DNA STRUCTURE,

STORAGE AND
COMPARTMENTALIZATION

TAU: An Innovative Centre of Excellence in Higher Medical Education & Research

DR MOHAMED ABDELBAKY
Associate Professor

1
 Objectives
By end of the lecture, students are able to:
Understand what is meant by genome organization.

Understand the nature of chromatin - how DNA and

histones interact to form nucleosomes?

Know the basic structures of the 10 nm chromatin

fiber and the 30 nm chromatin fiber.

Realize that chromosomes are single pieces of DNA

packaged into chromatin.

2
 Concepts of the Lecture
• Genetic information in Prokaryotic cells such as
viruses, bacteria, mitochondria, and chloroplasts is
most often is a short, circular DNA molecule,
relatively free of associated proteins.

• Eukaryotic cells, in contrast to viruses and bacteria,

contain relatively large amounts of DNA organized
into nucleosomes and present during most of the
cell cycle as chromatin fibers.

• Uncoiled chromatin fibers present in the interphase

coil up and condense into chromosomes during
eukaryotic cell division.
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 Concepts of the Lecture
• Eukaryotic genomes are characterized by both
unique and repetitive DNA sequences.

• Eukaryotic genomes consist mostly of noncoding

DNA sequences.

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 Size of DNA Molecules
• A prokaryotic cell contains a single chromosome
composed of double-stranded DNA that forms a
circle.

• These circular DNA molecules are extremely large.

The entire chromosome of the bacterium
Escherichia coli, composed of a single, circular
double-stranded DNA molecule, contains over 4 ×
106 bp.

• If this molecule were linear, its length would

measure almost 2 mm.
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 Size of DNA Molecules
• DNA from eukaryotic cells is approximately 1,000
times larger than that from bacterial cells.

• In eukaryotes, each chromosome contains one

continuous, linear DNA helix.

• The DNA of the longest human chromosome is

over 7 cm in length.

• If the DNA from all 46 chromosomes in a diploid

human cell were placed end to end, our total DNA
would span a distance of about 2 m (over 6 ft).

• Our total DNA contains about 6 × 109 bp.

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 Histones
• Chromatin consists of very long double-stranded DNA
molecules, nearly an equal mass of small basic proteins
termed histones, as well as smaller amounts of nonhistone
proteins, and a small quantity of ribonucleic acid (RNA).

• Histones are a heterogeneous group of closely related

basic proteins, which contain one fourth of amino acid
residues in the form of arginine- and lysine.

• These positively charged amino acids help histones to

bind tightly to the negatively charged sugar phosphate
backbone of DNA.

• Histones provide for the compaction of chromatin.

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DNA Packaging
o The nucleus of a human cell is typically 6 µm in diameter
and at least four levels of packaging of DNA take place
in order that DNA in individual chromosomes fits into the 1.4
µm chromosome seen at metaphase (a stage in mitosis in
the cell cycle where the DNA is most condensed).

o The double stranded DNA wraps twice around a histone

octamer formed by two molecules each of histone (H2A,
H2B, H3, and H4).

o This super-twisted helix forms a spherical particle of 10 nm

diameter; called nucleosome.

o The function of the nucleosome is to condense DNA and

this arrangement also stabilizes DNA.
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o Nucleosomes are the fundamental organization of the
higher order packing of chromatin.

o 146 base pairs (bp) of DNA are associated with the

nucleosome particle and a 50 to 70 bp span of linker DNA
bound by a linker histone H1 that separates each
nucleosome.

o Nucleosomes have a role in packaging DNA, also regulate

gene expression, or activity, by determining whether the
DNA sequences can be accessed by transcription
factors, allowing regulation of expression of a nearby gene.

o Nucleosomes are in turn successively packed into higher

order structures by coiling and looping.
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10
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o DNA fibrils; the supercoiled DNA with histones
(nucleosomes) will have a diameter of about 10 nm.

o About 6 such fibrils are further supercoiled to form 30 nm

diameter chromatin fibers or chromatin threads.

o Loops (300nm):
• The supercoiled DNA (zig-zag or solenoid) forms loops of
40-90kb DNA that radiate from the scaffold of non-histone
proteins at their base.

• Six to seven of such loops together form a rosette like

appearance.

