The document discusses nucleic acids and their role in genetics. It begins by defining nucleic acids as important biopolymers that contain genetic information and facilitate its transfer between generations. It then describes the two main types of nucleic acids: DNA and RNA. DNA contains the full genetic code and resides in the nucleus, while RNA carries messages from DNA and has various functions. The document proceeds to discuss the composition, structure, and functions of nucleic acids in more detail.

1. V.JAGAN MOHAN RAO M.S.Pharm., MED.CHEM
NIPER-KOLKATA
Asst.Professor, MIPER-KURNOOL
EMAIL- jaganvana6@gmail.com

2. It can be said that nucleic acid is one of the most important
biopolymers.
They are present in all organisms. Think of them as the
mother chip of your body. This is where
your genetic information is encoded and recorded.
The function of nucleic acid is to express this information
outside the cell to the future generation. So it felicitates the
transfer of genetic information from one generation to the next
and so onwards.
Now nucleic acids are big and complex molecules. They have
a linear binding between nucleotides. They are double-
stranded and have highly complex sequencing.
INTRODUCTION

3. TYPES OF NUCLEIC ACIDS

4. There are approximately 200 types of cells in our bodies like white
blood cells, neurons (brain cells), cardiac muscle cells etc.
But how do these cells know their particular function? Well, their
chemical compositions within their cells differ. The cells get their
instructions from this biopolymer that is Deoxyribonucleic Acid.
This information is the DNA code. This code forms due to the
sequencing of the nucleotides in the polymer chain. The DNA has
very long chains of nucleotides in their molecules and hence there
are billions upon billions of sequences possible. This is the reason all
of our DNA sequences are unique only to us.
Did you know that 99.9% of DNA is the same in all us humans?
Only 0.01% of our DNA coding is special and different for every
human. This is what makes every individual unique.
DEOXYRIBO NUCLEIC ACID (DNA)

5. RIBO NUCLEIC ACID (RNA)
Ribonucleic Acid is absolutely essential for our survival. RNA is
actually the blueprint of our DNAs.
While the DNA is always inside the nucleus of our cells, the RNA
travels outside the nucleus to perform its functions. There are
actually three types of Ribonucleic Acids, namely:
Ribosomal RNA: Is the main part of the ribosome, which is where
the protein maker of our bodies.
Messenger RNA: This RNA carries the message outside from the
nucleus. It carries the information about what type of protein cells
are to be manufactured.
Transfer RNA: It brings the amino acid to the ribosome for protein
production.

6. COMPOSITION OF NUCLEIC ACIDS
• Nucleic acid: A polymer of nucleotides.
• Nucleotide: A five-carbon sugar bonded to a
cyclic amine base and a phosphate group.

7.  DNA and RNA are two types of nucleic acids.
 In RNA (ribonucleic acid) the sugar is D-ribose.
 In DNA (deoxyribonucleic acid) the sugar is 2-
deoxyribose. (The prefix “2-deoxy-” means that an
oxygen atom is missing from the C2 position of
ribose.)
 Also may be spelled “desoxy ...”

8.  Five heterocyclic amines are found in nucleic acids.
 Thymine is present only in DNA molecules (with rare
exceptions).
 Uracil is present only in RNA molecules.
 Adenine, guanine, and cytosine are present in both
DNA and RNA.
 A, G are Purines & C, T, and U are Pyrimidine

9. • Nucleoside: A five-carbon sugar bonded to a
cyclic amine base; a nucleotide with no
phosphate group.
• Nucleosides are named with the base name
modified by the ending –osine for the purine
bases and -idine for the pyrimidine bases.

10. • Deoxy- is added to deoxyribose nucleosides.
• Numbers with primes are used for atoms in the sugar.
• Nucleotides are named by adding 5’-monophosphate
at the end of the name of the nucleoside.

11. • For example, adenosine 5’-monophosphate (AMP) and
deoxycytidine 5’-monophosphate (dCMP).
• Nucleotides that contain ribose are classified as
ribonucleotides and those that contain 2-deoxy-D-
ribose are known as deoxyribonucleotides
designated by leading their abbreviations with a lower
case “d”.

12. Phosphate groups can be added to nucleotides
to form diphosphate or triphosphate esters.
Adenosine triphosphate (ATP) plays an
essential role as a source of biochemical energy,
which is released during its conversion to
adenosine diphosphate (ADP).

