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What causes alleles to become dominant or recessive?


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#21 BabcockHall

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Posted 14 October 2016 - 01:48 PM

The answers here have  been helpful; I hope I won't muddy the waters.  For some enzymes a nonfunctional allele displays recessive genetics.  One might think at first blush that if you have one good and one bad copy of a gene, that the flux through this pathway will be down by 50%.  However, sometimes the flux is essentially unaffected, because the particular step of the pathway has a flux control coefficient of zero.


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#22 Itoero

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Posted 14 October 2016 - 04:37 PM

Why should a recessive allele be blocked in the first place? You are aware that in almost all the posts before we discussed how it is in a non-regulatory situation? If you still think that dominance is specifically a mechanisms that prevents expression of a recessive allele by the dominant one, then your model is flawed. The description is based on phenotype and the interaction can be simple. Examples were given above example (i.e. protein activity, did you understand that part or was that unclear) or due to regulatory influences, that may involve interactions with other gene products. These includes often transcription factors, though the role of small RNAs is getting more and more attention.
 
If you are really confused how gene regulation works, I would first look into transcription factors, which is a more canonical view as basis. Then expand into regulatory RNAs. I do feel that you may have quite some ground to cover in order to understand the elements and their interaction.

A dominant allele masks the contribution of a recessive allele on a phenotype. Since dominant alleles can block recessive alleles with sRNA, isn't it logic that most dominant alleles use that?
I don't know the exact system, but I'm not confused.
A recessive allele is masked by a dominant allele in a gene.
This is visible in the alleles which cause are blood type and alleles which cause the colors of mammals.
 

The simplest case is if an allele results in the loss or reduced function of the protein it codes for. Let's call the allele a and the phenotype p-. If an individual has two of this allele (aa) the individual has not functioning protein and the phenotype is p-. However, if he is heterozygote and carries a functional version (b) in addition to a, the functional one may be sufficient to cover the deficit, hence ab would be p+. Then there may be a third allele, c, which is functional, but not quite as efficient as b. If you have got cc, you have phenotype somewhere between p+ and p-, let's call it p+/-. So if you got bc, you got p+, as the more efficient b covers c. Thus b is dominant over a and c. But if you have ac, the somewhat functional c covers the deficit of a and you may have p+/-.

Do a and c modify the function of b? I thought this was only possible between genes and not alleles of a gene.

Edited by Itoero, 14 October 2016 - 06:35 PM.

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#23 CharonY

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Posted 14 October 2016 - 08:23 PM

You are still not getting it. Both alleles can express proteins (do you understand what a protein is and how it relates to a gene? If not, ask or look up, it is crucial for understanding). The proteins differ in sequence (as alleles may have different sequences). Different amino acid sequences can alter the function of the protein. This is the part that does not require additional regulatory control to explain dominance.


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#24 Itoero

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Posted 15 October 2016 - 10:06 AM

You are still not getting it. Both alleles can express proteins (do you understand what a protein is and how it relates to a gene? If not, ask or look up, it is crucial for understanding). The proteins differ in sequence (as alleles may have different sequences). Different amino acid sequences can alter the function of the protein. This is the part that does not require additional regulatory control to explain dominance.

Can you plz answer my questions?

*Do a and c modify the function of b? I thought this was only possible between genes and not alleles of a gene.

*A recessive allele is masked by a dominant allele in a gene.
This is visible in the alleles which cause our blood type, alleles which cause the colors of mammals, alleles which cause diseases...
Do you deny this?

*This is the Wikipedia definition:
"Dominance in genetics is a relationship between alleles of one gene, in which the effect on phenotype of one allele masks the contribution of a second allele at the same l"
This is wrong in your opinion?
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#25 BabcockHall

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Posted 15 October 2016 - 03:43 PM

Itoero,

 

I think that you are misconstruing the meaning of the word "mask."  For one thing to mask something else does not necessarily mean that there has to be a direct interaction between the two things.


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#26 Itoero

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Posted 15 October 2016 - 03:59 PM

Itoero,
 
I think that you are misconstruing the meaning of the word "mask."  For one thing to mask something else does not necessarily mean that there has to be a direct interaction between the two things.

There is a way a dominant allele can block a recessive allele, so why wouldn't that be used in most genes?

Edited by Itoero, 15 October 2016 - 04:00 PM.

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#27 CharonY

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Posted 15 October 2016 - 04:04 PM

I cannot help you if you just ignore the bulk of biological required to understand the process. Not understanding proteins is not understanding what a gene is. I do not sense any effort on your side to understand the process therefore I opt to not further waste my time.
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#28 Itoero

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Posted 15 October 2016 - 04:06 PM

I cannot help you if you just ignore the bulk of biological required to understand the process. Not understanding proteins is not understanding what a gene is. I do not sense any effort on your side to understand the process therefore I opt to not further waste my time.

Why do you refuse to answer my questions?

Edited by Itoero, 15 October 2016 - 04:07 PM.

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#29 CharonY

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Posted 15 October 2016 - 04:10 PM

Because you ignore my answers and questions. Asking the wrong questions won't help you understand the principles. Last try: to you understand the difference between gene and gene product?
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#30 Itoero

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Posted 15 October 2016 - 06:22 PM

Because you ignore my answers and questions. Asking the wrong questions won't help you understand the principles. Last try: to you understand the difference between gene and gene product?

