GCE A/LBiology

Main branches

• Zoology, Botany, Microbiology
• Cell biology, Histology (tissues), Anatomy (gross structure), Physiology (function)
• Biochemistry, Genetics, Ecology

Why biology matters today

• Understanding biodiversity (10 to over 100 million species)
• Understanding the human body and its functions
• Sustainable use of natural resources (pollution, biodiversity loss, desertification)
• Sustainable food production: high-yielding and disease-resistant varieties, better postharvest technology
• Understanding plant life (plants are primary producers)
• Understanding diseases; legal and ethical issues (DNA fingerprinting in parentage, crime, immigration)

Diseases named in the syllabus

Seven characteristics

1. Order and organisation: molecules → biosphere
2. Metabolism: sum of all chemical reactions (catabolism + anabolism)
3. Growth and development: growth = irreversible increase in dry mass; development = irreversible changes over the life span
4. Irritability and coordination: response to internal and external stimuli; together they produce movement
5. Adaptation: e.g. sunken stomata in xerophytes, vivipary in mangroves, splayed foot of camel
6. Reproduction
7. Heredity and evolution: evolution = change over time due to genetic modification

Hierarchy of organisation

The cell is the basic structural and functional unit of life. Nothing below the cell level is "living".

Diversity of form

• Size: bacteria 0.25–2 µm to giant sequoia ~100 m
• Shape: cylindrical (earthworm), streamlined (birds, fish)
• Form: unicellular (Amoeba), multicellular
• Habitat: terrestrial (rat), aquatic (fish), arboreal (loris), aerial (birds)

Elements

• ~92 natural elements; about 20–25% are essential (≈25 for humans, ≈17 for plants)
• C, H, O, N = 96% of living matter
• Ca, P, K, S make up most of the remaining 4%
• Trace elements (needed in minute amounts): B, Co, Cu, Cr, F, I, Fe, Mo, Mn, Se, Si, Sn, V, Zn
• Main role of trace elements: enzyme cofactors

Water: small, polar, angular

O is δ−, H is δ+, so hydrogen bonds form between molecules. H-bonds underlie all four key properties:

Monosaccharides (CH₂O)_n, n = 3–7

• Triose: glyceraldehyde (PGAL is a derivative)
• Tetrose: erythrose (rare)
• Pentose: ribose, deoxyribose, ribulose (RuBP derivative)
• Hexose: glucose, fructose, galactose
• Aldoses: glucose, galactose · Ketose: fructose
• All are reducing, water-soluble and crystalline

Disaccharides (glycosidic bond, condensation)

Sucrose is the form translocated in phloem and stored in sugarcane; lactose is milk sugar.

Polysaccharides

Fats (triacylglycerol)

• Glycerol (3C alcohol) + 3 fatty acids (16–18C) joined by ester bonds
• Saturated: no C=C; mostly animal; solid (butter)
• Unsaturated: ≥1 C=C; mostly plant; liquid (oils); cis or trans
• Excess saturated and trans fats → atherosclerosis

Phospholipids

• Glycerol + 2 fatty acids + phosphate (often + choline)
• Amphipathic: hydrophilic head, hydrophobic tails, so they form bilayers
• Major membrane component

Steroids and functions

• Cholesterol (animal membranes; regulates fluidity), steroid hormones
• Functions: energy store, membrane fluidity, signalling (hormones), insulation
• Test: Sudan III → red-stained oil droplets

Amino acids

• Central asymmetric C (except glycine), –NH₂, –COOH, H and an R group
• Amphoteric: basic amino + acidic carboxyl group
• Peptide bond forms by condensation

Four levels of structure

Functions and denaturation

• Catalytic (pepsin, amylase) · Structural (keratin, collagen) · Storage (ovalbumin, casein) · Transport (haemoglobin; serum albumin carries fatty acids) · Hormonal (insulin, glucagon) · Contractile (actin, myosin) · Defensive (immunoglobulins)
• Denatured by heat and high-energy radiation, strong acid or alkali, concentrated salts, heavy metals, organic solvents and detergents
• Test: Biuret → violet

Nucleotide = pentose + base + phosphate

• Nucleoside = no phosphate (adenosine, guanosine)
• Purines (2 rings): A, G · Pyrimidines (1 ring): C, T, U
• Phosphodiester bonds form the sugar–phosphate backbone
• DNA: antiparallel double helix, A=T (2 H-bonds), G≡C (3 H-bonds), 10 bp per turn

RNA types

ATP, NAD⁺, NADP⁺, FAD

• ATP: universal energy carrier
• NAD⁺: coenzyme, electron carrier, oxidising agent in respiration
• NADP⁺: coenzyme, electron carrier; NADPH is the reducing agent in photosynthesis
• FAD: coenzyme and electron carrier

Practical food tests

Key terms

• Magnification = image size ÷ actual size; light microscope (LM) max ≈ ×1000
• Resolution = minimum distance at which two points are seen as separate; LM = 0.2 µm
• Resolution is inversely proportional to wavelength, which is why electrons give better resolution
• Total magnification = objective × eyepiece (×40 × ×15 = ×600)
• The objective's image is the object for the eyepiece

TEM vs SEM

EM theoretical magnification 1×10⁸; practical just over 5×10⁵.

Light vs electron microscope

History and cell theory

• Hooke (1665): named "cell" (cork)
• Leeuwenhoek: first living cells (Euglena, bacteria)
• Schleiden (plants), Schwann (animals), Virchow (1855: cells from pre-existing cells)
• Theory: (1) all organisms are made of cells; (2) the cell is the basic structural and functional unit; (3) all cells arise from pre-existing cells

Prokaryote vs eukaryote

Shared by all cells: plasma membrane, cytosol, DNA, ribosomes.

Plasma membrane: fluid mosaic (Singer and Nicolson, 1972)

• ~7 nm; phospholipid bilayer with proteins (integral/transmembrane, peripheral)
• Glycoproteins and glycolipids; cholesterol in animal membranes (fluidity buffer)
• Protein functions: cell recognition, receptors, attachment to cytoskeleton (shape), enzymes, channels
• Phospholipids give fluidity; cholesterol modulates it

Cell wall

• Primary wall: thin, flexible, permeable, mainly cellulose
• Middle lamella: Ca and Mg pectates; glues cells together
• Secondary wall (between membrane and primary wall): lignin, suberin; rigid
• Pits and plasmodesmata connect cells

Cell junctions

Extracellular matrix (animals)

• Glycoproteins: collagen (most abundant) in a proteoglycan network
• Protects; links to cytoskeleton; signalling

Passive

• Diffusion: down a concentration gradient
• Facilitated diffusion: via channel or carrier proteins; passive (water and hydrophilic solutes)
• Osmosis: water across a selectively permeable membrane, from high to low water potential

Active and bulk

• Active transport: against a gradient, uses ATP (Na⁺/K⁺ pump, K⁺ uptake by root hairs)
• Endocytosis (phagocytosis, pinocytosis) and exocytosis

Meiosis I (reduction division)

• Prophase I: synaptonemal complex → synapsis → crossing over between non-sister chromatids → chiasmata
• Metaphase I: homologous pairs on the plate, random orientation
• Anaphase I: homologues separate; sister chromatids stay together
• Telophase I: two haploid nuclei, genetically different
• No DNA replication between meiosis I and II

Meiosis II (like mitosis)

• Plate perpendicular to that of meiosis I
• Anaphase II: sister chromatids separate
• Four haploid, genetically different cells

Significance: constant chromosome number across generations; variation through crossing over, independent assortment and random fertilisation.

