7402/2 · 2 hours · 91 marks · 35% of A-Level · Topics 5 – 8
Topic 5 - Energy transfers in and between organisms
Non-cyclic photophosphorylation (the main pathway; produces ATP, reduced NADP, and O2):
Products of the light-dependent stage: ATP, reduced NADP (NADPH), O2 (by-product)
Cyclic photophosphorylation (backup pathway; only PS I involved):
"Photophosphorylation" means ATP synthesised using light energy. It is not the same as oxidative phosphorylation (which uses energy from reduced NAD/FAD in respiration). The light-dependent stage does not fix CO2 - that happens in the Calvin cycle.
The Calvin cycle takes place in the stroma of the chloroplast. It uses ATP and reduced NADP from the light-dependent stage to fix CO2 into organic molecules.
Steps of the Calvin cycle:
Limiting factors of photosynthesis:
If light intensity falls: less ATP and reduced NADP are produced, so GP cannot be reduced to GALP. Therefore GP accumulates and GALP levels fall. RuBP cannot be regenerated, so RuBP levels also fall. This question type is common in exams - track which step is affected and which intermediates build up or fall.
Glycolysis takes place in the cytoplasm. It does not require oxygen and is the first stage of both aerobic and anaerobic respiration.
Net yield per glucose: 2 ATP, 2 reduced NAD, 2 pyruvate
Link reaction takes place in the mitochondrial matrix (aerobic respiration only):
Yield per pyruvate: 1 CO2, 1 reduced NAD, 1 acetyl CoA (no ATP produced directly)
Anaerobic respiration regenerates NAD so that glycolysis can continue when oxygen is absent:
Anaerobic respiration does not produce extra ATP beyond the 2 from glycolysis. Its sole purpose is to regenerate NAD from reduced NAD so that glycolysis can continue. The net ATP yield is only 2 per glucose (compared with ~32 for aerobic respiration).
The Krebs cycle takes place in the mitochondrial matrix. Each turn processes one acetyl CoA (so runs twice per glucose molecule).
Oxidative phosphorylation takes place on the inner mitochondrial membrane. It accounts for most of the ATP produced per glucose.
"Chemiosmosis" refers specifically to the flow of H+ down its electrochemical gradient through ATP synthase. "Oxidative phosphorylation" is the broader process (electron transport chain + chemiosmosis). If O2 is absent, the electron transport chain stops, H+ gradient collapses, and ATP synthase cannot function - aerobic ATP production ceases entirely.
Approximate ATP yield per glucose:
| Stage | Location | ATP produced |
|---|---|---|
| Glycolysis | Cytoplasm | 2 ATP (net, substrate-level) |
| Link reaction | Matrix | 0 directly |
| Krebs cycle | Matrix | 2 ATP (substrate-level) |
| Oxidative phosphorylation | Inner membrane | ~28–32 ATP (majority of total) |
Productivity is the rate of primary or secondary production: measured as biomass per unit area per unit time (e.g. kJ ha-1 yr-1). Primary productivity = by producers; secondary productivity = by consumers.
Energy losses between trophic levels (~90% lost at each step):
Only ~10% of energy at one trophic level is transferred to the next. This limits the length of food chains (usually 4–5 levels).
Nitrogen cycle:
Agricultural practices to increase efficiency of energy transfer:
Nutrient cycles - nutrients recycled within natural ecosystems. Microorganisms play a vital role.
Nitrogen cycle - key processes:
Mycorrhizae: mutualistic associations between fungi and plant roots. Fungal hyphae greatly increase the surface area for absorption of water and inorganic ions (especially phosphate), which are passed to the plant. Plant provides organic carbon to the fungus.
Phosphorus cycle (outline):
Fertilisers (natural: manure, compost; artificial: ammonium nitrate, superphosphate) replace nitrates and phosphates lost by harvesting plants and removing livestock. Environmental issue: leaching - soluble ions washed into rivers/lakes → eutrophication: algal bloom → blocks light → plants die → decomposers increase → BOD rises → oxygen depletion → aquatic organisms die.
Topic 6 - Organisms respond to changes in their internal and external environments
A receptor is a cell or organ that detects a stimulus and converts its energy into a nerve impulse (electrical energy). This conversion is called transduction.
