BY DR.

DALIA ALI
LECTURER OF MEDICAL BIOCHEMISTRY&MOLECULAR BIOLOGY,
HELWAN MEDICAL SCHOOL
1- Recognize linear structure of DNA with
respect to polarity, sugar phosphate
backbone and purine and pyrimidine base.
2- Describe base complementarity.
3- Describe the DNA double helix (Watson
and Crick model).
4- Describe factors affecting the stability of
the DNA double helix.
5- Explain denaturation/renaturation and how
CG content affect that.
6- Compare between A,B,Z forms of DNA.
7- Describe the organization & 3ry structure
of DNA.
8- Describe the nucleosome structure.
9- Compare gene, genome and chromosome.
Nucleic Acids
Nucleic acids are
required for: Storage
& Expression of the
genetic information.

They are 2 types:

DNA & RNA.
 DNA (Deoxy-Ribonucleic acid)

Polymer of
deoxynucleotides
linked together
by
phosphodiester
bonds
 DNA (Deoxy-Ribonucleic acid)

Repository of the genetic information

“The Genome”

Located in:
Chromosomes inside the nuclues
Mitochondria
Plants chloroplast
A. In euokaryotes:
i- In chromosome inside the nucleus
Carry genetic information that code for functional proteins or
functional RNA
ii- In chromosome inside mitochondria
Contains:
- genes encoded proteins of electron transport chains
- genes encode tRNA and small and large subunits of
ribosomal RNA

B. Plants:
In chloroplast

C. In prokaryotes:
i- In chromosomes
ii- In some prokaryotes in non chromosomal DNA (Plasmids
Eukaryotic & Prokaryotic DNA
Functions of DNA

a- Store genetic information and transmit it

to next cell generations.

b- Control selective protein synthesis

inside each cells to be able to perform its
physiologic functions.
“Differential gene expression”
Double stranded molecule: Each strand is
formed of many deoxynucleotides covalently
bounded by 3’-5’ phosphodiester bonds. The
nitrogenous bases of DNA are adenine, guanine
(purines) cytosine and thymine (pyrimidines)
Polarity:
One end of the DNA strand has a free phosphate
group at 5’ end and a free OH group at the other 3’
end.
- The nitrogenous bases between both ends are
written in a sequence from 5’ to 3‘.
The 2 DNA strands wind around each
othe forming right handed double helix.
 The 2 strands are anti parallel (5‘ end
of one strand is paired with 3’ end of the
other strand)
 DNA 2ry structure
The hydrophilic (polar) deoxyribose-
phosphate backbone of each chain is
outside of the chain and the hydrophobic
bases are stacked inside perpendicular to
the axis of the helix.
The overall structure resemble spiral
staircase (backbone: deoxy- ribose
phosphate and steps: nitrogenous
bases).

Each turn contains 10 base pairs ( 3.4

nm length, 1.9 nm width).
 On its exterior
surface, the
double helix of
DNA contains two
deep grooves
between the
ribose-phosphate
chains. These two
grooves are of
unequal size and
termed the major
& minor grooves.
 Read only slide
 The difference in their size is due to the
asymmetry of the deoxyribose rings and the
structurally distinct nature of the upper
surface of a base-pair relative to the bottom
surface.

 These grooves act as a binding sites for

regulatory proteins.
 
The double helix configuration of DNA is stabilized by
hydrogen bonds between nitrogenous bases.
Chargaff rule and base complementary bases:
1- In any sample of DNA the amount of adenine equal
thymine.

2- In any sample of DNA the amount of guanine equal

cytosine.

3- The total amount of purines equal the total amounts

of pyrimidines.
- The observation of Chargaff is explained by the fact
that the adenine and thymine base have only 2
electronegative atoms, while cytosine and guanine
have 3 electronegative atoms

- Accordingly adenine can pair with thymine with 2

hydrogen bonds while cytosine can pair with guanine
with 3 hydrogen bonds. This make C-G base pair is
more stable than A-T base pair.
Polymorphism of DNA
Polymorphism of DNA
Double stranded linear: Eukaryotic nuclear
chromosome).

Double stranded circular: Mitochondrial,

plasmid, viral and chloroplast).