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o Chromosome (1400nm):
 The above loops and rosettes along with the nuclear
scaffold or domain further undergo compaction to give rise
to the mitotic chromosome that is 1400 nm in size.

 It represents the most compacted form of DNA or the

highest order of its organization.

o By this time, the DNA is folded to about 100 times.

o In mitosis, DNA condenses to form chromosomes.

o Once the cell division accomplishes, the DNA reverts to its

less condensed form.
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o DNA and histone synthesis occurs during S phase.

o Mitochondria have their own DNA, which is circular

and with no histones.

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 Nucleosomes closely associate to form 30 nm
fiber (shortens total DNA by another 7 fold)
30 nm
30 nm

Core
histone
proteins
Irregular configuration
where nucleosomes
have little face-to-face
contact
Regular, spiral
configuration
containing six
nucleosomes per
turn

Solenoid model Zigzag model

Brooker, Fig 12.13

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
17
Levels of DNA Packaging in Eukaryotes
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Organization of DNA in Prokaryotes:
 In E. coli, the circular DNA is supercoiled and
attached to an RNA-protein core.

 DNA consists of a double helix, with the two

strands of DNA wrapping around each other to form
a helical structure.

 In order to compact, the DNA molecule coils about

itself to form a structure called a supercoil like a
telephone cord, which connects the handpiece to
the ancient landline phone.

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Organization of DNA in Prokaryotes:

 When the strands of a DNA molecule separate and

unwind over a small local region (which occurs
during DNA replication), supercoils are introduced
into the remaining portion of the molecule, thereby
increasing stress on this portion of the molecule.

 Enzymes known as topoisomerases relieve this

stress so that unwinding of the DNA strands can
occur.

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Histone Modification
o Each core histone has a structured domain and
an amino-terminal “tail” of 25 to 40 amino acid
residues.

o Enzymatic modification of the amino-terminal tails

(e.g., by acetylation, methylation, or
phosphorylation….etc) modifies the histones’ net
electric charge and shape.

o These modifications are physiologically reversible

and prepare the chromatin for DNA replication and
transcription.
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1. Acetylation and Deacetylation of
Lysine Residues
These processes are important in making DNA more
or less accessible to transcription factors (proteins
that regulate gene expression by direct binding to
DNA).

A.Histone acetylation:
•It catalyzed by (histone acetyl transferases or
HATs) is generally associated with transcriptional
activation.
•Lysine residue acetylation weakens the DNA
histone interactions and makes the DNA more
accessible to factors needed for transcription .
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1. Acetylation and Deacetylation of
Lysine Residues
B. Histone deacetylation:
C. Catalyzed by (histone deacetylase or HDAC) is
associated with gene silencing.

D. The interaction of acetylase and deacetylase

activities determine the transcriptional activity of a
given chromatin region.

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2. Other Processes of Histone
Modifications
• Phosphorylation is associated with condensation of
chromosomes.

• ADP-ribosylation is associated with DNA repair.

• Methylation generally occurs when the gene is

repressed, blocks lysine acetylation, maintains positive
charge, and promotes 30-nm fiber condensation.

• Sometimes histones are fixed to small ubiquitin related

modifier (abbreviated as Sumo), and the process is
called sumoylation. Sumoylation of histones is seen
during repression of transcription.
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3. Euchromatin and Heterochromatin

 These terms describe the compaction of DNA in the

chromosome and are used to classify chromatin.

 Heterochromatin; densely packed or compacted regions of

chromatin and are genetically inactive.

 Transcription is inhibited in heterochromatin because the

DNA is packaged so tightly that it is inaccessible to the
proteins responsible for RNA transcription.

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 For a gene to be transcribed, its gene sequence must
become available to the RNA polymerases and regulatory
proteins that influence the rate at which the gene is
transcribed.

 Euchromatin is less densely compacted chromatin regions

in a transcriptionally active nucleus and are commonly
undergoing, or preparing for, or have just completed
transcription.

 Euchromatin represents uncoiled chromatin structures that

allow RNA polymerases’ and regulatory proteins’ access to
DNA.

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 Heterochromatin typically is found at centromere
and telomere regions, which remain relatively
condensed during interphase.

 The inactivated copy of the X-chromosome (Barr

body) that occurs in cells in females also occurs as
heterochromatin.

