Chromosomes
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[edit] Introduction
In this article we shall discuss chromosomes with particular reference to their role in inheritance and their relationship to Mendel's principles of genetics. The reader who is unfamiliar with the principles of Mendelian genetics will probably do best to read that article first.
[edit] Diploidy
Sexually reproducing organisms are diploid: with the possible exception of their sex chromosomes, there are two non-identical copies of each chromosome: such pairs of chromosomes are said to be homologous.
The phrase "non-identical copies" may seem to be a contradiction in terms. To be more precise, two homologous chromosomes contain the same genes in the same positions on the chromosomes, but may have different alleles of these genes. So, for example, the two homologous copies of human chromosome 15 both have a gene controlling eye color: but the same individual may have the blue allele for eye color on one copy of chromosome 15 and the brown allele on its homologue.
This is the physical basis of Mendel's principle that there are two copies of each gene.
[edit] The cell cycle
The process is sketched out in the diagram to the left. These diagrams have been simplified to place emphasis on what is happening to the chromosomes in the cell, and omits details about the rest of the cellular apparatus involved in cell division.
The diagram here, and of meiosis below, represent the homologous chromosomes as being different shades of the same color.
At the top, we have a picture of a cell which has just divided. It is small, for that reason, and its chromosomes are long thin strands. The illustration does not do justice to how long and thin these strands really are: you have several meters of DNA in each cell, and they are so fine, in this phase of the cell cycle, that they cannot be seen using a light microscope.
The cell then undergoes the first gap phase: during this time it grows and performs its other metabolic functions. It then undergoes synthesis: an exact copy (exact, that is, barring the occasional mutation) is made of each chromosome, with the original and its copy being bound together along their length by protein links. Biologists describe such a structure as one chromosome consisting of two sister chromatids.
During synthesis, the cell continues to grow and function, and after synthesis comes a second gap phase, during which the cell continues to grow and function.
When the cell is large enough, it is ready to undergo mitosis, the process by which the sister chromatids divide. The phases of the process are shown on the diagram. The chromosomes contract into short stubby forms visible under a light microscope; the two sister chromatids in each chromosome remain attached at the centromere. They line up in the middle of the cell (as determined by the mitotic spindles, not pictured in the diagram) and then, in anaphase, the sister chromatids part, and one from each chromosome goes to each end of the cell, which elongates in that direction and then splits in two; at the same time, the chromosomes begin to unravel again. The result is that we're now back where we started except that we have two cells where previously we had one; each cell has its full diploid complement of genes.
[edit] Sexual reproduction
Although there are many differences in detail between the sexual reproduction of animals, plants, fungi, and algae, they all have one thing in common: the alternation between diploid cells and haploid cells --- that is, cells which only have one chromosome for each homologous chromosome pair. In animals, for example, the diploid stage (the animal) produces a haploid stage (a gamete: a sperm or an ovum) which then fuse together to produce a diploid cell, a zygote, which then grows into a full-grown animal by the process of diploid cell division, and produce more haploid gametes ... and so on.
This corresponds to the Mendelian principle of segregation that each parent contributes just one of each allele of each gene to its offspring.
The process by which diploid organisms produce haploid cells is known as meiosis, and as understanding the exact details is important for understanding some aspects of genetics, we shall describe it in some detail in the section below.
[edit] Meiosis
The process of meiosis is sketched out in the diagram to the right. As in the diagram of the cell cycle, we have pictured homologous chromosomes as being different shades of the same color.
We start when the cell has already gone through the first gap phase, synthesis phase, and second gap phase of the normal cell cycle, so that the cell is full grown and each chromosome consists of two sister chromatids.
As in mitosis, the chromosomes furl themselves up into stubby shapes joined at the centromere. But then they pair up and undergo a process known as recombination or crossing over. The arms of the chromosomes literally cross over one another, and the chromosomes exchange homologous strands of DNA --- that is, DNA containing the same genes, though possibly different alleles of each gene. The result is that although the cell ends up with homologous pairs of chromosomes, they are not the homologous pairs of chromosomes it started with. Note also that the sister chromatids needn't recombine with their homologues in exactly the same way, so that the sister chromatids of each chromosome needn't be identical after recombination.
Next, the homologous chromosomes line up in the center of the cell, and then each of the homologous pairs retreats to the opposite end of the cell, which then divides.
