Chroma: C O L O U R
Chromosome: Colored thread
up colour when stained)
• Located in nucleus as nuclear material
• Chromosomes seen in mitochondria and chloroplast are called organelle or extrachromosomal
• organized structure of DNA and protein that is found in cells.
• contain DNA-bound proteins, which serve to package the DNA and control its functions.
PARTS OF A CHROMOSOME
Chromosome consists of two threads held together in by
knot like structure
Each thread is called chromatid
The knot is called primary constriction or Centromere
The two threads of a single chromosome is called sister
The threads of pair of chromosome are called non sister
• Secondary constriction lead to formation of satellite
• The portions seen on either side of the centromere is called
arms of the chromosome
• One arm is called “p” or petite arm.
• Other arm is called “q” or quadran arm
• Chromosomes carry genes
• Chromosomes is made of DNA, histones and non-histone
Number CONSTANT for a given species
• 46/ 23 pairs
• 44/ 22 pairs
• 8/ 4 pairs
• 16/ 8 pairs
NUMBER OF SETS OF CHROMOSOMES – PLOIDY (n)
n – Monoploidy/ Haploidy
2n – Diploidy
3n – Triploidy
4n – Tetraploidy
5n – Pentaploidy
6n – Hexaploidy
7n - Heptaploidy
• In contrast to other cell organelles, the size of
chromosomes shows a remarkable variation
depending upon the stages of cell division.
• Interphase: chromosome are longest & thinnest
• Prophase: there is a progressive decrease in their
length accompanied with an increase in thickness
• Anaphase: chromosomes are smallest.
• Metaphase: Chromosomes are the most easily
observed and studied during metaphase when they
are very thick, quite short and well spread in the cell.
• Therefore, chromosomes measurements
generally taken during mitotic metaphase.
• Karyotype: is the general morphology of the somatic chromosome.
Generally, karyotypes represent by arranging in the descending order of
size keeping their centromeres in a straight line.
• Idiotype: the karyotype of a species may be represented
diagrammatically, showing all the morphological features of the
chromosome; such a diagram is known as Idiotype.
• Chromosomes may be identified by regions that stain in a particular manner when treated
with various chemicals.
• Several different chemical techniques are used to identify certain chromosomal regions by
staining then so that they form chromosomal bands.
• For example, darker bands are generally found near the centromeres or on the ends
(telomeres) of the chromosome, while other regions do not stain as strongly.
• The position of the dark-staining are heterochromatic region or heterochromatin.
• Light staining are euchromatic region or euchromatin.
• Heterochromatin is classified into two groups: (i) Constitutive and (ii) Facultative.
• Constitutive heterochromatin remains permanently in the heterochromatic stage, i.e., it does
not revert to the euchromatic stage.
• In contrast, facultative heterochromatin consists of euchromatin that takes on the staining and
compactness characteristics of heterochromatin during some phase of development.
• Satellite DNA consists of highly repetitive DNA with very high frequency of adenine & thymine. Satellite
DNA are of lower density hence when separated along with genomic DNA in a density gradient forms
a satellite Band.
• Its repeat length is several thousand Base pairs(Unit - 5-300 bp depending on species).
• Satellite DNA are organized as large clusters upto 100 million Base Pairs in the heterochromatic region of
chromosomes near centromeres & telomeres, these are also found abundantly on Y chromosome
• Satellite DNA shows exceptional variability among individuals particularly with regard to the number of
repeats at a given locus hence is the basis of most DNA typing systems used in Forensic medicine.
• Satellite DNA are not transcribed into RNA
• Do not have spacer sequences
• Satellite DNA are located on 1, 9, 16 & Y chromosomes & tiny short arms of chromosomes 13-15 & 21-22.
TYPES OF SATELLITE DNA
• SIMPLE SEQUENCE REPEATS or SIMPLE TANDEM REPEATS
These are of 2 types:
• TANDEM REPEATS
• A minisatellite (also referred as Variable Number Tandem Repeat, VNTR) is a section
of DNA that consists of a short series of nucleobases (10–60 base pairs). These occur at
more than 1,000 locations in the human genome.
• "Minisatellites" consist of repetitive, generally GC-rich, variant repeats that range in length
from 10 to over 100 base pairs.
• Some minisatellites contain a central (or "core") sequence of letters “GGGCAGGANG”
(where N can be any base) or more generally a strand base with Purines (Adenine (A)
and Guanine (G)) on one strand and Pyrimidines (Cytosine (C) and Thymine (T)) on the
• Application: minisatellites have been extensively used for DNA fingerprinting as well as
forgenetic markers in linkage analysis and population studies.
• Microsatellites, also known as Simple Sequence Repeats (SSRs) or Short Tandem
Repeats (STRs), are repeating sequences of 2-6 base pairs of DNA.
• It is a type ofVariable Number Tandem Repeat (VNTR). Microsatellites are typically codominant. They are used as molecular markers in STR analysis(Short tandem
repeat (STR) analysis is a molecular biology method used to compare
specific loci on DNA from two or more samples), for kinship, population and other
studies. They can also be used for studies of gene duplication or deletion, marker assisted
selection, and fingerprinting.
• CA nucleotide repeats are very frequent in human and other genomes, and are present
every few thousand base pairs. As there are often many alleles present at a microsatellite
locus, genotypes within pedigrees are often fully informative.
• In this way, microsatellites are ideal for determining paternity, population genetic studies
and recombination mapping. It is also the only molecular marker to provide clues about
which alleles are more closely related
• Located at telomeres & centromeres & may act as Protein binding sites.
