1.

At the start of glycolysis, glucose is phosphorylated to produce glucose 6-phosphate, which is converted into fructose 6-phosphate. A second phosphorylation reaction is then carried out, in which fructose 6phosphate is converted into fructose 1,6-bisphosphate. This reaction is catalyzed by the enzyme phosphofructokinase. Biochemists measured the enzyme activity of phosphofructokinase (the rate at which it catalyzed the reaction) at different concentrations of fructose 6-phosphate. The enzyme activity was measured with a low concentration of ATP and a high concentration of ATP in the reaction mixture. The graph below shows the results.

c o

c e n

t r a t i o

z y

a c t i v

i t y H i g h A T P c o n c e n t r a t i o n

r u

c t o

s e

- p

s p

a t e

c o

c e n

(a)

(i) Using only the data in the above graph, outline the effect of increasing fructose 6-phosphate concentration on the activity of phosphofructokinase, at a low ATP concentration. (i) increasing fructose 6-phosphate concentration (initially) causes an increase in activity; activity levels out / remains constant as (substrate) concentration continues to rise; (2) (ii) (ii) Explain how increases in fructose 6-phosphate concentration affect the activity of the enzyme. more collisions with active site as concentration rises; at high substrate levels all active sites are occupied so no further increase in rate / enzyme working at maximum rate; (2)

(b)

(i) Outline the effect of increasing the ATP concentration on the activity of phosphofructokinase. (i) decreases activity; at all fructose 6-phosphate concentrations; most effect at intermediate fructose 6-phosphate concentrations / little difference at high fructose 6-phosphate concentrations; ATP acts as an inhibitor; (2)

(ii)

Suggest an advantage to living organisms of the effect of ATP on phosphofructokinase. end-product inhibition; respiration rate decreased if ATP already available; (1) (Total 7 marks)

(ii)

2.

(a)

Define the term active site of an enzyme.

(a) the site (on the surface of an enzyme) to which substrate(s) bind / the site (on the enzyme) where it catalyzes a chemical reaction; (1) (b) (b) Outline how enzymes catalyze biochemical reactions. bring substrates close together in active site / in correct orientation; forms enzyme-substrate complex / substrate(s) bind to active site; lowers the activation energy for the reaction; weakens bonds in the substrate; (2)

(c) (c)

Explain the effect of pH on enzyme activity. enzymes have an optimal pH; lower activity above and below optimum pH / graph showing this; too acidic / basic pH can denature enzyme; change shape of active site / tertiary structure altered; substrate cannot bind to active site / enzyme-substrate complex cannot form; hydrogen / ionic bonds in the enzyme / active site are broken / altered (3) State three functions of lipids. energy storage / source of energy / respiration substrate; (heat) insulation; protection (of internal organs); water proofing / cuticle; buoyancy; (structural) component of cell membranes; electrical insulation by myelin sheath; (steroid) hormones; glycolipids acting as receptors; Three correct [2], one or two correct [1]. Use one tick to mark the first one or two correct answers. Use a second tick to mark the third correct answer. Mark the first three answers only. (2) (Total 8 marks)

(d) (d)

3. 3.

Explain the effects of temperature, pH and substrate concentration on enzyme activity. zymes have an active site; that fits the substrate precisely; changes in the chemical environment of the enzyme can lead to a shape / conformational change in the protein; leading to a change in the shape of the active site; may interfere with the binding of the substrate with the active site; altering pH can alter intermolecular interactions within the protein; or within the active site; enzymes have an optimum pH; increase in temperature can increase molecular motion leading to disruption of intermolecular interactions; increases chance of enzyme substrate collisions so enzyme activity increases; optimal temperature; temperature changes / pH changes can denature the protein;
3

the more substrate, the more product / more enzyme-substrate complex forms; after a point, all active sites are bound to substrate / all active sites occupied; additional substrate will not lead to a greater rate of product formation at this point; 8 max For full marks all three conditions must be included, otherwise award [6 max]. [Plus up to [2] for quality] (Total 8 marks)

4.

(a) State one named example of a fibrous protein and one named example of a globular protein. Fibrous: ........................................... Globular: ........................................... (a) Any two from the following. fibrous: eg fibrin, collagen (do not accept tendon); globular: eg hemoglobin, fibrinogen, amylase (do not accept enzyme); (2)

(b) (b)

Outline the effect of enzymes on the reactions they catalyse. a new reaction pathway is created; activation energy is reduced; the equilibrium for the reaction is achieved more quickly / the reaction is faster; (2)

(c)

The rate of cellular respiration is controlled by the allosteric inhibition of phosphofructokinase by ATP. Phosphofructokinase is the first enzyme in the respiration pathway. Explain the meaning of allosteric inhibition using this example. ATP inhibits phosphofructokinase at (allosteric) site away from the active site; inhibition alters the enzymes conformation / structure; the active site does not accept the substrate molecule; when respiration increases ATP levels phosphofructokinase is inhibited; respiration slows down; phosphofructokinase is the first enzyme in the respiration pathway so there is no build up of metabolic intermediates; as ATP is used up by the cell the inhibition of phosphofructokinase is reduced; respiration speeds up again; this is an example of negative feedback;

(c)

(4) (Total 8 marks)

5.

Consider the metabolic pathway shown below.

