RNA

Ms. Rima Dessai

CENTRAL DOGMA
Ribonucleic acid (RNA)
✓ Ribonucleic acid (RNA) is a molecule that is present in
the majority of living organisms and viruses.
✓ Ribonucleic acid (RNA) is a polymer of ribonucleotides
that contains the sugar Ribose and the bases Adenine,
Guanine, Cytosine, and Uracil (instead of thymine)and a
phosphate group
✓ The nucleotides are joined by a phosphodiester bond
✓ Strands of RNA are typically several hundred or several
thousand nucleotides in length, which is much shorter
than chromosomal DNA
✓ Transcription is the process of RNA formation from DNA,
and translation is the process of protein synthesis from
RNA.
✓ RNA molecules are Single stranded.

✓ However, an RNA strand can coil back on itself to form secondary structures

such as hairpins with complementary base pairing and helical

organization .

✓The helical structure of RNA molecules is due to the ability of complementary regions to
form base pairs between A and U and between G and C

✓Different types of structural patterns are possible such as bulge loops, internal loops,
multibranched junctions, and stem-loops (also called hairpins)

✓The structure of the RNA molecule was described by R.W. Holley in 1965.
Why is DNA is more Stable then RNA?
✓The presence of a chemically reactive hydroxyl (−OH) group attached to
the second carbon group in the Ribose sugar molecule makes RNA prone
to hydrolysis.

✓This chemical lability of RNA, compared with DNA, which does not have a
reactive −OH group in the same position on the sugar moiety
(deoxyribose), is thought to be one reason why DNA evolved to be the
preferred carrier of genetic information in most organisms.
DNA RNA
It is Double Stranded It is Single Stranded
DNA is larger with millions of RNA is smaller with hundred to
nucleotides thousands of Nucleotides
DNA has Deoxyribose Sugar RNA has Ribose Sugar
DNA is primarily located in the RNA is found in the nucleus or
Nucleus Cytoplasm
Nitrogenous bases : Adenine , Nitrogenous Bases : Adenine ,
Guanine, Cytosine and Thymine Guanine, Cytosine and Uracil
• Three main types of RNA are involved in protein
synthesis.
1. Messenger RNA (mRNA)
2. transfer RNA (tRNA) and
3. ribosomal RNA (rRNA).
 RNA

Coding Non Coding

RNA RNA

Act as cellular regulators

Encode proteins to act as without encoding proteins
various components including tRNA
enzymes , cell structures, rRNA
and signal transductors microRNA
mRNA siRNAs
mRNA
✓It is 1-5% of the cells total RNA

✓Discovery : Hoxley , Volkin , and Astrachan

✓It was produced by genetic DNA in Nucleus. this process is known as

Transcription.

✓They are synthesized from DNA by an RNA polymerase through a process

called as Transcription.

✓Messenger RNA (mRNA) is a single-stranded RNA molecule that is

complementary to one of the DNA strands of a gene
1. Messenger RNA (mRNA)
Functions:

✓mRNA carries the genetic information copied from DNA in the form of a series of
triplet codon , each of which specifies a particular amino acid.

✓mRNA – acts a template for protein synthesis .

✓During protein synthesis, ribosome moves along the mRNA, reads its base
sequence, and uses the genetic code to translate each three-base triplet, or codon,
into its corresponding amino acid.

✓mRNAs which represents only single gene are called Monocistronic mRNA and
mRNAs which represent more than one gene are called Polycistronic mRNA.
 Transcription
DNA 5’ ATGGGGCTCAGCGAC 3’
Sense or Coding
Strand

3’ TACCCCGAGTCGATG 5’ Antisense or template

Strand

5’ AUGGGGCUCAGCGAC 3’ mRNA with codon

mRNA
 Prokaryotic mRNA
✓They contain polycistronic mRNA

✓In prokaryotes, mRNA molecules often contain information for the amino acid
sequences of several different polypeptide chains; in this case, such a molecule is
called poly- cistronic mRNA.

✓A polycistronic mRNA contains multiple cistrons.

✓An intercistronic spacer sequence that is not translated separates the cistrons of
polycistronic mRNA.

✓Polycistronic mRNA contains multiple binding sites.