This leaves us with, in each of the two daughter cells, just one of each pair of homologous chromosomes. However, each of these still consists of two sister chromatids, which, thanks to the process of recombination, need not be identical. A further round of cell division is needed to fix this, which procedes more like the cell division familiar from the cell cycle: the chromosomes line up in the center of the cell, the sister chromatids part and retreat to opposite ends of the cell, which then divides.
So each round of meiosis produces four haploid cells from one diploid cell. What exactly happens next depends on the organism's sex and species. In male animals, all four haploid cells will become sperm; in female animals, in the process of meiosis one of the haploid cells will have ended up with more of the original cell's cytoplasm than the other three, and it will develop into an ovum while the other three, known as polar bodies, will be discarded. In plants, algae, and fungi, the details differ, but in each case the process of meiosis is much the same.
[edit] Meiosis and Mendel
The process of meiosis provides a physical basis for Mendel's law of segregation. Clearly, every allele of each gene of the diploid organism has a 50:50 chance of finding itself in any haploid cell produced by meiosis. Indeed, chance doesn't come into it: meiosis ensures that if an organism has two different alleles of the same gene, then when a cell undergoes meiosis, it will produce exactly two haploid cells having one allele, and two having the other allele.
The process of meiosis also explains why genes on non-homologous chromosomes should follow Mendel's law of independent assortment. When the homologous chromosome pairs separate (in anaphase I), and when, subsequently, the sister chromatids part (in anaphase II) there is no particular reason why two alleles on non-homologous chromosomes should end up at the same end of the cell when it divides, or at opposite ends of the cell: this is just how the genome. crumbles.
On the other hand, consider two alleles of genes that lie close together on the same chromosome. The process of recombination means that they don't always have to go around together. However, each pair of chromosomes will only cross over in a few places, exchanging lengthy strands of DNA, so the chances are that two alleles that lie close together on the same chromosome will tend to be inherited (or not inherited) together.
This means that genes lying close together will show a deviation from the results predicted by Mendel's law of independent assortment. This fact was used to make the first genetic maps: two genes which don't assort independently must lie on the same chromosome, and the greater the deviation from Mendel's prediction, the closer they must lie together; so by conducting a series of Mendel-style breeding experiments, and noting the divergence from Mendel's laws, it is possible to infer the relative position of genes on the chromosomes of a species.
[edit] Some exceptions
[edit] Asexual reproduction
In the article so far, we have discussed organisms that are diploid and reproduce sexually.
Organisms that are haploid and reproduce asexually have a much simpler time of it. In a bacterium, for example, the chromosome forms a single loop of DNA with a little protein packaging. The bacterium makes a copy of the chromosome, the two copies separate to opposite ends of the cell, which then divides, giving us two bacteria. There is no real difference here between reproduction and cell division.
This means that, barring the occasional mutation, the genes of the two daughter bacteria will be the same as the parental bacterium: this makes the genetics of asexually reproducing organisms very simple.
The mitochondia that live in, and symbiose with, the cells of animals also have a bit of DNA of their own, and reproduce asexually. Moreover, a zygote gets all its mitochondria from the ovum and none from the sperm. This makes possible an exception, or apparent exception to Mendel's laws. If a trait is controlled, not by diploid chromosomes in the cell nucleus, but by the chromosome of the mitochondria, then that trait will be passed down from a mother to all her children, but cannot be inherited on the paternal side.
Because mitochondrial DNA is reproduced asexually, without recombination, all the variation in it must be caused by mutation. This makes mitochondrial DNA useful in molecular phylogeny: for more information, see our article on Mitochondrial Eve.
[edit] Sex chromosomes
Sex chromosomes are chromosomes which by their presence or absence determine the sex of the organism carrying them. We have mentioned that sex chromosomes can be an exception to the rule that every chromosome in a diploid organism has a homologue. In humans, for example, whereas a female will have two homologous sex chromosomes (known as X chromosomes) a male will have an X chromosome and a Y chromosome, and the Y chromosome will not contain all the genes found on the X chromosome.
For a further discussion of sex chromosomes and their consequences, see the main article on Sex Chromosomes.
[edit] Polyploidy
We have given it as a rule that there are two copies of each chromosome in sexually reproducing organisms. This is not the case: some may have three copies of each chromosome (triploids) or four copies (tetraploids) or six copies (hexaploids) --- and so forth. More information will be found in our article on mutation.
