C1.1 Enzymes and metabolism. Practice questions with markscheme.

• A: anabolism builds larger molecules (condensation); catabolism breaks them down (hydrolysis/oxidation);

• D: heat-induced changes to tertiary structure are not reversed on cooling, so the active site remains non-functional;

• C: rate is inversely related to the time taken to reach the end point, so 1/time gives a value that increases as the reaction speeds up;

• B: the uncatalysed reaction does happen, but with a half-time of 78 million years it is far too slow to supply the cell; bound in the enzyme's active site the same reaction takes 0.018 s at the same temperature (about 10¹⁷ times faster), so enzymes allow the reactions of metabolism to run fast enough at the temperature of the cell;

B is refuted by the table itself (the uncatalysed reaction has a finite half-time); C tests scale (a few degrees raises rate by a small factor, not 10¹⁷); D confuses rate with yield. Data after Radzicka and Wolfenden (1995), orotidine 5'-phosphate decarboxylase: uncatalysed half-time 78 million years at 25 °C, kcat 39 s⁻¹ (half-time ln 2 ÷ 39 = 0.018 s).

• binding (in the active site) strains/distorts bonds in the substrate / holds substrates in the correct orientation;
• (this) stabilizes the transition state, so less energy is needed to reach it;
• local conditions in the active site (charged/acidic R-groups) assist the reaction, OWTTE;

• (a) [1]
  • (7.9 − 5.1) ÷ 5.1 × 100 = 55 %;

  Accept 54.9 %.

• (b) [2]
  • the same volume of small beads has a larger total surface area, so more of the enzyme lies close to the surface;
  • urea molecules have a shorter distance to move into a small bead to reach the enzyme;
  • so collisions between urea molecules and active sites are more frequent / more enzyme–substrate complexes form per unit time, OWTTE;
• (c) [2]
  • because the enzyme is immobilized, substrate molecules must move to the active sites for collisions to occur;
  • without stirring, urea close to the beads is used up faster than random movement replaces it / a layer of solution low in substrate forms round each bead;
  • stirring brings fresh urea solution to the surface of the beads / carries product away;
  • so collisions between substrate molecules and active sites are more frequent, OWTTE;
• (d) [1]
  • stirring moves only the solution outside the beads, so urea must still move slowly through the gel to reach enzyme deep inside a large bead;
  • enzyme near the centre of a large bead meets little substrate / a smaller proportion of the enzyme is close to the surface, OWTTE;

• substrate collides with / binds to the active site, forming an enzyme–substrate complex;
• the active site changes shape (slightly) to fit the substrate more closely / induced fit;
• the reaction occurs and products are released, leaving the enzyme unchanged (and reusable);

• they remain active / are not denatured at high temperatures;
• reactions can run faster at higher temperatures (more collisions) without loss of enzyme;
• less cooling of reaction vessels needed / lower contamination risk at high temperature / longer working life, OWTTE;

Any 2. Accept a named example such as Taq polymerase.

• (a) [1]
  • 75 °C;

  Accept 73–77 °C. Units required.

• (b) [2 max]
  • both show an optimum with activity falling either side / both reach a similar maximum rate;
  • enzyme B has a higher optimum than enzyme A / B remains active at temperatures that denature A;
  • A's activity falls to zero by ~45 °C, whereas B is still active (and rising towards its optimum), OWTTE;

  At least one similarity AND one difference required for full marks.

• (c) [2 max]
  • heat breaks (hydrogen/ionic) bonds maintaining the tertiary structure;
  • enzyme is denatured / active site changes shape;
  • substrate no longer binds / fewer enzyme–substrate complexes form;

• B: competitive inhibition is overcome at high substrate concentration;

• D: isoleucine normally binds an allosteric site on threonine deaminase, the first enzyme of the pathway, slowing the pathway as isoleucine accumulates (end-product inhibition); without that binding the pathway keeps running whatever the isoleucine concentration, so isoleucine is over-produced;

• B: enzymes are globular protein catalysts that lower activation energy and are not consumed;

• D: glycolysis is a linear chain of reactions from glucose to pyruvate, whereas the Krebs cycle (like the Calvin cycle) regenerates its starting compound;

• A: enzyme specificity means a separate enzyme is required for each reaction, so regulating the amount or activity of one enzyme regulates one step of the network; enzymes are not used up (A), they lower activation energy rather than supplying energy (B), and each enzyme catalyses only its own reaction (D);

• C: penicillin reacts covalently in transpeptidase's active site, permanently disabling wall cross-linking; resistant bacteria have altered transpeptidases or secrete β-lactamase, which destroys penicillin;

• A: the peak is the transition state, reached only when enough energy has been supplied to break bonds within the substrate; the drop after it is the energy yield from bond formation;

• C: the uncatalysed reaction does happen, but with a half-time of 78 million years it is far too slow to supply the cell; bound in the enzyme's active site the same reaction takes 0.018 s at the same temperature (about 10¹⁷ times faster), so enzymes allow the reactions of metabolism to run fast enough at the temperature of the cell;

B is refuted by the table itself (the uncatalysed reaction has a finite half-time); C tests scale (a few degrees raises rate by a small factor, not 10¹⁷); D confuses rate with yield. Data after Radzicka and Wolfenden (1995), orotidine 5'-phosphate decarboxylase: uncatalysed half-time 78 million years at 25 °C, kcat 39 s⁻¹ (half-time ln 2 ÷ 39 = 0.018 s).

• they remain active / are not denatured at high temperatures;
• reactions can run faster at higher temperatures (more collisions) without loss of enzyme;
• less cooling of reaction vessels needed / lower contamination risk at high temperature / longer working life, OWTTE;

Any 2. Accept a named example such as Taq polymerase.

• axes labelled: rate of reaction (y) against substrate concentration (x);
• rate rises (steeply) at low substrate concentrations;
• curve levels off / plateaus at high substrate concentration, annotated as enzyme/active sites saturated;

Award marks for correct shape even if freehand; both annotations and axis labels required for full marks.

• (a) [2]
  • variant G reaches half of Vmax only at a much higher substrate concentration (6.8 vs 2.1 mmol dm⁻³), so it binds substrate less tightly / has a lower affinity;
  • the two Vmax values are almost equal (~47–48), so the maximum catalytic rate is essentially unchanged, OWTTE;
• (b) [3]
  • the Vmax ranges overlap (≈46.8–49.2 vs 45.7–48.7), so that difference is not significant / could be due to chance;
  • the ½Vmax ranges do not overlap (≈1.9–2.3 vs 6.5–7.1), so the difference in substrate binding is (likely) significant;
  • a t-test (comparing two means) would test whether the difference is statistically significant;
• (c) [2 max]
  • the different R-group alters the shape/chemistry of the active site, so it is less complementary to the substrate / binds it less readily;
  • (so) fewer collisions lead to binding and a higher substrate concentration is needed to occupy half of the active sites, OWTTE;
  • at very high substrate concentration the active sites are still all occupied and, once bound, the substrate is still converted to product, so Vmax is (almost) unchanged, OWTTE;