Enzymes

Question 1

what is an enzyme

Answer 1

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

Question 2

Describe the structure of enzymes

Answer 2

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

Question 3

Explain why enzymes are specific

Answer 3

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

Question 4

enzyme _______ and _______down another molecule

Answer 4

enzyme attaches to and breaks down another molecule

Question 5

What is the substrate molecule

Answer 5

The molecule that the enzyme attaches to is called the substrate molecule

Question 6

What are the prodcuts

Answer 6

The molecules that are produced (from the reaction)

Question 7

what types of proteins are enzymes

Answer 7

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

Question 8

role of the active site

Answer 8

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

Question 9

when the substrate molecule binds to the enzyme’s active site what is made

Answer 9

when substrate binds to enzyme active site - enzyme-substrate complex

Question 10

what happens if a molecule with a structure which is different to the shape of active site

Answer 10

A molecule with a structure different to the substrate/shape of active site cannot successfully bind to the active site

Question 11

what happens when the substrate binds to the active site

Answer 11

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

Question 12

how do enzymes increase the rate of reaction

Answer 12

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

Question 13

what happens to the reaction rate in the presence of an enzyme

Answer 13

In the presence of an enzyme , the reaction rate increases.

Question 14

describe the lock and key model for enzyme function

Answer 14

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

Question 15

describe the induced fit model for enzyme function

Answer 15

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

Question 16

describe what would happen to molecules which are not the substrate

Answer 16

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

Question 17

Compare the lock and key model and the induced fit model for enzyme function

Answer 17

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

Question 18

describe what happens in an enzyme controlled reaction

Answer 18

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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Question 19

describe how the rate changes over the course of the enzyme controlled reaction

Answer 19

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

Question 20

draw graph of amount of product/time

draw graph amount of reactant/time

Answer 20

https://mmerevise.co.uk/app/uploads/2022/11/Rate-of-Reaction-Product-e1669108738140.png

https://mmerevise.co.uk/app/uploads/2023/01/mass-of-reactant.png

Question 21

explain why the rate changes as the reaction proceeds

rate of an enzyme controlled reaction

Answer 21

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

Question 22

describe how to calculate the rate of an enzyme controlled reaction

Answer 22

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

Question 23

factors which affect rate of enzyme controlled reactions

Answer 23

Temperature
pH
concentration of substrate molecules
concentration of enzyme molecules
concentration of competitive inhibitors
concentration of non-competitive inhibitors

Question 24

describe and explain the effect of temperature on enzymes

on the rate of an enzyme controlled reaction

Answer 24

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

Question 25

what does the pH of a solution depend on

Answer 25

The pH of a solution depends on the concentration of hydrogen ions (H+)

Question 26

describe the concentration of hydrogen ions in a solution with a low and high pH

Answer 26

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

Question 27

describe and explain the effect of pH on enzymes

on the rate of enzyme controlled reactions

Answer 27

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

Question 28

calculate the pH of a solution from the conc. of hydrogen ions

equation

Answer 28

pH = -log[H+]

negative log of the concentration of hydrogen ions
[] = concentration
H+ = hydrogen ions

Question 29

describe the effect of substrate concentration on the rate of an enzyme catalysed reaction

Answer 29

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

Question 30

describe the effect of enzyme concentration on the rate of an enzyme catalysed reaction

Answer 30

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

Question 31

the substrate is not the only molecule which can bind to an active site

what other molecules can bind to an active site

Answer 31

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

Question 32

role of competitive inhibitors

Answer 32

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

Question 33

how can we reduce the effect of a competitive inhibitor

Answer 33

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

Question 34

describe effect of increasing substrate concentration while keeping competitive inhibitor concentration the same

Answer 34

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

Question 35

effect of competitive inhibitors on the rate of an enzyme catalysed reaction

Answer 35

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

Question 36

draw a graph with enzyme with absence of completive inhibitor

then with a competitive inhibitor
rate of reaction and substrate conc.

Answer 36

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

Question 37

types of competitive inhibitors

Answer 37

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

Question 38

describe the effect of non-competitive inhibitors on the rate of an enzyme catalysed reaction

Question 39

how are non-competitive inhibitors different to competitive inhibitors

where do non-competitive inhibitors bind to

Answer 39

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

Question 40

Describe what happens when a non-competitive inhibitor binds to the allosteric site of an enzyme

Answer 40

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

Question 41

are the structure of a non-competitive inhibitor and the substrate similar

Answer 41

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

Question 42

can the effect of a non-competitive inhibitor be overcome

Answer 42

The effect of a non-competitive inhibitor cannot be overcome by increasing the substrate concentration

Question 43

draw and explain graph for non-competitive inhibitor

rate of reaction/substrate conc.

Answer 43

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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