ENZYMES
Definition
Enzymes are biological catalysts that speed up biochemical reactions by lowering activation energy
of a reaction
Structure
● Four categories of amino acid residues:
1) Catalytic amino acids (R groups are directly involved in catalytic activity, i.e. making
or breaking of chemical bonds once substrate is bound)
2) Binding amino acids (R groups hold substrate in position via non-covalent bonds
while catalysis takes place)
3) Structural amino acids (involved in maintaining specific 3D conformation of enzyme
and active site)
4) Non-essential amino acids (no specific functions)
● May interact with additional non-protein component (cofactors) via covalent bonds/weak
interactions
1) Inorganic metal ions
● Mostly small divalent ions (e.g. Ca2+)
● May be component of active site or alter enzyme activity via allosteric
regulation
● Usually bind reversibly to enzyme and alter enzyme’s active/allosteric site to
facilitate catalytic reaction
2) Coenzymes
● Loosely associates with enzyme during reaction
● Act as transient carriers of specific functional groups, hydrogen or electrons
● Enzyme + coenzyme = holoenzyme (without cofactor = apoenzyme)
3) Prosthetic groups
● Tightly bound to enzyme on a permanent basis
Mode of Action
[Enzyme specificity]
● Lock and key hypothesis
○ Enzyme viewed as a rigid structure; only substrates exactly complementary to active
site can bind
○ Explains substrate specificity of enzymes
● Induced fit hypothesis
○ Active site not in precise complementary conformation to substrate before binding
○ Upon binding of substrate, active site changes conformation to bind to substrate
more firmly
○ R groups of catalytic amino acids is moulded into precise conformation and brought
into close proximity to chemical bonds in substrate, facilitating catalysis
Copyright © 2019 tonyndr
, ○ Explains group specificity of enzymes (enzyme can catalyse reactions for substrates
with similar structural/chemical properties)
[Lowering of activation energy + formation of enzyme-substrate complex]
● Enzymes speed up rate of reaction by lowering activation energy
● Effective collision occurs when enzyme and substrate collide in correct orientation
○ Enzyme orientates substrates in close proximity and in the correct orientation to
undergo chemical reactions
● Substrate molecule bind to active site by forming non-covalent bonds (e.g. hydrogen bonds,
ionic bonds) with R groups of binding amino acid residues
○ Enzyme-substrate complex formed
● Enzyme provides a microenvironment that favours the reaction; R groups of catalytic amino
acids at active site catalyse conversion of substrate to product by straining critical bonds in
substrate, allowing substrate to attain an unstable transition state
● Product molecule formed is no longer complementary to active site and is released
Factors Affecting Rate of Reaction
● Limiting factor - factor in shortest supply that limits rate of reaction
[Substrate concentration]
At low substrate concentration,
● Increase in substrate concentration leads to proportional increase in rate of reaction
● Not all active sites of enzymes are occupied
● Substrate concentration is limiting factor
● Increase in substrate concentration increases frequency of effective collision between
enzyme active site and substrate molecules -> rate of enzyme-substrate complex formation
increases -> amount of product formed per unit time increases -> rate of reaction increases
At high substrate concentration,
● Any further increase in substrate concentration does not result in increase in rate of reaction
(graph reaches a plateau)
● Active site of every enzyme molecule is occupied at any given moment
● Enzyme concentration is limiting factor; rate of reaction can only increase with addition of
enzyme
[Enzyme concentration]
● Turnover number (Kcat) - maximum number of substrate molecules that an enzyme can convert
to product per catalytic site per unit time
At low enzyme concentration,
● Increase in enzyme concentration results in proportional increase in rate of reaction
● Enzyme concentration is limiting factor
● Increase in enzyme concentration provides more active sites -> increase in frequency of
effective collisions between substrates and active sites -> rate of enzyme-substrate complex
formation increases -> amount of product formed per unit time increases -> rate of reaction
increases
Copyright © 2019 tonyndr
Definition
Enzymes are biological catalysts that speed up biochemical reactions by lowering activation energy
of a reaction
Structure
● Four categories of amino acid residues:
1) Catalytic amino acids (R groups are directly involved in catalytic activity, i.e. making
or breaking of chemical bonds once substrate is bound)
2) Binding amino acids (R groups hold substrate in position via non-covalent bonds
while catalysis takes place)
3) Structural amino acids (involved in maintaining specific 3D conformation of enzyme
and active site)
4) Non-essential amino acids (no specific functions)
● May interact with additional non-protein component (cofactors) via covalent bonds/weak
interactions
1) Inorganic metal ions
● Mostly small divalent ions (e.g. Ca2+)
● May be component of active site or alter enzyme activity via allosteric
regulation
● Usually bind reversibly to enzyme and alter enzyme’s active/allosteric site to
facilitate catalytic reaction
2) Coenzymes
● Loosely associates with enzyme during reaction
● Act as transient carriers of specific functional groups, hydrogen or electrons
● Enzyme + coenzyme = holoenzyme (without cofactor = apoenzyme)
3) Prosthetic groups
● Tightly bound to enzyme on a permanent basis
Mode of Action
[Enzyme specificity]
● Lock and key hypothesis
○ Enzyme viewed as a rigid structure; only substrates exactly complementary to active
site can bind
○ Explains substrate specificity of enzymes
● Induced fit hypothesis
○ Active site not in precise complementary conformation to substrate before binding
○ Upon binding of substrate, active site changes conformation to bind to substrate
more firmly
○ R groups of catalytic amino acids is moulded into precise conformation and brought
into close proximity to chemical bonds in substrate, facilitating catalysis
Copyright © 2019 tonyndr
, ○ Explains group specificity of enzymes (enzyme can catalyse reactions for substrates
with similar structural/chemical properties)
[Lowering of activation energy + formation of enzyme-substrate complex]
● Enzymes speed up rate of reaction by lowering activation energy
● Effective collision occurs when enzyme and substrate collide in correct orientation
○ Enzyme orientates substrates in close proximity and in the correct orientation to
undergo chemical reactions
● Substrate molecule bind to active site by forming non-covalent bonds (e.g. hydrogen bonds,
ionic bonds) with R groups of binding amino acid residues
○ Enzyme-substrate complex formed
● Enzyme provides a microenvironment that favours the reaction; R groups of catalytic amino
acids at active site catalyse conversion of substrate to product by straining critical bonds in
substrate, allowing substrate to attain an unstable transition state
● Product molecule formed is no longer complementary to active site and is released
Factors Affecting Rate of Reaction
● Limiting factor - factor in shortest supply that limits rate of reaction
[Substrate concentration]
At low substrate concentration,
● Increase in substrate concentration leads to proportional increase in rate of reaction
● Not all active sites of enzymes are occupied
● Substrate concentration is limiting factor
● Increase in substrate concentration increases frequency of effective collision between
enzyme active site and substrate molecules -> rate of enzyme-substrate complex formation
increases -> amount of product formed per unit time increases -> rate of reaction increases
At high substrate concentration,
● Any further increase in substrate concentration does not result in increase in rate of reaction
(graph reaches a plateau)
● Active site of every enzyme molecule is occupied at any given moment
● Enzyme concentration is limiting factor; rate of reaction can only increase with addition of
enzyme
[Enzyme concentration]
● Turnover number (Kcat) - maximum number of substrate molecules that an enzyme can convert
to product per catalytic site per unit time
At low enzyme concentration,
● Increase in enzyme concentration results in proportional increase in rate of reaction
● Enzyme concentration is limiting factor
● Increase in enzyme concentration provides more active sites -> increase in frequency of
effective collisions between substrates and active sites -> rate of enzyme-substrate complex
formation increases -> amount of product formed per unit time increases -> rate of reaction
increases
Copyright © 2019 tonyndr
