These two sets chromosomes carry virtually all the thousands of genes each cell, with the exception of the tiny number in the mitochrondria, which are essential for generation of energy rich adenosine triphosphate (ATP), and a few plant chloroplasts, which are required for photosynthesis. Chromosomes can change their conformation and degree compaction throughout the cell cycle. During interphase, the major portion of the cycle, the DNA of active genes is available to the enzymes that are essential for ribonucleic acid (RNA) synthesis, and for a fraction of interphase (the DNA synthetic or S phase) all the DNA is available for DNA synthesis.

During interphase, chromosomes are not visible under the light microscope because, although they are very long, they are extremely thin.
However, during cell division (mitosis or meiosis), the chromosomes become compacted into shorter and thicker structures that can be seen under the microscope. At this time they appear as paired rods with defined ends, called telomeres, and they remain joined at a constricted region, the centromere, until the beginning of anaphase of cell division. Chromosomes are distinguished from one another by length and position of the centromere. Chromosomes are metacentric (the centromere is in the middle of the chromosome), acrocentric (the centromere is close to one end), or telocentric (the centromere is at the end, or telomere). The centromere thus usually lies between two chromosome arms, which contain the genes and their regulatory regions, as well as other DNA sequences that have no known function.
In many species, regional differences( in base composition and in the time at which the DNA replicated serve as the basis for special staining techniques that make visible a series of distinctive bands on each arm, and these can be used to identify the chromosome.
Composition
Chromosomes are made up essentially of DNA and proteins. The DNA is in the form of an extremely long, thread like double-stranded helix. Each strand has a continuous backbone (of millions of alternating phosphate and deoxyribose sugar units. A nucleotide base is attached to each sugar molecule and can be either adenine (A), cytosine (C), guanine (G), or thymine (T). The two complementary strands of the double helix are held together by hydrogen bonds between sped;
nucleotide base pairs: two hydrogen bonds between each GC base pair and three hydrogen bonds between each GC base pair. Since A can pair only with T, and G can pair only with C, each strand carries the information needed to make a new DNA strand complementary to itself (and identical to the other strand) in the process of DNA synthesis (replication), or to make a strand of RNA complementary to itself in the process of RNA synthesis (transcription).
A linear sequence of bases in a messenger RNA molecule translated into a linear series of amino acids in a polypeptide chain or protein on the basis of a nonoverlapping triplet code; that is, each successive amino acid in a growing polypeptide chain is specified by the next set of three nucleotide bases in an RNA message synthesized on a DNA template. Most of the estimated 5000-100,000 genes present in eukaryotes act by encoding proteins in this way.
For an important minority of the genes, the RNA transcript itself is the functional gel product. Examples are the small nuclear and nucleolar RNAs involved in preparing mature ribosomal and messenger RNAs, the ribosomal and transfer RNAs involved in protein synthesis, and the RNAs that mediate X-chromosome inactivation and the inactivation of one of the two copies of some autosomal genes (imprinting).
Each nucleus in the cell of a human or other mammal contains some 6 billion base pairs of DNA which, if stretched out, would form a very thin thread about 6 ft (2 m) long. This DNA has to be packaged into the chromosome within a nucleus that is much smaller than a printed dot. Each chromosome contains a single length of DNA comprising a specific portion of the genetic material of the organism. Tiny stretches of DNA, about 140 base pairs long and containing acidic phosphate groups, are individually wrapped around an octamer consisting of two molecules of each of the four basic histone proteins H2a, H2b, H3, and H4. This
Organization of DNA into chromosomes.

arrangement produces small structures called nucleosomes and results in a sevenfold compaction of the DNA strand. Further compaction is achieved by binding the histone protein HI and several nonhistone proteins, resulting in a supercoiled structure in which the chromosome is shortened by about 1600-fold in the interphase nucleus and by about 8000-fold during metaphase and anaphase, where the genetic material must be fully compacted for transport to the two daughter cells. At the point of maximum compaction, human chromosomes range in size from about 2 to 10 micrometers in length, that is, less than 0.0004 in.
Number
Each diploid (2n) organism has a characteristic number of chromosomes in each body (somatic) cell, which can vary from two in a nematode worm and one species of ant, to hundreds in some butterflies, crustaceans, and plants which have undergone polyploidization in their evolution (see table). The diploid number of chromosomes includes a haploid (n) set from each parent. Many one-celled organisms are haploid throughout most of their life cycle. The fission yeast (Schizosaccharomyces pombe) has n = 3 chromosomes, while the budding yeast (Saccharomyces cerevisiae), the common bread mold, has n = 16 chromosomes. See also: Polyploidy
Diploid numbers of chromosomes for selected species

