Lecture 12

Enzymes: biological
catalysts
Aims

 To understand the concept of biological catalyst

 To learn about the nomenclature and types of
enzymes
 To learn about the basic concepts of enzyme activity
as catalysts
 To understand the thermodynamics of enzymatic
action
Enzymes are catalysts
 They facilitate reactions BUT are not altered by them
 Enzymes are very effective catalysts:
– Specific for certain substrates
– Without secondary products
– Very high rate enhancements
Enzymes are biological catalysts
 Most of the enzymes are globular proteins
 All metabolic reactions require enzymes to take
place at optimal rates
 They catalyze reactions in biological conditions:
– 37 oC
– pH 7.0 Biological
– 1 at conditions are
– H2 O “weak”!!
A short trip into history…
 XVIII c., enzymatic action is described in
digestive fluids
1850, Pasteur characterizes fermentation
1880, Wurtz suggests the existence of the
enzyme-substrate complex
1897, Buchner discovers reactions do not
requiere cell integrity
1926, the first enzyme is isolated (urease)
1930, Haldane writes “Enzymes”
  XX-XXI c., many enzymes are isolated,
characterized and used in…

Medicine Biotechnology Research

– Diagnostic – Industry – Protein detection
– Treatments – Enviroment – genetic manipulation
 Nomenclature and classification
 Either the names are trivial (e.g. trypsin)
 or the names are related to their catalytic activity
Substrate + type of reaction + ase
Alcohol dehydrogen ase
Amino transfer ase

 EC (Enzyme Comission) classification according to 6 types

of reactions
An example
EC 1.1.1.1. (alcohol:NADH oxidoreductase)

1. Oxidoreductases
1.1 Acting on the CH-OH group of donors
1.1.1 With NAD+ or NADP+ as acceptor
1.1.1.1= Alcohol:NADH oxidoreductase
Also called: alcohol dehydrogenase; aldehyde reductase; ADH;
alcohol dehydrogenase (NAD); aliphatic alcohol
dehydrogenase; ethanol dehydrogenase; NAD-dependent
alcohol dehydrogenase; NAD-specific aromatic alcohol
dehydrogenase; NADH-alcohol dehydrogenase; NADH-
aldehyde dehydrogenase; primary alcohol dehydrogenase;
yeast alcohol dehydrogenase
 Enzymes: how is their structure?

 All of them present active centers

- They bind the

substrate
- Small pockets
- With key chemical
groups
- Usually without H2O
 Some enzymes have regulatory centers

- Different from active

centers
- They bind
modulators of
enzyme activity
- Modulator binding
can either increase
or decrease enzyme
activity
 Some enzymes require cofactors

Cofactor:
A nonprotein component of
enzymes that is required for
their catalytic activity
 Cofactors may be either inorganic
(metals)…
 or organic, called coenzymes; they may or may not be
stably bound to enzymes
 A single enzyme can have more than one coenzyme
(look at piruvate dehydrogenase complex!)
 Enzyme localization

 Inside the cell, some enzymes are present only in

certain organelles: mitochondria, cytosol, RER, etc.
 Some enzymes are present only in certain
cells/organs/tissues.
 Isoenzymes: different versions of
the same enzyme

Some tissues have isoforms of the same enzymes. They

may differ in:
– Tertiary or quaternary structure
– Regulation by modulators
– Kinetic properties (Km, Vmax)
 Enzymes: how do they work?
Two ways to study enzymatic activity:

Energy exchange of THERMODYNAMICS

reactions

Reaction rates KINETICS

Lets look at enzymatic thermodynamics…

 Things enzymes do not do:

 Enzymes do not alter the variation of free energy (DG) of a

reaction

G = H - TS

G =  G products -  G substrates
G < 0 exergonic or spontaneous
G = 0 in equilibrium
G > 0 endergonic or non-spontaneous
Characteristics of G
 It depends on the nature of substrates and products
 is independent of the mechanism of the reaction
 is not related to the reaction speed (spontaneous =
fast)
 is related to the equilibrium of the reaction
 in standard conditions (Go´) is a parameter that
defines the energy that a reaction can provide

Enzymes do not alter the thermodynamical

properties of a reaction
 Things enzymes do:
 Enzymes diminish the activation energy (Ea or ΔG‡)

Activation energy:
- Energy requiered to reach
the transition state
- Is related to the reaction
rate
- It saves molecules (and us!)
from destruction

Enzymes speed up reactions

 Enzymes: how do they work?

 By forming an enzyme-substrate complex

E+S ES EP
E+P
 Substrate is easier to find when it interacts with an enzyme

 The “protective” effect of water (solvatation) is removed

 binding energy is established between
enzyme and substrate due to geometric
and electrostatic complementarity
Two models for the enzyme-substrate complex

Lock and key model

Induced-fit model
 Enzymes bind with more stability to the transition state
than to the substrate: this facilitates the reaction
 Enzymes provide alternative ways for the reaction,
sometimes involving several sub-reactions
In summary

 Enzymes are biomolecules that catalyze biological

reactions in weak conditions
 The thermodynamic properties of reactions are not
altered by enzymatic catalysis
 Enzymes speed up reactions by diminishing activation
energy…
 …through the formation of a substrate-enzyme
complex