lecture_29legge - Structure & Properties of Water Bent...

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1 Comprehensive Exam Review 12/03/2009 Structure & Properties of Water Bent geometry, O-H bond length of 0.958Å Can form Hydrogen bonds Henderson - Hasselbalch equation ] [ ] ][ [ HA A H K + = From ] [ ] [ + = HA K H Rearrange ] [ A Take (-)Log of each ] [ ] [ log log HA A K pH + = ] [ ] [ log HA A pK pH + = The 6 step approach 1. Write the Henderson + Hasselbalch equation. 2. Write the acid base equation 3. Make sure either an H + or OH - is in the equation. 3. Find out what you are solving for 4. Write down all given values. 5. Set up equilibrium conditions. 6. Plug in H + H equation and solve. What is the pH of a solution of that contains 0.1M CH 3 COO - and 0.9 M CH 3 COOH? 1 ) pH = pK + Log [A - ] [HA] 2) CH 3 COOH CH 3 COO - + H + 3) Find pH 4) pK = 4.76 A - = 0.1 M HA = 0.9 M 5) Already at equilibrium 6) X = 4.76 + Log 0.1 0.9 Log 0.111 = -.95 X = 4.76 + (-.95) X = 3.81 Amino Acids You must know Table 4.1 p76-77: Their names Their structure Their three letter code Their one letter code Tyrosine, Tyr, Y, aromatic, hydroxyl
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2 The Fischer Convention Absolute configuration about an asymmetric carbon related to glyceraldehyde (+) = D -Glyceraldehyde (-) = L -Glyceraldehyde Newman Projection Threonine and Isoleucine Nucleophiles R NH 2 + H + RN + H H H Basic reaction of amine R NH 2 O R' R'' C OH R'' R' H Nucleophilic reaction of an amine Biologically important nucleophiles R NH 2 O R' R'' C OH R'' R' H Amine Ketone or aldehyde Carbinolamine intermediate R N H R' R'' + Imine Movement of an electron pair from a position and pointing to the electron deficient center attracting the pair.
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3 Common biological electrophiles Group transfer reactions Acetyl group transfer Nucleophile attack on an acyl carbonyl to form a tetrahedral intermediate P tid b d h d l i Y + AX Y A + X Peptide bond hydrolysis
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lecture_29legge - Structure & Properties of Water Bent...

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