2.1.4 Enzymes

Question 1

Describe the structure of enzymes

Answer 1

1. Enzymes are globular proteins (be able to describe the structure of a globular protein)
2. They have a specific tertiary structure that includes a cleft called the active site
3. Which is complementary in shape and chemical properties to its substrate
4. Some enzymes require cofactors, coenzymes or prosthetic groups to function

Question 2

Describe the mechanism of enzyme action

Answer 2

1. The enzyme collides with substrate
2. If there is enough energy, and the orientation of enzyme and substrate are suitable
3. The substrate will occupy the active site of the enzyme, forming an enzyme-substrate complex
4. The enzyme is specific because the shape of its active site is complementary to the shape of the substrate (lock and key hypothesis)
5. The induced-fit hypothesis states that the enzyme changes shape to accommodate the substrate, putting the substrate bonds under strain
6. Interactions between the substrate and active site cause the bonds within the substrate molecule to weaken.
7. The activation energy required for the reaction of the substrate(s) is thus lowered, increasing the rate of reaction
8. The substrate is converted to product in the enzyme (enzyme-product complex), which has a lower affinity for the enzyme and so is released (product formation)

Question 3

Describe the role of catalase, as example of an intracellular enzyme

Answer 3

1. Intracellular enzymes catalyse chemical reactions within the cell (think of all the chemical changes you know about that occur in the cell. Yeah.)
2. For example, catalase converts the toxic metabolic waste product hydrogen peroxide into harmless water and oxygen
3. 2H₂O₂ →(catalase)→ 2H₂O + O₂
4. Intracellular enzymes rely on their substrates being available in the cell and colliding with them
5. In many cases, the product of one enzyme is the substrate of another, which sets up a metabolic pathway

Question 4

Describe the role of amylase as an extracellular enzyme

Answer 4

1. Amylase is a hydrolytic enzyme
2. (the amylase gene is expressed in cells in the salivary glands and the pancreatic acinar cells, module 5)
3. Amylase gene is switched on, transcribed, translated, modified, packaged and released via exocytosis
4. When mixed with food, amylase breaks down starch into the disaccharide maltose
5. Which is hydrolysed again by maltase into glucose
6. Which is small enough to be absorbed into the bloodstream at the small intestine
7. This ensures dietary glucose is available to the body cells for respiration, and the liver to store as glycogen

Question 5

Describe the role of trypsin as an extracellular enzyme

Answer 5

1. Trypsin is a hydrolytic enzyme
2. The trypsin gene is expressed in pancreatic acinar cells, module 5
3. Trypsin gene is switched on, transcribed, translated, modified, packaged and released via exocytosis
4. Trypsin is released in the pancreatic juice as the precursor enzyme, trypsinogen, an inactive form, to ensure it is only active once in the small intestine
5. In the small intestine, the enzyme endopeptidase converts trypsinogen into active trypsin
6. Which hydrolyses polypeptides into shorter peptides
7. Other proteases hydrolyse peptides into amino acids, which can then be absorbed into the bloodstream

Question 6

Explain the effect of temperature on enzyme activity

Answer 6

1. At low temperatures the kinetic energy of enzymes and substrates is lower
2. The collide less frequently and with less energy
3. The rate of enzyme-substrate complex (ESC) formation (and thus product formation) is lower
4. As temperature increases, the kinetic energy of substrates and enzymes increases
5. There is a higher rate of collisions, ESC formation and product formation
6. At higher temperatures (above optimum) the available kinetic energy causes weak interactions in the enzyme’s tertiary structure to break
7. Changing the shape of the active site so it is no longer complementary to the substrate
8. Rate of ESC formation becomes lower, and so does product formation

Question 7

Explain what the temperature coefficient (Q10) tells us about an enzyme

Answer 7

1. Enzymatic activity increases as temperature increases until the optimum temperature
2. Different enzymes have different tertiary structures
3. So differ in their sensitivity to changing temperature
4. The temperature coefficient compares the enzyme activity (rate) at two temperatures separated by 10℃
5. The greater this value, the more sensitive the enzyme is to temperature

Question 8

Explain the effect of pH on enzyme activity

Answer 8

1. The tertiary structure of the enzyme is important in ensuring that the active site is complementary to the substrate.
2. At the optimum pH, the concentration of hydrogen ions and hydroxide ions ensures the correct active site shape
3. So that the rate ESC formation, and so product formation is highest
4. Away from the optimum pH, the concentration of positively charged hydrogen ions (low pH), or negatively hydroxide ions (high pH), will disrupt hydrogen and ionic bonding
5. Resulting in changes to the tertiary structure and alteration of the active site, so that it is no longer complementary to the active site
6. This reduces the rate of ESC, and so, product formation

Question 9

Explain the effect of substrate concentration on enzyme activity

Answer 9

1. At low substrate concentrations, the chances of successful collision between enzyme and substrate is relatively lower, and so the rate of ESC, and product formation, is low
2. As substrate concentration increases, the rate of ESC and product formation increases (as the substrate concentration is the limiting factor)
3. As substrate concentration becomes saturating, the enzyme reaches a maximum rate of activity, active sites are constantly occupied by substrate, and the rate of product formation can not increase further (reaches a maximum)
4. Substrate concentration is no longer the limiting factor

Question 10

Explain the effect of enzyme concentration on enzyme activity

Answer 10

1. At low enzyme concentrations, enzyme concentration is the limiting factor
2. As enzyme concentration increases, the chance of successful collisions, ESC formation and product formation increase
3. The more enzyme active sites available, the higher the capacity for ESC formation.

