that the r-allele is merely a defective version of the gene for red pigment. The r-allele is NOT a separate gene for making white color. In our hypothetical example, there is no enzyme that makes white pigment; there is simply a failure to make red pigment. Originally it was thought that each enzyme was either present or absent; that is, there were two alleles corresponding to Mendel's "yes" and "no" situations. In fact, things are often more complicated. An enzyme may be only partially active or even be hyperactive or have an altered activity and genes may actually have dozens of alleles, matters to be discussed later.A mutant allele that results in the complete absence of the protein is known as a null allele. [More strictly, a null allele is one that results in complete absence of the gene product. This includes the absence of RNA (rather than protein) in the case of those genes where RNA is the final gene product (e.g. ribosomal RNA, transfer RNA etc)—see Chapter 3].
Classical genetic analysis involves deducing the state of the genes by observing the outward properties of the organism.
In real life, most biochemical pathways have several steps, not just one. To illustrate this, extend the pathway that makes red pigment so it has three steps and three genes, called A, B, and C. If any of these three genes is defective, the corresponding enzyme will be missing, the red pigment will not be made, and the flowers will be white. Thus mutations in any of the three genes will have the same effect on the outward appearance of the flowers. Only if all three genes are intact will the pathway succeed in making its final product (Fig. 1.04).
Outward characteristics—the flower color—are referred to as the phenotype and the genetic make-up as the genotype. Obviously, the phenotype "white flowers" may be due to several possible genotypes, including defects in gene A, B, or C, or in genes not mentioned here that are responsible for producing precursor P in the first place. If white flowers are seen, only further analysis will show which gene or genes are defective. This might involve assaying the biochemical reactions, measuring the build-up of pathway intermediates (such as P or Q in the example) or mapping the genetic defects to locate them in a particular gene(s).
If gene A is defective, it no longer matters whether gene B or gene C are functional or not (at least as far as production of our red pigment is concerned; some genes affect multiple pathways, a possibility not considered in this analysis). A defect near the beginning of a pathway will make the later reactions irrelevant. This is known in genetic terminology as epistasis. Gene A is epistatic on gene B and gene C; that is, it masks the effects of these genes. Similarly, gene B is epistatic on gene C. From a practical viewpoint, this means that a researcher cannot tell if genes B or C are defective or not, when there is already a defect in gene A.
epistasis When a mutation in one gene masks the effect of alterations in another gene genotype The genetic make-up of an organism null allele Mutant version of a gene which completely lacks any activity phenotype The visible or measurable effect of the genotype
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