Lecture 5 (BOOK) – How
enzymes work (Thunnissen)
Chapter 3: page 140-151
As mentioned, enzymes bind to one or more ligands called substrates, and convert them to one or
more chemically modified products. Enzymes speed up reactions, that is they act as catalysts.
Enzymes can be grouped into functional classes that perform similar chemical reactions:
The first step in enzyme catalysis is substrate binding.
There is a limit tot the amount of substrate that a single enzyme molecule can process in a given
time. Although an increase in the concentration of substrate increases the rate at which product is
formed, this rate eventually reaches a maximum value. At that point, the enzyme molecule is
saturated with substrate. The rate of reaction (Vmax) depends only on how rapidly the enzyme can
process the substrate molecule, the turnover number can be calculated with the V max:
Vmax / [enzyme] = turnover number
Another parameter used to characterise enzymes is the concentration of substrate that allows the
reaction to proceed at one-half its maximum rate (0.5V max) expressed as Km. At low Km, the enzyme
reaches its maximum catalytic rate at low concentration of substrate, indicating tight binding,
whereas high Km corresponds to weak binding.
!!! STUDY PANEL 3-2 ABOUT METHODS USED TO STUDY ENZYMES !!!
Enzymes speed reactions
There are several reason for the efficiency of enzymes:
- Enzymes greatly increases the local concentration of both substrate molecules at the
catalytic sites, holding them in the correct orientation for the reaction.
- Enzymes have a much higher affinity for the transition state of the substrate than they have
for the stable form. The tight binding lower the energy of the transition state (activation
energy) and therefore the enzyme greatly accelerates a particular reaction.
, Acid and base catalysis
Enzymes not only bind tightly to a transition state, they also contain precisely positioned atoms that
alter the electron distributions in the atoms that participate directly in the making and breaking of
covalent bonds.
Enzymes are unique in being able to use acid and base catalysis simultaneously because the enzymes
framework prevents them from combining with each other.
Lysozyme
Lysozyme catalyses the cutting of polysaccharide chains in the cell walls of bacteria. The reaction that
lysozyme catalyses is hydrolyses, it adds a molecule of water to a bond between two adjacent sugar
groups in the polysaccharide chain. The reaction is energetically favourable because the free energy
in the severed polysaccharide chain is lower than the free energy of the intact chain.
An impressive increase in hydrolysis rate is possible because conditions are created in the
microenvironment of the lysozyme active site that greatly reduce the activator energy necessary for
the hydrolysis to take place.
Other enzymes use similar mechanisms. In reactions involving two ore more reactant, the active site
also acts like a template that brings the substrates together.
Tightly bound small molecules
Enzymes and other proteins often use small nonprotein molecules to perform functions that would
be difficult or impossible to do with amino acids alone. Carboxypeptidase for example, cuts
polypetide chains and carries a tightly bound zinc ion in its active site. The zinc ion forms a transient
bond with one of the substrate atoms, assisting the hydrolysis reaction.
When these small molecules are organic molecules, they are referred to as coenzymes which are
often vitamins or derivatives of vitamins. Examples are biotin found on enzymes that transfer a
carboxylate group from one molecule to another and retinal which assists the signal receptor protein
rhodopsin.
Another example is hemoglobin which carries four heme groups (ring-shaped molecules with a iron
atom) which give blood its red colour.
As mentioned, many vitamin derivatives are critical coenzymes for human cells:
Multi-enzyme complexes
If the rate of desirable reactions is not higher than the rate of competing side reactions, a cell would
die soon. Some rates reactions are so rapid because the enzyme catalysis is so effective, some even
can’t be improved. The factor that limits the reaction rate is no longer the intrinsic speed of action, it
the frequency at which the enzyme and substrate collide, these reactions are said to be diffusion-
limited.
