Genetics BZO3T06

Syllabus topics (RTMNU)

• 1.1 Mendelian Genetics: Mendel's laws of inheritance (Law of segregation, Law of independent assortment), Monohybrid and dihybrid crosses, Test cross and back cross.
• 1.2 Interaction of genes: Epistasis: dominant epistasis (12:3:1) e.g. coat colour in dog (Brown dog X white dog); recessive epistasis (9:3:4) e.g. coat colour in mice. Codominance e.g. Roan cattle; incomplete dominance e.g. Andalusian fowl.
• 1.3 Extracellular genome: Presence and functions of mitochondrial DNA. Plasmids- Types and significance.
• 1.4 Genetic Variation: Chromosomal aberrations (deletions, duplications, inversions, translocations), Spontaneous and induced mutations. Types of point mutation- deletion, insertion, substitution, transversion, transition, frameshift mutation.

1.1 Mendelian Genetics: Laws of Inheritance, Monohybrid and Dihybrid Crosses, Test Cross and Back Cross

Gregor Johann Mendel (1822–1884), an Austrian monk, is the Father of Genetics. He worked on the garden pea (Pisum sativum) for about 8 years and published his results in 1866. His work was rediscovered in 1900 by de Vries, Correns and Tschermak.

Law of Segregation (Law of purity of gametes)

The two alleles of a gene stay together in the individual but separate (segregate) during gamete formation, so each gamete gets only one allele. Gametes are always "pure".

Monohybrid cross (one character)

1. P: Tall (TT) × Dwarf (tt)
2. Gametes: T and t
3. F1: all Tall (Tt)
4. F1 selfed: Tt × Tt → F2: TT : Tt : tt = 1 : 2 : 1

Phenotypic ratio 3 : 1 (3 tall : 1 dwarf); genotypic ratio 1 : 2 : 1.

Law of Independent Assortment

When two or more pairs of characters are inherited together, the alleles of one pair assort independently of the other pair during gamete formation. (True for genes on different chromosomes.)

Dihybrid cross (two characters)

1. P: Round Yellow (RRYY) × Wrinkled Green (rryy)
2. F1: all Round Yellow (RrYy)
3. F1 forms 4 types of gametes in equal numbers: RY, Ry, rY, ry
4. F2 (16 boxes in Punnett square): 9 Round Yellow : 3 Round Green : 3 Wrinkled Yellow : 1 Wrinkled Green

Dihybrid phenotypic ratio = 9 : 3 : 3 : 1; genotypic ratio = 1 : 2 : 2 : 4 : 1 : 2 : 1 : 2 : 1 (9 genotypes).

Test cross and back cross

Every test cross is a back cross, but every back cross is not a test cross.

1.2 Interaction of Genes: Epistasis, Codominance and Incomplete Dominance

Gene interaction means two or more genes together control one character, so Mendel's 9 : 3 : 3 : 1 ratio gets modified.

Epistasis: one gene (epistatic) masks the effect of another non-allelic gene (hypostatic). It is different from dominance, which is between alleles of the same gene.

Dominant epistasis (12 : 3 : 1) – coat colour in dog

• Gene I (dominant inhibitor) stops pigment → dog is white, whatever the B gene is.
• Gene B = black, b = brown; they show only when genotype is ii.

1. P: Brown dog (iibb) × White dog (IIBB)
2. F1: all White (IiBb)
3. F2: 9 I_B_ (white) + 3 I_bb (white) = 12 White : 3 iiB_ Black : 1 iibb Brown

Recessive epistasis (9 : 3 : 4) – coat colour in mice

• Gene C is needed for any colour; cc = albino (masks gene A).
• Gene A = agouti (grey), a = black.

1. P: Agouti (AACC) × Albino (aacc)
2. F1: all Agouti (AaCc)
3. F2: 9 A_C_ Agouti : 3 aaC_ Black : 4 (3 A_cc + 1 aacc) Albino

Codominance – Roan cattle

Both alleles express fully and together in the heterozygote. Red cattle (RR) × White cattle (WW) → F1 Roan (RW) with a mixture of red and white hairs. F2: 1 Red : 2 Roan : 1 White. Other example: AB blood group.

