Module 2: Section 4 - Enzymes

Question 1

What do enzymes do and what do they affect in an organism?

Answer 1

1) enzymes speed up chemical reactions by acting as biological catalysts. They catalyse metabolic reactions - both at cellular level, e.g. respiration and for the organism as a whole, e.g for digestion in mammals
2) enzymes can affect structures in an organism (e.g. enzymes are involved in the production of collagen, an important protein in the connective tissues of animals) as well as functions (like respiration)

Question 2

Catalase is an example of an intracellular enzyme - what does it do?

Answer 2

1) hydrogen peroxide is the toxic by-product of several cellular reactions. If left to build up, it can kill cells
2) catalase is an enzymes that works inside cells to catalyse the breakdown of hydrogen peroxide to harmless oxygen and water

Question 3

Amylase and trypsin are examples of extracellular enzymes - what do they do?

Answer 3

1) amylase and tripsin both work outside cells in the human digestive system
2) amylase is found in saliva. It’s secreted into the mouth by cells in the salivary glands. It catalyses the hydrolysis of starch into maltose in the mouth
3) trypsin catalyses the hydrolysis of peptide bonds - turning big polypeptides into smaller ones. Trypsin is produced by cells in the pancreas and secreted into the small intestine

Question 4

What is the structure of an enzyme and how do they work?

Answer 4

1) enzymes are globular proteins
2) enzymes have an active site, which has a specific shape. The active site is the part of the enzyme that the substrate molecules bind to
3) the specific shape of the active site is determined by the enzyme’s tertiary structure
4) for the enzyme to work, the substrate has to fit into the active site. If the substrate shape doesn’t match the active site, the reaction won’t be catalysed. This means that enzymes work with very few substrates - usually only one

Question 5

Give two reasons why enzymes reduce activation energy

Answer 5

1) if two substrate molecules need to be joined, attaching to the enzyme holds them close together, reducing any repulsion between the molecules so they can bond more easily
2) if the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on bonds in the substrate. This strain means the substrate molecule breaks up more easily

Question 6

What is activation energy?

Answer 6

In a chemical reaction, a certain amount of energy needs to be supplied to the chemicals before the reaction will start. This is called the activation energy - it’s often provided as heat.

Question 7

What is it specifically about enzymes that reduce activation energy?

Answer 7

When a substance binds to an enzyme’s active site, an enzyme-substrate complex is formed. It’s the formation of the enzyme-substrate complex that lowers the activation energy.

Question 8

Draw and label the lock and key model

Answer 8

pg.43

Question 9

Draw and label the induced fit model

Answer 9

pg.43

Question 10

How does temperature influence enzyme activity?

Answer 10

The rate of an enzyme-controlled reaction increases when the temperature’s increased. More heat means more kinetic energy, so molecules move faster. This makes the enzyme more likely to collide with the substrate molecules. The energy of these collisions also increases, which means each collision is more likely to result in a reaction. But, if the temperature gets too high, the reaction stops.

Question 11

Explain a curve on a graph showing the relationship between temperature and rate of reaction of enzymes

Answer 11

1) the rise in temperature makes the enzyme’s molecules vibrate more
2) if the temperature goes above a certain level, this vibration breaks some of the bonds that hold the enzyme in shape
3) the active site changes shape and the enzyme and substrate no longer fit together
4) at this point, the enzyme is denatured - it no longer functions as a catalyst

Question 12

How does the temperature coefficient (Q10) show how rate changes with temperature?

Answer 12

1) the temperature coefficient (Q10) value for a reaction shows how much the rate of reaction changes when the temperature is raised by 10 degrees C
2) at temperatures before the optimum, a Q10 value of 2 means that the rate doubles when the temperature is raised by 10 degrees C. A Q10 value of 3 would mean that the rate trebles
3) most enzyme-controlled reactions have a Q10 value of around 2

Question 13

How does pH affect enzyme activity?

