How dna organize in prokaryotes and Eukaryotes...

1. Welcome

2. DNA Organization in prokaryotes
and eukaryotes
SUBMITTED TO: SUBMITTED BY:
DR. MANISH SHARMA DONGA AKHIL R.
REG. NO.- 04-AGRMA-2215-2020

3. What is DNA ?
 Deoxyribonucleic acid, more commonly known as DNA,
is a complex molecule that contains all of the
information necessary to build and maintain an
organism. All living things have DNA within their cells. In
fact, nearly every cell in a multicellular organism
possesses the full set of DNA required for that
 The molecule inside cells that contains the genetic
information responsible for the development and
function of an organism.
 The DNA molecule consists of two strands that wind
around one another to form a shape known as a
helix.
 People’s believe that American biologist James Watson
and English physicist Francis Crick discovered DNA in
1950s. In reality, this is not the case. Rather, DNA was
first identified in the late 1860s by Swiss chemist
Friedrich Miescher.

4.  Attached to each sugar is one of four bases-adenine (A), cytosine (C), guanine (G), and thymine (T).
The two strands are held together by bonds between the bases.
 Each DNA strand is 1.8 meters long but sueezed in to 0.09 micrometers.
Name of things Genome size
(MB)
Bacterium (Haemophilus influenzae) 1.83
Yeasts (Saccharomyces cerevisiae) 12
Bacterium (Escherichia coli) 5.5
Arabidopsis thaliana (Wild spp. Of mustard) 125
Paris japonica 148000
Pigeon pea 833.07
Cucumber 367
Rice 430 / 420
Castor 320
Tomato 900
Wheat 17000
Maize 2300
 The word “genome,” coined by German
botanist Hans Winkler in 1920, was derived
simply by combining gene and the final syllable
of chromosome.
 An organism’s genome is defined as the entire
collection of genes and all other functional and
non-functional DNA sequence in a haploid set
of chromosomes.
 It includes structural genes, regulatory genes
and non-functional nucleotide sequence.
 Genome is the entirety of an organism’s
hereditary organization. It is encoded either in
DNA, or for many types of viruses, in RNA.
The genome is the ultimate source of information about an organism.

5. What is GENE ?
 A piece of DNA (or in some cases RNA) that contains the primary sequence to produce a
functional Biological Gene product (RNA, Protein).
 "Genes" are units of genetic information present on the DNA in the chromosomes and chromatin.
 Structural genes :
DNA segments that code for some specific RNAs or proteins. Encode for mRNAs, tRNAs, snRNAs,
snoRNAs.
 Functional sequences :
Regulatory sequences- occur as regulatory elements (initiation sites, promoter sites, operator
sites, etc.)
 Nonfunctional sequences :
Introns and repetitive sequences. Needed for coding, regulation and replication of DNA. Much
more in no than functional sequences.

6. How DNA’s are
packed?

7. DNA Organization
in Prokaryotes

8. INTRODUCTION
 The term “prokaryote” means “primitive nucleus”, Cell in prokaryotes have no
nucleus.
 The prokaryotic chromosome is dispersed within the cell and is not enclosed
by a separate membrane.
 Much of the information about the structure of DNA has come from studies of
prokaryotes, because they are less complex (genetically and biochemically)
than eukaryotes.
 Prokaryotes are monoploid = they have only one set of genes (one copy of the
genome).
 In most viruses and prokaryotes, the single set of genes is stored in a single
chromosome (single molecule either RNA or DNA).
 The DNA is packaged into a region of the cell known as the nucleoid.

9. In Prokaryotic cells Genomic DNA forms a single circular chromosome, without
basic proteins , lies in the cell cytoplasm in nucleoid region.
In Prokaryotes, Plectonemic supercoils are predominant, because of the circular
chromosome and relatively small amount of genomic material. This structure is
called the Folded genome.
 Prokaryotic genomes are examplified by the E. coli chromosome. The bulk of
the DNA in E. coli cells consists of a single closed-circular DNA molecule of
length 4.6 million base pairs.
E.g., - E. Coli .,
 89% coding
 4285 genes
 122 structural RNA genes
 Operon: Polycistronic transcriptom units
 Haploid circular genome
 Usually asexual reproduction
 Transcription and translation take place in the same compartment.

