Biology 5: Chapter 17

GENE TRANSCRIPTION AND

RNA MODIFICATION

GENE TRANSCRIPTION

INTRODUCTION
n

Transcription is the first step in gene expression

!

It involves two fundamental concepts

n

1. DNA sequences provide the underlying information

n

Signals for the start and end of transcription

!
n

2. Proteins recognize these sequences and carry out the

process

n

Other proteins modify the RNA transcript RNA to

make it functionally active

5.1 TRANSCRIPTION: is the DNAdirected synthesis of RNA

n

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

n

It can continue to store information

4

Gene Expression Requires Base

Sequences
n

At the molecular level, a gene is a transcriptional

unit

n

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
5

 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

Bacterial mRNA may be polycistronic, which

means it encodes two or more polypeptides

Figure
6

Gene Expression Requires

Base Sequences
n

The strand that is actually transcribed is termed the

template strand

!

The opposite strand is called the coding strand

or the sense strand or

n

The base sequence is identical to the RNA transcript

n

Except for the substitution of uracil in RNA for thymine in DNA

7

The Stages of Transcription

n

Transcription occurs in three stages

n

Initiation

Elongation

Termination

!

These steps involve protein-DNA interactions

n

Proteins such as RNA polymerase interacts with

DNA sequences
8

Initiation
n

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
n

Figure

A termination signal is reached that

causes RNA polymerase to dissociated
from the DNA

Denature
9

Promoter and transcription unit

The DNA sequence where RNA polymerase

attaches is called the promoter; in bacteria, the
sequence signaling the end of transcription is called
the terminator

The stretch of DNA that is transcribed is called a
transcription unit = a gene

Copyright 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Promoters
n

Promoters are DNA sequences that promote gene

expression

n

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

n

The bases in a promoter sequence are numbered in

relation to the transcription start site

!

Refer to Figure
11

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
12

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 ()

13

Fig. 17-7a-4

Promoter

Transcription unit

5
3
Start point
RNA polymerase

3
5

DNA
1

Initiation

5
3

3
5

Unwound
DNA

RNA
transcript

Template strand
of DNA
2

Elongation

Rewound
DNA
5
3

3
5

3
5
RNA
transcript

3 Termination

5
3

3
5
5

Completed RNA transcript

Fig. 17-7b

Nontemplate
strand of DNA

Elongation

RNA
polymerase

RNA nucleotides

3 end

Direction of
transcription
(downstream)
Newly made
RNA

Template
strand of DNA

RNA Transcripts Have Different

Functions
RNA
n

Once they are made, RNA transcripts play

different functional roles (template and scaffold)

!

A structural gene is a one that encodes

a polypeptide

n

When such genes are transcribed, the product is an

RNA transcript called messenger RNA (mRNA)


!

Well over 90% of all genes are structural genes

16

Signal recognition particles: RNA as scaffold

17

5.2 TRANSCRIPTION IN BACTERIA

n

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

n

E. coli, of course

In this section we will examine the three steps of

transcription as they occur in bacteria

18

qqqqqq

Initiation of Bacterial Transcription

n

RNA polymerase is the enzyme that catalyzes the

synthesis of RNA

!

In E. coli, the RNA polymerase holoenzyme is

composed of

n

Core enzyme

n

Four subunits = 2

Sigma factor

n

One subunit =

!

These subunits play distinct functional roles

19

qqqqqq

Initiation of Bacterial Transcription

RNA polymerase binding and initiation of transcription
n

The RNA polymerase holoenzyme binds loosely to the

DNA

!

It then scans along the DNA, until it encounters a

promoter region

n

When it does, the sigma factor recognizes both the 35 and

10 regions

n

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

20

Amino acids within the

helices hydrogen bond
with bases in the promoter
sequence elements

Figure
21

qqqqqq
n

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

n

The sigma factor is released at this point

n

This marks the end of initiation

The core enzyme now slides down the DNA to

synthesize an RNA strand
22

qqqqqq

Figure

23

Elongation of RNA Strand in

Bacterial qqqqqq
n

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

(

n

It has the same base sequence as the RNA transcript

n

Except that T in DNA corresponds to U in RNA

24

Elongation in Bacterial Transcription

n

The open complex formed by the action of RNA

polymerase is about 17 bases long

n

Behind the open complex, the DNA rewinds back into the
double helix

On average, the rate of RNA synthesis is about 43

nucleotides per second!

!

Figure depicts the key points in the synthesis of the

RNA transcript
25

Similar to the
synthesis of DNA via
DNA polymerase

Figure

26

Termination of Bacterial
Transcription
n

Termination is the end of RNA synthesis

n

It occurs when the short RNA-DNA hybrid of the open

complex is forced to separate

n

This releases the newly made RNA as well as the RNA polymerase

27

5.3 TRANSCRIPTION IN
EUKARYOTES
n

Many of the basic features of gene transcription are

very similar in bacteria and eukaryotes

!

However, gene transcription in eukaryotes is more

complex

n

Larger organisms

Cellular complexity

Multicellularity
28

Fig. 17-8

A eukaryotic promoter
includes a TATA box

Promoter

Template

5
3

TATA box

Start point
2

Transcription
factors

3
5

Template
DNA strand

Several transcription factors must

bind to the DNA before RNA
polymerase II can do so.

5
3

3
5
3

Additional transcription factors bind to

the DNA along with RNA polymerase II,
forming the transcription initiation complex.

RNA polymerase II
Transcription factors
5
3

3
5

RNA transcript
Transcription initiation complex

TRANSCRIPTION IN EUKARYOTES
General transcription factors

30

Signal Transduction -

Specific Regulation of Eukaryotic Structural Genes

32