interpret and construct genetic diagrams, including Punnett squares, to explain and predict the results of test crosses

Objective

Interpret and construct genetic diagrams (Punnett squares, test‑cross diagrams, linkage maps) and, together with population‑genetics calculations, explain and predict the outcomes of genetic crosses and the inheritance of traits. The notes also integrate the core biological concepts required by the Cambridge IGCSE/A‑Level syllabus.

1. Cell Structure

• Prokaryotic vs. eukaryotic cells – no nucleus or membrane‑bound organelles in prokaryotes; eukaryotes have a nucleus, mitochondria, chloroplasts (plants), ER, Golgi, etc.
• Microscopy – light microscope (up to ~0.2 µm), electron microscope (TEM/SEM, up to ~0.01 µm) for organelle detail.
• Key organelles

  • Nucleus: DNA storage, nucleolus (rRNA synthesis).
  • Mitochondria: site of aerobic respiration (inner membrane folds – cristae).
  • Chloroplasts: thylakoid stacks (grana) for photosynthesis.
  • Endoplasmic reticulum: rough (ribosomes) – protein synthesis; smooth – lipid synthesis, detox.
  • Golgi apparatus: modification, sorting, packaging of proteins.
  • Vacuoles, lysosomes, peroxisomes – storage, digestion, detox.

2. Biological Molecules

3. Enzymes

• Structure – protein (or ribozyme) with a specific active site that binds substrate(s).
• Factors affecting activity

  • Temperature (optimum, denaturation)
  • pH (optimum, ionisation of active‑site residues)
  • Substrate concentration – Michaelis–Menten kinetics (Vmax, Km).

• Inhibition

  • Competitive – substrate analogue binds active site (increased Km, Vmax unchanged).
  • Non‑competitive – inhibitor binds elsewhere (Vmax ↓, Km unchanged).

• Cofactors & co‑enzymes – metal ions (Zn²⁺, Mg²⁺) or organic molecules (NAD⁺, coenzyme A).

4. Cell Membranes & Transport

• Fluid‑mosaic model – phospholipid bilayer with embedded proteins (integral, peripheral) that move laterally.
• Passive transport

  • Diffusion – movement down a concentration gradient.
  • Osmosis – diffusion of water across a semi‑permeable membrane.
  • Facilitated diffusion – carrier or channel proteins.

• Active transport

  • Primary – ATP‑driven pumps (Na⁺/K⁺‑ATPase).
  • Secondary – cotransport (symport/antiport) using ion gradients.

• Tonicity – hypertonic, hypotonic, isotonic solutions and their effects on animal cells (crenation, lysis) and plant cells (plasmolysis, turgor).

5. Mitotic Cell Cycle

• Interphase – G₁ (growth), S (DNA replication), G₂ (pre‑mitosis).
• Mitosis –

  1. Prophase – chromatin → chromosomes, spindle formation.
  2. Metaphase – chromosomes line up at the equatorial plate.
  3. Anaphase – sister chromatids separate to opposite poles.
  4. Telophase – nuclear envelopes reform, chromosomes de‑condense.

• Cytokinesis – division of cytoplasm (cleavage furrow in animal cells, cell plate in plant cells).
• Checkpoints & telomeres – G₁/S, G₂/M, spindle checkpoint; telomere shortening limits division (cellular ageing) and its maintenance by telomerase in cancer cells.

6. Nucleic Acids & Protein Synthesis

6.1 DNA Structure & Replication

• Double helix, antiparallel strands, complementary base pairing (A–T, G–C).
• Replication origins → replication fork; enzymes: helicase, DNA polymerase (5’→3’), primase, ligase, topoisomerase.
• Proofreading (exonuclease activity) reduces mutation rate.

6.2 Transcription (Nucleus)

1. RNA polymerase binds promoter (with transcription factors).
2. Elongation – synthesis of pre‑mRNA (5’→3’).
3. Termination – release of transcript.
4. RNA processing – 5’ cap, poly‑A tail, splicing (introns removed, exons joined).

6.3 Translation (Cytoplasm)

1. mRNA binds to ribosome (small subunit → start codon AUG).
2. tRNA anticodon pairs with codon; amino‑acid added to growing polypeptide chain (large subunit).
3. Termination at stop codons (UAA, UAG, UGA) – release factors release the protein.

6.4 Types of Mutations

7. Transport in Plants

• Xylem – water & mineral transport upward; tracheids & vessel elements; cohesion‑tension theory.
• Phloem – transport of photosynthates (sucrose) from source to sink; sieve‑tube elements + companion cells; pressure‑flow hypothesis.
• Water potential (Ψ) – Ψ = Ψ_s + Ψ_p; movement from higher to lower Ψ.
• Mass‑flow – bulk movement of solutes driven by osmotic pressure differences.