10.  DNA supercoiling refers to the over- or
under- winding of a DNA strand, and is an
expression of the strain on that strand.
 A super coiled form of DNA is the one in
which the double helix is further twisted
about itself, forming a tightly coiled
structure.
DNA SUPERCOILING & DNA DOMAINS :-
a) DNA Supercoiling :

11. Mechanism of DNA Supercoiling :
 A double helix of DNA undergoes additional twisting in the same direction as or in
the opposite direction from the turns in the original helix. Supercoiling results
when DNA is subject to some form of structural strain. A strain is introduced in the
DNA to induce supercoiling.
a) Original DNA form:
 The most common double helical structure found in nature is B-DNA in which the
double helix is right-handed with about 10–10.5 base pairs per turn.
b) Underwound DNA form:
 Underwound state occurs when the DNA has fewer helical turns than the normal B-
form.
I. Facilitate its compaction by coiling.
II. Enable the enzymes responsible for DNA metabolism to separate DNA strands.

12.  Negative supercoiling involves
twisting against the helical
conformation (twisting in a left-
handed fashion), which
preferentially underwinds and
"straightens" the helix at low
twisting stress, and knots the DNA
into negative supercoils at high
twisting stress.
a) NEGATIVE SUPERCOIL
(LEFT HANDED)
 Positive supercoiling of DNA occurs
when the right-handed, double-helical
conformation of DNA is twisted even
tighter (twisted in a right-handed
fashion) until the helix begins to
distort and "knot."
b) POSITIVE SUPERCOIL
(RIGHTHANDED)

13. DNA domains
 Experiments in which DNA from E.
coli is carefully isolated free of most
of the attached proteins and
observed under the electron
microscope reveal one level of
organization of the nucleoid.
 The DNA consists of 50–100 domains
or loops, the ends of which are
constrained by binding to a structure
which probably consists of proteins
attached to part of the cell
membrane. The loops are about 50–
100 kb in size.

14. DNA-binding proteins
 The most abundant of these are protein HU, a small basic (positively charged)
protein. It’s binds DNA nonspecifically by the wrapping of the DNA around the
protein, and H-NS (formerly known as protein H1), a monomeric neutral protein,
which also binds DNA nonspecifically in terms of sequence.
 These proteins are sometimes known as histone-like proteins, and have the effect
of compacting the DNA, which is essential for the packaging of the DNA into the
nucleoid, and of stabilizing and constraining the supercoiling of the chromosome.
 Half of this is constrained as permanent wrapping of DNA around proteins such as
HU. Only about half the supercoiling is unconstrained.
 RNA polymerase and mRNA molecules, site-specific DNA-binding proteins such as
integration host factor (IHF), a homolog of HU, which binds to specific DNA
sequences.

15. Model of E. coli Chromosome

16. DNA Organization
in Eukaryotes

17.  The nucleus is heart of the cell, which serves as the main distinguishing feature
of the eukaryotic cells. It is an organelle submerged in its sea of turbulent
cytoplasm which has the genetic information encoding the past history and
future prospects of the cell.
 DNA is associated with basic proteins(histones), form long chromatin fibers.
Chromatin fibers form a network, enclosed in a double layered nuclear envelop,
condenses into chromosomes during cell division.

18. Organization of Chromosome :
Centromere :
 DNA sequence that serve as an attachment for protein during mitosis
 In yeast these sequence (~ 130 nts) are very A+T rich.
 In higher eukaryotes centromeres are much longer and contain “Satellite
DNA”
 Based on position of the centromere on chromosome there many types of
chromosome 1) Metacentric 2) Sub metacentric 3) Sub telocentric 4)
Telocentric 5) Holocentric
 Based on the number of centromeres there many types of chromosome 1)
Acentric 2) Monocentric 3) Dicentric
Telomeres :
 At the end of chromosome , Help stabilize the chromosome
 In Yeast telomers are ~ 100 bp long (imperfect repeats)
 Repeats are added by a specific “Telomerase.”

19. Minichromosomes
Macrochromosomes
B Chromosomes (Extra chromosomes)
Lamp brush Chromosomes
Giant or Polytene or Salivary Gland
chromosomes
Isochromosomes
Special type of chromosomes

20. ORGANIZATION OF CHROMATIN :
 Nucleus contains many thread like coiled structures which remain suspended in the nucleoplasm
which are known as ‘chromatin substance’.
 Chromatin is the complex combination of DNA and proteins that makes up chromosomes. The
major proteins involved in chromatin are histone proteins; although many other chromosomal
proteins have prominent roles too.
 The functions of chromatin is to package DNA into smaller volume to fit in the cell, to strengthen
the DNA to allow mitosis and meiosis and to serve as a mechanism to control gene expression
and DNA replication.
 In resting non-dividing eukaryotic cells, the genome is in the form of nucleoprotein-complex-
the chromatin. (randomly dispersed in the nuclear matrix as interwoven network of fine
chromatin threads) The information stored in DNA is organized, replicated and read with the
help of a variety of DNA-binding proteins.
Two types of chromatins
1) Euchromatin which undergoes the normal process of condensation and decondensation in the
the cell cycle.
2) Heteochromatin which remain in a highly condensed state throughout the cell, even during
interphase.

