The set of chromosomes as viewed under the microscope is called a karyotype (“nuclear type”). The karyotype is defined by chromosome number and by other visible landmarks.
The microscopic study of chromosomes and analysis of their genetic properties is called cytogenetics, a discipline that combines cytology with genetics. Since a great deal of space in this book will be devoted to the properties of chromosomes, we will begin with a look at the visible morphology of chromosomes, the features that are commonly used in cytogenetic analysis for telling chromosomes apart.
Chromosomes can be viewed relatively easily under the microscope, but only just before, during, and immediately after cell division. When a cell divides, the nucleus and its chromosomes also divide. The topics of cell and nuclear division will be covered fully in Chapter 4. At present we need note only that chromosomes must become very compact during cell division, since they are moved around a great deal during their apportionment into daughter cells. Thus, the components of a chromosome (including its DNA) become condensed from the extended form found in nondividing cells into a shorter, fatter form that can be easily handled by the division apparatus of the cell. It is the landmarks of these condensed chromosomes that are seen under the microscope, but it can be presumed that these landmarks are in the same relative positions on the extended chromosomes of nondividing cells.
| Group | Number | Diagrammatic representation | Relative length* | Centromeric index† |
|---|---|---|---|---|
| Large chromosomes | ||||
| A | 1 |
 | 8.4 | 48 (M) |
| 2 |
 | 8.0 | 39 | |
| 3 |
 | 6.8 | 47 (M) | |
| B | 4 |
 | 6.3 | 29 |
| 5 |
 | 6.1 | 29 | |
| Medium chromosomes | ||||
| C | 6 |
 | 5.9 | 39 |
| 7 |
 | 5.4 | 39 | |
| 8 |
 | 4.9 | 34 | |
| 9 |
 | 4.8 | 35 | |
| 10 |
 | 4.6 | 34 | |
| 11 |
 | 4.6 | 40 | |
| 12 |
 | 4.7 | 30 | |
| D | 13 |
 | 3.7 | 17 (A) |
| 14 |
 | 3.6 | 19 (A) | |
| 15 |
 | 3.5 | 20 (A) | |
| Small chromosomes | ||||
| E | 16 |
 | 3.4 | 41 |
| 17 |
 | 3.3 | 34 | |
| 18 |
 | 2.9 | 31 | |
| F | 19 |
 | 2.7 | 47 (M) |
| 20 |
 | 2.6 | 45 (M) | |
| G | 21 |
 | 1.9 | 31 |
| 22 |
 | 2.0 | 30 | |
| Sex chromosomes | ||||
| X |
 | 5.1 (group C) | 40 | |
| Y |
 | 2.2 (group G) | 27 (A) | |
* Percentage of the total combined length of a haploid set of 22 autosomes.
† Percentage of chromosome’s length spanned by its short arm. The four most metacentric chromosomes are indicated by an (M); the four most acrocentric by an (A).
The tips of the chromosomes are called telomeres. The telomeres generally are not visibly distinct from the other parts of the chromosome. The telomeres and the centromeres have unique molecular structures that are crucial to normal chromosome behavior.
Nucleoli are spherical structures found associated with constrictions of the chromosomes called nucleolar organizers. Different organisms are differently endowed with nucleoli, which range in number from one to many per chromosome set. The diploid cells of many species have just a pair of nucleoli. Nucleolar organizers contain numerous tandem copies of the genes that code for ribosomal RNA, an untranslated RNA that is a component of the ribosomes. Ribosomal RNA is synthesized at the nucleolar organizers, deposited into the nucleoli, and later exported to the cytoplasm to become incorporated into ribosomes. The positions of nucleoli, like the positions of centromeres, are quite useful landmarks for cytogenetic analysis.
The chromomeres are beadlike, localized thickenings found along the chromosome during the early stages of nuclear division. The positions of chromomeres are the same in all homologous chromosomes. Although chromomeres can be useful as markers, their molecular nature is not known.
Chromosome 2 of tomato at pachytene of meiosis, showing the nucleous and the nucleolar organizer: (a) photograph; (b) interpretation. (Photo Peter Moens. From the genetic location of the centromere of chromosome 2 in the tomato. P. Moens and L. Butler. Can. J. Genet. Cytol. 5:364-370, 1963.)
When chromosomes are treated with chemicals that react with DNA, such as Feulgen reagent, distinct regions with different staining characteristics are revealed. Densely staining regions are called heterochromatin and reflect a high degree of compactness; poorly staining regions are called euchromatin and indicate less tightly packed regions. Most of the active genes are in euchromatin. Figure 5-15 shows examples of heterochromatin in the tomato.
Banding pattern of human chromosomes 1 and X, showing band nomenclature and the positions of some genes. (From V. A. McKusick, in S. J. O’Brien, ed., Genetic Maps, vol. 2. Cold Spring Harbor, N.Y. 1982.)
.
