Topic 5 - Energy transfers in and between organisms
5.1 Chloroplasts and the light-dependent reactions
Non-cyclic photophosphorylation (the main pathway; produces ATP, reduced NADP, and O2):
- Light absorbed by PSII; chlorophyll is photoionised: electrons are emitted from chlorophyll
- Photolysis of water: 2H2O → 4H+ + 4e- + O2; electrons replace those lost from PSII; O2 released as a by-product
- Electrons pass along the electron transport chain; energy released pumps H+ from the stroma into the thylakoid lumen (chemiosmosis)
- H+ flow back through ATP synthase (from lumen to stroma) → ATP formed (photophosphorylation)
- Light absorbed by PSI; chlorophyll is photoionised again: electrons emitted at a higher energy level
- Electrons combine with H+ and NADP+ → reduced NADP (catalysed by NADP reductase)
Products of the light-dependent stage: ATP, reduced NADP (NADPH), O2 (by-product)
Cyclic photophosphorylation (backup pathway; only PS I involved):
- Electrons from PS I cycle back to PS I via the electron transport chain
- Only ATP is produced; no reduced NADP and no photolysis (no O2)
- Occurs when NADP is unavailable (already fully reduced) but ATP is still needed
"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.
5.2 The Calvin cycle (light-independent reactions)
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:
- CO2 combines with RuBP (5C) → unstable 6C intermediate → 2 × GP (3C); catalysed by RuBisCO
- GP reduced to GALP using ATP + reduced NADP from the light-dependent stage
- Some GALP exported from the cycle to synthesise organic molecules (glucose, starch, amino acids, fatty acids)
- Most GALP (5 out of every 6 molecules) used to regenerate RuBP using ATP
Limiting factors of photosynthesis:
- Light intensity: limits rate of ATP and reduced NADP production in the light-dependent stage; at low light intensity GP accumulates, GALP and RuBP fall
- CO2 concentration: limits rate of CO2 fixation (the RuBisCO step); at low [CO2] RuBP accumulates, GP and GALP fall
- Temperature: affects enzyme activity (RuBisCO and other Calvin cycle enzymes); denaturation above optimum
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.
5.3 Glycolysis and the link reaction
Glycolysis takes place in the cytoplasm. It does not require oxygen and is the first stage of both aerobic and anaerobic respiration.
- Glucose (6C) phosphorylated to hexose bisphosphate using 2 ATP (phosphorylation activates the molecule)
- Hexose bisphosphate split into 2 × triose phosphate (3C)
- Each triose phosphate oxidised to pyruvate (3C): 2 reduced NAD produced and 4 ATP generated (substrate-level phosphorylation)
Net yield per glucose: 2 ATP, 2 reduced NAD, 2 pyruvate
Link reaction takes place in the mitochondrial matrix (aerobic respiration only):
- Pyruvate (3C) decarboxylated and dehydrogenated → acetyl CoA (2C) + CO2
- NAD reduced to reduced NAD
- Catalysed by the pyruvate dehydrogenase complex
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).
5.4 Krebs cycle and oxidative phosphorylation
The Krebs cycle takes place in the mitochondrial matrix. Each turn processes one acetyl CoA (so runs twice per glucose molecule).
- Acetyl CoA (2C) combines with oxaloacetate (4C) → citrate (6C)
- Citrate is decarboxylated and dehydrogenated in a series of steps → oxaloacetate (4C) regenerated
- Per turn: 3 reduced NAD, 1 reduced FAD, 1 ATP (substrate-level), 2 CO2
Other respiratory substrates: glucose is not the only substrate. The breakdown products of lipids (glycerol and fatty acids) and of amino acids can also enter the respiratory pathway and feed into the Krebs cycle, releasing more energy per gram in the case of lipids.
Oxidative phosphorylation takes place on the inner mitochondrial membrane. It accounts for most of the ATP produced per glucose.