✓Prokaryotic mRNA does not need to be processed and can proceed to synthesize
proteins immediately
Eukaryotic mRNA
✓They contain monocistronic mRNA.
✓Contains 1500 to 2000 nucleotides.
✓A monocistronic mRNA contains single ribosome-binding site.
✓In eukaryotes, a freshly transcribed RNA transcript is considered a pre-mRNA and needs
to undergo maturation to form mRNA. This process is called as Post transcriptional
Modifications
Structure of mRNA
• mRNAs contain two types of regions –
1. coding or translatable region- in all mRNAs it consists of codons starting with an
initiation or start codon and ending with an termination or stop codon.
Protein synthesis begins at initiation codon.

2. non-coding or untranslatable region- both the mRNA strands they contain

untranslatable sequences called 5’- UTR (5’ Untranslated regions) or leader
sequence and 3’ – UTR (3’ untranslated regions) or trailer sequence.

• mRNA is composed of contiguous, non overlapping strings of codons

called an Open Reading Frame (ORF).
• Genetic Code :
It is a trinucleotide sequence having a meaning for particular amino
acids.

• Open Reading Frame

• It is a continuous stretch of certain codons that starts with a start
codon and ends with a stop codon.
 Transfer RNA (tRNA)

• It is 10-15% of the total RNA

• It is synthesized in the Nucleus by DNA
• It is also known as Adaptor RNA

• Functions:
• At the time of protein synthesis , it acts a carrier of amino acids
• It carries a specific amino acid and corresponds to the codon of the mRNA
according to the genetic code.
• aa- tRNA synthetase enzyme are a group of enzymes that attach the
correct aa to the tRNA – Charged t-RNA
Transfer ribonucleic acid (tRNA)
✓It is a single chain of 73-93 nucleotides

✓Holley and his co-workers first determined the sequence of Yeast tRNA in 1965

✓It is also known as Adaptor RNA. The concept of an adaptor to provide the

interface between nucleic acid language and protein language was

introduced by crick in 1955

✓Transfer ribonucleic acid (tRNA) is a type of RNA molecule that helps

decode a messenger RNA (mRNA) sequence into a protein.

✓tRNA folds into cloverleaf leaf secondary structure with well defined stems and
loop that make up the accepted arm, D arm , anticodon arm and TѰC arm

✓This secondary structure in turn folds into an L-shaped tertiary structure , through
complex tertiary interactions. Including those between D loop and TѰC loop

✓The Acceptor arm always has a 7 bp and 4 unpaired nucleotide sequence ,

including an absolutely conserved CCA sequence.The 5’- CCA 3’ is universally
conversed for all the tRNA’s
Structure of tRNA
 Structure of tRNA
They have a cloverleaf structure that consists
of :
1. 3’ acceptor site-it is 7bp
-the 5’ end CCA and 3’ end is always conserved
for all tRNAs
2. D arm- it has 3-4 bp stem and 5-7 nucleotide
loop that always contain a modified base
Dihydrouridine
3. T arm- contains 5bp stem and a loop that
usually contains an unusual base
Pseudouridine.
Variable arm
4. Anticodon arm- 5bp stem and a loop
containing anticodon, a three nucleotide
sequence responsible for recognizing codon on
mRNA.
5. Variable arm- contains 4-5 nucleotides
✓All tRNA’s share the same secondary structure.

✓tRNA’s can be classified according to the length of the variable arm.

✓A Striking aspect of tRNA’s is the presence of several unusual bases in their

primary structure. these are derived post transcriptionally by enzymatic
modification of normal bases in the polynucleotide chain

✓Pseudouridine – Uridine (nucleoside)

✓Dihydrouridine – Uridine

✓Other unusual bases found in tRNA include Hypoxanthine , and Methylguanine,

Ribothymidine , Inosine
✓Each type of amino acids has its own type of tRNA, which binds it and carries it to
the growing end of the polypeptide chain

✓Prokaryotes contain 30-45 different tRNA’s and Eukaryotes have 50 or more

different tRNA’s

✓Since Standard amino acids are only 22 , two or more different tRNA’s that are
specific for same amino acids are termed as isoaccepting tRNA’s
Aminoacyl-tRNA synthetases
✓ Aminoacyl-tRNA synthetases are enzymes that attaches the appropriate amino acid onto a
free 3’ end of tRNA to synthesize proteins (Charging of tRNA).

✓ Once an amino acid is bound to tRNA, the tRNA is considered as an aminoacyl-tRNA.

