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Ch. 13 - The Genetic Code and Transcription
Chapter 13, Problem 17
Explain the features of the Initiator (Inr) elements, BREs, DPEs, and MTEs of focused promoters.

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The Initiator (Inr) element is a core promoter element that overlaps the transcription start site (TSS) and is often found in focused promoters. It is recognized by the transcription machinery and helps in the precise initiation of transcription.
BREs (TFIIB Recognition Elements) are sequences located either upstream (BREu) or downstream (BREd) of the TATA box in the promoter region. They are recognized by the TFIIB transcription factor, which is crucial for the recruitment of RNA polymerase II.
DPEs (Downstream Promoter Elements) are located downstream of the transcription start site, typically around +28 to +32. They are important for transcription initiation in promoters that lack a TATA box and are recognized by the transcription factor TFIID.
MTEs (Motif Ten Elements) are located downstream of the transcription start site, often overlapping with the DPE. They enhance the binding of the transcription machinery and are important for the efficiency of transcription initiation.
Focused promoters are characterized by having a single or a few closely spaced transcription start sites. They often contain a combination of these elements (Inr, BREs, DPEs, MTEs) to facilitate precise and efficient transcription initiation.

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Key Concepts
Here are the essential concepts you must grasp in order to answer the question correctly.
Initiator (Inr) Elements
Initiator (Inr) elements are DNA sequences located at the transcription start site of genes, playing a crucial role in the initiation of transcription. They are recognized by the transcription machinery, particularly RNA polymerase II, and help in positioning the polymerase correctly to start RNA synthesis. Inr elements can function independently or in conjunction with other promoter elements to enhance transcription efficiency.
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BREs (B Recognition Elements)
B Recognition Elements (BREs) are short DNA sequences found upstream of the transcription start site that assist in the binding of transcription factors and RNA polymerase II. They are important for the recruitment of the transcription machinery and can influence the strength of the promoter. BREs can be classified into two types: BREu (upstream) and BREd (downstream), each contributing to the regulation of gene expression.
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DPEs (Downstream Promoter Elements) and MTEs (Motif Ten Elements)
Downstream Promoter Elements (DPEs) and Motif Ten Elements (MTEs) are additional regulatory sequences located downstream of the transcription start site. DPEs are essential for the efficient binding of transcription factors and RNA polymerase II, while MTEs enhance transcriptional activity. Both elements work synergistically with Inr and BREs to form a robust transcriptional complex, ensuring precise gene expression.
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Related Practice
Textbook Question
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Textbook Question
Research indicates that promoters may fall into one of two classes: focused or dispersed. How do these classes differ, and which genes tend to be associated with each?
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Textbook Question
Define the process of transcription. Where does this process fit into the central dogma of molecular biology (DNA makes RNA makes protein)?
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Textbook Question
What observations suggested the existence of mRNA?
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Textbook Question
Many transcriptional activators are proteins with a DNA-binding domain (DBD) and an activation domain (AD). Explain how each domain contributes to transcriptional initiation. Would you expect repressors to also have each of these domains?
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Textbook Question
Describe the structure of RNA polymerase in bacteria. What is the core enzyme? What is the role of the σ subunit?
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