Human color vision is due to three opsin genes that encode proteins expressed in our eyes that absorb light of different wavelengths (generally called red, blue, and green opsins). The blue opsin gene is located on an autosome; red and green opsins are found on the X chromosome. Upon absorbance of light, opsin proteins then transmit signals to our brains to be interpreted. DNA mutations that cause amino acid changes in specific regions of opsin proteins can alter the specific colors absorbed by the opsin proteins, and thus fine-tune the colors of light that we can perceive.
In order to understand why color-blindness exhibits a sex-linked pattern (males have a much higher frequency of this disorder than females), we need to know something more about genetics. Because humans are diploid (have two copies of almost every chromosome), there are two copies per cell of the vast majority of genes. The benefit is that if one gene copy sustains a mutation (-), we still have one "good" (wild-type, +) copy of the gene to help our cells function. This tends to be true of color vision as well: if a retinal (eye) cell has one good copy and one mutant copy (+/-) of an opsin gene, the good version produces protein that allows "normal" color vision.
Because we have a "backup copy" of most genes, many mutations experienced by our genes are recessive: when there is still one good copy of the gene (+/-), we don't notice an effect of the mutation. Only when both copies of the gene have the mutation (-/-) do we exhibit the mutant trait. Under the (hopefully valid) assumption that very little inbreeding is occurring, the chance of inheriting the same mutation from both your mother and your father is very rare, which is why blue color-blindness is extremely rare in humans. But red-green color-blindness is fairly common in some human populations (and I'll address why this is important to scientists in a future post). This is entirely because of where the blue, red, and green opsin genes are found.
In order to understand why mutations on X-linked genes tend to cause higher incidence of mutant traits in men than women, we need to explore the history of the human X and Y chromosomes. Ages ago, our X and Y chromosomes were an autosomal pair and as genetically identical as any other pair of chromosomes. Then, a gene (called SRY) evolved to dictate which individuals would be male and which female. The rules here are simple: if you inherit SRY, you become male; if you don't have SRY, you become female. When SRY first came into existence, it was located on one member of an autosome pair (on the Y); the other member of the pair was thus defined as an X (lacking SRY).
Now the X and Y are (slightly) more genetically different: one has a gene that the other doesn't. This set off an amazing series of events that eventually caused the human Y chromosome to "degenerate." The human Y chromosome is physically much smaller than the X, and contains only a tiny fraction of the genes it used to share in common with the X - way back when they were still an autosome pair. The speciality field of sex chromosome evolution seeks to understand how this degenerative process occurs; this was the basis for my doctoral dissertation (but in stickleback fish, not humans).
Remember I said that we "have two copies of almost every chromosome" and "have a 'backup copy' of most genes." Human males (XY) do not have two functional copies of every chromosome: we have an XY "pair," but the X and Y are essentially genetically unrelated at this point in time. Our Y chromosome does not contain, for example, a red opsin gene or a green opsin gene. There are two tiny regions of DNA sequence similarity between the X and Y: the two "pseudoautosomal" regions (PAR1 and PAR2) that facilitate X and Y pairing at meiosis.
My best slides from this lecture (judging by student reaction) illustrate a very useful analogy for sex chromosomes:
This is entirely the basis for sex-linked traits: when a X-linked gene, like red opsin, is mutated, a mother can pass that mutant X chromosome to both her sons and daughters. However, the daughters (by virtue of also receiving an X from dad) don't exhibit the recessive trait. On the other hand, I received the Y chromosome from my father, by definition, and so my X from my mother. That X carries an opsin mutation, and I don't have a "normal" red opsin gene on my Y to provide me with "normal" color vision.
So, where did my mother get her mutant X chromosome from? Her color-blind father (my maternal grandfather). Hence, a typical pattern for X-linked traits: passed from affected grandfathers through their daughters to half of their grandsons. Why half? Because my mother has a wild-type X chromosome as well. I had a 50:50 chance of inheriting her "good" X, but I lost the coin toss.
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