Objective
Explain how a gene determines a protein, how mutations alter that protein, and how the resulting change in protein activity produces a specific phenotype. Use the following examples, linking each to its mode of inheritance:
- TYR → tyrosinase → oculocutaneous albinism (autosomal recessive)
- HBB → β‑globin → sickle‑cell anaemia (autosomal recessive)
- F8 → factor VIII → haemophilia A (X‑linked recessive)
- HTT → huntingtin → Huntington’s disease (autosomal dominant, anticipation)
1. Flow of Genetic Information (Central Dogma)
- Gene (DNA) – defined stretch of nucleotides on a chromosome.
- Replication – semi‑conservative copying of DNA before cell division.
- Transcription – synthesis of a complementary pre‑mRNA by RNA polymerase II.
- RNA processing – 5′‑capping, splicing of introns, poly‑A tail addition to give mature mRNA.
- Translation – ribosome reads mRNA codons; tRNAs deliver amino‑acids to build a polypeptide.
- Post‑translational events – folding (often with chaperones), cleavage, phosphorylation, glycosylation, etc., generate the functional protein.
- Phenotype – the observable trait or disease state that results from the protein’s activity (or its loss).
Key Enzymes & Molecular Players
| Step | Major Enzyme/Complex | Principal Function |
|---|
| DNA unwinding | DNA helicase (e.g., MCM complex) | Separates the two strands of the double helix. |
| Leading‑strand synthesis | DNA polymerase ε | Adds nucleotides continuously 5′→3′. |
| Lagging‑strand synthesis | DNA polymerase δ + primase | Produces Okazaki fragments. |
| Fragment joining | DNA ligase I | Seals nicks between Okazaki fragments. |
| Proofreading & repair | 3′→5′ exonuclease activity of Pol δ/ε; Mismatch‑repair (MSH, MLH) | Corrects mis‑incorporated bases. |
| Transcription initiation | RNA polymerase II + general transcription factors (TFIID, TFIIH) | Recognises promoter (TATA box) and begins RNA synthesis. |
| RNA capping | RNA 5′‑triphosphatase, guanylyltransferase, methyltransferase | Adds 7‑methyl‑G cap. |
| Splicing | Spliceosome (snRNPs U1, U2, U4/5/6) | Removes introns, ligates exons. |
| Poly‑A tailing | Poly‑A polymerase | Adds ~200 A residues to 3′ end. |
| Translation initiation | eIFs, 40S & 60S ribosomal subunits, Met‑tRNAi | Assembles ribosome at the 5′‑cap. |
| Elongation & termination | eEFs, release factors (eRF1/eRF3) | Adds amino‑acids and releases the polypeptide at stop codons. |
| Protein folding & modification | Chaperones (Hsp70, Hsp90), protein kinases, glycosyltransferases | Assists correct 3‑D structure; adds phosphate, carbohydrate, etc. |
2. Types of Mutations and Typical Molecular Consequences
| Mutation type | Mechanistic effect | Typical protein outcome | Cambridge‑relevant example |
|---|
| Missense (point) | Single‑base substitution changes one codon. | Single amino‑acid change; may alter activity, stability or localisation. | HBB Glu⁶→Val (sickle‑cell disease) |
| Nonsense (point) | Creates a premature stop codon. | Truncated protein; usually non‑functional or degraded. | TYR nonsense mutation → OCA1 |
| Frameshift (insertion/deletion) | Insertion/deletion not in multiples of three shifts the reading frame. | Aberrant amino‑acid sequence downstream; early stop codon. | ΔF508 in CFTR (cystic fibrosis – useful for technique comparison) |
| Repeat expansion | Increase in the number of tandem repeats (e.g., CAG). | Extended poly‑glutamine tract → protein misfolding, aggregation. | HTT CAG ≥36 repeats → Huntington’s disease |
| Large‑scale (deletion, duplication, inversion, translocation) | Loss or gain of whole exons/genes or rearrangement of chromosome segments. | Missing or extra protein domains; dosage effects. | Large deletion in F8 → severe haemophilia A |
| Regulatory / promoter mutation | Altered transcription factor binding. | Reduced or absent mRNA → little or no protein. | Promoter mutation in TYR reduces transcription. |
| Epigenetic modification | DNA methylation or histone modification without sequence change. | Gene silencing or up‑regulation. | Hypermethylation of tumour‑suppressor genes in cancer (contextual example). |
3. Case Studies – Gene → Protein → Phenotype
3.1 TYR Gene – Tyrosinase – Oculocutaneous Albinism Type 1 (OCA1)
- Gene: TYR (11q14.3), autosomal recessive.
- Protein function: Copper‑containing oxidase catalysing:
- Tyrosine → DOPA
- DOPA → DOPA‑quinone
These reactions initiate melanin synthesis. - Typical mutations: Missense, nonsense, frameshift or promoter lesions that abolish enzyme activity.
- Effect on protein: Little or no functional tyrosinase → melanin production stops.
- Phenotype: Pale skin, white hair, light irises, photophobia, reduced visual acuity; inheritance follows a classic 1:4 carrier ratio in families.
3.2 HBB Gene – β‑Globin – Sickle‑Cell Anaemia
- Gene: HBB (11p15.5), autosomal recessive.
- Normal protein: β‑globin pairs with two α‑chains to form adult haemoglobin (HbA, α₂β₂) for O₂ transport.
- Common mutation: A→T transversion in codon 6 (GAG → GTG) → Glu⁶→Val (β⁽ˢ⁾).
