LEC13 - Transcription factors bind DNA specifically and...

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Transcription factors bind DNA specifically and have DNA binding motifs
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Some transcription factors are dimers: doubles the number of contacts made with DNA
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Recognition sites are generally inverted repeats
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DNA binding motifs found in transcription factors Helix-turn-helix (mostly prokaryotic) Homeodomain Basic leucine zipper Basic helix-loop-helix (do not confuse with Ca binding motif) Zn finger
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The helix shown in red is called the recognition helix- its aa side chains H-bond with the sides of the bp Helix – turn – helix motif
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The homeodomain is similar but has an extension that binds in the minor groove Homeodomain
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Basic leucine zipper is always dimeric and grasps the DNA in a scissors grip
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Would you expect protein with a basic leucine zipper to bind to an inverted repeat? A. Yes B. No
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Basic Helix-loop-helix motif consists of two -helices with a loop in the middle
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The most common type of transcription factors contains 3 or more Zn fingers
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Several types of Zn fingers: Zn is coordinated with Cys and Hys residues and essential for structure
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Single polypeptide with 9 Zn fingers
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Some proteins have a mix of these motifs
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Transcription factors generally have at least two domains DNA binding domain Determines what sequences are recognized Activation domain Interact with RNA polymerase or other transcription factors to stimulate transcription Using fusion proteins these domains were shown to act independently
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Fusion: LexA DNA binding domain with Gal4p activation domain
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Activation domain is still functional when fused to LexA binding domain
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In the preceding experiment, why is there no -galactosidase activity
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