Enzymes Flashcards
what is an enzyme
an enzyme is a biological catalyst
- increase the rate of reaction/make reactions faster therefore they are catalysts
speeds up reactions/speeds up breakdown
e.g. catalase - speeds up breakdown of hydrogen peroxide into water and oxygen
since they are found in living organisms
Describe the structure of enzymes
on the surface of an enzyme molecule there is a groove called the active site
on the surface, the tertiary structure of the enzyme folds into a three dimensional shape called the active site
Explain why enzymes are specific
The tertiary structure of the active site is complementary to the tertiary structure of a specific substrate molecule
the substrate molecule fits perfectly into the active site
because of this each enzyme is specific for the substrate it binds to
enzyme _______ and _______down another molecule
enzyme attaches to and breaks down another molecule
What is the substrate molecule
The molecule that the enzyme attaches to is called the substrate molecule
What are the prodcuts
The molecules that are produced (from the reaction)
what types of proteins are enzymes
Enzymes are globular proteins
Hydrophilic amino acids on their surface
have any hydrophobic amino acids are buried within the centre of the protein
- this makes globular proteins soluble in water
role of the active site
The job of the active site is to attach to the substrate molecule
active site - part of the enzyme where the substrate molecule attaches to form the enzyme-substrate complex
when the substrate molecule binds to the enzyme’s active site what is made
when substrate binds to enzyme active site - enzyme-substrate complex
what happens if a molecule with a structure which is different to the shape of active site
A molecule with a structure different to the substrate/shape of active site cannot successfully bind to the active site
what happens when the substrate binds to the active site
The amino acids on the surface of the active site can form temporary bonds with the substrate molecule
these temporary bonds help to lower the activation energy of the reaction
The enzyme then catalyses the reaction to form the enzyme-product complex
now products are released from the active site
how do enzymes increase the rate of reaction
in any reaction - molecules must have a certain amount of energy before they can react. - CALLED THE ACTIVATION ENERGY
any molecules which dont have at least the activation energy cannot react
enzymes provide a pathway for the reaction with a lower activation energy barrier
in the presence of an enzyme, the activation energy barrier is lower than it would be without the enzyme
this means that more substrate molecules now have enough energy (at least the activation energy) to cross the activation energy barrier and react
what happens to the reaction rate in the presence of an enzyme
In the presence of an enzyme , the reaction rate increases.
describe the lock and key model for enzyme function
tertiary structure of the active site is fixed and does not change shape (scientists thought)
substrate slots perfectly into the active site
shape of active site does not change when substrate binds
describe the induced fit model for enzyme function
the tertiary structure of the active site changes as the substrate molecule approaches
As the substrate starts to form bonds with the amino acids in the active site, the tertiary structure of the enzyme adjusts so that the active site moulds itself tightly around the substrate
this change in the tertiary structure of the enzyme, ensures that the active site fits perfectly to the substrate
the bonds that the substrate forms with the active site help to catalyse the reaction
tertiary structure of enzyme changes as substrate approaches so the active site moulds around the substrate
describe what would happen to molecules which are not the substrate
Molecules which are not the substrate cannot form the correct bonds to the correct amino acids in the active site
Because of this, the tertiary structure of the enzyme does not change - means that the shape of the active site does not adjust to fit the molecules
explains why enzymes are specific for their substrate
Compare the lock and key model and the induced fit model for enzyme function
shape of active site does not change when substrate binds - lock and key
tertiary structure of enzyme changes as substrate approaches so the active site moulds around the substrate - induced fit
describe what happens in an enzyme controlled reaction
in an enzymes controlled reaction, a substrate molecule is converted into a product molecule
for this to happen - the substrate molecule must collide successfully with the active site of the enzyme
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describe how the rate changes over the course of the enzyme controlled reaction
at the start, the line is steep
This means that a large amount of product is produced in a short time
so the rate of reaction is rapid initially
Rapid initial rate
however as the reaction continues, the line becomes less steep
although we are still making product, the amount of product being formed in a given time is less than at the start
this tells us that at this point, the rate of reaction has decreased
reaction slowing down
at the end, the line is horizontal
this means that no more product is being made so the reaction has stopped
draw graph of amount of product/time
draw graph amount of reactant/time
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explain why the rate changes as the reaction proceeds
rate of an enzyme controlled reaction
rate of enzyme controlled reaction depends on the frequency of successful collisions between the substrate molecules and the active site
frequency = no. of collisions per second
at the start, there is a large amount of substrate molecules
this means that there is a high frequency of successful collisions between the substrate and the active site
this gives us a rapid initial rate of reaction
As the reaction takes place, some of the substrate is converted to product
this means that the amount of substrate molecules falls
So there is a lower frequency of successful collisions between the substrate and the active site (chance of them colliding is lower)
this is giving us a lower rate of reaction/reaction is slowing down
finally at a certain point - end of reaction
All of the substrate molecules have been converted to product
There are no more substrate molecules left to collide with the active site
frequency of successful collisions between the substrate molecules and active sire = 0
at this point, the reaction stops
describe how to calculate the rate of an enzyme controlled reaction
plotting the amount of product formed against time on a graph
then draw a tangent at the point of the reaction we are interested in
factors which affect rate of enzyme controlled reactions
Temperature
pH
concentration of substrate molecules
concentration of enzyme molecules
concentration of competitive inhibitors
concentration of non-competitive inhibitors
describe and explain the effect of temperature on enzymes
on the rate of an enzyme controlled reaction
the rate increases as we increase the temp
this is because, the kinetic energy of both enzyme and substrate are increasing
because they are moving more rapidly, the chance that the substrate will collide with the active site increases (there will be more frequent successful collisions - chance of this is higher)
This increase in the frequency of collisions between the substrate and the active site causes the rate of reaction to increase
At a certain temp., the ate of reaction is at its maximum
this is called the optimum temperature
At the optimum temperature, we have the maximum frequency of collisions between the substrate and the active site
as the temperature increases past the optimum, the rate of reaction decreases.
