lec3 note - LECTURE 3. 27 August 2010 (P. J. Hollenbeck)...

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-1- LECTURE 3. 27 August 2010 (P. J. Hollenbeck) BIOL 231 BIOLOGICAL CHEMISTRY Read: Chap 2: pp. 39-50; 59-63; Panels 2-1 (pp. 64-5), 2-2 (pp. 66-7); Panel 2-7 (pp. 76-7); DVD 2.4 Problem assignment: 8-10 <Last time we dealt with the boundaries of the cell and organelles. Now we’re ready to dive into the cell – but first, we need to understand its chemical building blocks. ..> 2 I. H O, protons and carbon 2 (A) H O the chemistry of cells is as much about WATER as it is about CARBON. (1) Water is a POLAR molecule, although it’s not charged. The two covalent bonds are both polarized, such that the O atom is negative relative to the H atoms. This asymmetric distribution of charge allows all 3 atoms to participate in interactions with other water molecules, so that. .. (2) Water is a very COHESIVE liquid. At each moment, each molecule in liquid water is interacting, on average, with 3.4 other molecules (This only rises to 4 when water freezes). (3) We call the part of the cell dominated by water a HYDROPHILIC environment. It is energetically favorable for molecules that are completely ionized or have asymmetrically-distributed charge to reside there. Examples are sodium ions or glucose. The other part of the cell (mainly membranes) is a HYDROPHOBIC environment. It excludes water and other molecules with asymmetrically-distributed charge, and contains molecules like lipids that have extended regions of uncharged 18 hydrocarbons. An example is stearic acid, a fatty acid with a C carbon chain. <Remember, the structure of molecules determines which environment – hydrophilic or hydrophobic – they will be found in. Hydrophilic locations include the cell’s cytoplasm, lumens of organelles and the extracellular space. It is no surprise that molecules with both polar and hydrophobic domains, such as phospholipids, are found at (and form) the hydrophobic boundaries between watery locations> (B) pH (1) Water dissociates, and we can think of the products as H and OH . In pure water, + ! W [H ] = [OH ] = 10 M, so the dissociation constant, K = [H ][OH ] = 10 . A useful + !! 7+ 14 measure of the [H ] that you know very well is pH. + (2) recall that pH = log(1/[H ]) = ! log[H ] ++ We need to be acutely aware of pH in biological chemistry because the most important ionizations of biological macromolecules involve losing or gaining H ! +
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-2- (C) C-C bonds, single and double (1) Carbon can make 4 equivalent single bonds. A C-C single bond allows free rotation of the connected C atoms and their constituents.
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lec3 note - LECTURE 3. 27 August 2010 (P. J. Hollenbeck)...

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