Download Module 14 Nucleic Acids Lecture 36 Nucleic Acids I

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Module 14 Nucleic Acids
Lecture 36 Nucleic Acids I
Nucleic acids are targets of many important drugs, including several anticancer agents.
There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). DNA encodes the hereditary details and controls the growth and division of the
cells. The genetic information stored in DNA is then transcribed into RNA, and the
details in RNA are then translated for the synthesis of the proteins.
14.1 Nucleosides and Nucleotides
• Nucleic acids are chains of five membered ring sugars linked by phosphate groups
(Figure 1). The anomeric carbon of each sugar is bonded to a nitrogen of heterocyclic
amine in a β-glycosidic linkage. In RNA, the five membered sugar is D-ribose. In
DNA, the five membered sugar is 2’deoxy-D-ribose.
base
O
Phosphodiester
base
O
O
O
O OH
O P Obase
O
O
O OH
O P Obase
O
O
Phosphodiester
β-glycosidic linkage
D-Ribose
O
O P Obase
O
O
β-glycosidic linkage
Anomeric Carbon
D-Deoxyribose
O
O P Obase
O
O
O
O OH
DNA
RNA
Figure 1
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• The difference in heredity among the species is determined by the sequence of the
bases in DNA. DNA has four bases: adenine, guanine, cytosine and thymine.
•
RNA also contains four bases. Three-adenine, guanine and cytosine- are same as
those in DNA. But the fourth base in RNA is uracil instead of thymine.
N
N
N
HN
N
H
N
NH2
O
NH2
adenine
N
N
H
N
H
O
O
O
guanine
O
HN
N
H
O
N
H
N
H
O
uracil
cytosine
Me
HN
thymine
• A compound with a base bonded to D-ribose or 2’-deoxy-D-ribose is called
nucleoside. Figure 2 shows an example using adenine as base. Similarly, other bases
(guanine, cytosine, uracil and thymine) can also make bond to the sugar to give the
corresponding nuleotides. The stereochemistry of the linkage between the base and the
ribose is most commonly β.
NH2
7
N
5
6
N1
8
N
9
5
HO
4
3
2
4
N
Me
NH
3
N
O
1'
2
OH OH
HO
O
adenine
(base)
ribose
(sugar)
5
HO
4
O
1'
3
2
Adenosine
(a ribonucleoside)
O
O
Thymine
(base)
OH OH
ribose
2-Deoxyribose HO
(sugar)
OH
2'-Deoxythymidine
(a deoxyribonucleoside)
OH
O
OH
OH
2'-deoxyribose
Nuleoside = base + sugar
Figure 2
• Nucleotide is nucleoside with either the 5’ or the 3’-OH group bonded in an ester
linkage to phosphoric acid. The nucletotide where the sugar is D-ribose is called
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ribonuleotide,
whereas
the
nucleotide
with
2’-deoxy-D-ribose
is
called
deoxyribonuleotide (Figure 3).
O
NH2
7
Phosphate Group
N
5
N
9
4
5
N1
2
N
adenine
(base)
N
3
5
HO
3
O
4
4
1'
2
OH OH
NH
6
8
O
O P O
O-
Me
ribose
(sugar)
Ester
Linkage
Adenosine 5'-monophosphate
O
1'
3
O
P O
O O-
2
O
2-Deoxyribose
(sugar)
2'-Deoxythymidine 3'-monophosphate
(a deoxyribonucleotide)
(a ribonucleotide)
Nuleotide = base + sugar + phosphate
Figure 3
14.2 Nucleic Acids
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Thymine
(base)
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• Nucleic acids are biopolymers composed of nucleotide subunits linked by
phosphodiester bonds. DNA and RNA are polynucleotides. Nucleotide triphosphate
serves as substrate precursor for the biosynthesis of nucleic acids. The nucleotides are
linked by the nucleophilic attack of 3’-OH of one nucleotide triphosphate on the