A rather specialized kind of banding occurs in a few organisms whose chromosomes can replicate their DNA many times without separating. This produces giant chromosomes, which are in essence magnified versions of the unreplicated forms. Consequently, the natural banding patterns of the chromosomes become readily visible and can serve as landmarks. These polytene chromosomes (polytene means “many-stranded”) are found in highly specialized cells of Malpighian tubules, rectum, gut, footpads, and salivary glands of the dipteran insects such as houseflies, mosquitoes, and fruit flies.
Polytene chromosomes form a chromocenter in a Drosophila salivary gland. (a) Mitotic metaphase chromosomes, with arms represented by different shades. (b) Hetero-chromatin coalesces to form the chromocenter. (c) Photograph of poly-tene chromosomes. (Tom Kaufman.)
) are present in most cells. However, in the cells of the
special organs that contain the polytene chromosomes we see some interesting
peculiarities (Figure 2-15b). First,
there are only four polytene chromosomes per cell (not eight) because during
the specialized replication process the members of each homologous pair
unexpectedly unite with each other. Second, all four polytene chromosomes
become joined at a structure called the chromocenter, which
is a coalescence of the heterochromatic areas around the centromeres of all
four chromosomes. The chromocenter of Drosophila salivary
gland chromosomes is shown in Figure
2-15b, where L and R stand for arbitrarily assigned left and
right arms.
). Polytene bands are much
more numerous than Q, G, or R bands, numbering in the hundreds on each
chromosome. The bands differ in width and appearance, so that the banding
pattern of each chromosome is unique and characteristic of that
chromosome.
Molecular studies have shown that in any chromosomal region of Drosophila there are more genes than there are polytene bands, so the bands do not represent genes. Similarly, the significance of the Q, G, and R patterns in other eukaryotic cells is not clear. They probably reflect the degree of compactness of the DNA, but it is not known how this pattern is maintained.
The landmarks that distinguish the chromosomes of corn.
shows a map of the chromosomal landmarks
of the genome of corn.
Such features as size, arm ratio, heterochromatin, number and position of chromomeres, number and location of nucleolar organizers, and banding pattern identify the individual chromosomes within the set that characterizes a species.
A human cell contains about 2 meters of DNA (1 m per chromosome set). The human body consists of approximately 1013 cells, and each cell is diploid; therefore, the body contains a total of about 2 × 1013 m of DNA. Some idea of the extreme length of this DNA can be obtained by comparing it with the distance from Earth to the sun, which is 1.5 × 1011 m. You can see that the DNA in your body could stretch to the sun and back almost 100 times. This peculiar fact makes the point that the DNA of eukaryotes is obviously efficiently packed. In fact, the packing occurs at the level of the nucleus, where the 2 m of DNA in a human cell are packed into 46 chromosomes, all inside a nucleus only 0.006 mm in diameter. How can such long molecules be packaged into to the wormlike structures, visible under the light microscope, that we call chromosomes? To answer this question we need to understand the three-dimensional structure of eukaryotic chromosomes.
Electron micrograph of metaphase chromosomes from a honeybee. The chromosomes each appear to be composed of one continuous fiber 30 nm wide. (From E. J. DuPraw, Cell and Molecular Biology. Copyright © 1968 by Academic Press.)
Composite electron micrograph of a DNA molecule from Drosophila. The overall length is 1.5 cm and is thought to correspond to one chromosome. (From R. Kavenoff, L. C. Klotz, and B. H. Zimm, Cold Spring Harbor Symp. Quant. Biol. 38, 1974, 4.)
. If such
chromosomes are studied carefully, it becomes clear that there are no ends
protruding from the fibrillar mass. This suggests that each chromosome is one
long, fine fiber folded up in some way. If the fiber somehow corresponds to a
DNA molecule, then we arrive at the idea that each chromosome is one densely
folded DNA molecule. Measurements of the elasticity of
Drosophila DNA in solution further support this concept, as
does electron microscopy (Figure
2-18).
Perhaps the best evidence that a chromosome consists of a single long DNA molecule comes from a technique called pulsed field gel electrophoresis. If DNA from a large number of cells is extracted, purified with great care to avoid breaking the molecules, and placed on a gelatinous matrix under the influence of powerful, alternating, crossed electric fields, the DNA molecules of each chromosome move through the gel at speeds proportional to their size. All the DNA of one chromosomal type ends up in one position (called a band), so if the gel is stained with a dye that binds to DNA, the number of bands of DNA is always equal to the number of chromosomes, whether the cell is diploid or haploid.
Each eukaryotic chromosome contains a single, long, folded DNA molecule.
