Models of Eucharyotic Chromosome Dr. Thirunahari Ugandhar.pptx

Models of Organization of
Eukaryotic Chromosomes
By
Dr. Thirunahari Ugandhar
Associate Prof of Botany
Department of Botany
Kakatiya Govt College (A) Hanamkonda

Organization of
Eukaryotic
Chromosomes
Eukaryotic chromosomes
are highly organized
structures that allow
long strands of DNA to
be compactly stored
within the cell nucleus.
This packaging is
essential for DNA
stability, accessibility for
gene expression, and
proper distribution
during cell division. The
organization occurs
through multiple
hierarchical levels

• Levels of Chromatin Organization
• 1. Nucleosome (Basic Unit of Chromatin):
• DNA wraps around a core of histone proteins,
forming a nucleosome.
• Each nucleosome consists of ~147 base pairs of
DNA wound around a histone octamer (2 copies
each of H2A, H2B, H3, and H4).
• Linker DNA connects individual nucleosomes,
and histone H1 helps stabilize this structure.
• 2. 30 nm Fiber (Higher-Order Packing):
• Nucleosomes are further folded into a more
compact fiber approximately 30 nanometers in
diameter.
• Two main models explain this structure:
• Solenoid model: Nucleosomes spiral in a helical
fashion.
• Zigzag model: Linker DNA passes through the
central axis, creating a more irregular structure.

• Euchromatin vs. Heterochromatin:
• Euchromatin: Loosely packed,
transcriptionally active regions of DNA.
• Heterochromatin: Densely packed,
transcriptionally inactive regions; often
found at centromeres and telomeres.
• 3D Chromatin Organization:
• Chromosomes are arranged in specific
territories within the nucleus.
• This spatial organization influences
gene expression and cellular function

• 3. Looped Domains:
• The 30 nm fiber forms loops of chromatin that attach to a
protein scaffold within the nucleus.
• These loops organize chromatin into functional domains
and play a role in regulating gene activity.
• 4. Metaphase Chromosome (Fully Condensed
Form):
• During cell division, looped domains are further
compacted into the tightly packed metaphase
chromosome, which is visible under a microscope.
• Key Features and Concepts
• Histones:
• Positively charged proteins essential for nucleosome
formation and chromatin organization.
• Linker DNA:
• The stretch of DNA between nucleosomes; its length and
flexibility affect chromatin structure.
• Non-Histone Proteins:
• These include structural and regulatory proteins that aid
in chromatin folding, gene regulation, and scaffold
formation.

Models of Eucharyotic Chromosome Dr. Thirunahari Ugandhar.pptx

Nucleosome Model –
Structure and Significance
Introduction
The nucleosome is the basic
structural and functional
unit of chromatin in
eukaryotic cells. It plays a
vital role in organizing and
compacting DNA within the
nucleus, while still allowing
access for gene expression,
replication, and repair

Historical
Background
• In 1974, R.D.
Kornberg proposed
the nucleosome
model to explain
chromatin
organization.
• In 1975, P. Oudet
coined the term
“nucleosome.”

What is a
Nucleosome?
• A nucleosome is made of
DNA coiled around a
core of histone proteins.
• It consists of
approximately 146 base
pairs of DNA wrapped
1.65 times around a
histone octamer.
• The histone octamer
includes two copies each
of the core histones: H2A,
H2B, H3, and H4.
• These positively charged
histones bind tightly to
the negatively charged
DNA, stabilizing the

Structure of the
Nucleosome
• Core DNA: 146 base pairs
wrapped around the histone
octamer.
• Linker DNA: ~54 base pairs
connecting one nucleosome to
the next.
• H1 histone: Binds at the
entry/exit point of DNA, securing
the structure but is not part of
the core histone octamer.
Shape: Each
nucleosome is disc-
shaped, with a height
of ~5.7 nm and a
diameter of ~11
nmRepeating Units:
Nucleosomes are
regularly spaced along
DNA, forming a “beads-
on-a-string” structure

Experimental
Evidence
• Scientists treated
chromatin with nuclease
enzymes.
• The DNA fragments
formed were multiples of
~200 base pairs, indicating
protected regions
(nucleosomes) and
exposed linker regions.
• In contrast, naked DNA
(not bound to histones)
was digested into random-
sized fragments.
• This confirmed the
presence of repeating
DNA-protein units in
chromatin—i.e.,
nucleosomes.