Answer 13

1) all enzymes have an optimum pH value. Most human enzymes work best at pH 7, but there are exceptions. Pepsin, for example, works best at acidic pH 2, which is useful because it’s found in the stomach.
2) above and below the optimum pH, the H+ and OH- ions found in acids and alkalis can mess up the ionic bonds and hydrogen bonds that hold the enzyme’s tertiary structure in place. This makes the active site change shape, so the enzyme is denatured

Question 14

How does enzyme concentration affect the rate of reaction?

Answer 14

1) the more enzyme molecules there are in a solution, the more likely a substrate molecule is to collude with one and form an enzyme-substrate complex. So increasing the concentration of the enzyme increases the rate of reaction.
2) but, if the amount of substrate is limited, there comes a point when there’s more than enough enzyme molecules to deal with all the available substrate, so adding more enzyme has no further effect

Question 15

How does substrate concentration affect rate of reaction up to a point?

Answer 15

1) the higher the substrate concentration, the faster the reaction - more substrate molecules means a collision between substrate and enzyme is more likely and so more active sites will be used
2) this is only true up until a ‘saturation’ point though. After that, there are so many substrate molecules that the enzymes have about as much as they can cope with (all the active sites are full), and adding more substrate makes no difference to the rate of reaction
3) substrate concentration decreases with time during a reaction (unless more substrate is added to the reaction mixture), so if no other variables are changed, the rate of reaction will decrease over time too. This makes the initial rate of reaction (the reaction rate right at the start of the reaction, close to time 0) the highest rate of reaction

Question 16

You need to know how the effects of pH, temperature, enzyme concentration and substrate concentration can be investigated experimentally. Give me two ways of measuring the rate of an enzyme-controlled reaction.

Answer 16

Example 1:
You can measure how fast the product of the reaction appears. The diagram on the right (see pg.45) shows how to measure this with the enzyme catalase. Catalase catalyses the breakdown of hydrogen peroxide into water and oxygen. It’s easy to collect the oxygen produced and measure how fast it’s given off.

Example 2:
You can also measure the disappearance of the substrate rather than the appearance of the product and use this to compare the rate of reaction under different conditions. For example, the enzyme amylase catalyses the breakdown of starch to maltose. It’s easy to detect starch using a solution of potassium iodide and iodine. You can time how long it takes for the starch to disappear by regularly sampling the starch solution. You can then alter the conditions of the reaction and compare rates. See pg 45 for diagram.

Question 17

Some enzymes will only work if there is another non-protein substance bound to them. These non-protein substances are called cofactors. Some cofactors are inorganic molecules or ions, how do these work?

Answer 17

Some cofactors are inorganic molecules or ions. They work by helping the enzyme and substrate bind together. They don’t directly participate in the reaction so aren’t used up or changed in any way. For example, chloride ions (Cl-) are cofactors for the enzyme amylase.

Question 18

Some cofactors are organic molecules - how do these work?

Answer 18

Some cofactors are organic molecules - these are called coenzymes. They participate in the reaction and are changed by it (they’re just like a second substrate, but they aren’t called that). They often act as carriers, moving chemical groups between different enzymes. They’re continually recycled during this process. Vitamins are often sources of coenzymes.

Question 19

What is a cofactor known as if it is tightly bound to the enzyme and give an example of this?

Answer 19

If a cofactor is tightly bound to the enzyme, it’s known as a prosthetic group. For example, zinc ions (Zn2+) are a prosthetic group for carbonic anhydrase (an enzyme in red blood cells, which catalyses the production of carbonic acid from water and carbon dioxide). The zinc ions are a permanent part of the enzyme’s active site.

Question 20

Enzyme activity can be prevent by enzyme inhibitors - molecules that bind to the enzyme that they inhibit. Inhibition can be competitive or non-competitive. How do competitive inhibitor molecules work?

