Understanding heredity requires separating what an organism carries in its DNA from what you can observe in its structure and function. This distinction underpins predictions about traits, inheritance patterns, and biological variation.

Core idea: what you have vs what you show

Genotype refers to the alleles an organism carries, while phenotype refers to the observable outcomes produced when those alleles are expressed in a particular biological context. The diagram highlights that phenotype is influenced by gene expression and can also be modified by environmental factors, so the same underlying DNA can yield different observable traits. Source

Genotype: inherited genetic makeup

Genotype is typically written using allele symbols (for example, two alleles at a locus in a diploid organism). In AP Biology, genotype is a statement about DNA-based information that can be transmitted to offspring.

Key points about genotype:

• A diploid organism usually has two alleles per autosomal gene (one from each parent).

• Alleles can be identical (homozygous) or different (heterozygous).

• Genotype is defined at a chosen scale:

  • Single-locus genotype (one gene)

  • Multi-locus genotype (several genes contributing to a trait)

  • Whole-genome genotype (all genetic variants)

Phenotype: observable characteristics

Phenotype includes traits you can measure or categorise, such as morphology (height, leaf shape), physiology (enzyme activity), and behaviour. Phenotype is not the DNA itself; it is the expression of genetic information through cells, tissues, and organs.

Common features of phenotype:

• Can be qualitative (e.g., purple vs white flowers) or quantitative (e.g., blood pressure, body mass).

• Can be described at different levels:

  • Molecular (amount of a protein)

  • Cellular (cell-surface markers)

  • Organismal (visible characteristics)

How genotype relates to phenotype

Gene expression links genotype to phenotype

This diagram traces how genetic information becomes phenotype through gene expression: DNA accessibility and transcription produce RNA, which is processed and translated into polypeptides that are modified into functional proteins. By marking multiple regulatory checkpoints, it clarifies why the same genotype can yield different phenotypes when expression levels, timing, or cell type differ. Source

Genes affect phenotype through gene expression, in which DNA information is used to build RNA and proteins that carry out cellular functions. The same genotype can lead to different phenotypes if expression differs across:

• Cell types (a liver cell vs a neuron)

• Developmental stages

• Physiological conditions

A useful chain of reasoning is:

• Genotype (alleles) influences protein structure or amount

• Proteins influence cell function

• Cell function contributes to traits (phenotype)

One genotype can produce multiple phenotypes

Phenotype is often shaped by more than genotype alone because biological systems integrate signals and conditions. Even when genotype is constant, phenotype may vary due to differences in:

• Regulation of transcription and translation

• Timing and location of gene expression

• Hormonal signalling and developmental pathways

This helps explain why phenotype is often a range rather than a single fixed outcome, especially for complex traits.

Different genotypes can produce similar phenotypes

Phenotypic similarity does not guarantee genetic identity. Similar phenotypes can arise when:

• Different alleles produce proteins with similar function

• Multiple genetic pathways converge on the same trait

• Some alleles have small phenotypic effects that are hard to detect without precise measurement

Distinguishing genotype and phenotype in data

What you can infer from observation

In inheritance problems, the phenotype is usually what is directly observed, while genotype is inferred using logic about allele behaviour. Important implications:

• A dominant phenotype may correspond to more than one genotype (often homozygous dominant or heterozygous).

• A recessive phenotype often reveals genotype more directly (commonly homozygous recessive in simple single-gene models).

Language precision for AP Biology

Use careful phrasing:

• “The organism has the phenotype of…” for observed traits.

• “The organism’s genotype is…” only when it is known from genetic testing, controlled crosses, or unambiguous inference.

• Avoid treating phenotype as purely visual; “observable” includes measurable biochemical or physiological outputs.

Why the distinction matters

Separating genotype from phenotype allows you to:

• Predict trait transmission while recognising that the same inherited alleles may not always look identical in every context.

• Interpret biological evidence correctly: measurements describe phenotype, while heredity is transmitted through genotype.

• Explain why classification by appearance can sometimes misrepresent underlying genetic variation.