General Genetics/Dominant and Recessive Genes
When Gregor Mendel studied pea plants, he studied one trait (height, flower color, etc.) at a time. As he studied different traits, he found that some versions of a trait tended to dominate over others. For example, he found that some plants produced wrinkled peas (r) instead of the round peas (R) typically observed, eventually attributed to a mutation affecting starch production. But not every plant that has the mutation to produce wrinkled peas. Because many organisms are diploid, which means they have two homologous chromosomes in each set, they have two copies of a locus (one on each chromosome). If one chromosome has the starch mutation (r) but the other chromosome doesn't (R), then the peas produce starch normally and have the rounded shape. In Mendelian genetics, this means that R is dominant over r.
Each individual pea plant has three possible genotypes: "RR," "Rr," and "rr."
This is a case of complete dominance, where the recessive trait is not seen as long as the organism has at least one copy of the dominant gene. This means that there are only two phenotypes: in this case, "round peas" or "smooth peas." Plants with either RR or Rr will produce round peas, whereas only rr plants will produce smooth peas.
The Molecular Basis of Dominance
We have said that organisms have "pairs" or "sets" of chromosomes, but what does that mean? To explain this point, let's consider humans, which have 23 pairs of chromosomes (for a total of 46 chromosomes). Within each pair, one chromosome was inherited from the maternal parent and the other from the paternal parent. When we say these chromosomes are "homologous," it does not mean they are genetically identical -- after all, most people do not have genetically identical parents. For chromosomes to be homologous, it simply means that the DNA sequences on each chromosome serve the same function, if not in the exact same way.
Any specific location on a chromosome can be referred to as a "locus" (pl: loci). Homologous chromosomes have the same loci, but they do not necessarily have the same DNA sequence at a given locus. Each unique variation of DNA sequence that can be found at a locus is an allele. In cases of complete dominance, the recessive allele is often nonfunctional. What makes Mendel's round and wrinkled peas a case of complete dominance is that pea plants can produce starch normally as long as they have at least one copy of the allele for normal starch formation.
Alternative Patterns of Inheritance
Not all loci show this simple dominance. If we represent phenotype on a plot then Complete Dominance would be like this:
AA/Aa aa Complete Dominance
Other types are:
AA Aa aa No Dominance
AA Aa aa Incomplete Dominance
Aa AA aa Over Dominance