about basic DNA structure

1. I am the chemical basis of life and
heredity
DNA

2. DNA structure:
• DNA is a polymer of deoxyribonucleoside
monophosphates covalently linked by 3´-5´
phosphodiester bond. With the exception a few virus that
contain single stranded (ss).
• DNA exists as a double strands wind around each other
forming a double helix.
• Nucleic acids (DNA & RNA) are require for storage and
expression of genetic information. DNA is the repository
of genetic information present in the chromosomes in the
nucleus of eukaryotic organism.

3. Central dogma of life/molecular biology
• The flow of information from DNA to RNA to protein is
termed the “central dogma” of life or molecular biology.
This is descriptive of all organisms with the exception of
some viruses that have RNA as the repository of their
genetic information.

4. Structure of DNA
• Polymer of deoxyribonucleoside monophosphate
covalently linked by 3´-5´ phosphodiester bond. DNA is
found associated with various protein known as
nucleoprotein present in the nucleus
• DNA chain with the nucleotide sequence written in the
5´-3´ and another 3´-5´ direction.
• DNA chain is more stylized form as sugar (ribose)-
phosphate backbone.

5. 3´-5´ phosphodiester bonds
• Phosphodiester bonds join the 3´-hydroxyl group of the
deoxypentose of one nucleotide to the 5´-hydroxyl
group of the deoxypentose of adjacent nucleotide
through a phosphate bond. The resulting long
unbranched chain chain has polarity with both a 5´ end
(free end with a free phosphate) & 3´ end with a free
hydroxyl group –that are not attached to other
nucleotides.
• The bases located along the resulting deoxyribose-
phosphate backbone are always written in sequence from
the 5´-end of the chain to the 3´-end, (5´-TACGTA-3´).

6. • Phosohodiester linkage between nucleotides (in DNA or
RNA) can be cleaved hydrolytically by chemicals or
hydrolyzed enzymatically by a family nucleases
deoxyribonucleases for DNA and ribonucleases for RNA
• ** only RNA is cleaved by alkali.

7. Double helix
• In the double helix the two chains are coiled around a
common axis called the axis of symmetry. The chains
are paired in an antiparallel manner- that 5´ end of one
strand is paired with 3´ end of the other strand.
• In the DNA helix, the hydrophilic deoxyribose
phosphate backbone of each chain is on the outside of
the molecule, whereas the hydrophobic bases are stacked
inside. The overall structure resembles a twisted ladder.
The spatial relationship between two strands relationship
between two strands in the helix creates major and minor
groove.
• This groove are the binding site for regulatory protein
and certain anticancer drug e.g. actinomycin

8. Base pairing
• The bases of one stand of DNA always bind with the
bases of the second strand. Adenine always binds with
thymine and cytosine with guanine.
• Chargaff rule: in any sample of dsDNA the amount of
adenine equals to the amount of thymine and the
cytosine equals to guanine and the total amount of
purines are equals to the total amount of pyrimidines.
• The base pair are held together by hydrogen bond. Two
hydrogen bond between A & T, and three hydrogen
bond between C & G. This hydrophobic interaction
stabilize the structure the double helix.

9. Separation of two DNA strand in the double helix
• The two strands of the double helix separate when
hydrogen bonds between the paired bases are disrupted.
• Disruption can occur in the laboratory by altered pH of
the solution, or by heating.
• DNA is heated, the temperature at which one half of the
helical structure is lost is defined as melting structure, the
loss of helical structure in DNA is called denaturation, can
be monitored by measuring its absorbance at 260 nm.

10. Structural form the double helix
• There are three major structural forms of DNA-
• B form described by watson and crick & right handed
helix.
• A form produced by moderate dehydration from B form
& right handed helix
• Z /zigzags form is left handed helix
• Transition between B and Z forms may play a role in
regulating gene expression.