The cell can increase reaction rates without raising substrate concentrations by bringing various
enzymes involved in a reaction sequence together to form a large protein assembly known as a
enzymes work (Thunnissen)
Chapter 3: page 140-151
As mentioned, enzymes bind to one or more ligands called substrates, and convert them to one or
more chemically modified products. Enzymes speed up reactions, that is they act as catalysts.
Enzymes can be grouped into functional classes that perform similar chemical reactions:
The first step in enzyme catalysis is substrate binding.
There is a limit tot the amount of substrate that a single enzyme molecule can process in a given
time. Although an increase in the concentration of substrate increases the rate at which product is
formed, this rate eventually reaches a maximum value. At that point, the enzyme molecule is
saturated with substrate. The rate of reaction (Vmax) depends only on how rapidly the enzyme can
process the substrate molecule, the turnover number can be calculated with the V max:
Vmax / [enzyme] = turnover number
Another parameter used to characterise enzymes is the concentration of substrate that allows the
reaction to proceed at one-half its maximum rate (0.5V max) expressed as Km. At low Km, the enzyme
reaches its maximum catalytic rate at low concentration of substrate, indicating tight binding,
whereas high Km corresponds to weak binding.
!!! STUDY PANEL 3-2 ABOUT METHODS USED TO STUDY ENZYMES !!!
Enzymes speed reactions
There are several reason for the efficiency of enzymes:
- Enzymes greatly increases the local concentration of both substrate molecules at the
catalytic sites, holding them in the correct orientation for the reaction.
- Enzymes have a much higher affinity for the transition state of the substrate than they have
for the stable form. The tight binding lower the energy of the transition state (activation
energy) and therefore the enzyme greatly accelerates a particular reaction.
, Acid and base catalysis
Enzymes not only bind tightly to a transition state, they also contain precisely positioned atoms that
alter the electron distributions in the atoms that participate directly in the making and breaking of
covalent bonds.
Enzymes are unique in being able to use acid and base catalysis simultaneously because the enzymes
framework prevents them from combining with each other.
Lysozyme
Lysozyme catalyses the cutting of polysaccharide chains in the cell walls of bacteria. The reaction that
lysozyme catalyses is hydrolyses, it adds a molecule of water to a bond between two adjacent sugar
groups in the polysaccharide chain. The reaction is energetically favourable because the free energy
in the severed polysaccharide chain is lower than the free energy of the intact chain.
An impressive increase in hydrolysis rate is possible because conditions are created in the
microenvironment of the lysozyme active site that greatly reduce the activator energy necessary for
the hydrolysis to take place.
Other enzymes use similar mechanisms. In reactions involving two ore more reactant, the active site
also acts like a template that brings the substrates together.
Tightly bound small molecules
Enzymes and other proteins often use small nonprotein molecules to perform functions that would
be difficult or impossible to do with amino acids alone. Carboxypeptidase for example, cuts
polypetide chains and carries a tightly bound zinc ion in its active site. The zinc ion forms a transient
bond with one of the substrate atoms, assisting the hydrolysis reaction.
When these small molecules are organic molecules, they are referred to as coenzymes which are
often vitamins or derivatives of vitamins. Examples are biotin found on enzymes that transfer a
carboxylate group from one molecule to another and retinal which assists the signal receptor protein
rhodopsin.
Another example is hemoglobin which carries four heme groups (ring-shaped molecules with a iron
atom) which give blood its red colour.
As mentioned, many vitamin derivatives are critical coenzymes for human cells:
Multi-enzyme complexes
If the rate of desirable reactions is not higher than the rate of competing side reactions, a cell would
die soon. Some rates reactions are so rapid because the enzyme catalysis is so effective, some even
can’t be improved. The factor that limits the reaction rate is no longer the intrinsic speed of action, it
the frequency at which the enzyme and substrate collide, these reactions are said to be diffusion-
limited.
The cell can increase reaction rates without raising substrate concentrations by bringing various
enzymes involved in a reaction sequence together to form a large protein assembly known as a