phosphorus of another nucleotide (Figure 4).
5'-end
O
O
O
P
P
P
O -O -O -O
O
O
O
Phosphate group
5'
base
O
O
O P OO
base
O
OH
O
O
O
P
P
P
O -O -O -O
O
O
O
Phosphate group
the 3'-OH group attacks the
α-phosphorus of the next
nucleotide
base
O
OH
3'-end
3'
Figure 4
•
Primary Structure: It describes the sequence of bases in the strand. By convention, the
sequence of bases is written in the 5’ to 3’ direction.
ATGAGCCATGTAGC
5' end
•
3' end
Secondary Structure: DNA consists of two strands of nucleic acids with the sugarphosphate backbone outside and the base inside. The chains are held together by H-
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bonding between the base of one strand with the base of another strand. Adenine pairs
with thymine, while guanine pairs with cytosine through two and three H-bonds,
respectively. This means if we know the sequences bases in one strand, we will be able
to sequence the bases in the other strand (Figure 5a). If the two strands run in opposite
directions, the strands are not linear. Instead they are twisted into a helix around
common axis, which is known as double helix (Figure 5b).
Figure 5
• Figure 6 shows the base pairing in DNA: adenine and thymine form two H-bonds;
cytosine and guanine form three H-bonds
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Two H bonds
H
H N
O
Me
N H
N
Sugar
Three H Bonds
N
N
N
Sugar
Sugar
N
N
N
H N
O
Sugar
H NH
cytosine
adenine
N
N
O
thymine
O
HN H
N
guanine
Figure 6
14.3 Stability of DNA and RNA
In RNA, the 2’-OH of ribose attacks the adjacent phosphodiester group that leads to the
cleavage of the strand (Figure 7). This reaction does not take place in DNA, because it
does not have the 2’-OH group. Thus, DNA remain intact throughout the life span of
cells
base
O
O
base
O
O
O P O-
HO P O-
O
O
O OH
OH
O O
O OH
O
base
O
O
base
O
O O
base
-
P
O
+
O OH
O
O OH
Figure 7
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base
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Module 14 Nucleic Acids
Lecture 37 Nucleic Acids II
14.4 Biosynthesis of DNA: Replication
Each strand of DNA acts as a template for the formation of complementary new strand
(Figure 1). The new (daughter) DNA molecules have the same genetic information as that
of the parent DNA. The synthesis of the identical copies of DNA is known as replication
(Figure 1).
Figure 1
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• The synthesis take place in a region where the strands have started to separate, because
a nucleic acid can be synthesized only in the 5’ to 3’ direction.
• The synthesis is catalyzed by enzyme is known as DNA polymerase, and the
fragments are joined together by an enzyme is called DNA ligase.
• In each of daughter DNA molecules, one strand comes from the parent DNA and
another strand is synthesized. This process is called semiconservative replication.
14.5 Biosynthesis of RNA: Transcription
• The synthesis of RNA from DNA blueprint is known as transcription. It starts by
DNA at a particular region to afford two single strands: (i) sense strand and (ii)
template strand (Figure 2).
• The template strand read in 3’ to 5’ direction, and the RNA is synthesized in 5’ to 3’
direction.
• The base in the template strand specifies the base sequence to be incorporated in
RNA.
sense strand
DNA
G C T G C A G C AG C A
T
5'
AT C G A T C G A
3'
TA G C T A G C T
A
template strand
G
AT C G A T
3'
TA G C T A
5'
C G A C G T C G T C G T C
G C U G C A G C A G C A
5' ppp G C U G C A G C A G C
OH 3'
RNA
transcription
Figure 2. Biosynthesis of RNA
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14.6 RNA
RNA is a single stranded polymer and does not form double helix. There are three types
of RNA:
• Messenger RNA (mRNA), whose base sequence specifies the amino acid sequence in
protein.
• ribosomal RNA (rRNA), that comprises the particles on which the biosynthesis of
protein occurs.
• transfer RNA (tRNA), which carries the amino acid that will be incorporated into the
protein.
 tRNAs are shorter than mRNA and rRNA, and folded into a characteristic
cloverleaf like structure (Figure 3). They have a CCA sequence at the 3’end, and
the three bases at the bottom are called anticoden.
 Each tRNA carries an amino acid as an ester to its terminal 3’OH. The amino
acid will be inserted into a protein during the protein synthesis.
3'
OH
A
C
tRNA contains CCA at the 3' end
Unusal base results from
C
5'
an enzymatic modifcation
A
of the four normal bases
G C
U A
C G
GG CG
G
G
C
U
A
A
A
A U C G A UG
U
G C U A G C U
UA G C U AG
AC GC
G C
A U
C G
G C
U A
G
The bottom three bases called anticodon
Figure 3. tRNA that carries alanine.
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NH2
NH2
R
+
H3N
COO-
+
N
O- OO
O
O O O
P
P
P
O
O
O
+
N
O
amino acid
N
R
N
N
O O O
P
O
O
H3N
O
N
N
N
OH OH
acyl adenylate
OH OH
3' OH
ATP
-
-
O 2 O P O
O
-
O
-
O
O O
O
P
P
O
O
pyrophosphate
HO ACC
5'
NH2
O
+
H3N
O ACC
R
5'
an amino acyl tRNA
N
O O O
P
O
N
-
+
O
N
tRNA
N
OH OH
AMP
Figure 4. Mechanism for amino acyl tRNA synthetase-the enzyme that catalyzes the attachment of an amino acid to tRNA
 Figure 4 shows the mechanism for the attachment of an amino acid in tRNA.

In the first step, the CO2- of amino acid attacks the α-phosphorus of ATP. The
carboxylic acid of amino acid is now activated with good leaving group.

The 3’-OH group of tRNA attacks the carbonyl carbon via nucleophilic addition to
give the amino acid attached tRNA.
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Amino acid
tRNA
A C
rRNA
G
Ribosome
U G C A A G
A C
A C G
U G C A AG
mRNA
U G
C A AG
mRNA
G
A C G A C G
U G C A AG
mRNA
mRNA
Protein
A C G
A C G A C G
U G C A AG
mRNA
A C
U G
G
A C G
C A A G
mRNA
Figure 5. The sequence of bases in mRNA that determines the sequence of amino acids in protein.
14.7 Biosynthesis of Proteins: Translation
During the synthesis, rRNA attaches to one end of the mRNA strand and travels along the
strand (Figure 5). As it travels, the nucleic acid bases of mRNA are read as triplets. The
tRNA that recognizes that triplet is bound and brings the amino acid coded by that triplet.
The protein is constructed on tRNA and transferred from one tRNA to the next until the
synthesis is completed.
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