Chromosomes are bundles of tightly coiled DNA located within the nucleus of almost every cell in our body. A chromosome is a DNA molecule with part or all of the genetic material (genome) of an organism. Chromosomes are normally visible under a light microscope only when the cell is undergoing the metaphase of cell division. Before this happens, every chromosome is copied once (S phase), and the copy is joined to the original by a centromere, resulting in an X-shaped structure. The original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, the X-shape structure is called a metaphase chromosome.

1. 1
Chromosome: A Complete Overview
1.1 Introduction
Chromosomes are bundles of tightly coiled DNA located within the nucleus of almost every cell
in our body. A chromosome is a DNA molecule with part or all of the genetic material (genome)
of an organism. Chromosomes are normally visible under a light microscope only when the cell
is undergoing the metaphase of cell division. Before this happens, every chromosome is copied
once (S phase), and the copy is joined to the original by a centromere, resulting in an X-shaped
structure. The original chromosome and the copy are now called sister chromatids. During
metaphase, when a chromosome is in its most condensed state, the X-shape structure is called a
metaphase chromosome.
1.2 Chromosome Structure and Function
Chromosome number and structure vary between species. Bacterial cells typically have a single
circular chromosome, but eukaryotes have several large linear chromosomes in their cell nuclei
(Table 1.1). The chromosome number and DNA content in a complex eukaryotic organism can
also vary, for example the gametes (sperm and egg cells) of mammals are specialized sex cells
which contain half the number of chromosomes (haploid) of the somatic cells (diploid). The
gametes arise from certain somatic cells in the ovary and testis which undergo a specialized form
of cell division called meiosis, which serves to reduce the chromosome number by half. Man has
a chromosomal number of 46, and in the sperm and egg cells this number is halved to 23,
comprising one sex chromosome X or Y, and 22 autosomes (non-sex chromosomes).

2. 2
Table 1.1: Chromosome number in different species of animals and plants
1.3 Chromosome Shape
Chromosomes in man consist of two separate arms, divided by a structure called
the centromere (see Figure 1.1) with the long arm being designated the 'q’ arm and

3. 3
the shorter arm the 'p’ arm. There are also three distinct shapes - metacentric
(where the centromere is central, such as in chromosomes 1 and 19),
submetacentric (where the centromere is slightly off-center, such as in
chromosomes 4, 6 and 12), and acrocentric (where the centromere is almost at the
top of the chromosome such as in chromosomes 13 and 22).
Figure 1.1 Chromosome shaped observed in the chromosome of men

4. 4
1.4 Chromosome Function
Chromosomes in mammals have two main functions: (a) perpetuating the hereditary material
during an individual’s development; and (b) to shuffle and move that material through successive
generations. There are three sequence elements of DNA responsible for the biological functions
of eukaryotic chromosomes.
Centromeres These are cis-acting DNA elements responsible for segregating the chromosomes
at mitosis and meiosis. If chromosomal segments lack a centromere (acentric fragments), they
will not become attached to the spindle so will fail to be included in the subsequent formation of
daughter cells. A chromosome needs a centromere to join in the fun of division.
Telomeres These seal the ends of the chromosomes and provide chromosome stability. They
maintain the structural integrity of the chromosome. If the telomere is lost, the chromosome
becomes unstable and tends to fuse with other broken chromosomes if it can. The telomeres also
ensure complete replication of the extreme ends of chromosome termini. They also play a role in
establishing the three-dimensional structure of the nucleus and chromosome pairing.
Origin of Replication DNA in most diploid cells replicates only once per cycle and the control
of this initiation of replication is governed by cis-acting sequences.
1.5 Chromosome Architecture and Transcriptional Activity
During mitosis, when the chromosomes condense, they are transcriptionally inactive, but during
interphase the chromatin fibers are less densely packed and the euchromatin observed dispersed
in the nucleus stains diffusely. The remaining chromatin comprises highly condensed fibers and
forms dark-staining regions called heterochromatin, and these regions are transcriptionally inert.

