The molecular organization of
chromosomes
BY
YEBOAH KWAKU OPOKU Ph.D
DEPARTMENT OF BIOLOGY EDUCATION
FACULTY OF SCIENCE EDUCATION
UNIVERSITY OF EDUCATION, WINNEBA
Eukaryotic chromosomes
• Each eukaryotic chromosome contains a single, uninterrupted molecule of DNA
that can be extremely long.
• The single uninterrupted DNA molecule of a chromosome contains genes
composed of coding sequences (exons) interspersed with noncoding
sequences (introns) as well as different levels of organizational units
that affect function
• The average length of a chromosome in the human genome is 130 million base
pairs (Mb), ranging from 250 Mb (chromosome 1, the longest) to 47 Mb
(chromosome 21, the shortest).
• If the DNA in chromosome 1 were extended to its full length, it would exceed
the diameter of the nucleus of an average human cell by a factor of about
15,000.
• How are the chromosomes packaged to fit into the nucleus fit into the
nucleus?
• DNA by itself does not have the ability to fold up small
enough to fi t in the cell nucleus.
• For sufficient compaction, it depends on interactions with two
categories of proteins:
• Histones and
• Nonhistone chromosomal proteins
• Chromatin is roughly 1/3 DNA, 1/3 histones, and 1/3
nonhistone proteins by weight
Histone proteins
• The major class of chromosomal proteins are the histone
proteins.
• Histones are largely responsible for the structure of chromatin.
• Five major types—H1, H2A, H2B, H3, and H4—are
present in the chromatin of nearly all eukaryotes
• Histones are small proteins (100 to 200 amino acids) that
differ from most other proteins in that from 20 to 30 percent of
the amino acids are lysine and arginine
• Both proteins confer a positive charge on chromosomes
• The DNA of all eukaryotic chromosomes is associated with
numerous protein molecules in a stable ordered aggregate
called chromatin.
• Some of the proteins present in chromatin determine
chromosome structure and the changes in structure that
occur during the division cycle of the cell.
• Other chromatin proteins appear to have important roles in
regulating chromosome functions.
• The positive charges enable histone molecules to bind to
DNA by electrostatic attraction to the negatively charged
phosphate groups in the sugar–phosphate backbone of
DNA.
• Placing chromatin in a solution with a high salt concentration
(e.g 2 molar NaCl) eliminates the electrostatic attraction
causing the histones to dissociate from the DNA.
• Histones also bind tightly to each other; both DNA–histone
and histone–histone binding are important for chromatin
structure
• The histone molecules from different organisms are remarkably
similar to one another, with the exception of H1.
• The amino acid sequences of H3 molecules from widely different
species are almost identical.
• For example, the sequences of H3 of cow chromatin and pea
chromatin differ by only 4 of 135 amino acids.
• The H4 proteins of all organisms also are quite similar;
• E.g Cow and pea H4 differ by only 2 of 102 amino acids.
• The sequence of other proteins vary so little from one species to
another
• When the variation is very small between organisms, the sequence is
highly conserved.
The extraordinary conservation in histone
composition through hundreds of millions of
years of evolutionary divergence reveals the
important role of these proteins in the structural
organization of eukaryotic chromosomes
Nonhistone proteins
• The chromatin of a diploid genome contains from 200 to
2,000,000 molecules of each kind of nonhistone protein
• Some nonhistone proteins play a purely structural role,
helping to package DNA into more complex structures.
• Some of these proteins are involved in segregation,
replication etc.
• Some regulate transcription and RNA processing
during gene expression
The nucleosome
• Chromatin resembles a regularly beaded thread formed into a coiled
fiber in the electron microscope known as the 30-nm chromatin fiber
• It has an average diameter ranging from 300 to 350 angstrom (Å).
• The beadlike units within the 30-nm chromatin fiber are called
nucleosomes.
• Each unit has a definite composition, consisting of two molecules
each of H2A, H2B, H3, and H4; a segment of DNA containing about
200 nucleotide pairs; and one molecule of histone H1
• The complex of two subunits each of H2A, H2B, H3, and H4, as well
as part of the DNA, forms each “bead,” and the remaining DNA
bridges between the beads.
• Histone H1 also appears to play a role in linking between the beads
• Each nucleosome is composed of a core particle,
additional DNA called linker DNA that links
adjacent core particle and one molecule of H1 that
binds to the histone octamer and to the linker DNA.
• Brief treatment of chromatin with certain Dnases yields a
collection of small particles of quite uniform size consisting only
of histones and DNA.
• The DNA fragments in these particles are of lengths equal to
about 200 nucleotide pairs or small multiples of that unit size
• These particles result from cleavage of the linker DNA segments
between the beads
• More extensive treatment with DNase results in loss of the H1
histone and digestion of all the DNA except that protected by the
histones in the bead.
• The resulting structure is called a core particle, which consists of
an octamer of pairs of H2A, H2B, H3, and H4 with some DNA
• The amino ends of the histone proteins are known as histone
tails.
• The tail end is accessible to enzymes that modify particular
amino acid residues such as by the addition of one or more
acetyl, methyl, or phosphate groups to the amino acid.
• Modifications of the histone tails are important to gene
activity.
• Acetylated histones tend to bind DNA more loosely and
usually render chromatin more accessible to
transcription, whereas methylated histones can either
promote or impede transcription depending on the
particular histone residue that is modified.
