Molecular Biology
Unit II
Organization of genome
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Chromatin:
Eukaryotic chromosomes are located within a separate cellular compartment termed as nucleus.
The length of DNA must be compacted by a remarkable amount in order to fit it inside nucleus.
The compacting of DNA is accomplished by the binding of the DNA to many different cellular proteins.
The formation of a highly organized DNA-protein complex, termed as chromatin, which is a nucleoprotein
complex completes the packing.
Chromatin is a dynamic structure capable of changing its shape and composition during the life of a cell
Chromatin can be defined as highly condensed chromosomes at metaphase stage, and very diffuse structures
in course of interphase.
Histones:
Histones are most abundant proteins in chromatin.
Histones are small and positively charged proteins and are of 5 major types: H1, H2A, H2B, H3 and H4.
Histones are characterized by the presence of high percentage of basic amino acids arginine and lysine.
These amino acids are positively charged that give the histones a net positive charge facilitating the binding
of histones to the negatively charged DNA.
Histone and DNA are present in equal amounts in chromatin.
A heterogenous variety of non-histone chromosomal proteins also are found in eukaryotic chromosomes.
There are times where variant histones, with different amino acid sequences, are integrated into chromatin in
place of one of the major histone proteins.
The amino acid sequences of histones H2A, H2B, H3 AND H4 are highly conserved, even between distantly
related species.
Evolutionary conservation of these amino acid sequences highly indicates that histones perform the same
basic role in organizing the DNA in the chromosomes of all eukaryotes.
Structural studies suggest that the histones classes do share a similar tertiary structure, showing that all
histones are ultimately evolutionarily related.
The Nucleosome: The basic structural unit of eukaryotic chromosomes is a DNA-protein
complex called the nucleosome . Nucleosomes consist of DNA associated with molecules of basic
proteins called histones. The mass of histones in chromatin is approximately equal to the mass of
DNA, except in chromosomes of sperm cells, where the histones are replaced by protamines.
The presence of basic amino acids in histones gives it a positive charge and their association with a
negatively charged DNA is stabilized by ionic bonds.
Each nucleosome bead or core particles is about 11 nm in diameter and consists of eight
histone molecules associated with 146 nucleotide pairs of DNA. The histones in the core particle
include two molecules each of H2A, H2B, H3 and H4 around which the DNA is wrapped in a
negative supercoil of almost two full turns
Nucleosome beads are separated by a length of nucleosome linker DNA or spacer spacer DNA
The number of nucleotides in the spacer or linker DNA averages about 50 − 60 and nucleosomes
are usually defined to include the spacer DNA too. Therefore, a typical nucleosome can be said to
include about 200 bp of DNA. Treatment of chromatin fibers with deoxyri-bonuclease results in
preferential digestion of the linker DNA and the release of free nucleosome beads.
Higher order structure of chromatin:
The next higher level of chromatin structure is represented by a series of loops of 30nm fibers, each
anchored at its base by proteins in the nuclear scaffold.
On average, each loop encloses some 20-100kb of DNA and measures about 300nm in length.
The 300nm loops are packed and folded to result a 250nm wide fiber.
Tight helical coiling of the 250 nm, in turn, yields the structure that is visible in metaphase- individual
chromatids approximately 700nm in width.
Overall, this packaging produces a chromosome that is about 10,000 times shorter and about 400 times
thicker, than naked DNA.
Cohesin:
Cohesin is a protein that holds sister chromatids together after DNA replication until anaphase occurs, and it
is the right time to separate sister chromatids from each other. Structurally, cohesin is a multi-subunit protein
complex which actually has four core subunits. Out of the four subunits, two are SMC proteins (SMC1
(structural maintenance of chromosome protein 1) and SMC3 (structural maintenance of chromosome
protein 3), which have two main structural domains as head and hinge domains. Other two subunits are two
long coiled-coil molecules. Due to cohesin protein, sister chromatids segregate to two poles correctly.
Otherwise, cells cannot control the segregation of sister chromatids into each pole during the
[Link] also facilitates the attachment of spindle fibres to chromosomes. In addition, cohesin
mediates DNA repairing by recombination.
Condensin:
Condensin is a pentameric protein complex needed for chromosome condensation. It consists of five
subunits, including two SMC proteins and three auxiliary subunits. SMC proteins in condensing are SMC2
and SMC4. Condensin fulfils several functions in genome regulation, including mitotic and meiotic division,
DNA repair, transcriptional control, and chromosome [Link] are two types of condensins as
condensin I and condensin II. Condensin I regulates the timing of chromosome condensation while
condensin II facilitates the compaction of the chromosome loops along the sister chromatid axes.
Structure of Mitochondrial DNA
Mitochondrial DNA is a double stranded circular molecule, which is inherited from the mother in all multi-
cellular organisms, though some recent evidence suggests that in rare instances mitochondria may also be
inherited via a paternal route.
Typically, a sperm carries mitochondria in its tail as an energy source for its long journey to the egg.
When the sperm attaches to the egg during fertilization, the tail falls off. The organisms mitochondria are
usually gets are from the egg its mother provided.
There are about 2 to 10 transcripts of the mt-DNA in each mitochondrion. Compared to chromosomes, it is
relatively smaller, and contains the genes in a limited number.
The size of mitochondrial genomes varies greatly among different organisms, with the largest found among
plants, including that of the plant Arabidopsis, with a genome of 200 kbp in size and 57 protein-encoding
genes.
The smallest mtDNA genomes include that of the protist Plasmodium falciparum, which has a genome of
only 6 kbp and just 2 protein- encoding genomes.
Mitochondrial DNA carry 16,569 base pairs with 37 genes (13 proteins, 22 t-RNAs and two r-RNA) which
are concerned with the production of proteins involved in respiration.
Out of the 37 genes, 13 are responsible for making enzymes, involved in oxidative phosphorylation, a
process that uses oxygen and sugar to produce adenosine tri-phosphate .
The other 14 genes are responsible for making molecules, called transfer RNA (t-RNA) and ribosomal RNA
(r-RNA). In some metazoans, there are about 100 – 10,000 separate copies of mt-DNA present in each cell.
Unlike nuclear DNA, mitochondrial DNA doesn’t get shuffled every generation, so it is presumed to change
at a slower rate, which is useful for the study of human evolution.
Mitochondrial DNA is also used in forensic science as a tool for identifying corpses or body parts and has
been implicated in a number of genetic diseases, such as Alzheimer’s disease and diabetes.
Changes in mt-DNA can cause maternally inherited diseases, which leads to faster aging process and
genetic disorders.
Mitochondria convert the potential energy of food molecules into ATP by the Krebs cycle, electron transport
and oxidative phosphorylation in presence of oxygen.
The energy from food molecules (e.g., glucose) is used to produce NADH and FADH2 molecules, via
glycolysis and the Krebs cycle.
The protein complexes in the inner membrane (NADH dehydrogenase, cytochrome c reductase, cytochrome
c oxidase) use the released energy to pump protons (FT) against a gradient.