Answer 20

1) competitive inhibitor molecules have a similar shape to that of the substrate molecules
2) they compete with the substrate molecules to bind to the active site, but no reaction takes place
3) instead they block the active site, so no substrate molecules can fit in

Question 21

What is the amount of enzyme inhibited dependent on during competitive inhibition?

Answer 21

1) how much the enzyme is inhibited depends on the relative concentrations of the inhibitor and the substrate
2) if there’s a high concentration of the inhibitor, it’ll take up nearly all the active sits and hardly any of the substrate will get to the enzyme
3) but if there’s a higher concentration of substrate, then the substrate’s chances of getting to an active site before the inhibitor increase. So increasing the concentration of substrate will increase the rate of reaction (up to a point).

Question 22

How do non-competitive inhibitors work?

Answer 22

1) non-competitive inhibitor molecules bind to the enzyme away from its active site. The site they bind to is known as the enzyme’s allosteric site
2) this causes the active site to change shape so the substrate molecules can no longer bind to it.
3) they don’t ‘compete’ with the substrate molecules to bind to the active site because they are a different shape
4) increasing the concentration of substrate won’t make any difference to the reaction rate - enzyme activity will still be inhibited

Question 23

Inhibitors can be reversible or non-reversible. Which one they are depends on the strength of the bonds between the enzyme and the inhibitor, please explain this

Answer 23

1) if they’re strong, covalent bonds, the inhibitor can’t be removed easily and the inhibition is irreversible
2) if they’re weaker hydrogen bonds or weak ionic bonds, the inhibitor can be removed and the inhibition is reversible

Question 24

Take a break

Answer 24

Go on, go running or make a cup of tea

Question 25

Some medicinal drugs are enzyme inhibitors, give two examples please

Answer 25

1) some antiviral drugs - e.g. reverse transcriptase inhibitors inhibit the enzyme reverse transcriptase, which catalyses the replication of viral DNA. This prevents the virus from replicating.
2) some antibiotics - e.g. penicillin inhibits the enzyme transpeptidase, which catalyses the formation of proteins in bacterial cell walls. This weakens the cell wall and prevents the bacterium from regulating its osmotic pressure. As a result the cell bursts and the bacterium is killed.

Question 26

Metabolic poisons interfere with metabolic reactions causing damage, illness or death - they’re often enzyme inhibitors. Give three examples please.

Answer 26

1) cyanide is an irreversible inhibitor of cytochrome c oxidase, an enzyme that catalyses respiration reactions. Cells that can’t respire die.
2) malonate inhibits succinate dehydrogenase (which also catalyses respiration reactions)
3) arsenic inhibits the action of pyruvate dehydrogenase, another enzyme that catalyses respiration reactions

Question 27

What is a metabolic pathway?

Answer 27

A metabolic pathway is a series of connected metabolic reactions. The product of the first reaction takes part in the second reaction - and so on. Each reaction is catalysed by a different enzyme.

Question 28

What is product inhibition?

Answer 28

Many enzymes are inhibited by the product of the reaction they catalyse. This is known as product inhibition.

Question 29

What is end-product inhibition, what does it regulate and give an example of how it works please

Answer 29

1) end-product inhibition is when the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the pathway
2) end-product inhibition is a nifty way of regulating the pathway and controlling the amount of end-product that gets made. For example:
3) both product and end-product inhibition are reversible. So when the level of product starts to drop, the level of inhibition will start to fall and the enzyme can start to function again - this means that more product can be made

Question 30

How can enzyme inhibition help to protect cells?

Answer 30

1) enzymes are sometimes synthesised as inactive precursors in metabolic pathways to prevent them causing damage to cells. For example, some proteases (which break down proteins) are synthesised as inactive precursors to stop them damaging proteins in the cell in which they’re made
2) part of the precursor molecule inhibits its action as an enzyme. Once this part is removed (e.g. via a chemical reaction) the enzyme becomes active