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Chromosomes are organized structures of DNA and proteins that are found in cells. Chromosomes contain a single continuous piece of DNA, which contains many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greek χρῶμα (chroma, color) and σῶμα (soma, body) due to their property of being stained very strongly by some dyes.
Chromosomes vary extensively between different organisms. The DNA molecule may be circular or linear, and can contain anything from tens of kilobase pairs to hundreds of megabase pairs. Typically eukaryotic cells (cells with nuclei) have large linear chromosomes and prokaryotic cells (cells without nuclei) smaller circular chromosomes, although there are many exceptions to this rule. Furthermore, cells may contain more than one type of chromosome; for example mitochondria in most eukaryotes and chloroplasts in plants have their own small chromosomes.
In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed structure called chromatin. This allows the massively-long DNA molecules to fit into the cell nucleus. The structure of chromatin varies through the cell cycle, and is responsible for the organisation of chromosomes into the classic four-arm structure during mitosis and meiosis.
"Chromosome" is a rather loosely defined term. In prokaryotes, a small circular DNA molecule may be called either a plasmid or a small chromosome. These small circular genomes are also found in mitochondria and chloroplasts, reflecting their bacterial origins. The simplest chromosomes are found in viruses: these DNA or RNA molecules are short linear or circular chromosomes that often lack any structural proteins.
This is a brief history of research in a complex field where each advance was hard won, and often hotly disputed at the time.
Visual discovery of chromosomes. Textbooks have often said that chromosomes were first observed in plant cells by a Swiss botanist named Karl Wilhelm von Nägeli in 1842. However, this opinion has been challenged, perhaps decisively, by Henry Harris, who has freshly reviewed the primary literature. In his opinion the claim of Nägeli to have seen spore mother cells divide is mistaken, as are some of his interpretations. Harris considers other candidates, especially Wilhelm Hofmeister, whose publications in 1848-9 include plates which definitely show mitotic events. Hofmeister was also the choice of Cyril Darlington.
The work of other cytologists such as Walther Flemming, Eduard Strasburger, Otto Bütschli, Oskar Hertwig and Carl Rabl should definitely be acknowledged. The use of basophilic aniline dyes was a new technique for effectively staining the chromatin material in the nucleus. Their behavior in animal (salamander) cells was later described in detail by Walther Flemming, who in 1882 "provided a superb summary of the state of the field". The name chromosome was invented in 1888 by Heinrich von Waldeyer. However, van Beneden's monograph of 1883 on the fertilised eggs of the parasitic roundworm Ascaris maglocephala was the outstanding work of this period. His conclusions are classic:
- Thus there is no fusion between the male chromatin and the female chromatin at any stage of division...
- The elements of male origin and those of female origin are never fused together in a cleavage nucleus, and perhaps they remain distinct in all the nuclei derived from them. [tranl: Harris p162]
"It is not easy to identify who first discerned chromosomes during mitosis, but there is no doubt that those who first saw them had no idea of their significance... [but] with the work of Balbiani and van Beneden we move away from... the mechanism of cell division to a precise delineation of chromosomes and what they do during the division of the cell." 
Van Beneden's master work was closely followed by that of Carl Rabl, who reached similar conclusions.  This more or less concludes the first period, in which chromosomes were visually sighted, and the morphological stages of mitosis were described. Coleman also gives a useful review of these discoveries.
Nucleus as the seat of heredity. The origin of this epoch-making idea lies in a few sentences tucked away in Ernst Haeckel's Generelle Morphologie of 1866. The evidence for this insight gradually acumulated until, after twenty or so years, two of the greatest in a line of great German scientists spelt it out. August Weismann proposed that the germ line was separate from the soma, and that the cell nucleus was the repository of the hereditary material, which he proposed was arranged along the chromosomes in a linear manner. Furthermore, he proposed that at fertilisation a new ombination of chromosomes (and their hereditary material) would be formed. This was the explanation for the reduction division of meiosis (first described by van Beneden).