Mitosis significance

• Genetic stability
• Growth and development
• Repair, replacement, regeneration
• Asexual reproduction

Cancer and galls

• Transformation → benign tumour (stays put) or malignant (invasive) → metastasis
• Galls: uncontrolled division when the auxin:cytokinin balance is upset (viruses, fungi, bacteria, insects, mites)

Energy relations

• Catabolism: breaks down molecules, releases energy (exergonic)
• Anabolism: builds molecules, absorbs energy (endergonic)
• ATP = ribose + adenine + 3 phosphates; hydrolysis of each terminal phosphate gives −30.5 kJ mol⁻¹
• Phosphorylation types: photo- (light), substrate-level (breakdown of a substrate), oxidative (ETC)

Enzyme properties

• Mostly globular proteins; lower activation energy
• Substrate-specific (active site); induced fit
• Not used up; do not change end products; most reactions reversible
• Heat-sensitive; affected by pH, temperature, substrate and enzyme concentration, inhibitors
• Only a few amino acids form the active site; the rest maintain shape

Cofactors

• Non-protein; bound permanently or temporarily
• Organic = coenzymes (vitamin derivatives: NAD, FAD, biotin)
• Inorganic: Zn²⁺, Fe²⁺, Cu²⁺

Factors

• Temperature: rate rises (more collisions) up to the optimum (~35–40 °C in humans; ~70 °C in hot-spring bacteria), then falls as H-bonds and ionic bonds break and the enzyme denatures
• pH: most 6–8; pepsin 2; trypsin 8
• Substrate concentration: rate rises, then plateaus when the enzyme is saturated

Inhibition

Regulation

• Allosteric: regulators bind a regulatory site non-covalently; enzyme has ≥2 subunits; one molecule affects all active sites
• ADP = allosteric activator; ATP = allosteric inhibitor (of catabolism)
• Cooperativity: one substrate binding raises the affinity of other sites (O₂ and haemoglobin)
• Feedback inhibition: the end product inhibits an early enzyme of its pathway

Pigments and spectra

• Chlorophylls absorb violet-blue and red, so leaves look green
• Chlorophyll a: main pigment, directly in the light reactions
• Chlorophyll b and carotenoids (carotenes, xanthophylls) are accessory pigments; carotenoids also give photoprotection (stop reactive oxidative molecules)
• Absorption spectrum = light absorbed by a pigment; action spectrum = effectiveness of each wavelength in driving photosynthesis

Photosystems (in thylakoid membranes)

• Each = reaction-centre complex (special chlorophyll a pair + primary electron acceptor) + light-harvesting complexes
• PS I = P700; PS II = P680

Photorespiration

• Rubisco acts as an oxygenase: RuBP + O₂ → one 3-PGA + 2-phosphoglycolate (toxic)
• Processed in chloroplast, peroxisome and mitochondrion
• Costs energy and releases CO₂; worse when hot, dry, bright and stomata are closed

C4 pathway

• Mesophyll: CO₂ → HCO₃⁻ (carbonic anhydrase); PEP + HCO₃⁻ → oxaloacetate (PEP carboxylase)
• OAA → malate or aspartate → diffuse to bundle sheath
• Bundle sheath: CO₂ released and re-fixed by Rubisco (Calvin cycle only here)
• Kranz anatomy; many plasmodesmata; bundle-sheath chloroplasts have few or no grana and little PS II
• PEP carboxylase is more efficient: uses HCO₃⁻ (50× more concentrated) and has no affinity for O₂

C3 vs C4

NIE ATP total

Fermentation (cytosol, no O₂)

Respiratory quotient

RQ = volume CO₂ produced ÷ volume O₂ used

Increasing order: fat < protein < carbohydrate.

Early Earth

• Earth formed ~4.6 billion years ago (bya)
• First atmosphere: water vapour, N₂ and its oxides, CO₂, CH₄, NH₃, H₂, H₂S; became reducing; little O₂
• Energy for abiotic synthesis: volcanic eruptions, lightning, intense UV, hydrothermal and alkaline vents
• Other organic sources: meteorites
• Evidence from chemistry, geology and physics; oldest microbial fossils ~3.5 bya

Biochemical evolution: 4 stages

Haldane: "primitive soup". Miller showed organic molecules form from inorganic gases. First genes and enzymes were probably RNA.

Timeline

Lamarck (1809)

• Use and disuse
• Inheritance of acquired characteristics (giraffe neck)

Darwin–Wallace: natural selection

Observations: heritable variation exists; every species produces more offspring than the environment can support.

Favourable traits: escaping predators, tolerating stress, obtaining food, disease resistance, fertilisation success, number of offspring.

Neo-Darwinism

Natural selection + Mendelian genetics + population genetics. Evolution = change in the genetic composition of a population over generations.

Artificial vs natural

Today's criteria: DNA base sequences of key genes and organelle DNA, rRNA sequences, protein amino-acid sequences, molecular structure of cell components.

History

Artificial groups today

• Protista: polyphyletic
• Viruses: no cellular organisation, so they belong to no kingdom

Hierarchy

Towards species, shared characteristics increase; towards domain, the number of individuals increases.

Species concepts

• Biological: interbreed → viable, fertile offspring
• Morphological: structural features
• Ecological: niche and interactions
• Phylogenetic: smallest group sharing a common ancestor

Rules of binomial nomenclature

• No two species share a name
• Genus + specific epithet; Latinised, Roman script
• Italics in print, underlined by hand
• Genus capitalised; epithet lower case
• Author added at the end, not Latinised: Cocos nucifera L.
• Third word for subspecies: Panthera pardus kotiya

Domain Bacteria

• Uni-, colonial or filamentous; 0.5–5 µm
• Peptidoglycan wall: Gram +/− by amount; often a capsule
• Flagella without membrane and without 9+2
• Diverse nutrition and O₂ needs; some fix N₂ (Rhizobium, cyanobacteria)
• Binary fission; some conjugate

Cyanobacteria: photosynthetic, O₂-producing, solitary or filamentous or colonial, some fix N₂.