(a) Model of a nucleosome showing the DNA wrapped twice around a histone octamer. (Alan Wolffe and Van Moudrianakis.) (b) Two views of a model of the 30-nm solenoid showing histone octamers as purple disks. (Left) Partially unwound lateral view. (Right) End view. The additional histone H1 is shown running down the center of the coil, probably acting as a stabilizer. With increasing salt concentrations, the nucleosomes close up to form a solenoid with six nucleosomes per turn. (From H. Lodish, D. Baltimore, A. Berk, S. L. Zipursky, P. Matsudaira, and J. Darnell, Molecular Cell Biology, 3d ed. Copyright © 1995 by Scientific American Books.)
. When salt
concentrations are higher, the nucleosome beaded necklace gradually assumes
a coiled form called a solenoid (Figure 2-19b). This solenoid, produced in vitro, is 30
nm in diameter and probably corresponds to the in vivo spaghetti-like
structures we saw in Figure 2-17. The
solenoid is stabilized by another histone, H1, that runs down the center of
the structure, as Figure 2-19b
shows.
We see then that to achieve its first level of packaging, DNA winds onto histones, which act somewhat like spools. Further coiling results in the solenoid conformation. However, it takes one more level of packaging to convert the solenoids into the three-dimensional structure we call the chromosome.
Drawings of chromosomes of a protozoan, demonstrating coiling and supercoiling visible with the light microscope. Two large chromosomes are shown: one orange and the other yellow; the chromosomes are duplicated because sexual cell division is about to occur. (From L. R. Cleveland, “The Whole Life Cycle of Chromosomes and Their Coiling Systems,” Trans. Am. Philosophical Soc. 39, 1949, 1.)
Electron micrograph of a metaphase chromosome from a cultured human cell. Note the central core, or scaffold, from which the DNA strands extend outward. No free ends are visible at the outer edge. At even higher magnification, it is clear that each loop begins and ends near the same region of the scaffold. (From W. R. Baumbach and K. W. Adolph, Cold Spring Harbor Symp. Quant. Biol., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1977.)
shows a good example from
the nucleus of a protozoan. Whereas the diameter of the solenoids is 30 nm,
the diameter of these “supercoils” is the same as the diameter of the
chromosome during cell division, often about 700 nm. What produces the
supercoils? One clue comes from observing chromosomes from which the histone
proteins have been removed chemically. After such treatment, the chromosomes
have a densely staining central core of nonhistone protein called the scaffold, as shown in Figure 2-21. Projecting laterally from
this protein scaffold are loops of DNA. The fibers forming these loops are
believed to be the solenoids. At high magnifications, it is clear from
electron micrographs that each DNA loop begins and ends at the scaffold. It
has been discovered that the central scaffold is largely composed of the
enzyme topoisomerase II, which has the ability to pass a strand of DNA
through another strand, rather like a magician’s rings. Evidently, the
central scaffold organizes the vast skein of DNA during replication, a time
when the two strands of DNA must unwind to allow new synthesis. Anyone who
has tried to unwind the two strands of a piece of rope has experienced the
difficulties inherent in this process.
Model for chromosome structure. On the left is shown a more relaxed supercoil, when the cell is not dividing. On the right, much tighter coiling is shown, representing a chromosome during cell division: here the loops are so densely packed, only their tips are visible. At the free ends the solenoids are shown uncoiled to give an approximation of relative scale.
, which shows a representation of a loosely coiled chromosome
from a nondividing cell and a more tightly coiled chromosome during cell
division. The loops attach to the scaffold by special regions along the DNA
called scaffold attachment regions, or SARs. Some SARs that
have been mapped in Drosophila are shown in Figure 2-23
.
, chromosomes
are much less supercoiled (but still not naked DNA) in the nondividing
nucleus than during cell division. Hence they are essentially invisible at
the light microscopic level. This more relaxed state is probably necessary
for most genes to be expressed.
In the progressive levels of chromosome packing
DNA winds onto nucleosome spools.
The nucleosome chain coils into a solenoid.
The solenoid loops, and the loops attach to a central scaffold.
Three different diagrammatic ways of representing chromosomes in nondividing cells. The first representation focuses on the coiled structure of chromosomes. The second emphasizes the fact that the genetic component of a chromosome is DNA. The third shows the chromosomes as wormlike structures with centromeres as white circles. No representation is perfectly accurate, but each has its uses in genetics.
shows three shorthand
representations of chromosomes in diploid and haploid nondividing cells,
focusing on coiled structure, linear DNA content, and chromosome length and
arm ratio. Shorthand representations such as these are used for illustrating
specific chromosomal properties under discussion, but it should be
emphasized that none is a perfect representation. Indeed the diagrams shown
in Figure 2-24 on the following page
are representations of the chromosomes in a nondividing cell, and as noted
before, at this stage the chromosomes are not even visible under the
microscope. It is important to note that in the diploid condition shown
homologous chromosomes constitute a pair, but they are generally not in a
paired configuration. In fact, homologous chro-mosomes pair physically only
during the specialized type of nuclear division that occurs during the
production of sex cells (meiosis), as we shall see in Chapter 4.
