The chromosome Y is 1 among the 2 sex chromosomes present in human beings while the other is the X chromosome. The sex chromosomes form 1 of the 23 pairs of human chromosomes in every cell. The Y chromosome consists of about 58 million building blocks of DNA (base pairs) and comprise of almost 2 % of the entire DNA in the cells. Each individual usually has 1 pair of sex chromosomes in each cell. The Y chromosome occurs in males, who have 1 X and 1 Y chromosome, while females have 2 X chromosomes. The Y chromosome was initially observed under a light microscope in 1923, and the scientists soon recognised its connection with maleness.

The Y chromosome has a characteristic structure on the whole with a short arm and a long arm. At both ends of the Y chromosome are the regions designated as 'pseudoautosomal regions', termed PAR 1 and PAR 2 and they include only 5% of the chromosome. The about sixty three pseudoautosomal genes are so called because they have counterparts on the chromosome X and can cross over with them. These genes code for a diversity of proteins that function in both sexes, taking part in or controlling the activities such as bone development, cell division, immunity, signal transduction, the production of hormones and receptors, fertility and metabolism.

The greater part of the Y chromosome is designated as the male specific region or MSY (the region was called formerly as non recombining region until the Y chromosome was sequenced in the year 2003). The MSY is located between the 2 pseudoautosomal regions and consists of 3 categories of DNA sequences, about 10 to 15% of male specific region (MSY) consists of X transposed sequences that are 99% identical to counterparts on the X chromosome and protein coding genes are limited in this region. Another 20% of MSY consists of X degenerate DNA sequences which have some common features to the X chromosome sequences and may be remainings of an ancient autosome that long back gave rise to X chromosome. The remaining of the MSY consists of the palindrome sections, known as amplicons. A few significant genes present in male specific region (MSY) are, the SRY gene (sex determining region of Y) which determines sex. AZF gene that codes a protein necessary to produce sperm and mutations in it leads to infertility.

The following chromosomal states are associated with changes in the Y chromosome:

- 46,XX testicular disorder of sex development - the state results from an abnormal swap over of genetic material between chromosomes (translocation). This swap over occurs as a chance event in the father of an affected person during the formation of sperm cells. The translocation affects the gene in charge that is SRY for development of a fetus into a male. The SRY gene, which is usually found on the Y chromosome, is mislaid in this disorder, almost always onto an X chromosome. Therefore the fetus with an X chromosome that carries the SRY gene will grow as a male despite not having a Y chromosome.

- 48,XXYY syndrome - it is due to the occurrence of an additional X chromosome and a Y chromosome in the cells of a male. Additional genetic material from the X chromosome intrudes with male sexual development, obstructing the testes from functioning usually and decreasing the levels of testosterone in adolescent and adult males. Additional copies of genes from the pseudoautosomal regions (PAR 1 and 2) of the extra X and Y chromosome contribute to the signals and symptoms of the syndrome.

- 47,XYY syndrome - male individuals with this syndrome have 1 X chromosome and 2 Y chromosomes in every cell, for a sum of 47 chromosomes. Symptoms include tall physique, learning problems, and other features in some boys and men. A few males with 47,XYY syndrome have an additional Y chromosome in only some of their cells. This incident is termed as mosaicism.

- Y chromosome infertility - Y chromosome infertility is generally results due to deletions of genetic material in areas of the Y chromosome known as AZF or azoospermia factor. Genes in these regions are thought to give information for making proteins that are concerned with sperm cell development.

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