Both RNA and DNA are made of nucleotides and take similar shapes. Both contain five-carbon sugars, phosphate groups, and nucleobases (nitrogenous bases). They both play important roles in protein synthesis. DNA has the five-carbon sugar deoxyribose and RNA has the five-carbon sugar ribose, hence their names
2. Nucleotides And Nucleic Acids
Nucleic acids are one of most giant molecules
found in the nucleus of cells. Friedrich Miescher
was first to isolate nucleic acids from pus cells. He
called them nuclein since these were obtained
from nucleus.
Altman 1899 replaced the term nuclein with nucleic
acid as these were acidic in nature.
There are two types of nucleic acid
Deoxyribonucleic acid (DNA)
Ribonuleic acid (RNA)
3. Nucleotides
Nucleic acid are linear polymers of nucleotides. A
nucleotide is composed of three components.
Nitrogenous Base
Pentose sugar
Phosphate group
5. Nucleotides :Nitrogenous bases
The base of DNA and RNA are heterocyclic
carbon and nitrogen containing ring with a
variety of substitutes.
These are either substituted purine or
pyrimidines.
6. Nucleotides :Pentose sugars
Nucleic acids have
two kinds of pentose
sugars.
1. Ribose sugar
2. 2’deoxyribose
The nucleotide units
of RNA contain
Ribose sugar.
The nucleotide units
of DNA contain
2’deoxyribose
O OH
CH2
OH
OH
HO HO O OH
CH2
OH
ribose deoxyribose
(no O)
7.
8.
9.
10.
11. Phosphodiester Bond Link Nucleotides In Nucleic Acids
3,5-phosphodiester bond
In DNA and RNA, nucleotides are joined into
polymers by the covalent linkage of a phosphate
group between the 5’hydroxyl of one ribose and
3’ hydroxyl of next.
This kind of linkage is called a phosphodiester
bond, since the phosphate is chemically in the
form of a diester.
A nucleic acid chain can hence be seen to have a
direction. Any nucleic acid chain of what ever length
has a free 5’end with or without attached phosphate
group and free 3’ end with hydroxyl group.
At neutral pH, each phosphate group has a single
negative charge, that is why nucleic acids are termed
as acids.
12. Both DNA and RNA have same
basic structure in which pentose
sugar and phosphate groups joined
through phosphodiester bond, form
the backbone of nucleic acids and
bases the side chains.
The polynucleotide chain has a
directional sense. One end of chain
has 5’- P and other end has 3’OH
which are not linked to other
nucleotides. These ends are called
as 5 prime and 3 prime ends and by
convention are always written with
5’ end on the left and 3’ end on the
right.
Nucleotides In Nucleic Acids
13.
14. Discovery OF Structure Of DNA
A most important clue to the structure of DNA came from the work of
Erwin Chargaff and his colleagues in he late 1940s.
They found that the four nucleotide bases of DNA occur in different
ratios in the DNAs of different organisms and that the amounts of
certain bases are closely related.
These data, collected from DNAs of a great many different species, led
Chargaff to the following conclusions:
1. DNA Molecules Have Distinctive Base Compositions. The base composition of DNA
generally varies from one species to another.
2. DNA specimens isolated from different tissues of the same species have the same base
composition.
3. The base composition of DNA in a given species does not change with an organism’s
age, nutritional state, or changing environment.
4. In all cellular DNAs, regardless of the species, the number of adenosine residues is equal
to the number of thymidine residues (that is, A= T), and the number of guanosine
residues is equal to the number of cytidine residues (G= C).
15.
16. Discovery OF Structure Of DNA
From these relationships it follows that the sum of the
purine residues equals the sum of the pyrimidine
residues; that is, A +G= T+ C (approx.). These
quantitative relationships, sometimes called “Chargaff’s
rules,” were confirmed by many subsequent
researchers.
Erwin Chargaff made key DNA observations that
became known as Chargaff’s rule.
Purines = Pyrimidines A = T and C = G
17. Discovery OF Structure Of DNA
In 1953 Watson and Crick postulated a three dimensional
model of DNA structure that accounted for all the
available data. The main feature of this model are
1. DNA has a double helical structure, in which
two poly nucleotide chains are coiled about
same axis.
2. The purine and pyrimidine bases of both
strands are stacked inside the double helix,
very close together and perpendicular to the
long axis. The offset pairing of the two strands
creates a major groove and minor groove on
the surface of the duplex.
18. MINOR AND MAJOR GROOVES
As the DNA strands wind around each
other, they leave gaps between each set
of phosphate backbones, revealing the
sides of the bases inside (see animation).
There are two of these grooves twisting
around the surface of the double helix:
one groove, the major groove, is 22 Å
wide and
2. the minor groove, is 12 Å wide
19. Discovery OF Structure Of DNA
3. Two polynucleotide chains run in opposite direction and
have complementary base sequences. Each nucleotide
base of one strand is paired in the same plane with a
base of the other strand. Bases of two chains are linked
by hydrogen bonds. Adenine is linked to thymine,
cytocine to guanine. This accounts for char gaff's rule
A+G=C+T as well as the constant diameter of the helix
i.e 20A0.
4. Nitrogenous bases are stacked inside of helix while
sugar phosphate forming the backbone of molecule is
outside.
5. The stacked bases inside the double helix are 3.4 Å and
there are 10 base pairs per turn of helix apart; the
secondary repeat distance of about 34 Å which account
for the periodicities observed in the xray diffraction
patterns of DNA fibers, In aqueous solution the
structure differs slightly from that in fibers, having 10.5
base pairs per helical turn
20.
21.
22.
23.
24.
25. The Watson - Crick Model Of DNA
Watson-Crick model for
the structure of DNA.
The original model
proposed by Watson and
Crick had 10 base pairs,
or 34 Å (3.4 nm), per turn
of the helix; subsequent
measurements revealed
10.5 base pairs, or 36 Å
(3.6 nm), per turn.
(a) Schematic
representation, showing
dimensions of the helix.
(b) Stick representation
showing the backbone
and stacking of the
bases.
(c) Space-filling model.
26.
27. DNA Strands
The opposing strands of DNA are not
identical, but are complementary.
This means: they are positioned to
align complementary base pairs:
You can thus predict the sequence of
one strand given the sequence of its
complementary strand.
28. Watson Crick Base pairing
Constant diameter can be explained by purine pyrimidine base
pairing only. Pairing of two purines would need too much space
whereas the pairing of two pyrimidines will occupy too little space
29. RNA Structure
RNA like DNA is a poly nucleotide: it is produced by
phosphodiester linkage between ribonucleotides in the
same manner as in case of DNA.
RNA nucleotides have ribose sugar in place of deoxyribose
in DNA. Thymine is absent in RNA, and uracil is found in its
place.
Usually RNA is single stranded, but double stranded RNA is
also found. In most of organisms RNA performs non genetic
functions through various species of RNA e.g. mRNA, tRNA,
rRNA but in some viruses it serves as genetic material.
RNA is transcribed from DNA by enzymes called RNA
polymerases and is generally further processed by other
enzymes. RNA is central to the synthesis of proteins.
30. Types of RNA: tRNA
Transfer RNA (tRNA)
Transfer RNA is a small RNA (usually about 74-95
nucleotides) that transfers a specific amino acid to a
growing polypeptide chain at the ribosomal site of protein
synthesis during translation.
It has a 3' terminal site for amino acid attachment. It also
contains a three base region called the anticodon that can
base pair to the corresponding three base codon region on
mRNA.
Each type of tRNA molecule can be attached to only one
type of amino acid,
31.
32. Types of RNA: tRNA
tRNA has a, clover leaf structure
secondary structure which has
following main features.
1. The acceptor stem is a 6-7-bp
stem made by the base pairing of
the 5'-terminal nucleotide with the
3'-terminal nucleotide The
acceptor stem may contain non-
Watson-Crick base pairs.
2. The CCA tail is a CCA sequence
at the 3' end of the tRNA
molecule amino acid get
attached. In prokaryotes, the
CCA sequence is transcribed. In
eukaryotes, the CCA sequence is
added during processing and
therefore does not appear in the
tRNA gene.
