Chromosomes

• Diploids in eukaryotes (one from each parent)

• Each chromosome has two arms : long `q arm’
and short `p arm’

d value = q-p
r value = q/p

• A constricted region- Centromere

Structure of Eukaryotic
Chromosomes

Three important structures

– Origins of replication

– Centromeres

– Telomeres
 Origins of replication
• Is a particular sequence in a genome at which replication is
initiated
• Eukaryotes have multiple origins of replication on each linear
chromosome that initiate at different times. (with up to 100,000
present in a single human cell).
• Many origins of replication helps to speed the duplication of
much larger genetic material.
• The origin of replication binds the pre-replication complex, a
protein complex that recognizes, unwinds, and begins to copy
DNA
• The segment of DNA that is copied starting from each unique
replication origin is called a replicon
 Centromeres

microtubules in green, chromosomes in blue,

kinetochores in pink
• Centromere: place for microtubule attachments
• Kinetochore: protein structure on chromatids where
the spindle fibers attach during cell division to pull
sister chromatids apart.
Types of chromosome based on centromere location,
1. Metacentric: centromere close to middle
2. Submetacnetric/acrocentric: between middle and
end
3. Telocentric: near to tip
• Genes are located between the centromeric and telomeric
regions along the entire chromosome
– A single chromosome usually has a few hundred to several
thousand genes

• In lower eukaryotes (such as yeast)

– Genes are relatively small
• They contain primarily the sequences encoding the polypeptides
• ie: Very few introns are present

• In higher eukaryotes (such as mammals)

– Genes are long
• They tend to have many introns
 Telomeres
• Telomere: region of repetitive
nucleotide sequences (TTAGGG) at
each end of a chromatid.
• Protects the end of the chromosome
from deterioration or from fusion
with neighbouring chromosomes.
• During chromosome replication, the
enzymes that duplicate DNA cannot
continue their duplication all the way
to the end of a chromosome, so in
each duplication the end of the
chromosome is shortened.
• Telomeres are replenished by an
enzyme Telomerase
 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.
Interphase chromatin
• During interphase (the period of the cell cycle where the cell
is not dividing), two types of chromatin can be distinguished:
• Euchromatin, which consists of DNA that is active, e.g., being
expressed as protein.
• Heterochromatin, which consists of mostly inactive DNA and
stains deeply.
 Chromosomes and cell division
• Multicellular organisms copy their
chromosomes before cell division.
• They must grow to a mature size. Interphase

• The nucleus divides, distributing the

chromosomes into two equal groups
(mitosis).
• The cytoplasm then divides
(cytokinesis) each part taking a
nucleus.
 The cell cycle
Cytokinesis Some cells may stay in
Division of the cytoplasm this stage for over a year
G0
M

G1 First growth phase.

Varies in length
G2
Second growth
phase

S Copying of
chromosomes

G1 + S + G2 = INTERPHASE
 Karyotype

• Karyotype: the number, size and shape of

metaphase chromosome
• G bands: chromosomes on mild heating and
stain with giemsa – areas with low G-C
content are stained.
• R bands: reverse of G bands, when
chromosomes treated with mild alkali and
giemsa stained
 Structural Organization of Eukaryotic
chromosome
Packaging of DNA
The total length of cellular DNA is up to a hundred thousand
times a cell’s length, the packing of DNA is crucial to cell
architecture.
 The compaction of linear DNA in eukaryotic chromosomes

involves interactions between DNA and various proteins

 Histones constitute the major protein complex.
 Histone proteins are basic
 They contain many positively-charged amino acids
 Lysine and arginine
 These bind with the phosphates along the DNA backbone

 There are five types of histones

 H2A, H2B, H3 and H4 are the core histones
 Two of each make up the octamer

 H1 is the linker histone

 Binds to linker DNA
 Also binds to nucleosomes
 But not as tightly as are the core histones
 Nucleosomes
 The repeating structural unit within eukaryotic chromatin is
the nucleosome

 It is composed of double-stranded DNA wrapped around

an octamer of histone proteins
 An octamer is composed two copies each of four different
histones
 146 bp of DNA make 1.65 negative superhelical turns around the
octamer
 Vary in length between 20 to 100 bp,
depending on species and cell type
Diameter of the
nucleosome

 Overall structure of connected nucleosomes resembles “beads on a string”