✓ Cells produce 20 different aminoacyl-tRNA synthetase enzymes, 1 for each of the 20 distinct
amino acids.

✓ The type of amino acid on a tRNA is dependent on the mRNA codon, which is a sequence of
three nucleotides that codes for an amino acid.

✓ The anticodon arm of the tRNA is the site of the anticodon, which is complementary to an
mRNA codon and dictates which amino acid to carry.

✓ Each aminoacyl-tRNA synthetase is named for the specific amino acid it attaches to tRNA.

✓ For example, alanyl-tRNA synthetase recognizes a tRNA with an alanine anticodon—

tRNAAla—and attaches an alanine to it.
• During mRNA-tRNA recognition, the anticodon in a tRNA molecule binds to a codon in
mRNA due to their complementary sequences.
• Importantly, the anticodon in the tRNA corresponds to the amino acid that it carries.
• For example, if the anticodon in the tRNA is 3ʹ–AAG–5ʹ, it is complementary to a 5ʹ–UUC–3ʹ
codon. According to the genetic code, the UUC codon specifies phenylalanine.
3. Ribosomal RNA (rRNA)
• rRNA (ribosomal RNA) associates with a set of proteins to form ribosomes.
• They are the most abundant form of RNA in the cell (80%).
70S Ribosome (Prokaryotic) 80S Ribosome(Eukaryotic)

60S 40S
50S 30S

23S 5S 28S 5.8 S 5S

16S 18S
S
Sedimentation
Coefficient/Svedberg Unit
Depends on the density and size of
ribosome
Ribosomal RNA (rRNA)
• It is 80% of the cell total RNA
• It was discovered by kuntze
• It is found in ribosomes
• Function :
• At the time of protein synthesis , rRNA provides an attachment site
for both tRNA and mRNA and attaches them on the ribosome
• It attaches t-RNA to the larger sub unit of ribosome and mRNA to the
smaller sub-unit of ribosome.
 ROLES OF rRNA IN PROTEIN SYNTHESIS
• 28S rRNA and 23S rRNA have a catalytic role.
It forms part of the peptidyl transferase activity of 60S and 50S subunit,
respectively.

• 18S rRNA and 16S rRNA has a recognition role.

It is involved in the correct positioning of the mRNA and small ribosomal
subunit.
Function
✓Initiation of protein synthesis in prokaryotes involves association of
30S and 50S Subunit
✓The Small and Large Subunit associate at the Ribosome Binding Site ,
a short nucleotide sequence that precedes the coding region .
✓It contains Shine Dalgarno sequence and and the initiation codon
✓Shine Dalgarno sequence is complementary to a region at the 3’ end
of 16s RNA(the one present in smaller subunit)
✓Base pairing between the two is involved in attachment of small
subunit to the mRNA
 Small regulatory RNAs
• The primary function of RNA is to create proteins via translation.
• Other functions includes RNA editing, gene regulation, and RNA interference.
• These processes are carried out by a group of small regulatory RNAs, which
include small nuclear RNA, microRNA, and small interfering RNA.

a. Small Nuclear RNA

• Small nuclear RNAs (snRNA) are non-coding RNAs that are responsible for
splicing introns.
• The snRNAs join with proteins to form small nuclear ribonucleoproteins
(snRNP), which most commonly contain U1, U2, U4, U5, and U6 snRNA
molecules.
RNA Interference (RNAi)
✓RNA interference (RNAi) is a biological process in which small
RNA molecules inhibit gene expression.

✓Historically, RNAi was known by other names, including co-suppression, Post-

transcriptional gene silencing (PTGS), and quelling.

✓It is observed in all eukaryotes , From yeast to mammals

✓They play an important role in Post Transcriptional gene regulation , Transposon

regulation and defending cells against viruses.

✓Two types of small RNA molecules – microRNA (miRNA) and small interfering
RNA(siRNA) – are central to RNA interference.
 d/S RNA Molecule

✓Although RNA is a single-stranded molecule, researchers soon discovered

that it can form double-stranded structures, which are important to its
function.

✓In 1956, Alexander Rich—an X-ray crystallographer and member of the

RNA Tie Club—and David Davies, both working at the National Institutes
of Health, discovered that single strands of RNA can "hybridize," sticking

together to form a double-stranded molecule (Rich & Davies, 1956).

