4. Core Concepts - Biological reactions are regulated by enzymes

Question 1

enzymes

Answer 1

globular proteins

tertiary structure (can have tertiary structure)

synthesised by living cells

can act inside the cell (intercellular enzymes) or can be secreted by cells (extracellular enzymes).

Question 2

What is a biological catalyst?

Answer 2

A biological catalyst is a substance (like an enzyme) that speeds up chemical reactions in living organisms without being used up or changed in the reaction.

Question 3

What type of protein is an enzyme?

Answer 3

A globular protein with a compact, spherical shape and typically a tertiary structure.

Question 4

Where are enzymes made and where do they act?

Answer 4

Enzymes are synthesised by living cells. They can act inside the cell (intracellular enzymes) or be secreted to act outside the cell (extracellular enzymes).

Question 5

What is the active site of an enzyme?

Answer 5

A 3D region within the enzyme where the specific substrate binds. It has a fixed shape determined by the enzyme’s amino acid sequence and folding.

Question 6

How does a substrate bind to the active site?

Answer 6

The substrate must be complementary to the active site and must collide successfully with it. Binding is due to interactions with R groups and polar atoms in the amino acids.

Question 7

What is an enzyme-substrate complex?

Answer 7

A temporary complex formed when the substrate binds to the enzyme’s active site.

Question 8

How do temperature and pH affect enzyme activity?

Answer 8

They affect the ability of R groups in the active site to form bonds with the substrate, altering enzyme efficiency and potentially denaturing the enzyme.

Question 9

How do enzymes reduce activation energy?

Answer 9

They distort bonds in the substrate (increasing chances of breaking them) and bring atoms closer together to facilitate bond formation, reducing the activation energy needed.

Question 10

What happens to the enzyme after the reaction?

Answer 10

The enzyme is unchanged and can be reused.

Question 11

What is the “lock and key” model?

Answer 11

The model where the substrate fits exactly into the enzyme’s fixed-shape active site, like a key into a lock.

Question 12

What is the overall sequence of an enzyme-catalysed reaction?

Answer 12

Substrate collides with active site.

Binds to form enzyme-substrate complex.

Chemical changes occur (bonds broken or formed).

Products released.

Enzyme reused.

Question 13

What is a biological catalyst?

Answer 13

A biological catalyst is a substance (like an enzyme) that speeds up chemical reactions in living organisms without being used up or changed in the reaction.

Question 14

active site

Answer 14

a 3D space in the molecule into which specific substrate molecule(s) can fit and bind.

The active site has a specific shape, which is determined by the sequence of amino acids in the polypeptide;

if the sequence of amino acids changes then the active site will change shape, substrate will not bind to the active site because they are no longer complementary.

Question 15

how is an enzyme substrate complex formed

Answer 15

substrate and enzyme collide successfully

substrate binds to active site by interactions with R groups/polar atoms of the amino acids in the active site - forms an enzyme substrate complex

Question 16

what does temperature and pH affect in enzymes

Answer 16

temp and pH affects ability of R groups and substrate to form bonds

bonds in substrate are distorted, puts strain on the bonds that are going to be broken, increase chance of breaking

breaking the bonds - brings new atoms in substrates closer together and new bonds can form

Question 17

how do enzymes affect activation energy

Answer 17

When an enzyme-substrate reaction forms,

the activation energy needed for the reaction to take place is reduced

– the reaction takes place faster - the enzyme acts as a biological catalyst.

enzyme is unchanged during the reaction.

Question 18

graph for enzyme activation energy

Answer 18

Question 19

lock and key hypothesis

Answer 19

active site - lock
substrate - key
substrate - is complimentary to active site so can bind

active site - fixed shape, substrate has to collide to form enzyme substrate complex

next - chemical changes take place, substrate molecule digested or combined (forming new products)

enzyme - not affected by reaction, can be reused

Question 20

diagram of lock and key

Answer 20

Question 21

anabolism

Answer 21

two substrate molecuels combined

forms a single product molecule

Question 22

catabolism

Answer 22

breaking down of complex substrate molecules into two or more product molecules

Question 23

induced fit hypothesis

Answer 23

As substrate molecule enters active site

forces attraction between substrate and R groups/polar atoms of amino acids in the active site are formed

