ProblemC1-2 - Computational Biology 03-310 Spring 2006 R F...

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Computational Biology 03-310, Spring 2006 R. F. Murphy Page 1 of 3 Problem C1 Modeling Acid-Base Equilibria Due: April 4, 2006 In this assignment you will make a model of the net charge on an amino acid by considering the pK's of its ionizable groups and entering appropriate equations into a spreadsheet program. Consider the amino acid lysine, which has three ionizable groups: the carboxyl group (with a pK of 2.2), the alpha amino group (with a pK of 9.2), and the epsilon amino group (with a pK of 10.8). Starting from a very low pH (e.g., pH 1) at which the fully protonated form ( H 3 Lys ++ ) would be the main species, we can identify the major species produced as each group loses a proton: first the carboxyl (yielding H 2 Lys + ), then the alpha amino group (yielding HLys ), and finally the epsilon amino group (yielding Lys - ). For any ionizable group, the ratio of the base and acid forms at any pH can be found using the Henderson-Hasselbalch equation: [ B ! HB ] = 10 ( pH ! pK ) If only the four species listed above are considered to be present (but see extra credit question 10 below!), the
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This note was uploaded on 03/04/2012 for the course BIO 510 taught by Professor Miller during the Fall '06 term at Carnegie Mellon.

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ProblemC1-2 - Computational Biology 03-310 Spring 2006 R F...

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