IMAT Biology · Biomolecules and Enzymes

Enzymes: Catalysis, the Active Site and Cofactors

Enzymes are biological catalysts, mostly globular proteins, that speed up reactions by lowering the activation energy and come out of the reaction unchanged.

All Biomolecules and Enzymes notes

Why this matters

The ministry papers keep returning to what an enzyme is: the definition of a catalyst (2025), the main job of enzymes in metabolism (2026) and which digestive enzymes act on proteins (2025). The older papers asked where in the cell enzymes are found (2021) and what shapes an active site (2018).

Concept 1 of 4: Enzymes as catalysts that lower the activation energy

Most reactions in a cell would be far too slow at 37 °C, because the molecules must first be pushed over an energy barrier, the activation energy. An enzyme offers a different route with a lower barrier, so far more molecules get over it each second. It does not change where the reaction ends up, only how fast it gets there, and it is free to work again afterwards.

Definition

A catalyst is a substance that increases the rate of a reaction and is found unchanged at the end of it.
Enzymes are biological catalysts. Almost all are globular proteins (a few are RNA, called ribozymes).
They work by lowering the activation energy $E_a$ , the energy needed to start the reaction.
They do not change the overall energy change of the reaction, the position of equilibrium or the amount of product finally formed; they only make equilibrium arrive sooner.
They are specific (one enzyme, one reaction or one type of substrate), work at body temperature and can be switched on and off, so the cell controls its metabolism through them.
Enzymes are not consumed, so a small amount can convert a very large amount of substrate.

Quantity	Changed by an enzyme?	Comment
Activation energy	Yes, lowered	This is how the enzyme speeds the reaction
Rate of reaction	Yes, increased	Often by millions of times
Overall energy released or taken in	No	Products and reactants are the same as without the enzyme
Position of equilibrium	No	Equilibrium is reached faster, not shifted
The enzyme itself	No	Unchanged at the end and used again

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Enzymes do not raise the temperature or supply energy

An enzyme speeds up a reaction at the same temperature by providing a route with a lower activation energy. It gives no energy to the reaction and is not used up. Options saying it heats the mixture, supplies energy, or turns into product are wrong.

Concept 2 of 4: The active site: lock-and-key and induced fit

The active site is a small pocket on the enzyme whose shape and charges match the substrate. The substrate binds, forming an enzyme-substrate complex, the reaction happens, and the products leave. The old lock-and-key picture says the pocket is a rigid exact fit. The newer induced-fit picture says the pocket moulds itself around the substrate as it binds, and that squeeze helps break or make bonds.

Definition

The active site is the region of the enzyme where the substrate binds and the reaction takes place. It is formed by a few amino acids, often far apart in the sequence, brought together by folding.
Enzyme-substrate complex: substrate bound in the active site. Then enzyme-product complex, then the products are released and the enzyme is free again.
Lock-and-key model: the active site has a fixed shape complementary to the substrate. It explains specificity.
Induced-fit model (the current model): the active site changes shape slightly as the substrate binds, giving a closer fit and putting strain on the substrate's bonds, which lowers the activation energy. It also explains why some enzymes accept a small family of similar substrates.
Because the shape of the active site depends on the protein's structure, anything that changes that structure (heat, pH, mutation, some inhibitors) can change the activity.

Model	Active site before binding	On binding	What it explains
Lock-and-key	Rigid, exactly complementary to the substrate	No change of shape	Specificity
Induced fit	Roughly complementary	Moulds around the substrate, straining its bonds	Specificity, the lowering of activation energy, broad specificity of some enzymes

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The active site is not built only from neighbouring amino acids

The amino acids that line an active site can be far apart in the primary sequence, or even on different chains. They meet only because the chain folds. That is why the higher levels of structure decide the shape of the active site.

Concept 3 of 4: Cofactors, coenzymes and prosthetic groups

Some enzymes cannot work with their protein alone; they need a small helper bound to them. If the helper is a metal ion, it is an inorganic cofactor. If it is a small organic molecule that comes and goes, carrying atoms or electrons between reactions, it is a coenzyme. If it is bound permanently, it is a prosthetic group. Many coenzymes are made from vitamins, which is one reason vitamins are needed in the diet.

Definition

A cofactor is a non-protein substance an enzyme needs in order to work.
Inorganic cofactors are metal or other ions, often from dietary minerals: $\mathrm{Zn^{2+}}$ in carbonic anhydrase, $\mathrm{Mg^{2+}}$ for enzymes that use ATP, $\mathrm{Cl^-}$ activates salivary amylase.
Coenzymes are small organic molecules that bind loosely and carry groups or electrons from one reaction to another. Many come from B vitamins: $\mathrm{NAD^+}$ from niacin (B3), FAD from riboflavin (B2), coenzyme A from pantothenic acid (B5).
A prosthetic group is a cofactor bound tightly and permanently, such as the haem in catalase and the cytochromes (haem also carries oxygen in haemoglobin, which is not an enzyme).
Apoenzyme: the protein part without its cofactor, inactive. Holoenzyme: apoenzyme plus cofactor, active.

Kind of helper	How it is bound	Example	Dietary source
Inorganic cofactor (ion)	Bound in or near the active site	$\mathrm{Zn^{2+}}$ in carbonic anhydrase	Minerals
Coenzyme	Loosely; moves between enzymes	$\mathrm{NAD^+}$ carrying electrons in respiration	Vitamins (niacin for NAD)
Prosthetic group	Tightly and permanently	Haem in catalase	Iron from the diet for the haem

Practice this conceptself-check · 3 quick reps

Every coenzyme is a cofactor, but not every cofactor is a coenzyme

Cofactor is the general word for any non-protein helper. Coenzymes are the organic ones. A metal ion such as

\mathrm{Zn^{2+}}

is a cofactor but never a coenzyme.

Concept 4 of 4: Where enzymes work, and the main enzyme classes

Every living cell runs on enzymes, so they are found in every compartment: in the cytoplasm, the nucleus, the mitochondria and the lysosomes. Some are sent out of the cell to work outside, like the digestive enzymes. Most enzyme names end in -ase and say what they act on or what they do.

Definition

Intracellular enzymes work inside the cell: glycolysis in the cytoplasm, DNA and RNA polymerases in the nucleus, Krebs cycle and respiratory chain enzymes in the mitochondria, hydrolytic enzymes in lysosomes.
Extracellular enzymes are secreted and work outside the cell: the digestive enzymes in the gut.
Names usually end in -ase, often after the substrate: amylase (amylose, starch), lipase (lipids), protease or peptidase (proteins, peptides), maltase, lactase.
The six main classes: oxidoreductases (redox reactions, such as dehydrogenases), transferases (move a group, such as transaminases moving amino groups), hydrolases (break bonds with water: all digestive enzymes), lyases (break bonds without water), isomerases (rearrange a molecule into an isomer), ligases (join molecules using ATP, such as DNA ligase).

Enzyme	Substrate	Products	Where it works
Amylase	Starch	Maltose	Mouth (saliva) and small intestine (from pancreas)
Pepsin	Proteins	Shorter polypeptides	Stomach, at about pH 2
Trypsin and other peptidases	Polypeptides	Short peptides and amino acids	Small intestine
Lipase	Triglycerides	Fatty acids and glycerol (or monoglycerides)	Small intestine, helped by bile
Catalase	Hydrogen peroxide	Water and oxygen	Inside cells, especially liver

Practice this conceptself-check · 4 quick reps

Amylase digests starch, peptidases digest proteins, lipase digests fats

The name tells you the substrate. A protein is broken down by proteases and peptidases, not by amylase or lipase. Isomerases and transaminases are not digestive enzymes at all: they rearrange molecules or move amino groups inside cells.

Summary — formulas & gotchas at a glance

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Reference tables (4)

Enzymes as catalysts that lower the activation energy5 rows

Quantity	Changed by an enzyme?	Comment
Activation energy	Yes, lowered	This is how the enzyme speeds the reaction
Rate of reaction	Yes, increased	Often by millions of times
Overall energy released or taken in	No	Products and reactants are the same as without the enzyme
Position of equilibrium	No	Equilibrium is reached faster, not shifted
The enzyme itself	No	Unchanged at the end and used again

The active site: lock-and-key and induced fit2 rows

Model	Active site before binding	On binding	What it explains
Lock-and-key	Rigid, exactly complementary to the substrate	No change of shape	Specificity
Induced fit	Roughly complementary	Moulds around the substrate, straining its bonds	Specificity, the lowering of activation energy, broad specificity of some enzymes

Cofactors, coenzymes and prosthetic groups3 rows

Kind of helper	How it is bound	Example	Dietary source
Inorganic cofactor (ion)	Bound in or near the active site	$\mathrm{Zn^{2+}}$ in carbonic anhydrase	Minerals
Coenzyme	Loosely; moves between enzymes	$\mathrm{NAD^+}$ carrying electrons in respiration	Vitamins (niacin for NAD)
Prosthetic group	Tightly and permanently	Haem in catalase	Iron from the diet for the haem

Where enzymes work, and the main enzyme classes5 rows

Enzyme	Substrate	Products	Where it works
Amylase	Starch	Maltose	Mouth (saliva) and small intestine (from pancreas)
Pepsin	Proteins	Shorter polypeptides	Stomach, at about pH 2
Trypsin and other peptidases	Polypeptides	Short peptides and amino acids	Small intestine
Lipase	Triglycerides	Fatty acids and glycerol (or monoglycerides)	Small intestine, helped by bile
Catalase	Hydrogen peroxide	Water and oxygen	Inside cells, especially liver

Watch out for (4)

Enzymes do not raise the temperature or supply energy
→ Enzymes as catalysts that lower the activation energy
The active site is not built only from neighbouring amino acids
→ The active site: lock-and-key and induced fit
Every coenzyme is a cofactor, but not every cofactor is a coenzyme
→ Cofactors, coenzymes and prosthetic groups
Amylase digests starch, peptidases digest proteins, lipase digests fats
→ Where enzymes work, and the main enzyme classes

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