AQA Paper 2 - Everything You Need To Know

Photosynthesis

  • Photosynthesis Overview:

    • Occurs in two stages: light-dependent and light-independent reactions.
    • Light-dependent reactions happen first, requiring light.
    • Light-independent reactions follow, also known as the Calvin cycle.

  • Chloroplast Structure (Locations of Photosynthesis):

    • Thylakoid stacks (granum): Folded membranes containing proteins for the electron carrier chain and ATP synthase, are the place of light-dependent reactions.
    • Stroma: The fluid-filled that surrounds the granum inside of the chloroplast; here occur light-independent reactions.
    • Inner and outer membranes: control the entering and exiting substances.

Light-Dependent Reactions

  • Occurs on the thylakoid membrane (or granum).
  • Light energy and water are converted into ATP and reduced NADP.
  • Key Steps: photolysis, photoionization of chlorophyll, and chemiosmosis.
  • Photolysis (Photo-lyse):
    • "Photo" means light, and "lysis" means splitting.
    • Light energy splits water into oxygen, electrons, and protons (H^+).
    • Protons are picked up by NADP to form reduced NADP (NADPH).
    • Electrons are passed along an electron carrier chain.
    • Oxygen is either used in respiration or diffuses out through the stomata.
  • Photoionization of Chlorophyll:
    • Light energy is absorbed by chlorophyll.
    • Electrons gain energy, becoming excited and rising to a higher energy level.
    • Excited electrons leave the chlorophyll, ionizing it.
    • Energy from released electrons is used in chemiosmosis to create ATP and reduced NADP.
  • Chemiosmosis:
    • Electrons move along a series of proteins in the thylakoid membrane, releasing energy.
    • Some energy is used to pump protons (H^+) from the stroma into the thylakoid lumen, creating an electrochemical gradient (charged molecules/ions present).
    • Protons move down the electrochemical gradient back to the stroma through ATP synthase.
    • ATP synthase phosphorylates ADP into ATP.
    • NADP coenzyme picks up electrons from the electron transport chain and protons after they pass through ATP synthase, forming NADPH.

Light-Independent Reactions (Calvin Cycle)

  • Occurs in the stroma and requires enzymes (e.g., Rubisco).
  • Temperature-sensitive but doesn't require light energy directly.
  • Uses carbon dioxide, ATP, and reduced NADP from the light-dependent reactions to create a hexose sugar.
  • ATP is hydrolyzed to provide energy, and reduced NADP donates hydrogen to reduce glycerate-3-phosphate within the cycle.
  • Steps:
    • Carbon dioxide reacts with RuBP (five-carbon compound), forming an unstable six-carbon compound that splits into two molecules of glycerate-3-phosphate (GP).
    • Both GP molecules uses ATP and hydrogen from NADPH and are then reduced to two molecules of triose phosphate (TP).
    • TP: one carbon is removed, leaving five carbons.
    • Five-carbon compounds are combined to regenerate RuBP, using ATP.
    • Cycle must occur six times to create one hexose sugar (e.g., glucose, sucrose).
    • Glucose/sucrose can be converted into other organic compounds (e.g., cellulose, starch, lipids, amino acids).

Limiting Factors of Photosynthesis

  • Anything that reduces the rate of photosynthesis: light intensity, carbon dioxide concentration, or temperature.
  • Identifying Limiting Factors on a Graph:
    • Positive correlation indicates the factor on the x-axis is limiting the rate.
    • Plateau indicates another factor is limiting the rate.
  • Temperature and Enzymes:
    • Low temperatures: Lower rate due to insufficient kinetic energy and fewer successful collisions.
    • High temperatures: Enzyme denaturation.
  • Reasons for Limitation:
    • Carbon Dioxide: Reactant in the Calvin cycle.
    • Light Intensity: Needed for photolysis and photoionization.
  • Maximum Photosynthesis in Agriculture:
    • Remove limiting factors to maximize profits in crop growth.
    • Artificial lighting, heating in greenhouses (burning fuels may also produce CO_2).
    • Cost-effectiveness must be considered to offset costs with additional profit.

Aerobic Respiration

  • Four stages: glycolysis, link reaction, Krebs cycle, and oxidative phosphorylation.
  • Each stage occurs in a specific location within the cell.
  • Glycolysis:
    • Occurs in the cytoplasm.
    • Does not require oxygen.
    • Produces a small amount of ATP.
    • Glucose is phosphorylated to glucose phosphate, using two ATP molecules.
    • Glucose phosphate is converted into triose phosphate.
    • Triose phosphate is oxidized to form pyruvate, producing four ATP and reduced NAD.
    • Net gain of 2 ATP molecules (four ATP produced, two ATP used).
    • Two molecules of pyruvate and two reduced NAD are needed for the next stages.
    • Pyruvate and reduced NAD are transported into the mitochondrial matrix.
  • Link Reaction:
    • Occurs in the mitochondrial matrix.
    • Pyruvate is oxidized to acetate.
    • NAD picks up hydrogen to create reduced NAD.
    • Carbon dioxide is produced.
    • Acetate combines with coenzyme A to create acetyl coenzyme A (acetyl-CoA).
    • For every glucose molecule, two pyruvates are created, and the link reaction happens twice.
    • One glucose molecule= two acetyl-CoA, two carbon dioxides, and two reduced NAD.
  • Krebs Cycle:
    • Occurs in the mitochondrial matrix.
    • Acetyl-CoA combines with a four-carbon molecule to create a six-carbon molecule.
    • Series of redox reactions generate reduced coenzymes, a small amount of ATP, and carbon dioxide.
    • Products Per Cycle: three reduced NAD, one reduced FAD, one ATP, and two carbon dioxides.
    • For every glucose, the cycle happens twice.
  • Oxidative Phosphorylation:
    • Occurs in the inner mitochondrial membrane.
    • Most of the ATP is produced.
    • Reduced coenzymes release hydrogen, which splits into protons (H^+) and electrons (e^-).
    • Electrons are transported along the electron transfer chain, releasing energy.
    • Energy is used to transport protons (H^+) from the mitochondrial matrix into the intermembrane space, creating an electrochemical gradient.
    • Protons (H^+) move down the gradient through ATP synthase, phosphorylating ADP to create ATP.
    • Oxygen picks up electrons and protons (H^+), forming water.
    • Creates 34 ATP molecules.