Question 11

Describe an investigation of a factor that affects enzyme activity

Answer 11

1. Set up a range of different (factor that you are investigating). For example, range of substrate concentrations (investigating substrate concentration), or range of pH buffers (investigating effect of pH)
2. Mix substrate and enzyme keeping all other factors constant across the experiment.
3. Measure the product formed or substrate disappearance (by colour change, gas produced etc.) at regular timed intervals for five minutes
4. Repeat this for the rest of the range of the independent variable
5. Plot the results on a graph (product formed or substrate used vs time)
6. For each of the range of conditions determine the initial rate by drawing a tangent at time zero
7. To see the effect of ‘the factor’ on enzyme activity, plot the range of the independent variable vs the initial rate

Question 12

Discuss the role of cofactors, giving examples

Answer 12

1. Some enzymes require a non-protein component in order to function (catalyse reactions)
2. Cofactors are non-protein, inorganic ions or molecules, that associate with enzymes to activate them
3. Cofactors are not permanently associated with the enzyme.
4. Mineral ion cofactors are obtained from the diet (forexample Cl- ions are cofactors for the enzyme amylase)

Question 13

Discuss the role of coenzymes, giving examples

Answer 13

1. Coenzymes are non-protein, but organic and not permanently attached to the enzyme, but are required for the enzyme to carry out a reaction.
2. For example the coenzymes NAD (respiration) and NADP (photosynthesis), are used to transfer hydrogen atoms in reactions carried out by a number of different enzymes
3. Many coenzymes are synthesised from vitamins obtained in the diet: NAD and NADP are synthesised from vitamin B12, coenzyme A from vitamin B5

Question 14

Discuss the role of prosthetic groups, giving examples

Answer 14

1. Prosthetic groups are non-protein (organic or inorganic) permanently associated molecules or ions which are required for the proper tertiary structure of the enzyme.
2. Example of prosthetic group is Zn2+ ions for carbonic anhydrase

Question 15

Describe the role of precursor enzymes in metabolism

Answer 15

1. Some enzymes are synthesised as precursor enzymes (apoenzymes) which are inactive
2. These are inactive until bound by the cofactor/coenzyme..
3. ..or an inhibitory portion is cleaved off by a protease..
4. ..or very specific pH or temperatures are encountered
5. This is a way to ensure enzymes are only active when and where required

Question 16

Describe and explain the effect of a competitive inhibitor on enzyme activity

Answer 16

1. Competitive inhibitor has a shape similar to the substrate
2. It binds to the active site, reducing the rate of formation of the ESC
3. This reduces the enzyme activity (rate of reaction)
4. Increasing the concentration of the substrate makes ESC more likely to form
5. The effect of the inhibitor can thus be reduced by increasing the substrate concentration
6. At an infinitely high substrate concentration the effect of the inhibitor is negligible, and a maximum enzyme activity can still be reached (at a higher substrate concentration)
7. Metabolic pathways are often regulated by negative feedback using end-products to inhibit earlier steps in the pathway, as products usually have similar shapes to enzyme substrates.

Question 17

Describe the effects of a non-competitive inhibitor

Answer 17

1. Non-competitive inhibitor binds to the enzyme at a location away from the active site
2. A location called the allosteric site
3. Binding causes a change to the shape of the tertiary structure
4. This makes the active site no longer complementary to the substrate
5. This reduces the rate of ESC formation, and thus the rate of reaction
6. This reduces the number of available active sites
7. Increasing the substrate concentration does not reduce the impact of the non-competitive inhibitor, and so the maximum enzyme activity is reduced
8. Many therapeutic drug molecules work by acting as competitive inhibitors of physiological enzymes

Question 18

Discuss reversible and non-reversible inhibition

Answer 18

1. Inhibitors may bind permanently to the enzyme in which case their effect will be irreversible.
2. If the inhibitor binds the enzyme temporarily, then its effects will be reversible
3. It important to remember that competitive and noncompetitive inhibition is not exactly the same as reversible and non-reversible
4. But in competitive inhibition, where the effects of the inhibitor can be reduced, that shows reversible inhibition
5. And often, non-competitive inhibitors bind permanently to enzymes, so their effects are non-reversible.
6. Many toxic and poisonous substances are extremely potent in small amounts because they act irreversibly.