Chromosomes as vectors of heredity. In a series of outstanding experiments, Theodor Boveri gave the definitive demonstration that chromosomes were the vectors of heredity. His two principles were:
- The continuity of chromosomes
- The individuality of chromosomes.
It was the second of these principles which was so original. He was able to test the proposal put forward by Wilhelm Roux, that each chromosome carries a different genetic load, and showed that Roux was right. Upon the rediscovery of Mendel, Boveri was able to point out the connection between the rules of inheritance and the behaviour of the chromosomes. It is interesting to see that Boveri influenced two generations of American cytologists: Edmund Beecher Wilson, Walter Sutton and Theophilus Painter were all influenced by Boveri (Wilson and Painter actually worked with him). In his famous textbook The Cell, Wilson linked Boveri and Sutton together by the Boveri-Sutton theory. Mayr remarks that the theory was hotly contested by some famous geneticists: William Bateson, Wilhelm Johannsen, Richard Goldschmidt and T.H. Morgan, all of a rather dogmatic turn of mind. Eventually complete proof came from chromosome maps – in Morgan's own lab! 
Chromosomes in eukaryotesEukaryotes (cells with nuclei such as plants, yeast, and animals) possess multiple large linear chromosomes contained in the cell's nucleus. Each chromosome has one centromere, with one or two arms projecting from the centromere, although under most circumstances these arms are not visible as such. In addition most eukaryotes have a small circular mitochondrial genome, and some eukaryotes may have additional small circular or linear cytoplasmic chromosomes.
In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin.
- Main article: Chromatin
Chromatin is the complex of DNA and protein found in the eukaryotic nucleus which packages chromosomes. The structure of chromatin varies significantly between different stages of the cell cycle, according to the requirements of the DNA.
- Euchromatin, which consists of DNA that is active, e.g., expressed as protein.
- Heterochromatin, which consists of mostly inactive DNA. It seems to serve structural purposes during the chromosomal stages. Heterochromatin can be further distinguished into two types:
- Constitutive heterochromatin, which is never expressed. It is located around the centromere and usually contains repetitive sequences.
- Facultative heterochromatin, which is sometimes expressed.
Individual chromosomes cannot be distinguished at this stage - they appear in the nucleus as a homogeneous tangled mix of DNA and protein.
Metaphase chromatin and division
In the early stages of mitosis or meiosis (cell division), the chromatin strands become more and more condensed. They cease to function as accessible genetic material (transcription stops) and become a compact transportable form. This compact form makes the individual chromosomes visible, and they form the classic four arm structure, a pair of sister chromatids attached to each other at the centromere. The shorter arms are called p arms (from the French petit, small) and the longer arms are called q arms (q follows p in the Latin alphabet). This is the only natural context in which individual chromosomes are visible with an optical microscope.
During divisions long microtubules attach to the centromere and the two opposite ends of the cell. The microtubules then pull the chromatids apart, so that each daughter cell inherits one set of chromatids. Once the cells have divided, the chromatids are uncoiled and can function again as chromatin. In spite of their appearance, chromosomes are structurally highly condensed which enables these giant DNA structures to be contained within a cell nucleus (Fig. 2).
The self assembled microtubules form the spindle, which attaches to chromosomes at specialized structures called kinetochores, one of which is present on each sister chromatid. A special DNA base sequence in the region of the kinetochores provides, along with special proteins, longer-lasting attachment in this region.
Chromosomes in prokaryotes
The prokaryotes - bacteria and archaea - typically have a single circular chromosome, but many variations do exist. Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii, to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum. Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome.
Structure in sequences
Prokaryotes chromosomes have less sequence-based structure than eukaryotes. Bacteria typically have a single point (the origin of replication) from which replication starts, while some archaea contain multiple replication origins. The genes in prokaryotes are often organised in operons, and do not contain introns, unlike eukaryotes.