Domain Archaea

• Prokaryotic, unicellular, no peptidoglycan
• Extreme halophiles and thermophiles; methanogens (including guts of cattle and termites)

Kingdom Protista (polyphyletic)

• Uni-, colonial or multicellular
• Photoautotrophs, heterotrophs, mixotrophs
• Freshwater, marine, damp soil; some symbionts

Kingdom Fungi

• Eukaryotic; chitin walls; absorptive heterotrophs secreting extracellular enzymes
• Decomposers, parasites, mutualists
• Hyphae → mycelium; septate (pores in septa) or coenocytic
• Haustoria in some; sexual and asexual spores
• Store glycogen

Fungal phyla

Innovations of vascular plants

• Xylem (tracheids, lignin) and phloem allow height
• Roots replace rhizoids (root tissues resemble stems of early vascular plants)
• Leaves: microphylls (single unbranched vein, small) vs megaphylls (branched veins)
• Sporophylls bear sporangia; heterospory: megaspores → ♀ gametophyte, microspores → ♂

Seed plant innovations

• Seeds: embryo + food + seed coat
• Reduced, protected gametophytes
• Heterospory
• Ovule = megasporangium + megaspore + integument(s)
• Pollen (sporopollenin wall) = male gametophyte; pollen tube delivers sperm, so no water needed

Monocots vs dicots

Chordate features (at some stage)

1. Notochord
2. Dorsal, hollow nerve cord
3. Pharyngeal slits
4. Muscular post-anal tail

Arthropod classes (keys)

Meristematic cells

• Living, isodiametric (roughly spherical), undifferentiated
• Central nucleus, dense cytoplasm, able to divide
• Three overlapping zones: division → elongation → differentiation (maturation)

Three meristem types

Root apex vs shoot apex

Root cells may elongate >10× and push the tip through soil.

Wood terms

Spring + summer wood = one annual ring (temperate trees can be aged).

Bark

All tissues outside the vascular cambium: secondary phloem (and any remaining primary phloem and cortex) + periderm. Only young secondary phloem conducts.

Shoot architecture and light capture

• Stem length and branching pattern are designed to capture maximum light; tall stems avoid shading; vines use supports
• Leaf size: largest in rain forests; smallest in dry or very cold habitats
• Phyllotaxy = arrangement of leaves on the stem
• Horizontal leaves capture light well in dim conditions; vertical leaves (grasses) avoid damage from intense light

Primary root (dicot vs monocot)

• Epidermis with root hairs → cortex (parenchyma, intercellular spaces; storage and transport)
• Endodermis: Casparian strip (suberin) in radial and transverse walls; no intercellular spaces
• Pericycle: 2–3 layers; in dicots meristematic (lateral roots, secondary growth); not meristematic in monocots
• Dicot: star-shaped xylem with phloem between arms
• Monocot: central pith with a ring of alternating xylem and phloem

Primary stem

• Dicot: epidermis with stomata; cortex with collenchyma below epidermis; vascular bundles in a ring (phloem outside, xylem inside, cambium between); sclerenchyma cap; large pith
• Monocot: ground tissue not divided into cortex and pith; scattered bundles each with a sclerenchyma sheath; no cambium

Leaf anatomy

Stomata

• Guard cells: only epidermal cells with chloroplasts; bean-shaped; inner wall thicker and less elastic; radial cellulose microfibrils form hoops
• Gas exchange also via lenticels and a little via cuticle; gases move by diffusion only

Practical: staining a T.S.

• Safranin stains lignified walls (xylem, sclerenchyma) red
• Use thin, even sections; mount in water or glycerol

Movement methods

Water potential Ψ (MPa)

Ψ = Ψs + Ψp

• Pure water at atmospheric pressure: Ψ = 0
• Ψs (solute potential) is always negative; more solute → more negative (0.1 M sucrose ≈ −0.23 MPa)
• Ψp positive in turgid cells; negative (tension) in xylem (< −2 MPa)
• Water moves from higher (less negative) to lower Ψ
• Incipient plasmolysis: Ψp = 0, so Ψ = Ψs
• Full turgor: Ψp = −Ψs, so Ψ = 0

Practical: Ψ of potato tissue

Ascent of sap: cohesion–tension

Root pressure and guttation

• At night (humidity near 100%, little transpiration), roots keep pumping ions into the stele → Ψ falls → water enters → root pressure
• Excess water exudes through hydathodes at leaf tips and margins = guttation (Alocasia, Colocasia)
• Not in daytime, not through stomata, not dew; root pressure lifts water only short distances

Phloem: pressure-flow hypothesis

Phloem sap ≈ 30% sucrose + amino acids, hormones, minerals. Sources: mature leaves. Sinks: growing roots, buds, fruits. Tubers can be either.

Transpiration

• Loss of water vapour from aerial parts: stomatal (~95%), cuticular, lenticular
• Path: xylem → mesophyll (3 routes) → evaporation into substomatal space → diffusion out through stomata → boundary layer ("diffusion shell")
• Importance: distributes water and minerals; drives ascent of sap and uptake by roots; cools leaves

Factors

Soil texture itself has little direct effect.

Stomatal opening: K⁺ influx

Closing: K⁺ leaves → water leaves → turgor falls. ABA (drought, from roots and leaves) triggers K⁺ loss and closure, preventing wilting. Low CO₂ in the substomatal cavity opens stomata. Guard cells also have an internal clock.

Modes of nutrition

• Photoautotrophs: all green plants
• Mutualism: legume + Rhizobium; mycorrhizae; coralloid roots of Cycas + Anabaena
• Commensalism: epiphytic orchids
• Parasitism: semi-parasite Loranthus; total parasite Cuscuta (dodder)
• Carnivorous (photosynthetic but take N and minerals from insects, in nutrient-poor soils): Nepenthes, Drosera, Utricularia (aquatic)

17 essential elements

Macronutrients (9): C, H, O, N, P, S, K, Ca, Mg

Micronutrients (8): Cl, Fe, Mn, B, Zn, Cu, Ni, Mo

C and O come from atmospheric CO₂. H comes from water. N is absorbed from soil as NO₃⁻ or NH₄⁺; atmospheric N₂ is not used directly by plants.

Alternation of generations (heteromorphic)

Gametangia and sporangia have sterile jackets against desiccation. Seedless plants need external water for sperm; seed plants do not. Trend: sporophyte becomes dominant, gametophyte reduced and dependent.

