RNA and DNA Differences

By
Miss Tooba
Kanwal
1Bacterial Genetics

RNA (Ribonucleic acid )
RNA is a
polymer of
ribonucleotides
linked together
by 3’-5’
phosphodiester
linkage
2Bacterial Genetics

RNA V/S DNA
3Bacterial Genetics

Differences between RNA and DNA
S.No. RNA DNA
1) Single stranded mainly except
when self complementary
sequences are there it forms a
double stranded structure (Hair
pin structure)
Double stranded (Except for
certain viral DNA s which are
single stranded)
2) Ribose is the main sugar The sugar moiety is deoxy
ribose
3) Pyrimidine components differ.
Thymine is never found(Except
tRNA)
Thymine is always there but
uracil is never found
4) Being single stranded structure-
It does not follow Chargaff’s rule
It does follow Chargaff's rule.
The total purine content in a
double stranded DNA is always
equal to pyrimidine content.
4Bacterial Genetics

S.No. RNA DNA
5) RNA can be easily destroyed by
alkalies to cyclic diesters of
mono nucleotides.
DNA resists alkali action due to
the absence of OH group at 2’
position
6) RNA is a relatively a labile
molecule, undergoes easy and
spontaneous degradation
DNA is a stable molecule. The
spontaneous degradation is
very 2 slow. The genetic
information can be stored for
years together without any
change.
7) Mainly cytoplasmic, but also
present in nucleus (primary
transcript and small nuclear
RNA)
Mainly found in nucleus, extra
nuclear DNA is found in
mitochondria, and plasmids
etc
8) The base content varies from
100- 5000. The size is variable.
Millions of base pairs are there
depending upon the organism
5Bacterial Genetics

S.No. RNA DNA
9) There are various types of RNA –
mRNA, r RNA, t RNA, Sn RNA, Si
RNA, mi RNA and hn RNA. These
RNAs perform different and
specific functions.
DNA is always of one type and
performs the function of
storage and transfer of genetic
information.
10) No variable physiological forms
of RNA are found. The different
types of RNA do not change
their forms
There are variable forms of
DNA (A to E and Z)
11) RNA is synthesized from DNA, it
can not form DNA(except by the
action of reverse transcriptase).
It can not duplicate (except in
certain viruses where it is a
genomic material )
DNA can form DNA by
replication, it can also form
RNA by transcription.
12) Many copies of RNA are present
per cell
Single copy of DNA is present
per cell.
6Bacterial Genetics

Types of RNA
In all prokaryotic and eukaryotic
organisms, three main classes of RNA
molecules exist-
1) Messenger RNA(m RNA)
2) Transfer RNA (t RNA)
3) Ribosomal RNA (r RNA)
7Bacterial Genetics

Messenger RNA (m-RNA)
Comprises only 5% of the RNA in the cell
Most heterogeneous in size and base sequence
All members of the class function as
messengers carrying the information in a gene to
the protein synthesizing machinery
8Bacterial Genetics

General features of mRNA
The m- RNA molecules are formed with the help
of DNA template during the process of transcription.
The sequence of nucleotides in mRNA is
complementary to the sequence of nucleotides on
template DNA.
The sequence carried on m -RNA is read in the
form of codons.
A codon is made up of 3 nucleotides
9Bacterial Genetics

• Prokaryotic mRNAs are made up of polynucleotide
chains of specific sequence endowed with 5’ to 3’
polarity.
• Size of the mRNAs is more or less proportional to the
gene from which it generates.
• The polypeptide chain it produces is directly
proportional to the coding size of the mRNA. Longer the
protein longer is the mRNA and vice versa.
• Average size of mRNA in bacterial systems is 1000 ntds
to 2000 with a mol. Wt. of 30,000 dal.
Bacterial Genetics 10

• Once translated, m-RNA is immediately degraded i.e
within 1 minute of the start of transcription.
• The 5’ terminus start decaying before the 3’ terminus
has been transcribed or translated. However the rate
of degradation is slower than the rate of
transcription.
• Out of 500 sites in E.coli, 300 sites are
transcriptional.

