2014 transcription biology 5
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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
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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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RNA transcript
3 Termination
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3Completed RNA transcript
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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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Figure 23
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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
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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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