The human diploid number is 46. Gorilla and chimpanzee chromosomes are very similar to those of the human, but both of these great apes have 48 chromosomes because only in the human was chromosome number 2 formed by fusion of two different acrocentric chromosomes characteristic of their common primate ancestor. Members of some groups of animals, such as the horses, show marked differences in chromosome number from one species to another. For example, the zebra has only half as many chromosomes as does the domestic horse. In other groups, such as the cats, all the member species share the same number of chromosomes.
There is some relationship between the number of chromosomes and their size. Marsupials, which are metatherians, usually have larger as well as fewer (14 -16) chromosomes than do most eutherian mammals. However, there are some interesting exceptions. For example, like other deer, the Chinese muntjak has 46 chromosomes, but the closely related Indian muntjak has only 6 much larger chromosomes in the XX female and 7 in the XY1 Y 2 male. Each of these large chromosomes is composed of several of the smaller Chinese muntjak chromosomes as a result of a massive reshuffling of the genome. Some of the chromosomes in certain classes of organisms with large numbers of chromosomes are very tiny, and have been called microchromosomes.

In birds and some reptiles, there are about 30-40 pairs of microchromosomes in addition to 5-7 or so pairs of regular­sized macrochromosomes. The number of microchromosomes is constant in any species carrying them, and only their size distinguishes them from the widespread macrochromosomes. At least seven microchromosomes in birds have been shown to contain genes, and all are thought to.

In some species of insects, plants, flatworms, snails, and rarely vertebrates (such as the fox), the number of chromosomes can vary because of the presence of a variable number of accessory chromosomes, called B chromosomes. It is not clear what role, if any, B chromosomes play, but they appear to be made primarily of DNA that neither contains functional genes nor has much effect on the animal or plant even when present in multiple copies.

Telomeres
Telomeres are essential for chromosome stability. A telomere caps each end of every chromosome and binds specific proteins that protect it from being digested by enzymes (exonucleases) present in the same cell. Most important, the telomere permits DNA replication to continue to the very end of the chromosome, thus assuring its stability. The telomere is also involved in attachment of the chromosome ends to the nuclear membrane and in pairing of homologous chromosomes during meiosis. The structure of telomeric DNA is very similar in virtually all eukaryotic organisms except the fruit fly (Drosophila).

One strand of the DNA is rich in guanine and is oriented 5’ to 3’ toward the end of the chromosome, and the other strand is rich in cytosine and is oriented 5' to 3' toward the centromere. Replication of DNA always occurs in the 5' to 3' direction, starting from an RNA primer complementary to the opposite strand of the DNA. Thus, in the absence of some provision for a special template structure, the end of the chromosome arm would be shortened by the length of the RNA primer each time the DNA is replicated. In order to avoid such shortening, in each replication cycle in the germ line, an enzyme called a telomerase adds additional telomere repeats on the G-rich strand at the end of each telomere.

Telomerase is not active in most somatic cells, and consequently their telomeres become shorter with repeated cell divisions, and hence with age. Fewer copies of the telomere repeat are present in human adult somatic cells than in human embryonic cells or sperm.

In most organisms, the telomere consists of multiple copies of a very short DNA repeat. For example, each human telomere contains about 2 million copies (10,000-15,000 kilobases) of a tandemly repeating TTAGGG sequence. Although the specific number and composition of the repeat units differ among various organisms, widely diverse organisms may share the same repeat unit, as do humans and slime molds. In fact, the telomere of one organism may function in a different organism; for example, a human telomere can function in a yeast cell. However, the sequences added to that telomere by yeast telomerase will be those specific for the yeast cell.