Structural Characteristics of m-RNA
 On both 5’ and 3’ end there are non coding sequences which
are not translated (NCS)
The 5’ non-coding region(5’UTR) is called leader sequence,
whose length and sequence varies from one species of mRNA
to the other.
The intervening region between non coding sequences
present between 5’ and 3’ end is called coding region or Open
Reading Frame (ORF). This region encodes for the synthesis of
a protein.
The 3’ non-coding region is called Trailor where the process
of translation stops.
12Bacterial Genetics

• The leader sequence in every mRNA contains an all-
important structured sequence called Shine-
Delgarno sequence, seven to nine nucleotides
upstream of the start codon AUG. These are also
called SPACERS which are usually 10 bases long.
• The coding region starts from the initiator codon
AUG (mostly) or GUG (rarely) and ends in a
terminator codon like UAG, UGA or UAA.
Structural Characteristics of
m-RNA(contd.)

Polycistronic mRNA with spacer between cistrons

• Cistron: a gene corresponding to one polypeptide
chain in addition to the translational start and stop
signals for protein synthesis.
• m-RNA encoding a single polypeptide is called
monocistronic m-RNA.
• Polycistronic m-RNA encodes proteins required to
carry out reaction of a single metabolic pathway.

Structural characteristics of m-RNA
(contd.)
• In the case of prokaryotes, the coding region is split
consisting of cistrons with initiating and terminator
sequences. In between two such coding regions one finds a
short spacer region, hence the name polycistronic.
• This spacer region is used for the translation termination of
the cistron and again initiates at the next cistron, the size
of the inter-cistronic space varies, but mostly very short.
5’---UAGGAGG—-AUG-----II-AUG---------II-AUG------UGA
• In prokaryotes transcription and translation are coupled.
• Half-life of mRNAs is very short ranging between 2-5
minutes.

Ribosomes and Ribosomal RNA
(r-RNA)
• Ribosome:
• Granular structures in cytoplasm.
• The ribosome of E.coli consists of r-RNA and protein
with the ratio of 2:1
• Mol.wt. of each ribosome is slightly less than 3
million daltons.
• ¼ of total cellular mass, 80% of cellular RNA and 10%
of total cell protein.

Structure of Ribosome
• Asymmetric aggregates of two subunits, differentiated
by their sedimentation of co-efficient.
• Larger S value, larger the particle.
• Bacterial ribosome sedimentation of coefficient is 70S,
divided into 30S and 50S subunits.
• Eukaryotic ribosome is 80S with 60S and 40S subunits.
• 30S SUB-UNIT:
In E.coli, 30S subunit has elongated and asymmetrical
shape composed of 21 different proteins(S1,S2…. S21)
and mol.wt ranges from 8500 to 61200 dal. A Single
16S molecule of rRNA of 1541 nucleotides is also
present. Bacterial Genetics 18

• 50S SUB-UNIT:
This subunit has a pentagonal outline and polyhedral
shape and 31 proteins (L1, L2… L31) with a mol. Wt.
of 11000 to 41500 dal. The r-RNA in this subunit is of
two types: 5S with 120 nucleotides and 23S with
2904 nucleotides.
• Ribosomal proteins are called r-proteins which are
responsible for creating several active sites for
protein synthesis and co-ordinates with r-RNA in
translation.

Prokaryotic Ribosome

General features of r-RNA
• Like all kinds of RNA, r-RNA is also transcribed from a
template strand of DNA.
• 0.1 to 0.2 % of the bacterial genome is estimated to
be responsible for transcription of r-RNA.
• Some well conserved regions usually contains
methylated residues.
• ~ 10 methyl groups are present in 16S r-RNA towards
it’s 3’ terminus and ~20 in 23S r-RNA.

General features of r-RNA (contd)
• The r-RNA participates in protein synthesis but
don’t code for proteins.
• Specific sequences in r-RNA play a role in
initial attachment of m-RNA to the 30S
subunit and assure the process of translation.
• The sequences in the 3’ terminus of r-RNA
interacts directly with m-RNA at initiation.

General features of r-RNA (contd).
• Specific regions at 16S rna interact directly
with the anticodon regions of t-RNA in both
the A site and P site.
• A specific sequence of 23S r-RNA interacts
with the CCA terminus of peptidyl-t-RNA.
• The 16S and 23S r-RNA are also involved in the
interaction of two sub units of ribosomes.

Transfer RNA (t- RNA)
Transfer RNA are the smallest of three major species of
RNA molecules
They have 74-95 nucleotide residues
They are synthesized by the nuclear processing of a
precursor molecule
They transfer the amino acids from cytoplasm to the
protein synthesizing machinery, hence the name t RNA.
They are also called Adapter molecules, since they act as
adapters for the translation of the sequence of nucleotides
of the m RNA in to specific amino acids
There are at least 20 species of t RNA one corresponding
to each of the 20 amino acids required for protein synthesis.