Four life cycles compared

Flower and gametophytes

• Sepals and petals are sterile; stamens are microsporophylls; carpels are megasporophylls
• Pollen grain (male gametophyte): tube nucleus + generative nucleus
• Ovule: 1 functional megaspore → embryo sac = 8 nuclei in 7 cells: 3 antipodals, central cell with 2 polar nuclei, 2 synergids, 1 egg
• The ovule itself is diploid (2n) tissue; megaspore, microspore, pollen and embryo sac are haploid

Double fertilisation (unique to angiosperms)

Ovule → seed; integuments → seed coat; ovary wall → pericarp; ovary → fruit. Significance: endosperm develops only if the egg is fertilised, so no nutrients are wasted.

Cross-pollination adaptations

• Self-incompatibility (self-infertility)
• Heterostyly
• Unisexual flowers
• (also dichogamy)

Monoecy and homostyly are not cross-pollination adaptations. Cross-pollination increases variation and supports evolution.

Parthenocarpy and parthenogenesis

• Parthenocarpy: fruit without fertilisation, so seedless. Natural in banana; induced with growth substances in grapes and oranges
• Parthenogenesis (plants): seed without fertilisation (some grasses)

Seeds, dormancy and germination

• Seed advantages: coat protects; food reserve; dormancy survives bad periods; dispersal
• Dormancy causes: inhibitors, hard seed coat, coat impermeable to water
• Germination needs water, O₂, suitable temperature
• Sequence: imbibition of water → enzymes activated → food mobilised → radicle emerges (positively gravitropic) → plumule (negatively gravitropic)

Natural vegetative propagation

Light (photomorphogenesis)

• Red and blue light matter most
• Blue-light photoreceptors: phototropism, light-induced stomatal opening, slowing of hypocotyl elongation as a seedling emerges
• Phytochromes (mainly red/far-red): seed germination, shade avoidance
• Shade under a canopy is rich in far-red, so plants grow taller. Direct sun (more red relative to far-red) stimulates branching and inhibits vertical growth
• Photoperiod controls flowering
• Phototropism: cells on the shaded side elongate faster

Gravity and touch

• Roots positively, shoots negatively gravitropic
• Statoliths = plastids with dense starch grains, in root-cap cells; settling redistributes Ca²⁺, which moves auxin to the lower side; high auxin inhibits root elongation there, so the root bends down
• Thigmomorphogenesis: wind-exposed trees are shorter and stockier
• Thigmotropism: tendrils coil around supports
• Thigmonasty: Mimosa pudica folds as pulvinus cells lose turgor
• Nyctinasty: flowers opening by day, closing at night

Abiotic stress

• Drought: ABA closes stomata; grass leaves roll; leaf shedding
• Cold: membranes lose fluidity below a critical temperature, so plants raise the proportion of unsaturated fatty acids. Freezing: extracellular ice draws water out of cells, so frost-tolerant plants accumulate sugars and other solutes
• Salt: low soil Ψ cuts water uptake; plants make compatible organic solutes; halophytes (mangroves) use salt glands

Biotic stress: defences

Connective tissues

Cells scattered in an extracellular matrix with fibres: collagen (strength), reticular (join to adjacent tissues), elastic. Cells include fibroblasts, macrophages, mast cells (heparin, histamine), fat cells and leucocytes.

Muscle tissues

Nervous tissue

• Neurone (structural and functional unit): cell body, dendrites (receive), axon (transmit)
• Neuroglia: nourish, insulate (myelin), replenish neurones, modulate function

Holozoic nutrition

Symbiosis: mutualism (cellulose digesters in ruminants and termites), parasitism (tapeworm, lice), commensalism (barnacles on whales).

Mouth

• Teeth: incisors, canines, premolars, molars (adult dental formula 2.1.2.3 per quadrant)
• Saliva: water (dissolves, aids taste), salivary amylase (starch → smaller polysaccharides + maltose), mucus (lubricates, cleans, protects), lysozyme and immunoglobulins (antimicrobial), buffers (neutralise acid, prevent tooth decay)
• Tongue (skeletal muscle) mixes and forms the bolus

Stomach

• Gastric glands: mucous cells (mucus), chief cells (pepsinogen), parietal cells (H⁺ and Cl⁻ separately → HCl)
• HCl activates pepsinogen → pepsin, which activates more (autocatalysis); pepsin: proteins → small polypeptides
• HCl kills microbes (non-specific defence)
• Self-protection: inactive enzyme secretion, mucus, new epithelium every 3 days
• Absorbs some water, alcohol, drugs; secretes gastrin; chyme leaves via pyloric sphincter

Absorption

• Surface area: circular folds → villi → microvilli (brush border)
• Glucose (mostly), amino acids, small peptides, vitamins: active; fructose: facilitated diffusion
• Into villus capillaries → hepatic portal vein → liver
• Fatty acids + monoglycerides → triglycerides re-formed in cells → chylomicrons → lacteal → lymph → blood
• ~2 L water drunk + ~7 L in juices; most reabsorbed in small intestine

Large intestine

• Caecum (with appendix): fermentation of undigested plant matter
• Colon: completes water and ion reabsorption; bacteria make vitamin K, some B vitamins and folic acid
• Rectum stores faeces; two anal sphincters

Pancreas and liver

• Pancreas: exocrine acini (juice: bicarbonate, amylase, lipase, nucleases, trypsinogen) + endocrine islets of Langerhans (insulin, glucagon); pancreatic + bile duct → hepatopancreatic duct
• Liver lobule (hexagonal): hepatocytes in columns radiating from a central vein; sinusoids with mixed portal and arterial blood; Kupffer cells; bile canaliculi; portal triad at corners

Hormonal regulation

Balanced diet

• Carbohydrates: energy, heat, stores, protein sparing
• Proteins: growth, repair, enzymes, antibodies, hormones. 8 essential amino acids (e.g. leucine, methionine, lysine); animal proteins are complete
• Lipids: most energy per gram; fat-soluble vitamins; steroid hormones; insulation, myelin; essential fatty acids
• Fibre: bulk, prevents constipation, protects against colorectal cancer
• Water ≈ 60% of body mass

Vitamins

Minerals

Energy and body mass

• BMR: minimum rate at rest, post-absorptive (≥12 h fast), no stress; ~1600–1800 kcal/day (men), 1300–1500 (women)
• Energy budget: C = M + U + F + P (food = metabolism + urine + faeces + production)
• BMI = mass (kg) ÷ height² (m²). <18.5 malnutrition; ≥30 obesity

Example: 50 kg, 1.53 m → 50 ÷ 2.3409 = 21.4. Minimum non-malnourished mass at 1.53 m = 18.5 × 2.3409 = 43.3 kg.

Disorders

• Gastritis: excess HCl damages mucosa; causes: prolonged starvation, mental stress, aspirin, Helicobacter pylori
• Constipation: slow faecal movement, too much water reabsorbed; prevent with fibre and regular habits

Open vs closed

No circulatory system: cnidarians, flatworms, nematodes (diffusion suffices).