Significance of the Nucleosome
• A diploid human cell contains around
6.4 billion base pairs of DNA.
• To compact this immense length, DNA
wraps into ~30 million nucleosomes.
• Nucleosomes enable efficient DNA
packaging while maintaining functional
accessibility.
• They are essential for:
o Chromosome structure
o Gene regulation
o DNA replication and repair

Features of the Nucleosome Model of Chromosomes
• In eukaryotes, DNA is tightly bound to an equal mass of histones,
which serve to form a repeating array of DNA-protein particles,
called nucleosomes.
• If it was stretched out, the DNA double-helix in each human
chromosome would span the cell nucleus thousands of time.
• Histones play a crucial role in packing this very long DNA
molecule in an orderly way (i.e., nucleosome) into nucleus only a
few micrometers in diameter.
• Thus, nucleosomes are the fundamental packing unit particles of
the chromatin and give chromatin a “beads-on-a-string”
appearance in electron micrographs taken after treatments that
unfold higher-order packing.
• Each nucleosome is a disc-shaped particle with a diameter of
about 11 nm and 5.7 nm in height containing 2 copies of each 4
nucleosome histones–H2A, H2B, H3, and H4.
• This histone octamer forms a protein core [(i.e., a core of histone
tetramer (H3, H4)2 and the apolar regions of 2(H2A and H2B)]
around which the double-stranded DNA helix is wound 1¾ time
containing 146 base pairs.

• n chromatin, the DNA extends as a
continuous thread from nucleosome to
nucleosome.
• Each nucleosome bead is separated from the
next by a region of linker DNA which is
generally 54 base pair long and contains
single H1 histone protein molecule.
• Generally, DNA makes two complete turns
around the histone octamers and these two
turns (200 bp long) are sealed off by H1
molecules.
• On average, nucleosomes repeat at intervals
of about 200 nucleotides or base pairs. For
example, a eukaryotic gene of 10,000
nucleotide pairs will be associated with 50
nucleosomes and each human cell with 6 x
109
DNA nucleotide pairs contains 3 x 107

The Folding of the DNA
The first step is the assembly of the DNA with a newly synthesized tetramer (H3-H4), are specifically
modified (e.g. H4 is acetylated at Lys5 and Lysl2 (H3-H4)), to form a sub-nucleosomal particle, which is
followed by the addition of two H2A-H2B dimers.
This produces a nucleosomal core particle consisting of 146 base pairs of DNA bind around the histone
octamer. This core particle and the linker DNA together form the nucleosome.
The next step is the maturation step that requires ATP to establish regular spacing of the nucleosome
cores to form the nucleo-filament.
During this step the newly incorporated his
tones are de-acetylated.
Next, the incorporation of linker histones is accompanied by folding of the nucleo-filament into the 30
nm fiber, the structure of which remains to be elucidated.
Two principal models exist- the solenoid model and the zig-zag.
Finally, further successive folding events lead to a high level of organization and specific domains in the
nucleus.

Function and Significance of Chromosomes
The number of the chromosomes is constant for a particular species. Therefore,
these are of great importance in the determination of the phylogeny and
taxonomy of the species.
Genetic Code Storage: Chromosome contains the genetic material that is
required by the organism to develop and grow. DNA molecules are made of
chain of units called genes. Genes are those sections of the DNA which code for
specific proteins required by the cell for its proper functioning.
Sex Determination: Humans have 23 pairs of chromosomes out of which one
pair is the sex chromosome. Females have two X chromosomes and males have
one X and one Y chromosome. The sex of the child is determined by the
chromosome passed down by the male. If X chromosome is passed out of XY
chromosome, the child will be a female and if a Y chromosome is passed, a male
child develops.
Control of Cell Division: Chromosomes check successful division of cells during
the process of mitosis. The chromosomes of the parent cells insure that the
correct information is passed on to the daughter cells required by the cell to
grow and develop correctly.
Formation of Proteins and Storage: The chromosomes direct the sequences of
proteins formed in our body and also maintain the order of DNA. The proteins
are also stored in the coiled structure of the chromosomes. These proteins
bound to the DNA help in proper packaging of the DNA.