Yes I do. I asked those questions because you are imo wrong.
In your example proteins decoded by alleles of the same gene modify each other's function.
The modification of proteins is a property of genes working together, not alleles in a gene. It's called post-translational modification.
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#31 BabcockHall

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Posted 15 October 2016 - 06:40 PM

There is a way a dominant allele can block a recessive allele, so why wouldn't that be used in most genes?

 

Asking why something would not happen in a certain way is starting out on the wrong track.  The question is what does or does not happen, based on evidence.


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#32 StringJunky

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Posted 15 October 2016 - 06:51 PM

I don't think you want to read what CharonY and I presented because you have your own pet theory... I suspect.

I wasn't wrong, was I? I think it's bad manners, dishonest and just plain  annoying for someone to apparently ask a question, as though they wish to learn something, then argue that the answers are wrong as the discussion proceeds.


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#33 Itoero

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Posted 15 October 2016 - 07:04 PM

Asking why something would not happen in a certain way is starting out on the wrong track.  The question is what does or does not happen, based on evidence.

A small RNA encoded by the first allele recognises a specific sequence on the second allele and blocks its expression.
http://www.inra.fr/e...gene-expression

I wasn't wrong, was I? I think it's bad manners, dishonest and just plain  annoying for someone to apparently ask a question, as though they wish to learn something, then argue that the answers are wrong as the discussion proceeds.

I asked the cause for dominance/recessiveness and found it myself.
And explaining how alleles behave dominant does not explain what causes it.
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#34 Delta1212

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Posted 15 October 2016 - 09:13 PM

A small RNA encoded by the first allele recognises a specific sequence on the second allele and blocks its expression.
http://www.inra.fr/e...gene-expression
I asked the cause for dominance/recessiveness and found it myself.
And explaining how alleles behave dominant does not explain what causes it.


Except in this case, where the explanation does in fact explain exactly what causes it. You're just ignoring the explanation.
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#35 Itoero

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Posted 16 October 2016 - 01:27 PM

Except in this case, where the explanation does in fact explain exactly what causes it. You're just ignoring the explanation.

That's not true.
Again, describing a dominant relationship does not explain what causes the relationship.
Many recessive alleles are just as functional as dominant alleles. Those recessive alleles must be blocked which is only possible if there is a chemical difference between dominant and recessive alleles, noticeable by RNA polymerase/mRNA.
A small RNA encoded by the first allele recognises a specific sequence on the second allele and blocks its expression. It's explained on this website: http://www.inra.fr/e...olution/(key)/2


RNA polymerase binds to promotor DNA and separates the double helix.
It then adds complementary RNA nucleotides at the correct allele. This is the start of mRNA.
A ribosome translates mRNA to an amino acid chain (protein)

This process is the main cause for the dominant relationship between alleles.

When I asked for the cause, I asked why mRNA is formed at the correct allele.
It seems that RNA polymerase forms mRNA at the correct allele by the presence of sRNA or RNA targets on the allele.
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#36 BabcockHall

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Posted 17 October 2016 - 07:02 PM

@OP,

 

E. coli is ordinarily a haploid organism; therefore, it has no need of any mechanism to make one allele silent.  Yet it can be made partially diploid by using plasmids.  The gene for the lactose repressor protein is sometimes given the symbol i.  Most lactose repressor mutants coding for a nonfunctional repressor i- are recessive to the wild type form i+.  A few mutants that code for a nonfunctional repressor, however, and dominant, i-d.  How do you explain these two observations?


Edited by BabcockHall, 17 October 2016 - 08:01 PM.

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#37 Itoero

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Posted 18 October 2016 - 01:28 PM

@OP,
 
E. coli is ordinarily a haploid organism; therefore, it has no need of any mechanism to make one allele silent.  Yet it can be made partially diploid by using plasmids.  The gene for the lactose repressor protein is sometimes given the symbol i.  Most lactose repressor mutants coding for a nonfunctional repressor i- are recessive to the wild type form i+.  A few mutants that code for a nonfunctional repressor, however, and dominant, i-d.  How do you explain these two observations?

-A haploid organism has no need for a mechanism to mask an allele but haploid organisms use RNA polymerase, just like diploid organisms. RNA polymerase has the ability to chose between 1 or 2 alleles, regardless in which organism it's used.
-Maybe they are codominant?
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#38 Itoero

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Posted 21 October 2016 - 10:31 AM

-A haploid organism has no need for a mechanism to mask an allele but haploid organisms use RNA polymerase, just like diploid organisms. RNA polymerase has the ability to chose between 1 or 2 alleles, regardless in which organism it's used.
-Maybe they are codominant?

Does this makes any sense?
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#39 BabcockHall

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Posted 21 October 2016 - 01:30 PM

You are arguing against the facts, which are that most mutations in the gene for the lactose repressor are recessive, but some are dominant.  I am not aware of any that are codominant.


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#40 Itoero

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Posted 21 October 2016 - 02:31 PM

You are arguing against the facts, which are that most mutations in the gene for the lactose repressor are recessive, but some are dominant.  I am not aware of any that are codominant.

ok, it just seems that a 100% dominant mutant that codes for a nonfunctional repressor is very unlikely so doesn't it make more sense that the mutant is codominant to the wildtype?

Edited by Itoero, 21 October 2016 - 02:46 PM.

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