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BI2.1-5 | Enzyme — Part 1

What Is an Enzyme? (BI2.1)

An enzyme is a biological catalyst — a molecule (usually a protein) that speeds up a specific chemical reaction without itself being permanently altered.

Figure: What Is an Enzyme? (BI2.1)

Key properties:

• Specificity — each enzyme catalyses a particular reaction on a particular substrate. The enzyme sucrase only breaks down sucrose; it won't touch lactose. This specificity comes from the shape of the enzyme's active site — the pocket or cleft where the substrate binds.
• Efficiency — enzymes accelerate reactions by factors of 10⁶ to 10¹⁴. They do this by lowering the activation energy (the energy barrier that must be overcome for a reaction to proceed).
• Regulation — enzyme activity can be turned up or down by the cell. This allows metabolic pathways to respond to changing conditions — you don't digest muscle protein while you're eating a meal.
• Mild conditions — enzymes work at body temperature (~37°C) and physiological pH. Industrial catalysts often require extreme heat and pressure; enzymes do not.

Most enzymes are proteins, but a few are RNA molecules called ribozymes (e.g., the ribosome's peptidyl transferase activity). For this module, when we say 'enzyme', we mean protein enzymes.

Holoenzyme, Apoenzyme, Cofactors and Coenzymes (BI2.1)

Many enzymes need a helper molecule to function. Here's the terminology:

Figure: Holoenzyme, Apoenzyme, Cofactors and Coenzymes (BI2.1)

• Apoenzyme — the protein part of the enzyme alone (inactive without its helper)
• Cofactor — the non-protein helper. It can be:
• An inorganic ion (e.g., Zn²⁺ in carbonic anhydrase, Mg²⁺ in kinases, Fe²⁺ in catalase)
• An organic molecule — called a coenzyme (e.g., NAD⁺, FAD, coenzyme A, thiamine pyrophosphate)
• Holoenzyme = apoenzyme + cofactor (the complete, active enzyme)

Apoenzyme + Cofactor → Holoenzyme (active)

A coenzyme that is tightly and permanently bound to the enzyme is called a prosthetic group (e.g., FAD in succinate dehydrogenase — it never leaves the enzyme). A coenzyme that binds loosely and acts as a co-substrate (carrying chemical groups between enzymes) is a co-substrate (e.g., NAD⁺ shuttles hydrogen atoms between dehydrogenases).

Figure: Apoenzyme + Cofactor → Holoenzyme (active)

Why do coenzymes matter? Many coenzymes are derived from vitamins:
• NAD⁺ and NADP⁺ ← from niacin (vitamin B₃)
• FAD ← from riboflavin (vitamin B₂)
• Coenzyme A ← from pantothenic acid (vitamin B₅)
• Thiamine pyrophosphate (TPP) ← from thiamine (vitamin B₁)
• Pyridoxal phosphate (PLP) ← from pyridoxine (vitamin B₆)

This is why vitamin deficiencies cause disease — without the vitamin, the coenzyme can't be made, the enzyme can't function, and the metabolic pathway stalls.

Isoenzymes — Same Reaction, Different Tissues (BI2.1)

Isoenzymes (isozymes) are different molecular forms of the same enzyme that catalyse the same reaction but differ in their structure, tissue distribution, or kinetic properties.

Figure: Isoenzymes — Same Reaction, Different Tissues (BI2.1)

The classic example is lactate dehydrogenase (LDH). LDH converts lactate to pyruvate (and vice versa). It exists as 5 isoforms (LDH1–LDH5), each a combination of two subunit types (H for heart, M for muscle):

• LDH1 (H₄) — predominates in heart muscle
• LDH2 (H₃M) — found in RBCs and heart
• LDH3 (H₂M₂) — found in lungs and lymphoid tissue
• LDH4 (HM₃) — found in kidneys and placenta
• LDH5 (M₄) — predominates in liver and skeletal muscle

Clinical use: If a patient's blood shows elevated LDH1 > LDH2 (the 'flipped' LDH pattern), it suggests myocardial infarction (heart attack). If LDH5 is elevated, think liver disease. Isoenzyme patterns tell you which organ is damaged.

Another important isoenzyme: creatine kinase (CK):
• CK-MM — skeletal muscle (elevated after muscle injury)
• CK-MB — heart muscle (elevated in myocardial infarction)
• CK-BB — brain (rarely measured in serum)

IUBMB Enzyme Classification — The Six Main Classes (BI2.1)

The International Union of Biochemistry and Molecular Biology (IUBMB) classifies all enzymes into six main classes based on the type of reaction they catalyse. Each enzyme gets an EC number (Enzyme Commission number) with four digits.

Figure: IUBMB Enzyme Classification — The Six Main Classes (BI2.1)

The six classes (with mnemonics and examples):

Class	Reaction Type	Example	Memory Aid
1. Oxidoreductases	Transfer electrons (oxidation-reduction)	Lactate dehydrogenase, Cytochrome oxidase	"Ox-Red" — they do redox
2. Transferases	Transfer a functional group from one molecule to another	Transaminases (ALT, AST), Kinases	"Transfer" — move a group
3. Hydrolases	Break bonds using water (hydrolysis)	Lipase, Amylase, Trypsin	"Hydro" — they use water
4. Lyases	Break bonds without water or oxidation (or form double bonds)	Aldolase, Decarboxylases	"Lyse" — they cleave
5. Isomerases	Rearrange atoms within a molecule (isomerisation)	Phosphoglucose isomerase, Racemases	"Iso" — they shuffle
6. Ligases	Join two molecules using ATP energy	DNA ligase, Glutamine synthetase	"Ligate" — they join (like a surgical ligature)

Mnemonic for the order: "Over The Hill, Liz Is Lazy" (Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases).

You don't need to memorise EC numbers — but you must know which class an enzyme belongs to based on what it does.