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DNA structure
1. DNA Structure
Presented By: Hadiah Bassam Al Mahdi
PhD. Student in Genetics
Faculty of Science , King Adulaziz University
Developmental Genetics Course Bio707
2. Outline
o History of DNA discovery .
o Chemical component of DNA structure.
o DNA as double helix.
o DNA packaging.
o Conclusion and References
3. DNA Abbreviation
D N A
Deoxyribo Nucleic Acid
Deoxyribonucleic acid
is the hereditary material in all organisms
4. Scientists Contributed in the
DNA Discovery
Friedrich Miescher
1869
DNA First Isolated
Erwin Chargaff
1950
Chargaff's rules
1951
X-ray diffraction
Rosalind Franklin
Francis Crick
James Watson
1953
3D DNA Structure
5. Building Blocks
• Nucleoside:
Nitrogenous Base+ Deoxyribose Sugar
• Nucleotide: (dNTPs)
Nucleoside + Phosphate
Adenine
Guanine
Cytosine
Thymine
Pyrimidine
Purine Two aromatic rings
One aromatic ring
Glycosidic bond
6. Polymer Chain
• Nucleotides considered as a monomer
• Backbone composed of repeating pentose-
phosphate units.
• The sugars are joined together by phosphate
groups that form phosphodiester bonds between
the third and fifth carbon atoms of adjacent sugar
rings.
• 5́ 3́ directionality
7. Nucleotides Percentage
• "Chargaff's Rules"
1. The amount of adenine = thymine
and the amount of guanine = cytosine.
2. The amount of dNTPs in DNA varies
between species.
8. DNA Helix
• X-ray diffraction patterns of DNA fibers which
showed that the geometric shape of DNA is a
right-handed helix.
• Usually, the two strands are coiled in a right-
handed fashion(Clockwise). The pitch of the
helix is 3.4 nm and there are roughly 10 bp in
each turn.
• Consequently, the distance between a bp in a
helix is approximately equal to 0.34 nm
9. DNA Double Helix
• Weston and crick constructed a 3D model of
DNA.
• DNA consists of two associated polynucleotide
strands that twist together to form a helix.
• B form (right handed).
• The orientation of the two strands is
antiparallel.
• The strands are held by formation of base pairs
between the two strands:
“complementary pairs”
A is paired with T through two hydrogen bonds
G is paired with C through three hydrogen bonds
• Hydrophobic and van der Waals interactions
between the stacked adjacent base pairs further
stabilize the double-helical structure.
10. DNA Grooves
• A DNA has two grooves that are not equal in size to each other.
• The angle at which the two sugars protrude out from the base (i.e. the angle
between the glycosidic bond.
• The patterns are important because they allow proteins to unambiguously
recognize DNA sequences without having to open and disrupt the double helix.
• Most sequence specific DNA binding
proteins bind to DNA via the major
groove.
• Many non specific DNA binding
proteins bind to the minor groove
• In major groove can distinguish
between 4 bases
11. DNA Different Conformation
3 forms of DNA could be
detected
B – form (Watson & Crick)
A – form
Z – form (Zigzag)
12. Physical Properties of Double-
Stranded DNA
Ultraviolet Absorption Spectra of DNA.
DNA absorbs ultraviolet (UV) light in a band
centered around 260 nm.
Denaturation and Renaturation.
To melt the two strands or denature the DNA,
all these stabilizing forces must be overcome.
The rest of the double helix renatures very
rapidly.
DNA Hybridization
Involves the formation of a double-stranded
nucleicacid, either a DNA double helix or an
RNA-DNA duplex.
Provides an extremely powerful tool in
molecular biology.
13. • Genome size is Related to complexity
of the organism when comparing
different groups
– Prokaryotes
– Single cell Eukaryotes
– Multi-cellular Eukaryotes
• Genome size complexity among
major groups
• Larger proteins
• More regulation needed
(regulatory sequences)
• Gene is discontinued by
introns
• Organism complexity 1/ Gene
density
DNA and complexity of the
Organism
14. Do all cells have the same DNA
structure ?
• Most Eukaryotes have linear DNA.
• mtDNA and plastid DNA are circular.
• Some viruses, most bacteria & plasmid have
circular DNA.
• phage can exist in both linear and circular
DNA because of sticky ends.
