and watch the rate meter, then warm the solution past 45 °C. What happens to the active sites, and to the rate?

C1.1.9 Measurements in enzyme-catalysed reactions

Measuring a rate

A rate of reaction is a change per unit time. For an enzyme, you can measure either how fast a product appears or how fast the substrate disappears. Catalase makes oxygen, which can be collected in a gas syringe and read in cm³ min⁻¹. Amylase uses up starch, which can be tested with iodine solution: you time how long it takes before a drop no longer turns blue-black.

Plot the product against time and the curve is steepest at the start, then flattens as the substrate is used up. The initial rate is the gradient at the very start, before the substrate runs low, and it measures the enzyme under the conditions you set. Draw a tangent to the curve at time zero and work out its gradient: rise over run, with units.

Where you only time an end point (the starch has gone, a paper disc has floated up), the rate is 1 ÷ time, in s⁻¹. Twice as fast means half the time.

One enzyme can be followed three ways. For catalase: the oxygen collected in a gas syringe; the oxygen collected over water in an upturned measuring cylinder; or a small filter paper disc soaked in extract, dropped into the peroxide and timed as it rises on the oxygen it makes.

A fair test changes one variable (the independent variable), measures the rate (the dependent variable) and keeps everything else the same: temperature in a water bath, pH with a buffer, the same volumes and concentrations. Repeat each value at least three times, and include controls, such as no enzyme and boiled enzyme.

You can also work out rates from secondary data: someone else's results in a table or graph. Reading the gradients is the same. The dry lab below is the place to do it all.

Watch out The total amount of product at the end measures how much substrate you put in, not how fast the enzyme works. Use the initial rate.

A drop of a starch and amylase mixture stops turning iodine blue-black after 40 s at 30 °C and after 80 s at 20 °C. Compare the rates.

01230510152025Time / minVolume of oxygen / cm³Results from the catalase dry laball the peroxide used: 21.2 cm³about 12 cm³1 mininitial rate = about 12 cm³ min⁻¹at 35 °C: about 22 cm³ min⁻¹25 °C35 °C
  1. Oxygen collected every 10 seconds.
  2. Fast at first, then slower as the substrate runs out.
  3. The initial rate is the gradient of a tangent at the start.
  4. Warmer: a steeper start, the same total.

C1.1.11 C1.1.13 Intracellular and extracellular reactions; linear and cyclical pathways

Chains, cycles, inside and out

Intracellular reactions happen inside cells, catalysed by enzymes that stay there. "Inside" means anywhere inside: in the cytoplasm, as glycolysis, the first stage of respiration, does, or inside an organelle, as the Krebs cycle does in the matrix of a mitochondrion. Extracellular reactions happen outside the cells that made the enzymes. The example is chemical digestion in the gut: cells of the salivary glands, the stomach lining and the pancreas make digestive enzymes and secrete them into the gut, where they hydrolyse food molecules.

The two kinds are made in different places. Enzymes that stay in the cytoplasm, such as those of glycolysis, are made by free ribosomes. Enzymes for export are made by ribosomes on the rough endoplasmic reticulum, packaged by the Golgi apparatus and released by exocytosis (B2.2).

Most metabolism runs as pathways, a series of steps each with its own enzyme. In a linear pathway the first substrate is turned, step by step, into a different end product. Glycolysis is the example: glucose goes in at the start and pyruvate comes out about ten steps later. A cyclical pathway ends by remaking the molecule it started from. Something is added at each turn and something leaves, but the carrier molecule comes back round, so a small amount of it keeps the cycle turning. The Krebs cycle (C1.2) and the Calvin cycle (C1.3) are the examples.

Why pathways, and not one leap? Each step needs only a small activation energy, energy is released or used a little at a time, and each step's enzyme is a point of control (chapter 13).

Watch out A cycle does not make something from nothing. Molecules join at each turn and products leave; what comes back round is the carrier molecule.

Glycolysis runs in the cytoplasm, the Krebs cycle inside mitochondria, and protein digestion in your stomach. Which are intracellular?

gut contentspancreas ductcell lining the gutmitochondrion

Tap a part of the gut wall, the gut contents or the duct.

Tap each pathway: does its starting molecule come back round, or leave as something new?

C1.1.12 Generation of heat by metabolism

Warm from the inside

No energy transfer in metabolism is 100% efficient. The efficiency of a transfer is the share of the energy that ends up where it is wanted. When respiration releases the energy in glucose, only about a third is captured in ATP, and the rest is released as heat. When the ATP is then used, to contract a muscle or to build a protein, most of that energy ends as heat too. Heat generation is inevitable.

The faster the metabolism, the more heat. You get hot when you run because your muscles respire faster, and a resting adult gives off about as much heat as a lamp of 80 to 100 watts.

Mammals and birds depend on this heat. They keep a high and constant body temperature, about 37 °C in most mammals and about 40 to 42 °C in most birds, mostly well above the air around them, by generating heat from their metabolism. They are endotherms. A few other animals warm themselves from their own metabolism at times: a bumblebee shivers its flight muscles to warm up before take-off.

This is how an endotherm keeps its temperature steady. When the air turns colder it loses heat faster, so its metabolic rate rises to replace what is lost, and its body temperature stays where it was (D3.3 shows how the change is controlled).

Why does it pay? Enzymes work fastest near their optimum, so a steady warm body keeps every reaction fast and predictable, whatever the weather (chapter 7).

Watch out Heat from metabolism is not a fault to be fixed. It is unavoidable, and for mammals and birds it is what keeps every enzyme near its optimum.

A mouse and a lizard of the same mass sit at 20 °C for a day. Which needs more food, and why?

energy released from glucose in respiration100 %in ATPheatabout a third is capturedwhen the ATP is usedheatwork done: movement, buildingall of it togetherheatalmost all ends as heat010203040010203040Air temperature / °CBody temperature / °Cbody = airmousepigeonlizardbaskingsheltering

No transfer is 100% efficient. About a third of the energy released from glucose is captured in ATP, and most of what the ATP does ends as heat too.

C1.1.14 Allosteric sites and non-competitive inhibition

A second site

An inhibitor is a molecule that binds to an enzyme and slows or stops its reaction. Many enzymes have, as well as the active site, a second site elsewhere on the molecule: an allosteric site. Like the active site, it is specific: only particular molecules fit and bind.

When one binds, it changes the interactions inside the enzyme, so the enzyme's shape changes, a conformational change, and that alters the active site enough to stop catalysis. The substrate no longer binds, or binds and does not react. This is non-competitive inhibition: the inhibitor does not compete with the substrate for the active site.

The binding is reversible. When the inhibitor leaves, the enzyme returns to its working shape. So the amount of inhibition depends on how much inhibitor there is: the more inhibitor, the bigger the share of enzyme molecules switched off at any moment.

Adding more substrate does not help, because substrate cannot push a molecule off a site it does not bind to (the graph is in chapter 12). And this is how a cell switches enzymes off and on (chapter 13).

Watch out Not every inhibitor blocks the active site. A non-competitive inhibitor never touches it.

An allosteric inhibitor binds nowhere near the active site. How can it stop the enzyme?

converted,quicklydoes not fitcannot bindactive siteallosteric site
  1. An active site, and a second site elsewhere: the allosteric site.
  2. Only a specific molecule fits the allosteric site.
  3. Binding changes the enzyme's shape, and with it the active site.
  4. The binding is reversible: the inhibitor leaves, the enzyme works again.

C1.1.15 Competitive inhibition

A look-alike in the active site

A competitive inhibitor is similar enough in shape and chemistry to the substrate to bind the active site. While it is there, no substrate can bind. It is not converted, and it leaves again, so the binding is reversible.

Substrate and inhibitor take turns: each active site is taken by whichever happens to collide with it first. So the effect depends on how much of each there is.

A non-competitive inhibitor is different (chapter 11): it binds elsewhere and changes the site. How do the two behave when you add more substrate? Make your prediction, then open the graph.

Statins are the example. They are taken to lower blood cholesterol. In liver cells the enzyme HMG-CoA reductase converts HMG-CoA to mevalonate, an early step on the pathway that makes cholesterol. Part of a statin molecule resembles HMG-CoA, so it binds the active site and blocks it. Less cholesterol is made in the liver, and the level in the blood falls. A statin binds the site far more tightly than the substrate does, so a small dose is enough.

Two samples of an enzyme: one with a competitive inhibitor, one with a non-competitive inhibitor. You add far more substrate to both. In which does the inhibitor's effect fade?

On a graph of rate against substrate concentration, a competitive inhibitor gives a curve that starts low but climbs towards the same plateau as the uninhibited enzyme. A non-competitive inhibitor gives a curve with a lower plateau.

Two more, not to learn Relenza, a drug for influenza, was designed in Australia from the shape of the active site of the virus's enzyme neuraminidase. The enzyme snips sugar ends off the cell surface so that new virus particles can float free; Relenza fills the site, so they stay stuck. It is a competitive inhibitor. Cyanide is a poison that stops the last enzyme of the respiration chain. It is often called a non-competitive inhibitor, but it binds the iron atom at the very spot where oxygen binds, so it is better described as blocking that site. Neither is in the syllabus: the examples to know are statins and penicillin.
membrane in a liver cellHMG-CoAreductasemevalonatecholesterolbloodHMG-CoAstatinHMG-CoA bounces offsites blocked:most of the time
  1. HMG-CoA reductase: an early step on the way to cholesterol.
  2. Part of a statin looks like the substrate and binds the active site.
  3. It binds and leaves: competitive and reversible.
  4. Less cholesterol is made, and blood cholesterol falls.
Substrate concentrationRate of reactionno inhibitorcompetitivenon-competitive

No inhibitor. The rate climbs with the substrate, then levels off at a maximum.

virusno drugsugars snipped: particle floats freeviruswith Relenzasugars not snipped: particles stuckFeFeoxygen binds hereCNnormalwith cyanideoxygen takes the iron atom's sitecyanide holds it: oxygen cannot bindthe last enzyme in a mitochondrion's respiration chain
  1. Relenza: a competitive inhibitor designed to fit a virus's enzyme.
  2. Cyanide: a poison that takes the place where oxygen binds.
Try each inhibitor, then add substrate. Which one does more substrate beat?

C1.1.16 Regulation of metabolic pathways by feedback inhibition

The end product shuts the gate

In feedback inhibition (end-product inhibition), the last product of a pathway inhibits an enzyme near its start, usually the first, by binding to its allosteric site (chapter 11). When the product builds up, more of the first enzyme's molecules have it bound, so the pathway slows. When the cell uses the product up, it leaves the allosteric sites, the enzyme works again and the pathway speeds up. The product's own level sets its rate of production. This is negative feedback.

The example is the pathway that makes the amino acid isoleucine. Plants and bacteria make it from another amino acid, threonine, in five steps, each with its own enzyme. Isoleucine binds the allosteric site of the first enzyme, threonine deaminase. Humans cannot make isoleucine (it is an essential amino acid, B1.2) and get it from food.

Nothing here is switched simply on or off. The share of enzyme that is inhibited follows the end product's concentration, so production matches use. In the valve, change how fast the cell uses isoleucine and watch the first enzymes (the six small ones with a notch) fill and empty.

Watch out Feedback inhibition is not permanent and not an on and off switch. It is reversible binding, and the share of the enzyme inhibited follows the end product's concentration.

Isoleucine inhibits the first enzyme of its five-step pathway, not the last. Why the first?