 In contrast, most transcribed genes are located in

regions of euchromatin.

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 Heterochromatin Euchromatin

Condensed, appears darker on Electron Less condensed

Microscope (EM) (labeled H in A - Nu,
nucleolus).

It is inaccessible to enzymes and so it is Appears lighter on EM (labeled E in

transcriptionally inactive; ↑methylation, A ).
↓acetylation.

Highly condensed such as Barr bodies It is accessible to enzymes and so

(inactive X chromosomes) may be visible on transcriptionally active.
the periphery of nucleus.

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3. Other Special Proteins Interact at
Specific Regions of DNA
o Apart from histones, there are many other special proteins
which will interact at specific regions of DNA.

o The protein–DNA interactions are mainly mediated by 3

motifs; Helix-turn-helix, zinc finger and leucine zipper motifs.

o Only small regions of the protein make direct contact with

the DNA (DNA Binding Domain); the rest of the proteins
are involved in other activities, like dimerization, ligand-
binding, interaction with coactivators and corepressors, etc.

o DNA binding and transactivation domains of most regulatory

proteins are separate and noninteractive.

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31
 Types of histone modifications
Chromatin Modifications Functions Regulated

Transcription, Repair, Replication,

Acetylation
Condensation

Methylation (lysines) Transcription, Repair

Methylation (arginines) Transcription

Phosphorylation Transcription, Repair, Condensation

Ubiquitylation Transcription, Repair

Sumoylation Transcription

ADP ribosylation Transcription

Post-translational modifications on histone proteins alter

chromatin structure and, consequently, chromatin function
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 Summary
• Chromatin is the sum of the protein and nucleic acid that
comprise the material of chromosomes.

• The basic unit of DNA packaging is the nucleosome,

composed of about 146-200 bp of DNA wrapped around a
histone octamer.

• The histone octamer contains a tetramer of histones H3-H4

and two dimers of histones H2A-H2B. The amino acid
sequences of the histones are highly conserved among
eukaryotes.

• Nucleosomes are linked together by DNA with one bound

molecule of H1.
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Textbook/ Course Reference
1) Genetics in Medicine, Thompson & Thompson, 8th Edition,
2016, ISBN-13: 978-1437706963.

2) Medical Genetics, Ian D. Young, ISBN-13: 9780199594610

2010.

3) Board Review Series (BRS)-GENETICS: Ronald W

Derduk- Published by Lippincott-Williams and Wilkins,
ISBN-13: 978-0781799942, 2013.

4) Biochemistry and Genetics PreTest.

5) Lippincott's Illustrated Reviews: Cell and Molecular

Biology.
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 Practice Questions
1. Define the following terms:
A. Genome
B. Nucleosome
C. Chromatin

2. Distinguish between the following:

A. Euchromatin and Heterochromatin
B. Core histone and Linker histone

3. Answer the following questions in short:

A. How does the charge of a histone help its function?
B. What is the composition of a nucleosome?

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4. Fill in the following blanks:
A. Histones are composed of --------- and …………..basic
amino acids.
B. Eukaryotic chromosome is maximally condensed during
…………..stage of mitosis.
C. …………………is the unit of chromatin.
D. The order of eukaryotic DNA compaction includes the
formation of ……………, …………….., …………….. and
finally the chromosome.

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 Answers to the Questions
1. A: It is defined as the one haploid set of
chromosome or the total nucleic acid content of a cell.

1. B: It is the basic unit of chromatin. It is a compact

structure formed by the wrapping of DNA around the
protein core formed of histones (two molecules each
of H2A, H2B, H3 and H4). The double stranded DNA
takes approximately 1.65 turns around the octamer.
The length of this wound DNA is 146bp.

1. C: Any given region of DNA with its associated

proteins is called as the chromatin.
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 Answers of Practice Questions
2. A: Euchromatin: is the uncondensed form of
eukaryotic DNA that is transcriptionally active. It takes
up a lighter color when stained with DNA dyes.

Heterochromatin: represents the highly condensed

region of eukaryotic chromosome that is
transcriptionally inactive and when stained with DNA
dyes imparts it a darker color. These are present near
the centromere and the telomere.

