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Enzymes: what a catalyst can and cannot do
A catalyst speeds a reaction up without being used up and without changing where the reaction finishes. Enzymes manage it with a pocket a few amino acids wide, and almost everything else in this topic follows from the shape of that pocket.
Before this Tertiary structure and the four bonds that hold it · Globular proteins and why they are soluble
Before you start
Enzymes speed up reactions by giving them energy — a push to get them going. It is a comfortable picture and it costs marks every summer. An enzyme is a protein sitting in solution at exactly the same temperature as everything around it, so it has no energy to hand out. What it does is cheaper than that. It offers a different route to the same destination, and the highest point on the new route is lower. The molecules still pay for the climb out of their own thermal motion; the difference is that far more of them can now afford it.
What you should be able to do
- State what an enzyme does to the activation energy of a reaction, and what it leaves alone.
- Describe the active site as a product of tertiary structure rather than of any one amino acid.
- Set out the lock-and-key and induced fit models, and give the evidence that decided between them.
- Use 'enzyme-substrate complex' and 'complementary' correctly in an explanation of specificity.
- Explain why changing one amino acid far from the active site can still stop an enzyme working.
A catalyst has a job description, and it is narrow
Reactions that look inevitable on paper often refuse to happen at any useful speed. Hydrogen peroxide in a brown bottle is decomposing into water and oxygen right now, and will still be at it next year, because before a molecule falls apart it has to be pushed into a strained, half-broken arrangement first. Only the small fraction of molecules moving fast enough at any instant can pay for that in-between state, and the size of the bill is the activation energy.
Drop a piece of liver into the same peroxide and the beaker foams over. Liver is full of catalase, one of the quickest enzymes anyone has measured: a single molecule of it deals with tens of millions of hydrogen peroxide molecules every second. Nothing has been added to the peroxide except a protein, and the protein comes out at the end exactly as it went in.
Read the figure carefully, because the parts that did not move are the examinable ones. Reactants start at the same energy either way and products finish at the same energy either way, so the overall energy change is identical. An enzyme therefore cannot make a reaction give out more energy, cannot make an unfavourable reaction favourable, and cannot shift an equilibrium: it catalyses the forward and reverse reactions to exactly the same degree, which is why the balance point stays where it was.
What an enzyme changes is how long you wait. That is not a small thing — a reaction that would take a century now takes a second — but it is only that.
- Catalyst
- A substance that increases the rate of a reaction by lowering its activation energy, and which is not used up in the process.
- Activation energy
- The minimum energy that colliding particles must have for a reaction to take place.
- Enzyme
- A globular protein that acts as a biological catalyst, with an active site complementary to its substrate.
The word globular is doing work there. Enzymes fold into compact shapes with hydrophilic side chains outwards, so they dissolve in cytoplasm and plasma, and their sequences are irregular, so the surfaces they present are irregular too. Collagen has neither property, which is why no fibrous protein is an enzyme.
The active site is a pocket that the fold creates
A typical enzyme is a few hundred amino acids long. The reaction happens in a dent on its surface perhaps a dozen amino acids across, and those amino acids are usually nowhere near each other in the chain. Lysozyme, the enzyme in tears and egg white that cuts bacterial cell walls, is 129 amino acids long, and the two side chains that do the chemistry are the 35th and the 52nd. Seventeen residues apart in the sequence; touching distance once the chain has folded.
That single fact carries most of the topic. The active site is not a component you could point to in the primary structure; it is something the tertiary structure builds. Anything that disturbs the fold disturbs the site, however far away the disturbance starts.
When the right molecule settles into the site, the pair is an enzyme-substrate complex. Use the phrase; it is usually worth a mark on its own, and 'joining' or 'reacting with' the enzyme is describing something else.
- Active site
- The region of an enzyme, formed by its tertiary structure, to which the substrate binds.
- Substrate
- The molecule on which an enzyme acts.
- Enzyme-substrate complex
- The temporary structure formed when a substrate binds to the active site.
- Specificity
- The property of an enzyme that it catalyses only one reaction, or one class of reaction, because only a substrate complementary to its active site can bind.
A mutation forty residues away
A single base substitution changes one amino acid in an enzyme. The changed amino acid is forty residues away from the active site along the chain. The enzyme no longer works. Explain how that is possible.
