NUCLEIC ACIDS BY VANA JAGAN MOHAN RAO

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

2. 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.

3.  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 ...”

4.  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

5. • 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.

6. • 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.

7. • 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”.

8. 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).

10. THE STRUCTURE OF NUCLEIC ACID CHAINS
• 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.

11. 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).

12. -12
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.

13. 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.

14. 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.

15. 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

16. 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?

17. 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.

18. (a) Notice that the base pairs are nearly  to the
sugar–phosphate backbones. (b) A space-filling
model of the same DNA segment. (c) An abstract
representation of the DNA double helix.

19. DNA, CHROMOSOMES AND GENES
• When a cell is not actively dividing, the DNA
(a polymer of deoxyribonucleic acid) is
twisted around proteins called histones –
this complex is called chromatin.
• During cell division, chromatin organizes
itself into chromosomes. Each chromosome
contains a different DNA molecule, and the
DNA is duplicated so that each new cell
receives a complete copy.

20. Each DNA molecule, in turn, is made up of
many genes—individual segments of DNA
that contain the instructions that direct the
synthesis of a single polypeptide.

21. • The duplication, transfer, and expression of
genetic information occurs as the result of
three fundamental processes: replication,
transcription, and translation.
• Replication: The process by which copies of
DNA are made when a cell divides.
• Transcription: The process by which the
information in DNA is read and used to
synthesize RNA.
• Translation: The process by which RNA
directs protein synthesis.

22. • (a) DNA unwinds,
exposing single
strands.
• (b) Single-
stranded DNA is
exposed at
numerous
replication forks
as DNA unwinds.
• (c) DNA
polymerase
enzymes
facilitate copying
of the single-
stranded DNA.
-22

23. • DNA polymerase
catalyzes the
reaction between
the 5’ phosphate
on an incoming
nucleotide and the
free 3’ –OH on the
growing
polynucleotide.
• The template
strand can only be
read in the 3’ to 5’
direction, and the
new DNA strand
can grow only in
the 5’ to 3’
direction.

24. • Only the leading
strand grows
continuously from
5’ to 3’ towards the
fork.
• The lagging strand
is replicated
from 5’ to 3’
in short segments
called Okazaki
fragments.
• These short
sections are joined
later by DNA ligase.

25. Two identical copies of the DNA double helix
are produced during replication. In each new
double helix, one strand is the template and the
other is the newly synthesized strand. We
describe the result as semi conservative
replication (one of the two strands is
conserved).

26. Structure and Function of RNA
• Ribosomal RNAs: Outside the nucleus but within the
cytoplasm of a cell are the ribosomes, small granular
organelles where protein synthesis takes place. Each
ribosome is a complex consisting of about 60%
ribosomal RNA (rRNA) and 40% protein, with a total
molecular weight of approximately 5,000,000 amu.
• The transfer RNAs (tRNA) are smaller RNAs that
deliver amino acids one by one to protein chains
growing at ribosomes. Each tRNA carries only one
amino acid.

27. The messenger RNAs (mRNA) carry
information transcribed from DNA. They are
formed in the cell nucleus and transported out
to the ribosomes, where proteins will be
synthesized. These polynucleotides carry the
same code for proteins as does the DNA.

28. 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.

29. • 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.

31. • 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.

32. • 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.

33. 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). )

35. 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.

36. • 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.

37. • 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.

38. • 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.

39. 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.