E1: threonine deaminasethreonine1234E2E3E4E5isoleucineused to makeproteins

Isoleucine is moderate: 4 of 6 first enzymes are inhibited, so the pathway runs at the speed the cell uses it.

Protein making
Five enzymes turn threonine into isoleucine, and the cell uses the isoleucine to make proteins. Change how fast it does that, then untick the box.

C1.1.17 Mechanism-based inhibition

A trap that springs once

In mechanism-based inhibition an inhibitor enters the active site as if it were a substrate, and the enzyme starts to act on it. But the reaction stops part way, with the inhibitor held by a covalent bond. The active site is chemically changed and stays blocked for good: the inhibition is irreversible. That enzyme molecule is out of action until the cell makes new ones.

Penicillin is the example, and it was the first widely used antibiotic (Fleming noticed it in 1928, and it came into use in the early 1940s). A bacterial cell wall (A2.2) is made of long sugar chains cross-linked by short peptides, and the enzyme transpeptidase makes those cross-links.

Penicillin looks like the end of the peptide that transpeptidase normally joins. It enters the active site and the enzyme attacks it: a ring in the penicillin molecule opens, and penicillin ends up bonded covalently to the active site. New wall is then built without cross-links, so it is weak. As the bacterium grows, water enters, the wall gives way and the cell bursts. Human cells have no cell wall, and so none of the wall-building enzyme that penicillin targets, so penicillin does not harm them (C3.2 returns to antibiotics).

Some bacteria are not harmed. They show antibiotic resistance: they carry a changed transpeptidase, whose active site has a different shape that penicillin binds poorly but that still makes cross-links, so their walls are built normally in penicillin. MRSA is the well-known case. Such variants arise by mutation and spread by natural selection when penicillin is used (C3.2). Other bacteria resist in another way, by making an enzyme that breaks penicillin down, but that is a different mechanism.

Remember it Three ways to stop an enzyme

  • CopycatCompetitivea look-alike takes the active site, reversibly
  • NudgeNon-competitivebinds the allosteric site and changes the active site, reversibly
  • MousetrapMechanism-basedsprings once in the active site and holds for good
Watch out Penicillin is not a competitive inhibitor that "stays a long time". It is bonded covalently and the enzyme never recovers.

A strain of bacteria keeps building strong walls in penicillin. Its transpeptidase still makes cross-links. What has most likely changed?

transpeptidasesugar chainsugar chaincross-linkthe enzyme joins two peptide ends: a new cross-linkpeptide endthe enzyme normally joinspenicillinthe same outlinecovalent bondring opened, held for goodenzyme out of actionactive site of transpeptidasewater inno cross-links: the new wall is weak, and the cell burstscellchanged shapeat the mouthpenicillin does not bindcross-link made: the wall stays whole
  1. Transpeptidase cross-links the wall's sugar chains.
  2. Penicillin looks like the peptide the enzyme joins.
  3. The enzyme starts to act on it, and is trapped by a covalent bond: irreversible.
  4. Without cross-links, the wall gives way and the cell bursts.
  5. A changed transpeptidase binds penicillin poorly: resistance.

02Dry lab: Catalase and hydrogen peroxide

Catalase in a potato extract breaks hydrogen peroxide down to water and oxygen. Collect the oxygen in a gas syringe, find the initial rate, then plan and write it up as an investigation with the coach under the bench.

Your questionHow does one factor change the initial rate at which catalase breaks down hydrogen peroxide? Start with temperature: where is the optimum, and what happens beyond it?
What you can changeOne independent variable at a time: temperature, pH, hydrogen peroxide concentration or extract concentration (and at higher level an inhibitor, competitive or non-competitive). Everything else stays fixed unless you change it on purpose.
What to recordThe volume of oxygen every 10 seconds, then the initial rate in cm³ min⁻¹: the gradient at the very start. At least three trials at each value (the bench allows five), a mean and a standard deviation, and a graph of the means with error bars. The coach under the bench helps you plan, process and evaluate.