- Reduced NAD and reduced FAD donate electrons to the electron transport chain
- Electrons pass along the chain (complexes I, II, III, IV); energy released at each step
- Energy used to pump H+ from the matrix to the intermembrane space (against concentration gradient)
- H+ diffuse back through ATP synthase (chemiosmosis) → ADP + Pi → ATP
- At the end of the chain: electrons + H+ + O2 → H2O; oxygen is the final electron acceptor
"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) |
5.5 Energy and ecosystems
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):
- Respiration: heat energy lost to surroundings
- Uneaten material: parts of organisms not consumed
- Undigested material: lost in faeces (egestion)
- Excretion: energy lost in urine and other nitrogenous waste (distinct from egestion)
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:
- Simplifying food webs: monocultures and removal of competing organisms (weeds, pests) reduce energy losses to non-human food chains; more energy available to the human crop
- Reducing respiratory losses: housing livestock indoors (controlled temperature); restricting movement; selective breeding for rapid growth; all reduce energy lost to respiration within the human food chain
- Fertilisers: replace minerals removed by harvest; increase plant growth; risk of eutrophication if leached into water
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):
- Phosphate ions in soil taken up by plants; passed to consumers through feeding
- Decomposers break down organic matter → inorganic phosphate returned to soil
- Phosphate can be locked in rocks (sedimentary); released by weathering over long timescales
- Leaching: soluble phosphate washed from soil into waterways → eutrophication
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
6.1 Stimuli, receptors and nervous communication
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):
- Concentric layers of connective tissue (lamellae) surround a sensory neurone ending
- Pressure deforms the lamellae, which stretch the neurone membrane
- Stretch-mediated Na+ channels open → Na+ enters → generator potential (local depolarisation)
- If the generator potential reaches the threshold → an action potential is triggered in the sensory neurone
Simple responses maintaining organisms in a favourable environment:
Simple (spinal) reflex arc - protective; rapid, involuntary, stereotyped response:
- Receptor detects stimulus → generator potential → action potential in sensory neurone
- Impulse travels to spinal cord → sensory neurone synapses with relay (interneurone) in dorsal horn
- Relay neurone synapses with motor neurone
- Motor neurone carries impulse to effector (muscle or gland) → 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.
6.2 Control of heart rate
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).
- SAN (in the right atrial wall) generates a wave of electrical excitation → spreads across both atria → atria contract
- Impulse reaches the atrioventricular node (AVN), which introduces a brief delay (allows atria to finish emptying)
- Impulse passes down the bundle of His (Purkyne fibres) in the interventricular septum → spreads through ventricular walls from the apex upward → ventricles contract
Extrinsic control - the cardiovascular centre in the medulla oblongata modifies heart rate via the autonomic nervous system:
Receptors providing feedback to the cardiovascular centre:
- Chemoreceptors: in the aortic arch, carotid bodies, and medulla. Detect changes in blood CO2, O2, and pH. Rising CO2 / falling pH → increased heart rate signal.
- Pressure receptors (baroreceptors): in the aortic arch and carotid sinus. Detect blood pressure. High pressure → increased parasympathetic impulses → heart rate decreases (and vice versa).
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.
6.3 Nerve impulses and synapses
Resting potential (−70 mV): the inside of the neurone is negative relative to the outside. Maintained by:
- Na+/K+ ATPase actively pumps 3 Na+ out and 2 K+ in per cycle
- K+ leak channels allow K+ to diffuse back out down its concentration gradient
- Net result: more positive ions outside than inside → inside is negative
Action potential (all-or-nothing; only fires if stimulus exceeds threshold of ~−55 mV):
- Depolarisation: voltage-gated Na+ channels open; Na+ rushes in; inside becomes positive (reaches ~+40 mV)
- Repolarisation: Na+ channels inactivate; voltage-gated K+ channels open; K+ rushes out; inside returns toward −70 mV
- Hyperpolarisation: K+ channels remain briefly open; slight overshoot below −70 mV
- K+ channels close; Na+/K+ pump restores resting potential
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.