Single vs double circulation

• Single (fish, including rays and sharks): 2-chambered heart; heart → gills → body; blood reaches organs at reduced pressure
• Double: pulmonary + systemic circuits. Amphibians and most reptiles: 3 chambers. Birds and mammals: 4 chambers, complete separation
• Double is better because systemic blood is re-pressurised, giving more efficient supply (brain, muscles)

Lymphatic system

• Lymph vessels (with valves), nodes (connective tissue + WBCs), tonsils, spleen, thymus
• Lymph composition = interstitial fluid
• Drains into veins at the base of the neck via two ducts
• Moved by vessel contraction and skeletal muscles
• Roles: return lost fluid and proteins; absorb fats and fat-soluble vitamins; immunity

Heart structure

• Wall: pericardium (fibrous + serous), myocardium (cardiac muscle + conducting fibres), endocardium (flat epithelium, continuous with endothelium)
• Left ventricle wall thickest (pumps to whole body)
• Tricuspid (right AV, 3 flaps); bicuspid/mitral (left AV, 2 flaps); chordae tendineae + papillary muscles stop inversion; semilunar valves at aorta and pulmonary artery
• Coronary arteries branch from the aorta just after the aortic valve; cardiac veins → coronary sinus → right atrium

Blood route

Head, neck, forelimbs → superior vena cava. Trunk and hind limbs → inferior vena cava. Hepatic artery → liver → hepatic vein → IVC.

Conducting system

• SA node (right atrium wall near SVC) = pacemaker: initiates and sets rhythm
• AV node (between atria) relays to ventricles
• AV bundle (bundle of His) → bundle branches → Purkinje fibres → contraction from apex upwards
• Heart is myogenic; rate modified by sympathetic (↑), parasympathetic (↓), adrenaline, thyroxine, temperature

Cardiac cycle (0.8 s at ~75 beats/min)

Resting rate 60–80 bpm. Stroke volume = blood pumped per ventricle per beat.

ECG

• P: atrial depolarisation (SA node impulse)
• QRS: ventricular depolarisation (spread from AV node)
• T: ventricular repolarisation
• Atrial repolarisation is hidden in QRS

Blood pressure

• Normal ~120/80 mmHg (systolic/diastolic); measured with a sphygmomanometer
• Hypertension risks: obesity, diabetes, family history, smoking, inactivity, salt, alcohol, stress, LDL deposits. Consequences: kidney damage, heart attack, stroke, vessel damage
• Hypotension: shock, dengue haemorrhagic fever, sudden standing, bleeding, fasting → fainting
• Atherosclerosis → angina (narrowing) or myocardial infarction (complete block) ± thrombosis; brain → stroke

Respiratory pigments

Pigments evolved because O₂ is poorly soluble in water.

Gas transport

Hb + 4O₂ ⇌ HbO₈ (lung capillaries, inside RBCs)

Blood components

• RBCs: biconcave, no nucleus, no mitochondria (anaerobic), ~120-day life, 4–6 million µL⁻¹; erythropoietin from kidney
• WBCs: neutrophils (phagocytes, first to arrive), monocytes → macrophages, lymphocytes (B, T, NK), eosinophils (parasites), basophils (histamine, heparin)
• Platelets: no nucleus; clotting
• Plasma: ions, albumin (buffer, osmotic), antibodies, fibrinogen; pH 7.4; serum = plasma without clotting factors

ABO groups

Anti-B is present in groups A and O.

Rhesus

• Rh⁺ = has Rh antigen on RBCs
• Rh⁻ people make anti-Rh antibodies only after exposure
• Rh⁻ mother, Rh⁺ first baby: sensitised at delivery; second Rh⁺ fetus: antibodies cross the placenta and destroy fetal RBCs
• B Rh⁺ can safely receive B or O, Rh⁺ or Rh⁻

Respiratory surfaces

• Needed because surface area to volume ratio falls as size increases. Animals with high SA:V (e.g. 8.3 cm⁻¹) can rely on the body surface
• Properties: moist, thin, permeable, large area, good blood supply
• Body surface: cnidarians, flatworms, earthworms
• External gills: marine annelids. Internal gills: fish, prawns
• Tracheae: insects. Book lungs: spiders, scorpions
• Lungs: reptiles, birds, mammals. Skin: amphibians

Human airway

Lungs

• Right lung 3 lobes; left lung 2 lobes and slightly smaller (heart apex)
• Visceral pleura (inner, on lung) and parietal pleura (outer, on thoracic wall) with fluid between
• Mucus escalator: goblet-cell mucus traps dust; cilia sweep it up to the pharynx to be swallowed
• Alveoli: single flattened, non-ciliated cells; moisture film; macrophages; surfactant lowers surface tension and prevents collapse

Ventilation (negative-pressure breathing)

Exercise recruits neck, back and chest muscles. The first pair of ribs is fixed to the sternum (manubrium) and barely moves.

Control of breathing (negative feedback)

O₂ has little effect unless very low (aortic and carotid sensors). Stretch receptors in lungs stop over-inflation. The pons modulates rhythm.

Lung volumes

TV 500, RV 1200, IRV 3100, ERV 1100 → VC = 4700 mL. TLC − VC = RV.

Smoking

• Nicotine: addictive; ↑ heart rate; vasoconstriction; temporary ↑ BP
• ↑ goblet-cell mucus; paralyses cilia (hydrogen cyanide) → bronchitis
• Phagocyte enzymes destroy alveoli (emphysema), so less gas-exchange area
• CO binds Hb irreversibly, so less O₂ carried
• Carcinogens: ~90% of lung cancers

Occupational and other disorders

• Silicosis: silica (quarrying, mining, masonry, glass, pottery) → fibrosis
• Asbestosis: asbestos fibres → fibrosis, pulmonary hypertension
• TB: Mycobacterium tuberculosis, airborne; weight loss, sweats, fever, cough, blood in sputum
• Asthma: bronchiolar smooth muscle contracts (immune over-reaction to pollen, dust, mites, cold air)

Innate (non-specific, vertebrates and invertebrates)

External barriers

• Keratinised skin; shedding
• Mucous membranes; mucus; cilia; coughing and sneezing
• Tears, saliva, mucus (washing); lysozyme
• Gastric acid; acidic skin (sweat and sebaceous secretions)

Internal defences

• Phagocytes: neutrophils (first), macrophages (larger)
• Natural killer cells: lymphocytes that release chemicals to kill virus-infected and cancer cells (no engulfing)
• Antimicrobial proteins: interferons (from virus-infected cells; neighbours make antiviral proteins), complement (cascade → lysis, phagocytosis, inflammation)
• Inflammation: mast cells release histamine → vasodilation (redness, heat) + permeability (swelling) → phagocytes and cytokines; pain; pus; fever if systemic