Higher-order packaging further condenses
chromosomes
• Packaging into nucleosomes condenses naked DNA about
sevenfold.
• With this condensation, the 2 m of DNA in a diploid human
genome shortens to approximately 0.25 m
• This is still much too long to fi t in the nucleus of even the
largest cell
• Therefore, additional compaction is required and several
models have been proposed
Supercoiling
• The first proposed model of additional compaction
beyond nucleosomal winding is supercoiling
• In this model, the 100 Å nucleosomal chromatin
supercoils into a 300 Å superhelix to achieve a
further six-fold chromatin condensation.
• Support for this model comes in part from electron
microscope images of 300 Å fibers that contain about
six nucleosomes per turn
The radial loop–scaffold model
• This model proposes that several nonhistone proteins, including
topoisomerase II, bind to chromatin at every 60–100 kb and tether the
supercoiled, nucleosome-studded 300 Å fiber into structural loops
• Evidence that nonhistone proteins fasten these loops comes from
chemical manipulations in which the removal of histones does not
cause the chromatin to unfold completely.
• A complex of proteins known as condensins may act to further
condense chromosomes for mitosis.
• These and other proteins may gather the loops into daisylike rosettes
compressing the rosette centers into a compact bundle
Hierarchical arrangement of the
• Thechromosome
hierarchical nature of chromosome structure is
• illustrated in FIGURE 3.16. Assembly of DNA andhistones
• is the first level, resulting in a sevenfold reduction
• in length of the DNA and the formation of a beaded
• flexible fiber 110 Å (11 nm) wide (part B), roughly five
• times the width of free DNA (part A). The structure of
• chromatin varies with the concentration of salts, and
• the 110-Å fiber is present only when the salt concentration
• is quite low. In the living cell, this is usually compacted
• into the 30-nm chromatin fiber (part C), which
• in the interphase nucleus is folded into 100-kb chromatin
• loops that are organized into 1-Mb chromatin
• domains that form the chromosome territories
A karyotype is a set of fully compacted homologous chromosomes
Each chromosomes is made up of two
unequal arms joined in the middle by the
centromere
The shorter arm is the P while the
longer arm is the q
Geneticists designate the chromosomal location
of a gene by describing its position in relation to
the bands on the p or q arm of the chromosome.
Chromosomal differences between species
• All placental mammals with diploid genome carries
roughly 6 billion base pairs, but packaged into different
numbers of chromosomes
• Deer - 4 chromosomes Cats – 38
• House mice – 40 Rabbits – 44
• Humans – 46 Dogs – 48
• Cattle – 60 Horses – 64
• Hippopotamuses - 96
Chromosomal Packaging and Function
• The compaction of DNA into chromatin presents a problem for
proteins that must recognize DNA sequences to carry out functions
such as transcription, replication, and repair.
• How do these proteins access bases within the genome to perform
these functions?
• The answer has two parts;
• First, chromatin structure is dynamic and can change to allow access
of specific proteins when they need to act.
• Second, variations exist in the molecules making up the basic
chromatin structure, and these variants recruit proteins that are
necessary for chromosomal functions
• In cells stained with certain DNA-binding chemicals, a small
proportion of chromosomal regions appear much darker than
others under the light microscope.
• Geneticists call these darker regions heterochromatin and
the lighter regions as euchromatin.
• euchromatin contains most of the sites of transcription and
thus almost all of the genes.
• By contrast heterochromatin appears to be transcriptionally
inactive for the most part because it is so tightly packaged
that the enzymes required for transcription of the few genes it
contains cannot access the correct DNA sequences
The centromere
• The centromere is a specific region of the eukaryotic chromosome
that becomes visible as a distinct morphological entity along the
chromosome during condensation.
• It serves as the point of assembly of the kinetochore
• In higher eukaryotes, each centromeric region encompasses 1
million base pairs or more.
• These regions of heterochromatin contain various kinds of repetitive
DNA sequences, as well as a patchwork of DNA sequences
derived from duplicated regions from elsewhere in the genome.
• Common to all human centromeres are hundreds of thousands of
copies of a 170-bp DNA sequence called alpha satellite
• The blocks of alpha-satellite DNA are associated with
chromatin composed of nucleosomes that contain a
specialized histone variant called CENPA that replaces the
normal histone 3.
• The presence of CENPA nucleosomes helps in the recruitment
of more than a dozen kinetochore proteins, resulting in a fully
assembled kinetochore
Telomere
• Each end of a linear chromosome is composed of a special
DNA–protein structure called a telomere that is essential for
chromosome stability.
• In Drosophila, chromosomes without ends formed by x-ray
breakage cannot be recovered
• In maize, broken chromosome ends frequently fuse with one
another and form new chromosomes with abnormal structures
(often having two centromeres)
• The mechanism of restoring the ends of a DNA molecule in a
chromosome relies on an enzyme called telomerase.
• This enzyme works by adding tandem repeats of a
simple sequence to the 3’ end of a DNA strand.
• In the ciliated protozoan Tetrahymena, in whichthe
enzyme was first discovered, the simple repeating
sequence is -TTGGGG-3’, and in humans and
other vertebrate organisms, it is -TTAGGG-3’
• The tandem repeats of these sequences constitute
the telomere
THE END