5. 5
There are two types of heterochromatin: (i) facultative heterochromatin, which can be genetically
active or inactive (i.e. in the special case of the mammalian X chromosome inactivation); and (ii)
constitutive heterochromatin, which is always inactive.
These regions are composed of certain repetitive DNA sequences observed in the centromeric
regions of the chromosomes and the p (short) arms of acrocentric chromosomes. Condensation of
chromatin is associated with loss of gene expression, although there is also a large amount of
transcriptionally inactive DNA in euchromatic regions. In fact it is known that dark-staining C-
bands contain more condensed chromatin than R-bands, and in situ hybridization has also shown
that 80% of genes in the human genome map to R-bands and only 20% to C-bands. It is almost
like imagining that the chromosome becomes pulled out in interphase but squeezed up like a
concertina during the process of division.
1.6 Staining and Bending of Chromosome Slides
Chromosomes display a banded pattern when treated with some stains. Bands are alternating
light and dark stripes that appear along the lengths of chromosomes. Unique banding patterns are
used to identify chromosomes and to diagnose chromosomal aberrations, including chromosome
breakage, loss, duplication, translocation or inverted segments. A range of different chromosome
treatments produce a range of banding patterns: Q-bands, G-bands, R-bands, C-bands, NOR-
bands and T-bands. In recent years a number of chromosome banding techniques have been
developed that employ molecular cytogenetic techniques, for example fluorescence in situ
hybridization (FISH).
Solid staining Although apparently outdated since the inception of banding, this still can be
applied to chromosome breakage syndromes and fragile site studies, as banding sometimes
masks small chromatid gaps and breaks in the chromosomes.

6. 6
G-banding The most widely used technique for the study and recognition of mammalian
chromosomes.
Q-banding This is a fluorescent staining technique using quinacrine, which produces a similar
banding pattern to C-banding. It is useful in the study of polymorphic variants on chromosomes,
regions such as those on chromosomes 1, 3, 9, 16, all the acrocentrics and the Y chromosome,
which usually fluoresce very brightly.
C-banding This produces dark staining of the constitutive heterochromatin located at the
centromeres of all the chromosomes. Again, as with Q-banding, polymorphic variants can be
studied with this technique the chromosomal DNA is preferentially denatured in alkali and lost
from the non-C-band regions.
R-banding This produces a pattern which is a reverse pattern of that observed with C-banding.
A few centers prefer to use this method rather than C-banding as their routine identification
banding. The advantage of this technique is that the telomeric regions of several chromosomes,
which stain faintly with C-banding, are stained darkly.
NOR staining The NOR of chromosomes are known to contain genes for 188 and 288RNA. The
active transcription sites of these chromosomes can be stained selectively using silver nitrate.
Distamycin A-4,6-diamino-2-phenyl-indole (DA-DAPI) banding This is a technique most
useful for identifying small marker chromosomes derived from chromosome 15, but also stains
the heterochromatic regions of chromosomes. Both DA and DAPI have an affinity for AT base
pairs, at similar but not identical sites.

7. 7
1.7 Types of chromosomal changes
Chromosomal changes can be present in cells throughout the body (i.e. an individual would be
born with the change) and this would be termed a constitutional abnormality. Alternatively, the
change can arise in a subset of cells or tissues, and these changes are known as acquired
abnormalities. The constitutional change would be present very early in development, probably
from an abnormality present in a sperm or egg cell, abnormal fertilization or an abnormal event
in the early embryo, whereas acquired abnormalities can occur at any time depending on the
disease type.
Normal chromosome constitutions in mammalian chromosomes are described by a karyotype
where the number of chromosomes is stated, which in humans is 46 and then the sex
chromosomes XX or XY. If there is an abnormality, this is also described in the karyotype
following guidelines laid down by the International System for Chromosome Nomenclature
(ISCN, 1995), as a result of several international conferences. Abnormalities fall into two main
categories, numerical and structural.
1. Numerical Chromosomal changes
Numerical changes involve a change in chromosome number without actual breakage of the
chromosome There are three different classes of numerical changes: polyploidy, aneuploidy and
mixoploidy.
Polyploidy The most commonly observed polyploidy is triplody (3n, where n is the haploid
number; in the case of human chromosomes n = 23) where two sperm fertilize the same egg, or
alternatively by fertilization with an abnormal diploid gamete.

8. 8
Figure 2: Types of chromosomal changes

9. 9
Aneuploidy Aneuploidy is the result of extra copies of a single chromosome being present (eg.
an extra copy in addition to the two normal homologs is termed trisomy, two extra copies would
be termed tetrasomy and so on), or alternatively the complete loss of a homolog, termed
monosomy. If both
homologs are missing this is called nullisomy.
Mixoploidy Mixoplody occurs because of mosaicism, a term applied to an individual who
possesses two or more genetically different cell lines from a single zygote, or occasionally
because of chimerism, where two or more differing cell lines have resulted from different
zygotes.