IA coach

Write it up as an investigation

Your results from this dry lab can be written up the way an IB scientific investigation is: four criteria, each worth 6 marks. Tick each line as your write-up does it. The coach on the page checks these as you go; it never gives a mark.

1 Research design

A focused question set in its biology; your choices of what to measure, how, over what range and how often, explained rather than listed; what you kept the same and how; safety, ethics and the environment; a method someone else could follow and repeat.

  • My question names what I changed.
  • It gives the range I used, with units.
  • It names what I measured and how.
  • It names the organism or system.
  • My background explains, with the biology, why the two should be linked.
  • I cite my sources, and each reference can be traced.
  • If I give a hypothesis, it predicts and explains.
  • Every variable has its How, Why and Units.
  • For each thing kept the same, I say how I kept it so.
  • I list at least three things I kept the same.
  • I name the apparatus that set what I changed, and the instrument that measured.
  • I test enough values.
  • My values spread wide enough.
  • I run at least three trials at every value.
  • I run a control.
  • I explain why these values, this many and this often.
  • Someone else could repeat my method.
  • I deal with safety, ethics and the environment.

2 Data analysis

Raw data recorded clearly, with titles, units, uncertainties and the same decimal places down a column; what you saw as well as what you measured; processing that suits the question, shown with a worked example; the spread shown; a graph a reader can trust.

  • Each table has a numbered title that says what it shows.
  • Every heading has its quantity and its unit.
  • Every raw data heading has its uncertainty.
  • Each uncertainty is realistic for the instrument.
  • Each uncertainty has the same decimal places as its readings.
  • I record what I saw as well as what I measured.
  • I show one worked example of my processing, and it is right.
  • I say why I left out any trial.
  • My error bars show a spread my repeats can support.
  • My graph has a numbered title and labelled axes with units.
  • I say what the error bars show.
  • A straight line, if I draw one, has its R².
  • A statistical test, if I run one, has its hypotheses and suits the data.

3 Conclusion

Your question answered from the processed data, with numbers quoted and the spread taken into account; the biology that explains the pattern; a comparison with published work; no claim bigger than the data.

  • I answer my question in a sentence, naming both variables.
  • I quote my processed numbers.
  • I say how sure the spread lets me be.
  • I say whether my hypothesis is supported.
  • I explain the pattern with biology.
  • I compare my result with published work, and cite it.
  • I claim no more than my data show.

4 Evaluation

Weaknesses and limitations of this method (not slips in carrying it out), with evidence from your own data, the effect each had on the results, which mattered most and why, and a realistic improvement for each.

  • I give at least three weaknesses or limitations.
  • Every row is filled in.
  • No slips in carrying it out: weaknesses of the method itself.
  • Each improvement is specific: which instrument, how many, what changes.
  • Each effect says what it did to my data.
  • At least two rows point to evidence in my own data.
  • At least one limitation: what this experiment cannot tell me.
  • I say which mattered most, and why.
  • I deal with what stands out in my data.
  • My improvements improve this investigation, not a new one.

Variables

VariableHow?Why?Units
Independent: temperature
Dependent: initial rate of oxygen production
Kept the same: pH of the buffer
Kept the same: concentration of hydrogen peroxide
Kept the same: volume of hydrogen peroxide
Kept the same: concentration of the extract
Kept the same: the same potato extract for every run
Kept the same: inhibitor (none)

Evaluation

Weakness or limitationWhich?Evidence in my dataEffect on my resultsImprovement

Data generated with the catalase dry lab, biologybybradford.com (a simulation). These checks catch what is missing. They cannot judge how good it is: that is what your teacher does.

