Transcription and RNA

processing
 The first stage in the expression of
genetic information is transcription of
the information in the base sequence
of DNA molecule to form the base
sequence of a molecule of RNA.
• For any particular gene, only one
strand of the DNA molecule called the
template strand, is copied by RNA
polymerase as it synthesizes RNA in
the 5ʹ to 3ʹ direction.
 Because RNA polymerase moves in the
3ʹ to 5ʹ direction along the template
strand of DNA, the RNA product is
antiparallel and complementary to the
template.
 RNA polymerase recognizes start
signals (promoters) and stop signals
(terminators) for each of the
thousands of transcription units
(genes) in the genome of an organism.
Promoter
Terminator
Transcription
5ʹ 3ʹ

Gene 1 Gene 2

3ʹ 5ʹ
Transcription
Promoter
Terminator
1. Ribosomal RNA (rRNA):- The most
abundant type of RNA in the cell. It is
used as structural component of the
ribosome.
2. Transfer RNA (tRNA):- The second
most abundant type of RNA.

 Its function to carry amino acids to

the ribosome, where they will be
linked together during protein
synthesis.
3. Messenger RNA (mRNA):- carry the
information specifying the amino acid
sequence of a protein to the
ribosome.

 It is the only type of RNA that is

translated.
4. Heterogeneous nuclear RNA (hnRNA)
or (pre-mRNA):- found only in the
nucleus of eukaryotic cells.
5. Small nuclear RNA (snRNA):- found
only in the nucleus of eukaryotes.

 One of its major functions is to

participate in splicing mRNA (removal
of introns).
6. Ribozymes: which are RNA molecules
with enzymatic activity. Found in both
prokaryotes and eukaryotes.
• RNA is synthesized by a DNA-
dependent RNA polymerase (uses DNA
as a template for synthesis of RNA).
 RNA polymerase locates genes in DNA
by searching for promoter regions.

 The promoter is the binding site for

RNA polymerase.
 No primer is required.

• The RNA product is synthesized in the

5ʹ to 3ʹ direction using NTPs (ATP,
GTP, UTP, CTP) as substrate.
 It is complementary and antiparallel to
the template strand.

 RNA polymerase does not proofread

its work.
 The coding (antitemplate) strand is
not used during transcription.

 It is identical in sequence to the RNA

molecule, except that RNA contain
uracil instead of the thymine found in
DNA.
 Transcription ends when RNA
polymerase reaches a termination
signal.
 Transcription unit

Start site terminater

Antitemplate
₋10 ₊1 (coding) strand
5ʹ ₊10 3ʹ
DNA promoter RNA
3ʹ 5ʹ polymerase
Template strand
transcribes
RNA 5ʹ 3ʹ
DNA template
strand
RNA transcript is
synthesized 5ʹ to
3ʹ
• There is a single prokaryotic RNA
polymerase that synthesizes all types
of RNA in the cell.

• This enzyme has the subunit structure

α₂ββʹ, a protein factor called sigma (σ)
is required for the initiation of
transcription at a promoter.
• This enzyme is inhibited by rifampin.

• Actinomycin D binds to the DNA,

preventing transcription.
1. RNA polymerase I: is located in
nucleolus and synthesizes most
rRNAs.

