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Biology - Enzymology course
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Enzymology course of French Licence 2
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I. Introduction and Definitions1. Enzyme
= Protein that catalyses a biochemical reaction
Enzymology: since the 19ème century
→ Reactions taking place only in living beings (e.g. Fermentation)
Enzymes = Agents of metabolism (catalyse all reactions in the body)
• E.g. Glucose used to produce energy via 10x2 reactions (Catabolism)
→ Reaction enabled by an enzyme by lowering the activation energy
Reaction without catalysis: need for more
activation energy (e.g. more heat)
→ Catalysis = lowering the energy level
required
Enzymes: act in a coordinated cascade (product of
one = substrate of the other)
E.g. Glycolysis = sequence of 10 steps
1 glucose→ 2 pyruvates
Notion of Specificity: Enzyme specific to a given substrate and reaction
• Linked to a structure-activity relationship: type of reaction characterised by a particular part of the
enzyme (active site)
• More or less narrow specificity: 2 models (key-lock + induced shape model)
Key-lock model (Fischer) : Good structural
conformation
Induced Form Model (Koshland): Derives from the
Keyhole and supports protein plasticity
Classification and Nomenclature :
- EC x.y.z.w
→ x = Class number (type of reaction): 6 classes
→ y = Subclass number (type of substrate function)
→ z = Sub-subclass number (type of acceptor)
→ w = Order number (in the sub-subclass)
Class number :
- 1: Oxidoreductases: e.g. Alcohol dehydrogenase (EC 1.1.1.1)
- 2: Transferases: e.g. Hexokinase (EC 2.7.1.1)
- 3: Hydrolases: e.g. -galactosidase (EC 3.2.1.23)
- 4: Lyases: e.g. Pyruvate decarboxylase (EC 4.1.1.1)
- 5 : Isomerases : e.g. Glucose isomerase (EC 5.3.1.5)
- 6: Ligases: e.g. Pyruvate carboxylase (EC 6.4.1.4)
, 2. Substrate
Substrate: S: molecule involved in an enzymatic reaction and transformed by the action of an enzyme
• One enzyme for one or more substrates
3. Product
Product : P: molecule that appears as a result of the reaction catalysed by an enzyme
• A reaction for one or more products
4. Ligand
Ligand = chemical body with a specific binding to a protein
• One or more specific ligand binding sites on the protein
5. Cofactor
Cofactor = chemical body essential for an enzymatic reaction
• Is not permanently transformed by the reaction
E.g. Mineral elements: Cu2+ , Mg2+ , Zn2+ ...
6. Coenzyme
Coenzyme = biological molecule acting as a cofactor
• Free Coenzymes: "Stoichiometric Intervention":
→ [Free Coenzymes] same order as [Substrate].
• Linked coenzymes (prosthetic groups): "Catalytic Intervention":
→ [Linked Coenzymes] same order as [Enzyme].
, II. Notion of Active Site
= Region of the enzyme where the substrate molecules bind and undergo the chemical reaction
• Consists of AA residues forming temporary bonds with the substrate:
→ Liaison site
• Consists of AA residues that catalyse a
reaction of this substrate:
→ Catalytic site
*Some diseases are caused by mutations in the
active site of certain enzymes
• Ex. Phenylketonuria (Phenylalanine
hydroxylase PAH mutation)
Catalytic Triads: 3 AA residues which are involved in the active site of some Hydrolases (3) and
Transferases (2):
E.g. peptidases, amidases, esterases, lipases, -lactamases...
• Mechanism:
→ An acidic residue (aspartate,
glutamate): alignment + polarisation
of the basic residue...
→ A basic residue (Histidine):
Reduction of the pKa thanks to the
action of the acid residue + activation
of the nucleophilic residue...
→ Nucleophilic residue (Serine,
Cysteine, Threonine): Catalysis of the
reaction
III. Enzymatic reaction
1. Writing the Reaction
*Changing the direction of the enzymatic
reaction means making the product the
substrate and vice versa...
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