Incomplete dominance – Andalusian fowl

Neither allele is fully dominant; the heterozygote is intermediate. Black fowl × Splashed-white fowl → F1 Blue (bluish-grey). F2: 1 Black : 2 Blue : 1 White. Here phenotypic and genotypic ratios are the same, 1 : 2 : 1.

1.3 Extranuclear (Extracellular) Genome: Mitochondrial DNA and Plasmids

The syllabus says "extracellular genome"; it means the genome outside the nucleus (extranuclear/extrachromosomal).

Mitochondrial DNA (mtDNA)

• Double-stranded, circular, naked (no histones), present in many copies in each mitochondrion.
• Human mtDNA = 16,569 bp with 37 genes: 13 for proteins of the respiratory chain, 22 tRNA and 2 rRNA genes.
• Maternal inheritance: passed only from mother to all children, because the egg gives the cytoplasm.
• Functions: codes some proteins for ATP production (oxidative phosphorylation); mitochondria are semi-autonomous.
• Uses: tracing maternal lineage, human evolution ("Mitochondrial Eve"), forensic identification.
• Diseases from mtDNA mutation: LHON (Leber's hereditary optic neuropathy), MERRF.

Plasmids

Small, circular, double-stranded DNA in bacteria (and yeast) that replicates independently of the main chromosome. A plasmid that can join the bacterial chromosome is called an episome (e.g. F factor).

Significance: spread of antibiotic resistance; used as cloning vectors in genetic engineering (pBR322, pUC19); Ti plasmid used to make transgenic plants.

1.4 Genetic Variation: Chromosomal Aberrations and Mutations

Chromosomal aberrations (structural changes)

• Deletion: loss of a segment (terminal or interstitial). E.g. cri-du-chat syndrome (5p deletion).
• Duplication: a segment repeated. E.g. Bar eye in Drosophila.
• Inversion: segment breaks and rejoins after turning 180°. Paracentric (centromere outside the segment) and pericentric (centromere inside).
• Translocation: segment moves to a non-homologous chromosome. Reciprocal (exchange) or Robertsonian (fusion of two acrocentrics). E.g. Philadelphia chromosome t(9;22).

Mutation

A sudden, heritable change in the genetic material (term by Hugo de Vries).

• Spontaneous mutation: occurs naturally without known cause, at a low rate – errors in replication, tautomeric shifts of bases, depurination.
• Induced mutation: caused by mutagens. Physical: X-rays, gamma rays, UV (forms thymine dimers). Chemical: base analogues (5-bromouracil), nitrous acid (deamination), alkylating agents (EMS), acridine dyes (frameshift). H. J. Muller first induced mutations with X-rays in Drosophila (1927).

Types of point mutation (gene mutation)

• Substitution: one base replaced by another.
  • Transition: purine → purine or pyrimidine → pyrimidine (A↔G, C↔T).
  • Transversion: purine ↔ pyrimidine (e.g. A→T, G→C).
• Insertion: one or more extra bases added.
• Deletion: one or more bases lost.
• Frameshift mutation: insertion or deletion of bases (not in multiples of 3) shifts the reading frame, so all codons after it change. E.g. THE CAT ATE THE RAT → delete one letter → THE ATA TET HER AT.

Effects of substitution: silent (same amino acid), missense (new amino acid, e.g. sickle-cell: GAG→GTG, glutamic acid → valine), nonsense (stop codon formed).

Likely exam questions

1. (Long, 8 marks) State Mendel's law of independent assortment and explain it with a dihybrid cross and Punnett square.
2. (Long, 8 marks) What is epistasis? Explain dominant epistasis in dog and recessive epistasis in mice with suitable crosses.
3. (Short, 4 marks) Differentiate between test cross and back cross.
4. (Short, 4 marks) Write a note on plasmids – types and significance.
5. (Short, 4 marks) Explain transition, transversion and frameshift mutation with examples.

