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It's dependent on protein expression relative to the recessive allele. So will it be determined by factors controlling the rate of expression of that gene, It's transcription factors, the % of guanisine-Cytosine within the gene, it's structural availibility for transcription, It's epigentic modifications (DNA methylation) and many many more factors which control Gene expression.

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If one gene has more benenficial factors expression or if the other has as negative expression factors, the dominant gene's trait will be produced.

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The simplest explanation usually for how alleles are either recessive or dominant is based on whether the protein they express has a higher than average function (gain of function) or lower than average function (loss of function).

Think about it through the lens of genetic disease. Oftentimes dominant genes are gain of function mutations. In Huntington’s disease, patients express a version of the protein huntingtin that is toxic to neurons and causes the condition. If you have two copies of alleles for huntingtin, but only one of them makes a toxic protein, you’d still have the toxic effect even though it represents only half of the expressed protein. That’s because this toxic effect is a “gain of function.” That’s what makes this allele dominant.

On the other hand, cystic fibrosis is a recessive disease. The gene for cystic fibrosis encodes a protein that transports sodium across cell membranes. Defects in this gene, called CFTR, can cause non-functional protein to be expressed and decrease the transport of sodium leading to a whole bunch of systemic effects. This is a loss of function. However, if you only have one mutant copy of the allele, then the other allele expresses a functional protein that can still do what the gene is supposed to do. This makes the disease recessive, because you need two “broken” alleles for a complete loss of this protein function.

Edit: punctuation

Was the same type of thing going on with Mendel's peas?

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More or less.

Mendel's peas are a simpler example. For Mendel's peas, the dominant traits in peas are 'active' alleles, and the recessive traits are 'inactive' alleles.

A trait for larger leaves or taller stalks (dominant) requires an active protein function to generate the growth, while the smaller leaves or stalks (recessive) merely requires nothing to happen. Purple flowers (dominant) are the result of a particular pigment, while white flowers (recessive) lack the pigment.

Having one copy of the dominant allele is enough for this protein production to occur fully, hence why the heterozygote (one of each) displays the dominant trait.

> , the % of guanisine-Cytosine within the gene

How does this affect expression?

Sorry my mistake guanine- cytosine

Higher GC content has been shown to affect polymerase efficiency in DNA elongation. It's not 100% understood why because it has been shown not to be due to the more stable bonds of GC and the better annealing which we exploit in primer design.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1463026/

https://www.pnas.org/doi/10.1073/pnas.1518976113

https://pubmed.ncbi.nlm.nih.gov/20203083/

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Dominant alleles are alleles that overtake the other one in their function. The body doesn't know which is which, its an inherent trait to the gene.

Nearly all genes come as pairs, and if one of the pair can outperform the other, then its considered dominant. There are many different ways this can happen both normally and in disease. Here are some examples:

Blood type - In the ABO blood type group there are three alleles, A, B and O. A and B are dominant over O in that if you are AO or BO then your blood type is A or B. On a cellular level, the ABO locus encodes a glycoprotein. A and B alleles will express this glycoprotein (although slightly differently) while O will express no glycoprotein. Thus if you have an A or B allele, it will dominant over the O allele.

Eye color - The OCA2 gene has a large role in eye color determination. The brown eye allele will cause the cells in your iris to produce melanin and turn your irises brown while the blue eye allele will produce much less melanin. Thus if you have one brown eye allele, it will dominant over the blue eye allele by producing a lot of melanin.

Alzheimer's disease - The protein APP is involved in forming amyloid plaques seen in patients with Alzheimer's. In some families, this protein is mutated such that it forms these plaques much faster than normal. Faster plaque formation means faster disease onset and progression. Since only one allele is needed to be mutated to cause disease (it doesn't matter there's a normal one), this mutation is considered to be dominant.

Like others have mentioned, there is a tendency for dominant alleles to be "gain-of-function" which means these mutations (or normal variations) cause a new function. In ABO alleles, its production of a glycoprotein. In eye color, its production of melanin in the iris. In APP, it's the increased tendency to aggregate into plaques. This tendency is because of the redundancy of having two copies of your genes. If one loses its function, you already have another copy to take its place. Thus loss-of-function mutations are less likely to cause disease. But this isn't always the case.

Hemophilia A - This clotting disorder is caused by a mutation in the factor VIII gene. This gene is located on the X chromosome the mutation is considered recessive. If you have at least one copy of the normal factor VIII gene, you won't develop disease. However, if you have only one copy of the X chromosome (IE males) and you have the factor VIII mutation, then you will develop the disease as you only have one copy of those genes.

Cancer - The protein p53 is an important cancer preventing gene in your body. It's involved in making sure your cells are dividing at an appropriate time and rate. It functions by oligomerizing (four of the proteins get together). If there is a mutation in p53, then the mutant form will poison the complex and prevent its function. IE if one of the four proteins that get together to form the complex is mutant, the whole complex won't function. Thus having a normal allele will not prevent disease.

ABO blood group - https://www.ncbi.nlm.nih.gov/books/NBK2267/

Eye color - https://www.sciencedirect.com/science/article/pii/S0002929707626822

Alzheimer's genetics - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453386/

Hemophilia A - https://medlineplus.gov/ency/article/000538.htm

p53 mutations - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135636/

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May I ask in the case of Hemophilia A, why isnt the recessive gene getting expressed alongside of the dominant? If the dominant is outperforming the recessive why does the recessive gene have zero impact instead of a lesser one. In the case of eye colour I can understand that higher melanin -> darker eye colour, so even if you have blue and brown genes you end up with brown eyes just maybe little bit lighter due to there only being one brown eyes gene. Is it the same with Hemophilia A or is there another reason why the recessive gene has no impact? Is it because one gene alone can encode for enough proteins so that overproduction in the case of the gene being there two times gets mitigated by some other factor?

Great question. This is a special case since the hemophilia A gene is only on the X chromosome and not on the Y chromosome. Since XY males will only have one copy of the X chromosome, they only need to inherit one mutant allele to develop disease. The Y chromosome doesn't have a copy of that gene to make up for the mutant one. In XX females, they have two copies of the gene and thus will need two copies of the recessive disease allele to develop disease (just like genes on any other chromosome).

All chromosomes except sex chromosomes are symmetrical so this is a special case that makes XY males more susceptible to certain genetic diseases.

Does that imply that someone who is heterozygous for the cystic fibrosis allele will have poorer lung function than average?