Enzymology 1
Learning objectives
• General introduction to enzymes
• Mode of action
• Stereospecificity - chirality
• Classification of enzymes
• Introduction to coenzymes
What are enzymes
• Proteins/biological catalysts that facilitate/mediate reaction mechanism
o Stabilizes transition state (highest energy species in rxn)
• Nearly all proteins are enzymes; but do not have absolute monopoly on catalysis
o ¼ of genes in human genome encode enzymes
• Characteristics:
o Specificity: no byproducts, greater specificity in terms of substrate and products
o Catalytic power (↑ rate of reaction in range of 106 - 1012 greater than uncatalysed)
o Allow milder conditions e.g. neutral pH, atmospheric pressure, ~ ambient T
o Capacity to control system: responds to conc. of substances (see allosteric control/covalent
modification)
Why study enzymes?
• Crucial in many cellular functions
• Facilitate reactions that otherwise would not take place inside a cell (see above)
• Linked to diseases if their function is altered/interrupted/lowered/increased
• Obtain crystal structure → define active site (a.a., cofactors involved) and substrate binding; by making
mutant versions of protein → kinetics → propose possible reaction mechanisms → develop drugs/ inhibitors
Active site
• Region of an enzyme that binds to substrate
• Substrate: reactant(s) in an enzyme-catalyzed reaction
• Small relative to the total volume
o Usually occurs in clefts/crevices (narrow opening) (buried
inside enzyme)
• It excludes solvents (would otherwise reduce catalytic activity)
• A.a. in active site defines specificity
• Other a.a. and cofactors may be involved in binding
o These are held in precise arrangement with respect to substrate
3 methods of binding
• Lock and key model
• Induced fit
• Transition state stabilization
Lock and Key
• Structure of ligand binding site (i.e. active site) complementary to substrate (like lock and key)
o Shape determined by tertiary and quarternary structure of protein – is rigid
Induced fit
• Active site present but not properly formed
• Conformational change (shape) and adapts (interaction with substrate) to make perfect fit
• Most have some degree of flexibility
• Example: hexokinase, binds to G6P
Without and with substrate: it closes around substrate to catalyze rxn
Learning objectives
• General introduction to enzymes
• Mode of action
• Stereospecificity - chirality
• Classification of enzymes
• Introduction to coenzymes
What are enzymes
• Proteins/biological catalysts that facilitate/mediate reaction mechanism
o Stabilizes transition state (highest energy species in rxn)
• Nearly all proteins are enzymes; but do not have absolute monopoly on catalysis
o ¼ of genes in human genome encode enzymes
• Characteristics:
o Specificity: no byproducts, greater specificity in terms of substrate and products
o Catalytic power (↑ rate of reaction in range of 106 - 1012 greater than uncatalysed)
o Allow milder conditions e.g. neutral pH, atmospheric pressure, ~ ambient T
o Capacity to control system: responds to conc. of substances (see allosteric control/covalent
modification)
Why study enzymes?
• Crucial in many cellular functions
• Facilitate reactions that otherwise would not take place inside a cell (see above)
• Linked to diseases if their function is altered/interrupted/lowered/increased
• Obtain crystal structure → define active site (a.a., cofactors involved) and substrate binding; by making
mutant versions of protein → kinetics → propose possible reaction mechanisms → develop drugs/ inhibitors
Active site
• Region of an enzyme that binds to substrate
• Substrate: reactant(s) in an enzyme-catalyzed reaction
• Small relative to the total volume
o Usually occurs in clefts/crevices (narrow opening) (buried
inside enzyme)
• It excludes solvents (would otherwise reduce catalytic activity)
• A.a. in active site defines specificity
• Other a.a. and cofactors may be involved in binding
o These are held in precise arrangement with respect to substrate
3 methods of binding
• Lock and key model
• Induced fit
• Transition state stabilization
Lock and Key
• Structure of ligand binding site (i.e. active site) complementary to substrate (like lock and key)
o Shape determined by tertiary and quarternary structure of protein – is rigid
Induced fit
• Active site present but not properly formed
• Conformational change (shape) and adapts (interaction with substrate) to make perfect fit
• Most have some degree of flexibility
• Example: hexokinase, binds to G6P
Without and with substrate: it closes around substrate to catalyze rxn
