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I am not ignoring the function of genes, or the gene-environment interactions. What I want to know is if behind every "observable characteristic" we can find a protein -or a group of proteins- which is responsible for that trait. The idea comes from a school curriculum, and it is expressed as follows:

In this unit the core topic is the central role of proteins as executors of fundamental biological functions and thus as responsible of an organism phenotype...

Thank you in advance.

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  • $\begingroup$ Yes proteins are executors of our fundamental biology. But the proteome is the critical word here (takes into account spacial and temporal features of all proteins). For example if you had a perfectly functional ion channel, but with low expression, then a different phenotype would be exhibited than a perfectly functional ion channel that was expressed in higher amounts. The proteins are the same but the proteomes are different. $\endgroup$
    – James
    Jul 11 '16 at 9:45
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A general note on phenotype

I think that the meaning of phenotype has become more complicated over time compared to what it was when it was first coined. As you said, in simple words, a phenotype is an observable characteristic of an organism. However, for Mendel, an observable characteristic would have been only an obviously gross change in the morphology whereas with the current state of technology we can observe the assembly of macromolecules inside a cell. We can also study the physiology of an organism/tissue/cell in real time using various sensors. We can also observe the gene expression profile using different technologies (with different levels of sensitivity and resolution). The question now is, can you call such a characteristic (for e.g. an assembly of some complex in a cell observed by cryo-EM) a phenotype? In other words "what is an observable"?


Coming back to your question:

Can it be said that proteins determine phenotypic traits?

Yes.

Are they the sole determinants of phenotypic traits?

No. A phenotype is usually determined by many factors. Many genes are involved, which may code for proteins as well as functional non-coding RNAs. However, if you make a comparison, proteins seem to be more versatile than ncRNAs (also most of them are involved in direct action). So you may say that proteins are the primary determinants of most phenotypic traits, but I would generally advise that such generalizations should be used cautiously. I'll give a counter example in favour of RNAs. If there is a mutation in a tRNA or a rRNA, you'll see a great effect on the phenotype.

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  • $\begingroup$ About the question "what is an observable?", I would agree with this: "...the term phenotype includes traits or characteristics that can be made visible by some technical procedure." (en.wikipedia.org/wiki/Phenotype#Difficulties_in_definition) In the case of an tRNA/rRNA mutation, that would lead to a change in the amino acid sequence, am I wrong? $\endgroup$
    – PiQ
    Jul 11 '16 at 21:49
  • $\begingroup$ @PiQ It may not necessarily cause a change in the amino acid sequence (it could increase the error rate). It might just reduce the rate of protein synthesis. $\endgroup$
    – WYSIWYG
    Jul 31 '16 at 11:10
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Yep, that is correct in general. However, sometimes proteins indirectly determine phenotype. For example, the skin colour is dependent on melanin (not a protein) but the melanin producing cells work because of proteins. Further, melanin production is also controlled by proteins. Thus, skin colour is not DIRECTLY determined by proteins but because proteins produce the pigment melanin, proteins are ultimately the reason behind our skin colour phenotype.

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  • $\begingroup$ You might modify your answer to clarify your statements "…is controlled by proteins" and "proteins produce pigments". I don't think a novice would understand them. I would say that non-protein substances responsible for a phenotype are produced in reactions that are catalysed by protein enzymes. That's why proteins determine the phenotype. $\endgroup$
    – David
    Jul 9 '16 at 17:35
  • $\begingroup$ When you say "in general", is it explained in the next sentence? Or were you referring to something else? $\endgroup$
    – PiQ
    Jul 11 '16 at 21:53

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