Giant chromosomes
• Found in certain tissues e.g., salivary
glands of larvae, gut epithelium,
Malphigian tubules and some fat
bodies, of some Diptera (Drosophila,
Sciara, Rhyncosciara)
• These chromosomes are very long and
thick (upto 200 times their size during
mitotic metaphase in the case of
Drosophila)
• Hence they are known as Giant
chromosomes.

They are first discovered by Balbiani in 1881 in
dipteran salivary glands and thus also known
as salivary gland chromosomes.
But their significance was realized only after
the extensive studies by Painter during 1930’s.
Giant chromosomes have also been discovered
in suspensors of young embryos of many
plants, but these do not show the bands so
typical of salivary gland chromosomes.

• He described the morphology in
detail and discovered the
relation between salivary gland
chromosomes and germ cell
chromosomes.
• Slides of Drosophila giant
chromosomes are prepared by
squashing in acetocarmine the
salivary glands dissected out
from the larvae.
• The total length of
D.melanogater giant
chromosomes is about 2,000µ.

• Giant chromosomes are made up
of several dark staining regions
called “bands”.
• It can be separated by relatively
light or non-staining “interband”
regions.
• The bands in Drosophila giant
chromosome are visible even
without staining, but after staining
they become very sharp and clear.
• In Drosophila about 5000 bands
can be recognized.

• Some of these bands are as thick as
0.5µ, while some may be only 0.05µ
thick.
• About 25,000 base-pairs are now
estimated for each band.
• All the available evidence clearly
shows that each giant chromosome is
composed of numerous strands, each
strand representing one chromatid.
• Therefore, these chromosomes are
also known as “Polytene
chromosome”, and the condition is
referred to as “Polytene”

• The numerous strands of these
chromosomes are produced due to
repeated replication of the paired
chromosomes without any nuclear or
cell division.
• So that the number of strands
(chromatids) in a chromosome doubles
after every round of DNA replication
• It is estimated that giant chromosomes
of Drosophila have about 1,024 strands
• In the case of Chironomus may have
about 4,096 strands.
• The bands of giant chromosomes are
formed due to stacking over one
another of the chromomeres of all
strands.

Since chromatin fibers are highly coiled in
chromosomes, they stain deeply.
On the other hand, the chromatin fibers in the
interband regions are fully extended, as a result
these regions take up very light stain.
In Drosophila the location of many genes is
correlated with specific bands in the connected
chromosomes.
In interband region do not have atleast functional
genes

During certain stages of development,
specific bands and inter band regions are
associated with them greatly increase in
diameter and produced a structure called
Puffs or Balbiani rings.
Puffs are believed to be produced due to
uncoiling of chromatin fibers present in the
concerned chromomeres.
The puffs are sites of active RNA synthesis.

•Figure 3. Polytene chromosome map of
Anopheles gambiae

Lampbrush
Chromosome
It was given this name because it is similar in appearance to the
brushes used to clean lamp chimneys in centuries past.
First observed by Flemming in 1882.
The name lampbrush was given by Ruckert in 1892.
These are found in oocytic nuclei of vertebrates (sharks, amphibians,
reptiles and birds)as well as in invertebrates (Sagitta, sepia,
Ehinaster and several species of insects).
Also found in plants – but most experiments in oocytes.

• Lampbrush chromosomes are up to
800 µm long; thus they provide very
favorable material for cytological
studies.
• The homologous chromosomes are
paired and each has duplicated to
produce two chromatids at the
lampbrush stage.
• Each lampbrush chromosome
contains a central axial region, where
the two chromatids are highly
condensed
• Each chromosome has several
chromomeres distributed over its
length.
• From each chromomere, a pair of
loops emerges in the opposite
directions vertical to the main
chromosomal axis.

• One loop represent one
chromatid, i.e., one DNA
molecule.
• The size of the loop may
be ranging the average of
9.5 µm to about 200 µm
• The pairs of loops are
produced due to uncoiling
of the two chromatin
fibers present in a highly
coiled state in the
chromomeres.

One end of each loop is
thinner (thin end) than
the other end (thick
end).
There is extensive RNA
synthesis at the thin
end of the loops, while
there is little or no RNA
synthesis at the thick
end.

Phase-contrast and fluorescent micrographs of
lampbrush chromosomes

Dosage
Compensatio
n
• Sex Chromosomes:
females XX, males XY
• Females have two copies of
every X-linked gene; males
have only one.
• How is this difference in
gene dosage compensated
for? OR
• How to create equal amount
of X chromosome gene
products in males and
females?

