A species of beetle expresses a pigment protein as an adult but not as a juvenile. The pigment is encoded by the gene PIG. A protein called KID, which is only present in juveniles, is a transcription factor that binds to the DNA near the protein-coding sequence for PIG. Do you think KID is a negative regulator of PIG or a positive regulator? Why? Some individuals in the species never express the pigment (neither as a juvenile or as an adult). Do you think they have a mutation in the KID gene, the KID binding site, or in the protein-coding part of the PIG gene? Why? (the ‘why’ part of the question will only be used to help us give possible credit for answers different than what we think is the clearest answer)

Given the information, KID appears to be a negative regulator of the PIG gene. Here is why: since KID is only present in juveniles and the pigment protein encoded by the PIG gene is not expressed in the juvenile stage but is in the adult stage, it suggests that KID is inhibiting the expression of the PIG gene. When KID is absent in the adult stage, the regulatory inhibition is lifted, and the PIG gene is expressed, allowing for the production of the pigment.

Regarding the individuals that never express the pigment, the mutation could potentially be in any of the three areas mentioned: the KID gene, the KID binding site, or the protein-coding part of the PIG gene. However, if the KID protein were mutated such that it could not bind to the DNA or it failed to be produced at all, one might expect that the PIG gene would be expressed in both juveniles and adults (assuming KID is indeed a negative regulator), which is not the case here. A mutation in the KID binding site might result in a similar outcome, where the PIG gene expression is no longer controlled by KID and thus might be expressed at all stages of life. But individuals never express the pigment, implying the inability to produce an active pigment protein at any stage of life. Therefore, the most plausible explanation is a mutation in the protein-coding part of the PIG gene that results in the loss of pigmentation. This mutation could affect the proper formation of the pigment protein, rendering it nonfunctional.

Extra: The regulation of gene expression is a complex process controlled by various factors, including transcription factors such as KID. Transcription factors are proteins that can bind to specific DNA sequences and regulate the transcription of genes—transcription being the first step in gene expression, where a segment of DNA is copied into RNA.

Negative regulators or repressors, like the hypothetical KID protein, bind to DNA and inhibit gene expression. They may do this by blocking the binding site for RNA polymerase (the enzyme responsible for transcribing DNA to RNA), modifying the structure of the DNA so it's less accessible, or recruiting other proteins that complicate the transcription machinery.

Conversely, positive regulators or activators enhance gene expression by facilitating the binding of RNA polymerase to DNA or by altering DNA conformation to make it more accessible for transcription.

When a gene mutation occurs in the protein-coding region, it can alter the amino acid sequence of the resultant protein, potentially leading to a loss of function or change in function of the protein. Mutations in the gene's regulatory regions (such as the promoter or enhancer where transcription factors like KID bind) can lead to upregulation or downregulation of gene expression.

In genetics, understanding the role of regulatory elements and mutations is crucial for piecing together the reasons why certain phenotypes, like the absence of pigment in the mentioned beetles, manifest in organisms.