Prokaryotes do not possess nuclei, instead their DNA is organized into a structure called the nucleoid. The nucleoid is a distinct structure and occupies a defined region of the bacterial cell. This structure is however dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome. In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes.
Bacterial chromosomes tend to be tethered to the plasma membrane of the bacteria. In molecular biology application, this allows for its isolation from plasmid DNA by centrifugation of lysed bacteria and pelleting of the membranes (and the attached DNA).
Number of chromosomes in various organisms
Normal members of a particular eukaryotic species all have the same number of nuclear chromosomes (see the table). Other eukaryotic chromosomes, i.e., mitochondrial and plasmid-like small chromosomes, are much more variable in number, and there may be thousands of copies per cell.
Asexually reproducing species have one set of chromosomes, which is the same in all body cells.
Sexually reproducing species have somatic cells (body cells), which are diploid [2n] having two sets of chromosomes, one from the mother and one from the father. Gametes, reproductive cells, are haploid [n]: they have one set of chromosomes. Gametes are produced by meiosis of a diploid germ line cell. During meiosis, the matching chromosomes of father and mother can exchange small parts of themselves (crossover), and thus create new chromosomes that are not inherited solely from either parent. When a male and a female gamete merge (fertilization), a new diploid organism is formed.
Some animal and plant species are polyploid [Xn]: they have more than two sets of homologous chromosomes. Agriculturally important plants such as tobacco or wheat are often polyploid compared to their ancestral species. Wheat has a haploid number of seven chromosomes, still seen in some cultivars as well as the wild progenitors. The more common pasta and bread wheats are polyploid, having 28 (tetraploid) and 42 (hexaploid) chromosomes compared to the 14 (diploid) chromosomes in the wild wheat.
Prokaryote species generally have one copy of each major chromosome, but most cells can easily survive with multiple copies. Plasmids and plasmid-like small chromosomes are, like in eukaryotes, very variable in copy number. The number of plasmids in the cell is almost entirely determined by the rate of division of the plasmid - fast division causes high copy number, and vice versa.
Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karotypes, which are often highly variable. There may be variation between species in chromosome number and in detailed organization. In some cases there is significant variation within species. Often there is variation 1. between the two sexes. 2. between the germ-line and soma (between gametes and the rest of the body). 3. between members of a population, due to balanced genetic polymorphism. 4. geographical variation between races. 5. mosaics or otherwise abnormal individuals. Finally, variation in karyotype may occur during development from the fertilised egg.
The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division (in metaphase) in vitro (in a reaction vial) with colchicine. These cells are then stained, photographed and arranged into a karyogram, with the set of chromosomes arranged, autosomes in order of length, and sex chromosomes (here XY) at the end: Fig. 3.
Investigation into the human karyotype took many years to settle the most basic question: how many chromosomes does a normal diploid human cell contain? In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XO sex determination mechanism. Painter in 1922 was not certain whether the diploid number of man was 46 or 48, at first favouring 46. He revised his opinion later from 46 to 48, and he correctly insisted on man having an XX/XY system. Considering their techniques, these results were quite remarkable.
New techniques were needed to definitively solve the problem:
It took until the mid 1950s until it became generally accepted that the karyotype of man included only 46 chromosomes. Rather interestingly, chimpanzees (our closest living relatives) have 48 chromosomes.
Chromosomal aberrations are disruptions in the normal chromosomal content of a cell, and are a major cause of genetic conditions in humans, such as Down syndrome. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of having a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, aneuploidy, may be lethal or give rise to genetic disorders. Genetic counseling is offered for families that may carry a chromosome rearrangement.
Chromosomal mutations produce changes in whole chromosomes (more than one gene) or in the number of chromosomes present.
Most mutations are neutral - have little or no effect
A detailed graphical display of all human chromosomes and the diseases annotated at the correct spot may be found at .
Human cells have 23 pairs of large linear nuclear chromosomes, giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database. Number of genes is an estimate as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions.