Biochem Connections notes

Biochem Connections notes - BioChem Connections Boxes Exam...

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BioChem Connections Boxes Exam I Fall 2006 Extremophiles: p.23 -Archaebacteria live in extreme environments Three Groups: -methanogens - strict anaerobes, produce methane from CO2 and H2 -halophiles - require high [salt] (like in Dead Sea) for growth -thermacidophiles - require high temps and acidic conditions for growth -80-90 C and pH 2 -since these organisms can tolerate these extremes, so can their proteins/enzymes -these enzymes make many biochemical processes in the laboratory possible -like PCR uses Thermus aquaticus (Taq polymerase) 1
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BioChem Connections Boxes Exam I Fall 2006 Importance of H-bonding -h-bond essential for the evolution of life. (much like polymers, carbon, and stereochemistry) -individually, h-bonds are weak -but collectively, h-bonds are VERY strong -all unique properties of H2O (high melting point, surface tention, ise and density characteristics, solvent potency) are all contributed to h-bonding -Water is polar -20 or more water molecule per dissolved molecule of Na+ or Cl- -H-bonding in polymers determines shape -Single helices like starch or the alpha-helix are stabilized by intrachain H-bonds -Double and 3x helices, like DNA or Collagen, respectively, involve H-bonds b/t 2 or 3 respective groups -also important in transferring genetic material -dentists use fluorouracil to treat cold sores -the herpes simplex virus causes these sores and the fluorouracil causes mutations so sores will not appear. 2
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BioChem Connections Boxes Exam I Fall 2006 Buffer Selection: -most of biochem is carried out in vitro which need to be buffered. -also, enzyme isolation and growth of cells in tissue culture are buffered -For selecting a buffer, the following must be considered: 1. Suitable pKa for buffer 2. no interference w/ reaction or w/ assay 3. suitable ionic strength of buffer 4. no precipitation of reactants or products due to presence of buffer 5. non-biological nature of buffer -the perfect pH buffer for a reaction would have a pH equal to its pKa -if reaction is known to produce acidic product, pKa needs to be below reaction pH -if reaction is known to produce basic product, pKa needs to be above reaction pH. In both cases, buffering capacity increases as reaction proceeds. -Sometimes a buffer can interfere w/ a reaction or w/ assay methods -a reaction that requires/produces CO2/phosphate will be inhibited if too much phosphate or carbonate in mixture -phosphate or carbonate buffers are prepared from Na+ or K+ salt. -many enzymes that react w/ nucleic acids are activated by one of these ions and inhibited by the other, so the choice of Na+ or K+ is very important -buffer can also effect spectrophotometric determination of colored assay product. -buffers w/ poor buffering capacity at desired pH can be assisted by increasing their concentration, but enzymes are sensitive to high [salt]. -buffers w/ no biological activity are desired, i.e. TRIS
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Biochem Connections notes - BioChem Connections Boxes Exam...

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