Enzymes

Question 1

What are enzymes?

Answer 1

Enzymes catalyse reactions that affect metabolism at a cellular and whole organism level. Enzymes are globular proteins and act as biological catalysts. They speed up reactions but are not used in the reactions, themselves.

Question 2

Describe the role of enzymes.

Answer 2

The enzyme has an active site with a specific shape and only a substrate with a complementary shape can bind to the active site

Question 3

What are intracellular reactions?

Answer 3

Enzymes catalyse reactions inside the cell – i.e. hydrolases in lysosomes.

Question 4

Give an example of an intracellular reaction.

Answer 4

Catalase is an enzyme that catalyses intracellular reactions – it is found in vesicles, called peroxisomes, inside eukaryotic cells. Catalase breaks down hydrogen peroxide (H2O2), a harmful by-product of metabolic reactions, and protects the cell. It also is used to kill pathogens, when they are ingested by white blood cells.

Question 5

What are extracellular reactions?

Answer 5

Enzymes catalyse reactions outside the cell – i.e. digestive enzymes that are released into the alimentary canal.

Question 6

Give an example of an extracellular reaction.

Answer 6

Amylase and trypsin are enzymes that catalyse extracellular reactions. Amylase digests starch into maltose and is produced in the salivary gland. Trypsin digests proteins into smaller polypeptides, by hydrolysing peptide bonds – made in the pancreas, but used in the small intestine.

Question 7

What is a turnover number?

Answer 7

The number of reactions per second an enzyme catalyses.

Question 8

What is anabolic reaction?

Answer 8

Anabolic reactions – energy is used to synthesise larger molecules from smaller ones.

Question 9

What is a catabolic reaction?

Answer 9

Catabolic reactions – metabolites are broken down into smaller molecules to release energy.

Question 10

Describe the mechanism of enzymes.

Answer 10

Each enzyme has an active site with a specific shape, due to the specific tertiary structure, and therefore the shape of substrate must be complementary to the specific shape of the enzyme’s active site to bind to the active site.

Question 11

Describe the lock-and-key model.

Answer 11

The shape of the active site will only allow one shape of molecule to fit it, like a key fitting into a lock. The shape of the substrate is complementary to the shape of the active site.

Question 12

Describe the induced-fit model.

Answer 12

Substrate collides with the enzyme active site and the enzyme molecule changes its shape slightly. The active site will now fit more closely around the substrate and an ESC forms. The changing shape destabilises the substrate molecule and the reaction occurs more easily, forming products and an EPC. The products are a different shape from the substrate and so, no longer fit the active site so the products leave the active site.

Question 13

Why do enzymes lower the activation energies of reactions?

Answer 13

Enzymes lower the activation energy of a reaction so less energy is needed for the reaction to take place.

Question 14

How does pH affect enzyme activity?

Answer 14

Different enzymes can have a different optimum pH to each other (see graph on the right) – i.e. pepsin: pH 2, amylase: pH 7, trypsin: pH 9. Reducing/increasing the pH away from the optimum pH, will reduce the rate of reaction. This is because the concentration of the H+/OH- ions in the solution affects the tertiary structure of the enzyme, by breaking bonds between the amino acids. The substrate can no longer fit into the active site of the enzyme and therefore, ESCs will not be able to form. Extreme of pH can and will lead to denaturation of the enzyme.

Question 15

How does temperature affect enzyme activity?

Answer 15

As temperature rises, the enzyme and substrate molecules move faster due to the increased kinetic energy. Successful collisions between the substrate and the enzyme’s active site occur more often and as a result, more ESCs form. The successful collisions also have a sufficient activation energy to react. But if the temperature is too high, the activity of the enzyme will be reduced. The structure of the enzyme molecule vibrates energetically, so the bonds between R-groups (especially hydrogen bonds or ionic bonds), holding the enzyme in its specific shape will break. The enzyme will lose its tertiary shape and is irreversibly, denatured – the substrate is no longer complementary to the active site.

Question 16

How does the substrate concentration affect enzyme activity?

Answer 16

At first, the substrate concentration is the limiting factor. Collisions between the substrate and enzymes occur more frequently, more ESCs and products formed, the rate of reaction increases. Then, all the enzyme molecules are forming ESCs, as fast as possible but all the active sites are occupied.
Therefore, an increased rate of substrate concentration has no further effect on the rate of reaction. The enzyme concentration is now the limiting factor.

Question 17

How does enzyme concentration, with excess substrate concentration, affect enzyme activity?

Answer 17

If there is excess substrate or substrate is continually added, there are more enzyme molecules that can react with more substrates. The rate of reaction will increase. The limiting factor will be the enzyme concentration.

Question 18

What is the optimum temperature for enzymes?

Answer 18

An optimum temperature for enzymes is the temperature at which an enzyme catalyses at the maximum rate. It is 40C in human – but some enzymes work best in cool temperatures (i.e. psychrophilic bacteria) and some work best in high temperatures (i.e. thermophilic bacteria – found in hot springs/volcanoes).

Question 19

How does enzyme concentration, with a fixed substrate concentration, affect enzyme activity?

