RNA (Ribonucleic acid )

RNA (Ribonucleic
acid )
❑RNA is a long unbranched macromolecule.
❑RNA is a polymer of ribonucleotides linked together by
3’-5’ phosphodiester linkage.

Structure of RNA
Molecular Structure of DNA and RNA
 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 (rRNA)
The other are –
o small nuclear RNA (SnRNA)
o micro RNA(mi RNA) and
o small interfering RNA(Si RNA) and
o heterogeneous nuclear RNA (hnRNA)
 FUNCTIONS OF RNA

❖RNA is synthesized by DNA for the transportation of

genetic information to the protein building apparatus
in the cell.
❖RNA also directs the synthesis of new proteins using
the genetic information it has transported.
❖ mRNA (messenger ribonucleic acid) is used to
transfer genetic information through plasma
Membranes.
❖ It carries genetic formation of DNA (Gene) for
protein synthesis from nucleus to ribosome of genetic
code.
 FUNCTIONS OF RNA
❖tRNA – Acts as adapter molecule ,carries Amino
Acid and drops it to particular location by
recognizing codon on mRNA by virtue of having
anticodon.
❖rRNA – It makes complex with proteins and form
ribosomal subunits which provide space for
protein synthesis ,single ribosomal RNA of smaller
subunit helps correct orientation of mRNA during
attachment with respect to P and A sites.
❖ snRNA – play significant role in eukaryotic
mRNA processing by splicing of exons as snRNPs
or snurps U1,U2, U4,U5 &U6.
 FUNCTIONS OF RNA

❖scRNA – being component of Signal

Recognition Particle (SRP) helps in targeting of
secretary proteins.
❖ snoRNA – Plays role in gene silencing
(regulates gene expression).
❖ miRNA – play important role in gene silencing
by blocking mRNA and preventing translation.
❖ Si RNA – Plays important role in gene silencing
interfering transcription.
❖ gRNA- help in RNA editing in mitochondria ,
forms part of gene edit and some hybridize with
matching sequence of mRNA.
 1. Messenger RNA (m-RNA)

1. Comprises only 5% of the RNA in the cell

2. Most heterogeneous in size and base sequence
3. All members of this class function as messengers carrying the
information in a gene to the protein synthesizing machinery
4. If the RNA codes for only one peptide, the m-RNA is
monocistronic. If it codes for two or more different
polypeptides, the m RNA is polycistronic.
 Structural Characteristics of m-
RNA
✓ The 5’ terminal end is capped by 7- methyl
guanosine triphosphate cap.
✓ The cap is involved in the recognition
of mRNA by the translating machinery.
✓ It stabilizes m-RNA by protecting it from 5’
exonuclease.
✓ The 3’end of most m-RNAs have a polymer of
Adenylate residues( 20-250).

Contd…..
Structural Characteristics of m-RNA

5’ cap and 3’ tail impart stability to m RNA by

protecting from specific exo nucleases.
 Structural Characteristics of m-
RNA
✓ The tail prevents the attack by 3’ exonucleases
✓ Histones and interferons do not contain poly A
tails
✓ On both 5’ and 3’ end there are non coding
sequences which are not translated (NCS)
✓ The intervening region between non coding
sequences present between 5’ and 3’ end is
called coding region. This region encodes for
the synthesis of a protein.
 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 easily soluble hence called “Soluble
RNA or s RNA.

Contd…
 Transfer RNA (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.
 Structural characteristics of t-
RNA
1) Primary structure- The nucleotide sequence of all the
t-RNA molecules allows extensive intrastand
complimentarity that generates a secondary structure.

2) Secondary 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 and is a consistent feature.
 Structural characteristics of t-
RNA
Secondary structure (Clover leaf structure)
All t-RNA contain 5 main arms or loops which are as
follows-
a) Acceptor arm
b) Anticodon arm
c) D HU arm (dihydrouridine (D)
d) TΨ C arm (ribothymidine (T) and pseudouridine (Ψ,
psi)
e) Extra arm
The arms have base paired stems and unpaired loops. The
structure of tRNA molecules
is maintained by the base pairing in these arms or stem regions.
• The acceptor arm consists of a base paired stem that terminates
in the sequence CCA at the 3' end. This is the attachment site for
the amino acid.
• The D arm is named for the presence of the base dihydrouridine
(D).
• The anticodon arm contains the anticodon that base pairs with
the codon on mRNA. Anticodon has
nucleotide sequence complementary to the codon of mRNA and is
responsible for the specificity of the tRNA.
• The TΨC arm contains both ribothymidine (T) and
pseudouridine (Ψ, psi)
The extra arm is also known as variable arm because it varies in
size, is found between the anticodon and TΨC arms.
Function of tRNA
tRNA carries amino acids in an activated form to the ribosome for
the protein synthesis.
 Secondary structure of t-
RNA