Pacinian corpuscle (example of a mechanoreceptor):
Simple responses maintaining organisms in a favourable environment:
Simple (spinal) reflex arc - protective; rapid, involuntary, stereotyped response:
The reflex bypasses conscious processing (though the brain is informed via collateral fibres). This gives a very short response time, which is protective (e.g. withdrawal from pain).
The human retina - rods vs cones:
Visual acuity depends on one-to-one connections (cones at fovea). Sensitivity at low light depends on summation (many rods share one ganglion cell). The fovea has no rods, so looking directly at a dim star makes it disappear - use peripheral vision to keep it visible.
Myogenic stimulation: the heart generates its own rhythmic electrical impulses - it does not require nerve input to beat (intrinsic control). This originates in the sinoatrial node (SAN).
Extrinsic control - the cardiovascular centre in the medulla oblongata modifies heart rate via the autonomic nervous system:
Receptors providing feedback to the cardiovascular centre:
Do not confuse myogenic (intrinsic) rhythm with extrinsic control. The SAN sets the basic rate; the autonomic nervous system adjusts it. A transplanted heart still beats because SAN activity is intrinsic - but it cannot speed up quickly during exercise without nerve control.
Resting potential (−70 mV): the inside of the neurone is negative relative to the outside. Maintained by:
Action potential (all-or-nothing; only fires if stimulus exceeds threshold of ~−55 mV):
Refractory period: Na+ channels remain inactivated; another action potential cannot be generated immediately. This ensures unidirectional transmission (the impulse cannot travel backwards) and limits the maximum firing frequency.
The all-or-nothing principle means stimulus intensity is coded by frequency of action potentials, not by the size of each impulse. A stronger stimulus produces more impulses per second, not larger ones.
Cholinergic synapse (events at an excitatory synapse using acetylcholine):
Inhibitory synapses: release inhibitory neurotransmitters (e.g. GABA) that open Cl- or K+ channels on the post-synaptic membrane → the membrane becomes hyperpolarised (more negative, e.g. −80 mV) → threshold is harder to reach → action potential less likely. Inhibitory and excitatory post-synaptic potentials summate; the net effect determines whether an action potential fires.
Neuromuscular junction (NMJ) vs cholinergic synapse:
Sarcomere structure (the contractile unit, between two Z lines):
Sliding filament mechanism:
Relaxation: Ca2+ pumped back into the sarcoplasmic reticulum (active transport; requires ATP) → tropomyosin returns → myosin-binding sites covered → no cross-bridges → sarcomere lengthens.
ATP has two roles in muscle contraction: (1) its hydrolysis by myosin ATPase powers the detachment of the myosin head after the power stroke; (2) it powers the active transport of Ca2+ back into the sarcoplasmic reticulum during relaxation. Rigor mortis occurs after death because ATP is depleted - myosin heads cannot detach from actin.
Phosphocreatine (PCr): a short-term store of phosphate in muscle. At the onset of intense exercise, when ATP demand exceeds supply from respiration: PCr + ADP → creatine + ATP (catalysed by creatine kinase). This rapidly regenerates ATP but stores last only ~10 seconds. PCr is resynthesised during recovery using ATP from aerobic respiration.
Slow and fast skeletal muscle fibres:
Antagonistic muscle pairs: muscles work in antagonistic pairs against an incompressible skeleton. When one muscle contracts (agonist), the other relaxes (antagonist). Example: biceps (flexor) and triceps (extensor) at the elbow - biceps contracts to flex; triceps contracts to extend. Muscles can only pull, not push - they generate force only when shortening.
Homeostasis is the maintenance of a stable internal environment (temperature, blood glucose, water potential) within narrow limits, despite changes in the external environment.
Negative feedback loop: receptor detects deviation from the set point → control centre (e.g. hypothalamus) processes signal → effectors act to reverse the change → receptor detects return to set point → effectors switched off.
Thermoregulation in mammals (hypothalamus acts as thermostat):
Too hot:
Too cold:
Blood glucose is monitored by alpha (α) and beta (β) cells in the islets of Langerhans of the pancreas.
High blood glucose (e.g. after a meal):
Low blood glucose (e.g. during fasting or exercise):
Adrenaline (released from the adrenal medulla in response to stress or exercise):
Second messenger model (for adrenaline and glucagon - both use cAMP as second messenger):
The hormone cannot enter the cell (too large/hydrophilic), so cAMP acts as the intracellular signal. This system amplifies the signal: one hormone molecule → many adenylate cyclase molecules activated → many cAMP molecules → many enzyme molecules activated.
Glucagon has no effect on muscle because muscle cells lack glucagon receptors. Muscle cannot release glucose back into the blood (it lacks glucose-6-phosphatase). Only the liver can export glucose during glycogenolysis and gluconeogenesis. Adrenaline, however, does act on muscle (muscle cells have adrenaline receptors) to stimulate glycogenolysis for local energy use.
Nephron regions and their roles:
Ultrafiltration:
Selective reabsorption (PCT):
Loop of Henle (countercurrent multiplier):
Osmoregulation (ADH):
Auxin (IAA) and phototropism (Cholodny-Went hypothesis):
Gravitropism (geotropism):
Gibberellins:
IAA promotes growth in shoots but inhibits growth in roots (at the same concentration). This is because root cells are more sensitive to IAA; the concentration that is optimal for shoot elongation is supraoptimal (inhibitory) for roots. Do not confuse auxin with gibberellin: auxin drives tropisms; gibberellin drives stem elongation and seed germination.
Topic 7 - Genetics, populations, evolution and ecosystems
Epistasis: one gene masks or suppresses the expression of another gene at a different locus. The masking gene is epistatic; the masked gene is hypostatic. This produces modified dihybrid ratios (e.g. 9:3:3:1 becomes 9:7, 12:3:1, 9:3:4, or 15:1 depending on the type of epistasis).
F2 expected ratios: monohybrid (Aa × Aa) → 3 dominant : 1 recessive; dihybrid (AaBb × AaBb, unlinked) → 9:3:3:1.
Chi-squared test (χ2): tests whether observed ratios differ significantly from expected ratios (e.g. 3:1 or 9:3:3:1).
If χ2 is less than the critical value: difference is not significant; due to chance; the null hypothesis (data fits the expected ratio) is accepted. If greater than the critical value: difference is significant; data does not fit the expected ratio.
The Hardy-Weinberg principle states that, in a population where certain conditions are met, allele frequencies do not change between generations.
Conditions for Hardy-Weinberg equilibrium:
Application: if the frequency of a recessive phenotype (q2) is known, calculate q = √q2, then p = 1 − q, and find carrier (heterozygous) frequency = 2pq.
If allele frequencies change between generations, one or more Hardy-Weinberg conditions must be violated and evolution is occurring. This makes H-W a useful null hypothesis for detecting selection or other evolutionary forces in real populations.
Natural selection:
Evolution is defined as a change in allele frequency in a gene pool over generations.
Sources of genetic variation:
Genetic drift: random changes in allele frequency due to chance sampling effects. Most significant in small populations (where chance events have a proportionally larger effect). An allele may be lost entirely or become fixed regardless of whether it is advantageous. Genetic drift is not directional - unlike natural selection. Example: the founder effect (a small group colonises a new area; limited gene pool represents chance allele frequencies of the founders).
Speciation = the formation of new species through the development of reproductive isolation.
Allopatric speciation:
Sympatric speciation: reproductive isolation within the same geographic area (due to ecological niche differences, seasonal breeding differences, behavioural isolation, or polyploidy in plants).
A community = all the populations of different species in an area. An ecosystem = community + its non-living (abiotic) environment.
Within a habitat, each species occupies a niche - its role and position in the ecosystem, determined by all the biotic and abiotic conditions to which it is adapted (what it eats, when it is active, where it lives, etc.). Two species cannot occupy exactly the same niche indefinitely (competitive exclusion).
Biotic factors (living): predation, competition, disease, parasitism, mutualism. Abiotic factors (non-living): temperature, light intensity, pH, water availability, mineral concentration, oxygen levels.
Population size is determined by:
Succession: progressive change in species composition over time as organisms modify their environment.
Each seral stage modifies the abiotic environment (adds organic matter, alters microclimate, reduces hostility), making it more suitable for other species. The new species may in turn make conditions less suitable for the previous pioneer species. Succession continues until a stable climax community is reached. Conservation of habitats frequently involves management of succession (e.g. mowing, coppicing, controlled burning) to maintain an earlier seral stage with greater biodiversity than the climax.
Estimating population size:
Assumptions of mark-release-recapture:
Both in-situ and ex-situ conservation are needed. In-situ is preferred because it maintains natural selection and ecological relationships; ex-situ is a safety net when in-situ is not viable. Maintaining biodiversity is important for food security, medicine (e.g. drug discovery), gene pool preservation for selective breeding, and ecosystem services.
Topic 8 - The control of gene expression
A gene mutation is a change to the base sequence of DNA. Mutations occur spontaneously during DNA replication; the rate is increased by mutagenic agents (ionising radiation, UV light, certain chemicals such as base analogues and intercalating agents).
Frame-shift mutations (addition/deletion of non-multiples of 3) are usually more severe than substitutions because every codon after the mutation is altered. Substitutions affect only a single codon - and may have no effect at all if the new codon codes for the same amino acid (degenerate code).
Cell differentiation is the process by which an unspecialised cell becomes structurally and functionally specialised. All cells in an organism contain the same DNA; different cells express different genes (differential gene expression).
Induced pluripotent stem cells (iPSCs): adult somatic cells reprogrammed back to a pluripotent state by introducing specific transcription factors (Yamanaka factors). Avoids the ethical issues associated with destroying embryos. Potential for patient-matched cell therapies (low rejection risk).
Therapeutic uses of stem cells: bone marrow transplants (haematopoietic stem cells) to treat leukaemia; potential future applications include replacing damaged cardiac tissue, neural repair in spinal cord injury, and generating insulin-secreting β cells for type 1 diabetes. Ethical issues surround the destruction of embryos to obtain pluripotent cells.
Transcription factors: proteins that bind to specific DNA sequences (promoter or enhancer regions) to activate or inhibit transcription. They control which genes are expressed in a given cell.
Example: oestrogen (a steroid hormone) diffuses through the cell membrane → binds to an intracellular receptor → the hormone-receptor complex enters the nucleus and acts as a transcription factor → activates transcription of target genes.
Epigenetics: heritable changes in gene expression that do not involve changes to the DNA base sequence itself.
Epigenetic changes can be influenced by environmental factors: diet, lifestyle, stress, and toxins can alter methylation and acetylation patterns. Some epigenetic marks are heritable across cell divisions.
The lac operon (prokaryotic gene regulation in E. coli):
The operon contains structural genes lacZ, lacY, and lacA encoding enzymes for lactose metabolism, controlled by a single promoter and operator.
Catabolite repression (glucose effect):
RNA interference (RNAi): in eukaryotes (and some prokaryotes), small double-stranded RNA molecules (siRNA or miRNA) can inhibit translation of specific mRNA sequences. The siRNA binds to complementary mRNA → the mRNA is cleaved and degraded by the RISC complex → protein is not produced. RNAi is a natural mechanism for gene regulation and protection against viruses; it is also exploited as a research tool to silence specific genes.
Gene expression and cancer:
Oestrogen and breast cancer: increased oestrogen concentrations can stimulate the transcription of genes that promote cell proliferation in breast tissue. Some breast cancers have oestrogen receptors; treatments such as tamoxifen block oestrogen receptor activity to slow tumour growth.
Producing DNA fragments - three methods:
Amplifying DNA fragments:
Recombinant DNA technology:
PCR (polymerase chain reaction) exponentially amplifies a specific DNA target sequence:
Each cycle doubles the number of target copies; after 30 cycles, approximately 109 copies are produced.
Gene therapy:
Delivery methods:
Ethical issues in gene technology: somatic gene therapy is generally accepted; germ-line raises concerns about consent (unborn individuals cannot consent), unknown long-term effects, and "designer baby" implications. GM crops raise issues about biodiversity, corporate control of food supply, and ecological effects of gene flow to wild relatives.
Genome projects and sequencing:
DNA probes and personalised medicine: