Biology 5: Chapter 17
GENE TRANSCRIPTION AND
RNA MODIFICATION
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GENE TRANSCRIPTION
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DNA Microarry: DNA 微陣列
Application of DNA Microarry: DNA 微陣列的運
用
Transcriptome 轉錄體
INTRODUCTION

Transcription is the rst step in gene expression

It involves two fundamental concepts
1. DNA sequences provide the underlying information


Signals for the start and end of transcription
2. Proteins recognize these sequences and carry out the
process

Other proteins modify the RNA transcript （RNA轉錄產物） to
make it functionally active
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fi

5.1 TRANSCRIPTION: is the DNAdirected synthesis of RNA

Transcription literally means the act or process of
making a copy

In genetics, the term refer to the copying of a DNA
sequence into an RNA sequence

The structure of DNA is not altered as a result of
this process

It can continue to store information
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Gene Expression Requires Base
Sequences

At the molecular level, a gene is a transcriptional
unit

It (DNA) can be transcribed into RNA

During gene expression, different types of base
sequences perform different roles

Figure shows a common organization of sequences
within a bacterial gene and its transcript
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• Start codon: specifies the first amino acid in a
protein sequence, usually a formylmethionine
(in bacteria) or a methionine (in eukaryotes)
Signals the end of
protein synthesis
Figure
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Gene Expression Requires
Base Sequences

The strand that is actually transcribed is termed the
template strand

The opposite strand is called the coding strand （編碼股）
or the sense strand （義股or意股）

The base sequence is identical to the RNA transcript（轉錄產
物）

Except for the substitution of uracil in RNA for thymine in DNA
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The Stages of Transcription


Transcription occurs in three stages

Initiation

Elongation

Termination
These steps involve protein-DNA interactions

Proteins such as RNA polymerase interacts with
DNA sequences
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Promoter and transcription unit
• The DNA sequence where RNA polymerase
attaches is called the promoter; in bacteria, the
sequence signaling for the end of transcription is
called the terminator
• The stretch of DNA that is transcribed is called a
transcription unit （轉錄單位）= a gene
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
Promoters （啟動子）

Promoters are DNA sequences that “promote” gene
expression


More precisely, they direct the exact location for the
initiation of transcription
Promoters are typically located just upstream of the
site where transcription of a gene actually begins


The bases in a promoter sequence are numbered (編碼) in
relation to the transcription start site
Refer to Figure
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Sequence elements that play
a key role in transcription
Bases preceding
this are numbered
in a negative
direction
There is no base
numbered 0
Bases to the right are
numbered in a
positive direction
Sometimes termed
the Pribnow box,
after its discoverer
(David Pribnow, 1975)
Figure The conventional numbering system of promoters (編碼系統)
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The nding of promoter
For many bacterial
genes, there is a good
correlation between
the rate of RNA
transcription and the
degree of agreement
with the consensus
sequences
The most commonly
occurring bases
Figure Examples of –35 and –10 sequences within a variety of bacterial promoters
fi
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Initiation

The promoter functions as a recognition site
for transcription factors

The transcription factors enable RNA
polymerase to bind to the promoter forming a
closed promoter complex

Following binding, the DNA is denatured into a
bubble known as the open promoter complex,
or simply an open complex
helicase
Elongation
RNA polymerase slides along the DNA in
an open complex to synthesize the RNA
transcript

Termination

Figure
A termination signal is reached that
causes RNA polymerase to dissociated
from the DNA
Denature：變性
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TRANSCRIPTION IN BACTERIA

Our molecular understanding of gene transcription
came from studies involving bacteria and
bacteriophages

Indeed, much of our knowledge comes from studies
of a single bacterium


E. coli, of course
In this section we will examine the three steps of
transcription as they occur in bacteria
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Initiation of Bacterial Transcription

RNA polymerase is the enzyme that catalyzes the
synthesis of RNA

In E. coli, the RNA polymerase holoenzyme is
composed of

Core enzyme


Sigma factor


Four subunits = α2ββ’
One subunit = σ
These subunits play distinct functional roles
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qqqqqq
Initiation of Bacterial Transcription
RNA polymerase binding and initiation of transcription

The RNA polymerase holoenzyme binds loosely to the
DNA

It then scans along the DNA, until it encounters a
promoter region

When it does, the sigma factor recognizes both the –35 and
–10 regions


A region within the sigma factor that contains a helix-turn-helix
structure is involved in a tighter binding to the DNA
Refer to Figure
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Binding of σ factor protein to DNA double helix
Amino acids within the α
helices hydrogen bond
with bases in the -35
and -10 promoter
sequences
Figure 12.5
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qqqqqq

The binding of the RNA polymerase to the promoter
forms the closed complex

Then, the open complex is formed when the TATAAT
box is unwound

A short RNA strand is made within the open complex


The sigma factor is released at this point
 This marks the end of initiation
The core enzyme now slides down the DNA to
synthesize an RNA strand
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qqqqqq
DNA/RNA hybrid
Figure
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Elongation of RNA Strand in
Bacterial
qqqqqq

The RNA transcript is synthesized during the
elongation step

The DNA strand used as a template for RNA
synthesis is termed the template or noncoding strand

The opposite DNA strand is called the coding strand
(編碼股）

It has the same base sequence as the RNA transcript

Except that T in DNA corresponds to U in RNA
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Similar to the
synthesis of DNA
via DNA polymerase
DNA/RNA hybrid
Figure
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Termination of Bacterial
Transcription

Termination is the end of RNA synthesis

It occurs when the short RNA-DNA hybrid of the open
complex is forced to separate


This releases the newly made RNA as well as the RNA polymerase
E. coli has two different mechanisms for termination

1. rho-dependent termination


Requires a protein known as ρ (rho)
2. rho-independent termination

Does not require ρ
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Termination of Bacterial Transcription
Rho dependent and Rho indipendent
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rho utilization site
Rho protein is a
helicase
Figure 12.8
ρ-dependent termination
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Figure 12.8
ρ-dependent termination
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
ρ-independent termination is facilitated by two sequences in the RNA

1. A uracil-rich sequence located at the 3’ end of the RNA

2. A stem-loop structure upstream of the Us
NusA
URNA-ADNA hydrogen bonds
are very weak
Stabilizes the
RNA pol
pausing
No protein is required to physically
remove the RNA from the DNA
This type of termination is also called
intrinsic
Figure 12.9
ρ-independent termination
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