This is because at higher temperatures, the enzyme molecules are vibrating more rapidlyy
These vibrations cause bonds within the enzyme such as hydrogen bonds to break.
Because of this, the tertiary structure of the enzyme molecules begins to change
as the shape of the active site changes, there comes a point where it is no longer complementary to the substrate
now the substrate can no longer fit into the active site
At this point the enzyme has denatured and no longer functions.
so rate falls to 0
when an enzyme denatures due to high temperatures, it cannot renature if we cool it back down
this is because its tertiary structure has been changed so much that it cannot be reversed
what does the pH of a solution depend on
The pH of a solution depends on the concentration of hydrogen ions (H+)
describe the concentration of hydrogen ions in a solution with a low and high pH
A solution with a low pH, e.g. pH 2, contains a high concentration of H+
A solution with a higher pH e.g. pH6, has a lower concentration of hydrogen ions
describe and explain the effect of pH on enzymes
on the rate of enzyme controlled reactions
each enzyme works fastest at a specific optimum pH
enzyme optimum pH of 2 - suggests that this enzyme works in an acidic environment e.g. the stomach
if the pH changes away from the optimum pH, then the rate of reaction decreases
pH depends on conc. of h+ ions present
hydrogen ions can bond with R groups of amino acids in the protein
Includes amino acids within the active site which form temporary bonds to the substrate
because this can prevent these R groups from bonding with the substrate - this can reduce how effectively the substrate binds to the active site, reducing the rate of reaction
hydrogen ions can also bond with the R groups on amino acids in the rest of the enzyme molecule
This can break the bonds holding the tertiary structure of the enzyme in place/which are essential for the enzyme tertiary structure
this can change the shape of the active site making it less likely that the substrate can attach successfully
if the pH changes significantly, then the active site may change shape so much that it is no longer complementary to the substrate
in this case, the enzyme has denatured
calculate the pH of a solution from the conc. of hydrogen ions
equation
pH = -log[H+]
negative log of the concentration of hydrogen ions
[] = concentration
H+ = hydrogen ions
describe the effect of substrate concentration on the rate of an enzyme catalysed reaction
when there is a low concentration of substrate, there is a low frequency of collisions between the substrates and the active sites
So in this example, the rate of reaction will also be relatively low
When concentration of substrate molecules has doubled/increased, the frequency of collisions between substrate molecules and active sites also doubles/increases
Because of this, the rate of reaction will also double
When doubling the substrate concentration again, this will double the frequency of collisions between the substrate and the active site
This causes the rate to double
As you can see we produce a graph with a straight line through 0
what this means is that the rate of an enzyme catalysed reaction is directly proportional to the substrate concentration
if we continue to increase substrate concentration, then there comes a point where the rate stops increasing any further
At this point, the enzyme is working at its fastest rate
This is called Vmax (max is subscript)
At any given time, every active site will be colliding with a substrate molecule
So if we add more substrates then there are no free active sites for the extra substrate molecules to collide with
Now any increase in the substrate will not increase the rate of reaction any further
IT IS SAID THAT THE ENZYME IS SATURATED
describe the effect of enzyme concentration on the rate of an enzyme catalysed reaction
When there is a low conc. of enzyme molecules (but large conc. of substrate)
All of the active sites will be colliding with the substrate molecules all of the time
So at any time, a large number of substrate molecules will be unable to collide with a free active site.