A 1 B 2 C 3 D

If there is end-product inhibition, which product (B to E) would inhibit which enzyme (1 to 4)? Product A. B. C. D. C B B E Enzyme 4 3 4 1 (Total 1 mark) 6. (a) Explain the significance of secondary structure to the structure of a protein. a) held together by hydrogen bonds; between CO and NH groups; (-helix for) structure of fibrous proteins / keratin; one of four levels of structure; provides stability of structure; helix; sheet; (3) (b) State the name of a competitive enzyme inhibitor. malonate / Prontosil (1)

(c) (c)

Outline the difference between competitive and non-competitive enzyme inhibitors. competitive similar to substrate and non-competitive not;
5

competitive attaches to the active site, non-competitive does not bind to the active site; non-competitive changes enzyme shape, competitive does not; competitive change reversible; (2) (Total 6 marks) 7. Alcohol dehydrogenase is an enzyme that catalyses the reversible reaction of ethanol and ethanal according to the equation below. NAD+ + CH3CH2OH ethanol CH3CHO + NADH + H+ ethanal

The initial rate of reaction can be measured according to the time taken for NADH to be produced. In an experiment, the initial rate at different concentrations of ethanol was recorded (no inhibition). The experiment was then repeated with the addition of l mmol dm3 2,2,2-trifluoroethanol, a competitive inhibitor of the enzyme. A third experiment using a greater concentration of the same inhibitor (3 mmol dm3) was performed. The results for each experiment are shown in the graph below.
1 . 2 1 . 1 1 . 0 0 . 9 0 . 8 0 . 7 I n i t i a l r a t e0 . o6 f r e a c t i o n / a r b i t r a r0 y . 5 u n i t s 0 . 4 0 . 3 0 . 2 0 . 1 0 . 0 0 1 0 2 0 3 0 4 E t h a n

n 1 3 0 o 5 l 0 6 0 n 7

o m m 0
3

i n h i b m 3o l m 3o l 8 0 9 0 1

i t i o d m d m 0 n 0 /

n i n i n h h i i

c o

c e n

t r a t i o

[Source: R Taber, Biochemical Education, (1998) 26, pages 239-242]

(a) (a)

Outline the effect of increasing the substrate concentration on the control reaction (no inhibition). directly proportional / greater concentration, greater rate of reaction; at high concentrations the increase is smaller / plateau / levels-off (at approximately 70 mmol dm3); (2)

(b)

(i)

State the initial rate of reaction at an ethanol concentration of 50 mmol dm3 in the presence of the inhibitor at the following concentrations. 1 mmol dm3: 0.70 ( 0.02) 3 mmol dm3: 0.55 ( 0.02) (1)

(ii)

State the effect of increasing the concentration of inhibitor on the initial rate of reaction. lower reaction rate at inhibitor concentration of 3 mmol dm3 / the greater the inhibitor concentration the slower the rate of reaction; trend / overall shape are the same / increases but then levels-off; but lower at greater concentration of inhibitor;

(ii)

(c) (c)

Explain how a competitive inhibitor works. substrate and inhibitor (structurally) similar; inhibitor binds to active site; prevents substrate from binding; activity of enzyme prevented; named example (eg malonate inhibits succinate dehydrogenase as it is similar to succinate); (3) (Total 7 marks)

8.

What can reduce the effect of a competitive inhibitor of an enzyme? A. B. Decrease the temperature at which the reaction takes place. Increase the temperature at which the reaction takes place.

C. D.

Increase the substrate concentration. Add a non-competitive inhibitor. (Total 1 mark)

Ans : C

9.

Outline enzyme-substrate specificity.

active site of enzyme binds to specific substrate; shape of the active site and substrate fit / complement each other; lock and key model; chemical properties of substrate and enzyme attract / opposite charges; enzyme / active site is not rigid and substrate can induce slight changes in shape; allows substrates of similar structure to bind with same enzyme; induced fit; causes weakening of bonds in substrate to lower activation energy; (Total 5 marks) 10. Explain how allosteric control of metabolic pathways by end-product inhibition includes negative feedback and non-competitive inhibition. allosteric enzyme has binding site(s) away from / other than the active site; (shape of an) allosteric enzyme alternates between active and inactive (form); non-competitive inhibitor binds to allosteric site / away from active site; non-competitive inhibitor changes shape of active site; non-competitive inhibitors do not compete with substrate for the active site; end-product can inhibit enzyme needed for early / first step in metabolic pathway; negative feedback since increased level of product decreases rate of its own production; metabolic pathway regulated according to the requirement for its end-product; idea that inhibition is reversible; Award [1] for named enzyme and [1] for its non-competitive / end-product inhibitor. (Total 8 marks)

11. Explain the effect of substrate concentration on enzyme activity. (Total 3 marks) 11. as substrate concentration increases enzyme activity increases; at high substrate concentration enzyme reaches maximum activity; active sites saturated; labelled sketch-graph showing above relationship;

12. (a)

(a)

Outline the induced fit model of enzyme activity. (3) substrate binds / approaches active site; shape of active site changes; bonds in substrate weaken; activation energy decreases; explains broad specificity of some enzymes; eg proteases;

(b) (b) (i)

(i) State two products of the light-dependent reactions of photosynthesis. oxygen; NADPH / NADPH + H+ / NADPH2; ATP; (ii) (ii) Explain the light-independent reactions in photosynthesis. occurs in stroma of chloroplast; ribulose disphosphate / RuBP / 5-C sugar combines with CO2; catalyzed by rubisco / ribulose biphosphate carboxylase; splits into two 3-C sugars / glycerate 3-phosphate; ATP and NADPH supply energy and H; 3-C sugars join to form glucose / 6-C sugar; RuBP regenerated (with use of ATP); (4) (Total 9 marks)

13. What effect do enzymes have on the activation energy of exergonic and endergonic reactions? Activation energy of exergonic reactions A. B. C. D. increases decreases increases decreases Activation energy of endergonic reactions increases decreases decreases increases (Total 1 mark)
9

Ans : B

14. Outline two examples of the commercial application of enzymes in biotechnology. the name of the enzyme and the substrate; the name(s) of the product(s); a statement as to why the application is useful commercially; Award [3 max] per example, eg pectinase acts on (soluble) pectin; produces smaller, more soluble carbohydrates; used in fruit juice clarification / to increase yield; eg endonuclease DNA acts on DNA; produces DNA fragments; used in genetic engineering; eg protease acts on (insoluble) proteins; produces amino acids; washing powders - stain removal; (Total 6 marks)

15. The enzyme aspartate carbomyltransferase (ACTase) is a key regulatory enzyme in nucleotide metabolism in bacteria. The activity of this enzyme was studied in the bacterium Helicobacter pylori, an important human pathogen. ACTase activity and the growth of H. pylori were measured at different concentrations of carbomoyl aspartate (CAA), the end product of the reaction catalysed by ACTase.
1 7 A % C 0 5 0 1 7 5 2 0 0 a m o y l a s p 0 5 0 G % 5 r o w t h / o f c o n t r o 0

T a s e 5 a0 c t i v i t y / o f c o n t r o l K e y : 2 5 A C T a s e a c t i v i t y H . p y l o r i g r o w t h 0 0 C o 1 n 0 2 c e n 0 3 0 4 n 0 o f 5 0 6

t r a t i o

c a r 3b

a r t a t

[Source: Burns, et al, Biological Procedures Online, (1998), http://www.biologicalprocedures.com]

(a)

(i)

State the growth of H. pylori at a CAA concentration of 30 mmol dm3. (i)72.5 (.1.0)% (1) (ii) Calculate the change in ACTase activity between CAA concentrations of 20 and 40 mmol dm3. (ii) 40% (decrease) (1)

(b) (b)

Compare the effect of increasing CAA concentration on the growth of H. pylori and ACTase activity. both are inversely proportional / as CAA concentration increases both activity and growth decrease; growth is more irregular at low concentrations; ACTase activity decreases more at higher concentration / after 30 mmol dm3 than growth; both show linear decreases between 10 and 30 mmol dm3; 2 max Any other valid comparisons. (2)

(c) (c)

Explain the effect of CAA on ACTase activity. end-product is slowing enzyme activity; allostery / non-competitive inhibition; (2)

(d) Suggest a direct medical application of this information. (d) use CAA to control / inhibit bacterial growth / antibiotic functions; use CAA to treat H. pylori infection; (1) (Total 7 marks)

11

16. The graph below shows the effect of changing the substrate concentration on an enzyme controlled reaction.
4 0 % 2 0 % 1 A m o u n t o f p r o d u c t f o 0 s u % r m 5 % b s t r a t e s u b s t r a t e s u e d s u b s t r a t e b s t r a t e

2 0 T i m e

. 5 %

% s u

s u b

s t r a t e

s t r a t e

What is the correct interpretation of these data? A. B. C. D. The rate of reaction increases continuously with increase in substrate concentration. The rate of reaction decreases continuously with increase in substrate concentration. The rate of reaction increases up to a point and then remains constant. The rate of reaction is not affected by any change in the substrate concentration. (1) Ans : C

17. In the enzyme controlled pathway shown below, which compound is most likely to inhibit enzyme (w)?
enzyme w Precursor I enzyme x II enzyme y III enzyme z IV

A. B. C.

I II III

D.

IV (1) (1)

Ans : D

18. Which of the following could cause denaturation of an enzyme? A. B. C. D. Ans : C . (1) 19. Enzymes are used by living organisms to catalyse reactions. Some of these reactions occur in the cytoplasm of cells. Other reactions take place outside cells, for example the digestion of foods in the human gut. (a) State the name used by biochemists for the chains and cycles of reactions that occur inside cells. (a) metabolic pathways / metabolic reactions / metabolism / anabolism and catabolism (1) (b) Enzymes of digestion in humans are secreted by glands. They have a pH optimum which allows them to work efficiently in the part of the gut into which they are secreted. (i) In the table below, identify the missing enzyme, the two glands, and the pH optimum Gland secreting the enzyme Substrate Products pH optimum Substrate concentration A competitive inhibitor High temperature Low salt concentration (1)

Name of enzyme amylase

starch triglycerid es

maltose fatty acids and glycerol / ( 7

(i) salivary pH lipase;

gland 7.5 (accept

pancreas; 0.5); lipidase)

13

pancreas; (4) (ii) (ii) Outline the effect of pH values above and below the optimum on enzyme structure. ionic bonds / polar bonds broken / disrupted / charge distribution altered; ionization of amino / carboxyl groups altered; conformation / shape of enzyme / active site altered / tertiary structure altered; enzyme denatured; (2) (c) Enzymes that work inside cells are sometimes affected by noncompetitive inhibitors. Explain how a non-competitive inhibitor affects the activity of an enzyme. inhibitor binds (to the enzyme) away from the active site / at allosteric site; shape / (intramolecular) bonding / conformation of the protein / enzyme is altered; shape / properties of active site altered; substrate no longer fits the active site / no enzyme-substrate / ES complex formed; no enzyme activity / works more slowly (until the inhibitor dissociates); (3) (Total 10 marks) 20. Outline two examples of the commercial application of named enzymes in the name of the enzyme and the substrate; the name(s) of the product(s); a statement as to why the application is useful commercially; Award [3 max] for each example. eg pectinase acts on soluble pectin; produces smaller, more soluble carbohydrates; used in fruit juice clarification / improving fruit juice yield; eg DNA endonuclease acts on DNA; produces DNA fragments; used in genetic engineering; eg protease acts on insoluble proteins; produces amino acids; washing powders stain removal; Accept other suitable examples. (Total 6 marks)

(c)

21. Explain competitive and non-competitive inhibition, including allostery. (Total 8 marks) competitive: a molecule structurally similar to the substrate binds to the active site; preventing substrate binding; eg inhibition of butanedioic acid (succinate) dehydrogenase by propanedioic acid (malonate) in the Krebs cycle / other valid example; competitive inhibition is reversible; non-competitive: an inhibitor molecule binds to an enzyme; not at the active site; causes a conformational change in the active site; preventing substrate binding; eg CN inhibition of cytochrome oxidase by binding to SH groups / other valid example; Award [6 max] for explanation of competitive and non-competitive inhibition. most allosteric enzymes have multiple allosteric sites; allosteric inhibition is a form of non-competitive inhibition; metabolites can act as allosteric inhibitors of enzymes earlier in a metabolic pathway to regulate metabolism; binding (of end product) to an allosteric site changes shape of enzyme;

22. The graphs below show the energy changes during endergonic and exergonic reactions, with and without enzymes.

15

Which line represents an endergonic reaction, without an enzyme? A. B. C. D. I II III IV

Ans :; C (Total 1 mark) 23. What determines the specificity of an enzyme for its substrate? A. B. C. D. The temperature at which it is operating The optimum pH of the enzymes The concentration of the substrate The structure of the enzyme molecule (Total 1 mark) Ans :D 24. (a) State why each step in a biochemical pathway often requires a separate enzyme. (a) enzymes are specific for their substrate / lock and key model / energy requirements for reactions with substrates vary; each step of the pathway is unique / different substrate at each step; finer control of metabolic pathways; (2) (b) Explain the effects of either changing temperature or pH on enzyme activity. (b) Either, temperature: [3 max] each enzyme has an optimal temperature for its maximum activity; (small) temperature increases result in increased enzyme activity to a point / optimum; increase activity due to increased movement of molecules / increased kinetic energy or conversely stated; temperature increases above the optimum causes (progressive) loss of activity due to denaturation / shape changes or, pH: [3 max] each enzyme has an optimal pH for its maximum activity; as pH varies from optimal pH, enzyme activity diminishes / becomes inhibited;

loss of activity is due to denaturation / shape changes; gain or loss of hydrogen ions distorts tertiary shape of enzyme; homeostatic mechanisms maintain optimal conditions for enzyme activity;3 max Credit marking points above if illustrated by a suitably annotated graph. (3) (Total 5 marks) 25. The hydrolysis of inorganic phosphate (PPi) by phosphatase enzyme provides energy for a wide range of reactions. A phosphatase (PPase) occurs bound to thylakoid membranes. This enzyme was purified from the thylakoid membranes of spinach leaves using chromatography. The activity of the membrane bound enzyme and the purified enzyme was measured. The effect of the concentration of magnesium ions (Mg2+) on the relative activity of these enzymes was determined using different concentrations of magnesium chloride. The concentration of inorganic phosphate used in both cases was of 1 mmol dm3. Activity of phosphatase (arbitary units) Membrane Purified bound 12 618 1215
P u r i f e d b d r a n e

M e m b o u n R e l a t i v / % e a c t i v i t y

a g

e s i u

c h

l o

r i d 3e

c o

c e n

t r a t i o

[Reprinted from Po-Yin Cheung et al., Thiols Protect the Inhibition of Myocardial Aconitase by Peroxynitrite, Archives of Biochemistry and Biophysics, vol. 350, issue 1, pp. 104-108 1998, with permission from Elsevier.]

(a)

State the percentage of relative activity of the purified enzyme when the concentration of magnesium chloride is

17

i) (i) (ii) (ii) (b) (b)

1 mmol dm3 ................................... 27 (1) 2 mmol dm3 ................................... 90 (1) (2)

Outline the effect of magnesium chloride on the relative activity of the membrane bound enzyme. as the concentration of Mg increases the rate increases; most rapid increase between 1 and 2 mmol dm3; peaks at 4 mmol dm3: until it plateaus (at 5 mmol dm3 ) / no more increase / drops slightly; (2)

(c)

Calculate the approximate ratio of inorganic phosphate to magnesium chloride concentration needed to achieve maximum activity in membrane bound enzymes. 1:4 (1)

(d)

(i) State the difference in phosphatase activity when membrane bound and when purified. (i) membrane bound is 10 times more efficient (12000 to 1200); difference is (12618-1215) 11403 arbitrary units greater in membrane bound; about 1000% greater / 938.5% greater; (1) (ii) Suggest a reason for this difference. (ii) purification could have affected structure of protein; bound to membrane allows interactions / other molecules in membrane may help it / be acting as coenzymes; (1) (Total 7 marks)

26. The reaction below shows the energy changes in a chemical reaction.

What would happen to the changes in energy if this reaction was controlled by an enzyme? A. B. C. D. I would increase. II would decrease. I and IV would decrease. II and III would decrease. (Total 1 mark) Ans : D

27. According to the induced fit model of enzyme function, which of the following statements is correct? A. B. C. D. Active sites on enzymes are specific to a single substrate. The shape of the active site can be changed by the binding of an allosteric inhibitor. The binding of the substrate changes the shape of the active site slightly. Competitive inhibitors can change the shape of enzymes. (Total 1 mark)
19

Ans : C

28. What is an active site? A. B. C. D. The part of an enzyme that binds only to the product molecules. The sequence of amino acids responsible for the catalytic activity of enzymes. The sequence of amino acids responsible for the structure of an enzyme. The specific area responsible for the activity of all proteins. (Total 1 mark) 29. Which types of enzyme are found in the human digestive system? I. II. III. A. B. C. D. Amylases Proteases Lipases

Ans : B

I and II only I and III only II and III only I, II and III (Total 1 mark)

Ans : D

30. Which statement describes how allosteric enzymes work? Reversible A. B. C. D. Competitive inhibition Endproduct inhibition Active and inactive forms

Key: Ans : B

= yes

= no (Total 1 mark)

31. Which diagram shows how enzymes change the activation energy in an endergonic reaction? A . X Y E n e r g y E n e r g y B . Y X

P C .

r o

r e s s

r e a c t i o D .

r o

r e s s

r e a c

X Y E n e r g y E n e r g y

Y X

r o

r e s s

r e a c t i o

r o

r e s s

r e a c

Key: X = without enzyme Ans : C

Y = with enzyme (Total 1 mark)

32. Phenylketonuria (PKU) is a disease caused by a gene mutation that makes too much phenylalanine which may cause brain damage. The enzyme phenylalanine ammonia lyase (PAL), converts phenylalanine into harmless products. Mice with PKU were injected with PAL. The levels of phenylalanine in blood plasma were measured immediately after the injection (0 hour) and every hour for the next three hours. Different groups of mice with PKU were injected with three different doses of PAL. The
21

results are shown below as a percentage of the levels of phenylalanine before the PAL injection.

0 p

p l a s m a h e n y l a l a n / %

0 t i m h o 1 u e 2 / r 3 2 d o 2 0 1 1 0 0

s e s / o u f n P i At s L

[Source: C. Sarkissian et al., A different approach to treatment of phenylketonuria: Phenylalanine degradation with recombinant phenylalanine ammonia lyase, Proceedings of the National Academy of Sciences (1999), vol. 96, pp. 23392344. Copyright (1999) National Academy of Sciences, U.S.A.]

(a)

Calculate the approximate percentage reduction in phenylalanine at 0 hour when the mice were injected with a dose of two units of PAL. (a) (100% 60% = ) 40 (4) (units not required) (1)

(b) Outline the effect of a dose of twenty units of PAL on phenylalanine levels. (b) no reaction immediately after injection; decreases then remains steady / constant / plateaus / between 1 hour and 2 hours; rises again at 3 hours; (2)

(c) (c)

Discuss the effectiveness of the different doses of PAL to treat PKU mice. all doses reduce amount of phenylalanine / positive correlation;

100 units reduce it the most / 2 units reduce it the least; at 2 hours level remains lower except for the 2 units of PAL / rise at 2 hours for 2 units of PAL; 2 units of PAL will be the most appropriate as less enzyme needed / 2 units of PAL reacts the fastest (0 hour); effect of 100 units lasts longer; no knowledge of possible side effects / more data on time / units / dosage required; (3) (d) Outline how the type of mutation that causes PKU differs from Klinefelters syndrome. (d) (PKU is a gene mutation while) Klinefelters is a chromosome mutation (1) (Total 7 marks) 33. (a) (a) Explain the secondary and tertiary levels of protein structure. secondary structure: [2 max] folding / pleating of polypeptides to form - pleated sheets / coiling of polypeptides to form -helix; held in place by hydrogen bonds; make structure stable; contributes to strength of fibrous proteins; provide structural role in organisms; eg -helix is keratin / -sheet is silk; tertiary structure: [2 max] 3-D shape; due to bonding between amino R-groups / residues; hydrogen bonds / disulphide bridges / sulphur bonds / ionic bonds; form globular proteins; which are soluble; eg lysozyme / enzymes; (4) (b) Outline the induced fit model for enzyme action. (b) change in shape of enzymes active site; improves fit of enzyme and substrates; brought about when the substrate molecules bind with the enzyme; enzyme changes from inactive to active form; permits some enzymes to bind with several substrates; distorts / weakens bonds in substrates; lowers activation energy: 2 max Accept any of the above if clearly explained in a labelled diagram.

23

(2) (Total 6 marks) 34. Scientists have long been concerned about the effect of heavy metals in foods that we eat. Aquatic filter feeders including bivalves, such as mussels and oysters, are especially prone to accumulation of heavy metals. Calcium is taken into bivalves through protein channels, but other nonessential elements may also be taken in. To investigate the relationship between the uptake of calcium and other elements, the bivalves Hyridella depressa and Velesunio ambiguous were placed in solutions containing ten times the normal level of calcium (Ca). The elements manganese (Mn), lead (Pb), cadmium (Cd) and cobalt (Co) were also present in the solutions at normal concentrations. The results are shown below.
1 1 8 F a c t o 6r o f i n c r e a4 s e / r e d u c t i o n 2 0 2 4
C a i n w C a a t e i rn t i s s u M n e i n Pt i bs s iu n e t Ci s d s u i en t C i s o s u i ne t i s s u e

2 0

e p

r e s s a

M V . a

e t a l m b i g u o u s

1 1 8

2 0

6 F a c t o r o f i n c r e a4 s e / r e d u c 2t i o n 0 2 4
M n i n Pt i bs s iu n e t Ci s d s u i en t C i s o s u i ne t i s s u e C a i n w C a a t e i rn t i s s u e

e t a l

[Source: Reprinted from Markich Scott J. and Jeffree Ross A., Absorption of divalent trace metals as analogues of calcium by Australian freshwater bivalves: an

explanation of how water hardness reduces metal toxicity, Aquatic Toxicology (August 1994), vol. 29, issue 34, pp. 257290, 1994 with permission from Elsevier] (a) (a) (i) Outline the effect of increasing calcium levels in the water on calcium levels in the tissue of the bivalves. (i) leads to an increase in calcium in tissues / accept numerical data (1) (ii) Outline the effect of increasing calcium levels in the water on metals other than calcium in the tissue of the bivalves. (ii) leads to a decrease in other metals in tissues (1) (b) Suggest reasons for the effects of calcium on the levels of the other metals in the tissues. (b) competitive inhibition / calcium and the other metals compete for the transport mechanism; as calcium concentration within the cell increases, uptake of the other metals is prevented; entry of calcium into cells may be linked to increased export of the other metals; (2) (c) Evaluate the implications of these results for monitoring water quality in regions where bivalves are harvested. (c) monitoring of water quality for metals can indicate amount of metals in tissue; (toxic) metals found in water will (most likely) be found in bivalves; analysis of bivalve tissue could be used as a measure of water quality; high levels of heavy metals in bivalves may poison consumers; (3) (Total 7 marks) 35. (a) (a) State the function of a named protein. name and function; eg hemoglobin carries oxygen (1) (b) Outline the significance of the primary structure in a protein. (b) order of amino acids in polypeptides; primary structure determines higher structure; primary structure reflects genetic information / is coded for by the DNA; (2)

25

(c)

Discuss the statement, Enzyme inhibitors function by binding to the active site of the enzyme competitive inhibitors are structurally similar to the substrate; competitive inhibitors bind / block active site; non-competitive inhibitors do not bind to the active site / bind somewhere else on enzyme; they function by changing the shape of the enzyme so the substrate cannot fit in to the active site; (3) (Total 6 marks)

(c)

36. The graph below shows enzyme activity plotted against temperature. What is happening at point I?

I E n z y m e a c t i v i t y / a r b i t r a r y u n i t s

e m

e C r a t u

r e

A. B. C. D.

The enzyme is being denatured. pH changes are slowing the reaction. The concentration of the substrate remains constant. The reaction is increasing in speed. (Total 1 mark)

Ans : A 37. What occurs in the induced fit model for enzyme catalysed reactions? A. There is an exact fit between a specific substrate and a specific

enzyme. B. C. D. The enzyme can change shape to accommodate the substrate. The substrate can change its shape to fit a number of enzymes. Other substrates can bind away from the active site. (Total 1 mark) Ans : B 38. (a) The table below compares prokaryotic and eukaryotic cells. Place a tick ( ) wherever the organelle is present. Organelle Nucleus Mitochondrio n Ribosomes (a) Organelle Nucleus Mitochondrion Ribosomes Award [1] for each correct column. (2) Prokaryotic Eukaryotic Prokaryotic Eukaryotic

(b)
E

(i) The graph below shows the energy changes in a reaction.

n e r g y

r o

r e s s

r e a c t i o

On the above graph draw the result you would obtain in this same reaction if an enzyme that catalyses this reaction were added.
27

(b)
E n e r g

(i)
y

1
K e :y o w r i g i t h i n e n a l r e a e c t z y m

Award [1] if drawn line is same shape as original, starting and finishing in same place and activation energy lower. (1) (ii) Explain how the enzyme produces this effect. (ii) enzyme binds to substrate; lowers activation energy; by weakening bonds; making substrate more likely to react; (3) (c) (c) Outline the process of glycolysis. one hexose sugar / glucose is converted to two 3-carbon compounds / pyruvate; at start 2 ATP are used / phosphorylation of glucose; net gain of 2 ATP / 4 ATP produced in total; production of 2NADH + H+ / reduced NAD; (3) (Total 9 marks) =39. Up to two additional marks are available for the construction of your answers. (2) (a) Explain why enzymes are substrate specific and why their activity is affected by substrate concentration. (a) specificity: (active site works as a) lock and (substrate as a) key; (enzyme has) a specific shape; active site;

(substrate has) a specific / complementary shape; (active site) fits substrate molecule / part of molecule / enzyme-substrate complex formed; activation energy lowered; substrate concentration: lower / medium concentration activity increases; directly proportional to concentration of substrate; random collisions more frequent; activity levels off / plateau; high concentration no change in activity; as all active sites fully utilised; Award [6 max] if only specificity or substrate concentration aspects addressed.

8 max

(8) (b) (b) Outline the use of restriction enzymes (endonucleases) and DNA ligase in gene technology. restriction enzyme: bacteria / E. coli has plasmids; plasmids / DNA cleaved / cut by enzyme; at specific points; leaving sticky ends; other species DNA cleaved / cut out by enzyme at same base sequence; suitable example; ligase: DNA added to plasmid / other DNA; spliced to plasmid / other DNA by enzyme; at sticky ends; recombinant plasmids / DNA inserted into (new) host cells; (new) host cells may be cloned; 6 max Award [4 max] if only restriction enzyme or ligase aspects addressed. (6) (c) (c) Type / Specific example eg amylase / salivary amylase; egprotease / pepsin; eglipase / pancreatic lipase; Substrat e starch; proteins; lipid; Product maltose; polypeptides / short peptide chains; glycerol and fatty acids; 4 max Outline the role of two enzymes found in the digestive system of humans.

