110C LEC 10 Regulation of eukaryotic gene expression (overview)

110C LEC 10 Regulation of eukaryotic gene expression (overview)

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BCH 110C LECTURE 10 Regulation of Gene Expression (Overview) Lodish 6 th ed. Pages 273 & 275; Chapters 7.3-7.5
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How to identify transcription-control regions near a eukaryotic gene? Deletion-transfection analysis
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How do sequence specific gene regulatory proteins work? • How do they find their specific DNA binding sites? • How do they stimulate or repress transcriptional initiation in eukaryotes ?
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How do regulatory proteins bind to specific DNA sequences • The shape of the protein fits DNA • Multiple interactions between positive amino acid sides of the protein and the negatively charged DNA phosphate oxygens • Contact involves ~20 ionic, hydrogen-bond or hydrophobic interactions in the major or minor groves • Usually protein α -helices or β -sheets interact with the DNA major grove • Relatively few structural motifs are used for DNA binding by proteins
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In bacteria and eucaryotes a common, simple DNA binding motif: “Helix-Turn-Helix” Two α -helical barrels separated by a turn The recognition helix interacts in the major grove ~20 amino acids in both helices
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Helix-turn-helix Proteins Usually Bind as Dimers in Adjacent Major Groves of Repeated DNA Sequences
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Subunits of dimers often bind “half-sites” in the DNA arranged in palindromes
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Subunits of dimers often bind “half-sites” in the DNA arranged in palindromes mirror
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Base Pairs Can be Recognized by Their Edges
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What Does a DNA Binding Protein See?
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One Contact Between a Regulatory Protein and a DNA Base Pair
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One of the most common protein-DNA interactions Learn this
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the Major Grove: Bacteriophage 434 Repressor
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110C LEC 10 Regulation of eukaryotic gene expression (overview)

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