Most chromosomes come in pairs that match in shape and size. The members of each pair are known as homologous chromosomes because they have the same genes along their length (Chapter 11). One member of each pair of homologous chromosomes is inherited from the mother and the other from the father. In many animal species, however, the sex of an individual is determined by a distinctive pair of unmatched chromosomes known as the sex chromosomes, which are usually designated as the X chromosome and the Y chromosome (Chapter 13). Chromosomes other than the sex chromosomes are known as autosomes.

In humans, a normal female has two copies of the X chromosome (a sex-chromosome constitution denoted XX), and a normal male has one X chromosome and one Y chromosome (XY). The sizes of the human X and Y chromosomes are very different from each other (Fig. 17.1). The X chromosome DNA molecule is more than 150 Mb long, while the Y chromosome is only about 50 Mb long. Except for a small region near each tip, the gene contents of the X and Y chromosomes are different from each other. The X chromosome, which includes more than 1000 genes, has a gene density similar to that of most autosomes. The vast majority of these genes have no counterpart in the Y chromosome. In contrast to the X chromosome, the Y chromosome contains only about 50 protein-coding genes.

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The regions of homology between the X and Y chromosomes consist of about 2.7 Mb of DNA near the tip of the short arm and about 0.3 Mb of DNA near the tip of the long arm. These regions of homology allow the chromosomes to pair during meiosis (Chapter 11). In most cells undergoing meiosis, a crossover (physical breakage, exchange of parts, and rejoining of the DNA molecules) occurs in the larger of these regions. The crossover allows the chromosomes to move as a unit to align properly at metaphase I so that when their centromeres separate from each other at anaphase I the X and Y chromosomes go to opposite poles.

The relative size and gene content of the X and Y chromosomes differ greatly among species. In some species of mosquitoes, the X and Y chromosomes are virtually identical in size and shape, and the regions of homology include almost the entire chromosome. This situation is unusual, however. In most species, the Y chromosome contains many fewer genes than the X chromosome. Some species, like grasshoppers, have no Y chromosome:Females in these species have two X chromosomes, and males have only one X chromosome. The total number of chromosomes in grasshoppers therefore differs between females and males. In birds, moths, and butterflies, the sex chromosomes are reversed: Females have two different sex chromosomes and males have two of the same sex chromosome.