14. FORMATION OF NUCLEIC ACID BACKBONE
• Nucleic acids are polymers of nucleotides. The
nucleotides are connected in DNA and RNA by
phosphate diester linkages between the group
on the sugar ring of one nucleotide and the
phosphate group on the next nucleotide.
• The “repeat unit” of the monomer is the sugar
ring and phosphodiester unit – because the
base changes, we can think of this as a
copolymer. The chemistry of the backbone is
identical for all of the nucleotides.

15. A nucleotide chain commonly has a free
phosphate group on a 5’ carbon at one end
(known as the 5’ end) and a free –OH group
on a 3’ carbon at the other end (the 3’ end).

16. 16
A nucleotide
sequence is read
starting at the 5’
end and
identifying the bases in order
of occurrence. One-letter
abbreviations of the bases are
commonly used : A for
adenine, G for guanine, C for
cytosine, T for thymine, and U
for uracil in RNA. The
trinucleotide at right would
be represented by T-A-G or
TAG.

17. Base Pairing in DNA: Watson-Crick
• The double helix resembles a twisted ladder,
with the sugar–phosphate backbone making
up the sides and the hydrogen-bonded base
pairs, the rungs. The sugar–phosphate
backbone is on the outside of this right-
handed double helix, and the heterocyclic
bases are on the inside, so that a base on
one strand points directly toward a base on
the second strand.

18. The two strands of the DNA double helix run in opposite
directions, one in the 5’ to 3’ direction, the other in the 3’ to
5’ direction.

19. a-Helix
Hydrogen bonds are between the C=O of peptide bond and
the H-N of another peptide linkage 4 AA’s further along
the chain.
Grey = C
Blue = N
Red = O
Yellow = R-
group
White = H

20. Hydrogen bonds connect the pairs of bases; thymine with adenine, cytosine
with guanine. Thus a Purine always pairs with a pyrimidine. What would
happen if not? What would happen if we had C-A or G-T pairs?

21. The pairing of the bases along the two strands of
the DNA double helix is complementary. An A
base is always opposite a T in the other strand, a
C base is always opposite a G. This base pairing
explains why A and T occur in equal amounts in
double-stranded DNA, as do C and G. To
remember how the bases pair up, note that if the
symbols are arranged in alphabetical order the
outer 2 and inner 2 pair up.

22. Chemical and Physical Properties of Nucleic Acids
1. Stability of Nucleic Acids
2. Effect of Acid & applications
3. Effect of alkali & applications
4. Chemical denaturation
5. Viscosity & applications
6. Buoyant density & application
Chemical properties
Physical properties

23. Stability of Nucleic Acids
1. Hydrogen bonding
• Does not normally contribute the stability of nucleic acids or
protein
• Contributes to specific structures of these macromolecules.
For example, a-helix, b-sheet, DNA double helix, RNA
secondary structure
2. Stacking interaction/hydrophobic interaction between
aromatic base pairs/bases contribute to the stability of nucleic
acids.
• It is energetically favorable for the hydrophobic bases to
exclude waters and stack on top of each other
• This stacking is maximized in double-stranded DNA

24. Effect of Acid
Strong acid + high temperature: completely
hydrolyzed to bases, riboses/deoxyrobose, and
phosphate
pH 3-4 : apurinic nucleic acids [glycosylic bonds
attaching purine (A and G) bases to the ribose
ring are broken ], can be generated by formic acid

25. Effect of Alkali & Application
keto form enolate form keto form
enolate form
Base pairing is not stable anymore because of the change of tautomeric states of
the bases, resulting in DNA denaturation
1. High pH (> 7-8) has subtle (small) effects on DNA structure
2. High pH changes the tautomeric state of the bases

26. RNA hydrolyzes at higher pH because of 2’-OH
groups in RNA
RNA is unstable at higher pH
OH free 5’-OH
2’, 3’-cyclic
phosphodiester
alkali

27. Chemical Denaturation
Urea (H2NCONH2) : denaturing PAGE
Formamide(HCONH2) : Northern blot
Disrupting the hydrogen bonding of the bulk
water solution
Hydrophobic effect (aromatic bases) is reduced
Denaturation of strands in double helical structure

28. Viscosity
Reasons for the DNA high viscosity
1. High axial ratio
2. Relatively stiff
Applications:
Long DNA molecules can easily be shortened by
shearing force. Remember to avoid shearing
problem when isolating very large DNA molecule.