Award [2 max] for all three parts correct for one enzyme and
29

[1 max] for correct enzyme and substrate or enzyme and product. (Plus up to [2] for quality) (4) (Total 20 marks)

40.

(a) (a) (i) (i)

State the name and function of Both name and function required for [1]; a fibrous protein fibrous: collagen, structural / strength / flexibility; actin / myosin, contraction of muscles; keratin, in hair; silk in spider webs; elastin in ligaments; (1) a globular protein globular: a named enzyme eg pepsin, accept general function eg speeds up reaction; hemoglobin, carries oxygen; antibodies, for immunity; albumin, osmotic balance; (1)

(ii) ii)

(b)

Annotate the graph representing an exergonic enzyme catalysed reaction.

(b)

a + E n e r g y

b ;

r e a c t a n

t s ;

a c t i v

a t i o

e n

c +

e n e r g y r e l e a s e r o d u c t s ;

t i m

r o

r e s s

r e a c t i o

One mark for each correct annotation. The marks for a+b / reactants or substrates or c+d / products can only be awarded if the label is on the horizontal parts of the line. (2) (c) Explain how end-product inhibition controls metabolic pathways. (c) example of negative feedback eg ATP inhibition of phosphofructokinase, in glycolysis; controls rate of product synthesis / amount of product produced / inhibits earlier stage / switches off pathway when too much product made; binds to enzyme but not active site / allostery / allosteric site;
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enzyme changes shape / substrate cannot bind / enzyme cannot catalyse; (3) (Total 7 marks) 41. The diagram below shows the energy levels of a reaction in the presence or absence of an enzyme. What is the best explanation of the different energy levels labelled I, II and III?

I
E n e rg y le v e l

I I
E n e r g y r e a c t a n o f t s

I I I

E P r o g r e s s o

n f

e r g

f n

r o

c t s

r e a c t i o

I A. B. C. D. Absence of an enzyme Presence of an enzyme Absence of an enzyme Presence of an enzyme

II Presence of an enzyme Absence of an enzyme Presence of an enzyme Absence of an enzyme

III Endergonic reaction Exergonic reaction Exergonic reaction Endergonic reaction

Ans : B (Total 1 mark) 42. What happens during end product inhibition of the pathway shown below?

s t a n e n z y

c e m c e m c e m c e e e e

W I X I I Y I I I Z

s t a n e n z y

s t a n e n z y

S A. B. C. D.

s t a n

Enzyme I is inhibited by substance X. Enzyme I is inhibited by substance Z. Enzyme III is inhibited by substance W. Enzyme III is inhibited by substance Y. (Total 1 mark)

Ans : B 43. Up to two additional marks are available for the construction of your answers. (2) (a) Outline the first three levels of protein structure, including the types of bonding within each and the significance of each level. (a) primary structure / level: order / sequence of amino acids; linked by peptide bonds; determines the type / function of protein / 2 and 3 structures; secondary structure / level: regular folding / beta-pleated sheets / spiralling / alpha-helices; held through hydrogen bonding; tertiary structure / level: 3-dimensional conformation of a polypeptide / protein; held with ionic bonds, hydrogen bonds, disulfide bonds / bridges and hydrophobic bonds; (must give at least two bonds) determines overall shape / a named example eg: active sites on enzymes; 5 max To receive full marks the candidate must mention each of the three levels, otherwise award [4 max]. (5) (b) Using a table, compare competitive and non-competitive inhibition
33

and give one named example of each. (b) Characteristic inhibitor: Competitive inhibition structurally / chemically very similar to substrate Non-competitive different from substrate;

site of binding: effect:

effect:

example:

effect of substrate concentration: (c) (c)

binds to different site / not active site active site / allosteric site; changes 3 structure of blocks active site enzyme / conformational change of active site; substrate cannot bind / competes with substrate / reaction not catalyzed / decreased prevents substrate enzyme binding activity; Butanedioic acid metal ions / Hg+ / Ag+ / Cu2+ (succinate) / dehydrogenase by CN inhibit enzymes propanedioic (malonate) (cytocrome acid oxidase) by breaking disulfide in the Krebs cycle / any linkages / any valid example; valid example eg Folic acid synthesis in bacteria by sulfonamide Prontosil; increasing substrate can be reduced by concentration increasing does not reduce effect of substrate concentration inhibitor;

Explain the production of antibodies. antigens stimulate an immune response; antibodies are produced in response to specific antigens; antibodies are made by B-cells / lymphocytes / plasma cells; antigen is engulfed by macrophages; antigen is presented on macrophage membrane; helper T-cells bind to antigen (on macrophage); helper T-cells are activated; helper T-cells activate B-cells; B-cells clone; into plasma cells and memory cells; plasma cells produce specific antibodies to the antigen; memory cells for long-term immunity; a faster / stronger response later;

(8) (Total 20 marks) 44. Up to two additional marks are available for the construction of your answers. (2) (a) Draw and label a diagram of the digestive system.

