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Lecture 8

BIO130H1 Lecture Notes - Lecture 8: Tata Box, Transcription Factor Ii D, Transcription Factor Ii H

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John Coleman

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Lecture 8 Notes
Transcription Initiation in Eukaryotes Requires Many Proteins
Unlike bacteria, eukaryotes have three different polymerase each with different functions (see
Bacterial RNA polymerase vs. eukaryotic RNA polymerase II:
1.While bacterial RNA polymerase requires only a single additional protein ( factor) for
transcription initiation to occur, eukaryotic RNA polymerases require many additional proteins,
collectively called the general transcription factors.
2.Eukaryotic transcription initiation must deal with the packing of DNA into nucleosomes
and higher-order forms of chromatin structure, features absent from bacterial chromosomes.
RNA Polymerase Requires General Transcription Factors
The general transcription factors help to position eukaryotic RNA polymerase correctly at the
promoter, aid in pulling apart DNA to begin transcription, and release RNA polymerase from the
promoter into the elongation mode once transcription has begun—similar to the factor in
bacterial RNA polymerase
The assembly process begins when the general transcription factor TFIID (transcription factor for
pol ii) binds to a short double-helical DNA sequence primarily composed of T and A nucleotides—
TATA box/sequence
o The subunit of TFIID that recognizes it is called TBP (for TATA- binding protein).
oThe TATA box is located 25 nucleotides upstream from the transcription start site.
The binding of TFIID causes a large distortion in the DNA which serves as a physical landmark for
the promoter.
Other factors assemble, along with RNA polymerase II, to form a complete transcription
initiation complex.
After forming the complex on the promoter DNA, RNA polymerase II must gain access to the
template strand at the
transcription start point.
TFIIH, which contains a

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DNA helicase hydrolyzes ATP, unwinds the DNA, exposing the template strand.
Next, RNA polymerase II remains at the promoter synthesizing short lengths of RNA until it
undergoes a conformational change, moves away from the promoter and enters the elongation
phase of transcription.
oA key step in this transition is the addition of phosphate groups to the tail of the RNA
polymerase (known as the CTD or C-terminal domain).
oIn humans, the CTD consists of 52 tandem repeats of
a seven-amino-acid sequence, which extend from the
RNA polymerase core structure. During transcription
initiation, the serine located at the fifth position in
the repeat sequence (Ser5) is phosphorylated by
The polymerase can then disengage the factors, and
begin transcription
Polymerase II Also Requires Activator, Mediator, and Chromatin
Since eukaryotic DNA is packaged into nucleosomes, and further into higher-
order chromatin, it requires other proteins before the GTF attach to
the TATA box
First, gene regulatory proteins known as transcriptional activators
must bind to specific sequences in DNA and help to attract RNA
polymerase II to the start point of transcription.
Second, eukaryotic transcription initiation requires the presence of a protein
complex known as Mediator, which allows the activator proteins to
communicate properly with the polymerase II and with the GTFs.
Finally, transcription initiation in a eukaryotic cell typically requires
the local recruitment of chromatin- modifying enzymes, including chromatin
remodelling complexes and histone-modifying enzymes.
Transcription Elongation Produces Superhelical Tension in DNA
There is another barrier to elongating polymerases because of DNA supercoiling: a conformation
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