Genotypes, Phenotypes, and Alleles Revision Notes | A Level AQA Biology

1. Why Genotype and Phenotype Are Not the Same Thing

Two organisms can carry identical DNA sequences yet look, behave, or function differently. Equally, two organisms can look identical yet carry different genetic instructions. This apparent paradox sits at the heart of genetics — and resolving it requires you to separate two concepts that students frequently conflate: genotype and phenotype.

The genotype is the genetic constitution of an organism — the actual alleles it carries. The phenotype is the expression of that genetic constitution and its interaction with the environment — what you can observe or measure. Genotype is the instruction set; phenotype is the outcome.

Consider human height. A person may carry alleles that predispose them to tall stature, yet poor nutrition during childhood can result in a shorter adult height. The genotype has not changed — the environment has altered the phenotype. This interaction is fundamental to AQA's definition and must appear in any full-mark answer about phenotype.

A classic biological example is the Himalayan rabbit. Its genotype codes for dark fur, but the enzyme responsible for pigment production is temperature-sensitive. In cold extremities (ears, paws, nose), the enzyme is active and dark fur is produced. In warmer body regions, the enzyme is inactive and fur is pale. One genotype; a phenotype shaped by temperature.

This example also illustrates why phenotype cannot be read directly from genotype without considering context. Examiners regularly award marks specifically for mentioning the environmental component — so always include it when defining or explaining phenotype.

2. Alleles — Variants of a Gene

A gene occupies a specific position on a chromosome called a locus (plural: loci). Different versions of that gene — arising through mutation over evolutionary time — are called alleles. The AQA specification states explicitly that there may be many alleles of a single gene, and this is a point students often underestimate.

Human ABO blood groups are the textbook example of multiple alleles. The gene controlling ABO blood type has three common alleles in the population: $I^A$, $I^B$, and $i$. Any individual carries two of these (one inherited from each parent), but the population as a whole maintains all three. Multiple alleles increase phenotypic diversity without requiring multiple genes.

• A gene occupies a fixed position (locus) on a chromosome.
• Alleles are alternative forms of the same gene, differing in their nucleotide sequence.
• A population may contain many alleles of a single gene; any one individual carries at most two (in a diploid organism).
• New alleles arise through gene mutation.

3. Dominant, Recessive, and Codominant Alleles

Not all alleles contribute equally to the phenotype. The relationship between alleles at the same locus determines which traits are expressed — and this is where the terms dominant, recessive, and codominant become essential.

A dominant allele is one whose associated phenotype is expressed whenever the allele is present — whether the organism carries one copy or two. By convention, dominant alleles are written with a capital letter (e.g. B). A recessive allele, written in lower case (e.g. b), only produces its associated phenotype when two copies are present — that is, when no dominant allele is there to mask it.

Codominance is a distinct relationship in which neither allele masks the other. Both are fully expressed in the heterozygote, producing a phenotype that shows characteristics of both alleles. This is not the same as blending — each allele still produces its own product.

In the ABO blood group system, the $I^A$ allele codes for the A antigen on red blood cells, and $I^B$ codes for the B antigen. An individual with genotype $I^A I^B$ produces both antigens — giving blood group AB. Neither allele is dominant over the other; both are fully expressed. The $i$ allele, however, is recessive to both $I^A$ and $I^B$: only individuals with genotype $ii$ have blood group O.

Sickle cell anaemia provides a powerful example that links all three allele types. The allele for normal haemoglobin ($H^N$) and the allele for sickle haemoglobin ($H^S$) are codominant: a heterozygous individual ($H^N H^S$) produces both normal and sickle haemoglobin, resulting in sickle cell trait. Neither allele is fully dominant over the other at the molecular level, because both gene products are present in the red blood cells.

4. Homozygous and Heterozygous Genotypes

Now that you can describe individual alleles, the next step is to describe the combination of alleles an organism carries at a specific locus. Two terms are used: homozygous and heterozygous. Both apply specifically to diploid organisms, which carry two alleles at each locus.

A heterozygous organism carries two different alleles at the same locus — for example, Bb. In a dominant-recessive relationship, the heterozygote expresses the dominant phenotype but still carries the recessive allele, which can be passed to offspring. This is why recessive conditions can persist in a population even when they are not expressed.

The distinction between homozygous and heterozygous is particularly important when analysing inheritance patterns. Two parents who are both heterozygous (carriers) for a recessive condition have a 1 in 4 chance of producing a homozygous recessive offspring — the only genotype that expresses the recessive phenotype.

Worked example: Identifying Genotype, Phenotype, and Zygosity from a Cross

In pea plants, the allele for purple flowers (P) is dominant over the allele for white flowers (p). A plant with genotype Pp is crossed with a plant with genotype pp. For the offspring: (a) State all possible genotypes. (b) State the phenotype of each genotype. (c) Identify whether each genotype is homozygous or heterozygous.

1. Parent genotypes: Pp × pp Gametes from Pp: P or p Gametes from pp: p only — Each parent produces gametes containing one allele from each pair. The homozygous recessive parent (pp) can only contribute p.
2. p p P | Pp | Pp | p | pp | pp | — Crossing the gametes gives two genotype classes: Pp and pp, each with a frequency of 50%.
3. Pp: pp = 1: 1 50% Pp, 50% pp — There are only two possible genotypes from this cross. Note that PP is not possible here because the pp parent cannot contribute a P allele.
4. Pp → purple flowers (P is dominant, so one copy is sufficient) pp → white flowers (no dominant allele present) — The dominant allele P masks the recessive allele p in the heterozygote. Only the homozygous recessive genotype expresses the recessive phenotype.
5. Pp → heterozygous (two different alleles at the locus) pp → homozygous recessive (two identical alleles at the locus) — Zygosity describes whether the two alleles at a locus are the same (homozygous) or different (heterozygous). This is independent of which phenotype is expressed.

Answer: Offspring genotypes: 50% Pp (heterozygous, purple flowers) and 50% pp (homozygous recessive, white flowers).

5. Bringing It Together — Genotype, Phenotype, and Environment

You now have all the components. The genotype sets the potential range of phenotypes an organism can express. Which phenotype actually appears depends on which alleles are present (and their dominance relationships) and on the environmental conditions the organism experiences.

This means phenotype is not a fixed readout of genotype. Identical twins share the same genotype, yet differences in diet, exercise, stress, and exposure to pathogens mean their phenotypes can diverge significantly over time. At A Level, you are expected to articulate this interaction — not treat genotype as a direct blueprint for phenotype.

The relationship between genotype and phenotype also explains why the same phenotype can arise from different genotypes. In a dominant-recessive system, both BB and Bb produce the dominant phenotype — you cannot determine genotype from phenotype alone without additional information such as a test cross.

6. Exam Technique and Mark-Winning Precision

AQA questions on this topic are precise about terminology, and marks are frequently lost through vague or incomplete answers. The guidance below targets the most common errors seen in mark schemes.

For extended-response questions asking you to explain how genotype relates to phenotype, structure your answer as: genotype (alleles present) → dominance relationship → phenotype expressed → environmental modifier. This chain of reasoning demonstrates the analytical depth that secures marks in the top band.