22. Chemical composition of chromatin :
 DNA= 20-40 %- most important chemical constituent of chromatin.
 RNA=05-10 %-associated with chromatin as; Ribosomal RNA-( rRNA)
Messenger RNA- (mRNA) Transfer RNA- (tRNA).
 PROTEINS=55-60%-associated with chromatin as,
I. Histones : - Very basic proteins +ve charged at neutral PH, constitute about
60% of total protein, almost 1:1 ratio with DNA. FIVE TYPES: 1:H1, 2:H2a,
2:H2b, 2:H3 and 2:H4.
II. Non-Histones : - They are 20% of total chromatin protein

23.  Structural Proteins- Histones(Packing proteins):
 Main structural proteins found in eukaryotic cells.
 Low molecular weight basic proteins with high proportion of positively charged
amino acids.
 Bound to DNA along most of its length.
 The positive charge helps histones to bind to DNA and play a crucial role in packing
of long DNA molecules.
 Functional Proteins- Non- Histones:
 Associated with gene regulation and other functions of chromatin.
 50% structural (actin, L & B tubulin and myosin)-contractile proteins, function during
chromosome condensation and in the movement of chromosomes during mitosis and
meiosis.
 50% include all enzymes and co-factors –involved in replication, transcription and
regulation of transcription.

24.  Nucleosomes :
 Nucleosomes are condensed several time to
form the intact chromatids.
 Nucleosomes contain 2 copies of H2A, H2B,
H3 and H4 (Octomer).
 147 bp of DNA is wrapped around
nucleosome
 Histone tails emanate from are.
 Some nucleosomes contain histone variants.
 H1 is a linker histone and it is on the outside
at the point of DNA entry/exit to the core
particle.
 Linker DNA between core particles gives
total of about 200 bp per nucleosome.
 Humans have about 25 million
nucleosomes/cell.

25. 1) Multi-strand model
2) Folded fiber model
3) Nucleosome model-( R. D. Kornberg & O. Thomas-1974 widely
accepted)
Three levels of organization :
DNA wrapping around “Nucleosomes”- The string on beads structure.
A 30 nm condensed chromatin fiber consisting of nucleosome arrays in their
most compact form- The solenoid structure.
Higher levels of packing into metaphase chromosome- The loops, domains
and scaffold structure.
 Ultrastructure and organization :

26.  Proposed by E. J. Dupraw
 Chromosome consists of tightly
folded fiber of 20-30nm diameter.
 Folded fiber consists of DNA
histone helix of 3nm in a
supercoiled conditions.
 Histones were attached on the
outside of the DNA coils that is
histone shells around DNA.
Folded Fiber Model
Each chromatin fiber consists of one DNA molecule
and has average diameter of 230 A˚. This model is
widely accepted.

27. Nucleosome Model
 Proposed by R. D. Kornberg and
confirmed by P. Outdet.
 This is the lowest level of
organization.
 Nucleosome consists of a disc
shaped of 11 nm in diameter.
 Comprising of the two parts: A
core particle and a small or linker
DNA.

28. Repetitive DNA
Highly repetitive
Satellite DNA
Minisatellites
Microsatellites
Moderately
repetitive
Interspersed retrotransposome
SINEs
Alu
LINEs
L1
DNA sequences that are repeated in the genome.

29. Highly repetitive :
1) Satellite DNA
 Satellite DNA is highly repetitive and consists of short repeated sequences.
 Found in centromeres and telomeres.
 Used to DNA Fingerprinting to identify individuals.
i) Minisatellite DNA: Repeats of 14-500 bp, 1-5 Kb long, Scattered throughout
genome.
ii) Microsatellites: Repeats up to 13 bp, 1 Kb long, 106 copies, around
centromeres & telomeres, Short repeats (6bp), 250-1000 at ends of
chromosomes
 Eukaryotic chromosomes demonstrate complex organization characterized by
Repetitive DNA.
 Repetitive DNA sequences are repeated many times within eukaryotic
chromosomes. Mainly Two types following.