 This structure shortens the DNA length about seven-fold
Beads on string
 Nucleosomes Join to Form a 30 nm
Fiber
 Nucleosomes associate with each other to form a
more compact structure termed the 30 nm fiber

 Histone H1 plays a role in this compaction

The 30 nm fiber
shortens the total
length of DNA
another seven-fold
 Nucleosomes are thought to be packed into an irregular
spiral or solenoid arrangement, with approximately six
nucleosomes per turn

Regular, spiral
configuration
containing six
nucleosomes per
turn

Irregular
configuration
where
nucleosomes
have little face-to-
face contact
 Further compaction
• The 30nm fibre form loops to make 300 nm
coiled chromatin fibers radial loops
• The 300nm loops are compressed and folded
to form 700nm fibres
• Form scaffold from nuclear matrix and further
compaction to 1400nm, that constitute the
chromatids.
 Compaction level
in euchromatin

During interphase
most chromosomal Compaction level
regions are in heterochromatin
euchromatic
 Giant chromosomes
2 types of giant chromosomes
1. Lampbrush chromosome
2. Polytene chromosome
 Lampbrush chromosome
•The amphibian oocyte (germ cells in the ovary) has certain periods of
very active RNA synthesis.
•During this stage, certain chromosomes stretch out large loops of
DNA, causing the chromosome to resemble a lamp brush
•These chromosomes show RNA synthesis and form unusual
chromatin loops consisting of transcriptionally active DNA.
•They are 400–800 μm long and are visible under the light microscope
 Polytene Chromosomes

• many of the cells of certain fly larvae grow

to an enormous size through multiple cycles
of DNA synthesis without cell division.
• In several types of secretory cells of fly
larvae, all the homologous chromosome
copies are held side by side, creating a single
giant polytene chromosome.
• Polytene chromosome have a distinct
pattern of chromosome banding readily
visible under the light microscope.
• These chromosomes, first observed in cells
of insect salivary glands of Drosophila .
Chromatin Packing
 Repetitive Sequences
• Sequence complexity refers to the number of times
a particular base sequence appears in the genome

• There are three main types of repetitive sequences

– Unique or non-repetitive
– Moderately repetitive
– Highly repetitive
 Repetitive Sequences
• Unique or non-repetitive sequences
– Found once or a few times in the genome
– Includes structural genes as well as intergenic areas

• Moderately repetitive
– Found a few hundred to a few thousand times
– Includes
• Genes for rRNA and histones
• Origins of replication
• Transposable elements
 Repetitive Sequences
• Highly repetitive
– Found tens of thousands to millions of times
– Each copy is relatively short (a few nucleotides to several hundred
in length)

– Some sequences are interspersed throughout the genome

• Example: Alu family in humans

– Other sequences are clustered together in tandem arrays

• Example: AATAT and AATATAT sequences in Drosophila
• These are commonly found in the centromeric regions
 Further Compaction of the
Chromosome
 The two events we have discussed so far have
shortened the DNA about 50-fold

 A third level of compaction involves interaction

between the 30 nm fiber and the nuclear matrix

 The nuclear matrix is composed of two parts

 Nuclear lamina
 Internal matrix proteins
 10 nm fiber and associated proteins
 The third mechanism of DNA compaction involves
the formation of radial loop domains

Matrix-attachment
regions
or
25,000 to
Scaffold-attachment 200,000 bp
regions (SARs)

MARs are anchored

to the nuclear matrix,
thus creating radial
loops
 Further Compaction of the
Chromosome
 The attachment of radial loops to the nuclear matrix
is important in two ways
 1. It plays a role in gene regulation

 2. It serves to organize the chromosomes within the

nucleus
 Each chromosome in the nucleus is located in a discrete and
nonoverlapping chromosome territory
 Heterochromatin vs Euchromatin
 The compaction level of interphase chromosomes
is not completely uniform
 Euchromatin
 Less condensed regions of chromosomes
 Transcriptionally active
 Regions where 30 nm fiber forms radial loop domains

 Heterochromatin
 Tightly compacted regions of chromosomes
 Transcriptionally inactive (in general)
 Radial loop domains compacted even further
 Play a role in the
organization and compaction
of the chromosome
 Regular, spiral
configuration
containing six
nucleosomes per turn

Irregular
configuration where
nucleosomes have
little face-to-face
contact
 The 30 nm fiber shortens the total length of DNA
another seven-fold
Chromatin Packing