SizesLecture1

Sizing up ecoli estimate n h 2 o in an ecoli cell

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Sizing up e.coli Estimate N H 2 O in an E.coli cell: fact: 70% m E.coli m H 2 O => m total H 2 O 0.7 pg N H 2 O 0.7 × 10 -12 g / (18 g/mol) × (6 × 10 23 molecules/mol) 2 × 10 10 water molecules Estimate N inorganic ions in a typical bacterial cell: assume a typical concentration of inorganic ions (e.g., K + ) is 100 mM => N inorganic ions (100 × 10 -3 mol) / (10 15 μ m 3 ) × (6 × 10 23 molecules/mol) × 1 μ m 3 6 × 10 7 N H 2 O 2 × 10 10 1 L Cell volume N ions 6 × 10 7
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Image: D.Goodsell Sizing up e.coli : an outcome Observed molecular census of an E .coli cell. (Data from Neinhardt et al., 1990, and Schaechter et al., 2006)
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Taking the molecular census of e.coli : how ? An important tool: gel break open cells, keep only protein components separate complex protein mixture into individual molecular species: 1. Load the mixture at one end of the gel, apply el. field across the gel => diff. proteins migrate at rates ~ net charge; 2. Add charged detergent that binds to all proteins => N of detergent molecules associated with a protein ~ the protein’s size; 3. Apply el. field; net charge on the detergent molecules >> original charge of the protein => diff. proteins migrate at rates ~ protein size; stain proteins with a non-specific dye to locate cut each spot out, elute protein, determine size and AA-content with mass spectrometry Use similar tricks to characterize RNA, lipids, etc. Protein census of E.coli using 2D polyacrylamide gel electrophoresis. Each spot represents an individual protein with a unique size and charge distribution. (Swiss Inst. of Bioinformatics) large, – small, +
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Census in Yeast
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Mass Spec and census in spirochete
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We think about the microbes that are responsible for 40% of the overall photosynthesis on Earth. Ocean water census tells us between 10,000 and 100,000 cyanobacteria per mL. This yields estimate of roughly 10 26 cyanobacteria doing 10% (ish) of the overall carbon fixation. Conclusion: 10 4 rubisco per cyanobacterium. Using relatively few facts: 1 pg in 1fL with 30% of the mass ``dry’’. 30,000 Da “typical” protein tells us 3 x 10 6 proteins. Prochlorococcus (Iancu et al, JMB, 2007)
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Every time I show you a picture of a cell, ask yourself how the architecture works. For cyanobacteria, we are going to examine several remarkable specializations related to their ability to perform photosynthesis. (Cannon et al.) (Iancu et al, JMB, 2007)
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One of the intriguing features of these organisms is their membrane disposition. Membrane area is roughly 5 microns 2 . This means that the number of lipids in the outer leaflet of the bilayer is roughly 10 7 , yielding a total of roughly 10 8 . Membrane management: interesting and challenging. (Liberton et al.) Thylakoid membrane in Synechocystis Prochlorococcus
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Sizing up ecoli Estimate N H 2 O in an Ecoli cell fact 70 m...

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