33. Types of RNA: tRNA
1. The D arm is a 4 bp stem
ending in a loop that often
contains dihydrouridine (act
as a recognition site for aminoacyl-tRNA
synthetase).
2. The anticodon arm is a 5-
bp stem whose loop
contains the anticodon.
3. The T arm is a 5 bp stem
containing the sequence
TΨC where Ψ is a
pseudouridine (expected to play a role
in association with aminoacyl transferases).
4. Bases that have been
modified, especially by
methylation, occur in
several positions outside
the anticodon.
35. Types of RNA: mRNA
• Messenger ribonucleic acid
(mRNA) is a molecule of RNA
encoding a chemical "blueprint" for
a protein product. mRNA is
transcribed from a DNA template,
and carries coding information to
the sites of protein synthesis.
• Here, the nucleic acid polymer is
translated into a polymer of amino
acids: a protein. In mRNA as in
DNA, genetic information is
encoded in the sequence of
nucleotides arranged into codons
consisting of three bases each.
36. Types of RNA: mRNA
Each codon encodes for a
specific amino acid, except
the stop codons that
terminate protein
synthesis.
This process requires two
other types of RNA;
transfer RNA (tRNA)
mediates recognition of the
codon and provides the
corresponding amino acid.
ribosomal RNA (rRNA) is the
central component of the
ribosome's protein
manufacturing machinery.
37. Types of RNA: mRNA
Prokaryotic mRNA
In prokaryotes, a single mRNA contains the information
for synthesis of many proteins.
It does not contain non coding intron sequences.
Eukaryotic mRNA
In eukaryotes, a single mRNA codes for just one protein
DNA is transcribed to produce heterogeneous nuclear
RNA which contain introns and exons.
intron - intervening non coding sequence
exon - coding sequence
Splicing produces final mRNA without introns
38. Types of RNA: rRNA
Ribosomal RNA (rRNA) is the central
component of the ribosome, the protein
manufacturing machinery of all living cells. rRNA
molecules make up about 2/3 of ribosome
The function of the rRNA is to provide a
mechanism for decoding mRNA into amino acids
and to interact with the tRNAs during translation
by providing peptidyl transferase activity.
39.
40.
41. A-DNA
The A form is favored in many solutions that are
relatively devoid of water.
The DNA is still arranged in a right-handed double helix,
but the helix is wider and the number of base pairs per
helical turn is 11, rather than 10.5 as in B-DNA.
The plane of the base pairs in A-DNA is tilted about 200
with respect to the helix axis. These structural changes
deepen the major groove while making the minor groove
shallower.
The reagents used to promote crystallization of DNA
tend to dehydrate it, and thus most short DNA molecules
tend to crystallize in the A form.
42.
43. Z-form DNA
Z-form DNA is a more radical departure from the B structure; the most obvious
distinction is the left-handed helical rotation.
There are 12 base pairs per helical turn, and the structure appears more
slender and elongated. The DNA backbone takes on a zigzag appearance.
Certain nucleotide sequences fold into left-handed Z helices much more
readily than others. Prominent examples are sequences in which pyrimidines
alternate with purines, especially alternating C and G or 5-methyl-C and G
residues.
To form the left-handed helix in Z-DNA, the purine residues flip to the syn
conformation, alternating with pyrimidines in the anti conformation. The major
groove is barely apparent in Z-DNA, and the minor groove is narrow and
deep.
Whether A-DNA occurs in cells is uncertain, but there is evidence for some
short stretches (tracts) of Z-DNA in both prokaryotes and eukaryotes. These
Z-DNA tracts may play a role (as yet undefined) in regulating the expression
of some genes or in genetic recombination.
it is a transient structure that is occasionally induced by biological activity and
then quickly disappears
46. Forms of the Double Helix
0.26 nm
2.8 nm
Minor
groove
Major
groove
1.2 nm
A DNA
1 nm
Major
groove
Minor
groove
A T
T A
G C
C G
C G
G C
T A
A T
G C
T A
A T
C G
0.34 nm
3.6 nm
B DNA
11 Bp/turn 12 Bp/turn
+
10.5 Bp/turn
0.57 nm
6.8 nm
0.9 nm
Z DNA
47. Secondary structures of DNA/RNA
role in
•replication
•transcription regulation
•used as recombination sites.