15. DNA is compacted into
chromosomes
1. To fit DNA inside the cell
2. To protect DNA from damage.
3. To transmit DNA efficiently to daughter cells.
4. To Facilitate gene expression.
5. To ensure that recombination takes place between
homologous chromosomes only
16. DNA Packaging
• 2 nm = DNA structure
• 11 nm = String on beads form of chromatin
• “Nucleosomes primary structural units of
chromatin”
• 30 nm= chromatin fibers
“ Nucleosomes fold”
• 300 nm = chromosome scaffold
“long loops of chromatin extending from the
scaffold”
• 700 nm = chromatid structure
• 1400 nm= chromosomal structure
17. String on beads
• During interphase, the genetic material exists as
a nucleoprotein complex called chromatin.
• Proteins associated with eukaryotic DNA are
histones.
• The five major types of histone proteins (H1,
H2A, H2B, H3, and H4).
• Histones rich in positively charged basic amino
acids, which interact with the negatively charged
phosphate groups in DNA.
• The string is composed of free DNA called
“linker” DNA connecting the beadlike structures
termed nucleosomes.
• Nucleosome consists of a protein core with DNA
wound around its surface like thread around a
spool.
• The core is an octamer containing two copies
each of histones H2A, H2B, H3, and H4
18. Chromatin fibers
• A chromatosome is a result
of histone H1 binding to
a nucleosome, which contains
a histone octamer and DNA.
19. Chromosome scaffold
• Nonhistone proteins provide a structural scaffold for long chromatin
loops.
• Folding of the scaffold has been proposed to produce the highly
condensed structure characteristic of metaphase chromosomes.
22. Conclusion
Deoxyribonucleic acid (DNA), the genetic material, carries information to
specify the amino acid sequences of proteins.
DNA contains four types of adjacent nucleotides in a polynucleotide are linked
by phosphodiester bonds .
Natural DNA (B DNA) contains two complementary antiparallel polynucleotide
strands wound together into a regular right-handed double helix.
The bases in nucleic acids can interact via hydrogenbonds. The standard
Watson-Crick base pairs are G·C, A·T (in DNA).
Each eukaryotic chromosome contains a single DNA molecule packaged into
nucleosomes and folded into a 30-nm chromatin fiber, which is attached to a
protein scaffold at specific sites
23. References
o SINDEN, R. R. 2012. DNA structure and function,
Elsevier.
o WATSON, J. D., BAKER, T. A., BELL, S. P., GANN, A.,
LEVINE, M., & LOSICK, R. M. (2004). Molecular
biology of the gene.
o LODISH, H., BERK, A., KAISER, C. A., KRIEGER, M.,
SCOTT, M. P., BRETSCHER, A., PLOEGH, H. &
MATSUDAIRA, P. 2008. Molecular cell biology,
Macmillan.
Hinweis der Redaktion
First step in central dogma
which triggered the idea that DNA was a helix.
Perhaps the most important aspects of DNA structural variation are
likely to be found in the mechanics of molecular recognition and manipulation
by proteins.
Deoxyribose is the five-carbon sugar molecule that helps form the phosphate backbone of DNA molecules
Guanine + thymine = keto
Cytosine + Thymine = Amino
Glycosidic bond between sugar and base
A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms.
DNA polymarase
Negative charge
Hydrogen bond is non covalent
Negative charge
Antiparallel means one strand is orientated from 5 to 3 and other orientated from 3 to 5
Hydrogen bond is non covalent
Antiparllel means one strand is orientated from 5 to 3 and other orientated from 3 to 5
Rosalind Franklin and Maurice Wilkins used a method of X-ray diffraction to investigate the structure of DNA
DNA was purified and then fibres were stretched in a thin glass tube (to make most of the strands parallel)
The DNA was targeted by a X-ray beam, which was diffracted when it contacted an atom
The scattering pattern of the X-ray was recorded on a film and used to elucidate details of mole
(a nanometer is one billionth of ameter, that is 10-9 m)
Weston and crick constructed a 3D model of DNA.
Used information from experiments conducted by other scientist
Determined the structure of DNA was a double helix made of two nucleotides
Won Nobel Prize 1962
The narrow angle = minor groove.
The large angle =major grove.
Dehydrating condition. (A)
High salt concentration.(Z)
6 um diameter of nucleolus
Lysine and arginine amino acid
Linker 147 b.b
Each chromosome consists of a single,
long molecule of DNA up to ~280 Mb
in humans, organized into increasing
levels of condensation by the histone
and nonhistone proteins with which it
is intricately complexed.