Syllabus topics (RTMNU)

• 2.1 Chromosome Theory of Inheritance: Linkage and crossing over: types and significance, Chromosomal mapping in eukaryotes.
• 2.2 Cytoplasmic inheritance: Kappa particles in Paramecium, CO2 sensitivity in Drosophila, milk factor in mice.
• 2.3 Pedigree analysis: Pedigree analysis, Autosomal Recessive Inheritance, Autosomal Dominant Inheritance, X-linked recessive Inheritance, X-linked dominant Inheritance, and Y linked inheritance.
• 2.4 Concepts of genes: Classical concept of gene, Molecular concept of gene- Cistron, Muton and Recon.

2.1 Chromosome Theory of Inheritance, Linkage, Crossing Over and Chromosomal Mapping

Chromosome theory of inheritance

Proposed by W. S. Sutton and T. Boveri (1902–03). It states that genes are located on chromosomes, and the behaviour of chromosomes in meiosis explains Mendel's laws.

• Chromosomes, like genes, occur in pairs (homologous pairs).
• Homologous chromosomes separate in meiosis → explains segregation.
• Different pairs orient randomly at metaphase I → explains independent assortment.
• Gametes get one chromosome of each pair; fertilisation restores the pair.

T. H. Morgan proved it experimentally with sex-linked white eye in Drosophila.

Linkage

Linkage is the tendency of genes located on the same chromosome to be inherited together. Discovered by Bateson and Punnett (1906) in sweet pea (they called it coupling and repulsion); explained by Morgan (1910) in Drosophila.

• Complete linkage: linked genes always stay together; only parental types are formed. E.g. male Drosophila (no crossing over in males).
• Incomplete linkage: linked genes sometimes separate by crossing over, so a few recombinants appear. E.g. female Drosophila, maize.

Closer the genes, stronger the linkage. All genes on one chromosome form a linkage group; the number of linkage groups = haploid chromosome number (4 in Drosophila, 23 in humans).

Crossing over

Exchange of segments between non-sister chromatids of homologous chromosomes during pachytene of prophase I of meiosis. The visible cross point (seen at diplotene) is the chiasma.

Steps: synapsis (zygotene) → duplication into four chromatids (tetrad) → breakage and exchange of segments, enzyme recombinase (pachytene) → chiasma formation and terminalisation (diplotene, diakinesis).

Types:

• Single, double and multiple crossing over (one, two or more chiasmata).
• Germinal (meiotic) – in germ cells, common; somatic (mitotic) – in body cells, rare (Stern, Drosophila).

Significance: produces new combinations of genes (variation) – raw material for evolution; proves genes are arranged linearly; frequency of crossing over is used to make chromosome maps; helps plant and animal breeders get useful recombinants.

Chromosomal mapping in eukaryotes

A linkage map (genetic map) shows the order of genes and relative distances between them on a chromosome. First made by A. H. Sturtevant (1913).

• Recombination frequency (RF) = (number of recombinants ÷ total offspring) × 100.
• 1% recombination = 1 map unit = 1 centiMorgan (cM).
• Done by a three-point test cross.

Example: a–b = 10%, b–c = 4%, a–c = 14%. Since 10 + 4 = 14, gene b lies between a and c: a —10— b —4— c.

Interference: one crossover reduces the chance of another nearby. Coefficient of coincidence = observed double crossovers ÷ expected double crossovers; Interference = 1 − coefficient of coincidence.

2.2 Cytoplasmic Inheritance: Kappa Particles, CO₂ Sensitivity and Milk Factor

Cytoplasmic (extranuclear) inheritance is controlled by genes or particles present in the cytoplasm. Features: reciprocal crosses give different results; inheritance is usually maternal; Mendelian ratios are not seen.

Kappa particles in Paramecium (T. M. Sonneborn, 1938)

• "Killer" strains of Paramecium aurelia have kappa particles in the cytoplasm; they release a toxin, paramecin, that kills "sensitive" strains.
• Kappa particles are now known to be symbiotic bacteria (Caedibacter taeniospiralis), containing DNA.
• Kappa can multiply only when the nuclear dominant gene K is present (KK or Kk). In kk animals kappa is lost.