50. 1. Almost all DNA molecules in cells (prokaryotes) can be
considered as circular, and are on average negatively
supercoiled.
Negative supercoils favor local
unwinding of the DNA
favour the transition between B-DNA
and Z-DNA,
51.
52. SUPERCOILS:
Winding of the deoxyribonucleic acid duplex on itself so that it crosses its own axis;
may be in the same (positive) direction as, or opposite (negative) direction to, the
turns of the double helix.
54. 2. Negative supercoiled DNA has a higher torsional energy than
relaxed DNA, which facilitates the unwinding of the helix, such as
during transcription initiation or replication
3. Topoisomer: A circular dsDNA molecule with a specific linking
number which may not be changed without first breaking one or
both strands.
Twists: In a "relaxed" double-helical segment of DNA, the two strands twist
around the helical axis once every 10.4-10.5 base pairs of sequence.
‘Writhes' is the number of coils
Lk= Tw+Wr
55. The linking number L of DNA, a topological property, determines the degree of
supercoiling;
The linking number defines the number of times a strand of DNA winds in the right-
handed direction around the helix axis when the axis is constrained to lie in a plane;
If both strands are covalently intact, the linking number cannot change;
For instance, in a circular DNA of 5400 basepairs, the linking number is 5400/10=540,
where 10 is the base-pair per turn for type B DNA.
Linking number
56. 1. Twist T is a measure of the helical winding of the DNA strands around each
other. Given that DNA prefers to form B-type helix, the preferred twist = number
of basepair/10;
2. Writhe W is a measure of the coiling of the axis of the double helix. A right-
handed coil is assigned a negative number (negative supercoiling) and a left-
handed coil is assigned a positive number (positive supercoiling).
3. Topology theory tells us that the sum of T and W equals to linking number:
L=T+W
4. For example, in the circular DNA of 5400 basepairs, the linking number is
5400/10=540
1. If no supercoiling, then W=0, T=L=540;
2. If positive supercoiling, W=+20, T=L-W=520;
The twist and writhe
63. Topoisomerases can fix topological problems and are separated into two
types separated by the number of strands cut in one round of action:
Type I topoisomerase cuts one strand of a DNA double helix and then reanneals
the cut strand. Type I topoisomerases are subdivided into two subclasses:
type IA topoisomerases which share many structural and mechanistic features
with the type II topoisomerases,
type IB topoisomerases, which utilize a controlled rotary mechanism. Examples
of type IA topoisomerases include topo I and topo III. Historically, type IB
topoisomerases were referred to as eukaryotic topo I, but IB topoisomerases are
present in all three domains of life.
Interestingly, type IA topoisomerases form a covalent intermediate with the 5' end
of DNA, while the IB topoisomerases form a covalent intermediate with the 3' end
of DNA. Recently, a type IC topoisomerase has been identified, called topo V.
While it is structurally unique from type IA and IB topoisomerases, it shares a
similar mechanism with type IB topoisomerase.
64.
65. Type II topoisomerase cuts both strands of one DNA double helix,
passes another unbroken DNA strand through it, and then reanneals
the cut strand. It is also split into two subclasses:
type IIA and type IIB topoisomerases, which share similar structure
and mechanisms. Examples of type IIA topoisomerases include
eukaryotic topo II, E. coli gyrase, and E. coli topo IV. Examples of type
IIB topoisomerase include topo VI.
66. Topoisomerases exist in cell to regulate the level of
supercoiling of DNA molecules.
Type I topoisomerase: breaks one strand and
change the linking number in steps of ±1.
TypeII topoisomerase: breaks both strands and
change the linking number in steps of ±2.
Gyrase: introduce the negative supercoiling
(resolving the positive one and using the energy from ATP
hydrolysis.
70. Ethidium bromide (intercalator): locally
unwinding of bound DNA, resulting in a
reduction in twist and increase in writhe.
Topoisomerases
Type I: break one strand of the DNA , and
change the linking number in steps of ±1.
Type II: break both strands of the DNA , and
change the linking number in steps of ±2.
71. The sterically allowed orientations of purine and pyrimidine bases
with respect to their attached ribose units.