The carboxyl group of amino acid is attached to 3’OH group of Adenine

nucleotide of the acceptor arm. The anticodon arm base pairs with the
codon present on the m- RNA.
a) Acceptor arm
❑ The acceptor arm is at 3’ end
❑ It has 7 base pairs
❑ The end sequence is unpaired
Cytosine, Cytosine-Adenine at the 3’ end
❑ The 3’ OH group terminal of Adenine binds with
carboxyl group of amino acids
❑ The t RNA bound with amino acid is called
Amino acyl t RNA.
 Secondary structure of t-
RNA

The carboxyl group of amino acid is attached to 3’OH group of Adenine

nucleotide of the acceptor arm. The anticodon arm base pairs with the
codon present on the m- RNA.
b) Anticodon arm
1. Lies at the opposite end of acceptor arm
2. 5 base pairs long
3. Recognizes the triplet codon present in
the m RNA
4. Base sequence of anticodon arm is
complementary to the base sequence of
m RNA codon.
5. Due to complimentarity it can bind
specifically with m RNA by hydrogen
bonds.
c) DHU (Dihyrouridine) arm
❑It has 3-4 base pairs

❑Serves as the recognition site for the enzyme (amino

acyl t RNA synthetase) that adds the amino acid to the
acceptor arm.
d) TΨC arm (T-loop arm)
❑This arm is opposite to DHU arm

❑Since it contains pseudo uridine that is why it is so

named
❑It is involved in the binding of t RNA to the ribosomes
e) Extra arm or Variable arm
1. About 75 % of t RNA molecules possess a short extra
arm
2. If about 3-5 base pairs are present the t-RNA is
said to be belonging to class 1. Majority t - RNA
belong to class 1.
3. The t –RNA belonging to class 2 have long extra arm,
13-21 base pairs in length.
 Tertiary structure of t- RNA
1. The L shaped tertiary structure is formed by further folding of
the clover leaf due to hydrogen bonds between T and D arms.

2. The base paired double helical stems get arranged in to two

double helical columns, continuous and perpendicular to one
another.
 tRNA Function
❖tRNA plays an important role in protein synthesis.
❖It acts as an adapter molecule for linking amino acids to its
specific codon present in mRNA.
❖Aminoacylation of tRNA is the first step in protein
synthesis.
❖tRNA is specific to each amino acid and carries them
during the translation process in the ribosomal subunits.
❖The tRNA transfers the amino acid to the growing
polypeptide chain in the ribosomes, which has three
binding sites for tRNA, namely A, P and E, which
correspond to aminoacyl, peptidyl and exit, respectively.
❖This decoding of codons of mRNA by specific tRNAs
continues until the entire sequence for a polypeptide
chain is translated.
 3. Ribosomal RNA (rRNA)
The mammalian ribosome contains two major nucleoprotein
subunits—a larger one with a molecular weight of 2.8 x 106 (60S)
and a smaller subunit with a molecular weight of 1.4 x 106 (40S).
1. The 60S subunit contains a 5S ribosomal RNA (rRNA), a 5.8S
rRNA, and a 28S rRNA; there are also probably more than 50
specific polypeptides.
2. The 40S subunit is smaller and contains a single 18S rRNA and
approximately 30 distinct polypeptide chains.
3. All of the ribosomal RNA molecules except the 5S rRNA are
processed from a single 45S precursor RNA molecule in the
nucleolus .
4. 5S rRNA is independently transcribed.
Ribosomal
RNA (rRNA)
 Functions of Ribosomal RNA (rRNA)
1. The functions of the ribosomal RNA molecules in the
ribosomal particle are not fully understood, but they
are necessary for ribosomal assembly and seem to
play key roles in the binding of mRNA to ribosomes
and its translation

2. Recent studies suggest that an rRNA component

performs the peptidyl transferase activity and thus is
an enzyme (a ribozyme).
 Small RNA
❑Most of these molecules are complexed
with proteins to form ribonucleoproteins
and are distributed in the nucleus, in the
cytoplasm, or in both.
❑They range in size from 20 to 300
nucleotides and are present in 1,00,000–
10,00,000 copies per cell.
 Small Nuclear RNAs (snRNAs)
1. snRNAs, a subset of the small RNAs, are significantly
involved in mRNA processing and gene regulation Of
the several snRNAs, U1, U2, U4, U5, and U6 are
involved in intron removal and the processing of
hnRNA into mRNA.

2. The U7 snRNA is involved in production of the correct

3' ends of histone mRNA—which lacks a poly(A) tail.
 Small Nuclear RNAs (snRNAs)

Sn RNA s are involved in the process of splicing (intron removal) of

primary transcript to form mature m RNA. The Sn RNA s form
complexes with proteins to form Ribonucleoprotein particles called
snRNPs
 Micro RNAs, miRNAs, and Small
Interfering RNAs, siRNAs
❑These two classes of RNAs represent a subset
of small RNAs; both play important roles in gene
regulation.

