Biology 5: Chapter 17

GENE TRANSCRIPTION AND RNA MODIFICATION

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GENE TRANSCRIPTION

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INTRODUCTION

n Transcription is the first step in gene expression

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nIt involves two fundamental concepts

n 1. DNA sequences provide the underlying information

nSignals for the start and end of transcription

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n2. Proteins recognize these sequences and carry out the process

n Other proteins modify the RNA transcript RNA to

make it functionally active

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n Transcription literally means the act or process of making a copy

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n In genetics, the term refer to the copying of a DNA sequence into an RNA sequence

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nThe structure of DNA is not altered as a result of this process

n It can continue to store information

5.1 TRANSCRIPTION: is the DNA-directed synthesis of RNA

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n At the molecular level, a gene is a transcriptional unit

n It (DNA) can be transcribed into RNA

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n During gene expression, different types of base sequences perform different roles

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n Figure shows a common organization of sequences within a bacterial gene and its transcript

Gene Expression Requires Base Sequences

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Figure

Bacterial mRNA may be polycistronic, which means it encodes two or more polypeptides

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

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n The strand that is actually transcribed is termed the

template strand

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n 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

Gene Expression Requires Base Sequences

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n Transcription occurs in three stages

n Initiation

n Elongation

n Termination

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n These steps involve protein-DNA interactions

n Proteins such as RNA polymerase interacts with

DNA sequences

The Stages of Transcription

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nThe promoter functions as a recognition site for transcription factors

nThe transcription factors enable RNA polymerase to bind to the promoter forming a closed promoter complex

nFollowing binding, the DNA is denatured into a bubble known as the open promoter complex, or simply an open complex

Initiation

Elongation

n RNA polymerase slides along the DNA in an open complex to synthesize the RNA transcript

Termination

n A termination signal is reached that causes RNA polymerase to dissociated from the DNA

Figure9

Denature

helicase

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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

Promoter and transcription unit

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n Promoters are DNA sequences that promote gene expression

n More precisely, they direct the exact location for the

initiation of transcription

n 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

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n Refer to Figure

Promoters

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Figure Examples of 35 and 10 sequences within a variety of

bacterial promoters

The most commonly occurring bases

For many bacterial genes, there is a good

correlation between the rate of RNA

transcription and the degree of agreement with the consensus

sequences

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Figure The conventional numbering system of promoters ()

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)

Sequence elements that play a key role in transcription

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Fig. 17-7a-4Promoter Transcription unit

DNAStart pointRNA polymerase

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Initiation

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RNA transcript

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Unwound DNA

Template strand of DNA

2 Elongation

Rewound DNA

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5 5 3 33

RNA transcript

3 Termination

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3Completed RNA transcript

Fig. 17-7b

Elongation

RNA polymerase

Nontemplate strand of DNA

RNA nucleotides

3 end

Direction of transcription (downstream) Template

strand of DNANewly made RNA

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n Once they are made, RNA transcripts play different functional roles (template and scaffold)

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n 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)

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n Well over 90% of all genes are structural genes

RNA Transcripts Have Different Functions

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RNA

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Signal recognition particles: RNA as scaffold

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nOur molecular understanding of gene transcription came from studies involving bacteria and bacteriophages

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nIndeed, much of our knowledge comes from studies of a single bacterium

n E. coli, of course

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n In this section we will examine the three steps of transcription as they occur in bacteria

5.2 TRANSCRIPTION IN BACTERIA

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n RNA polymerase is the enzyme that catalyzes the synthesis of RNA

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n In E. coli, the RNA polymerase holoenzyme is composed of

n Core enzyme

n Four subunits = 2

n Sigma factor

n One subunit =

!n These subunits play distinct functional roles

Initiation of Bacterial Transcription

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n The RNA polymerase holoenzyme binds loosely to the DNA

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n 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

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n Refer to Figure

Initiation of Bacterial Transcription RNA polymerase binding and initiation of transcription

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Figure

Amino acids within the helices hydrogen bond

with bases in the promoter sequence elements

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n The binding of the RNA polymerase to the promoter forms the closed complex

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n Then, the open complex is formed when the TATAAT box is unwound

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n 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

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n The core enzyme now slides down the DNA to synthesize an RNA strand

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n The RNA transcript is synthesized during the elongation step

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n The DNA strand used as a template for RNA synthesis is termed the template or noncoding strand

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n 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

Elongation of RNA Strand in Bacterial

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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

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n On average, the rate of RNA synthesis is about 43 nucleotides per second!

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n Figure depicts the key points in the synthesis of the RNA transcript

Elongation in Bacterial Transcription

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Similar to the synthesis of DNA via

DNA polymerase

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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

Termination of Bacterial Transcription

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nMany of the basic features of gene transcription are very similar in bacteria and eukaryotes

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nHowever, gene transcription in eukaryotes is more complex

n Larger organisms

n Cellular complexity

n Multicellularity

5.3 TRANSCRIPTION IN EUKARYOTES

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Fig. 17-8A eukaryotic promoter includes a TATA box

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Promoter

TATA box Start point

Template

Template DNA strand

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Transcription factors

Several transcription factors must bind to the DNA before RNA polymerase II can do so.

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Additional transcription factors bind to the DNA along with RNA polymerase II, forming the transcription initiation complex.

RNA polymerase IITranscription factors

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RNA transcript

Transcription initiation complex

TRANSCRIPTION IN EUKARYOTES General transcription factors

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Signal Transduction -

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Specific Regulation of Eukaryotic Structural Genes

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