8. Transport in Mammals (Circulatory System & Heart)

• Blood vessels – arteries (thick muscular walls), veins (valves), capillaries (thin walls for exchange).
• Blood composition – plasma (water, proteins, nutrients), cells (RBCs, WBCs, platelets).
• Hemoglobin – tetrameric protein, each subunit binds one O₂; cooperative binding (sigmoidal O₂‑dissociation curve).
• Heart cycle – atrial systole, ventricular systole, diastole; valves prevent backflow; cardiac output = HR × SV.

9. Gas Exchange

• Lung anatomy – trachea → bronchi → bronchioles → alveolar sacs; alveolar walls thin, surrounded by capillaries.
• Diffusion – driven by partial pressure gradients of O₂ and CO₂ (Fick’s law).
• Ventilation – inhalation (diaphragm contraction, thoracic cavity expansion) and exhalation (relaxation).
• Control of breathing – medulla oblongata chemoreceptors (pCO₂, pH) and stretch receptors.

10. Infectious Diseases

• Antibiotic resistance – selective pressure, plasmid‑borne resistance genes.
• Vaccination – active immunity (attenuated, subunit, mRNA vaccines).

11. Immunity

• Innate immunity – physical barriers, phagocytes (macrophages, neutrophils), complement, inflammation.
• Adaptive immunity

  • B‑cells → plasma cells → antibodies (IgM, IgG, IgA, IgE, IgD).
  • T‑cells – cytotoxic (CD8⁺) kill infected cells; helper (CD4⁺) coordinate response.
  • Memory cells → faster secondary response.

• Vaccination – mimics primary exposure without disease, generates memory.

12. Energy & Respiration

• ATP – energy currency; produced by substrate‑level phosphorylation and oxidative phosphorylation.
• Glycolysis (cytoplasm) – glucose → 2 pyruvate + 2 ATP + 2 NADH.
• Link reaction & Krebs cycle (mitochondrial matrix) – pyruvate → Acetyl‑CoA → CO₂, NADH, FADH₂, GTP.
• Electron transport chain (ETC) – inner mitochondrial membrane; proton gradient drives ATP synthase (≈34 ATP).
• Respiratory quotient (RQ) – CO₂ produced / O₂ consumed; RQ ≈ 1 for carbohydrates, 0.7 for fats.

13. Photosynthesis

• Chloroplast structure – outer/inner membranes, stroma, thylakoid stacks (grana).
• Light‑dependent reactions – water splitting (O₂ released), NADPH and ATP formed; photosystems II & I, electron transport, photophosphorylation.
• Calvin cycle (light‑independent) – CO₂ fixation (Rubisco), reduction phase (G3P), regeneration of RuBP; consumes ATP & NADPH.
• Pigments – chlorophyll a (primary), chlorophyll b, carotenoids; absorb 400–700 nm (visible spectrum).

14. Homeostasis

• Feedback mechanisms – negative feedback (most common, e.g., blood glucose regulation), positive feedback (e.g., oxytocin during labour).
• Osmoregulation – kidney nephrons, ADH control of water re‑absorption.
• Temperature control – hypothalamic set‑point, vasodilation/constriction, sweating, shivering.

15. Control & Coordination

• Nervous system – neurons (axon, dendrite, synapse), action potential, reflex arc, CNS vs PNS.
• Endocrine system – hormones (peptide, steroid, amine); target‑cell receptors; examples: insulin, glucagon, adrenaline, thyroid hormones.
• Integration – hypothalamus links nervous and endocrine responses.

16. Mendelian Genetics & Genetic Diagrams

16.1 Monohybrid Punnett Square

1. Write parental genotypes.
2. List possible gametes for each parent.
3. Place one parent’s gametes across the top, the other’s down the side.
4. Combine gametes to fill the squares – each square = a possible genotype.
5. Convert genotype ratio to phenotype ratio using the dominance relationship.

Result: 100 % Aa (heterozygous). Phenotype = dominant trait.

16.2 Dihybrid Punnett Square (Independent Assortment)

Cross: RrYy × RrYy (R = round, r = wrinkled; Y = yellow, y = green).

Phenotypic ratio (9:3:3:1): 9 round yellow : 3 round green : 3 wrinkled yellow : 1 wrinkled green.

