Transcription of the

Genetic Code: The

Biosynthesis of RNA
Chapter Outline
(11-1) Overview of transcription
(11-2) Transcription in prokaryotes
(11-3) Transcription regulation in prokaryotes
(11-4) Transcription in eukaryotes
(11-5) Transcription regulation in eukaryotes
(11-6) Noncoding RNAs
(11-7) Structural motifs in DNA-binding proteins
(11-8) Posttranscriptional RNA modifications
(11-9) Ribozymes

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Transcription
• Controls the expression of genes and the production
of proteins
• General features of RNA synthesis

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Overview: Transcription in Prokaryotes: RNA
Polymerase in Escherichia coli (E. coli)
• RNA polymerase:
• MW ~ 470,000 Da
• Has a multisubunit structure - α, ω, β, β′,σ
• Core enzyme: α2ωββ′
• Enzyme that lacks the σ subunit
• Holoenzyme: α2ωββ′ σ
• Enzyme that has all component parts, including
coenzymes + all subunits

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RNA polymerase

Bacterial RNA polymerase:

• Large complex enzyme
• Composed of multiple
polypeptides

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RNA polymerase: structure and function
α2ββ’ω Core Polymerase
Mr = 390 000

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RNA polymerase: structure and function
α2ββ’ω Core Polymerase
α2ββ’ω + σ Holoenzyme

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Architecture of RNA Polymerase
• Bacterial RNA polymerase core

Image Credit: David Clode

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Transcription in Prokaryotes: RNA Polymerase
(Pol) in Escherichia coli (E. coli) (continued)
• Holoenzyme binds to specific DNA sequences and
transcribes only the template strand
• σ-subunit recognizes the promoter + is released after
transcription begins
• Promoter: Portion of DNA to which RNA pol binds at
the start of transcription

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Fig. 11.1 - Basics of Transcription
• Template strand (antisense, or [–] strand)
• Serves as a template for RNA synthesis
• Coding strand (sense, [+], or nontemplate strand)
• Contains the same sequence as the RNA that is synthesized from the template

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Promoter Structure
• Simplest of organisms contain a large amount of DNA that is
not transcribed
• RNA pol needs to know which strand is the template strand,
which part to transcribe, and where the 1st nucleotide of the
gene to be transcribed is located
• Promoters - DNA sequences that provide direction for RNA pol

Fig. 11.2 - Sequences of Representative Promoters from E. coli

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Promoters
• Note: there is no zero

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Chain Initiation
• Part of transcription where RNA pol binds to DNA,
the strands are separated, and the first nucleotide
binds to its complement

• Begins when RNA pol binds to the promoter + forms

closed complex
• Closed complex: Complex that initially forms between
RNA pol and DNA before transcription begins
• Requires formation of open complex
• Open complex: Form of the complex of RNA pol and
DNA that occurs during transcription

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Fig. 11.3 - Initiation and Elongation Phases
of Transcription

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Chain Elongation
• After strands are separated, transcription bubble of
about 17 base pairs moves down the DNA sequence
to be transcribed
• RNA pol catalyzes formation of phosphodiester
bonds between the incorporated ribonucleotides

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Chain Elongation
• Topoisomerases relax the supercoils in front of +
behind the transcription bubble
• Occurs when the RNA pol is able to launch itself off
the DNA promoter
• RNA pol scrunches the DNA into itself, causing
torsional strain of the separated DNA strands

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Chain Termination Mechanisms
• Intrinsic termination: Not dependent on the rho
protein and is controlled by termination sites
• Termination sites: Areas in DNA that cause
termination of transcription by generating hairpin loops
and a zone of weak binding between DNA and RNA
• Other type of termination involves rho () protein
• Rho-dependent
termination
sequences
cause a hairpin
loop to form

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Fig. 11.7 - The Rho-Factor Mechanism of
Transcription Termination

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Ways to Control Transcription in Prokaryotes

Alternative σ
Enhancers
factors

Transcription
Operons
attenuation

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 Examples of σ factors

• σ factors are global recognition factors

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Enhancers
• DNA sequences that bind to a transcription factor and
↑ transcription rate
• Transcription factors: Proteins or other complexes
that bind to DNA sequences and alter the basal level
of transcription
• Certain E. coli genes include sequences upstream of
the extended promoter region
• Genes for ribosomal RNA production have 3 upstream
sites, called Fis sites

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Fig. 11.9 - Elements of a Bacterial Promoter

• Fis sites - Binding sites for the protein called Fis

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Operon
• Group of operator, promoter, and structural genes
• Structural gene: Directs the synthesis of a protein
under the control of some regulatory gene
• Physically adjacent to the structural gene in the DNA
• Not transcribed all the time
• Regulated by induction
• Induction: Triggering of the production of an enzyme
by the presence of a specific inducer
• Inducer: Molecule that turns on the transcription of a
gene

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Gene Protein
• lacI = (codes for) repressor protein (LacI)
• lacZ = (codes for) b-galactosidase (LacZ)
• lacY = (codes for) lactose permease (LacY)
• lacA= thiogalactoside transacetylase (LacA)

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lac operon

lacZ

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Summary: Operon (continued)
• β-galactosidase, an inducible protein
• Coded for by a structural gene, lacZ
• Structural gene, lacY
• Structural gene, lacA
• Expression of the three structural genes is controlled
by the regulatory gene (lacI)
• Regulatory gene: Directs the synthesis of a repressor
protein
• Can be quite far from the operon

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lac repressor
• Repressor: Protein that binds to an operator gene,
blocking the transcription + eventual translation of
structural genes under the control of that operator

• lacI
• lacI produces an inhibitor that exerts neg control over
lacZ and lacY

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Repression in Lac Operon
• Repressor protein made by lacI gene forms a
tetramer when it is translated and then binds to
operator portion of operon
• Operator (O): DNA element to which a repressor of
protein synthesis binds
• When the repressor is bound to the operator, RNA
pol cannot bind to the adjacent promoter region
• Operator and promoter together form the control sites
• Control sites: Modulate the production of proteins
whose amino acid sequence is specified by the
structural genes under their control

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Fig. 11.10 - The Mode of Action of the Lac
Repressor

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Transcription in Eukaryotes
• Each RNA polymerase transcribes a different set of
genes + recognizes a different set of promoters
• RNA polymerase I
• Found in the nucleolus
• synthesizes precursors of most ribosomal RNAs
• RNA polymerase II
• Found in the nucleoplasm
• synthesizes mRNA precursors
• RNA polymerase B (RPB)
• RNA polymerase III
• Found in the nucleoplasm
• synthesizes tRNAs, precursors of 5S ribosomal RNA, and
other RNA molecules involved in mRNA processing and
protein transport
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Table 11.2 - Yeast RNA Polymerase II Subunits

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α-amanitin

• a toxin produced by the death cap mushroom

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Pol II Promoters
• Upstream elements

• TATA box
• Located 25 bases upstream of the transcription start
site

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Pol II Promoters (continued)
• Initiator element: Loosely conserved sequence
surrounding the transcription start site in eukaryotic
DNA
• Downstream regulator - More rare than upstream
regulators

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Initiation of Transcription
• Any protein regulator of transcription that is not itself
a subunit of pol II is a transcription factor
• Begins by forming the preinitiation complex, where
most of the control of transcription occurs
• Preinitiation complex: Phase where RNA pol and the
general transcription factors bind to the DNA
• General transcription factors (GTFs): 6 transcription
factors that bind to DNA to initiate transcription

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Table 11.3 - General Transcription Initiation
Factors

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Fig. 11.21 - A Schematic Representation of
the Order of Events of Transcription

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