This causes - change in shape of active sit , streonger bonds formed with substrate

weakesn bonds in substrate, lowers activation energy is reaction

when products released from substrate, active site returns to original shape

eg with enzyme lysozyme
-enzyme not affected by reaction, can be reused

Question 24

diagram of induced fir hypothesis

Answer 24

Question 25

how do changes in pH affect amino acids

Answer 25

amino acids - contain basic and acidic groups change of pH changes bonding causes changes to secondary and tertiary structure of a protein reduces ability of substrate to bind to side groups of animo acid lining active site

Question 26

how does changes in charge on side groups affect ability of enzymes active site

Answer 26

change in charges on side groups bonds may not be formed enzyme may not be able to lower activation energy enzyme is denatured

Question 27

how do small changes in pH affect enyzmes

Answer 27

cause small reversible changes in enzymes structure - inactivation large changes are irreversible – new bonds form that permanently change the 3D shape of the polypeptide chain- denaturation ionic an dhydrogen bonds are disrupted

Question 28

why do we use a buffer solution when investigating effect of pH on enzymes

Answer 28

buffer - maintians constant pH

Question 29

diagram to show - how substrate molecules form an enzyme substrate complex via bonding to amino acid side groups in the active site of enzymes

Answer 29

Question 30

how do changes in temperature affect enzymes

Answer 30

temperature increases, particles gain KE, up to optimun temp below optimum temp, as temp increase enzymes and substrates have more KE, more successful collisions, more enzymes substrate complexes form, as RofR increases above optimum temp, as temp increase, more energy given to particles, bonds in enzymes vibrate and they break (weak hydrogen bonds are broken first) then loss of secondary and tertiary structure, 3D shape of active site changes, is denatured

Question 31

diagram to show effect of increased temperature on enzymes

Answer 31

Question 32

amino group

Answer 32

Question 33

hydrogen bond

Answer 33

Question 34

carboxyl group

Answer 34

Question 35

investigating reactions involving enzymes what can you measure

Answer 35

the disappearance of substrate the appearance of product

Question 36

During enzyme investigations you decide on the independent variable to change:

Answer 36

pH temperature concentration of substrate concentration of enzyme.

Question 37

during enzyme investigations what are the DVs you can measure

Answer 37

time volume mass absorbance/transmission.

Question 38

What happens as a substrate enters the active site?

Answer 38

Attractive forces form between the substrate and R groups or polar atoms of amino acids in the active site.

Question 39

How does enzyme binding lower activation energy?

Answer 39

The binding weakens bonds in the substrate, making them easier to break, and thus lowers activation energy for the reaction.

Question 39

How does substrate binding affect the active site?

Answer 39

The active site slightly changes shape to form stronger bonds with the substrate (induced fit model).

Question 40

enzyme investigations what can you do with DVs

Answer 40

You can then use these measurements to calculate the rate at which substrate disappears or product is made.

Question 41

how to calculate rate from time

Answer 41

rate = 1 / time If the dependent variable is a quantity: rate = quantity / time

Question 42

how to caluclate rate from a graph: rate between two times initial rate rate at a particular part

Answer 42

Question 43

why is initial rate always highest

Answer 43

the concentration of substrate is the highest, so there is the highest frequency of successful collisions and the highest rate.

Question 44

what happens to rate as reaction progresses

Answer 44

substrate is converted to product so concentration decreases. There is a lower frequency of successful collisions and the rate decreases. When all the substrate has been converted to product, the rate will decrease to zero.

Question 45

Explain RofR at A

Answer 45

as temperature increases, substrate molecules gain kinetic energy increased frequency of successful collisions between substrate and enzyme molecules increased frequency of enzyme-substrate complex formation rate of reaction therefore increases.

Question 46

Explain RofR at B

Answer 46

at the optimum temperature, the maximum number of enzyme-substrate complexes are forming at the same time the rate reaches a maximum – called Vmax at this point substrate will be used up/product will be produced fastest.

Question 47

Explain RofR at C

Answer 47

at temperatures above the optimum, increased kinetic energy causes bonds in the enzyme to vibrate so much that they break active sites of enzymes change shape and increasing numbers of enzyme molecules become denatured the frequency of enzyme-substrate complex formation decreases until all enzyme molecules are denatured and the reaction stops.

Question 48

Explain RofR at A

Answer 48

at the optimum pH, the shape of the active site enables bonds to form successfully with the substrate greatest frequency of enzyme-substrate complex formation and highest rate of reaction.

Question 49

Explain RofR at B

Answer 49

in low pH there is a high concentration of H + ions (acid conditions) more amino groups will have a positive charge so will affect hydrogen and ionic bonding in the protein this will change the 3D shape of the active site as the pH becomes more acidic fewer bonds can form between the active site and the substrate molecules fewer enzyme-substrate complexes form and the rate decreases.

