(a) (i) Explain the factors affecting enzyme activity. (10 marks) (ii) Describe the mechanism of enzyme action. (10 marks) (b)…

(a)(i) Factors affecting enzyme activity (10 marks)

• Substrate concentration: at low concentration the rate rises with substrate, and at high concentration it levels off at Vmax, when all enzyme molecules are saturated, giving a hyperbolic curve (Michaelis-Menten). Km, the substrate concentration at half Vmax, measures the affinity of the enzyme.
• Enzyme concentration: with excess substrate, rate is directly proportional to enzyme concentration.
• Temperature: rate roughly doubles for a 10 °C rise (Q₁₀ about 2) up to an optimum (about 35 to 40 °C for many enzymes), and above it the enzyme is denatured and activity falls sharply. Low temperature slows but does not destroy enzymes.
• pH: each enzyme has an optimum pH (pepsin about 2, salivary amylase about 6.8, trypsin about 8), giving a bell-shaped curve, since pH alters the ionisation of the active site and the shape of the protein.
• Inhibitors: competitive inhibitors resemble the substrate and raise Km without changing Vmax, non-competitive inhibitors lower Vmax, and irreversible inhibitors (heavy metal ions, poisons) bind permanently.
• Activators and cofactors: metal ions (Mg²⁺, Zn²⁺, Mn²⁺) and coenzymes are needed for activity of many enzymes.
• Products and regulators: accumulation of the product, allosteric effectors and feedback inhibition change the rate, and radiation, high salt and water content also affect it.

(a)(ii) Mechanism of enzyme action (10 marks)

Enzymes are biological catalysts that speed up reactions by lowering the activation energy, without changing the equilibrium or being consumed. The enzyme's active site, a cleft made of a few amino acid residues, binds the substrate to form an enzyme-substrate complex (ES), which goes to the enzyme-product complex and then releases the product: E + S ⇌ ES → EP → E + P.

Models of binding:

• Lock-and-key (Fischer, 1894): the substrate fits rigidly into an active site of complementary shape.
• Induced fit (Koshland, 1958): the active site is flexible and changes shape after the substrate binds, giving a closer fit.

How catalysis is achieved:

• Proximity and orientation: the substrates are brought close together in the correct orientation.
• Strain and stabilisation of the transition state: the enzyme binds the transition state more tightly than the substrate, distorting bonds.
• Acid-base catalysis: amino acid side chains donate or accept protons.
• Covalent catalysis: a temporary covalent intermediate forms with a residue.
• Metal ion catalysis: a metal or cofactor stabilises charges or takes part in electron transfer.

For example, in chymotrypsin a serine-histidine-aspartate triad forms an acyl-enzyme intermediate to hydrolyse peptide bonds.

(b)(i) Acid rain (5 marks)

Acid rain is rain, snow or dry deposition with a pH below 5.6, the pH of normal rain in equilibrium with atmospheric CO₂. It arises from sulphur dioxide and nitrogen oxides, released by coal-burning power plants, smelters and vehicles, which are oxidised in the atmosphere to sulphuric and nitric acids. Effects: acidification of lakes and death of fish, leaching of calcium and magnesium from soil and release of toxic aluminium, damage to forests and crops, and corrosion of buildings and marble monuments. Control: flue gas desulphurisation, low-sulphur fuel, catalytic converters and liming of lakes.

(b)(ii) Biocide as a pollutant (5 marks)

Biocides, such as insecticides, herbicides and fungicides, are chemicals that kill living organisms. They become pollutants because they are spread beyond the target through drift, run-off and leaching into soil, water and air. Persistent ones (DDT, BHC, aldrin) are not biodegradable, are fat-soluble, and accumulate in tissues and are magnified along food chains (DDT thinned the eggshells of birds of prey). They kill non-target organisms such as bees and natural enemies, produce resistant pests, contaminate groundwater and food, and harm health (cancer, endocrine disruption; endosulfan). Control is by integrated pest management, biopesticides and bans on persistent chemicals (Stockholm Convention, 2001).

(b)(iii) Photochemical smog (5 marks)

Photochemical smog is a brownish haze that forms in warm, sunny, still air over cities with heavy traffic, as in Los Angeles. The primary pollutants are nitrogen oxides and volatile organic compounds (hydrocarbons) from vehicle exhaust. Sunlight splits NO₂ into NO and atomic oxygen, which combines with O₂ to make ozone; hydrocarbons react with NO and O₃ to form peroxyacetyl nitrate (PAN), aldehydes and other oxidants. Effects: eye irritation, respiratory illness, damage to leaves of crops and trees (bleaching and necrosis), and cracking of rubber. It differs from the sulphurous smog of London, which is a reducing type. Control is by catalytic converters and emission standards.

(c)(i) Seed dormancy and its regulation (8 marks)

Seed dormancy is the failure of a viable seed to germinate even under favourable moisture, temperature and oxygen. It ensures germination at a suitable season and spreads it over time.

Causes:

• Hard, impermeable seed coats (legumes, Cassia), or coats that resist the embryo's growth or exclude oxygen.
• An immature (rudimentary) embryo, as in orchids and Fraxinus.
• Physiological dormancy from germination inhibitors, such as abscisic acid, phenolics and coumarin, which may be in the coat or fruit pulp, and a need for after-ripening.
• Light requirement (photoblastic seeds such as lettuce, through phytochrome) or a temperature requirement.

Regulation. The balance between ABA, which maintains dormancy, and gibberellins, which promote germination, is central; transcription factors ABI3 and ABI5 and the gene DOG1 act in it. Light acts through phytochrome, and low temperature (stratification), nitrate, ethylene and smoke compounds lower ABA or raise GA sensitivity. Dormancy is broken by scarification (mechanical or with sulphuric acid), stratification at 0 to 5 °C, leaching of inhibitors, light, and treatment with GA₃, KNO₃ or thiourea.

(c)(ii) Biochemical changes during seed germination (7 marks)

• Imbibition of water rehydrates the seed, followed by a lag phase and then radicle emergence, and respiration rises sharply, with repair of mitochondria and more ATP.
• Reserves are mobilised by hydrolytic enzymes. Gibberellin, released by the embryo, induces alpha-amylase in the aleurone layer (as in barley), and starch is converted to maltose and glucose. Proteases break proteins into amino acids, lipases break fats into fatty acids and glycerol, and in oily seeds the glyoxylate cycle (isocitrate lyase, malate synthase) converts fat to sugar. Phytase releases phosphate, calcium and magnesium.
• These soluble products move to the embryo, where new proteins, RNA and DNA are made, partly from stored mRNA, and cell division and expansion begin.
• The level of ABA falls, and gibberellins and cytokinins rise.
• Dry weight of the seed falls at first, because of respiration, and rises when the seedling begins photosynthesis.