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SizesLecture1

Image nobelprizeorg drawing of the structure of cork

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Image: nobelprize.org Drawing of the structure of cork as it appeared under the microscope to Hooke. Microscopic section through 1-yr old ash tree wood, drawing by Leeuwenhok 17th cent.: microscopic observations by Hooke and Leeuwenhoek 19th cent.: modern cell theory by Schwann, Schleiden, Virchow; confirmed by Pasteur
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Taking the molecular census of e.coli : why ? For most cases of interest, it suffices to attribute to E.coli V E.coli 1 μ m 3 = 1 fL A E.coli 6 μ m 2 femto = 10 -15 Estimating the number of molecules of diff. kinds that are in an E.coli cell… …Why care about these numbers? a realistic physical picture of a bio phenomena demands understanding of the individual particles involved + the spatial dimensions over which they can interact ( crowded? dilute? homogeneous? ) a prerequisite to beginning to answer questions such as: How fast is a genome replicated? What is the aver. rate of protein synthesis? How do the ribosomes maintain this rate? To understand many experiments in biology. Most experimentation is comparative (“normal” behavior vs. “perturbed” behavior, compared by observing some measurable property) “a lot” vs. “a few” copies of a molecule => describe concentration vs. influence of stochasticity (random chance) on cellular function
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Sizing up e.coli Estimate N protein in an E.coli cell: N protein = m total protein / m per protein V E.coli 1fL, assume ρ E.coli H 2 0 = 1 g/mL => m E.coli 1 pg from exp.: cell’s dry weight = 30% cell’s total weight, protein = 50% of dry weight => m total protein 0.15 pg Aver.protein = 300 AA, m AA 100 Da => m per protein = 30,000 Da; 1Da 1.6 × 10 -24 g => m per protein = 5 × 10 -20 g N protein = m total protein / m per protein (15 × 10 -14 g) / (5 × 10 -20 g) 3 × 10 6 1/3 proteins coded in a typical genome = membrane proteins => N cytoplasmic protein 2 × 10 6 , N membrane protein 10 6 N protein 3 × 10 6
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Sizing up e.coli Estimate N ribosome in an E.coli cell: N ribosome = m total ribosome / m per ribosome facts: ribosomal protein = 20% cell’s total protein, m per ribosome 2.5 MDa, m per ribosome (1/3 protein + 2/3 RNA) N ribosome = m total ribosomal protein / m protein per ribosome (0.2 × 0.15 × 10 -12 g) / (830,000 Da) × (1 Da) / (1.6 × 10 -24 g) 20,000 ribosomes d ribosome 20 nm => volume taken up by 20,000 ribosomes: V total ribosome 10 8 nm 3 <=> 10% of total cell volume Ribosome - cellular machine that synthesizes proteins 20% of cell’s protein is ribosomal 15% of cell’s mass is protein cell mass 1/3 of the ribosomal mass is protein N ribosome 20,000
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Sizing up e.coli or or => surface area A E.coli 6 μ m 2 Estimate N lipid associated with the inner and outer membranes of an E.coli cell: N lipid = 4 × 0.5 × A E.coli / A lipid 4 × 0.5 × (6 × 10 6 nm 2 ) / 0.5 nm 2 2 × 10 7 roughly half of the surf. area is covered by membrane proteins rather than lipids N lipid 2 × 10 7
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Image nobelprizeorg Drawing of the structure of cork as it...

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