(a) Award [1] for each structure correctly drawn and labelled. esophagus attached to both mouth and stomach; stomach j-shaped sac attached to esophagus and u-shaped portion of small intestine; large intestine wider diameter than small intestine, attached to small intestine; pancreas leaf-shaped, in u-shaped region of small intestine with small duct connected to small intestine; liver large, triangular, to left of stomach; gall bladder small sac drawn on top of liver with tube connected to small intestine at same region as duct from pancreas; anus at end of large intestine but narrower in diameter; (4) (b) (b) Discuss factors that affect enzyme activity. at low temperatures, rate of reaction increases as temperature increases (or vice versa); more kinetic energy / faster movement of molecules means more collisions between enzyme / active site and substrate; optimum temperature is temperature at which rate of enzyme-catalyzed reaction is fastest; at high temperatures enzymes are denatured and stop working; denatured means change of structure in enzyme / protein resulting in loss of its biological properties / no longer can carry out its function; too much kinetic energy / vibrations breaks bonds that give enzyme specific shape; optimum pH is one at which rate of enzyme-catalyzed reaction is fastest; rate of reaction reduced as increase or decrease pH (from optimum); strong acids and alkalis can denature enzymes; affect (weak, ionic, hydrogen) bonds that hold enzyme in specific shape; at low substrate concentrations, as increase concentration get increase in rate of reaction; more chance of collision between substrate and enzyme / active site; at high substrate concentration, have no change in rate as increase concentration; (9)
35

all active sites occupied;

(c) (c)

Outline one industrial use of lactose. lactose intolerance high in some human populations / Asian / African / native American and Australian aboriginal populations; lactase used to produce lactose-free / low-lactose milk; lactase breaks down lactose to glucose and galactose; source of lactase is usually yeast / many sources such as bacteria, moulds; milk passed over immobilized lactase / lactase bound to inert substance; increase sweetness of milk; no need to add extra sugar in manufacture of flavoured milk drinks / frozen desserts; can add (harmless) bacterium such as L.acidophilus which has same effect on lactose as in yoghurt; 5 max (5) (Total 20 marks)

45. Inflammation of human tissues often causes pain. Cyclooxygenases (COX) are a group of enzymes that play a role in causing inflammation. Analgesics are drugs that can reduce pain. The graph below shows how increasing concentrations of the analgesic drug dipyrone, affects the activity of three different cyclooxygenases, COX-1, COX-2 and COX-3.
K E n z y m e a c tiv ity / a rb itra ry u n its 1 1 8 6 4 2 0 2 0 0 0 0 0 0 D 1 i p y 1 0 r o 1 n e 0 0 1 0 0 10 0 0 0 0 c o n c 3e n t r a t i o 0 0 e y : C O C O C O X X X - 1 - 2 - 3

[Source: Adapted from N V Chandrasekharan, et al, (2002), Proceedings of the National Academy of Sciences, USA, 99, (21), pages 1392613931]

(a)

Outline the relationship between dipyrone concentration and COX-3 activity. (a) at low dipyrone concentrations, there is no effect on enzyme function; as concentration of dipyrone increases, increased inhibition of

enzyme activity; (2)

(b) (b)

Deduce whether dipyrone is an inhibitor of COX-2. over range of concentrations in the experiment appears to have no effect on enzyme function (of COX-2); may be inhibited at concentrations higher than those used in the experiment; (2)

(c) Evaluate the potential of dipyrone as an analgesic using the data in the graph. (c) it would limit inflammation due to COX-1 and COX-3; but not COX-2; effective only at high doses; (2) (Total 6 marks) 46. Which graph shows the relationship between the substrate concentration and the rate of an enzyme controlled reaction?
A . B . R a te o f re a c tio n S c o D .

R a te o f re a c tio n

S c o C .

u n

b s t r a t e c e n t r a t i o

u n

b s t r a t e c e n t r a t i o

(Total 1 mark)

Ans : B 47. Consider the metabolic pathway shown below.

37

V WXYZ

If there is end-product inhibition, which product would inhibit which enzyme? Produc t A. B. C. D. Ans : D 48. Up to two additional marks are available for the construction of your answers. (2) (a) Draw a labelled diagram showing the structure of the digestive system. (a) Award [1] for each structure correctly drawn and labelled. esophagus attached to both mouth and stomach; stomach j-shaped sac attached to esophagus and u-shaped portion of small intestine; large intestine wider diameter than small intestine, attached to small intestine; pancreas leaf-shaped, in u-shaped region of small intestine with small duct connected to small intestine; liver large, triangular, to left of stomach; gall bladder small sac drawn on top of liver with tube connected to small intestine at same region as duct from pancreas; anus at end of large intestine but narrower in diameter; (4) (b) (b) Outline the need for enzymatic hydrolysis in the digestive process. large molecules cannot be absorbed; mechanical digestion only to break down food physically; enzymes breakdown large molecules into smaller ones (that can be absorbed); need several enzymes as they are substrate specific; enzymes speed up the rate of digestion considerably; higher speeds at low / normal body temperature; named example of enzyme; example of named enzymes action; (6) (c) Explain how the kidney prevents the body from losing important materials absorbed from the digestive system. X W W Z Enzym e 4 3 2 1 (Total 1 mark)

(c)

important that some products of digestion not lost; products in the blood stream; ultrafiltration in the glomerulus; fenestrated capillaries / podocytes; basement membrane acts as the filter; proteins too large to pass through; importance of proximal convoluted tubule; reabsorption of salts / glucose / ions / other named substance; microvilli; details of active transport; osmosis is the reabsorption of water;\ detail of osmoregulation; (8)
(Total 20 marks)

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