FAR EASTERN UNIVERSITY – NICANOR REYES MEDICAL FOUNDATION BIOCHEMISTRY AUGUST 2019

LESSON 6: DNA TRANSCRIPTION The Basics of Transcription

Overview of Transcription
 RNA is synthesized on a DNA template,
catalyzed by DNA-dependent RNA
polymerase.
 ATP, GTP, CTP, and UTP are required,
as is Mg2+.
 No RNA primer is required.
 The RNA chain is synthesized in the 5’
→ 3’ direction; the nucleotide at the 5’
end of the chain retains its triphosphate
(ppp) group.
 RNA polymerase unwinds the helix.
Promoter Sequence
 The DNA base sequence contains
 Simplest of organisms contain a lot of
signals for initiation and termination of
DNA that is not transcribed.
RNA synthesis; the enzyme binds to and
 RNA polymerase needs to know which
moves along the DNA template in the 3’
→ 5’ direction. strand is template strand, which part to
transcribe, and where first nucleotide of
 The DNA template is unchanged.
gene to be transcribed is.
 Promoter:
Transcription in Prokaryotes
o A DNA sequence that provides
 E. coli RNA Polymerase:
direction for RNA polymerase.
 Four different types of subunits: α, β, β+,
and σ.
Parts of a Gene
 The core enzyme is α2ββ+.  Promoter Region
 The holoenzyme is α2ββ+σ.
 Coding Region
 The role of the σ subunit is recognition  Termination Region
of the promoter locus; the σ subunit is
released after transcription begins.
 Of the two DNA strands, the one that
serves as the template for RNA
synthesis is called the template strand
or antisense strand; the other is called
the coding (or nontemplate) strand or
sense strand.

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Promoter Sequence

Initiation and Elongation Transcription

 σ-subunit initiates strand separation

(melting) of the DNA at about -10 from
the start site.

Eukaryote Promoter

 Upstream Elements – Enhancers and

silencers
o GC Box (-40): GGGCGG
consensus
o CCAT Box (extending to -110):
GGCCAATCT
 TATA Box (-25) – TATAA (T/A)
 +1 – Transcription start site (with initiator
element – Inr)
 Downstream Regulator

Transcription Start Site Chain Elongation

 If the RNA polymerase followed the
template strand around the axis of the
DNA duplex, there would be no strain,
and no supercoiling of the DNA would
occur, but the RNA chain would be
wrapped around the double helix once
every 10 base pairs. This possibility
seems unlikely because it would be
difficult to disentangle the transcript from
the DNA complex.
 Alternatively, topoisomerases could
remove the supercoils. A topoisomerase

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capable of relaxing positive supercoils DNA-RNA hybrid in the

situated ahead of the advancing transcription bubble.
transcription bubble would “relax” the  Releasing the nascent RNA.
DNA. A second topoisomerase behind
the bubble would remove the negative
supercoils.

Chain Termination
Organization of Eukaryote Genes: Post
 Two types of termination mechanisms:
Transcriptional Modification
1. Intrinsic Termination – Controlled
by specific sequences, termination
sites.
 Termination sites
characterized by two inverted
repeats.

Parts of a Gene
 Exon – Coding region.
2. Termination by Rho (ρ) Protein –  Intron – Non-coding – removed after
Rho-dependent termination transcription.
sequences cause hairpin loop to o Prokaryotic Gene
form.
 The rho-factor mechanism of
transcription termination.
 Rho factor attaches to a
recognition site on mRNA
and moves it along behind
RNA polymerase.
 When RNA polymerase
pauses at the termination
site, rho factor unwinds the

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o Eukaryotic Gene

Eukaryotic mRNA Spacing

 Splice Site: GU – AG
 Branch Site: 18 to 40 bases; invariant A

Eukaryotic mRNA
 5’ Cap: 7-mG cap (7-methyl GTP)
 5’ Untranslated Region – 40-150
bases
 AUG – Initiation codon
 3’ Untranslated Region – 40-150
bases
 3’ Poly(A) Tail

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