9-15-08_lecture_bioenergetics2A

9-15-08_lecture_bioenergetics2A - If someone points out to...

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If someone points out to you that your pet theory of the universe is in disagreement with Maxwell's equations - then so much worse for Maxwell's equations. If it is found to be contradicted by observation -well, these experimentalists do bungle things sometimes. But if your theory is found to be against the second law of thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation. -- Arthur S. Eddington (British Astrophysicist, 1882-1933) In this house, we obey the laws of thermodynamics! -- Homer Simpson
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Announcements First test this Friday, Sep. 19, 7:30 am in Matthews 210 (this room). Exam will cover through today’s lecture and potentially part of Wednesday’s lecture. Answers to the review questions will be posted on Blackboard after class. Review session in MJIS 1001, Sep. 18 from 7:30-9 pm. The TAs and I will answer specific questions but not lecture.
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Mass spectrometry 2 Vaporized peptide fragments pass through a magnetic field that separates them by their mass/charge ratio (m/z ratio). The ions are accelerated and then deflected by the magnet according to their mass. Lighter fragments are deflected more. The ion flux (number of ions/unit time) is detected at the detector for each mass
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Mass spectrometry 3 Each protein will have a signature in the mass spectrometer Can be compared with a database Or some fragments can undergo another round of mass spectrometry at a finer level of detail to reveal the amino acid sequence, which is called tandem mass spectrometry
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Gel electrophoresis Can be one or two dimensional Separate proteins by size and/or isoelectric point Similar to chromatography in that a matrix alters movement of a protein. Commonly use SDS-PAGE, or sodium dodecyl sulfate polyacrylamide gel electrophoresis. Negatively charged SDS attach all over proteins and put in a voltage gradient. Larger proteins move slower
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Two-dimensional gel electrophoresis Two dimensions are typically mass and isoelectric point , the point at which the protein is neutral. Can segregate most proteins in a cell simultaneously like this.
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picture of protein tertiary crystal structure Sample must be a crystal, because need ordered repeating structure. Crystal creation lies at the science/magic interface (kidding, mostly) A very short wavelength x-ray beam produces an interference pattern based on the positions of the atoms in the sample The sample or beam can be moved to get the structure from all angles. Typical diffraction pattern
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9-15-08_lecture_bioenergetics2A - If someone points out to...

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