- Effect on protein: Valine creates a hydrophobic patch; de‑oxygenated HbS polymerises, distorting RBCs into a sickle shape.
- Phenotypic consequences: Chronic haemolytic anaemia, vaso‑occlusive pain crises, splenic infarction, increased infection risk. Homozygotes (ss) are affected; heterozygotes (AS) show carrier advantage against malaria (balanced polymorphism).
3.3 F8 Gene – Factor VIII – Haemophilia A
- Gene: F8 (Xq28), X‑linked recessive.
- Protein function: Large glycoprotein co‑factor for factor IXa; together they form the intrinsic tenase complex (VIIIa·IXa) that activates factor X → Xa, leading to thrombin generation and fibrin clot formation.
- Typical mutations: Large deletions, nonsense mutations, splice‑site changes, or intron‑13 inversion that abolish functional factor VIII.
- Effect on protein: Factor VIII absent or non‑functional → intrinsic pathway cannot generate sufficient factor Xa.
- Phenotype: Prolonged activated partial thromboplastin time (aPTT), spontaneous joint haemorrhages, excessive bleeding after minor trauma. Males are affected; carrier females may show mild symptoms due to lyonisation.
3.4 HTT Gene – Huntingtin – Huntington’s Disease
- Gene: HTT (4p16.3), autosomal dominant with anticipation.
- Normal protein: Huntingtin – cytoplasmic protein involved in vesicular transport, transcription regulation and mitochondrial function.
- Mutation type: Expansion of a CAG trinucleotide repeat in exon 1.
- Normal: 10–35 repeats
- Pathogenic: ≥36 repeats (often >40)
- Pathogenic mechanism: Poly‑glutamine tract causes misfolding and intracellular aggregation; aggregates interfere with transcription, mitochondrial respiration and axonal transport, leading to selective loss of medium spiny neurons in the striatum.
- Phenotype: Progressive chorea, dystonia, cognitive decline, psychiatric disturbance; age of onset inversely correlated with repeat length. Each generation tends to inherit a longer repeat (anticipation).
4. Inheritance Patterns & Population Genetics (Cambridge Topic 16)
4.1 Mendelian Segregation
- Autosomal recessive (TYR, HBB):
- Genotype ratios in offspring of two heterozygotes: 1 AA : 2 Aa : 1 aa.
- Phenotypic ratio: 3 normal : 1 affected.
- X‑linked recessive (F8):
- Autosomal dominant with anticipation (HTT):
- One affected parent transmits the mutant allele to 50 % of children.
- Repeat expansion during meiosis leads to earlier onset in successive generations.
4.2 Pedigree Analysis Tips (Cambridge Exam)
- Identify the mode of inheritance by looking for:
- Sex bias (X‑linked),
- Vertical transmission (dominant),
- Horizontal transmission with skipped generations (recessive).
- Use symbols: squares = male, circles = female, filled = affected, half‑filled = carrier (for X‑linked).
- Calculate carrier risk: e.g., for an autosomal recessive disorder, two unaffected parents with an affected child each have a 2⁄3 chance of being carriers.
4.3 Hardy–Weinberg Equilibrium (Population Genetics)
For a single‑gene, two‑allele system (p = frequency of normal allele, q = frequency of mutant allele):
Use Hardy–Weinberg to predict disease prevalence, carrier rates, and the impact of selection (e.g., sickle‑cell heterozygote advantage in malaria‑endemic regions).
5. Summary Table – Gene → Protein → Mutation → Phenotype → Inheritance
| Gene | Protein (function) | Typical mutation | Effect on protein | Phenotype | Inheritance pattern |
|---|
| TYR | Tyrosinase – catalyses first steps of melanin synthesis | Missense / nonsense / frameshift / promoter loss‑of‑function | Enzyme activity reduced or absent | Oculocutaneous albinism type 1 (pale skin, visual defects) | Autosomal recessive |
| HBB | β‑globin – part of adult haemoglobin (O₂ transport) | Missense (GAG→GTG) → Glu⁶→Val | HbS polymerises under low O₂, distorts RBCs | Sickle‑cell anaemia (anaemia, pain crises, organ damage) | Autosomal recessive (balanced polymorphism in malaria zones) |
| F8 | Factor VIII – co‑factor in intrinsic clotting cascade | Large deletions, nonsense, splice‑site, intron‑13 inversion | Factor VIII absent or non‑functional | Haemophilia A (excessive bleeding, joint haemorrhages) | X‑linked recessive |
| HTT | Huntingtin – vesicle transport, transcription regulation, mitochondrial support | CAG repeat expansion (≥36 repeats) | Poly‑Q tract causes misfolding & aggregation | Huntington’s disease (chorea, cognitive decline, psychiatric symptoms) | Autosomal dominant with anticipation |
6. Key Take‑aways
- Genes encode proteins; the structure and activity of those proteins determine cellular function and thus the organism’s phenotype.
- Mutations can alter the amount of protein produced (null alleles, promoter defects) or its structure (missense, nonsense, frameshift, repeat expansion).
- The phenotypic outcome reflects the normal physiological role of the protein – loss of pigment, altered oxygen transport, impaired clotting, or neurotoxicity.
- Understanding the gene → protein → phenotype chain is essential for diagnosis, genetic counselling, and the development of targeted therapies (enzyme replacement, gene therapy, small‑molecule modulators).
- Linking each disorder to its mode of inheritance and to population‑genetics concepts (Hardy–Weinberg, carrier frequency, selection) satisfies Cambridge AS & A Level requirements for Topics 6 and 16.