2. RNA polymerase II: is located in the

nucleoplasm and synthesizes
hnRNA/mRNA and some snRNA.
3. RNA polymerase III: is located in the
nucleoplasm and synthesizes tRNA,
some snRNA and one type of rRNA
subunit.
1. With the help of sigma factor, RNA
polymerase recognizes and binds to
the promoter region.
2. The RNA polymerase separates the
two strands of DNA as it reads the
base sequence of the template
strand.
3. Sigma factor is released as soon as
transcription is initiated.
4. The core polymerase (α₂ββʹ)
continues moving along the template
strand in the 3ʹ to 5ʹ direction,
synthesizing the mRNA in the 5ʹ to 3ʹ
direction
5. RNA polymerase reaches a
transcription termination signal, at
which point it will stop transcription
and release the completed mRNA
molecule.
1. In eukaryotes, most gene are
composed of coding segments
(exons) interrupted by non coding
segments (introns).
2. With the help of proteins called
transcription factors, RNA polymerase
II recognizes and binds to the
promoter region.
3. RNA polymerase II separates the two
strands of the DNA over a short
region to initiate transcription and
read the DNA sequence.
4. The template strand is read in the 3ʹ
to 5ʹ direction as the RNA product
(pre mRNA) is synthesized in the 5ʹ to
3ʹ direction.
5. Both exons and introns are
transcribed.

6. RNA polymerase II ends transcription

when it reaches a termination signal.
 Genes encoding other classes of RNA
are also transcribed ( in eukaryotes by
using different RNA polymerase
enzymes), but the RNA products are
not translated to produce proteins.
 Processing of Eukaryotic
mRNA

(Posttranscriptional Modification)
 In eukaryotic, premature RNA
(hnRNA) should be processed in order
to give mature mRNA

 (Note; prokaryotic RNA not requires

these processes).
1. Capping: addition of 7-
methylguanosine cap to the 5ʹ end.
This cap serves as a ribosome binding
site and also helps to protect the
mRNA chain from degradation.
2. Tailing: a poly- A tail is attached to
the 3ʹ end to protects the message
against rapid degradation and aids in
its transport to the cytoplasm.
3. Splicing: introns are removed from
hnRNA by splicing, and then the
neighboring exons are joined
together to assemble the coding
region of the mature mRNA.
 Transcription unit
Promoter Intron Intron 2
Exon 2 Exon Exon 3
1 2
Gene
Transcription
(template
strand)
Primary RNA E1 E2 E3
transcript

Cleavage
at and
discard
introns

Mature E1 E2 E3
mRNA
 DNA polymerase RNA polymerase

 Nucleic acid  Nucleic acid

synthesized synthesized
(5ʹ to 3ʹ) (5ʹ to 3ʹ)
 Required DNA  Required DNA
template template
(copied 3ʹ to 5ʹ) (copied 3ʹ to 5ʹ)
 Required
 Required
substrates: ATP,
substrates: dATP,
GTP, CTP, UTP.
dGTP, dCTP, dTTP.
 Required primers:  Required primers:
RNA or DNA. None
 Proofreading  Proofreading
activity (3ʹto 5ʹ activity (3ʹto 5ʹ
exonuclease): Yes exonuclease): No

DNA Polymerase RNA Polymerase

 Prokaryotic Eukaryotic
 Gene : genes are  Gene: genes have
continuous coding exons and introns.
regions.
 RNA polymerases:
 RNA polymerase: 1. RNA polym. I : rRNA
core enzyme α₂ββʹ, 2. RNA polym. II:
synthesizes all types mRNA, snRNA.
of RNA. 3. RNA polym. III:
tRNA, one type of
rRNA subunit.
 Prokaryotic Eukaryotic

 Initiation of  Initiation of
transcription: sigma transcription:
subunit is used to Transcription factors
recognize promoter. recognize and bind
promoter.
 Relationship of RNA  Relationship of RNA
transcript to DNA: RNA transcript to DNA:
is antiparallel and Also
complementary DNA
template strand; RNA
is identical (except U
substituted for T) to
DNA coding strand.
 Prokaryotic Eukaryotic

 Posttranscriptional  Posttranscriptional
processing of hnRNA processing of hnRNA
(pre mRNA): None (pre mRNA):
1. 5ʹ cap (7-MeG).
2. 3ʹ tail (poly A
sequence.
3. Removal of introns
from hnRNA.

 Ribosomes: 70S (30S +  Ribosomes: 80S (40S

50S) rRNA + protein + 60S) rRNA + protein