Acquired (specific, vertebrates only)

• Specificity, self/non-self recognition, memory
• B and T cells both arise in bone marrow; T cells mature in the thymus, B cells in bone marrow
• Antigen receptors on membrane (~100,000 per cell)
• Antigen: provokes a response. Epitope: small part bound by a receptor; one antigen has several epitopes
• T cells recognise antigen fragments only on antigen-presenting cells (macrophages, dendritic cells, B cells); B cells bind free antigen

Antibodies (immunoglobulins)

• Proteins secreted by plasma cells
• Same Y shape as B-cell receptors, but soluble
• Neutralise, mark for destruction, activate complement and phagocytosis; do not kill directly

Types of acquired immunity

Disorders

• Allergy: allergen → antibodies on mast cells → histamine release on re-exposure (sneezing, bronchoconstriction, anaphylaxis)
• Autoimmune: attack on self. Type 1 diabetes (T cells destroy β cells), multiple sclerosis (T cells attack myelin), rheumatoid arthritis (antibodies attack joint lining)
• Immunodeficiency: inborn or acquired (drugs, HIV/AIDS)

Nitrogenous wastes

Excretory products depend on the substrate, enzymes, O₂ availability and habitat. Defecation is not excretion.

Excretory structures

Kidney and nephron

• Posterior abdominal wall, behind peritoneum; right kidney slightly lower
• Renal artery from aorta; renal vein to IVC
• Cortex (granular, glomeruli), medulla (pyramids), pelvis → ureter
• Nephrons: cortical (majority) and juxtamedullary (deep loops)
• Afferent arteriole wider than efferent, so high glomerular pressure
• Efferent arteriole → peritubular capillaries (around convoluted tubules) and vasa recta (around loop)

Urine formation

Hormones and homeostasis

• ADH (hypothalamus, released from posterior pituitary): blood osmolarity ↑ → ADH ↑ → DCT and collecting duct more permeable → less, concentrated urine
• Aldosterone (adrenal cortex): ↑ Na⁺ and water reabsorption, ↑ K⁺ excretion; driven by renin → angiotensin (↑ BP)
• Kidney roles: water and electrolyte balance, excretion, pH, blood volume and pressure, erythropoietin, renin

Disorders

• Renal calculi (oxalates, phosphates): dehydration, alkaline urine, infection, metabolism, family history; prevent by drinking water
• Kidney failure / CKD: diabetes, hypertension, family history, age; prevent with low-salt, low-fat diet, exercise, check-ups, no smoking
• Dialysis: artificial removal of wastes, solutes and toxins
• CKDu (Sri Lanka: NCP, Uva, Eastern and other provinces): suspected As, Cd, fluoride, pesticides, poor utensils, genetics, dehydration

Nervous vs hormonal coordination

Shared: both use chemical signals and coordinate responses for homeostasis.

Nervous organisation in phyla

CNS protection

• Skull and vertebrae
• Meninges: dura mater (outer), arachnoid, pia mater (inner)
• CSF in 4 ventricles (3 in forebrain, 1 in hindbrain) and central canal: uniform pressure, shock absorber, nutrients and wastes

Peripheral nervous system

• Cranial and spinal nerves + autonomic ganglia
• Afferent (sensory) → CNS → efferent (motor)
• Spinal nerves carry axons of both sensory and motor neurones
• Somatic (motor) system: skeletal muscle, voluntary
• Autonomic: smooth muscle, cardiac muscle, glands

Sympathetic vs parasympathetic

Sympathetic nerves leave the spinal cord only and release noradrenaline. Parasympathetic nerves leave brain and sacral cord and release acetylcholine.

Resting potential (≈ −70 mV)

• Unequal ion distribution: K⁺ high inside, Na⁺ high outside; Cl⁻ and large anions inside
• More K⁺ channels than Na⁺ channels open
• Na⁺/K⁺ pump (ATP): 3 Na⁺ out for every 2 K⁺ in

Action potential

Duration ~2 ms. Speed ↑ with axon diameter and myelin (saltatory conduction between nodes of Ranvier).

Chemical synapse

Transmitters: acetylcholine (motor neurones), biogenic amines (noradrenaline, dopamine, serotonin), amino acids, neuropeptides.

Reflex arc

Disorders

Sensory receptors

• Specialised cell, organ or subcellular structure; always connected to the nervous system
• Respond at or above threshold; transduce stimulus to membrane potential
• Amplification and sensory adaptation (e.g. smell fades)
• Detect both external and internal stimuli

Eye structure

Rods: rhodopsin, sensitive, night vision, no colour. Cones: photopsin, three types (red, green, blue), colour, need bright light.

Vision

• Accommodation (near): ciliary muscle contracts → ligaments slacken → lens more convex (parasympathetic)
• Distant: ciliary muscle relaxes → lens flatter
• Pupil constricts in bright light and for near vision; convergence for near objects
• Binocular vision: overlapping fields fused in occipital lobe → 3-D, judging speed and distance
• Blocked aqueous drainage → glaucoma

Ear

• Outer: pinna, auditory canal (wax), tympanic membrane
• Middle (air, temporal bone): malleus → incus → stapes (on oval window); round window; Eustachian tube to pharynx equalises pressure
• Inner: vestibule (utricle, saccule), 3 semicircular canals, cochlea
• Cochlea: vestibular canal and tympanic canal (perilymph) + cochlear duct (endolymph) with basilar membrane and organ of Corti; tectorial membrane

Hearing and balance

Utricle and saccule (otoliths of CaCO₃) sense gravity, tilt and linear movement. Semicircular canals sense angular movement. Endolymph-filled: cochlear duct, utricle, saccule (membranous labyrinth).

Skin

• Epidermis: keratinised stratified squamous; germinative layer; melanocytes (melanin vs UV); no blood vessels
• Dermis: areolar tissue, collagen and elastic fibres; hair, arrector pili, sweat and sebaceous glands, blood vessels, receptors
• Subcutaneous layer: adipose + areolar
• Functions: protection, temperature regulation, sensation, vitamin D synthesis, minor excretion (NaCl, urea)

Feedback

• Negative (most): response reduces stimulus (insulin and glucose)
• Positive: oxytocin in labour (cervix stretch → more oxytocin) and in milk ejection (suckling → oxytocin → milk → more suckling); oestradiol → LH surge

Disorders

Body temperature (36.5–37.5 °C)

Blood glucose (70–110 mg/100 mL fasting)

Osmoregulation

Hypothalamic osmoreceptors detect ↑ osmolarity → thirst + ADH release (posterior pituitary) → more water reabsorbed → concentrated urine. Low volume or Na⁺ → angiotensin II → aldosterone → Na⁺ and water retained.

Asexual reproduction in animals

• Mitosis only; rapid; no mate needed; identical offspring; good in stable environments; risky when conditions change
• Budding: Hydra
• Fragmentation and regeneration: some annelids, sponges, cnidarians, flatworms
• Parthenogenesis: bees, ants, aphids, wasps; rarely some lizards and fish. Honey-bee drones are haploid parthenogenetic males; queens and workers come from fertilised eggs

Sexual reproduction

• Hermaphrodite (earthworm) vs dioecious
• External fertilisation: water needed (many invertebrates, amphibians, most bony fish)
• Internal: insects, reptiles, birds, mammals; fewer gametes, higher zygote survival, more protection
• Variation gives an advantage when conditions change

Male system

• Testes in scrotum, ~2 °C below core temperature
• Seminiferous tubules: Sertoli cells (nourish and attach developing sperm; inhibin). Leydig cells between tubules (testosterone)
• Epididymis (~6 m, ~3 weeks): sperm mature, become motile and are stored
• Pathway: seminiferous tubules → epididymis → vas deferens → ejaculatory duct → urethra
• Semen 2–5 mL; 40–100 million sperm per mL; sperm <10% of volume; sperm survive 48–72 h

Accessory glands

Spermatogenesis (~7 weeks; from puberty)

Sperm: head (nucleus + acrosome with trypsin and hyaluronidase), midpiece (mitochondria), tail (9+2 flagellum). Diploid cells in testis: spermatogonia, primary spermatocytes, Leydig and Sertoli cells.

Male hormonal control

Female system

• Ovary: cortex (follicles at various stages; germinal epithelium) and medulla
• Oviduct: ciliated; fertilisation in the upper part
• Uterus: muscular; vascular endometrium; cervix
• Vagina: muscular, elastic, stratified epithelium

Oogenesis

Ruptured follicle → corpus luteum (oestradiol + progesterone) → corpus albicans if no pregnancy. Primordial germ cells come from the yolk sac.

Early development

Extra-embryonic membranes

Placenta and pregnancy

• Fetal chorionic villi + maternal endometrium; blood does not mix
• Exchange; immune protection; hormones (hCG, progesterone, oestrogen)
• Umbilical cord: 2 arteries (O₂-poor, to placenta), 1 vein (O₂-rich, to fetus)
• ~38 weeks from fertilisation (40 from last period); embryo for the first 8 weeks, then fetus
• T1: organogenesis; heart beats by week 4 (detectable at 8–10 weeks); hCG pregnancy test; morning sickness
• T2: hCG falls, placenta takes over progesterone; fetus ~30 cm, movements felt
• T3: rapid growth to ~50 cm, 3–4 kg

Birth and lactation

• Labour: prostaglandins, oestradiol, oxytocin (positive feedback); stages: cervical dilation → delivery of baby → delivery of placenta
• Prolactin (milk synthesis) after oestradiol and progesterone fall; oxytocin ejection via suckling (positive feedback)
• Colostrum: less lactose, no fat, rich in antibodies
• Breast milk: lactose, fatty acids, casein, lactalbumin, antibodies, WBCs, lower Na⁺ than cow's milk; fewer allergies; bonding

Birth control

Prenatal diagnosis and ART

• Ultrasound; amniocentesis; chorionic villus sampling; fetal DNA in maternal blood
• Infertility treatments: hormone therapy; surgery; ART
• IVF: oocytes + 50,000–100,000 sperm per oocyte in the lab → culture to ≥8 cells → transfer to uterus
• ICSI: a single selected sperm (or spermatid nucleus) injected into the oocyte cytoplasm → transfer; for male infertility

Skeleton types

Common functions: support, protection, movement. Human extras: Ca and phosphate storage and release; blood-cell production.

Moving through water and air

• Legs as oars (insects, tetrapods); jet propulsion (squid); side-to-side body and tail (fish); up-and-down undulation (whales)
• Fusiform shape reduces drag in water and air; wings act as aerofoils

Skull (21 bones: 8 cranial + 13 facial)

• Cranium (8): frontal, 2 parietal, occipital, 2 temporal, ethmoid, sphenoid
• Face: 2 zygomatic, maxilla, 2 nasal, 2 lacrimal, vomer, 2 palatine, 2 inferior conchae, mandible (only movable bone); the frontal also contributes to the face
• Fontanelles: soft areas allowing compression at birth; ossify in 1–2 years
• Sutures: immovable joints
• Sinuses (sphenoid, ethmoid, maxillary, frontal): voice resonance, lighter skull
• Mandible: condyloid process (temporomandibular joint), coronoid process (muscle attachment)
• Temporal bone: zygomatic, mastoid and styloid processes
• Zygomatic arch: zygomatic + temporal bones; muscle attachment for lower jaw
• Occipital condyles + atlas: nodding

Vertebral column: 26 bones

24 separate vertebrae + sacrum + coccyx. Curvatures: primary (thoracic, sacral; concave anteriorly) and secondary (cervical ~3 months, lumbar ~7–8 months; convex anteriorly) maintain upright posture.

Thorax

• Sternum: manubrium (clavicles + first 2 rib pairs), body, xiphoid (diaphragm); red marrow
• 12 rib pairs: 7 true, 3 false (indirect), 2 floating
• First rib fixed, so it does not move in inspiration

Upright posture

• Secondary curvatures
• Vertebrae enlarge downwards
• Large fused sacrum
• Occipital condyles and foramen magnum centred under the skull
• Foot arches

Upper limb (30 bones per limb)

• Pectoral girdle: scapula + clavicle
• Humerus, radius, ulna, 8 carpals, 5 metacarpals, 14 phalanges
• Shoulder: shallow ball-and-socket (head of humerus in glenoid cavity of scapula): widest range
• Elbow: hinge (humerus with radius and ulna; two articular surfaces); flexion and extension only
• Wrist: radius + 3 proximal carpals; pronation and supination
• Metacarpal–phalangeal joints: power grip. Joint between carpal and first metacarpal: opposable thumb, precision grip

Lower limb (30 bones per limb)

• Pelvic girdle: 2 hip bones
• Femur (longest, strongest), tibia, fibula, patella, 7 tarsals, 5 metatarsals, 14 phalanges (excluding patella = 29)
• Hip: ball-and-socket in acetabulum; sturdy, bears weight when standing
• Knee: femur + tibia + patella; flexion, extension and a locking rotation for long standing
• Ankle: tibia and fibula with a tarsal
• Arches (2 longitudinal, 1 transverse) spread weight whether stationary or moving

Joints and disorders

• Osteoporosis: ↓ bone density (menopause, low Ca)
• Osteoarthritis: degenerative, non-inflammatory; cartilage thins
• Slipped disc: disc core protrudes; may press on a nerve

Skeletal muscle structure

• Muscle → bundles → fibres (multinucleate cells) → myofibrils → sarcomeres (Z line to Z line)
• Thin (actin) and thick (myosin) filaments; A band (myosin length) stays constant; I band and H zone shorten
• Properties of all muscle: contractility, excitability, extensibility, elasticity
• Accepted model: sliding filament theory

Contraction

Cross-bridge order: ATP hydrolysed (high-energy head) → binds actin → power stroke (ADP, Pi released) → new ATP detaches.