This means that the rate of reaction will be relatively low
If I double the enzyme conc. then I double the number of active sites, doubles the frequency of collisions between the substrates and the active sites
So this doubles the rate
The rate is directly proportional to the enzyme concentration provided that there is more substrate than enzyme
If the amount of substrate becomes limited, then increasing the enzyme conc. further will no longer increase the rate
this is because there will not be enough substrate molecules to collide with all of the available active sites
the substrate is not the only molecule which can bind to an active site
what other molecules can bind to an active site
this molecule has a similar but not identical structure to the substrate
just like the substrate, this molecule can also bind to the active site
but because it is not the substrate, no reaction happens
so after a short time, the molecule leaves the active site
molecule called a competitive inhibitor
By occupying the active site for a short time, this molecule prevents the actual substrate from colliding with the active site
because the frequency of collisions between the substrate and the active site is reduced, the effect of this molecule is to reduce the rate of reaction
e.g.
succinate is the substrate for an enzyme involved in respiration.
The molecule malonate has a similar structure to succinate
Because of this, malonate can act as a competitive inhibitor preventing succinate from colliding with the active site of the enzyme
this means that malonate can inhibit respiration
role of competitive inhibitors
a competitive inhibitor competes with the substrate molecules for the active site
effect of this is to reduce the rate of the enzyme catalysed reaction
how can we reduce the effect of a competitive inhibitor
a competitive inhibitor competes with the substrate molecules for the active site
this means that we can reduce the effect of a competitive inhibitor by increasing the concentration of the substrate
describe effect of increasing substrate concentration while keeping competitive inhibitor concentration the same
increasing substrate concentration while keeping competitive inhibitor concentration the same
means that there is now a much greater chance that a substrate molecule will occupy the active site and form an enzyme-substrate complex rather than the competitive inhibitor
so by increasing the concentration of substrate we can reduce effect of competitive inhibitor
only applies if the competitive inhibitor does not bind permanently to the active site
effect of competitive inhibitors on the rate of an enzyme catalysed reaction
this molecule has a similar but not identical structure to the substrate
just like the substrate, this molecule can also bind to the active site
but because it is not the substrate, no reaction happens
so after a short time, the molecule leaves the active site
molecule called a competitive inhibitor
By occupying the active site for a short time, this molecule prevents the actual substrate from colliding/binding with the active site
effect of this is to reduce the rate of the enzyme catalysed reaction
a competitive inhibitor competes with the substrate molecules for the active site
this means that we can reduce the effect of a competitive inhibitor by increasing the concentration of the substrate
draw a graph with enzyme with absence of completive inhibitor
then with a competitive inhibitor
rate of reaction and substrate conc.
normal rate of reaction and substrate conc.
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lower line shows the same experiment, except that we have added a fixed concentration of a competitive inhibitor
As you can see, the competitive inhibitor reduces the rate of reaction
By temporarily blocking the active site, the competitive inhibitor prevents the substrate from binding and forming an enzyme-substrate complex
However, as we increase the substrate concentration, the effect of the competitive inhibitor reduces (e.g. at higher concentrations, the competitive inhibitor has only reduced the rate of reaction by around 20% compared to about 50% inhibition at lower concentrations of substrate)
at a very high concentration, the rate of reaction is almost the same as when there is no competitive inhibitor present
lower amount of products being formed per second with competitive inhibitor
types of competitive inhibitors
reversible competitive inhibitor
irreversible competitive inhibitor
some competitive inhibitors bind irreversibly to the active site of enzymes
Because irreversible competitive inhibitors bind permanently to the active site, we cannot reverse the effect of these inhibitors by increasing the substrate concentration
This is because once an irreversible competitive inhibitor enters the active site, it never leaves no matter what the substrate concentration
describe the effect of non-competitive inhibitors on the rate of an enzyme catalysed reaction
how are non-competitive inhibitors different to competitive inhibitors
where do non-competitive inhibitors bind to
unlike a competitive inhibitor, non-competitive inhibitors do not bind to the active site of an enzyme
instead, a non-competitive inhibitor binds to a different site on the enzyme molecule
This is called an allosteric site
Describe what happens when a non-competitive inhibitor binds to the allosteric site of an enzyme
When the non-competitive inhibitor binds to the allosteric site it causes the tertiary structure of the enzyme to change
This means that the shape of the active site changes, so it is no longer complementary to the substrate
now the substrate molecule cannot bind to the active site to form the enzyme substrate complex
the effect of this is to reduce the rate of the reaction
are the structure of a non-competitive inhibitor and the substrate similar
Unlike a competitive inhibitor, a non-competitive inhibitor does not have a similar structure to the substrate
This is because a non-competitive inhibitor does not bind to the active site
can the effect of a non-competitive inhibitor be overcome
The effect of a non-competitive inhibitor cannot be overcome by increasing the substrate concentration
draw and explain graph for non-competitive inhibitor
rate of reaction/substrate conc.
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even if we increase the substrate concentration, the non-competitive inhibitor reduces the rate of reaction by the same amount
this is because the non-competitive inhibitor causes the shape of the active site to change
So even if we increase the conc. of substrate, the substrate molecules still cannot bind successfully with the active site