Conjugation experiment: Killer (KK + kappa) × Sensitive (kk). Both exconjugants become Kk.

1. Short conjugation (no cytoplasm exchange): the killer-side exconjugant stays killer (Kk + kappa); the sensitive-side one stays sensitive (Kk, no kappa).
2. Long conjugation (cytoplasm exchanged): both get kappa → both killers.
3. After autogamy, Kk gives KK or kk; kk lines lose kappa and become sensitive.

So the killer trait needs both the nuclear gene K and cytoplasmic kappa.

CO₂ sensitivity in Drosophila (L'Héritier and Teissier, 1937)

• Normal flies recover from CO₂ exposure; sensitive flies become permanently paralysed or die even after a short exposure.
• Cause: a virus-like particle, sigma (σ) virus, in the cytoplasm.
• Transmitted mainly through the egg cytoplasm: sensitive female × normal male → offspring sensitive; normal female × sensitive male → offspring mostly normal (rarely sensitive by sperm).

Milk factor in mice (J. J. Bittner, 1936)

• Some mouse strains show high incidence of mammary (breast) cancer.
• High-cancer female × low-cancer male → young get cancer; reciprocal cross → young mostly free of cancer.
• Foster-nursing: young of a high-cancer mother nursed by a low-cancer mother are mostly cancer-free, and vice versa.
• So the factor passes through the mother's milk – the "milk factor", now known as mouse mammary tumour virus (MMTV).
• Cancer also needs a susceptible genotype and hormones.

2.3 Pedigree Analysis and Modes of Inheritance

Pedigree analysis is the study of a trait over several generations of a family using a chart (pedigree). It is used in humans because controlled crosses are not possible.

Symbols: square = male, circle = female, shaded = affected, half-shaded or dot = carrier, horizontal line = marriage, double line = consanguineous marriage, vertical line = offspring; generations in Roman numerals (I, II, III).

2.4 Concepts of Gene: Classical and Molecular (Cistron, Muton, Recon)

Classical concept

• Mendel called genes "factors"; W. Johannsen (1909) coined the word "gene".
• Morgan: genes are arranged linearly on chromosomes like beads on a string.
• The gene was thought to be one indivisible unit of function, mutation and recombination.
• Beadle and Tatum (1941, Neurospora): one gene–one enzyme hypothesis (later one gene–one polypeptide).

Molecular concept (Seymour Benzer, 1955–61)

Benzer studied the rII locus of T4 bacteriophage and showed the gene is divisible. He named three sub-units:

• Cistron: unit of function; a DNA segment coding one polypeptide; identified by the cis-trans complementation test. Most like the modern gene.
• Muton: smallest unit of mutation; can be a single nucleotide pair.
• Recon: smallest unit of recombination; one nucleotide pair, as crossing over can happen between adjacent nucleotides.

Today a gene is a DNA sequence coding a functional product (polypeptide or RNA).

Likely exam questions

1. (Long, 8 marks) What is linkage? Explain complete and incomplete linkage. Describe the mechanism and significance of crossing over.
2. (Long, 8 marks) What is cytoplasmic inheritance? Explain kappa particles in Paramecium and milk factor in mice.
3. (Short, 4 marks) Write the characteristics of X-linked recessive inheritance with a pedigree example.
4. (Short, 4 marks) Explain cistron, muton and recon.
5. (Short, 4 marks) How is a chromosome map prepared? Explain with an example.

Syllabus topics (RTMNU)

• 3.1 Population Genetics: Gene pool and allele frequency, Hardy-Weinberg principle and its applications, Factors affecting genetic equilibrium (mutation, migration, selection, genetic drift).
• 3.2 Quantitative Genetics: Polygenic inheritance and continuous variation e.g. Skin colour in human, eye colour in human, sickle-cell anaemia. Inbreeding and outbreeding, hybrid vigor.
• 3.3 Speciation and Evolution: Species concepts and speciation mechanisms (Parapatric, Sympatric and Allopatric Speciation), Adaptive radiation, divergent and convergent evolution.
• 3.4 Human Genetics: Karyotyping and chromosomal disorders (Down syndrome, Turner syndrome, Klinefelter syndrome), Genetic counseling and prenatal diagnosis (Aminocentesis and Chorionic villi test).

3.1 Population Genetics: Gene Pool, Allele Frequency, Hardy–Weinberg Principle

• Population (Mendelian population): a group of interbreeding individuals of one species living in one area.
• Gene pool: the total of all alleles of all genes present in a population at a given time.
• Allele (gene) frequency: the proportion of one allele among all alleles of that gene in the population.

Allele frequency of A = (2 × number of AA + number of Aa) ÷ (2 × total individuals).

Hardy–Weinberg principle (G. H. Hardy and W. Weinberg, 1908)

In a large, randomly mating population, allele and genotype frequencies remain constant from generation to generation if no evolutionary forces act. This state is called genetic equilibrium.

• If p = frequency of A and q = frequency of a, then p + q = 1.
• Genotype frequencies: p² + 2pq + q² = 1 (p² = AA, 2pq = Aa, q² = aa).

Conditions (assumptions): large population; random mating; no mutation; no migration (gene flow); no natural selection; no genetic drift.

Worked example: In 1000 people, 160 are albino (aa). q² = 160/1000 = 0.16 → q = 0.4, p = 0.6. AA = p² = 0.36 (360 people); carriers Aa = 2pq = 0.48 (480 people).

Applications: calculating carrier frequency of recessive diseases (useful in genetic counselling); testing whether a population is evolving (a change from equilibrium = evolution); estimating mutation rates and effect of selection.

Factors affecting genetic equilibrium

• Mutation: adds new alleles; changes allele frequency slowly.
• Migration (gene flow): entry or exit of individuals brings in or removes alleles.
• Natural selection: individuals with favourable alleles leave more offspring, so those alleles increase.
• Genetic drift: random change in allele frequency, strongest in small populations. Founder effect – few individuals start a new population; bottleneck effect – population size crashes.

3.2 Quantitative Genetics: Polygenic Inheritance, Inbreeding, Outbreeding and Hybrid Vigour

Polygenic inheritance

A character controlled by many genes (polygenes), each with a small additive effect, is a quantitative trait. It shows continuous variation – many intermediate forms instead of clear classes – and the graph is a bell-shaped (normal) curve.

Skin colour in humans (Davenport): controlled by about 3 gene pairs (A, B, C); each dominant allele adds melanin.

1. P: Very dark (AABBCC) × Very fair (aabbcc)
2. F1: AaBbCc – intermediate colour (mulatto)
3. F2: 7 classes in ratio 1 : 6 : 15 : 20 : 15 : 6 : 1 (from 0 to 6 dominant alleles)

(Davenport's first model used 2 gene pairs → 1 : 4 : 6 : 4 : 1.)

Eye colour in humans: also polygenic. Amount of melanin in the iris decides brown, hazel, green or blue; main genes are OCA2 and HERC2 on chromosome 15, so many shades occur.

Sickle-cell anaemia (listed in syllabus): note that it is actually a single-gene (monogenic) trait, given here as a contrast – it shows discontinuous classes: normal (HbA HbA), sickle-cell trait carrier (HbA HbS) and diseased (HbS HbS). Details in Unit 4.1.

Inbreeding and outbreeding

• Inbreeding: mating between closely related individuals (4–6 generations in the same breed). It increases homozygosity, helps make pure lines and exposes harmful recessive genes so they can be removed. Too much causes inbreeding depression (low fertility and vigour).
• Outbreeding: mating of unrelated animals. Types: outcrossing (same breed, no common ancestor for 4–6 generations), cross-breeding (two breeds, e.g. Hisardale sheep), interspecific hybridisation (two species, e.g. mule = male donkey × female horse). Increases heterozygosity.

Hybrid vigour (heterosis)

The superiority of the F1 hybrid over both parents in growth, yield, fertility or resistance. Term "heterosis" by G. H. Shull (1914). Examples: mule, hybrid maize, cross-bred cows (Karan Swiss, Frieswal) giving more milk.

• Dominance hypothesis: harmful recessive alleles of one parent are masked by dominant alleles of the other.
• Over-dominance hypothesis: the heterozygote (Aa) itself is superior to both homozygotes.

Heterosis is highest in F1.

3.3 Speciation and Evolution: Species Concepts, Modes of Speciation, Adaptive Radiation

Species concepts

• Morphological: similar-looking individuals (Linnaeus).
• Biological species concept (Ernst Mayr, 1942): groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups. Most accepted.
• Evolutionary / phylogenetic: a lineage with its own evolutionary history and common ancestry.

Speciation = formation of new species, mainly through reproductive isolation.

Adaptive radiation

Evolution of many different forms from one ancestor, each adapted to a different habitat or way of life. Examples: Darwin's finches (different beaks for seeds, insects, cactus); Australian marsupials.

Divergent and convergent evolution

• Divergent evolution: related species become different as they adapt to different needs; produces homologous organs (same origin, different function) – forelimbs of man, whale, bat, horse.
• Convergent evolution: unrelated species become similar because they live in similar conditions; produces analogous organs (different origin, same function) – wings of insect and bird, eyes of octopus and vertebrates, flippers of penguin and dolphin.

3.4 Human Genetics: Karyotyping, Chromosomal Disorders, Genetic Counselling, Prenatal Diagnosis

Karyotyping

Karyotype is the chromosome set of an individual arranged in pairs by size and centromere position; its photo-chart is an idiogram. Method: culture blood lymphocytes → add colchicine to stop cells at metaphase → hypotonic treatment → fix and stain (Giemsa, G-banding) → photograph and arrange. Normal human: 46 chromosomes (44 autosomes + XX or XY), placed in groups A–G.

These arise by non-disjunction (failure of chromosomes to separate) during meiosis.

Genetic counselling

Advice by a trained expert to families with risk of a genetic disease: studying family history (pedigree), calculating risk, explaining the disease, tests available and options. Useful for consanguineous couples and families with sickle-cell.

Prenatal diagnosis

• Amniocentesis (written "aminocentesis" in the syllabus): at about 15–18 weeks, a little amniotic fluid is drawn by a needle through the abdomen; foetal cells are cultured for karyotype and biochemical tests.
• Chorionic villus sampling (CVS): at about 10–12 weeks, a small piece of chorionic villi is taken through the cervix or abdomen; gives earlier results.

In India, using these tests for sex determination is a crime under the PCPNDT Act, 1994.

Likely exam questions

1. (Long, 8 marks) State and explain the Hardy–Weinberg principle. Describe the factors that affect genetic equilibrium.
2. (Long, 8 marks) What is karyotyping? Describe Down, Turner and Klinefelter syndromes. Add a note on prenatal diagnosis.
3. (Short, 4 marks) Explain polygenic inheritance with the example of skin colour in man.
4. (Short, 4 marks) What is hybrid vigour? Give its explanation and examples.
5. (Short, 4 marks) Differentiate between allopatric and sympatric speciation.

Syllabus topics (RTMNU)

• 4.1 Genetic Disorders and Inborn Errors of Metabolism: Single-gene disorders (e.g., cystic fibrosis, sickle-cell anemia), Inborn errors of metabolism (e.g., phenylketonuria, alkaptonuria).
• 4.2 Cancer Genetics: Mechanism of activation of oncogenes (point mutation, gene amplification and chromosomal translocations); mechanism of inactivation of tumor suppressor genes (mutation, deletions and epigenetic silencing).
• 4.3 Epigenetics and Environmental Influence on Genes: Role of environment in gene expression, Epigenetic changes in response to environmental stimuli, Developmental plasticity and gene-environment interactions, Impact of nutrition, stress, and toxins on gene expression.
• 4.4 Applications of Genetics in Medicine and Agriculture: Gene therapy: principles and challenges, Genetic modification in livestock; Ethical, social, and legal issues in genetic research and biotechnology.

4.1 Genetic Disorders and Inborn Errors of Metabolism

Single-gene (monogenic) disorders

Caused by mutation in one gene; they follow Mendelian patterns.

(a) Cystic fibrosis

• Inheritance: autosomal recessive; gene CFTR on chromosome 7.
• Most common mutation: ΔF508 (deletion of 3 bases → phenylalanine at position 508 lost).
• CFTR protein is a chloride ion channel; when faulty, Cl⁻ and water do not move out of cells, so thick, sticky mucus forms.
• Symptoms: blocked airways and repeated lung infections, blocked pancreatic ducts (poor digestion), very salty sweat.
• Diagnosis: sweat chloride test.

(b) Sickle-cell anaemia

• Inheritance: autosomal recessive; β-globin gene (HBB) on chromosome 11.
• Point mutation (transversion): codon GAG → GTG at 6th position of β-chain, so glutamic acid is replaced by valine; normal HbA becomes HbS.
• At low oxygen, HbS polymerises and RBCs become sickle-shaped, block capillaries, and break early → anaemia, pain crises, organ damage.
• HbA HbS = sickle-cell trait (carrier, usually healthy, resistant to malaria); HbS HbS = disease.
• Common in tribal belts of central India including Vidarbha; screening and counselling are important.

Inborn errors of metabolism

Term by Sir Archibald Garrod (1908). A gene mutation causes deficiency of one enzyme, so a metabolic pathway is blocked; the substance before the block accumulates.

4.2 Cancer Genetics: Oncogenes and Tumour Suppressor Genes

Cancer is uncontrolled cell division with invasion and spread (metastasis). It results from mutations in genes that control the cell cycle.

• Proto-oncogenes: normal genes that promote cell growth (growth factors, receptors, signal proteins). When mutated/over-active they become oncogenes – a gain of function, acting dominantly (one mutant copy is enough).
• Tumour suppressor genes: normal "brakes" of cell division (e.g. RB1, p53, BRCA1). Cancer needs loss of function of both copies (recessive at cell level).

Activation of oncogenes

1. Point mutation: one base change makes the protein permanently active. E.g. RAS gene: change in codon 12 (glycine → valine) keeps Ras protein "switched on" – found in bladder, lung, colon cancers.
2. Gene amplification: many extra copies of a proto-oncogene → excess protein. E.g. N-MYC in neuroblastoma, HER2/neu in breast cancer.
3. Chromosomal translocation: (a) forms a new fusion gene – Philadelphia chromosome t(9;22) joins BCR and ABL → BCR-ABL protein, an always-active tyrosine kinase → chronic myeloid leukaemia (CML); (b) moves a gene near a strong promoter – Burkitt's lymphoma t(8;14) brings MYC next to the immunoglobulin gene → over-expression.

Inactivation of tumour suppressor genes

Knudson's two-hit hypothesis (1971, retinoblastoma): both alleles must be lost. In hereditary cases one faulty copy is inherited, so only one more "hit" is needed.

1. Mutation: point or nonsense mutations make an inactive protein. E.g. p53 ("guardian of the genome", chromosome 17) is mutated in about half of all human cancers; normally it stops the cell cycle or causes apoptosis when DNA is damaged.
2. Deletion: loss of a chromosome part removes the gene (loss of heterozygosity). E.g. deletion of 13q14 removes RB1 in retinoblastoma.
3. Epigenetic silencing: DNA sequence is normal, but hypermethylation of the promoter (CpG islands) switches the gene off. E.g. p16 (CDKN2A), MLH1, BRCA1 silenced in many cancers.

4.3 Epigenetics and Environmental Influence on Genes

Epigenetics (term by C. H. Waddington, 1942) is the study of heritable changes in gene expression that do not involve a change in the DNA sequence.

Mechanisms

• DNA methylation: methyl group added to cytosine at CpG sites by DNA methyltransferases → gene switched off.
• Histone modification: acetylation loosens chromatin → gene on; deacetylation and some methylations tighten it → gene off.
• Non-coding RNAs (miRNA) block mRNA.

Role of environment in gene expression

• Himalayan rabbit: enzyme for black pigment works only at low temperature, so only the cooler parts (ears, nose, feet, tail) are black.
• Temperature-dependent sex determination in turtles and crocodiles: nest temperature decides sex.

Epigenetic changes in response to environmental stimuli

• Agouti mouse: pregnant mothers given methyl-rich food (folic acid, B₁₂) had more brown, lean, healthy pups instead of yellow, obese ones – because the agouti gene got methylated (silenced).
• Identical twins have the same DNA, but their methylation patterns differ more with age and lifestyle.

Developmental plasticity and gene–environment interactions

• Developmental plasticity: one genotype produces different phenotypes depending on conditions during development.
• Honeybee: the same larva becomes a queen if fed royal jelly and a worker if not – due to different DNA methylation.
• Gene–environment interaction: PKU babies are normal if given a low-phenylalanine diet – the effect of a gene depends on environment.

Impact of nutrition, stress and toxins

• Nutrition: Dutch Hunger Winter (1944–45) – children of starved mothers had higher obesity, diabetes and heart disease later, linked to changed methylation.
• Stress: rat pups with less maternal licking and grooming showed higher methylation of the stress-hormone (glucocorticoid) receptor gene and became more anxious.
• Toxins: smoking, alcohol, arsenic, bisphenol A (BPA) and pesticides alter methylation and are linked to cancer and developmental defects.

4.4 Applications of Genetics in Medicine and Agriculture

Gene therapy

Principle: correcting a genetic disease by inserting a normal, functional gene into the patient's cells (or editing the faulty gene).

• Somatic gene therapy: body cells; not passed on. Germline gene therapy: eggs/sperm/embryo; inherited – not allowed in most countries.
• Ex vivo: cells removed, gene added in the lab, returned. In vivo: gene delivered directly into the body.
• Vectors: retrovirus, adenovirus, adeno-associated virus (AAV), liposomes.
• First case (1990, USA): a 4-year-old girl with ADA deficiency; her lymphocytes were given a normal ADA gene and returned (ex vivo).
• Newer tool: CRISPR-Cas9 gene editing.

Challenges: safe delivery to the right cells; immune reaction against the vector; insertion at a wrong place can cause cancer; short-lived effect needing repeat doses; very high cost.

Genetic modification in livestock

Transgenic animals carry a foreign gene introduced on purpose (e.g. by microinjection into the fertilised egg).

• More milk, meat and wool; faster growth – AquAdvantage salmon with a growth hormone gene.
• Biopharming (medicines in milk): Rosie (1997), the first transgenic cow, gave milk with human α-lactalbumin; transgenic goats give antithrombin.
• Disease-resistant animals and animal models for human diseases.

Ethical, social and legal issues

• Ethical: animal suffering; germline editing and "designer babies"; consent of patients.
• Social: genetic data may lead to discrimination in jobs or insurance; high costs mean unequal access; misuse of prenatal tests for sex selection.
• Legal: patenting of genes and biopiracy (e.g. basmati rice, turmeric and neem patent cases); in India, GM organisms are approved by the GEAC (Genetic Engineering Appraisal Committee); international Cartagena Protocol on Biosafety.

Likely exam questions

1. (Long, 8 marks) What are inborn errors of metabolism? Describe phenylketonuria and alkaptonuria with the metabolic pathway.
2. (Long, 8 marks) Explain the mechanisms of activation of oncogenes and inactivation of tumour suppressor genes.
3. (Short, 4 marks) Write a note on sickle-cell anaemia.
4. (Short, 4 marks) What is epigenetics? Explain the effect of nutrition and stress on gene expression.
5. (Short, 4 marks) What is gene therapy? Write its principle and challenges.