Key terms

Why Mendel succeeded (garden pea, Pisum sativum)

• Short generation time, many seeds per cross
• Naturally self-pollinating, yet easy to cross artificially (emasculation)
• Seven clear-cut contrasting characters
• Started with true-breeding lines; studied one character at a time
• Large samples, counted offspring, applied statistics; kept careful records

Mendel's two laws

• Law of segregation: the two alleles of a gene separate during gamete formation, so each gamete carries one allele (basis: separation of homologues in anaphase I)
• Law of independent assortment: alleles of different genes segregate independently (basis: random orientation of bivalents in metaphase I) — true only for genes on different chromosomes or far apart

Single-gene human traits

Reading a pedigree

• □ male, ○ female; shaded = affected; horizontal line = mating; vertical = offspring
• Autosomal recessive: skips generations; two unaffected parents can have an affected child
• Autosomal dominant: every affected child has an affected parent; no skipping
• X-linked recessive: mostly males; passed from carrier mothers; never father → son

Incomplete dominance

Heterozygote is intermediate. Mirabilis jalapa (four o'clock): red × white → all pink F₁; F₂ 1 red : 2 pink : 1 white. Phenotype ratio = genotype ratio.

Codominance

Both alleles fully expressed in the heterozygote. ABO blood group: I^AI^B → group AB (both A and B antigens).

Multiple alleles (polyallelism)

More than two alleles in the population (each person still has two). ABO: I^A, I^B, i. I^A = I^B (codominant) > i.

Epistasis

One gene masks/modifies the expression of another (non-allelic) gene.

• Dominant epistasis — fowl plumage: dominant inhibitor allele suppresses colour → 13 : 3 (white : coloured)
• Recessive (complementary) epistasis — sweet pea flower colour: purple needs at least one dominant allele of both genes → 9 : 7 (purple : white)

Polygenic inheritance

Many genes with additive small effects → continuous variation, normal (bell-shaped) distribution. Examples: human skin colour, height. Environment adds further spread.

Pleiotropy

One gene → multiple phenotypic effects.

• Sickle-cell: one Hb mutation → anaemia, pain, organ damage, malaria resistance in carriers
• Cystic fibrosis: autosomal recessive, defective CFTR chloride channel → thick mucus in lungs, pancreas, sterility

Epigenetics & environment

• Heritable change in gene expression without change in DNA sequence — DNA methylation (silences), histone modification
• Identical twins can differ (e.g. only one develops schizophrenia)
• Environment shapes phenotype: Hydrangea colour with soil pH; Himalayan rabbit fur with temperature

Linkage

• Genes on the same chromosome tend to be inherited together → violate independent assortment
• Morgan's Drosophila: body colour (grey G / black g) and wing size (normal N / vestigial n)
• Test cross GgNn × ggnn gives mostly parental types plus few recombinants

Crossing over & maps

• Exchange between non-sister chromatids at chiasmata (prophase I) → recombinants
• Recombination frequency = recombinants ÷ total offspring × 100
• 1% recombination = 1 map unit (centimorgan); farther apart → more crossing over (max ≈ 50%)

Sex determination (humans)

• XX female, XY male — the male is heterogametic; father's sperm decides the sex
• SRY gene on Y triggers testis development
• Other systems: ZW (birds — female ZW), XO (grasshopper), haplodiploidy (bees)

X-linked recessive disorders

• Red–green colour blindness, haemophilia
• Males hemizygous (X^hY affected); females need two copies
• Carrier mother × normal father → ½ sons affected, ½ daughters carriers
• Affected father → all daughters carriers, no sons affected

Five conditions for equilibrium

1. No mutation
2. Random mating
3. No natural selection
4. Very large population (no genetic drift)
5. No migration (gene flow)

Any violation → allele frequencies change = microevolution.

Worked example

If p = 0.8, q = 0.2:
AA = p² = 0.64 · Aa = 2pq = 0.32 · aa = q² = 0.04

Typical question: 1 in 100 people is affected by a recessive trait → q² = 0.01, q = 0.1, p = 0.9, carriers = 2pq = 0.18 (18%).

Agents of change

• Natural selection — peppered moth (Biston betularia): dark form rose during industrial soot pollution
• Genetic drift — bottleneck, founder effect (small populations)
• Gene flow — migration
• Mutation — the ultimate source of new alleles
• Non-random mating — changes genotype, not allele, frequencies

Disadvantages of artificial breeding

• Loss of genetic diversity → vulnerability to new diseases
• Inbreeding depression
• Negative correlated responses: bulldog skull (breathing problems), Texel sheep and Belgian Blue cattle (double muscling → calving difficulty)

Prokaryote vs eukaryote genome

Levels of packing

Chromatin

• Euchromatin — loosely packed, transcriptionally active
• Heterochromatin — tightly packed, mostly inactive (e.g. centromeres, Barr body)

Transcription

• RNA polymerase binds the promoter (TATA box in eukaryotes), unwinds DNA
• Reads the template (antisense) strand 3′→5′; makes RNA 5′→3′; no primer needed
• mRNA sequence = coding (sense) strand with U for T
• Ends at terminator; DNA rewinds

Eukaryotic RNA processing

• 5′ cap (modified G) and 3′ poly-A tail — protect and aid export/translation
• Splicing: introns removed, exons joined (spliceosome)
• Alternative splicing → several proteins from one gene

Genetic code

• Triplet codons; 64 codons, 61 sense, 3 stop (UAA, UAG, UGA)
• Start codon AUG = methionine
• Degenerate (redundant), unambiguous, non-overlapping, comma-less, nearly universal

Ribosome sites

• A site — aminoacyl-tRNA enters
• P site — peptidyl-tRNA holds growing chain
• E site — empty tRNA exits
• Small subunit binds mRNA; large subunit catalyses peptide bonds (rRNA = ribozyme)

tRNA

Clover-leaf; anticodon loop pairs with codon; 3′ CCA end carries the amino acid (attached by aminoacyl-tRNA synthetase using ATP).

Polyribosomes & fate of proteins

• Many ribosomes translate one mRNA at once
• Free ribosomes → cytosolic proteins; ER-bound → secreted / membrane proteins
• Faulty or unneeded proteins tagged with ubiquitin → destroyed in proteasomes