Questions on cofactors, coenzymes and where enzymes work

Question 1

A prolonged dietary shortage of vitamin B3 damages tissues that respire heavily, such as the nervous system and the lining of the gut. Suggest why.

Accepted Answer

B1 vitamin B3 (nicotinamide) is the raw material from which cells make the coenzyme NAD B1 NAD carries hydrogen from the oxidation reactions of respiration to the electron transport chain B1 with too little NAD those reactions slow, so less ATP is made by respiration B1 tissues with a high demand for ATP are affected first, because active transport, synthesis and impulse transmission all depend on it

Question 2

Compare an intracellular enzyme with an extracellular enzyme, giving a named example of each and comparing the conditions each must tolerate.

Accepted Answer

B1 an intracellular enzyme catalyses reactions inside the cell that made it, such as catalase acting in peroxisomes, whereas an extracellular enzyme is secreted from the cell that made it and acts outside it, such as trypsin acting in the small intestine B1 an intracellular enzyme need only tolerate the conditions inside its own cell, whereas an extracellular enzyme must remain active in conditions the secreting cell never itself experiences, such as the strongly acidic stomach B1 intracellular enzymes are not released by exocytosis, whereas extracellular enzymes are B1 both classes are made by ribosomes inside a cell; what differs is only where each subsequently acts

Question 3

A patient's diet is severely deficient in vitamin B5. Suggest the effect this has on the Krebs cycle, and suggest why a wide range of tissues would be affected rather than just one.

Accepted Answer

B1 vitamin B5 is the raw material from which cells make coenzyme A, so a deficiency would limit the supply of coenzyme A available B1 coenzyme A carries the two-carbon acetate group from the link reaction into the Krebs cycle, so with too little of it fewer acetate groups could be delivered and the Krebs cycle would slow B1 a slower Krebs cycle would reduce the ATP a cell can make by aerobic respiration B1 because every respiring cell in the body needs coenzyme A for this step, a wide range of tissues, not just one, would be affected, especially those with the highest demand for ATP

Question 4

Compare a coenzyme with a prosthetic group, giving a named example of each.

Accepted Answer

B1 both are non-protein partners that an enzyme needs in order to function B1 a coenzyme binds and is released and recycled, whereas a prosthetic group is tightly bound to the protein and may be organic or inorganic B1 NAD or coenzyme A as the coenzyme, against the haem group of catalase or the zinc ion of carbonic anhydrase as the prosthetic group

Question 5

A purified sample of amylase hydrolyses starch only when chloride ions are present in the solution. Explain this observation.

Accepted Answer

B1 the chloride ion is a cofactor that amylase requires in order to function B1 without the ion the active site does not take, or hold, the shape complementary to starch, so few enzyme-substrate complexes form B1 the ion is not the substrate and is not used up: it binds near the active site and allows the reaction to be catalysed

Question 6

Explain why the enzymes that digest food in the gut must be extracellular, and name two such enzymes.

Accepted Answer

B1 food molecules such as starch and proteins are too large to cross the cell surface membrane, so they cannot be digested inside a cell B1 the enzymes are therefore secreted, by exocytosis, and hydrolyse the food outside the cells, so only the small soluble products are absorbed B1 salivary amylase and trypsin, or another correct pair of secreted digestive enzymes

Question 7

Two enzymes, P and Q, act on the same substrate and have similar Vmax values. Enzyme P has a Km of 0.2 mmol dm⁻³ and enzyme Q a Km of 4.0 mmol dm⁻³. Explain which enzyme has the higher affinity for the substrate, and which converts more substrate when the substrate concentration is low.

Accepted Answer

B1 enzyme P has the higher affinity, because affinity runs opposite to Km B1 a low Km means the enzyme reaches half of its maximum rate while the substrate is still scarce, which is only possible if it binds the substrate readily B1 at low substrate concentration P works at a far higher fraction of Vmax than Q, so with similar Vmax values P converts more substrate

Question 8

Name the vitamin from which coenzyme A is made, name the stage of aerobic respiration in which coenzyme A picks up acetate, and name the pathway it carries that acetate into.

Accepted Answer

B1 pantothenic acid, vitamin B5 B1 the link reaction, where acetate made from pyruvate is picked up B1 the Krebs cycle, which it feeds acetate into

Question 9

Explain why carbonic anhydrase's zinc ion is classed as a prosthetic group rather than as a cofactor that visits and leaves, even though it is a single inorganic ion.

Accepted Answer

B1 the distinction between a visiting cofactor and a prosthetic group is about how tightly and permanently it is bound, not about whether it is organic or inorganic B1 the zinc ion in carbonic anhydrase never leaves the active site once the enzyme has folded around it, unlike a coenzyme, which binds and is released repeatedly B1 because it remains permanently bound, it is classed as a prosthetic group, in the same category as the organic haem group of catalase, despite being an inorganic ion

Question 10

Describe the role of NAD in aerobic respiration, and describe what happens to the coenzyme once it has delivered its hydrogen.

Accepted Answer

B1 NAD collects hydrogen released during the oxidation reactions of glycolysis and the Krebs cycle B1 it delivers that hydrogen to the electron transport chain, where the energy carried is used to make ATP B1 having released its hydrogen, NAD is free to collect more from a further oxidation reaction, which is why only a small quantity is needed despite being used repeatedly

Question 11

Explain why a cofactor is not counted as a substrate of the reaction it makes possible, even though the reaction could not proceed without it.

Accepted Answer

B1 a substrate is converted into product and used up, whereas a cofactor is not consumed by the reaction it enables B1 it may be required simply to be present, as the chloride ion is for amylase, or it may bind, leave carrying what the reaction removed, and be restored to its original form at another enzyme, as a coenzyme does B1 because it is regenerated or unaffected rather than consumed, only a small quantity of a cofactor is needed relative to the amount of substrate the enzyme processes

Question 12

Hexokinase has a Km far below the normal blood glucose concentration. Explain what this tells us about how close to Vmax hexokinase is working under normal conditions, and explain why its rate barely changes when blood glucose rises after a meal.

Accepted Answer

B1 a Km far below the normal blood glucose concentration means the enzyme is already working close to its maximum rate under normal conditions, since Km is the concentration needed to reach only half of Vmax B1 because glucose concentration is already well above the level needed to saturate hexokinase, only a small proportion of active sites are ever free at any moment B1 raising glucose concentration further after a meal makes little difference, because there is little room for the rate to rise

Question 13

State what is meant by a coenzyme, and name the vitamin from which the coenzyme NAD is made.

Accepted Answer

B1 a coenzyme is an organic cofactor: a small non-protein organic molecule that binds to an enzyme, carries hydrogen or chemical groups between reactions and is released again B1 NAD is made from nicotinamide, which is vitamin B3

Question 14

State what is meant by a prosthetic group, and state one named example of one.

Accepted Answer

B1 a prosthetic group is a cofactor that is tightly bound to a protein, and may be organic or inorganic B1 haem in catalase, or the zinc ion of carbonic anhydrase

Question 15

Name the organelle in which catalase acts, and name the class, intracellular or extracellular, that this makes catalase.

Accepted Answer

B1 the peroxisome, inside the cell B1 intracellular, acting in the same cell