❑miRNAs and siRNAs cause inhibition of gene

expression by decreasing specific protein
production albeit apparently via distinct
mechanisms
 Micro RNAs (miRNAs)
•miRNAs are typically 21–25 nucleotides in length and
are generated by nucleolytic processing of the products
of distinct genes/transcription units
•The small processed mature miRNAs typically
hybridize, via the formation of imperfect RNA-RNA
duplexes within the 3'- untranslated regions of specific
target mRNAs, leading via unknown mechanisms to
translation arrest.
 Micro RNAs (miRNAs)

microRNAs, short non-coding RNAs present in all living organisms, have

been shown to regulate the expression of at least half of all human
genes. These single-stranded RNAs exert their regulatory action by

binding messenger RNAs and preventing their translation into proteins.

 Small Interfering RNAs (siRNAs)
1. siRNAs are derived by the specific nucleolytic cleavage of
larger, double-stranded RNAs to again form small 21– 25
nucleotide-long products.
2. These short siRNAs usually form perfect RNA-RNA hybrids with
their distinct targets potentially anywhere within the length of
the mRNA where the complementary sequence exists.
3. Formation of such RNA-RNA duplexes between siRNA and
mRNA results in reduced specific protein production because
the siRNA-mRNA complexes are degraded by dedicated
nucleolytic machinery;
4. some or all of this mRNA degradation occurs in specific
organelles termed P bodies.
 Small Interfering RNAs (siRNAs)

Small interfering RNA (siRNA) are 20-25 nucleotide-long double-

stranded RNA molecules that have a variety of roles in the cell.
They are involved in the RNA interference (RNAi) pathway, where
it interferes with the expression of a specific gene by hybridizing
to its corresponding RNA sequence in the target mRNA. This then
activates the degrading mRNA. Once the target mRNA is degraded,
34
the mRNA can not be translated in to protein.
 Heterogeneous nuclear RNA (hnRNA)
1.In mammalian nuclei , hnRNA is the immediate
product of gene transcription
2.The nuclear product is heterogeneous in size
(Variable) and is very large.
3.Molecular weight may be more than 107, while
the molecular weight of m RNA is less than 2x
106
4.75 % of hnRNA is degraded in the nucleus, only
25% is processed to mature m RNA.
 Heterogeneous nuclear RNA (hnRNA)

• Mature m –RNA is formed from primary transcript by capping,

tailing, splicing and base modification.
 Significance of mi RNAs and si
RNAs
1. Both miRNAs and siRNAs represent exciting new
potential targets for therapeutic drug development
in humans.

2. In addition, siRNAs are frequently used to decrease

or "knock-down" specific protein levels in
experimental procedures in the laboratory, an
extremely useful and powerful alternative to gene-
knockout technology.
 Summary
1.RNA exists in several different single-
stranded structures, most of which are
directly or indirectly involved in protein
synthesis or its regulation.
2.The linear array of nucleotides in RNA
consists of A, G, C, and U, and the sugar
moiety is ribose.
 Summary
• The major forms of RNA include messenger RNA
(mRNA), ribosomal RNA (rRNA), transfer RNA
(tRNA), and small nuclear RNAs (snRNAs;
miRNAs).
• Certain RNA molecules act as catalysts
(ribozymes).
• miRNAs and siRNAs represent exciting new
potential targets for therapeutic drug
development in humans.
 Differences between RNA and DNA
S.No. DNA RNA
Single stranded mainly
except when self
Double stranded (Except for
1) complementary sequences
certain viral DNAs which are
are there it forms a double
single stranded)
stranded structure (Hair pin
structure)
The sugar moiety is
2) Ribose is the main sugar
deoxy ribose
Pyrimidine components
Thymine is always there
3) differ. Thymine is never
but uracil is never found
found(Except tRNA)
It does follow Chargaff's rule.
The total purine content in a Being single stranded
4) double stranded DNA is structure- It does not
always equal to pyrimidine follow Chargaff’s rule
content.
 Differences between RNA and
DNA
S.No. RNA DNA
5) RNA can be easily destroyed by DNA resists alkali action due
alkalies to cyclic diesters of to the absence of OH group
mono nucleotides. at 2’ position
6) RNA is a relatively a labile DNA is a stable molecule. The
molecule, undergoes easy and spontaneous degradation is
spontaneous degradation very 2 slow. The genetic
information can be stored for
years together without any
change.
7) Mainly cytoplasmic, but also Mainly found in nucleus,
present in nucleus (primary extra nuclear DNA is found in
transcript and small nuclear mitochondria, and plasmids
RNA) etc
8) The base content varies from Millions of base pairs are
100- 5000. The size is variable. there depending upon the
organism
 Differences between RNA and
S.NDNA
RNA DNA
o
9) There are various types of RNA – DNA is always of one type
mRNA, r RNA, t RNA, Sn RNA, Si and performs the function of
RNA, mi RNA and hn RNA. These storage and transfer of
RNAs perform different and specific genetic information.
functions.
10) No variable physiological forms of There are variable forms of
RNA are found. The different DNA (A to E and Z)
types of RNA do not change
their forms
11) RNA is synthesized from DNA, it DNA can form DNA by
can not form DNA(except by the replication, it can also form
action of reverse transcriptase). It RNA by transcription.
can not duplicate (except in certain
viruses where it is a genomic
material )
12) Many copies of RNA are present Single copy of DNA is
per cell present per cell.