The fruit fly is an exception. Its telomere is composed of several types of very long DNA repeats, one called HeT and another called a TART sequence. These can act as transposable elements and are not synthesized by a telomerase. Instead, the infrequent addition of a single copy several thousand base pairs long to each telomere counteracts the gradual shortening of the chromosome end at each cycle of DNA replication.

Centromeres
The centromere is the chromosome structure which is responsible for proper segregation of each chromosome pair during cell division. The chromatids in mitosis and each pair of homologous chromosomes in meiosis are held together at the centromere until anaphase, when they separate and move to the spindle poles, thus being distributed to the two daughter cells. The kinetochore, which is the attachment site for the microtubules that guide the movement of the chromosomes to the poles, is organized around the centromere.

The molecular composition of the centromere is known in detail in only two species, the budding yeast and the fission yeast. In the budding yeast, the entire sequence necessary for centromeric function is no more than 120 base pairs long and consists of two short protein-binding regions flanking a longer AT-rich sequence. The DNA sequence of the centromere of each of the 16 chromosomes in this budding yeast differs, but the centromere of one chromosome can substitute for that of a different chromosome in this species.

In the fission yeast, the centromeric DNA is much more complex, consisting of long, direct and inverted repeats flanking a core element of approximately 5,000 base pairs. Each of the three centromeres in the fission yeast is a different length, ranging from 40,000 to 120,000 base pairs. A centromere from a chromosome of one organism cannot function in the other.

The molecular structures of centromeres in other species, including mammals, are still unclear, although most appear to be even larger and more complex than those of fission yeast. All centromeres seem to contain sequences that bind proteins, and these are contained in a series of short, highly repetitive DNA sequences.

In a wide variety of species, some of the proteins bound to the centromere are sufficiently similar that they can be detected by antibodies present in the serum of humans with an autoimmune disease, the CREST type of scleroderma. As a general rule, only closely related species share similar centromeric sequences. In humans and great apes, one of these repetitive families is called alpha satellite DNA. The precise sequence of its repeats of 170-base-pair length differs slightly even on different human chromosomes, so that the type of alpha satellite present can be used to identify specific human chromosomes by in situ hybridization. The repetitive DNA making up and surrounding the centromere is called heterochromatin because it remains condensed throughout the cell cycle and hence stains intensely. In humans, this region includes multiple copies of the alpha satellite DNA as well as several other types of satellite DNA. Satellites I, II, and III consist of many copies of short repeat units, some only five to eight base pairs long, and they can be partially purified by density-gradient centrifugation because their average base composition, and thus their density, differs from that of the rest of the DNA.

Such repetitive-sequence DNAs can undergo changes in composition and in number, with the result that the size of the centromeric heterochromatin region can vary between chromosomes, and even between members of the same pair of homologous chromosomes, usually without any apparent effect on centromeric function.

Nucleolus organizer regions
One or more pairs of chromosomes in each species have a region called a secondary constriction which does not stain well. This region contains multiple copies of the genes that transcribe, within the nucleolus, the ribosomal RNA (rRNA), which is an essential component of the ribosomes on which proteins are synthesized. In humans, all five pairs of acrocentric chromosomes usually have a cluster of rRNA genes, each containing up to 40 or more gene copies. These genes are clustered in other species as well, often on a single pair of chromosomes. The rRNA genes take part in forming a nucleolus, and as a result the nucleolus organizer regions can often be found still associated during metaphase, although rRNA synthesis, like that of all other genes, ceases during cell division.

The presence of such associations has been used as an indication that the rRNA genes on chromosomes in association were active. A silver-staining technique is used to identify only active rRNA gene clusters. The number of active rRNA genes may be regulated, and an organism that has too few copies of the rRNA genes may develop abnormally or not survive. Chromosome bands and staining methods

The classical chromosome stains, such as orcein or Giemsa, produce intense, uniform staining of every chromosome, except for the centromere which is less intense, and are particularly effective for demonstrating the ends of each arm and the position of the centromere.
This type of stain can be used to identify specific chromosomes only in species in which the chromosomes in the complement differ quite a bit in length or in the position of the centromere.

