16.2 The Roles of Genes in Determining Phenotype
- Syllabus
- 9700–2028–2029
- Topic
- 16.2
- Level
- A2
Learning objectives
16.2.1Core genetic terms• Terms: gene, locus, allele, dominant, recessive, codominant, linkage, test cross, F1, F2, phenotype, genotype, homozygous, heterozygous16.2.2Genetic diagrams• Genetic diagrams and Punnett squares for:- Monohybrid crosses: dominance, codominance, multiple alleles, sex linkage- Dihybrid crosses: dominance, autosomal linkage, epistasis- Test crosses16.2.3Chi-squared test in genetics• Chi-squared test for significance of differences between observed and expected results16.2.4Genes, proteins and phenotype• Relationship between genes, proteins, and phenotype:- TYR gene, tyrosinase, albinism- HBB gene, haemoglobin, sickle cell anaemia- F8 gene, factor VIII, haemophilia- HTT gene, huntingtin, Huntington's disease16.2.5Gibberellin role in stem elongation• Gibberellin role in stem elongation: Le allele (functional enzyme) vs le allele (non-functional enzyme)
Genetic terms locate alleles, describe expression and track generations
| Term | Precise meaning |
|---|---|
| gene | DNA base sequence that codes for a polypeptide or functional RNA |
| locus | position of a gene on a chromosome |
| allele | alternative form of a gene at the same locus |
| dominant | allele whose phenotype is expressed in a heterozygote |
| recessive | allele whose phenotype is masked by a dominant allele in a heterozygote |
| codominant | two different alleles both contribute to the heterozygote phenotype |
| genotype / phenotype | allele combination / observable characteristics produced by genotype and environment |
| homozygous / heterozygous | two identical / two different alleles at a locus |
| linkage | loci on the same chromosome tend to be inherited together |
| F1 / F2 | first filial generation / offspring produced from an F1 cross or selfing |
| test cross | cross with a homozygous recessive individual to reveal an unknown dominant-phenotype genotype |
Dominant does not mean common, beneficial or stronger. Codominance means both alleles are expressed in the heterozygote; it does not mean the alleles blend into a new allele.
Choose the inheritance model before building a genetic diagram
For every cross: define allele symbols and relationships → write parental phenotypes and genotypes → list every possible gamete → combine one gamete from each parent in a Punnett square → state offspring genotypes and phenotypes with probabilities or ratios → check probabilities sum to 1.
| Inheritance model | Required diagram decision |
|---|---|
| monohybrid complete dominance | one locus; heterozygote has dominant phenotype |
| codominance / multiple alleles | use distinct superscripts; both codominant alleles appear in a heterozygote; a population may have more than two alleles although one individual has at most two |
| sex linkage | write alleles as X-chromosome superscripts; track male and female offspring separately because the Y usually lacks the locus |
| unlinked dihybrid dominance | list four gamete types from a double heterozygote if loci assort independently |
| autosomal linkage | write linked alleles together on homologues, e.g. AB/ab; parental gametes usually exceed recombinant gametes when crossing over occurs |
| epistasis | determine how one locus masks or modifies another before converting genotypes to phenotypes; do not assume or memorise one universal ratio |
| test cross | cross the unknown dominant-phenotype individual with a homozygous recessive individual; offspring phenotypes reveal its gametes |
The Punnett square combines gametes; it does not decide which gametes are possible. A 3:1 or 9:3:3:1 ratio applies only when its dominance, segregation, viability and independent-assortment assumptions are satisfied.
Chi-squared tests whether count deviations exceed chance expectation
\chi^2=\sum\frac{(O-E)^2}{E}
- State the null hypothesis: observed and expected counts do not differ significantly; any difference is due to chance.
- Convert the genetic ratio to expected counts with the same total as the observations.
- Calculate (O−E)²/E for every category and sum the contributions.
- Use degrees of freedom = number of categories − 1.
- Compare χ² with the critical value at the chosen probability, commonly p=0.05. Above the critical value: reject the null; at or below it: fail to reject the null.
For observed 78 dominant and 22 recessive offspring under a 3:1 expectation (total 100), E=75 and 25. χ²=(3²/75)+(−3)²/25=0.48. With df=1, 0.48 is below 3.841 at p=0.05, so fail to reject the null: the deviation is compatible with chance.
Failing to reject does not prove the genetic model true. Use independent count categories—not percentages—and check that expected counts and the biological assumptions are suitable.
Four gene variants alter proteins and produce distinct phenotypes
| Gene and inheritance | Protein consequence | Phenotypic consequence |
|---|---|---|
| mutant TYR alleles; albinism is recessive | little or no functional tyrosinase, so the melanin pathway is blocked | little/no melanin in skin, hair and eyes; visual effects can occur |
| HBB allele HbS; HbA and HbS are codominantly expressed at protein level | altered beta-globin forms haemoglobin S, which is less soluble and can form fibres at low oxygen | red cells sickle, carry oxygen less effectively and may block capillaries; HbS/HbS causes sickle-cell anaemia |
| mutant F8 allele; X-linked recessive | little or no functional factor VIII | clotting cascade is impaired, fibrin formation is reduced and bleeding lasts longer |
| mutant dominant HTT allele with expanded CAG repeats | abnormal huntingtin protein is produced | progressive damage to nervous tissue causes movement, cognitive and behavioural changes |
For each example, explain the full direction: DNA allele changes the amount or structure of a named protein; altered protein function changes a cellular or physiological process; that process produces the phenotype.
Do not jump directly from gene name to symptom. The four proteins have different jobs—enzyme, oxygen-carrying protein, clotting factor and neuronal protein—so their mechanisms are not interchangeable.
Le controls a gibberellin-synthesis enzyme and stem height
| Genotype/allele | Enzyme and gibberellin | Stem phenotype |
|---|---|---|
| Le_ (LeLe or Lele) | dominant Le codes for a functional enzyme in the gibberellin-synthesis pathway, so enough active gibberellin is produced | gibberellin promotes internode cell elongation and the plant is tall |
| lele | recessive le codes for a non-functional enzyme, reducing/blocking gibberellin synthesis | internode elongation is reduced and the plant is dwarf |
Applying gibberellin can restore stem elongation in an lele dwarf if its receptors and downstream response pathway are functional. This shows that the mutation affects hormone synthesis upstream, rather than preventing cells from responding to gibberellin.
Le is an allele coding for an enzyme; it is not the hormone itself. Dominance means one functional Le allele supplies sufficient pathway activity for the tall phenotype.