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Biology: Unit F212: Molecules, Biodiversity, Food and Health
Enzymes
o Enzymes are biological catalysts – they speed up reactions but are not
used up or changed in any way. They are globular proteins with lots of
hydrophilic amino acids, making them soluble in water. They have a
very specific tertiary structure determined by the sequence of amino
acids in the primary structure.
o Enzymes have benefits as catalysts, because they are specific to one
reaction and do not produce a range of unwanted by-products.
o Some enzymes are intracellular – they catalyse reactions on the inside
of cells, like DNA polymerase.
o Extracellular enzymes catalyse reactions on the outside of cells – like
amylase which digests amylase in saliva.
o The whole of the primary, secondary and
tertiary structure of an enzyme is involved in
achieving a very specific shape for the active
site.
o The active site is the region of an enzyme to
which a substrate binds due to its
complementary shape and charge.
o Enzymes are specific because the shape of
their active site is complementary to only one
substrate molecule.
o The lock and key mechanism is how the enzyme and substrate fit
together. The enzyme and its substrate have complementary shapes
and charges. The substrate
molecule is bound tightly to the
enzyme’s active site. The
reaction occurs and the
substrate is converted into two
products. The product
molecules have a changed shape and charge, so they are no longer
complementary to the enzyme’s active site. The opposite charges
cause the products to be pushed out.
o The induced fit mechanism suggests that when the substrate binds,
the enzyme changes shape slightly, causing the active site to fit more
closely around the substrate. The enzyme’s change in shape causes a
strain to be put on the bonds in the substrate – this destabilises it so
it will react more easily.
o Enzymes lower the activation energy of a reaction:
this means that they reduce the amount of energy
required for a reaction to occur. The hold substrates
together at the right angles top react and have
structural flexibility – their shape can change in order
to bring substrates together in the correct sequence.
o The changing rate of an enzyme catalysed reaction
left to completion:
At the start of the
reaction, there are a
large number of
substrate molecules,
and so there is a high
frequency of collisions.
This means that the rate
is high.
As the reaction proceeds, there
are fewer collisions as more
reactant is turned into product.
The rate of reaction continues
to decrease in rate as more
substrate is turned to product,
because there are fewer and
fewer collisions. When there is
no reactant left, the reaction
stops.
o The effect of temperature on enzyme activity:
At the optimum temperature, the
rate of reaction is at its maximum.
As temperature increases,
molecules have more
kinetic energy. The
enzymes and substrates
therefore have more
frequent successful
collisions and there is an
increased rate of reaction.
When the temperature exceeds the
optimum, rate of reaction
eventually falls to zero. This is
because the enzyme becomes
denatured…
Denaturation is caused when the molecules vibrate due to high
temperatures and the hydrogen and ionic bonds
may break. These are the bonds responsible for
holding the tertiary structure in place. If the
bonds break, and the tertiary structure breaks
down, the specific shape of the active site is
lost and is no longer complementary to the
substrate. Enzyme substrate complexes can’t
form, so the reaction stops.
o The effect of pH on enzyme activity:
If the pH is lowered, there is a greater
concentration of H+ ions. These H+ ions can
interfere with the hydrogen and ionic bonds
which hold the tertiary structure in place. H+ ions
are attracted to negatively charged R groups
which are part of the amino acids making up the
active site. They cluster around the negative
group, and this interferes with the binding of the
substrate to the active site.
If the substrate cannot bind,
rate of reaction falls.
At the optimum
temperature, the
concentration of
hydrogen ions in solution
gives the enzyme its best
overall shape. This shape
holds the active site in the
shape that best fits the
substrate.
o The effect of substrate concentration on enzyme activity:
As the concentration of substrate
increases, there are more frequent
successful collisions between
enzymes and substrates. More
enzyme-substrate complexes form,
so more product is formed and rate
of reaction increases.
The rate of reaction will reach a
maximum value, V max, when
all active sites are occupied at
all times.
o The effect of enzyme concentration on enzyme activity:
As the enzyme
concentration increases,
more active sites become
available. More enzyme
substrate complexes can
form so more product can
form, and the rate of
reaction increases.