• Tandem repeats occur in DNA when a pattern of two or more nucleotides is repeated and the
repetitions are directly adjacent to each other.
• An example would be:
• ATTCG ATTCG ATTCG---------> in which the sequence ATTCG is repeated three times.
• When between 10 and 60 nucleotides are repeated, it is called a minisatellite. Those with fewer are
known as microsatellites or short tandem repeats.
• When exactly two nucleotides are repeated, it is called a dinucleotide repeat (for example:
ACACACAC…). The microsatellite instability in hereditary nonpolyposis colon cancer most
commonly affects such regions.
• When three nucleotides are repeated, it is called a trinucleotide repeat (for example:
CAGCAGCAGCAG…), and abnormalities in such regions can give rise to trinucleotide repeat
• When the number is not known, variable, or irrelevant, it is sometimes called a variable number tandem
• Tandem repeat describes a pattern that helps determine an individual's inherited traits.
• Tandem repeats can be very useful in determining parentage. Short tandem repeats are
used for certain genealogical DNA tests.
• DNA is examined from microsatellites within the chromosomal DNA. Minisatellite is
another way of saying special regions of the loci. Polymerase chain reaction (or PCR)
is performed on the minisatellite areas. The PCR must be performed on each organism
being tested. The amplified material is then run through electrophoresis. By checking
the percentage of bands that match, parentage is determined.
• In the field of Computer Science, tandem repeats in strings (e.g., DNA sequences) can
be efficiently detected using suffix trees or suffix arrays.
• Studies in 2004 linked the unusual genetic plasticity of dogs to mutations in tandem
• Centromeres and telomeres are two essential features of all eukaryotic chromosomes.
• Each provide a unique function i.e., absolutely necessary for the stability of the chromosome.
• Centromeres are required for the segregation of the centromere during meiosis and mitosis.
• Teleomeres provide terminal stability to the chromosome and ensure its survival
• The region where two sister chromatids of a chromosome appear to be joined or
“held together” during mitatic metaphase is called Centromere
• When chromosomes are stained they typically show a dark-stained region that is
• Also termed as Primary constriction
• During mitosis, the centromere that is shared by the sister chromatids must divide so
that the chromatids can migrate to opposite poles of the cell.
• On the other hand, during the first meiotic division the centromere of sister
chromatids must remain intact
• whereas during meiosis II they must act as they do during mitosis.
• Therefore the centromere is an important component of chromosome structure
• As a result, centromeres are the first parts of chromosomes to be seen moving towards the
opposite poles during anaphase.
• The remaining regions of chromosomes lag behind and appear as if they were being pulled
by the centromere.
• Within the centromere region, most species have several locations where spindle fibers attach,
and these sites consist of DNA as well as protein.
• The actual location where the attachment occurs is called the kinetochore and is composed of
both DNA and protein.
• The DNA sequence within these regions is called CEN DNA.
• Typically CEN DNA is about 120 base pairs long and consists of several sub-domains, CDEI, CDE-II and CDE-III.
• Mutations in the first two sub-domains have no effect upon segregation,
• but a point mutation in the CDE-III sub-domain completely eliminates the ability of the
centromere to function during chromosome segregation.
• Therefore CDE-III must be actively involved in the binding of the spindle fibers to the
• The protein component of the kinetochore is only now being characterized.
• A complex of three proteins called Cbf-III binds to normal CDE-III regions but can not bind
to a CDE-III region with a point mutation that prevents mitotic segregation.
• Chromosomes may differ in the position of the Centromere, the place on the chromosome
where spindle fibers are attached during cell division.
• In general, if the centromere is near the middle, the chromosome is metacentric
• If the centromere is toward one end, the chromosome is acrocentric or submetacentric
• If the centromere is very near the end, the chromosome is telocentric.
• The centromere divides the chromosome into two arms, so that, for example, an acrocentric
chromosome has one short and one long arm,
• While, a metacentric chromosome has arms of equal length.
• All house mouse chromosomes are telocentric, while human chromosomes include both
metacentric and acrocentric, but no telocentric.
metacentrics acrocentric or telocentric
M – Metacentric; A – Acrocentric
• The two ends of a chromosome are known as telomeres.
• It required for the replication and stability of the chromosome.
• When telomeres are damaged or removed due to chromosome breakage, the damaged
chromosome ends can readily fuse or unite with broken ends of other chromosome.
• Thus it is generally accepted that structural integrity and individuality of chromosomes is
maintained due to telomeres.
• McClintock noticed that if two chromosomes were broken in a cell, the end of one
could attach to the other and vice versa.
• What she never observed was the attachment of the broken end to the end of an
• Thus the ends of broken chromosomes are sticky, whereas the normal end is not
sticky, suggesting the ends of chromosomes have unique features.
Until recently, little was known about molecular structure of telomeres. However, during
the last few years, telomeres have been isolated and characterized from several sp.
Tetrahymena - protozoa organism.
• The telomeres of this organism end
in the sequence 5'-TTGGGG-3'.
• The telomerase adds a series of 5'TTGGGG-3' repeats to the ends of
the lagging strand.
• A hairpin occurs when unusual base
pairs between guanine residues in
the repeat form.
• Finally, the hairpin is removed at the
• Thus the end of the chromosome is
RNA Primer - Short stretches of ribonucleotides
(RNA substrates) found on the lagging strand during
DNA replication. Helps initiate lagging strand