MicroRNAs (miRNAs)
▪ MicroRNAs (miRNAs) are small , noncoding RNA molecules(19-25 nucleotides) that
are found in the genome of plants , animals, and their viruses.

▪ They are small Silencing RNA

▪ Victor Ambros and his colleagues identified the first mi-RNA , lin 4 in C.elegans over
a decade ago.

▪ These highly conserved 20-25 nt long RNA appear to regulate gene expression post-
transcriptionally by binding to the 3’ UTR region of target mRNA

▪ miRNA resemble the small interfering RNAs (siRNA) of the RNA interference (RNAi)
pathway except miRNA derive from regions of RNA transcripts that fold back on
themselves to form short hairpin ,whereas siRNA derive from longer regions of
dsRNA.
▪ mi - RNA genes are already present in the Nucleus.

▪ mi – RNA will be synthesized in the nucleus by RNA Pol II enzyme as pro-pre-mi-

RNA, which is a hair pin loop structure.

▪ An RNAase III enzyme Drosha (endonuclease) in conjugation with ds RNA binding

protein Pasha (drosophila) and DGCR8(Mammals) bind to pro-pre-mi-RNA ,
forming a Microprocessor complex

▪ Microprocessor complex carries out processing of pro-pre-mi-RNA into pre-mi-

RNA

▪ Pre-mi-RNA is then transported from nucleus to cytoplasm by exportin -5

▪ In the cytoplasm , Dicer protein which is an endonuclease cleaves the pre-mi-RNA

into small mi-RNA fragments
▪ mi-RNA contains two strands , Guide strand and Passenger Strand or Anti-

Guide Strand of which passenger strand will be selectively degraded

▪ Some Argonaute family proteins will bind to guide strand of mi-RNA forming

RISC (RNA induced Silencing Complex) Complex.

▪ RISC Complex binds to target mRNA, and carries out degradation of mRNA

▪ Gene Silencing will occur either via mRNA degradation or by preventing the

mRNA from being translated.

▪ miRNA interact with the 3’ UTR of target mRNAs to suppress expression.

Pre-pro
mi-RNA
Small Interfering RNA (Si-RNA)
▪ Small Interfering RNAs (siRNA) are double-stranded, non-coding RNAs that are
processed into 21-25 nucleotide long Si-RNA
▪ They inhibit gene expression through RNA interference.
▪ They interfere with gene expression by degrading mRNA and preventing the Translation
of proteins.
▪ They are 21-25 nucleotide long
▪ They had an accidentals discovery .They were first discovered in C. elegans ( Nematode).
Scientist introduced d/s RNA into the embryo of C. elegans. As soon as they introduced
d/S RNA into C. elegans , some developmental defects were seen.
▪ Small interfering RNAs have the potential to be therapeutic agents for diseases due to
their potency and ability to knock down genes.
Small Interfering RNA (Si-RNA)

▪ Si-RNA’s are formed from double Stranded RNA with the assistance of an
enzyme called as DICER.
▪ DICER is an endonuclease , which is basically an RNAse III family enzyme that
degrades double stranded RNA into 21-25 nucleotide fragments called as Si-RNA
▪ Si-RNA has two Strands , Guide Strand and Passenger Strand.
▪ Anti-guide or Passenger Strand is relatively degraded during RISC (RNA
Induced Gene Silencing ) activation
▪ Only Guide Strand directs the gene silencing.
▪ A group of Argonaute family proteins bind to the guide strand of Si-RNA
▪ Together they form (RNA induced Silencing Complex) RISC Complex.
▪ Si-RNA –RISC Complex will go and bind to target mRNA
Small Interfering RNA (Si-RNA)

▪ After binding to the mRNA, two different things may happen.

▪ In some cases, the RISC may direct the degradation of the mRNA through
complementary base.

▪ Alternatively, the RISC may inhibit translation.

 Guide Strand

Passenger Strand

Guide Strand-RISC Passenger Strand is

Complex degraded
References
• Robert J. Brooker; Genetics : analysis & principles ; fourth Edition
(2012)
• Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith
Roberts, Peter Walter; Molecular biology of the cell; fifth edition
• Wang D, Farhana A. Biochemistry, RNA Structure. [Updated 2020 Jun
23]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls
Publishing; 2021 Jan-. Available from:
https://www.ncbi.nlm.nih.gov/books/NBK558999/