Answer 19

If there is a fixed concentration of the substrate, at first there are more active sites available, so there are more successful collisions occurring between the substrate and enzyme, forming more ESCs. The limiting factor, at first, will be the enzyme concentration but the rate of reaction is increasing. When the plateau begins, all the substrate molecules have been converted into product so increased enzyme concentration will have no effect. The limiting factor now is the substrate concentration but there is no further effect on the rate of reaction.

Question 20

What is a temperature coefficient (Q10)?

Answer 20

This refers to the increase in the rate of a process when the temperature is increased by 10C. For every increasing in 10C, the rate of reaction is approximately doubled, from 0-40C but above the optimum temperature, the Q10 will drop.

Question 21

What is a cofactor?

Answer 21

A cofactor is a non-protein substance that are sometimes required to make an enzyme-controlled reaction take place at an appropriate rate. They alter the shape of the enzyme’s active site so that the substrate can fit more easily.

Question 22

What is a coenzyme?

Answer 22

Vitamins are a source of coenzymes – i.e. vitamin B3.

Question 23

What is a prosthetic group?

Answer 23

A cofactor that is a permanent part of an enzyme molecule. Contribute to the final 3D shape and charges. Zinc ions (Zn2+) are a prosthetics group for carbonic anhydrase.

Question 24

What is an inorganic ion cofactor?

Answer 24

The presence of certain ions can increase the rate of reaction. The ions combine with the enzyme/substrate and ESCs form more easily – as the cofactor (ions) will affect the charge distribution and shape of the complex. Chlorine ions (Cl-) acts as a cofactor for amylase.

Question 25

What is an enzyme inhibitor?

Answer 25

An enzyme inhibitor is any substance that slows or stops an enzyme-controlled reaction, by affecting the enzyme in some way. It influences how the substrate binds to the active site and the enzyme’s turnover number.

Question 26

What is a competitive inhibitor?

Answer 26

Compete with the substrate for the active site. The inhibitor has a similar shape to the substrate and will fit into the active site, blocking it so that the substrate cannot enter. They form an enzyme-inhibitor complex, which is catalytically inactive. Fewer ESCs are formed and so, the increasing concentration of the substrate will increase the chance of a substrate binding to an enzyme. Competitive inhibitors do not alter the shape of the enzyme and so can be reversible and increasing substrate concentration, can cancel their effect. If a competitive inhibitor binds irreversibly to an active site, it is an inactivator.

Question 27

What is a non-competitive inhibitor?

Answer 27

Attaches to the allosteric site (not the active site). This distorts the tertiary structure and so, the 3D shape is also changed. The active site’s shape is also changed so it is no longer complementary to the substrate. This reduces the rate of reaction and increasing the substrate concentration has no effect. The Vmax (maximum rate of reaction) is not reached. The level of inhibition depends on the number of inhibitor molecules present, and if there are enough to bind to all the enzymes, the reaction will stop. Some bind reversibly, others bind irreversibly.

Question 28

What is end-product inhibition?

Answer 28

Enzyme-catalysed reactions are regulated by end-product inhibition. At the end of a catalysed reaction, the product molecules stay tightly bound to the enzyme. Therefore, the enzyme cannot form more of the product, than it needs – this an example of negative feedback. Many metabolic processes involve a series of enzyme-catalysed reactions and the product of one reaction can be the substrate of another. The end-product may be a non-competitive inhibitor for the first enzyme – but it binds reversibly – as the end-product accumulates, it will eventually stop the reaction, until the cell has used all the product.

Question 29

What is an inactive precursor?

Answer 29

Some enzymes are synthesised and produced in an inactive precursor form. Before they are active, some of their amino acids are to be removed. Digestive enzymes are made like this so they do not digest their cell’s molecules. Trypsin is produced as trypsinogen – a portion is then removed by another enzyme and it turns into trypsin. Pepsin is produced as pepsinogen – it is activated by HCl in the stomach.

Question 30

Name and describe a metabolic poison.

snake venom

Answer 30

Contains inhibitor of AChE – acetylcholinesterase, which breaks down the neurotransmitter acetylcholine (Ach) at neuromuscular synapses. If the enzyme is inhibited, the ACh stays attached to the receptors on the muscle membrane and keeps the muscles contracted. Causes paralysis, including breathing muscles. Death by suffocation.

Question 31

Name and describe a metabolic poison.

cyanide

Answer 31

CN- ions bind irreversibly to an enzyme (cytochrome oxidase) in the mitochondria involved in the final stages of aerobic respiration. Inhibits catalase too – breaks down toxic H2O2 in the liver. Death in seconds. Non-competitive inhibitor.

Question 32

Name and describe a metabolic medicinal drug.

aspirin

Answer 32

Salicylic acid binds to the enzyme that catalyses the formation of prostaglandins – cell-signalling molecule produced by cells that are damaged/infected and make nerve cell more sensitive to pain. Reduces risk of blood clots forming in vessels – reduces risk of stroke.

Question 33

Name and describe a metabolic medicinal drug.

ACE inhibitors

Answer 33

Drugs can inhibit the angiotensin converting enzyme (ACE), which operates in a metabolic pathway that increases blood pressure. They can lower blood pressure of people with hypertension – but cannot take beta-blockers. To treat heart failure. Minimise risk of stroke/a second myocardial infarction in patients who previously have had a myocardial infarction.