Anaerobic Respiration

  • Occurs without oxygen only in the cytoplasm.
  • In plants and microbes, it produces ethanol and carbon dioxide; in animals, it produces lactate and lactic acid.
  • Reoxidizes NAD so that glycolysis can continue.
  • Glycolysis occurs because no oxygen is needed; now the pyruvate is reduced to form lactate.
  • Reduced coenzymes are reoxidized to NAD, which is then reused in glycolysis. This allows at least some ATP to be continually made.
  • Lactic acid denatures enzymes and other proteins.
  • Anaerobic respiration cannot occur for long because of the buildup of lactic acid.
  • Microbes produces ethanol and carbon dioxide.

Energy Transfer in Ecosystems (Food Webs)

  • Food webs begin with producers which are plants to make their own organic compounds through photosynthesis.
  • Energy Loss:
    • The majority of energy is lost between each trophic level through respiration and excretion.
    • Remaining energy forms the biomass.
  • Biomass:
    • Mass of carbon within the organism.
    • Dry mass.
    • Given per area.
  • Productivity Using GPP and NPP:
    • Depends on abiotic and biotic factors.
    • High productivity ecosystems have : water, light, warmth, and green plants for photosynthesis.
  • GPP (Gross Primary Production):
    • Chemical energy stored in plant biomass in a given area or volume.
    • Total energy resulting from photosynthesis.
  • NPP (Net Primary Production):
    • The GPP minus the energy lost by respiration.
    • The energy left to make biomass.
  • Consumer Net Production ("N") Formula:
    • N = I - (F + R)
      • N = Net production of consumer.
      • I = Chemical energy stored in ingested food.
      • F = Chemical energy loss to the environment in feces and urine.
      • R = Respiratory losses.
  • Units for Recording Productivity Rates: kJ {ha}^{-1} {year}^{-1}
    • kJ: Unit of energy.
    • Per unit area ( {ha}^{-1}): Standardizes results to enable environments to be compared.
    • Per year ( {year}^{-1}): Accounts for the impact of seasons.

Nutrient Cycles

  • Nitrogen Cycle

    • Nitrogen is within proteins, ATP, and nucleic acids (DNA and RNA).
    • Plants cannot gain nitrogen gas directly because it has a triple bond that they cannot break.
    • Key Processes:
      • Ammonification
      • Nitrification
      • Nitrogen fixation
      • Denitrification
    • Saprophytic nutrition and microbes are essential for those stages.
    • Cycle Steps:
      • Nitrogen gas in the atmosphere converted to ammonia by nitrogen-fixing bacteria.
        • Nitrogen-Fixing Bacteria: Directly convert nitrogen into ammonia in nodules by the Leguminous plants.
        • Free-Living Nitrogen-Fixing Bacteria: Bacteria found in the soil to fix nitrogen converts to ammonium.
      • Nitrification: Bacteria oxidizes ammonium into nitrites and then into nitrates.
      • Absorbed: Plants absorb nitrates through active transport. Animals absorb nitrates through digestion and absorption.
      • Decomposers: They are breaking down the waste to release nitrogen and can convert Ammonium for recycling in the process.
      • Denitrifying Bacteria: Will convert nitrates back into nitrogen gas.
    • Except for denitrifying bacteria, all other stages are oxidation and need oxygen.

  • Phosphorus Cycle

    • Phosphorus compounds include phosphate groups of DNA, RNA, ATP, and phospholipids in phospholipid bilayer.
    • There is no gaseous phase unlike carbon and nitrogen cycles.
    • Main source of phosphate ions is sedimentary rock.
    • Mycorrhizae:
      • Mutualistic Fungal associations spread to increase surface area for absorption in roots.
      • Plants provide carbohydrates to the fungus using photosynthesis.
    • Absorbed: Plants absorb phosphate ions through root hair cells by active transport.
    • Cycle Steps:
      • Phosphate ions are transported into the oceans or the soil from waste, deposition and decomposition.
      • Guano are bird feces rich in phosphates also add to the cycle.
      • Sedimentary Rocks are formed from phosphates due to soil compaction over time.
    • Erosion: Sedimentary rocks are eroded to release the phosphate ions back into the soil or oceans.
    • Leaching: Phosphate from fertilizers can leach into water sources or remains in the soil.

  • Fertilizers (Natural and Artificial):

    • Crops harvest removes nutrients from the cycle.
    • Fertilizers added to soils replace minerals and nutrients that are being removed when crops harvest.
    • Natural: Animal manure is cheaper but doesn't accurately contain the exact proportions of the minerals needed.
    • Artificial: Soluble chemicals contain known quantities of minerals but are inorganic, which leads to leaching and run-off in the water sources which then causes eutrophication.

  • Eutrophication (Nitrogen Fertilizer Leaching):

    • Nitrates stimulate growth of algae, blocks light.
    • Plants cannot photosynthesize and die.
    • Bacteria feed and respire on dead plant matter.
    • With bacteria thriving, oxygen gets used.
    • Animals will die without the oxygen.