Question 50

Explain RofR at C

Answer 50

at pH values above the optimum, not enough H + ions are present increasing number of carboxylic acid groups have a negative charge hydrogen and ionic bonding are affected and the 3D shape of the active site changes making it less able to form bonds with the substrate as the pH becomes more basic, fewer bonds can form between the active site and the substrate molecules fewer enzyme-substrate complexes form and the rate decreases.

Question 51

Explain RofR at A

Answer 51

at low substrate concentration, the number of substrate molecules is low and not all the active sites on the enzyme molecules are occupied as the concentration of substrate increases, there is a greater frequency of enzyme-substrate complex formation and an increase in the rate of reaction at low substrate concentrations the number of molecules of substrate acts as a limiting factor.

Question 52

Explain RofR at B

Answer 52

at higher substrate concentrations, more of the active sites become occupied at the same time the frequency of enzyme-substrate complex formation increases at a slower rate there is a smaller increase in the rate of reaction.

Question 53

Explain RofR at C

Answer 53

because there are a fixed number of active sites, eventually you reach a maximum rate of reaction – Vmax all the active sites on the enzyme molecules are occupied – the active sites are said to be saturated adding more substrate cannot cause an increase in the rate of reaction as no more active sites are available at high substrate concentrations the number of molecules of enzyme acts as a limiting factor only by adding more enzyme can the Vmax be increased.

Question 54

Explain RofR at A

Answer 54

at low enzyme concentrations, the number of enzyme molecules is low and all the active sites on the enzyme molecules are occupied as the concentration of enzyme increases, more active sites become available there is a greater frequency of enzyme-substrate complex formation and an increase in the rate of reaction at low enzyme concentrations, the number of molecules of enzymes acts as a limiting factor.

Question 55

Explain RofR at B

Answer 55

at higher enzyme concentrations, more active sites become available substrate concentration is limited the frequency of enzyme-substrate complex formation increases at a slower rate there is a smaller increase in the rate of reaction.

Question 56

Explain RofR at C

Answer 56

because there are a fixed number of substrate molecules eventually you reach a maximum rate of reaction – Vmax adding more enzyme cannot cause an increase in the rate of reaction as no more substrate molecules are available at high enzyme concentrations, the number of molecules of substrate acts as a limiting factor only by adding more substrate can the Vmax be increased.

Question 57

Inhibition of enzymes

Answer 57

Inhibition of an enzyme occurs when enzyme action is slowed down or stopped by another substance. This is needed in cells to control reactions by slowing down or stopping reactions which are no longer needed.

Question 58

Competitive inhibition

Answer 58

This occurs when a substance has a close structural resemblance (is a similar shape) to a substrate molecule and can bind temporarily to the active site instead of the normal substrate. This means that the active site is blocked for the substrate so the substrate cannot bind to the active site and there are fewer enzyme-substrate complexes and the rate of reaction is decreased. This is reversible. ----- As substrate concentration is increased, there are fewer inhibitor molecules in proportion to the number of substrate molecules. Less competition occurs for the active site and the maximum rate of the enzyme-controlled reaction can be achieved.

Question 59

Diagram of a competitive enzyme inhibitor Eg competitive inhibitor

Answer 59

Question 60

Non-Competitive Inhibition:

Answer 60

This occurs when a substance has no structural resemblance to a substrate molecule but binds to the enzyme at a point other than the active site. This is called the allosteric site. This changes the structure/3D shape of the active site. This means that the substrate cannot bind to the active site so fewer enzyme-substrate complexes are made and the rate of reaction is decreased. Sometimes non-competitive inhibition is reversible, but the rate of reaction is not affected by substrate concentration, i.e. you cannot get back to the maximum rate of reaction by using higher concentrations of substrate. Some non-competitive inhibitors are non-reversible.

Question 61

Diagram for action of a non-competitive enzyme inhibitor

Answer 61

Question 62

effect of substrate concentration on effect of enzyme inhibitors

Answer 62

Competitive inhibitor: the Vmax of the enzyme is not affected by adding increasing concentrations of substrate, Vmax is eventually reached as more active sites become occupied by the substrate rather than the competitive inhibitor. Non-competitive inhibitor: Vmax is reduced even at high substrate concentrations fewer active sites are available as fixed concentration of enzymes.