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 Answers of Practice Questions
2. B: Core histone: It is composed of the histone
octamer, i.e., two molecules each of H2A, H2B, H3
and H4. It is wrapped around by 1.67 turns of DNA
with a length of 146bp. It forms the nucleosome.

Linker histone: It is composed of one molecule of H1

histone. It associates with the linker DNA that
connects two nucleosomes and is 50-70bp long. It
helps the DNA to assume 30nm solenoid or zig-zag
model.

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 Answers of Practice Questions
3. A: Histones are positively charged proteins that
interact with the negatively charged DNA. The
negative charge of DNA is due to the phosphate
groups.

3. B: Nucleosome is a compact structure formed by

the wrapping of DNA around the protein core formed
of histones (two molecules each of H2A, H2B, H3 and
H4). The double stranded DNA takes approximately
1.65 turns around the octamer. The length of this
wound DNA is 146bp.

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Answers of Practice Questions
4. A: Lysine; arginine

B: Metaphase

C: Nucleosome

D: Nucleosome; solenoid/ 30nm fiber and loops.

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4. Which of the following are components
of nucleotides?
A. Deoxyribose
B. Amino acids
C. Phosphate
D. Enzymes
E. Organic bases

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4. Which of the following are components
of nucleotides?
A. Deoxyribose
B. Amino acids
C. Phosphate
D. Enzymes
E. Organic bases

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5. Which of the following are organic
bases?
A. Valine
B. Guanine
C. Thymine
D. Serine

45
5. Which of the following are organic
bases?
A. Valine
B. Guanine
C. Thymine
D. Serine

46
6. A nucleotide triplet codes for:
A. a protein
B. an amino acid
C. an enzyme
D. an organic base

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6. A nucleotide triplet codes for:
A. a protein
B. an amino acid
C. an enzyme
D. an organic base

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7. Which of the following represent a correct
pairing of bases?
A. Adenine with thymine
B. Adenine with guanine
C. Uracil with adenine
D. Guanine with cytosine

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7. Which of the following represent a correct
pairing of bases?
A. Adenine with thymine
B. Adenine with guanine
C. Uracil with adenine
D. Guanine with cytosine

50
8. The sequence of part of a DNA strand is the
following: –ATTCGATTGCCCACGT–. When this
strand is used as a template for DNA synthesis,
the product will be which one of the following?
A. TAAGCTAACGGGTGCA
B. UAAGCUAACGGGUGCA
C. ACGUGGGCAAUCGAAU
D. ACGTGGGCAATCGAAT

51
8. The sequence of part of a DNA strand is the
following: –ATTCGATTGCCCACGT–. When this
strand is used as a template for DNA synthesis,
the product will be which one of the following?
A. TAAGCTAACGGGTGCA
B. UAAGCUAACGGGUGCA
C. ACGUGGGCAAUCGAAU
D. ACGTGGGCAATCGAAT

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8. The answer is D: ACGTGGGCAATCGAAT. The product of
DNA replication will be complementary to the template, and
antiparallel.
Reading from the 5′ end of the template, the product will be 3′-
TAAGCTAACGGGTGCA.
When written 5′–3′ (standard notation) one has -
ACGTGGGCAATCGAAT-. Recall that uracil (U) is not placed
into DNA by DNA polymerase.

53
9. Deoxyribonucleic acid (DNA) is a nucleic
acid; a polymer of nucleotide made of a
nitrogenous base, phosphate group and:
A. deoxyglucose sugar
B. deoxyribose sugar
C. glucose sugar
D. ribose sugar

54
9. Deoxyribonucleic acid (DNA) is a nucleic
acid; a polymer of nucleotide made of a
nitrogenous base, phosphate group and:
A. deoxyglucose sugar
B. deoxyribose sugar
C. glucose sugar
D. ribose sugar

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10.Modification of histone proteins by
acetylation will:
A. Add methyl groups to the regulatory region
of the target genes
B. Increase the condensation of chromatin
C. Increase the affinity of histones for DNA
D. Increase the transcription of target genes
E. Inhibit RNA polymerase activity

56
10.Modification of histone proteins by
acetylation will:
A. Add methyl groups to the regulatory region
of the target genes
B. Increase the condensation of chromatin
C. Increase the affinity of histones for DNA
D. Increase the transcription of target genes
E. Inhibit RNA polymerase activity

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THANK YOU

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