9-14-09_lecture_proteinIDA

9-14-09_lecture_proteinIDA - Poets say science takes away...

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Poets say science takes away from the beauty of the stars - mere globs of gas atoms. I, too, can see the stars on a desert night, and feel them. But do I see less or more?” - Richard Feynman “Marge: Homer! There's someone here who can help you. .. Homer: Is it Batman? Marge: No, he's a scientist. Homer: Batman's a scientist?! Marge: It's not Batman!”
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Announcements Answers to the review questions will be passed out today Papers for your research article summary are available in Blackboard. First exam – This Friday, September 18 th
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Noncovalent bonds are critical for the formation of protein secondary and tertiary structures from a given amino acid chain (primary structure)
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Hydrophobicity also plays an important role in determining protein structure Alberts et al. Molecular Biology of the Cell
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All structures are Gibbs free energy minimizers, and proteins are particularly studied in this manner 2200 G= E +p V –T S, where G is the Gibbs free energy, E is the energy (assume constant pressure), V is volume, T is temperature in Kelvin, and S is entropy Given some starting configuration of a structure, want to minimize G (make G as negative as possible) Changes in potential energy result from electrostatic interactions (covalent, hydrogen bonds, van der Waals) “Hydrophobicity results from depriving water molecules of some of their configurational entropy” (from Physical Biology of the Cell)
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Can compute energetic cost function of different protein configurations to determine stable states Computationally very expensive for a realistic sized protein Can have a stable state without having a global free energy minimum Relative minimum (stable) Global minimum (stable) Local minimum (unstable)
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Changes in free energy paths are dynamic due to a changing environment and changing protein conformation In this analogy, we can consider the offense as trying to find a low energy path for the ball to reach the stable state of the endzone, while the defense is trying to find a “low” energy path to reach the stable state of the ground or a change in possession. The point is that, from the ball’s point of view, the free energy paths to stable states are in constant flux due to changes in the conformations of the different components www.directsnapfootball.com
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Second string: One major type of secondary structure is the alpha helix conformation • Discovered by Linus Pauling and Robert Corey and confirmed using X-ray crysallography •Stable conformation due to large number
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This note was uploaded on 02/09/2010 for the course BIOL 230 taught by Professor Bartlett,e during the Fall '08 term at Purdue.

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9-14-09_lecture_proteinIDA - Poets say science takes away...

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