The nucleic acids

1. THE NUCLEIC ACIDS
By- Sanju Sah
St. Xavier’s College, Maitighar, Kathmandu
Department of Microbiology

2. FRIEDRICH MIESCHER IN 1869
•isolated what he called nuclein from the nuclei of pus cells
•Nuclein was shown to have acidic properties, hence it
became called nucleic acid
Discovery of the DNA double helix
A. Frederick Griffith – Discovers that a factor in
diseased bacteria can transform harmless
bacteria into deadly bacteria (1928)
B. Rosalind Franklin - X-ray photo of DNA. (1952)
C. Watson and Crick - described the DNA
molecule from Franklin’s X-ray. (1953)

3. Central dogma of molecular biology

4. FUNCTIONS OF NUCLEIC ACIDS
• Chemical basis of heredity and reserve bank of genetic
information.
• Responsible for maintaining the identity of different
species of organisms.
• Every aspect of cellular function is under the control of
DNA.
• DNA is organized into genes (fundamental units of
genetic information).
• Genes control the protein synthesis through the
mediation of RNA.

5. OTHER FUNCTIONS
• They are the building blocks of DNA, RNA.
• They are structural units of cofactors such as
NAD, FAD, FMN and NADP
.
• Some nucleotide act chemical messenger such
as cAMP
, cGMP
.
• Nucleotides are also energy rich compounds for
example ATP
, ADP
, GTP
.
• flavin adenine dinucleotide
• Nicotinamide adenine dinucleotide
• Flavin mononucleotide
• Nicotinamide adenine dinucleotide phosphate

6.  TWO TYPES OF NUCLEIC ACID ARE
FOUND
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
 The distribution of nucleic acids in the eukaryotic cell
• DNA is found in the nucleus with small amounts in
mitochondria and chloroplasts
• RNA is found throughout the cell
 NUCLEIC ACID STRUCTURE
• Nucleic acids are polynucleotides
• Their building blocks are nucleotides

7. NUCLEOTIDES
Nucleic acids consist of nucleotides that have a sugar,
nitrogen base, and phosphate
7
Sugar
Base
PO4
nucleoside

8. NITROGENOUS BASES
• PURINES
1. Adenine (A)
2. Guanine (G)
• PYRIMIDINES
3. Thymine (T)
4. Cytosine (C)
T or C
A or G

9. NUCLEOSIDES IN DNA
Base Sugar Nucleoside
Adenine (A) Deoxyribose Adenosine
Guanine (G) Deoxyribose Guanosine
Cytosine (C) Deoxyribose Cytidine
Thymine (T) Deoxyribose Thymidine
9
Nucleosides in RNA
Base Sugar Nucleoside
Adenine (A) ribose Adenosine
Guanine (G) ribose Guanosine
Cytosine (C) ribose Cytidine
Uracil (U) ribose Uridine

10. NUCLEOTIDE STRUCTURE
PHOSPATE SUGAR
Ribose or
Deoxyribos
e
NUCLEOTIDE
BASE
PURINES PYRIMIDINES
Adenine (A)
Guanine(G)
Cytocine (C)
Thymine (T)
Uracil (U)

11. RIBOSE IS A PENTOSE
C1
C5
C4
C3 C2
O

12. RIBOSE DEOXYRIBOSE
CH2OH
H
OH
C
C
OH OH
C
O
H H
H
C
CH2OH
H
OH
C
C
OH H
C
O
H H
H
C
Spot the difference

13. THE SUGAR-PHOSPHATE BACKBONE
• The nucleotides are all
orientated in the same direction
• The phosphate group joins the
3rd Carbon of one sugar to the
5th Carbon of the next in line.
P
P
P
P
P
P

14. ADDING IN THE BASES
• The bases are attached to
the 1st Carbon
• Their order is important
It determines the genetic
information of the molecule
P
P
P
P
P
P
G
C
C
A
T
T

15. DNA IS MADE OF TWO
STRANDS OF
POLYNUCLEOTIDE
P
P
P
P
P
P
C
G
G
T
A
A
P
P
P
P
P
P
G
C
C
A
T
T
Hydrogen bonds

16. DNA IS MADE OF TWO STRANDS OF
POLYNUCLEOTIDE
• The sister strands of the DNA molecule run in opposite
directions (antiparallel)
• They are joined by the bases
• Each base is paired with a specific partner:
A is always paired with T
G is always paired with C
Purine with Pyrimidine
• This the sister strands are complementary but not identical
• The bases are joined by hydrogen bonds, individually weak
but collectively strong

17. • Chargaff’s Rule: His data showed that in each species, the
percent of A equals the percent of T, and the percent of G
equals the percent of C.

18. WATSON & CRICK BASE
PAIRING

19. DOUBLE HELIX OF DNA19
Francis Crick and
James Watson with
Maurice Wilkins
received the 1962
Nobel Prize for
discovering the
molecular structure of
deoxyribonucleic acid
(DNA).

20. CONFORMATIONS OF DNA DOUBLE
HELIX
• The double helical structure of DNA exsits in at least 6
different forms A to E and Z.
• Among these B, A and Z forms are common.
B-form:
• B-form of DNA double helix, described by Watson and
Crick, is the most predominant form under physiological
conditions.
• Exists when plenty of water surrounds the molecule and
there is no usual base sequence in the DNA.
• Each turn of the B-form has 10 base pairs, each pair
placed at a distance of about 3.4 nm.
• The width of the double helix is 2 nm.

21. A-form:
• Right-handed helix.
• Exits when less water is present.
• Contain 11 base pairs per turn.
• It is shorter and wider than B- DNA
Z-form:
• Left-handed helix.
• Contain 12 base pairs per turn.
• Phosphodiester bridges are formed zig zag and are
thinnest

22. C-DNA:
• Right handed with an axial rise of 3.32 A
• There are 9.33 base pair per turn of helix.
• Tilt of base pairs is 7.8 degree.
D-DNA:
• 8 base pairs per helical turn.
• An axial rise of 3.03 A per base pair.
• Tilting of 16.7 degree from the axis of the helix.

23. OTHER TYPES OF DNA
STRUCTURE
• Besides double helical
structure, DNA also exists in
certain unusual structure.
Triple stranded DNA:
• Occur due to additional
hydrogen bonds between the
bases.
• Less stable than double helix
due to three negatively
charged back bone strands
results in increased
electrostatic repulsion.

24. • Usually found in polypyrimidine or polypurine
segments that contains within themselves a mirror
repeat.
• Example is a long stretch of alternating T and C
residues in fig.
• Triple- helical DNA is produced only within long
sequences containing only pyrimidines or purines
in one strand.
• Two of the three strands in the triple helix contain
pyrimidines and the third containes purines.

25. Bent DNA
• Produces whenever 4 or more adenine residue appear
sequentially in one of the two strands.
• Six adenine in a row produce a bends of about 18 degree.
• Bending may important in the binding of some proteins to
Four stranded DNA:
• G-quadruplexes (also known as G-tetrads) are nucleic acid
sequences that are rich in guanine and are capable of forming
a four-stranded structure.
• The ends of eukaryotic chromosomes namely telomeres are
rich in guanine, and therefore form G-tetraplexes.
• The formation of these quadruplexes in telomeres has been
shown to decrease the activity of the enzyme telomerase,
which is responsible for maintaining length of telomeres.

27. Denaturation of dsDNA:
• Double stranded DNA is held together by hydrogen bonds
• the double helix can be denatured in different ways: heat, pH
(acid & alkali), chemicals etc
• dissociation by heating is also named melting
hyperchromicity effect : disruption of the stacking
=> 30 to 40 % increase of UV (260 nm)absorption
Decrease in specific optical rotation:
Decrease in viscosity:

28. Tm : melting temperature
• position in melting profile where 50% is single-
• pseudo-monomolecular reaction: strands are not
physically separated (but A-T rich zones 'melt' first)
(dynamic equilibrium)
- linear relationship between Tm and % G+C of a duplex
- physical separation requires temperatures far above Tm
- upon fast chilling : nucleic acid remains single-stranded
- slow cooling is necessary to enable the base-pairs (and
stacking) to rebuild

29. Renaturation
- renaturation is not simply the reverse of denaturation
- collision of complementary strands required
- nucleic acid strands are negatively charged in the phosphate
moiety
- charge per nucleotide => repulsion
=> hence : requires shielding to allow strands to
approach one another (use of Na+ or K+ salts)
- four parameters in renaturation kinetics
1) concentration of cations
2) incubation temperature (usually 20 to 25 °C below Tm)
3) DNA concentration (related to complexity of the DNA
see below)
4) size of the fragments