Question 63

immobilising enzymes

Answer 63

in an inert (non-reactive) substance eg alginate - a gel membrane stabalises enzyme, reduces the ability of polypeptide chain to move changes of temperature and pH have less effect of 3D shape

Question 64

uses of immobilised enzymes in industry

Answer 64

The enzyme can be recovered and reused: * this reduces costs * it also means that only small amounts of an enzyme are needed * the product is also not contaminated by the enzyme * several enzymes can be used at once each acting on a specific substrate. Lower/higher temperatures can be used and still have higher yields than using the free enzyme. An industrial example is the use of immobilised lactase, which is used to produce lactose-free milk: * the enzyme is immobilised in alginate gel beads * milk is passed over the beads and the enzymes digest the lactose into glucose and galactose * the milk is not contaminated by the enzyme and the beads can be used many times.

Question 65

uses of immobilised enzymes in medicine

Answer 65

Because enzymes are specific to a particular substrate, they can be used as biosensors or analytical reagents. The glucose oxidase electrode is one example of a biosensor that is important for diabetics, as it can detect glucose levels in the blood. The biosensor works as follows: * the enzyme glucose oxidase is immobilised in a gel * a small sample of blood is passed over the enzyme * when glucose in the blood comes into contact with the enzyme, a reaction occurs, which releases energy (chemical) * the energy released is converted into electrical impulses * the more energy released, the higher the concentration of glucose in the blood * a digital display of accurate concentration is available by referring to reference data stored in the processing unit.

Question 66

risk of hydrogen peroxide

Answer 66

Hazard Risk Control Measure hydrogen peroxide is corrosive can irritate / damage skin and eyes when pouring hydrogen peroxide into test tube wear safety glasses / use a pipette to fill test tubes – don’t pour

Question 67

improving enzymes investigations

Answer 67

no instruction to wash forceps between dipping disc into potato paste / peroxide solution enzyme / peroxide could be on forceps so reaction could start before timing improve by washing and drying forceps each time after picking up a paper disc length of time dipped into potato paste not specified different amount of potato paste containing catalase absorbed onto different discs could increase / decrease time improve by keeping time paper disc held in potato disc the same each time, e.g. 5 seconds. experiment carried out in the lab temperature not controlled / could vary which would change the kinetic energy of the molecules and affect rate improve by using a thermostatically controlled water bath

Question 68

A student concluded that the CuSO4 was acting as a non-competitive inhibitor. To what extent do your results agree with this conclusion? Explain your answer.

Answer 68

agree - non-competitive inhibitor time taken with copper sulphate did not decrease at higher concentration of peroxide if competitive you would expect time for disc to sink and rise at higher concentrations of peroxide

Question 69

Explain what is meant by an immobilized enzyme

Answer 69

an immobilised enzyme is attached to an inert matrix so cannot move freely.

Question 70

State two advantages of using immobilized enzymes in industry.

Answer 70

Any 2 from: ● the enzyme can be recovered and reused ● can use smaller quantities of enzyme ● the product is also not contaminated by the enzyme ● several enzymes can be used at once each acting on a specific substrate ● lower / higher temperatures pH can be used and still have higher yields than using free enzyme

Question 71

What happens to the enzyme after the reaction?

Answer 71

The products are released, and the active site returns to its original shape; the enzyme remains unchanged and reusable.

Question 72

name for enzyme which works outside of cells

Answer 72

extracellular

Question 73

Answer 73

Question 74

Answer 74

Question 75

Answer 75

Question 76

Answer 76

Question 77

Answer 77

Question 78

Answer 78

Alternate monomers rotated 180° / forms long straight chains (1 mark): Explains that alternate monomers are rotated 180°, producing long, straight cellulose chains. Enables hydrogen bonding between adjacent/parallel chains (1 mark): Indicates that the straight chains align to allow hydrogen bonds between them. Hydrogen bonds are weaker compared to peptide/covalent bonds, resulting in increased strength upon cross-linking (1 mark): Compares the relatively weak hydrogen bonds in cellulose to the stronger peptide bonds in peptidoglycan, highlighting how cross-linking enhances cell wall rigidity.

Question 79

Answer 79

The bond formed is a peptide bond. Two different dipeptides can form because either amino acid can provide its amine group (—NH₂) or carboxyl group (—COOH). The peptide bond forms between the —COOH of one amino acid and the —NH₂ of the other, so the order matters: Methionine–glycine and Glycine–methionine have different sequences and structures.

Question 80

Answer 80

Question 81

4 or 3

Answer 81