If the enzyme concentration
increases further, a point will
be reached where all substrate
molecules are occupying
enzyme active sites. The
maximum possible rate has
been reached for this reaction
with a fixed substrate
concentration.
o A competitive inhibitor has a similar shape to that of the
substrate molecule. The competitive inhibitor can bind with
the enzyme to make an enzyme-inhibitor complex. This means
that the active site is filled, and so the substrate can’t bind.
The enzyme doesn’t catalyse a reaction, so the rate of reaction
decreases. The level of inhibition depends on the
concentrations of inhibitor and substrate. If the number of
substrate molecules is greater than the number of inhibitor molecules,
the level of inhibition decreases, because the enzyme is more likely to
collide with a substrate molecule than with an inhibitor molecule.
The rate of reaction with a
non competitive inhibitor
present is reduced; there are
fewer collisions between
enzymes and substrates, so
fewer enzyme-substrate
complexes form, and less
product is produced.
o A non competitive inhibitor does not compete with the
substrate for a place in the active site. Instead, they
attach to the allosteric site elsewhere on the enzyme.
This binding distorts the tertiary structure and the shape
of the active site changes. The shape of the active site is
no longer complementary, so enzyme-substrate complexes
cannot form, and rate of reaction decreases. This type of
inhibition is generally irreversible – changing the substrate
concentration will have no effect.
o Poison as a competitive inhibitor: Ethylene Glycol
Ethylene glycol is found in car anti-freeze. When it is taken into the
body, the ethylene glycol is broken down by the alcohol dehydrogenase
enzyme into oxalic acid. This is
extremely toxic and can lead to death. In
order to reduce the rate at which
ethylene glycol is broken down, it must be
‘diluted’ with ethanol alcohol. If the
concentration of ethanol is increased,
there will be a greater chance of collision
between the enzyme and the ethanol, so
the rate at which oxalic acid is produced
will be reduced.
o Some medicinal drugs work by inhibiting the activity of enzymes.
Infections by viruses, including HIV, are treated using chemicals that
act as protease inhibitors. These prevent the viruses from replicating
by inhibiting the activity of the protease enzyme, which the viruses
need in order to build new virus coats.
o Antibiotics as a competitive inhibitor: Penicillin
Penicillin is an inhibitor of a bacterial
enzyme that forms cross links in the
bacterial cell wall of some bacteria. Penicillin
is structurally similar to peptidoglycan, of
the substrates used in wall building. The
penicillin is introduced into the cell wall, which makes them weak. The
walls collapse and fall apart, killing the bacteria.
There is an increasing problem with treating bacterial infections because
some strains of bacteria are becoming resistant. Among a population of
bacteria, there may be an individual with mutations and altered enzymes.
This individual will be naturally selected when the bacterial population is
exposed to antibiotics. It will survive and reproduce, so that all then have
then altered enzymes capable of producing the enzyme, beta lactamase
that breaks down penicillin.
o A cofactor is any substance which must be present to ensure that an
enzyme controlled reaction takes place at the appropriate rate. Some
cofactors are part of the enzyme (prosthetic groups); others affect
the enzyme on a temporary basis (coenzymes and inorganic ion
cofactors).
o Coenzymes are small organic non-protein molecules that bind for a
short period to the active site. They may bind at the same time or just
before the substrate. Coenzymes often carry chemical groups
between enzyme and substrate so that they link together enzyme
controlled reactions which must take place in a sequence.
o Prosthetic groups are coenzymes which are permanently a part of
the enzyme. They contribute to the overall shape and charge of
the molecule. An example is the zinc prosthetic group in carbonic
anhydrase.
o Inorganic ion cofactors – “activators” – in the presence of certain
charged ions, some catalysed reactions can be speeded up.
The binding of the ion makes the enzyme substrate complex
form more easily because it affects the charge distribution
and shape of the enzyme substrate complex. Amylase will
not function without chloride ions.