Start where the change is, not where the effect is. A different amino acid means a different R group, so the interactions available at that point along the chain are different: a hydrogen bond or an ionic bond that used to form may not form, a hydrophobic side chain may be replaced by a charged one, a cysteine that used to make a disulfide bridge may be gone.
Those interactions are what hold the tertiary structure, and tertiary structure is not local. Folding brings distant parts of the chain into contact, so a bond that fails at residue 90 can move residue 50 by a fraction of a nanometre.
If one of the residues that moved lines the active site, the site is now a different shape, the substrate is no longer complementary to it, no enzyme-substrate complex forms, and the reaction proceeds only at its uncatalysed rate. The distance quoted in the question is the point of the question: primary structure is a line, tertiary structure is not.
Lock and key, and the evidence that retired it
Emil Fischer proposed the first serious model in 1894. A substrate fits its enzyme, he suggested, the way a key fits a lock: one rigid shape, one rigid complementary shape, and no other combination will turn. As an account of specificity it was excellent, and it is still the quickest way to explain why lactase will not touch sucrose.
As an account of catalysis it has a hole in it. A rigid pocket that grips a substrate explains why the substrate sticks. It does not explain why sticking should make the reaction any faster. Something has to happen to the substrate once it is in there, and a shape that never moves cannot do anything to it.
Three lines of evidence pushed the model on. When enzyme structures began to be solved by X-ray crystallography in the 1960s, several were photographed in both states, and they were not the same shape: hexokinase closes around a glucose molecule the way a hand closes around a marble, shifting by a large fraction of a nanometre. Second, molecules built to resemble the strained half-reacted transition state rather than the relaxed substrate bind far more tightly than the substrate itself, which only makes sense if the site is shaped to grip the strained form. Third, plenty of enzymes accept a family of related substrates — lipases will hydrolyse triglycerides with a range of different fatty acid tails — and a lock that accepts several keys is a poor lock.
Daniel Koshland's answer in 1958 was induced fit. The active site is close to complementary before binding and becomes exactly complementary as the substrate arrives, because the substrate's arrival makes it move.
| Lock and key | Induced fit | |
|---|---|---|
| Active site before binding | Already exactly complementary | Close to complementary, not exact |
| What moves | Nothing | The active site, as the substrate binds |
| Explains specificity | Yes | Yes |
| Explains why the rate rises | No | Yes: binding strains the substrate |
| Supported by structures? | Not by enzymes photographed with and without substrate | Yes — hexokinase closes around glucose |
Both models say the enzyme finishes unchanged, and both say one enzyme handles one substrate. Do not present them as rivals over specificity. They differ over whether the site is rigid, and over whether the model has anything to say about catalysis.
Where the lower barrier actually comes from
Once you accept that the site closes on the substrate, the mechanism stops being mysterious. Four things happen inside a shut active site, and any of them will lower an activation energy.
Binding holds two substrates in the right orientation: in solution they collide in every wrong way first, and in an active site they are already lined up. Closing also strains the bonds that are about to break, so they are partly broken before the reaction starts. The pocket excludes water. And charged R groups lining it can donate or accept protons, creating a local chemical environment no beaker could reproduce.
None of that is required in detail at A level, but knowing it stops you writing the sentence examiners see most often — that the enzyme 'gives the substrate energy'. The energy account never changes. Only the route does.
TRY IT — A conclusion that goes one step too far
Hydrogen peroxide decomposes into water and oxygen on its own at room temperature, slowly. A student adds catalase, sees the mixture foam, and writes that catalase 'makes the decomposition possible'. Comment on that conclusion.
Check your answer
The decomposition was already possible; the student's own control shows it, because peroxide left alone still gives off oxygen. What was missing was speed, not permission.
The reaction releases energy overall, so it is energetically favourable with or without catalase. Its slowness comes from a high activation energy: at room temperature only a tiny proportion of molecules have enough energy at any moment to reach the transition state. Catalase provides an alternative route with a lower activation energy, so a much larger proportion of collisions are now successful and the rate rises enormously.
The same mass of peroxide yields the same volume of oxygen either way; catalase changes how long you wait for it, not how much you get. 'Catalase makes the decomposition fast' is the sentence that scores.
In the exam
- The mark is 'lowers the activation energy'. 'Speeds up the reaction' repeats the question back at the examiner and earns nothing on an explain command.
