Section 4: Enzymes

Question 1

What are enzyme inhibitors?

Answer 1

Enzyme activity can be prevented by enzyme inhibitors - molecules that bind to the enzyme that they inhibit. Inhibition can be competitive or non-competitive.

Question 2

What are competitive inhibitors?

Answer 2

Competitive inhibitor molecules have a similar shape to that of substrate molecules. They compete with the substrate molecules to bind to the active site, but no reaction takes place. Instead they block the active site, so no substrate molecules can fit in it.
How much the enzyme is inhibited depends on the relative concentrations of the inhibitor and substrate. If there’s a high concentration of the inhibitor, it’ll take up nearly all the active sites and hardly any of the substrate will get to the enzyme. 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 3

What are non-competitive inhibitors?

Answer 3

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. This causes the active site to change shape so the substrate molecules can no longer bind to it.
Non-competitive inhibitor molecules don’t ‘compete’ with the substrate molecules to bind to the active site because they are a different shape. Increasing the concentration of substrate won’t make any difference - enzyme activity will still be inhibited.

Question 4

What are cofactors and coenzymes?

Answer 4

Some enzymes only work if there is another non-protein substance bound to them. These non-protein substances are called cofactors.

Question 5

What are inorganic cofactors and give an example.

Answer 5

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

Question 6

What are organic cofactors (coenzymes)?

Answer 6

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. For example, the coenzymes NAD is derived from vitamin B3.

Question 7

What is a prosthetic group? Give an example.

Answer 7

If a cofactor is tightly bound to the enzyme, it’s known as a prosthetic group.
For example, zinc ions (Zn 2+) are a prosthetic group for carbonic anhydrase (an enzyme in red blood cells, which catalysed the production of carbonic acid from water and carbon dioxide). The zinc ions are a permanent part of the enzyme’s active site.

Question 8

What does it mean if an inhibitor is reversible or non-reversible.

Answer 8

Inhibitors can be reversible (not bind permanently to an enzyme) or non-reversible (bind permanently to an enzyme). Which one they are depends on the strength of the bonds between the enzyme and the inhibitor.
> If they’re strong, covalent bonds, the inhibitor can’t be removed easily and he inhibition is irreversible.
> If they’re weaker hydrogen bonds or weak ionic bonds, the inhibitor can be removed and the inhibition is reversible.

Question 9

How can drugs be used as inhibitors?

Answer 9

Some medicinal drugs are enzyme inhibitors, for example:
> Some antiviral drugs (drugs that stop viruses) - e.g. reverse transcriptase inhibitors are a class of antiviral developed to treat HIV. They work by inhibiting the enzyme reverse transcriptase, which catalyses the replication of viral DNA. This prevents the virus from replicating.
> 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 10

What are metabolic poisons?

Answer 10

Metabolic poisons interfere with metabolic reactions (the reactions that occur in cells), causing damage, illness or death - they’re often enzyme inhibitors.

Question 11

Give three examples of metabolic poisons.

Answer 11

Cyanide is a non-competitive, irreversible inhibitor of cytochrome c oxidase, an enzyme that catalyses respiration reactions. Cells that can’t respire die.
Malonate is a competitive inhibitor of succinate dehydrogenase (which also catalyses respiration reactions).
Arsenic is a non-competitive inhibitor of pyruvate dehydrogenase, yet another enzyme that catalyses respiration reactions.

Question 12

What is product inhibition? What is a metabolic pathway?

Answer 12

Metabolic pathways are regulated by end-product inhibition. 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. Many enzymes are inhibited by the product of the reaction they catalyse. This is known as product inhibition.

Question 13

What is end-product inhibition?

Answer 13

End-product inhibition is when the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the pathway.
End-product inhibition is a nifty way of regulating the pathway and controlling the amount of end-product that gets made.

Question 14

Give an example of product inhibition?

Answer 14

Phosphofructokinase is an enzyme involved in the metabolic pathway that breaks down glucose to make ATP. ATP inhibits the action of phosphofructokinase - so a high level of ATP prevents more ATP from being made.
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 15

How does enzyme inhibition protect cells? Give an example.

Answer 15

Enzymes are sometimes synthesised as inactive precursors in metabolic pathways to prevent them causing damage to cells. 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.
Some proteases (which break down proteins) are synthesised as inactive precursors to stop them damaging proteins in the cell in which they’re made.

Question 16

Explain how enzymes are biological catalysts.

Answer 16

Enzymes speed up chemical reactions by acting as biological catalysts. A catalyst is a substance that speeds up a chemical reaction without being used up in the reaction itself - biological catalysts are those found in living organisms. They catalyse metabolic reactions - both at a cellular level (e.g. respiration) and or the organism as a whole (e.g. digestion in mammals)
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). Enzyme action can be intracellular - within cells, or extracellular - outside cells.

Question 17

Give examples of intracellular enzymes.

Answer 17

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

Question 18

Give examples of extracellular enzymes.

Answer 18

Amylase and trypsin both work outside cells in the human digestive system.
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 (a sugar) in the mouth.
Trypsin catalyses the hydrolysis of peptide bonds - turning big polypeptides into smaller ones (which then get broken down into amino acids by other enzymes). Trypsin is produced by cells in the pancreas and secreted into the small intestine.