Single stranded circular DNA: (small

viruses).
Stacking interaction:
Stack arrangement of bases in DNA facilitated
mainly by hydrophobic interactions between
bases.
Def.:
- Separation of the 2 DNA strands by
disruption of H- bonds between the 2 DNA
strands.
Denaturating factors:
1- Change in pH:
Change the pH ionization of base
disruption of H-bonds.
2- Heating (thermal denaturation):
- Heating will disrupt hydrogen bonds.
- The base composition of DNA varies widly
from molecule to molecule, and even within
different regions of the same molecule.
- So regions that have predominantly A-T
base-pair will be less stable than those rich
in G-C base-pairs.
- Melting temperature (TM):
Temperature at which 50% of the DNA molecule
exist as single strands.
N.B.: The TM differ according to base composition of
the DNA molecule, with high TM value in DNA
molecule rich in C-G base pair.

- DNA denaturation can be monitored by measuring

its absorbance at 260 nm. Single stranded DNA
has a higher relative absorbance at this wave
length.
Complementary DNA strands separated by
denaturation can reform double helix if
treated well (cooling).
DNA Organization
 A typical human cell
contains 46
chromosomes (23 pair).
 Each chromosome is
composed of 2
chromatids joined at
centromer.
 Each chromatid contains
a double stranded DNA
molecule.
Organization of DNA

 The length of DNA inside the

cell measure approximately 1.6
meters. How this molecule
packed inside invisible
nucleus?!!!
 Chromatin is a term designing the 3ry structure in
which DNA exists within cells.

 The structure of the chromatin is determined and

stabilized through the interaction of the DNA with
the DNA-binding proteins.

 There are 2 classes of DNA-binding proteins

involved in maintaining the compact structure of
chromatin:
a- Histones b- Non histones
Eukaryotic chromatin structure

Nuclear DNA
bound to
Histones proteins
+
smaller amounts of non histone proteins
(Enzymes involved in DNA replication and transcription)
+
Small amount of RNA
(snRNA)
HISTONES

 Basic proteins that form ionic bonds

with the negatively charged acidic DNA
phosphate group.

5 types: H1, H2A, H2B, H3, H4.

Functions:
1. They help condensation of the DNA into
more compact chromosomes.
HISTONES

2. Protect the DNA from digestion by

exonucleases.
3. Modified histones: Has an important role
in changing the structure of chromatin
and chromatin function e.g. acetylation of
H3 and H4 is associated with activation
or inactivation of gene expression.
 The
Nucleosome
contains DNA &
Histones
Chromatin

is built from repeating

nucleosomes units
If the chromatin is placed in low salt buffer and
viewed with E/M (i.e If the chromatin is pulled
into a linear strucrure)→→→→ It resembles a
string of beads( with the beads
representing nucleosome cores and the string
representing the DNA linker)
Compaction of Chromatin
1- DNA core:
Formed of supercoiled DNA surrounding histone
octamer (2 molecules of each of H2A, H2B, H3,
H4). The nucleosome core contains
approximately 150 bp of DNA.
2- Linking region:
It joins one nucleosome core to the next
Formed of 20-200 bp of DNA and 1 molecule of
histone (H1) which protects the linker DNA from
digestion by exonucleases.
Compaction of chromatin

Condensation of the nucleosomes with histone

H1 in the centre, form the 10 nm fibril which
represents 7 fold shortening of the linear ß- form
DNA.

Supercoiling of the 10 nm fibril with 6-7

nucleosomes per turn form the 30 nm fiber
which represents 50 fold shortening of the
length of DNA.
Read only slide

 Supercoiling of the 30 nm fiber into

superloops (700 nm in diameter).
 Each 6 superloops attached to a
protein scaffold form a rosette.
 Each 30 rosette form one coil.
 Each 10 coils form one chromatid.
 Nucleosome fate during DNA
Replication (cell division)??
Before the cell divides & for DNA to
replicate, nucleosomes are
disassembled to allow access &
copying of DNA.

Once DNA synthesis is complete, they

reassemble rapidly.
 The protein-DNA structure of chromatin is
stabilized by attachment to a non histone protein
scaffold called nuclear matrix.

 This class of proteins includes the various

transcription factors, polymerases, hormone
receptors and other nuclear enzymes. In any living
cell there are more than 1000 different types of
non histone proteins bound to the DNA.
Genome: The total DNA content in the
chromosomes of a cell. It contains approximately
100,000 functional genes (1% of human genome
which has 1.5 million genes).
Gene: a segment of DNA that code for polypeptide
chain or RNA. The gene is formed of exons and
entrons.
Exons: are coding sequences of gene that can be
translated to polypeptides
Introns: Are stretch of nucleic acid sequence that
separate the coding sequence of a gene. Part of its
functions is it involved in control of gene expression.
Enjoy your day!