Week 6 enzymes and catalysis Flashcards
Enzymes
Biological catalysts that speed up specific enzymatic reactions, every chemical reaction within cells is regulated by enzymes
Enzymes 2
Nearly all enzymes are proteins
-Some enzymes are single polypeptide chains
-Others are complexes of more subunits
Enzymes - Relevance for MPharm students
Enzymes as a catalyst
Their catalytic activity depends on the integrity of their protein conformation ->
If enzymes are denatured or dissociated, catalytic activity is usually lost
Enzyme properties
-Specific
-Catalytic power - fast
-Efficient
-Regulated
Substrate specificity
-Ability of the enzyme to specifically recognise the proper substrate (reactant)
-Enzyme-substrate recognition and specificity is based on structural complementarity ->
3-D fit
->Substrates bind to a specific region of the enzyme called the active site
Enzyme–substrate complex
Enzyme–substrate complex (ES) is the first step in enzymatic catalysis
E + S ⇄ ES
2 models of substrate-active site binding
-Lock and key
-Induced-fit
Lock and key
The active site and substrate are perfectly complementary for each other, like “a key into its lock”
Induced - fit
Substrate is not exactly
complementary to the active site. The binding induces a conformational change allowing a better fit, like “a hand in a glove”
Active site
The active site, is a three-dimensional pocket, located in
a small enzyme region (~10–20%), which is composed of:
-Substrate binding site
-Catalytic site
The correct folding of the enzymes is required
Substrate-enzyme binding alters the structure of the substrate to promote the formation of the transition state
Substrate binding site
Amino acids side chains interact with the substrate
-Through H-bonds and other electrostatic interactions
-To orientate the substrate within the active site
Catalytic site
Amino acids that catalyse the reaction
Catalytic power
-Increase the rate (speed) of a chemical reaction
-Between 10^6 up to 10^17 times faster than their absence
-Enzymes achieve catalysis of a reaction by reducing the activation energy of the transition state (the energy barrier to the reaction, ΔG‡)
Activation energy
To initiate any chemical reaction, energy is required the minimum amount of energy required
-Essential to cause molecules to react with each other
-The lowest activation energy, the faster rate of a reaction
Efficiency and reusability
Enzymes are extremely efficient to catalyse specific reaction and remain unaffected throughout this process
Not altered or consumed during
or after the reaction
Extremely efficient -> active at very low concentrations
Enzymatic modulation (regulated)
Various conditions affect enzyme function (reaction rate);
-Temperature
-Ionic conditions
-pH
-Substrate concentration
-Presence of inhibitors
Temperature
-Highest rate at a certain optimum temperature -> usually 37 °C in humans
-Lower activity at lower temperatures -> molecules have low kinetic energy
-Lose activity at high temperatures -> denaturation (loss of native folding, active site and the substrate no longer
matches, loss of catalytic activity)
pH and enzymatic activity
Enzymes are most active at an optimum pH;
-About pH 7.5 for enzymes in the small intestine
-About pH 1.5 for stomach enzymes (Pepsin)
-About pH 4 - 5 for digestive lysosomal enzymes
Contain R groups of amino acids with proper charges at optimum pH
Lose activity in low or high pH as the tertiary structure is disrupted
Substrate concentration
-At a constant concentration of
enzyme, an increase in substrate
concentration will increase the
reaction rate until the enzyme
becomes saturated
-At a constant concentration of
enzyme, an increase in substrate
concentration will increase the
reaction rate until the enzyme
becomes saturated
-At steady state, increasing substrate concentration will not change the reaction rate
-E + S ⇄ ES ⇄ E+P
Vmax, Km and principles of enzyme kinetics
-Kinetics is the study of reaction rates
-From Michaelis–Menten equation: Km = the concentration of substrate at
which the reaction rate is half-maximal
Km is an inverse measure of how tightly the enzyme binds its substrate
The higher the Km, the weaker the binding
The lower the Km, the stronger the binding
Enzyme inhibition
-Competitive inhibitors
-Non-competitive inhibitors
Competitive inhibitors
-They compete with the substrate by binding the active site and blocking it
-Can be reversible or irreversible
Non-competitive inhibitors
-Binding to a site (allosteric) far from the active site. It causes a conformational change of the enzyme and its active site
resulting in the block of the activity
-Usually reversible
Enzyme Cofactors
Some enzymes do not require additional chemical groups for activity
Other enzymes require cofactors providing additional NON-PROTEIN reactive groups that are essential for their catalytic activity
Coenzymes
Non-protein organic cofactors
-Cosubstrates
-Prosthetic groups
Cosubstrates
-Weakly/temporarily bound to an enzyme
-Consumed and transformed during the reaction and dissociate from the active site (regenerated in another enzymic
reaction and recycled)
Prosthetic groups
-Tightly or permanently bound to the enzyme
-Are not consumed or altered during the reaction
Holoenzymes and Apoenzymes
-A complete catalytically-active enzyme together with its cofactor is called a HOLOENZYME
-The protein part of the enzyme on its own without its cofactor is
called an apoenzyme (not active)
Enzymes nomenclature
> 5,000 enzymes classified by the reactions they catalyse
-Trivial names are more used, but each enzyme has unique code number
Oxidoreductases
Oxidation and reduction (REDOX) reactions
Transferases
Functional group transfer reactions
->Includes kinases
Hydrolases
Cleavage of chemical bonds through the addition of water molecules (proteases, phosphatases, etc)
Lyases
Breaking of chemical bonds within a molecule, without the involvement of water
Isomerases
Conversion of one isomer into another one
Ligases
Joining of two molecules
Translocases
Movement of molecules or ions across membranes