Staining with quinacrine mustard produces consistent, bright and less bright fluorescence bands (Q bands) along the chromosome arms because of differences in the relative amounts of CG or AT base pairs. The distinctive Q-band pattern of each chromosome makes it possible to identify every chromosome in the human genome. Quinacrine fluorescence can also reveal a difference in the amount or type of heterochromatin on the two members of a homologous pair of chromosomes, called heteromorphism or polymorphism. Such differences can be used to identify the parental origin of a specific chromosome, such as the extra chromosome in individuals who have trisomy 21.

Many methods have been devised to enhance the banding patterns inherent in chromosome structure in mammals, birds, reptiles, and other organisms. Two methods involve treating chromosomes in various ways before staining with Giemsa. Giemsa or G-band patterns are essentially identical to Q-band patterns; reverse Giemsa or R-band patterns are the reverse, or reciprocal, of those seen with Q or G banding.

In humans, most other mammals, and birds (macrochromosomes only), the Q-, G-, and R-banding patterns are so distinctive that each chromosome pair can be individually identified, making it possible to construct a karyotype, or organized array of the chromosome pairs from a single cell. The chromosomes are identified on the basis of the banding patterns, and the pairs are arranged and numbered in some order, often based on length. In the human karyotype, the autosomes are numbered 1 through 22, and the sex chromosomes are called X and Y. The short arm of a chromosome is called the p arm, and the long arm is called the q arm; a number is assigned to each band on the arm. Thus, band 1q23 refers to band 23 on the long arm of human chromosome 1.
Fig. G-banded metaphase karyotype of a human male cell. Every chromosome pair can be identified by its banding pattern. Chromosome 1 is about 12 pm long.

G and R bands
G bands and R bands differ in a variety of ways. In humans, each R band may contain up to 100 or more genes. The majority of genes appear to be in the R bands, including all the housekeeping genes, which are active in all cells, and some of the tissue-specific genes, which are active in only certain cell types. R bands are rich in many short interspersed repeat DNA sequences. In contrast, only tissue-specific genes (those that are active in only certain types of cells) are located in the G bands. G bands are replicated later than R bands, although not as late as heterochromatin. G bands are rich in long interspersed repeat DNA sequences.
The polytene chromosomes present in Drosophila or other dipteran fly salivary glands (Fig. 2b) are also banded, but these bands have a different origin than G and R bands. Polytene chromosomes are produced by multiple (up to 10 or 13) rounds of DNA replication, or endoreduplication, of the genes in somatically paired dipteran chromosomes, without any separation of the duplicated strands. Thus, each of the approximately 5000 bands may contain a single gene, or very few genes at most. The activity of a gene may result in the formation of a puff in the polytene chromosome. Polytene chromosomes are present not only in dipteran insects but also in specialized tissues of plant embryos. Endoreduplication also occurs in certain specialized cells in mammals, notably in trophoblast cells of the placenta, but the endoreduplicated chromosomes do not remain attached to each other, so the cells are polyploid, with increased numbers of chromosome sets rather than polytene chromosomes.
There are methods which make it possible to stain only selected regions of chromosomes. For example, C-banding techniques produce dark staining of heterochromatin (especially in the centromeric regions) and light staining of the euchromatin. Heterochromatin does not contain genes and is replicated very late. Restriction-enzyme banding is useful for distinguishing different types of repeated-sequence DNAs, in heterochromatin.
Replication banding is used to determine when DNA in a particular band is replicated during the cell cycle. It is based on the incorporation of radioactive molecules (for example, tritium) which can later be detected by autoradiography or, for better resolution, bromodeoxyuridine, detectable by specific antibodies or by selective destruction of DNA that has incorporated bromodeoxyuridine. Replication banding is particularly useful because it occurs even in many species in which standard G- or R-banding techniques do not produce banding. This diverse group includes fish, amphibia, and some plants.
In many of these organisms, replication banding is the best method to identify individual chromosomes in the complement. Replication banding has also been used to identify the inactive X chromosome in mammalian female cells, because the inactive X replicates later than the active X.
Fig. Chromosomes of the fungus gnat (Sciara coprophila). (a) Mitotic metaphase spread from an XO male fly, showing somatic pairings of homologous chromosomes. Chromosome IV is about 5mm long. (b) Polytene chromosome (containing identical chromosomes) spread from a female fly.