Factors affecting conduction speed: myelination (saltatory conduction is faster than continuous conduction); axon diameter (wider axons conduct faster, as there is less resistance to ion flow); and temperature (higher temperature speeds ion diffusion and raises the rate, up to the point of denaturation).
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):
- Action potential arrives at the pre-synaptic knob → voltage-gated Ca2+ channels open → Ca2+ enters
- Ca2+ causes synaptic vesicles to fuse with the pre-synaptic membrane → ACh released by exocytosis
- ACh diffuses across the synaptic cleft → binds to ligand-gated Na+ channels on the post-synaptic membrane
- Na+ channels open → depolarisation → new action potential generated (if threshold is reached)
- Acetylcholinesterase (in the cleft) hydrolyses ACh → choline + acetate; response ends; cleft cleared
- Choline taken back into the pre-synaptic knob and recycled into ACh (using acetyl CoA)
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:
6.4 Skeletal muscle contraction
Sarcomere structure (the contractile unit, between two Z lines):
Sliding filament mechanism:
- Action potential arrives at the neuromuscular junction; ACh released; T-tubule membrane depolarised
- Ca2+ released from the sarcoplasmic reticulum into the sarcoplasm
- Ca2+ binds troponin → conformational change → tropomyosin displaced → myosin-binding sites on actin exposed
- Myosin head (cocked, with ADP + Pi bound) attaches to actin → cross-bridge formed
- Power stroke: Pi then ADP released → myosin head pivots → actin filament pulled toward M line → sarcomere shortens
- ATP binds to myosin head → cross-bridge detaches
- Myosin ATPase hydrolyses ATP → ADP + Pi; myosin head recocked to original position
- Cycle repeats while Ca2+ and ATP are present
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.
6.5 Homeostasis and negative feedback
Homeostasis is the maintenance of a stable internal environment within restricted limits, despite changes in the external environment, through physiological control systems.
Why it matters:
- A stable core temperature and a stable blood pH keep enzymes working near their optimum; extremes denature enzymes or slow reaction rates, disrupting metabolism.
- A stable blood glucose concentration ensures a reliable respiratory substrate for ATP production and maintains the water potential of the blood (preventing osmotic damage to cells).
Negative feedback restores a system to its original (set point) level: a receptor detects a deviation → a control centre (e.g. the hypothalamus) coordinates a response → effectors act to reverse the change → the return to the set point is detected and the effectors are switched off.
Possessing separate mechanisms that control departures in different directions from the set point (one to raise the level, a different one to lower it) gives a greater degree of control than a single mechanism could.
Positive feedback amplifies a change away from the original level rather than reversing it (e.g. the surge in events during an action potential, or oxytocin during labour). It is not used to maintain a stable internal environment.
6.6 Blood glucose regulation and diabetes
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):
- β cells secrete insulin
- Insulin binds to receptors on liver, muscle, and adipose cells
- More glucose transporter proteins inserted into cell membranes → increased glucose uptake
- Glycogenesis: glucose → glycogen (stored in liver and muscle)
- Increased cellular respiration; increased fat synthesis
- Blood glucose falls
Low blood glucose (e.g. during fasting or exercise):
- α cells secrete glucagon
- Glucagon binds to receptors on liver cells only
- Glycogenolysis: glycogen → glucose
- Gluconeogenesis: amino acids, lactate, and glycerol converted to glucose
- Blood glucose rises
Adrenaline (released from the adrenal medulla in response to stress or exercise):
- Binds to receptors on liver (and muscle) cell surfaces
- Activates enzymes that convert glycogen → glucose (glycogenolysis) → rapid rise in blood glucose for "fight or flight"
Second messenger model (for adrenaline and glucagon - both use cAMP as second messenger):
- Hormone (first messenger) binds to a G-protein coupled receptor on the cell surface
- Receptor activates adenylate cyclase (via G protein) in the cell membrane
- Adenylate cyclase converts ATP → cyclic AMP (cAMP) inside the cell
- cAMP activates protein kinase A, which phosphorylates target enzymes
- Phosphorylation activates glycogen phosphorylase (breaks down glycogen) and inhibits glycogen synthase → blood glucose rises
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.
6.7 Kidney structure and osmoregulation
Nephron regions and their roles:
- Bowman's capsule / glomerulus: ultrafiltration
- Proximal convoluted tubule (PCT): selective reabsorption of all glucose, amino acids, and most water
- Loop of Henle: creates an osmotic gradient in the medulla (countercurrent multiplier)
- Distal convoluted tubule (DCT): fine adjustment of ion and water balance; responds to aldosterone and ADH
- Collecting duct: variable water reabsorption regulated by ADH
Ultrafiltration:
- Afferent arteriole is wider than the efferent arteriole → high hydrostatic pressure in the glomerular capillary
- Small molecules forced through the fenestrated endothelium, basement membrane, and podocyte foot processes into Bowman's capsule
- Filtrate contains: water, glucose, urea, amino acids, ions
- Retained in blood: red blood cells, large proteins (too large to pass through the basement membrane)
Selective reabsorption (PCT):
- All glucose and amino acids reabsorbed by co-transport with Na+ (secondary active transport)
- Na+/K+ ATPase on basolateral surface maintains low [Na+] inside cell; Na+ diffuses in with glucose
- PCT cells have microvilli (brush border) to increase surface area; many mitochondria for ATP supply
- Most water reabsorbed by osmosis
Loop of Henle (countercurrent multiplier):
- Descending limb: permeable to water, impermeable to ions; water leaves by osmosis → filtrate becomes more concentrated
- Ascending limb: impermeable to water; Na+ and Cl- actively pumped out → medullary interstitium becomes increasingly concentrated
- Creates a steep osmotic gradient (low water potential) in the medulla → concentrated urine possible
Osmoregulation (ADH):
- Osmoreceptor cells in the hypothalamus detect blood water potential
- Low water potential (dehydration): more ADH released from the posterior pituitary; collecting duct becomes more permeable to water (more aquaporin water channels inserted); more water reabsorbed; concentrated urine produced
- High water potential: less ADH; fewer aquaporins; more dilute urine produced
6.8 Plant responses
Auxin (IAA) and phototropism (Cholodny-Went hypothesis):
- IAA produced in the shoot tip
- Unilateral light causes IAA to migrate laterally to the shaded side
- Higher IAA concentration on shaded side promotes cell elongation (IAA activates proton pumps → cell wall acidifies and loosens → cells elongate)
- Shaded side elongates more than the illuminated side → shoot bends toward the light
Gravitropism (geotropism):
- Shoots: negative gravitropism (grow away from gravity); roots: positive gravitropism (grow toward gravity)
- Roots are more sensitive to IAA than shoots; high IAA concentration on the lower side inhibits growth on that side; root bends downward
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. The spec requires only the effect of IAA on cell elongation to explain phototropism and gravitropism.
Topic 7 - Genetics, populations, evolution and ecosystems
7.1 Inheritance
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.
7.2 Hardy-Weinberg principle
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:
- Large population size (minimises genetic drift)
- Random mating (no sexual selection)
- No natural selection (all genotypes equally fertile and viable)
- No mutation (no new alleles introduced)
- No migration (no gene flow in or out)
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.
7.3 Evolution and speciation
Natural selection:
- Variation exists in a population (from mutations and sexual reproduction)
- A selection pressure (predation, disease, climate) favours individuals with certain phenotypes
- Favoured individuals are more likely to survive and reproduce (differential reproduction)
- Advantageous alleles passed to more offspring → allele frequency increases over generations
Evolution is defined as a change in allele frequency in a gene pool over generations.