29. Buoyant density (DNA)
1.7 g cm-3, a similar density to 8M CsCl
Purifications of DNA: equilibrium density gradient centrifugation
RNA pellets at the bottom
Protein floats

30. CENTRAL DOGMA PROCESS

31. Transcription: RNA Synthesis
• Only one of the two DNA strands is transcribed
during RNA synthesis. The DNA strand that is
transcribed is the template strand; its
complement in the original helix is the
informational strand.
• The mRNA molecule is complementary to the
template strand, which makes it an exact RNA-
duplicate of the DNA informational strand, with
the exception that a U replaces each T in the
DNA strand.

32. • The transcription process begins when RNA
polymerase recognizes a control segment in
DNA that precedes the nucleotides to be
transcribed.
• The sequence of nucleic acid code that
corresponds to a complete protein is known as
a gene.
• The RNA polymerase moves down the DNA
segment to be transcribed, adding
complementary nucleotides one by one to the
growing RNA strand as it goes.
• Transcription ends when the RNA polymerase
reaches a codon triplet that signals the end of
the sequence to be copied.

34. • Some of these bases, however, do not code
for genes. It turns out that genes occupy
only about 10% of the base pairs in DNA
• The code for a gene is contained in one or
more small sections of DNA called an exon.
• The code for a given gene may be
interrupted by a sequence of bases called an
intron. Introns are sections of DNA that do
not code for any part of the protein to be
synthesized.

35. • The initial mRNA strand contains both exons
and introns, and is known as heterogeneous
nuclear RNA (or hnRNA).
• In the final mRNA molecule released from the
nucleus, the intron sections have been cut out
and the remaining pieces are spliced together
through the action of a structure known as a
spliceosome.

36. The Genetic Code
• Codon: A sequence of three ribonucleotides in the messenger RNA chain
that codes for a specific amino acid; also a three-nucleotide sequence that
is a stop codon and stops translation.
• Genetic code: The sequence of nucleotides, coded in triplets (codons) in
mRNA, that determines the sequence of amino acids in protein synthesis.
• Of the 64 possible three-base combinations in RNA, 61 code for specific
amino acids and 3 code for chain termination.
• A codon is the triplet sequence in the messenger RNA (mRNA) transcript
which specifies a corresponding amino acid (or a start or stop command).
An anticodon is the corresponding triplet sequence on the transfer RNA
(tRNA) which brings in the specific amino acid to the ribosome during
translation. The anticodon is complementary to the codon, that is, if the
codon is AUU, then the anticodon is UAA. (No T (Thymine) in mRNA. It's
replaced by U (Uridine). )

38. Translation: Transfer RNA and Protein Synthesis
• Overview: The codons of mature
mRNA are translated in the
ribosomes, where tRNAs deliver
amino acids to be assembled into
proteins (polypeptides).
• The three stages in protein
synthesis are initiation,
elongation, and termination.
• Just like there can be many
replication forks, more than one
ribosome can attach to long
mRNA, and translate more than
one copy of the protein at once.

39. • Structure of tRNA.
(a) The cloverleaf
shaped tRNA
contains an
anticodon triplet and
a covalently bonded
amino acid at its 3’
end.
• Notice that ssRNA
can base pair to form
hydrogen-bonded
stretches. These
sections stabilize the
tRNA’s folded
structure making the
codon and AA
available for binding
and reaction.

40. • Initiation: Protein synthesis begins when an mRNA,
the first tRNA, and the small subunit of a ribosome
come together.
• The first codon on the end of mRNA, an AUG, acts as
a “start” signal for the translation machinery and
codes for a methionine carrying tRNA. In some
organisms this is “fmet” – N-formylmethionine. fMet
is found only as AA 1 in proteins (if it is found).
• Initiation is completed when the large ribosomal
subunit joins the small one and the methionine-
bearing tRNA occupies one of the two binding sites
on the united ribosome.
• If it is not needed, the methionine from chain
initiation is removed by post-translational
modification before the new protein goes to work.

41. • The three elongation
steps now repeat:
• The next tRNA binds
to the ribosome.
• Peptide bond
formation attaches
the new amino acid to
the chain and the first
tRNA is released.
• Ribosome position
shifts to free the
second binding site
for new tRNA.

42. Termination: A “stop” codon signals the end of
translation. An enzyme called a releasing factor
then catalyzes cleavage of the polypeptide
chain from the last tRNA. The tRNA and mRNA
molecules are released from the ribosome, and
the two ribosome subunits again separate.