NUCLEIC ACID

Nitrogenous
base + sugar = Nucleosides + Phosphoric
acid =Nucleotides

Cytosine

Purine Pyrimidine Thymine

Uracil
Adenine Guanine

Nucleic acid

DNA
• Nitrogenous base
• Pentose sugar
• Phosphoric acid

RNA
• Nitrogenous base
• Pentose sugar
• Phosphoric acid
 Double helical structure of DNA –Watson –Crick Model
• Purine –purine pairing is too long to get accommodated in the
prescribed groove in Watson –Crick Model
• Pyrimidine-pyrimidine pairing is too short in the prescribed
groove diameter of Watson –Crick Model
• Therefore, most appropriate base pairing is Purine-pyrimidine
Chargaff’s Rule
Adenine must pair with Thymine
Guanine must pair with Cytosine
The bases form weak hydrogen bonds
• 10 base pairing stacked upon each other like coins in a groove
• Purine and pyrimidine bases are stacked inside with their
hydrophobic planar ring structure with very close proximity and
perpendicular to central axis
• Sugar and phosphate groups joined by phosphodiester bonds
are in outward direction facing the surrounding water
• DNA backbone are bonded together by phosphodiester linkage
between 3΄& 5ʹcarbons.
• Right handed helix
• Rise= 0.33 nm/nt
Why DNA is helix?The tendency towards a helix comes from the stacking of the individual bases on top of one
• Pitch=3.4 nm/turn another. Both the sugar and phosphate which constitute the backbone are quite soluble in water. However, the
• DNA bases which are in the middle of the helix are relatively hydrophobic and insoluble. the bases are flat, they
10.4 nt/turn
stack on top of each other in order to form a more hydrophobic ‘mini-environment’. Thus the reason for a helix in
• Two grooves-major and minor DNA is primarily due to the hydrophobic stacking interactions of the bases.
 Directionality of DNA
Carbons are numbered clockwise 1’ to 5’

Antiparallel orientation: DNA molecule has “direction.“

One strand of DNA goes from 5’ to 3’ (sugars)
The other strand is opposite in direction going 3’ to 5’
(sugars)
Complementary strands run in opposite directions.
• DNA has to be copied before a cell Replication: Facts
divides
• New cells will need identical DNA
strands
• DNA is copied during the S or synthesis
phase of interphase
• Nucleus of eukaryotes
• Replication fork movement is
bidirectional
• 3 proposed Models of Replication S e m i co n s e r va t i v e r e p l i c a t i o n

• Semiconservative: New duplex is

1/2 parent template &
1/2 new DNA
Co n s e r va t i v e
replication

Dispersive
re p lica t i o n
 • Begins at Origins of Replication
• Region is AT rich to allow easy separation
• As the 2 DNA strands open at the origin,
Replication Bubbles form
• Prokaryotes (bacteria) have a single bubble
• Eukaryotic chromosomes have MANY bubbles
• Two strands open forming Replication Forks (Y-
shaped region)
• New strands grow at the forks
3’

Parental DNA Molecule

5’ Replication
Fork
3’
 Large team of enzymes coordinates replication
• Helicase unwinds and separates the 2 DNA strands by breaking the weak hydrogen
bonds
• Single-Strand Binding Proteins attach and keep the 2 DNA strands separated and
untwisted
• DNA gyrase prevents tangling upstream from the replication fork i.e. relieve topological
stress on the DNA molecule as it separates
 Elongation: 2nd Step
• Before new DNA strands can form, there must be RNA primers present to start the
addition of new nucleotides
• Primase is the enzyme that synthesizes the RNA Primer to the 3’ end of template
DNA
• DNA polymerase can only add the new nucleotides to existing strands of DNA
• This causes the NEW strand to be built in a 5’ to 3’ direction
• RNA primer serves as starter sequence for DNA polymerase III. RNA Primer has a
free 3’OH group to which the first Nucleotide is bound. 5

3 5 3
5
3
3 5

growing 3 primase
replication fork DNA polymerase III
5

RNA 5

3
 Leading & Lagging strands
Limits of DNA polymerase III
 can only build onto 3 end of
an existing DNA strand 5


rag ments
ki f
Okaza 5
3 5 5 3
3
5 Lagging strand
3
ligase
growing 3
replication fork
5
Leading strand

Lagging strand
3
5

3
DNA polymerase III
 Okazaki fragments
 joined by ligase Leading strand
 “spot welder” enzyme  continuous synthesis
 • Replacement of RNA primer done by DNA polymerase I (i.e. exonuclease
activity)
• Strands are glued by Ligase by forming phosphodiester bonds between
nucleotides DNA polymerase I
5
• DNA Pol has a proofreading mechanism built in
3

3
5 ligase
growing 3
replication fork
5

RNA 5

3

ALL DNA Pol’s have 2 properties

Only synthesize DNA in one direction 5’ to 3’ (i.e. 5’ to 3’polymerase activity)
Only add to the end of existing double stranded DNA

Therefore they CANNOT start synthesis of DNA from scratch.

RNA polymerases can, but not DNA polymerases
Differences between DNA Polymerase I, II and III
 • In prokaryotes:
• DNA replication terminates when replication forks reach specific “termination sites”.
• the two replication forks meet each other on the opposite end of the parental circular DNA .
DNA
polymerase III lagging strand
DNA
polymerase I
3’
Okazaki primase
fragments 5’
5’ ligase
3’ 5’ SSB

3’ helicase

DNA
polymerase III
5’ leading strand
3’
direction of replication
SSB = single-stranded binding proteins
In Eukaryotes:

In eukaryotic replication, following removal of RNA Primer from the 5’end of lagging strand; a gap is
left.
This gap exposes DNA strand to attack of 5’ exonucleases.
This problem is overcome by Telomerase.