DR VISHNU KUMAR

1. Dr. Vishnu Kumar
Professor & Head, Department of
Biochemistry, MPTMC, SIDDHARTH NAGAR
vkawasthi@hotmail.com
madhwapur1976@gmail.com
Nucleic Acid Chemistry
Competency Number BI: 7.1
CORE COMPETENCY

2. LEARNING OBJECTIVES
After completion of this lecture learner
should be able to define/ describe
 Structure of DNA
 Types of DNA
 Structure of RNA
 Types of RNA
 Primary transcript

3. Structure of DNA
 Consists of 2 helical chains wound round
the same axis to form a right handed
double helix.
 Monomeric units are dAMP, dGMP , dCMP,
and TMP linked by 3’ 5’ phospho diester
bonds
 Base pairing—A &T with 2 hydrogen
bonds and G & C with 3 hydrogen bonds.


4. DNA Structure
 Two strands are anti parallel.
 In the double helix d ribose &
phosphate groups are on the outside
facing the water, and bases are present
inside.
 The structure resembles a twisted
ladder, producing Major & Minor
grooves.

7. Physical properties of DNA
 Denaturation– separation of two strands by
increasing temperature--Hydrogen bonds are
broken, loss of viscosity.
 Hyperchronicity of denaturation– increase of
optical absorbance of bases.
 Melting temperature (Tm)– temperature at
which half the d/s structure is lost.
 Hybridization.– Pairing between DNA& RNA--
formation of DNA-RNA hybrid.
 DNA super coiling.

8. Types of DNA
 A, B, C, D, E &Z.
 B form--, 10 bp/ turn. 3.4 nm/ turn, 2 nm in
width, Rt. Handed double helix. Vast majority
of DNA in living cells exist in B – form.
 A form– 11 bp/ turn. Rt. Handed double
helix.
 Z form– Zigzag structure, 12 bp/ turn. Left
handed double helix.

10. Circular DNA
 Prokaryotic organisms contain d/s
circular chromosomal DNA.
 Eukaryotic organisms have circular DNA
in mitochondria.
 Extra chromosomal circular DNA
present in bacteria.

11. Mitochondrial DNA
 Human Mitochondria contains 2-10
copies of small circular DNA.
 Constitutes 1% of cellular DNA.
 Codes for mitochondrial rRNA,
mitochondrial tRNA and 13 proteins of
respiratory chain.
 Maternal inheritance.

14. RNA
 Definition– polymer of purine and pyrimidine
ribonucleotides ( A,G,C,U,) linked by phospho
diester linkage.
 Single stranded. RNA strand is
complementary to one strand of DNA called
the template strand. It is identical with the
other strand called the coding strand except it
has U for T.

15. Difference between RNA &
DNA
 RNA DNA
 Ribose Deoxy ribose.
 A,G,C,U. A,G,C,T.
 Single strand. Double strand.
 G is not equal to C G=C.
 A is not equal to T A=T.
 Alkali hydrolysis + negative.
 Protein synthesis. Transmits genetic
information.

16. Types of RNA.
 Messenger RNA- mRNA.
 Heterogeneous nuclear RNA- hn RNA.
 Transfer RNA- tRNA.
 Ribosomal RNA- rRNA.
 Small nuclear RNA- snRNA

17. Types of RNA.
 RNA as enzyme- Ribozyme.
 RNA as genetic material- RNA virus.
 Micro- RNA- mi RNA.
 Small interfering RNA- si RNA.

18. m RNA
 Heterogeneous in size, abundance and
stability.
 All members of this class function as
messengers conveying the information in a
gene to the protein synthesizing machinery,
where each mRNA serves as a template on
which a specific sequence of amino acids is
polymerized to form specific protein molecule.

19. Structure of mRNA
 5’ end is ‘capped’ by 7 methyl
guanosine tri phosphate which stabilizes
the mRNA. Also involved in recognition
of mRNA by the protein synthesizing
machinery.
 3’ end has a polymer of 20-250
nucleotides called ‘poly A’ tail. It
stabilizes the mRNA.

21. Primary transcript.
 In mammalian cells the mRNA
molecules are not synthesized directly
from DNA.
 From DNA pre-RNA is formed which is
processed to form the mRNA.
 This primary transcript or pre-RNA is
called heterogeneous nuclear RNA.

22. Transfer RNA.
 74-95 nucleotide in length.
 Generated by nuclear processing of a
precursor molecule.
 Function– Translation of information
present in the nucleotide sequence of
mRNA into amino acid sequence of
protein.
 20 species in each cell.

23. Structure of t RNA
It has five arms.
 Accepter arm.
 Anticodon arm.
 D-arm.
 T C arm.
 Extra arm.
 Clover leaf appearance.

25. Ribosome
 Cytoplasmic nucleoprotein, that acts as
machinery for protein synthesis. On the
ribosome mRNA &tRNA molecule
interact to translate the information in a
gene into a specific protein molecule.
 Mammalian ribosome has sedimentation
velocity coefficient of 80 S. It contains 2
subunits 60 S & 40 S.

27. Ribosomal RNA
 Contributes to the formation of
ribosome.
 60 S ribosomal subunit contains 5S,
5.8S& 28S ribosomal RNA and 50
polypeptides.
 40S ribosomal subunit contains 18S
rRNA and 30 distinct polypeptides.

28. Small RNA
 A large number of small RNA species
are found in eukaryotic cells.
 Most of them are complexed with
protein, and distributed in the nucleus,
the cytoplasm ,or both.
 20- 300 nucleotides in length.

29. Small nuclear RNA
 Sn RNA– A subset of small RNAs,
involved in mRNA , rRNA processing
and gene regulation.
 U1, U2, U4, U5 & U6 are involved in
intron removal.
 Uracil rich .

30. Other RNAs
 Ribozymes – SnRNA, peptidyl transferase,
RNAse P are example.
 RNA acting as genetic material- - RNA
virus.
 Micro RNAs– 21-25 nucleotide in length.
They cause inhibition of gene expression.
 Si RNAs– also cause inhibition of gene
expression.
 Both mi RNAs & si RNAs are potential
targets for therapeutic drug development.

31. Nucleases
 Enzymes capable of degrading nucleic
acids.
 Two classes– deoxy- ribonucleases &
ribonucleases.
 Both classes have endonucleases &
exonucleases.