• Levels of enzymes or
proteins encoded by genes
on the X chromosome are
the same in both males
and females
• Even though males have 1
X chromosome and
females have 2.

G6PD, glucose 6 phosphate
dehydrogenase, gene is carried
on the X chromosome
This gene codes for an enzyme
that breaks down sugar
Females produce the same
amount of G6PD enzyme as
males
XXY and XXX individuals
produce the same about of
G6PD as anyone else

In cells with more than two X
chromosomes, only one X remains
genetically active and all the others
become inactivated.
In some cells the paternal allele is
expressed
In other cells the maternal allele is
expressed
In XXX and XXXX females and XXY males
only 1 X is activated in any given cell the
rest are inactivated

Barr
Bodies
1940’s two Canadian scientists
noticed a dark staining mass in
the nuclei of cat brain cells
Found these dark staining
spots in female but not males
This held for cats and humans
They thought the spot was a
tightly condensed X
chromosome

Barr Bodies •Barr bodies represent the inactive X chromosome and
are normally found only in female somatic cells.

•A woman with the
chromosome
constitution 47, XXX
should have 2 Barr
bodies in each cell.
•XXY individuals are
male, but have a Barr
body.
• XO individuals are
female but have no Barr
bodies.

Which chromosome is inactive is a
matter of chance, but once an X has
become inactivated , all cells arising
from that cell will keep the same
inactive X chromosome.
In the mouse, the inactivation
apparently occurs in early in
development
In human embryos, sex chromatin
bodies have been observed by the 16th
day of gestation.

Mechanism
of X-
chromoso
me
Inactivation
A region of the p arm of the X
chromosome near the
centromere called the X-
inactivation center (XIC) is the
control unit.
This region contains the gene
for X-inactive specific
transcript (XIST). This RNA
presumably coats the X
chromosome that expresses it
and then DNA methylation
locks the chromosome in the
inactive state.

This occurs about
16 days after
fertilization in a
female embryo.
The process is
independent from
cell to cell.
A maternal or
paternal X is
randomly chosen
to be inactivated.

• Rollin Hotchkiss first
discovered methylated DNA in
1948.
• He found that DNA from
certain sources contained, in
addition to the standard four
bases, a fifth: 5-methyl
cytosine.
• It took almost three decades
to find a role for it.
• In the mid-1970s, Harold
Weintraub and his colleagues
noticed that active genes are
low in methyl groups or under
methylated.
• Therefore, a relationship
between under methylation
and gene activity seemed
likely, as if methylation helped
repress genes.

This would be a valuable means of
keeping genes inactive if methylation
passed on from parent to daughter cells
during cell division.
Each parental strand retains its methyl
groups, which serve as signals to the
methylating apparatus to place methyl
groups on the newly made progeny
strand.
Thus methylation has two of the
requirements for mechanism of
determination:
1. It represses gene activity
2. It is permanent.

Strictly speaking, the DNA is
altered, since methyl groups are
attached, but because methyl
cytosine behaves the same as
ordinary cytosine, the genetic
coding remain same.
A striking example of such a role
of methylation is seen in the
inactivation of the X chromosome
in female mammal.
The inactive X chromosome
become heterochromatic and
appears as a dark fleck under the
microscope – this chromosome
said to be lyonized, in honor of
Mary Lyon who first postulated
the effect in mice.

An obvious explanation is that
the DNA in the lyonized X
chromosome is methylated,
where as the DNA in the active,
X chromosome is not.
To check this hypothesis Peter
Jones and Lawrence Shapiro
grew cells in the presence of
drug 5-azacytosine, which
prevents DNA methylation.
This reactivated the lyonized the
X chromosome.
Furthermore, Shapiro showed
these reactivated chromosomes
could be transferred to other
cells and still remain active.

Enhancing Learning
Analytics and Teaching
Quality with Generative
AI
by
Dr. Thirunahari Ugandhar
Associate Prof of Botany
Department of Botany
Kakatiya Govt College (A) Hanamkonda

Enhancing Learning
Analytics and Teaching
Quality with Generative AI
• Generative AI, like
ChatGPT, uses
machine learning to
create new content.
• While generative AI
tools can help
explore new ideas,
write text, and get
feedback, there are
important
limitations to these
tools to keep in
mind.

