5) Helical Wheel (10 pts) CIEBP-alpha is a transcription factor, meaning it prom

Question

5) Helical Wheel (10 pts) CIEBP-alpha is a transcription factor, meaning it promotes the synthesis of RNA for a specific gene based on binding to a DNA sequence called a promoter. We will learn more about promoters and DNA binding proteins later in the course. The following sequence is a fragment of a long ( 70 amino acid) alpha helix from C/EBPa amino acids 1-80 32 NH2- DKNSNEYRVR RERNNAVRK SHDKAKORNV ETQQKVLELT SDNDRLRKRV EOLSRELDTL RGIFROLPES SLVKAMGNCA-COOH 67 a) How long (in A) is a helix that contains 70 amino acids? (show your work) b) Construct a helical wheel diagrams for the 2 underlined segments. Color code your helical wheels to determine whether one or both segments of this extended helix are amphipathic. Use the hydropathy values (in your text and on your amino acid handout) as your guide. c) 5 amino acids have been indicated with arrows between residues 45-62 of the alpha helix. Describe the potential interactions between these 5 amino acids and comment on whether these interactions stabilize or destabilize the helical structure.

Explanation / Answer

a) Alpha-helices have 3.6 amino acid residues per turn.

The separation of residues along the helix axis is 5.4/3.6 or 1.5 Angstroms i.e. the alpha-helix has a rise per residue of 1.5 Angstroms.

So, for 70 residues it will be (70 x 1.5) = 10.5 Angstroms long.

b) Potential interactions are - intramolecular hydrogen bonding and hydrophobic forces.

They make the helical structure stabilized.

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