3.3.

The structure of RNA

-Comprised of polynucleotide chains.

-Present in nucleus and cytoplasm

- Enzyme activity- Ribozymes

-Hydrolysis by alkaline because of OH-group

-
-useful for protein synthesis

-Ribose instead of deoxyribose.

-Uracil in place of thymine.

- Most RNA Contain a single polynucleotide strand ( exception some viruses dsRNA)

- Folding back on itself – to form double helical regions- containing A:U and G:C bps.
- Has stem-loop or hairpin structure  Create small base- paired stretches

- Ten times as much RNA as DNA in a cell- due to large variety of roles
Features of RNA
• RNA: polymer composed of a combination of four nucleotides
– adenine (A)
– cytosine (C) 3 Hydrogen Bonds – more stable

– guanine (G)
– Uracil (U)
• Canonical Base Pairs
– A-U
– G-C
– G-U
“wobble” pairing
Three major types of RNA
1) Ribosomal RNA (rRNA)-
- Present in the ribosomes
- Contain equal mass of protein
- Makes 80% of total cell RNA
- Role in Binding mRNA and Protein synthesis
► Three size types in prokaryotic cell (bacteria) and eukaryotic mitochondria
- 5S, 16S, 23S,
►Four rRNA size species in eukaryotic cytosol (ribosome)
- 5S, 5.8S, 18S. 28S.

► S = Svedberg unit – sedimentation rate in ultracentrifuge

- related to their molecular weight

► Most rRNA molecules synthesized in nucleolus ( 5.8S, 18S, 28S)

From one precursor molecule + 5S rRNA + Ribosomal protein
Form pre 40S and 60S ribosomal subunits
Role of rRNA molecules

a) The 28S rRNA

- has a catalytic role as part of peptidyl transferrase
activity of the 60S subunits
b) The 18S rRNA
- has a recognition role involved in correct positioning of
the mRNA and peptidyl tRNA

c) rRNA molecules have structural role

- Fold into 3D shapes forming scaffold for the assembly
of ribosomal proteins
2) Messenger RNA (mRNA)
• Copy of information carried on the gene
• Synthesized in the nucleus - Heterogeneous in size and Role – transfer
the genetic info. in DNA to translational machinery
• High Mwt and short life span
• In eukaryotes synthesized as heterogeneous nuclear RNA (hnRNA) in
nucleus
• hnRNA- contains Introns and exons
• Introns are removed by RNA splicing
• Exons joined together to give information

►RNA editing – process of adding neucleotides in the mRNA sequence

hnRNA & mRNA- bound to cation and proteins in the cell
Forming riboneucleoprotein complex (RNPs)
Cont’d

• The 3‘ end of mRNA is contain polymers of adenlyate

residue called Poly (A) tail
• At the 5‘ mRNA is capped with 7-methyl guanosine
triphosphate and 2‘O-methyl purine
The 5‘ cap & 3‘ tail
provide stability to mRNA

-The cap serves to identify this RNA molecule as mRNA to

the translational machinery
Prokaryotic mRNA. Schematic diagrams
(a) monocistronic and
(b) polycistronic mRNAs of prokaryotes.

- Red segments represent RNA coding for a gene product; gray segments
represent noncoding RNA.
- In the polycistronic transcript, noncoding RNA separates the three
gene
•Monocistronic: coding for only one polypeptide

•Polycistronic: coding fro two or more different polypeptide

►Small nuclear RNA (snRNA)- Component of splicesome

-refers to a number of small RNA molecules in nucleus
- important in many processes
RNA splicing- removal of introns from hnRNA
Maintenance of telomeres (chromosome ends)
Found in association with specific proteins to form small nuclear
ribonucleoproteins (SNRNPs) or as snurps.

Antibodies against snurps found in autoimmune diseases

 Small Nucleolar RNA( snoRNA)
- takes part in RNA processing

Function of snoRPA:
(~ 100 in number)
• Participate in making ribosome during splicing by helping to
cut the large RNA precursors (28S,18S.5.8S molecules)
• Some Modify many nucleotides in these molecules
by adding methyl groups to ribose
• Serve as a template for the synthesis of telomeres.
Major Classes of Non translated RNA

Name Function
Rbosomal RNA Component of ribisomes, Synthesis
of polypeptide chain
tRNA Carrier amino acids to ribosomes
Recognizes codon on mRNA
snRNA Splicing of mRNA (in eukaryotes)
Guide RNA Involved in processing of RNA or
DNA in some organisms
Regulatory RNA (RNAi ) Regulation of gene expression by
binding to proteins of DNA or to
other RNA molecules
Antisense RNA Regulating gene expression by base
pairing to mRNA
Recognition RNA Part of few enzymes (telomerase)
enable them to recognize short DNA
sequence
Ribozymes Enzymatically active RNA molecule
3) Transfer RNA (tRNA)
• The smallest of RNA molecule (4S)
• Has 73-93 nucleotides.
• One specific type of tRNA for each of the 20 amino acids, >20 different
tRNA molecules
• Make up 15% of total RNA in the cell
• Each tRNA serve as an “adaptor” molecule that carries amino acids to
the site of protein synthesis.
• It recognizes the genetic code word and add specific amino acid to the
growing polypeptide chain.
• tRNA – the direct interface between amino-acid sequence of a protein
and the information in DNA
• It decodes the information in DNA
• All tRNA from all organisms have similar structure
• There are – 4 arms
- 3 loops
Processes in which RNA is involved

•Translation
•Transcription
•RNA splicing
• RNA processing and editing
• cellular localization
•catalysis
Secondary structure of the RNA

• Intermediary between a linear molecule

and a three-dimensional structure
• Composed of double-stranded RNA regions formed by folding the
single-stranded RNA molecule back on itself.
Stem Loops (Hairpins)-Loops generally at least 4 bases long
Bulge Loops- occur when bases on one side of the
structure cannot form base pairs
Interior Loops

• occur when bases on both sides of the structure cannot form base
pairs
Junctions (Multiloops)

• two or more double-stranded regions converge to form a

closed structure
Single stranded bases within a stem are called a bulge of bulge loop if the
single stranded bases are on only one side of the stem.

If single stranded bases interrupt both sides of a stem, they are called an
internal (interior) loop.
Hierarchical organization of RNA molecules
• Primary structure: order of nucleotides in a chain

5’ ACCACCUGCUGA 3
Tertiary structure: Secondary Structure
(Conformation of - Pattern of baser-pairing
Molecules in 3D)
Tertiary Interactions
• Kissing Hairpins-
• unpaired bases of two separate hairpin
loops base pair with one another
Pseudoknots
Hairpin-Bulge Interactions
Complete RNA structure

Pseudoknot

Stem

Interior
Loop

Single-Stranded

Bulge Loop
Hairpin loop Junction (Multiloop)
Structure of tRNA

• secondary structure of tRNA. Blue color indicates modified nucleotides,

with "m" representing "methylated". Anticodon is the trinucleotides
complementary to a codon on mRNA.
Cont’d

• Some nucleotides in tRNA have been modified, such as

dihydrouridine (D),pseudouridine (ψ ), and inosine (I).
• In dihydrouridine, a hydrogen atom is added to each C5
and C6 of uracil.
• In pseudouridine, the ribose is attached to C5, instead of
the normal N1.
• Inosine plays an important role in codon recognition. In
addition to these modifications, a few nucleosides are
methylated
• 3‘termianl is acceptor stem where aa attaches
Ribosome

• In prokaryotes, the ribosomal RNA (rRNA) has three types: 23S, 5S,
and 16S
• In mammals, four types of rRNA have been found : 28S, 5.8S, 5S
and 18S.
• In prokaryotes, the size of a ribosome is 70S, consisting of two
subunits: 50S and 30S.
• The size of a mammalian ribosome is 80S, comprising a 60S and a
40S subunit.
• Proteins in the larger subunit are designated as L1, L2, L3, etc. (L =
large). In the smaller subunit, proteins are denoted by S1, S2, S3,
• The composition of ribosomes
Ribosome binds to mRNA and tRNA –only the tRNA containing the

anticodon which matches mRNA's codon may join the complex

• The mRNA-ribosome-tRNA complex formed during protein synthesis

 O
• RNA C N G
HN C
CH
H2N-C C
N N
5’
5’ end HO-CH2 NH2
O C
4’ 1’
N CH
C
3’ 2’
C
GCUAp
OH CH
O O N
O P O CH2 O
O
O C
HN CH U
OH C CH
O O N
O P O CH2 NH2
O
O C N
N C
A
CH
HC C
O OH N N
O P O CH2
O
O
3’
OH
3’ end O-PO32
 O
• DNA C N
HN C G
CH
H2N-C C
N N
5’
5’ end HO-CH2 NH2
O C
4’ 1’
N CH
C
3’ 2’
C
GCTAp
CH
O O N
O P O CH2 O
O
O C CH3
HN C T
C CH
O O N
O P O CH2 NH2
O
O C N
N C
A
CH
HC C
O N N
O P O CH2
O
O
3’
3’ end O-PO32
Summary
• Nucleotides have three parts: sugar (ribose in RNA,
deoxyribose in DNA), base (purine,A, G, and pyrimidine, C, T
or U), and phosphate group.
• Nucleotide can polymerise to form polynucleotides, or
“strands”.
• DNA (deoxyribo nucleic acid) is a double stranded helix,
where the two strands run in opposite directions and are
maintained together by hydrogen bonds. Base pairs include
one purine and one pyrimidine (A-T and G-C).
• There are three main forms of DNA helices: A, B and Z.
• DNA molecules have topological constraints, such as
supercoiling.
Cont´d
• Only one DNA strand is used for RNA synthesis: the “template” strand,
which is complementary to the coding strand. The sequence of the mRNA
is the sequence of the coding strand, where T are replace by U.

• Three types of RNA are involved in protein synthesis: messenger RNA

(mRNA, carries the information), transfer RNA (tRNA, brings the correct
amino acid during synthesis), and ribosomal RNA (rRNA, major consituent
of the ribosome, where protein synthesis occurs.

• The message carried by the mRNA is read as a collection of “words” of 3

letters, or codons. There are 64 codons, that code for 20 amino acids. AUG
is the initiation codon, which codes for Methionine. UAA, UAG and UGA
are stop codons. There is redundancy in the genetic code, related to the
third base in the codon.
Cont'd
• RNA bases can be free, involved in base pairs, or base triplets.

• RNA contains single stranded regions, hairpin loops, bulges, and

internal loops (secondary structures)

• RNA secondary structures can interact to form pseudoknots,

kissing hairpins, or hairpin-bulge complexes.

• The wobble hypothesis is based on the presence in some tRNA of

Inosine at the 5’ end of the anticodon. It is one possible
explanation of the degeneracy of the genetic code.
RNA processing

-To generate a mature mRNA (for protein genes) or a

functional tRNA or rRNA from the primary transcript

►Processing of pre-mRNA involves the following steps:

-Capping - add 7-methylguanylate (m7G) to the
5'end.
-Polyadenylation - add a poly-A tail to the 3' end.
-Splicing - remove introns and join exons.
The procedure of RNA processing
5'-Capping
• Modifications at the 5' end.
• occurs shortly after transcription begins
• m7G is linked to the first nucleotide by a
special 5'-5' triphosphate linkage

Sometimes
methylated
3'-Polyadenylation
• A stretch of adenylate residues are added to the 3' end
• Poly-A tail contains ~ 250 A residues in mammals, and ~ 100 in yeasts.

• Polyadenylation at the 3' end. The major signal for the 3' cleavage is the
sequence AAUAAA. Cleavage occurs at 10-35 nucleotides downstream from
the specific sequence. A second signal is located about 50 nucleotides
downstream from the cleavage site. This signal is a GU-rich or U-rich region.