Transfer RNA (t- RNA)
1) Primary structure-
The nucleotide sequence of all the t RNA molecules
allows extensive intra-strand complimentarity that
generates a secondary structure.
• It contains a number of unusual nucleotides due the
presence of one or more methyl groups.
• Restructuring of purine ring
• About 50 bases are modified.
• Some modification is common and some is found in
particular t-RNAs
• Another imp feature of base modification is codon-
anticodon pairing.

Structural characteristics of t- RNA
2) Secondary structure (Clover leaf structure) –
Each single t- RNA shows extensive internal base
pairing and acquires a clover leaf like structure. The
structure is stabilized by hydrogen bonding between
the bases on the same chain into a double stranded
helical arrangement which is a consistent feature.
The clover leaf model shows the base-pairing
structure of t-RNA and reveals four base paired
regions that define the three loops of t-RNA.

Structural characteristics of t- RNA
• All t-RNA contain 5 main arms or loops which
are as follows-
a) Acceptor arm
b) TΨ C arm
c) Anticodon arm
d) D arm
e) Extra arm

Secondary structure of t- RNA
a) Acceptor arm
 The acceptor arm is at 3’ end and always ends in a
C.C.A.
 The nucleotide at 5’ end is usually G.
 These two termini base pair with each other to form
the acceptor arm.
 It has 7 base pairs
 The end sequence at the C.C.A remains unpaired.
 The 3’ OH group terminal of Adenine binds with
carboxyl group of amino acids later.
 The t RNA bound with amino acid is called Amino acyl t
RNA
 CCA attachment is done post transcriptionally

Secondary structure of t- RNA
b) TΨC arm
As we move along the t-RNA molecule from the 3’
terminus, we encounter the first loop, TΨC loop.
It is so named because it contains the three bases,
T,C and a modified Ψ(Psi) base. (Psi stands for a
modified uridine base into psuedouridine.)
 It is involved in the binding of t RNA to the
ribosomes
This loop is made up of seven unpaired bases.

Secondary structure of tRNA
(contd.)
c) Anticodon arm
 Lies at the opposite end of acceptor arm
It consists of seven unpaired bases which
contains the anti-codon triplet in it’s center.
Recognizes the triplet codon present in the m
RNA
Base sequence of anticodon arm is
complementary to the base sequence of m RNA
codon.
 Due to complimentarity it can bind specifically
with m RNA by hydrogen bonds.

Secondary structure of t-
RNA(contd.)
d) D arm
 D arm is named after modified base
dihydrouridine (D).
It consists of 8-12 unpaired bases.
It has 3-4 base pairs
It serves as the recognition site for the
enzyme (amino acyl t RNA synthetase) that
adds the amino acid to the acceptor arm.

Secondary structure of t-
RNA(contd.)
e) Extra arm or Variable arm
 This arm lies between the TΨC and anticodon arms.
 About 75 % of t RNA molecules possess a short extra
arm
 It is variable in size, depending upon the number of
bases can b divided into:
• Class I:
If about 3-5 base pairs are present, it is called small extra
arm. Majority t -RNA belong to class 1.
• Class II:
It is a long extra arm having 13-21 base pairs.
The function of extra arm is unknown.

Tertiary structure of t- RNA
 The L shaped tertiary
structure is formed by further
folding of the clover leaf due
to hydrogen bonds between T
and D arms.
 The base paired double
helical stems get arranged in
to two double helical
columns, continuous and
perpendicular to one another.

Tertiary structure of t- RNA
 The amino acid
acceptor arm is located
at one end of the L,
from where the
anticodon loop lies at
the opposite end.
The D loop and T loop
form the corner of the
L.

Summary
RNA exists in several different single-stranded structures, most of
which are directly or indirectly involved in protein synthesis or its
regulation.
The linear array of nucleotides in RNA consists of A, G, C, and U,
and the sugar is ribose.
 All types of RNA has a 5’ and 3’ terminal.
m-RNA is in linear form, hetrogenous in size and is immediately
degraded after translation.
Prokaryotic ribosomes are 70S having two small and large
subunits of 30S and 50S respectively.
Ribosomal RNA is found in ribosomes in linear structure.
Transfer RNA is helical, folded structure and is the smallest in all
RNAs.
30s ribosome contains linear strand of 16s RNA whereas 50s
ribosome contains two linear sets of RNA, 5s and 23s.
The major forms of RNA include messenger RNA (mRNA),
ribosomal RNA (rRNA), transfer RNA (tRNA) 36Bacterial Genetics

RNA and DNA Differences

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