RNA: Structure &

Synthesis
By
Amr S. Moustafa, M.D.; Ph.D.

Objectives
The differences between DNA and RNA
The structure and functions of RNAs
RNA synthesis (Transcription)
Post-transcriptional events (modifications)

RNA & DNA: Similarity

Both RNA & DNA:
Unbranched polymers
Nucleoside monophosphate
Phosphodiester bonds

RNA & DNA: Differences

RNA

DNA

Single-Strand (mostly)
Cytoplasm (mainly)
AGCU (exception)
Modified bases
Ribose
Protein Biosynthesis
Post-transcriptional events

Double
Nucleus
d AGCT
Deoxyribose
Storage &transfer
DNA Repair

Gene Expression - 1

Gene Expression - 2
Information
Pathway
From Nucleus
to
Cytoplasm

DNA(Gene)
(1) mRNA
(2) Protein

RNA: Types
Major types:
Ribosomal RNA (rRNA)

80%

Transfer RNA (tRNA)

15%

Messenger RNA (mRNA)

5%

Others:
Small nuclear RNA (snRNA)

The rRNA
Nucleoprotein
complexes
of ribosomes
Svedberg Unit:
Related to
Molecular weight
& Shape

The tRNA
Smallest RNA
4S (74 95)
At least 20 species
Unusual bases
Secondary structure
Intra-chain base pairing
Adaptor molecule
Carries its sp. a.a. to site
of protein biosynthesis

The mRNA
Size:Heterogeneous
(500 6000)
Primary (precursor):
hnRNA
Post-transcriptional
Processing of
Euokaryotic mRNA
Carries genetic information
from nucleus to cytoplasm
(Template of protein synthesis)

RNA Synthesis
(Transcription)
Transcription: the copying process which uses
one of the two DNA strands (template strand)
to form RNA
Other DNA strand: coding strand
Similar to RNA strand (with exception)
Transcription is highly selective:
Some DNA regions form many,
other form few or no transcripts

Transcription - 2
The selectivity is due to
signals in the DNA nucleotide sequence
The signals convey a message to
RNA polymerase to define:
Where polymerase should start?
How often? (frequency)
Where to stop? (termination)

Transcription 3
Prokaryotic RNA
polymerase

Transcription 4
Prokaryotic RNA
polymerase

One species for all RNAs

(Except primase for RNA primer)
No exonuclease or proofread activity
Transcription:
Initiation: Recognition of promoter sequence
Elongation: 5 3 polymerizing activity
Termination: (rho)-independent

Transcription 5
Complementary
and
antiparallel
DNA and RNA

Transcription 6
Prokaryotic Promoter
Promoter is DNA sequence recognized by ()
Sigma factor of RNA polymerase holoenzyme
where transcription should start
Consensus, highly conserved sequences
-10 Pribnow box (TATAAT)
-35 Sequence (TTGACA)
(as read 5 3 on nontemplate coding strand)
Mutant promoter affects transcription of its gene

Transcription 7
Prokaryotic Promoter

Consensus, highly conserved sequences

Transcription 8
Transcription Unit
Transcription Unit:
DNA region from promoter to termination
The product: primary transcript

Transcription 9
Initiation
Binding of RNA polymerase holoenzyme to promoter
Local unwinding
Supercoils (Topoisomerases I & II)
Denovo synthesis: No primer required
Substrate: Ribonucleoside triphosphate
Usually begins with a purine
No proofreading
Once promoter is recognized,
Sigma () factor is released

Transcription 10
Elongation
Direction: 5 3, antiparallel
Complementarity: as DNA, but for A there is U
release of pyrophosphate
Relaxation of supercoils:
Topoisomerases I and II

Transcription 11
Termination
A-The rho ()-dependent termination:
The -factor binds to C-rich near 3-end of RNA
It has ATP-dependent DNA-RNA helicase activity
Hydrolyzes ATP (Energy-dependent)
Unwind 3-end of the transcript from template
Movement of () protein along RNA/DNA hybrid 5-3
Displacement of DNA template at termination site,
releasing of RNA transcript

Transcription 12
Termination (Contd)
B-The rho-independent termination:

Transcription 13
Inhibitors (Antibiotics)
Rifampin (anti-tuberculous):
binds to the -subunit
interferes with formation of first phosphodiester bond
inhibit RNA synthesis and bacterial growth

Dactinomycin (Actinomycin D):

binds to minor groove of DNA template
interferes with movement of RNA polymerase
inhibits prokaryotic transcription (antibiotic)
inhibits euokaryotic replication (anticancer)

Transcription
14
Rifampin inhibits
RNA polymerase
and transcription