 Artificial intelligence (AI) refers to the capability of
computer systems to perform tasks typically requiring
human intelligence, such as learning, reasoning,
problem-solving, and decision-making.
 AI aims to simulate human intelligence in machines,
enabling them to learn from experience, adapt to new
inputs, and perform human-like tasks.

Definition
Generative AI is a type of
artificial intelligence that creates
new content, such as text, images,
and music, by learning patterns
from data. Unlike traditional AI,
it can generate human-like
responses and assist in tasks like
writing, coding, and problem-
solving. Examples include
ChatGPT, Google Bard, and
DALL-E. While useful, it requires
human oversight for accuracy.

• Definition of Generative AI
• Generative AI, like ChatGPT,
utilizes advanced machine
learning algorithms to
generate new content,
making it a powerful tool in
scientific research and
innovation.
• AI-driven platforms, such as
Google Bard, Claude, and
Bing AI, enhance productivity
by assisting in data analysis,
literature reviews, and
experimental design.
• These tools can accelerate
discoveries by identifying
patterns in complex datasets,
simulating scientific models,
and generating research
summaries.

Role of AI in
Education
AI is transforming
education by making
learning more
personalized, efficient,
and accessible. Key areas
include:
Personalized
Learning: AI
adapts lessons to
students' strengths
and weaknesses.
Intelligent Tutoring: AI-
driven tutors provide
instant support and
explanations.
Automated
Grading: AI speeds
up assessment and
feedback.
Smart Classrooms: AI
enhances digital learning with
interactive tools.
Administrative
Support: AI automates
scheduling,
attendance, and
student queries.
Accessibility: AI assists
students with disabilities
through speech-to-text and
translation tools.
Career Guidance:
AI recommends
courses and career
paths based on
skills and interests.
While AI improves education,
challenges like data privacy, bias,
and cost must be addressed. It
should support, not replace,
educators, ensuring a balanced
learning experience.
Role of AI in
Education

Learning Analytics and AI
Learning Analytics: The process of
collecting and analyzing student
data to improve learning outcomes.
AI in Student Performance: AI
tracks progress, identifies patterns,
predicts success, and provides real-
time feedback.
Personalized Learning: AI adapts
lessons, recommends resources, and
tailors study plans for individual
needs.
AI-driven analytics make education
more efficient, data-driven, and
personalized, enhancing student
success
Learning Analytics and
AI

AI in Teaching and Classroom
Improvement
AI is transforming education by
assisting teachers in lesson
planning, assessments and
providing personalized feedback.
AI-powered chatbots help students
with instant answers to queries,
enhancing engagement and
learning.
Additionally, automation of
administrative tasks like
attendance, grading, and
scheduling allows educators to
focus more on teaching, improving
overall classroom efficiency.

Additionally, it supports educators in
content creation and curriculum design,
making teaching more efficient and
innovative.
It provides instant feedback and
performance insights, helping students
track progress and improve.
Generative AI enhances student
engagement by creating interactive and
personalized learning experiences.
Benefits of Generative AI in Education

Challenges and
Ethical
Considerations
AI-generated content may
sometimes lack accuracy and can
be influenced by biases, leading
to misinformation.
There's also a concern about
overdependence on technology,
potentially hindering the
development of critical thinking
skills.
Ethical issues, such as data
privacy and the responsible use
of AI, need careful attention to
ensure fairness, transparency,
and the protection of personal
information.

Future of AI in Education
• AI will continue to evolve in
personalized learning,
tailoring lessons to
individual student needs and
learning styles.
• Integration with augmented
and virtual reality will create
immersive, interactive
educational experiences,
enhancing engagement and
comprehension.
• Potential research areas
include developing more
adaptive AI systems,
exploring AI’s role in
emotional and social
learning, and improving AI-
driven tools for assessment
and feedback.

Conclusion
In summary, AI has the
potential to revolutionize
education by enhancing
student engagement,
providing personalized
learning experiences, and
supporting educators in
content creation and
administrative tasks.
However, challenges related to
accuracy, bias, and ethical
concerns must be addressed to
ensure responsible use.
As AI continues to evolve, its
integration with emerging
technologies like AR/VR offers
exciting possibilities for the
future of education.

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