Simplifying a lot, in a case of complete dominance one allele (dominant) masks the contribution of the second (recessive); so if you are referring to "expression" meaning "visibility" in the phenotype, in case of simply dominance, by definition, the recessive allele is never "expressed". Considering "expression" from another point of view, a recessive allele may be correctly translated, and a protein may be produced (generally misfolded or un-functional, or somehow diverse from the normal protein); it may be not expressed at all of course.

There are two forms of dominance.  There is compete dominance and incomplete dominance.  They way you determine what you are observing is by the presence of either two or three phenotypes.  In complete dominance, you only see two phenotypes as the heterozygote is identical to the homozygous dominant.  In incomplete dominance, there are three phenotypes as the heterozygote produces a unique phenotype.  But, if you do a molecular analysis, you may be able to see some expression by a totally recessive allele in the heterozygous state, but it produces no observable phenotypic expression.

It is often thought that a dominant D gene codes for a functional protein while a recessive R gene/allele does not but the concept of dominance is confusing for two reasons. Firstly because dominant and recessive refer to the effect of an allele/gene…its phenotype and not to any inate property of the allele itself. As such there are no regulatory elements or DNA sequences that make an allele dominant D or recessive R because any sequence may be D to another allele (s) but R to yet another allele so the concept of D and R exists only when you have defined which 2 ( or group) of alleles that you are discussing. Thus you cannot ask the question “ why does a D mask a R allele” because alleles may be dominant or recessive depending on which other allele you are comparing it with. We also have a problem with expression in that alleles code for proteins and production and usage of protein is not an absolute so in many disorders the production of an important protein may be 5% to 100% of expected but the body copes and there is no phenotype but at less than 5% there is a phenotype ( for instance PKU) and then we talk about the inheritance of the disorder but really there was nothing to distinguish some of the affecteds from the normal.

So in partial answer to your question there is nothing about a D allele that makes it expressed preferentially. Both of the D and R alleles will be expressed ( forget null alleles)

But sometimes the R will produce a less active enzyme or less functional protein and the D allele will manage on its own. Sometimes also the protein is multimeric and the D and R alleles will each make strands of the protein which will combine to form the complete dimer or tetramer and again, sometimes the shape of the multimer will not change and it will be functionally active and with other changes the multimer may be the wrong shape and inactive or partially inactive so again it is only when you can see or measure a phenotype that you can say whether an allele/gene is D or R in a family.

Sometimes both alleles are equally expressed and this is codominance ( blood groups)

Concerning recessive R alleles it is useful to have the concept of haploinsufficiencey. Again there is no absolute definition of recessive for the same reasoning as above but for many molecules having one functional gene produces enough product to let the body function normally. But if we have parents (carriers) each with one allele which produces a non functional protein then the NN, NM and MN combinations of alleles will all be phenotypically normal as they all have on normal allele but 1 in 4 children will have the MM combination, will not produce protein which works and will be classically described as a result of recessive inheritance but referring back to your question the recessive allele is expressed normally it is just that the gene product does not work very well.

Naturally selective pressure over many generations may increase or remove some mutations so R and D are not naturally more common than each other. For instance most people think that the sickle cell mutation is all bad but the is a population of Arabs who benefitted historically by having the sickle trait which protects against malaria quite well and also a second mutation which increases the level of fetal haemoglobin in adults which make the sickling asymptomatic by stopping polymerisation of the globin molecules. So sometimes it is not even easy to classify a mutation as good or bad let alone dominant or recessive in absolute terms.

Hello Paul Rutland If there is no difference between protein function due to the translation of D and R allele, can the recessive R translate into protein? Or is there a possibility that the recessive R protein will be degraded since it's recessive?

Hi Vikram Thimaradka ,

It is the phenotype that is D or R so it is normal that the gene expresses one or more proteins which can be different shapes so exhibit different activities or sometimes no activity at all.. One of these proteins could be more susceptible to degradation but it is not a necessary condition in the production of either a D or R phenotype

Paul Rutland Thanks for your answer. Let me clarify a bit more. Say I performed a knock-in experiment in mouse. Then I will cross it with a WT mouse to obtain a heterozygous (WT/Knock-in) mouse. So in the heterozygous mouse, for the same protein to be expressed, will there be some proteins of Wildtype (Call it dominant?) and some proteins of new Knock-in type (call it recessive?). So my question was in the presence of WT protein (which I call it dominant) will the Knock-in protein survive/expressed? (also, can we call translation of a gene as phenotype?).

You should not use the term phenotype Vikram Thimaradka ( pheno = Showing ) because in most cases a knock in/out may not cause any discernible difference in the host. What you have changed is the genotype of the organism and unless it results in a shape or behavioural change then it is probably not a phenotype change. As in my answer above to Akila Wijerathna Yapa a gene change is not absolutely dominant or recessive but its phenotype may be dominant compared to another allele but recessive against a different allele. With a knocked in gene I would expect that both the original and the knocked in gene will be expressed if the proper regulatory sequences are present unless you have previously knocked out the original gene in which case only the knock in will be expressed

Paul Rutland I see. Thank you very much.

Hello Paul Rutland , thank you for your answers here, I've learned a lot!

I have a quick question, if I have a cell line that its heterozygous for an specific gene (WT/Mut), Would both isoforms (WT and Mut) express in each individual cell? or would some cells express the WT isoform and others the Mut isoform?

Hello Paul Rutland, thanks for the answers, I read them and learned more.

But I have one question. If the dominant allele produces the functional protein and the recessive allele do not, do we mean that the genetic codes for the dominant allele and recessive allele for a gene are different? If the two alleles are the same in their genetic code, why they are different in their function? If they are different in their genetic code, what is the actual difference of the two allele in terms of their codes and functions?

Thanks!