- Never write that an enzyme gives energy to a reaction, provides activation energy, or makes a reaction possible. All three are the same error and all three are penalised.
- Say complementary, not 'the same shape'. A substrate and an active site are complementary the way a foot is complementary to a footprint.
- If the question names induced fit, the phrase 'the active site changes shape as the substrate binds' has to appear somewhere in your answer. A lock-and-key description will not be credited on an induced fit question, however well written.
- Mutation questions want the chain of causation in order: R group → bonds between R groups → tertiary structure → active site shape → substrate no longer complementary. Skipping to the last step loses the middle marks.
Check yourself
An industrial process converts substrate S into product P using an enzyme. At 25 °C the reaction reaches equilibrium with 90% P and 10% S. A colleague suggests doubling the amount of enzyme in order to push the yield above 90%. Evaluate that suggestion.
Answer
It will not work, and the reason is worth stating precisely: an enzyme changes the rate at which equilibrium is reached, not where equilibrium lies.
The 90:10 split is fixed by the energy difference between S and P. An enzyme lowers the activation energy of the route between them, and it lowers it by the same amount in both directions, so the forward and reverse reactions are both speeded up in the same proportion and the balance point does not move. Doubling the enzyme will get the mixture to 90% P sooner — which may well be worth doing — but it will stop there.
To change the yield you have to change something the equilibrium responds to: remove P as it forms, raise the concentration of S, or alter the temperature — remembering that a temperature high enough to help the equilibrium may be high enough to denature the enzyme. More enzyme is a rate decision; yield is a different question.
Questions
Question 14 marks
Explain why a given enzyme catalyses only one reaction, using the terms active site, complementary and enzyme-substrate complex in your answer.
Mark scheme
- B1 the active site is a region formed by the tertiary structure of the enzyme, with a particular shape
- B1 only a substrate whose shape is complementary to the active site can bind to it
- B1 when it binds, an enzyme-substrate complex forms and the reaction is catalysed
- B1 a molecule that is not complementary cannot enter the site, so no complex forms and that reaction is not catalysed
Question 24 marks
Compare the lock-and-key model of enzyme action with the induced fit model.
Mark scheme
- B1 in lock and key the active site is already exactly complementary to the substrate, whereas in induced fit it is only close to complementary before binding
- B1 in lock and key nothing moves, whereas in induced fit the active site changes shape as the substrate binds
- B1 both models account for specificity, but only induced fit accounts for the rise in rate, because the closing of the site strains the substrate's bonds
- B1 induced fit is supported by enzymes photographed with and without their substrate, such as hexokinase closing around glucose, which lock and key is not
Question 33 marks
Explain why every enzyme is a globular protein, and why a fibrous protein such as collagen cannot be one.
Mark scheme
- B1 a globular protein folds with hydrophilic side chains facing outwards, so it dissolves in cytoplasm or plasma where the reaction happens
- B1 its amino acid sequence is irregular, so the surface it presents is irregular and can carry an active site of a particular shape
- B1 a fibrous protein has a repetitive sequence and forms long insoluble strands, so it is neither soluble nor able to present such a pocket
Question 43 marks
A molecule built to resemble the strained, half-reacted form of a substrate binds to its enzyme far more tightly than the substrate itself does. Suggest what this tells us about the shape of the active site, and suggest why such a molecule would slow the enzyme down.
Mark scheme
- B1 the active site must be complementary to the strained transition state rather than to the relaxed substrate
- B1 this supports induced fit, in which the site moulds around the substrate and strains the bonds that are about to break
- B1 the molecule occupies the active site, so substrate cannot bind there and fewer enzyme-substrate complexes form
Question 52 marks
State what an enzyme does to the activation energy of a reaction, and state one quantity that an enzyme does not change.
Mark scheme
- B1 an enzyme lowers the activation energy of the reaction
- B1 it does not change the energy of the reactants or of the products, and so does not move the position of equilibrium
Worth remembering
- An enzyme lowers activation energy. It does not change the energy of the reactants or of the products, and it does not move an equilibrium.
- The active site is built by tertiary structure, so anything that changes the fold changes the site.
- Substrate and active site are complementary, not identical.
- Induced fit: the site moulds around the substrate as it binds, and that moulding is where the catalysis comes from.
- A catalyst finishes the reaction in the state it started it, ready to go again.