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An allele is dominant when its phenotype appears in a heterozygote (Aa), masking the expression of the recessive allele. Dominance reflects molecular mechanisms: often the dominant allele produces a functional protein and the recessive allele does not, so one functional copy is sufficient. The genotype describes the two alleles present; the phenotype is the observable trait. Homozygous dominant (AA) and heterozygous (Aa) individuals share the same phenotype under complete dominance, but heterozygotes can be identified through test crosses with homozygous recessive (aa) individuals.
Work through test cross problems to determine unknown genotypes. Connect dominant/recessive patterns to molecular mechanisms such as loss-of-function vs. gain-of-function mutations.
From Mendelian genetics, you know that organisms carry two copies of each gene (one from each parent) and that these copies — alleles — may differ. Dominance and recessiveness describe what happens when those two alleles are different. If an individual with genotype Aa looks the same as one with genotype AA, then the A allele is dominant and the a allele is recessive. The heterozygote's phenotype is determined entirely by the dominant allele; the recessive allele is present in the genome but invisible in the organism's appearance or function.
The molecular reason for dominance is usually straightforward. Most genes encode enzymes or structural proteins, and for many genes, one functional copy produces enough protein to do the job. Consider an enzyme in a metabolic pathway: an individual with genotype Aa has one allele making functional enzyme and one making nonfunctional enzyme. If half the normal enzyme quantity is still sufficient to catalyze the reaction at a normal rate, the heterozygote is indistinguishable from the homozygous dominant — this is called haplosufficiency. The recessive allele is typically a loss-of-function mutation (a broken version of the gene), and dominance simply reflects the fact that one working copy is enough. This is why most newly arising deleterious mutations are recessive: they break one copy, but the other copy compensates.
The critical distinction to master is between genotype and phenotype. Two individuals can look identical (same phenotype) while carrying different genotypes — AA and Aa both show the dominant phenotype under complete dominance. The only way to distinguish them is a test cross: mate the unknown individual with a homozygous recessive (aa). If any offspring show the recessive phenotype, the unknown parent must have been Aa, because the recessive offspring must have received an a allele from each parent. If all offspring show the dominant phenotype, the parent is likely AA (though large sample sizes are needed for confidence, since Aa × aa produces 50% dominant and 50% recessive on average).
Finally, complete dominance is not the only possibility — it is just the simplest case. In incomplete dominance, the heterozygote has an intermediate phenotype (red × white flowers producing pink). In codominance, both alleles are fully expressed simultaneously (AB blood type, where both A and B surface antigens are present). These variations do not violate Mendel's laws of segregation; they simply reflect cases where one functional copy of a gene is not enough to produce the full dominant phenotype, or where both allele products are independently detectable. Understanding these allelic interactions prepares you for the more complex inheritance patterns — epistasis, polygenic traits, and sex-linkage — that build on this foundation.