What makes an allele dominant on the molecular level?

This was a question, I have been asked yesterday.

Although dominance is the property an allele, dominance is not”regulated” on the genomic level but a function of the resulting protein. According to the largely citied Wilkie paper there are numerous mechanisms

  • reduced gene dosage expression or protein activity
  • increased gene dosage
  • ectopic or temporally altered mRNA expression
  • increased or constitutive protein activity
  • dominant negative effects
  • altered structural proteins
  • toxic protein alterations
  • new protein functions

In lay terms also explained at biology.stackexchange

… the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fibrosis.