16.3 Test Crosses

• Purpose – determine the genotype of an individual that shows the dominant phenotype.
• Method – cross the unknown dominant individual with a homozygous recessive (aa) partner.
• Interpretation

  • All offspring dominant → unknown parent is AA.
  • ≈1:1 dominant : recessive → unknown parent is Aa.

16.4 Linkage & Recombination

• Genes on the same chromosome may be linked and do not assort independently.
• Cross‑overs during meiosis produce recombinant gametes.
• Recombination frequency (RF) = (Number of recombinant progeny / Total progeny) × 100 %.
• 1 % ≈ 1 centiMorgan (cM); genetic maps are built by adding distances between linked loci.
• Example: In a test cross, 400 progeny give 40 recombinants → RF = 10 % → genes are 10 cM apart.

16.5 Epistasis & Polygenic Traits

• Epistasis – one gene masks or modifies the expression of another (e.g., Labrador coat colour: B = black/brown pigment, E = pigment deposition). Typical phenotypic ratios: 9:7, 12:3:1, 15:1.
• Polygenic inheritance – many genes contribute additively (e.g., human skin colour, height) → continuous variation rather than discrete ratios.

17. Quantitative Genetics – Hardy–Weinberg Equilibrium

17.1 Equation

For a diploid population with two alleles A (frequency p) and a (frequency q):

\[

p^{2}+2pq+q^{2}=1

\]

• p² = frequency of AA
• 2pq = frequency of Aa
• q² = frequency of aa

Assumptions: large population, random mating, no mutation, migration or selection.

17.2 Worked Example

Population: 200 pea plants; 180 tall (dominant), 20 short (recessive).

• Short plants are aa → q² = 20/200 = 0.10 → q ≈ 0.316.
• p = 1 – q ≈ 0.684.
• Predicted genotype frequencies:

  • AA = p² ≈ 0.468 ≈ 94 plants
  • Aa = 2pq ≈ 0.432 ≈ 86 plants
  • aa = q² = 0.10 ≈ 20 plants

• If the population mates at random, these frequencies remain constant in the next generation (no evolutionary forces).

18. Genetic Technology

• Polymerase Chain Reaction (PCR) – exponential amplification of a specific DNA fragment using primers, Taq polymerase, and thermal cycling.
• Gel electrophoresis – separates DNA fragments by size; visualises PCR products or restriction digests.
• DNA sequencing – Sanger (chain‑termination) and next‑generation methods reveal nucleotide order.
• CRISPR‑Cas9 – targeted genome editing; guide RNA directs Cas9 to cut at a specific locus, enabling knock‑out or insertion.
• Genetically Modified Organisms (GMOs) – transgenic plants/animals with introduced traits (e.g., Bt cotton, insulin‑producing bacteria).

19. Evolutionary Context

• Natural selection – differential survival/reproduction of phenotypes with a genetic basis; advantageous alleles increase in frequency.
• Genetic drift – random changes in allele frequencies, especially in small populations (bottleneck, founder effects).
• Gene flow – migration of individuals or gametes introduces new alleles.
• All three mechanisms can be illustrated with deviations from Hardy–Weinberg expectations.

20. Biodiversity, Classification & Conservation

• DNA barcoding – short mitochondrial COI (animals) or rbcL (plants) sequences used to identify species.
• Microsatellites & RAPD markers – assess genetic diversity within and between populations; important for managing endangered species.
• Conservation strategies often aim to maintain genetic variability to enhance adaptive potential.

21. Common Pitfalls

• Confusing genotype with phenotype – always state both.
• Assuming independent assortment for linked genes; check map distance first.
• Overlooking epistatic interactions that alter expected Mendelian ratios.
• Applying Hardy–Weinberg without confirming its assumptions (e.g., small population = drift).
• Neglecting gene regulation, environmental effects, or post‑translational modifications when linking genotype to phenotype.

22. Summary Checklist

1. Identify the relevant cell structures and molecules for the process being studied.
2. State the type of inheritance (complete, incomplete, codominant, sex‑linked, polygenic, epistatic).
3. Construct the appropriate Punnett square (mono‑, di‑, or test cross) and derive genotype ↔ phenotype ratios.
4. Determine whether genes are linked; calculate recombination frequency and draw a linkage map if required.
5. Apply Hardy–Weinberg equations to calculate allele frequencies and test for equilibrium.
6. Consider possible mutations, environmental influences, and regulatory mechanisms that could modify the expected outcome.
7. Use genetic technology (PCR, sequencing, CRISPR) to verify genotypes or create experimental crosses.
8. Relate the genetic outcome to evolutionary processes (selection, drift, gene flow) and to conservation concerns.