30. b) Moderately Repetitive :
 Functional (Protein coding, tRNA coding)
 Unknown function.
1) SINEs (Short interspersed elements): 200-300 bp , 100,000 copies, Alu
(~ 5% of human DNA)
2) LINEs (Long interspersed elements): ~ 6000- 7000 bp, 10-10,000
copies, L1 (~ 5% of human DNA)

31. Mitochondrial genome (mtDNA) :
Multiple identical circular chromosomes.
Size ~ 15 kb in animals.
Over 95% of mitochondria proteins are
encoded in the nucleus genome.
Often A+T rich genomes.
MtDNA is replicated before or during
mitosis or meiosis.
Chloroplast genome (cpDNA) :
 Multiple identical circular chromosomes.
 Size ranges from 120 kb to 160 kb.
 Similar to mtDNA.
 Many chloroplast proteins are encoded in
the nucleus.

32. A Geometrical Model for DNA Organization in Bacteria
Mathias Buenemann and Peter Lenz, 2010
 Caulobacter crescentus aquatic gram –ve bacteria used in this research.
 Eukaryotic cells have an elaborate machinery that organizes the genome over
several length scales.
 Namely, self-avoidance of DNA, specific positioning of one or few DNA loci (such as
origin or terminus) together with the action of DNA compaction proteins (that
organize the chromosome into topological domains) are sufficient to get a linear
arrangement of the chromosome along the cell axis.
 They develop a Monte-Carlo method that allows us to test model numerically and to
analyze the dependence of the spatial ordering on various physiologically relevant
parameters.
 In this model for compacted DNA the chromosome configuration is represented by a
self-avoiding walk. Each step is given by a spherical blob of diameter db as a local
representation of the compacted structure. Every step of the random walk now
represents a rather extended part of the DNA self-avoidance of the walk has to be

33. Results
 The correlation between the position of a gene
on the chromosome and inside the cellular
volume can be explained by a purely
model.
 The shape of the DNA is approximated by a
random walk on a three-dimensional cubic
lattice with grid spacing.
 Proteins such as H-NS, HU, FIS etc. bind to
certain regions of the chromosome and give it
compact local structure such that the
chromosome consists of a chain of compact
units which is compact DNA.
 Persistant length:
Non Compact DNA ζp=50nm,
Compact DNA ζp=20nm
Fig. Typical DNA configuration of an
individual C. crescentus cell belonging to a
population that has an average DNA
configuration showing the linear correlation
between position of genes on the
chromosome and position in the cell.

34.  In eukaryotes, genomic information is encoded in chromosomes, which occupy distinct
territories within the nucleus.
 Inside these territories, chromosomes are folded in a hierarchical set of topological
structures, called compartments, topologically associated domains and loops.
 Phase separation and loop extrusion are the mechanisms indicated to mediate the 3D
organization of the genome, and gene activity and epigenetic marks determine the
activity level of the formed chromatin domains.
 Chromatin fiber is organized inside chromosome territories is now being uncovered via
large-scale genome-wide analysis, mainly by using 3C (Chromosome Conformation
Capture ) based technologies. 3C technologies, such as Hi-C, are based on proximity
ligation and determine the relative frequency at which genomic regions physically interact.
 Hi-C, but especially its derivatives (e.g. in situ Hi-C and Capture-C), generate high-
resolution contact maps that provide detailed insights into the 3D genome organization,
from individual locus up to the entire genome. FISH and 3C technology indicated that
within territories, the chromatin fiber is folded in loops spanning tens of kb up to
megabases, in mammalian cells, Drosophila and plant cells.
3D genome organization: a role for phase separation and loop
extrusion
Maike Stam. et al. ,

35. Results:
 The main difference between plants and
animals may be the absence of canonical
insulator elements in plants. Comparison
across plant species indicates that the
identification of chromatin domains is
affected by genome size, gene density,
the linear distribution of genes and
transposable elements.
 Together these factors establish the 3-
dimensional organization (3D) of the genome
that facilitates an efficient regulation of the
genome, including interactions between
distant DNA elements.
Fig. Hierarchical topological structures
Topiological
Associated
Domians

36. Sources:
 Genome 4 by T. A. Brown
 Life Science (Fundamental and practice) by Pranav Kumar and Usha meena
 Buenemann, M. and Lenz, P
. (2010). A geometrical model for DNA organization in
bacteria. PLoS One, 5(11), e13806.
 Stam, M.; Tark-Dame, M. and Fransz, P
. (2019). 3D genome organization: a role for
phase separation and loop extrusion?. Current opinion in plant biology, 48, 36-
Thank you !