Sources of genetic variation:
- Gene mutation: random, heritable changes to DNA base sequences; produce new alleles
- Chromosome mutation: non-disjunction during meiosis produces gametes with an abnormal number of chromosomes (e.g. trisomy), creating new combinations of genetic material
- Meiosis: independent assortment of chromosomes produces new combinations of alleles; crossing over during prophase I creates recombinant chromosomes
- Random fertilisation: any two gametes may fuse, further shuffling allele combinations
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:
- A geographical barrier (mountain range, sea, river) separates a population into two sub-populations
- Sub-populations evolve independently: different selection pressures act; genetic drift also occurs
- Allele frequencies diverge; different mutations accumulate
- Reproductive isolation develops; if the barrier is removed, the two groups can no longer interbreed to produce fertile offspring
- New species formed
Sympatric speciation: reproductive isolation within the same geographic area (due to ecological niche differences, seasonal breeding differences, behavioural isolation, or polyploidy in plants).
7.4 Ecosystems, succession and conservation
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:
- Birth rate (natality) and death rate (mortality)
- Immigration (individuals entering) and emigration (individuals leaving)
- Carrying capacity (K): maximum stable population size the environment can support; set by availability of resources
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:
- Mark does not affect survival, behaviour, or probability of recapture
- Sufficient time for marked individuals to randomly mix back into population
- No significant immigration, emigration, births, or deaths between the two samples
- Marks are not lost between capture events
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
8.1 Gene mutations
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).
8.2 Stem cells and cell differentiation
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.
8.3 Epigenetics and gene regulation
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.
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.
8.4 Gene technologies
Producing DNA fragments - three methods:
Amplifying DNA fragments:
- In vitro (PCR): rapid amplification outside cells (see below)
- In vivo: DNA fragment inserted into a vector → vector transformed into host cells (bacteria or yeast) → host cells cultured; replicate and produce millions of copies of the recombinant DNA
Recombinant DNA technology:
- DNA fragment produced (cDNA, restriction enzyme cut, or gene machine)
- Fragment ligated into a vector using DNA ligase; promoter and terminator regions added flanking the gene so it is expressed in the host
- Vector (plasmid or viral) introduced into host cells by transformation (electroporation, heat shock, or liposomes)
- Marker genes (antibiotic resistance or fluorescent markers) used to identify GM cells that have taken up the vector
- Transgenic organism produces the desired protein (e.g. human insulin from bacteria)
PCR (polymerase chain reaction) exponentially amplifies a specific DNA target sequence:
- Denaturation: ~95°C; hydrogen bonds broken; two strands separate
- Annealing: ~55–65°C; short complementary primers bind to either end of the target sequence on each strand
- Extension: ~72°C; Taq DNA polymerase (heat-stable; isolated from Thermus aquaticus) extends from the primers, copying the template (5'→3')
Each cycle doubles the number of target copies; after 30 cycles, approximately 109 copies are produced.
Gene therapy:
Delivery methods:
- Retroviral vectors: integrate into host genome; persistent effect; risk of insertional mutagenesis
- Adenoviral vectors: do not integrate; shorter-term expression; lower integration risk
- Liposomes: non-viral; encase DNA in lipid vesicle that fuses with cell membrane; lower immune response than viral vectors
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:
- Sequencing projects have determined the complete genome of many organisms including humans. Sequencing methods are continuously updated and have become automated (e.g. next-generation sequencing).
- In simpler organisms: because most DNA codes for protein, the genome sequence can be translated into the full proteome (all proteins an organism can produce). Applications include identifying potential antigens for vaccine production.
- In complex (eukaryotic) organisms: the presence of large amounts of non-coding DNA (introns, regulatory sequences, repetitive sequences) and regulatory genes means knowledge of the genome cannot easily be translated into the proteome. Alternative splicing adds further complexity.
DNA probes and personalised medicine:
- Labelled DNA probes (fluorescent or radioactive) are used in DNA hybridisation to locate specific alleles of genes in a patient's DNA
- Probes can screen patients for: heritable conditions (e.g. BRCA1/2 alleles for breast cancer risk), drug responses (pharmacogenomics), and health risks
- This information is used in genetic counselling (informing patients of risks and reproductive choices) and personalised medicine (tailoring drug choice and dose to a patient's genotype)