1. Enzymes: Basic concepts
CHMI 2227E Biochemistry I
Enzymes:
Basic concepts
CHMI E.R. Gauthier, Ph.D.

2. Enzymes Enzymes: Catalysts:
Proteins
RNA
Catalysts:
Fully active enzyme is regenerated at the end of the reaction
Speed-up chemical reactions in cells by placing the substrate in an environment that facilitates the reaction
So: proper 3D structure (tertiary and, when applicable, quaternary) is ABSOLUTELY ESSENTIAL for the function of enzymes;
CHMI E.R. Gauthier, Ph.D.

3. Enzymes Very powerful catalysts; Very specific for their substrate;
Can distinguish between enantiomers
Some enzymes require additional chemicals or groups to function:
Metal ions
Prosthetic groups:
Heme
Co-factors
ATP
CHMI E.R. Gauthier, Ph.D.

4. Classes of enzymes
Only 6 types of chemical reactions are catalyzed by enzymes:
1. oxido-reduction: oxidoreductases
2. Transfer of chemical groups: transferases
3. Hydrolysis: hydrolases
4. Removal of chemical groups: lyases
5. Isomerisation: isomerases
6.Linking two groups together: ligases
Enzymes are classified according to the type of reaction they catalyse:
each enzyme is given a systematic name and a IUBMB number (EC XXXX)
IUMBM = International Union of Biochemistry and Molecular Biology
The complete list of enzymes can be found at the following website:
CHMI E.R. Gauthier, Ph.D.

5. IUBMB enzyme nomenclature
Example: ATP: D-glucose-6 phosphotransferase (aka hexokinase) EC
2 = transferase
7 = phosphotransferase
1 = acceptor group is OH
1 = glucose binds the phosphate group
ATP +
D-glucose
ADP
D-glucose-6-phosphate
CHMI E.R. Gauthier, Ph.D.

6. Classes of enzymes 1- Oxidoreductases 2- Transferases 3- Hydrolases
4- Lyases
5- Isomerases
6- Ligases
CHMI E.R. Gauthier, Ph.D.

7. Classes of enzymes 1- Oxidoreductases 2- Transferases 3- Hydrolases
4- Lyases
5- Isomerases
6- Ligases
A- + B
A + B-
A-B + C
A + B-C
A-B + H2O
A-H + B-OH
A=B + X-Y
A-B X Y
A-B X Y
A + B
A-B
CHMI E.R. Gauthier, Ph.D.

8. Oxidoreductases Example: Lactate dehydrogenase (EC 1.1.1.27)
Lactate = substrate
Pyruvate = product
NAD+/NADH = co-factor
CHMI E.R. Gauthier, Ph.D.

9. 2. Transferases Example: Alanine transaminase (EC 2.6.1.2)
Alanine / a-ketoglutarate = substrates
Pyruvate / L-glutamate = products
CHMI E.R. Gauthier, Ph.D.

10. 3. Hydrolases Example: diphosphate phosphohydrolase (EC 3.6.1.1)
Pyrophosphate / H2O = substrates
Phosphate = product
CHMI E.R. Gauthier, Ph.D.

11. 4. Lyases (aka synthases) Example: Pyruvate decarboxylase (EC 4.1.1.1)
Pyruvate = substrate
Acetaldehyde and CO2 = products
CHMI E.R. Gauthier, Ph.D.

12. 5. Isomerases Example: Alanine racemase (EC 5.1.1.1)
L-alanine = substrate
D-alanine = product
CHMI E.R. Gauthier, Ph.D.

13. 6. Ligases (aka synthetases) Example: L-glutamine synthetase (EC 6. 3
L-glutamate / NH4+ = substrates
L-glutamine = product
ATP = co-factor
CHMI E.R. Gauthier, Ph.D.

14. How do enzymes work?
Enzymatic reactions take place in multiple steps involving reaction intermediates:
E + S ES EP E + P
Note that, while in theory these reactions are reversible, in practice, the low levels of the one of the reactants (S or P) usually pushes the equilibrium in one direction;
Enzymes increase the rate of chemical reactions, but do NOT alter the direction of the equilibrium.
CHMI E.R. Gauthier, Ph.D.

15. Enzymes and the energy barrier
In chemical reactions, three conditions must be met for a reaction to take place:
1. the molecules must collide to react. If two molecules simply collide, however, they will not always react; therefore, the occurrence of a collision is not enough.
2. there must be enough energy (energy of activation) for the two molecules to react. If two slow molecules collide, they might bounce off one another because they do not contain enough energy to reach the energy of activation and overcome the transition state (the highest energy point).
3. the molecules must be orientated with respect to each other correctly.
CHMI E.R. Gauthier, Ph.D.

16. Enzymes and the energy barrier
The transition state is not a reaction intermediate: it is a transitory molecular structure that is no longer the substrate, but not yet the product.
G = Gibbs free energy
the ability of the molecule to react
The greater the free energy, the more unstable the molecule is.
DG = Gproduct – Gsubstrate:
If DG > 0 = reaction does not occur spontaneously (because S is more stable that P)
If DG < 0 = reaction occurs spontaneously (because P is more stable than S)
In other words: the more negative the DG, the more likely the reaction will take place;
DGŧ DG
CHMI E.R. Gauthier, Ph.D.

17. Enzymes and the energy barrier
In the absence of an enzyme (or catalyst), the substrate (here the metal stick) requires a substantial amount of energy in order to reach the activation state and react;
CHMI E.R. Gauthier, Ph.D.

18. Enzymes and the energy barrier
In the presence of an enzyme, the reaction is facilitated because the enzyme provides a better environment for the reaction to occur:
Close proximity of substrate and chemical groups of the enzyme
Proper orientation of the chemical groups with respect to the substrate
The formation of the transition state is favoured;
This results in a lowering of the activation energy required for the reaction to occur.
CHMI E.R. Gauthier, Ph.D.

19. The « lock and key » myth…
The « lock and key » thing is a MYTH:
If the enzyme and substrate were perfectly complementary, like a lock and key, the interaction between E and S would be so stable that the reaction would not occur!
CHMI E.R. Gauthier, Ph.D.

20. The « lock and key » myth…
Instead, the 3D shape of the enzyme is complementary to the transition state;
by doing so, the enzymes favours the formation of the transition state, lowers the energy of activation, and accelerates the reaction…COOL!
CHMI E.R. Gauthier, Ph.D.