The Sex Chromosomes

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There are twenty three pairs of chromosomes in the human genome. In twenty two pairs, the homologous pairs match closely in size and shape. Homologous chromosomes carry corresponding genes aligned in corresponding positions. One member of each pair is the maternal chromosome received from the mother and the other is the paternal chromosome received from the father. While homologous chromosomes carry genes for the same trait, there are often small variations in the nucleotide sequences that result in different versions of that trait. Different versions of the same gene are called alleles. The variety of different alleles in the human genome are responsible for the variation in traits from person to person.

During meiosis, the homologous pairs of autosomal chromosomes entwine and exchange bits and pieces of their DNA. The end result is a patchwork chromosome carrying some paternal alleles and some maternal alleles. This mixing and shuffling, called recombination or crossover, insures that each individual receives a unique assortment of their parents' alleles. These 22 pairs of chromosomes are called autosomal chromosomes or simply autosomes.

In order for sperm or egg formation to occur, there must be at least one cross over event between each homologous pair during meiosis.

The 23rd chromosome pair is unique. The chromosomes differ in both size and shape. The larger X chromosome is similar to the autosomes. It is much larger than the Y chromosome spanning 155 million DNA base pairs. The X chromosome makes up about 5% of the human genome. Over thousands of years, the Y chromosome has lost many of its genes. some have moved to other chromosomes and others just deteriorated. The result is a human Y chromosome that is smaller than its partner, only about 59 million base pairs in length. It is also somewhat misshapen—looking more like the letter Y than the X shape of the other chromosomes.

All females have two X chromosomes with similar genes aligned in a similar fashion. A pair of X chromosomes can function as a normal homologous pair. Like the autosomes, they can entwine with their homologous genes aligned in such a way that they can exchange substantial lengths of homologous DNA during the process of egg cell formation.

The X chromosome contains 800 - 900 genes whereas the Y chromosome is variously reported to contain only 50 to 60 genes. With such disparity in base pair and gene number, it is not surprising to learn that the X and Y chromosomes are mismatched along much of their lengths.

There is not much homology between the X and the Y chromosome. However, there is a bit of homology near both ends where they contain some of the same genes. We call these “matching” ends of the X and Y chromosomes the pseudoautosomal regions. Figure 2 is a micrograph of an X and Y chromosome pair stained with green fluorescent dye to show their pseudoautosomal ends. With some contortion, it is possible for limited crossover to occur between the X and Y in these pseudo-autosomal regions. This is fortunate because they are not exempt from the requirement for at least one cross-over to occur before meiosis can proceed and sperm or egg cells can be produced.

fluorescently labeld pseudoautosomal regions of X and Y chromosomes
Fig. 2

Their awkward pairing notwithstanding, these two chromosomes play an important role in human development. They are the sex chromosomes.

Y Chromosome

Y chromosome showing pseudoautosomal region
Fig. 3

Despite its unassuming appearance, the Y chromosome contains the SRY gene that alone determines that a fertilized egg will develop into a male.

Early in the development process, the SRY gene starts a cascade of gene expression by activating genes on other chromosomes that are necessary for male development. Those genes then activate other male developmental genes and so on. For example, the SRY gene activates a gene called SOX9 that is locate on chromosome 17. Both males and females carry this gene on chromosome 17 but it can only be activated by the SRY gene. There is no SRY gene on the X chromosome. Without the SRY gene, this cascade will not start. If the SRY gene is missing or impaired, the fertilized egg will develop as a female even if there is a Y chromosome present.

All males have one X chromosome received from their mother. The unpaired genes on that chromosome are sufficient for all the the functions they control. Unlike genes residing on the paired autosomal (and paired X) chromosomes, there is no provision for masking of a deleterious recessive gene by a corresponding dominant gene that may code for a normal trait.

This unpaired state guarantees that which ever version of an allele that is present on the Y chromosome will be expressed. In most cases this is not a problem. However there is an assortment of genes on the X chromosome that may exist in some deleterious state though they are recessive. It would be rare for a female to have a copy of this allele on both of her X chromosomes. In most cases, the harmful version is masked by the presence of a more benign dominant version. However, if a mother passes the X chromosome with the harmful, recessive allele to her son, it will be expressed as there is no chance for masking it. Familiar conditions that can arise from such X linked recessive alleles are hemophilia and color blindness and Duchenne muscular dystrophy.

Hemophilia in the Descendants of Queen Victoria of England
Chart showing helophilia in descendants of Queen Victoria
Fig. 4

Idosyncrasies of the X Chromosome

The mismatch of the X and Y chromosomes also results in a quirk in the expression of genes on the X chromosome in females. Since the male has only one X, over time cells have evolved to need only one copy of each X linked gene. This leads to a potential imbalance of X chromosome gene expression between male and females. To remedy this dilemma, very early in the development of the female embryo, one X chromosome in each cell is deactivated. This is accomplished by compacting the superfluous X chromosome in such a way that it cannot be unwound and made accessible for transcription to mRNA. This process is called lyonization and the resulting deactivated X chromosomal material is called heterochromatin. The deactivated X chromosome of each cell is sometimes called a Barr body.

Once an X chromosome is deactivated, it is deactivated for the life of the organism and remains inactive in all descendant cells in the organism.

The deactivation of one X chromosome occurs randomly in each cell so that the cells of a female are a mosaic of their maternal and paternal X chromosomes. A classic example of this is the Calico cat. Each colored patch on a calico cat has a different X chromosome turned on. This explains why calico cats are rarely male as they only the same X chromosome in each cell. A less well known example is women who have some patches of skin that are missing sweat glands.

An excellent, more detailed discussion of X chromosome deactivation can be found at

Calico cat
Fig. 5
Image credits

Figure 1 By Ashwin Kelkar , Vivek Thakur , Ramakrishna Ramaswamy , Deepti Deobagkar [CC BY 2.5 (], via Wikimedia Commons

Figure 2 By Steffen Dietzel, Dietzel65 (Own work) [CC BY 3.0 (], via Wikimedia Commons

Figure 3 By John W. Kimball [CC BY 3.0 (], via Wikimedia Commons

Figure 4 By Shakko (Own work) [CC BY-SA 4.0 (], via Wikimedia Commons

Figure 5 By Britchi Mirela (Own work) [CC BY-SA 3.0 (], via Wikimedia Commons

Where Can I Go From Here?

©️2002 - 2017 is a not for profit, educational website.

Where Can I Go From Here?

©️2002 - 2017 is a not for profit, educational website.