Find out

  • Where is the optimum? Temperature, 0 to 80 °C in 10 °C steps, three trials each; then every 5 °C around the peak. Record the optimum to the nearest 5 °C and what a run at 70 °C does after its first 20 seconds.
  • When does more peroxide stop helping? Substrate, 0.25% to 10%. Then halve the extract and run it again. Where does each curve level off?
  • Which pH suits catalase? pH 3 to 11, three trials each.
  • Run the controls. Boiled extract and water, no extract, beside a normal run at 25 °C.
  • Beat the inhibitor. A substrate series with no inhibitor, then a competitive inhibitor at 1 mmol dm⁻³, then a non-competitive one at 1 mmol dm⁻³. Compare the runs at 0.5% and at 10%.

Record

  • For every run: the settings, and which one you changed.
  • Change one setting at a time and keep the rest fixed.
  • Three to five repeats at each value, with a mean and its standard deviation.
  • Use Graph your results under the bench, or download the CSV and plot it yourself.
  • When you are done, the coach under the bench helps you write it up as an investigation.

At 70 °C the oxygen collected rises for the first 20 seconds and then hardly at all, far short of what the peroxide could give. Why?

What does the boiled extract tube rule out?

At 10% peroxide, the run with the competitive inhibitor is almost as fast as the run with none, but the non-competitive run is still at about half. Why?

03Check

A fresh paper from the exam bank on this guide's topics each time: past-paper style questions, marked as you go, and saved to your Exam practice progress when you are signed in. It opens on biologybybradford.com, so it needs the internet.

Exam practice

Exam questions on C1.1, marked

Start 15 marks of exam questionsYour exam practice

04Downloads

This file is the guide, saved to run without the internet.

Saved from biologybybradford.com/guides/ib-biology-c1-1-enzymes-and-metabolism, where the guide is kept up to date with the notes, the revision guide and, for the teacher, the lesson plans and slides.

05Teacher resources

The guide as three one-hour lessons, and two more at higher level. Each has a plan to print (the timings, what to project and where to stop, the activities with what they need, what students get wrong) and slides to teach it from, in the same order, with the teacher's moves in the notes.

LessonCoversFocusChaptersLesson planSlides
1Why life needs enzymes C1.1.1, C1.1.2, C1.1.3, C1.1.1060 min What enzymes are for, metabolism as a web, anabolic and catabolic, and the activation energy hill 1, 2, 3 Lesson planPDF 700 KB SlidesPPTX 2.3 MB
2Fit, collisions and shape C1.1.4 to C1.1.860 min The active site and induced fit, collisions, specificity and denaturation, and the three graphs 4, 5, 6, 7 Lesson planPDF 737 KB SlidesPPTX 5.2 MB
3Measuring a rate C1.1.960 min How to measure an enzyme's rate, the initial rate, and planning, running and evaluating the catalase investigation 7, 8, dry lab Lesson planPDF 701 KB SlidesPPTX 5.1 MB
4Pathways, places and heat HL C1.1.11 to C1.1.1460 min Enzymes inside and outside cells, linear and cyclical pathways, heat from metabolism, and the allosteric site 9, 10, 11 Lesson planPDF 662 KB SlidesPPTX 1.4 MB
5Stopping enzymes HL C1.1.15 to C1.1.1760 min Competitive inhibition and statins, feedback inhibition of the isoleucine pathway, and penicillin 12, 13, 14 Lesson planPDF 699 KB SlidesPPTX 5.3 MB
PDFEvery lesson planAll five plans in one PDF, with this overview at the front. 1.4 MB KEYNote template, filled inThe class’s note template with every gap filled. 1.9 MB

The note template, the revision guide and the offline copy are in Downloads, for you and the class.

PRACTISE AND REVISE

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How this was made. The course structure, the activities and the teaching choices come from my own classroom, my presentations and my years of teaching IB and AP Biology. I use Claude, an AI, to help write and build the interactive guides, lesson plans, slides and practice questions, and to draw the diagrams and code the interactives. I direct the work and review it against the IB and AP specifications before it goes live.