Question 19

Describe the structure of enzymes.

Active site, substrate,etc

Answer 19

Enzymes are globular proteins. They have an active site. The active site is the part of the enzyme where the substrate molecules (the substance that the enzyme interacts with) bind to. The active site has a specific shape, which is determined by the enzyme’s tertiary structure.
For the enzyme to work, the substrate has to fit into the active site (its shape has to be complementary). If the substrate shape doesn’t match the active site, the reaction won’t be catalysed . This means that enzymes are very specific and work with very few substrates - usually only one. When a substrate binds to an enzyme’s active site, an enzyme-substrate complex is formed.

Question 20

How do enzymes speed up reaction?

Answer 20

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. Enzymes reduce the amount of activation energy that’s needed often making reactions happen at a lower temperature than they could without an enzyme. This speeds up the rate of reaction.
When a substance binds to an enzyme’s active site, an enzyme-substrate complex is formed - it’s this that lowers the activation energy. Here are two reasons why:
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 21

Describe the ‘lock and key’ model.

Answer 21

Enzymes are a bit picky - they only work with substrates that fit their active site. Early scientists studying the action of enzymes came up with the ‘lock and key’ model. This is where the substrate fits into the enzyme in the same way that a key fits into a lock - the active site and substrate have a complementary shape.
Scientists soon realised that the lock and key model didn’t give the full story. The enzyme and substrate do have to fit together in the first place, but new evidence showed that the enzyme-substrate complex changed shape slightly to complete the fit. This locks the substrate even more tightly to the enzyme. Scientists modified the old lock and key model and came up with the ‘induced fit‘ model.

Question 22

Describe the ‘induced fit’ model.

Answer 22

The ‘induced fit’ model helps to explain why enzymes are so specific and only bond to one particular substrate. The substrate doesn’t only have to be the right shape to fit the active site, it has to make the active site change shape in the right way as well. This is a prime example of how a widely accepted theory an change when new evidence comes along. The ‘induced fit’ model is still widely accepted.

Question 23

How does temperature affect enzyme activity?

Answer 23

Like any chemical reaction, 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 substrate molecules more likely to collide with the enzymes’ active sites. The energy of these collisions also increases, which means each collision is more likely to result in a reaction. The rate of reaction continues to increase until the enzyme reaches its optimum temperature - this is the temperature at which the rate of an enzyme-controlled reaction is at its fastest.
But, if the temperature gets too high, the reaction stops. The rise in temperature makes the enzyme’s molecules vibrate more. If the temperature goes above a certain level, this vibration breaks some of the bonds that hold the enzyme in shape. The active site changes shape and the enzyme and substrate no longer fit together. At this point, the enzyme is denatured - it no longer functions as a catalyst.

Question 24

What is the temperature coefficient?

Answer 24

The temperature coefficient value for the reaction shows how much the rate of reaction changes when the temperature is raised by 10° C. You can calculate the temperature coefficient value using the equation:
rate at higher temperature divided by rate at lower temperature.

Question 25

How does the pH affect enzyme activity?

Answer 25

All enzymes have an optimum pH value – this is the pH at which the rate. of an enzyme controlled reaction is at its fastest. Most human enzymes work best at pH 7 (neutral), but there are exceptions. Pepsin, for example, works best at acidic pH 2, which is useful because it’s found in the stomach. Above and below the optimum pH, the hydrogen and OH ions found in acids and alkalis can break that ionic bonds and hydrogen bonds that hold the enzymes tertiary structure in place. This makes the active site change shape, so the enzyme is denatured.

Question 26

How does enzyme concentration affect enzyme activity?

Answer 26

The more enzyme molecules that are in a solution, the more likely a substrate molecule is to collide with one and form an enzyme substrate complex. So increasing the concentration of the enzyme increases the rate of reaction. But, if the amount of substrate is limited, there comes a point when there is more than enough enzyme molecules to deal with all the available substrate, so adding more enzyme has no further affect.

Question 27

How does substrate concentration affect enzyme activity?

Answer 27

The higher the substrate concentration, the faster the reaction. More substrate molecules means a collision between substrate an enzyme is more likely, so more active sites will be occupied and more enzyme substrate complexs will be formed. This is only true up until the 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 makes no difference – the enzyme concentration becomes the limiting factor. 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 overtime to.This makes the initial rate of reaction (The reaction right at the start of the reaction, close to time zero) the highest rate of reaction.

Question 28

How do you estimate the initial rate of reaction?

Answer 28

You can use a tangent to estimate the initial rate of reaction from a graph. As you know, the initial rate of reaction is the rate of reaction right at the start of the reaction, close to time equals 0 (t=0) on the graph. To work out the initial rate of reaction, carry out the following steps:
1. Draw a tangent to the curve at t=0, using a ruler. Do this by positioning the ruler so it’s an equal distance from the curve at both sides of where it’s touching it. Here you’ll have to estimate where the curve would continue if it carried on below 0. Then draw a line along the ruler.
2. Calculate the gradient of the tangent - this is the initial rate of reaction. The equation for the gradient of a straight line is:
Gradient = change in y axis / change in x axis.
3. Finally, you need to work out the units of the rate. The units will vary depending on what was measured in the experiment. To work out the units of rate from a graph, divide the units of the y-axis by the units of the x-axis (which should always be time).