January 27 th and 29 th , 2010 Biochemistry Recitation MBioS 303 - PDF document

1/29/2010 January 27 th and 29 th , 2010 Biochemistry Recitation MBioS 303 Spring 2010 Today’s Main Topics � Acid/Base chemistry � pK and pH, ionizable groups, and pI � Calculating a net charge on a pentapeptide � Electrophoresis � Basic � Isoelectric focusing � The peptide bond � Formation � Characteristics 1

1/29/2010 Acid and Base Chemistry: p K s � p K a = acid dissociation constant Do you recognize this molecule? Which form is the acid and which is the base? A B � What is the proportion of acid and base forms when the pH of the environment is equal to the p K a of the group you are looking at? Acid and Base Chemistry: ionizable groups on amino acids � Why do we care about ionizable groups on amino acids? � What amino acids have ionizable R groups? � Y, Tyr � C, Cys � K, Lys � H, His � R, Arg � D, Asp � E, Glu 2

1/29/2010 Acid and Base Chemistry: ionizable groups on amino acids A B (1) What is the amino acid? (2) What is the ionizable group? Would ionization give the acid or base form? (3) What is the classification of each amino acid? Acid and Base Chemistry: ionizable groups on amino acids Given that the p K R for this amino acid is 10.07, what pH is -2 pH units? +2 pH units? What would be the predominant form at pH 7? pH 3? pH 13? What would be the charge on the R group at pH 7? pH 13? 3

1/29/2010 Acid and Base Chemistry: calculating pI � pI = isoelectric point � What does this mean? � How do you determine the pI? � Where there is no charge � pK1 = 2.19, pKR = 4.25. pI = (2.19+4.25)/2 = 3.22 Calculating the Net Charge of a Pentapeptide Following is the example worked in recitation this week. 4

1/29/2010 Calculating the Net Charge of a Pentapeptide See Lehninger for the appropriate p K values. (1) Name the above pentapeptide using one- or three-letter amino acid abbreviations. (2) At pH 6, would each ionizable group be in the acid or base form? (3) What is the net charge of the pentapeptide? (HINT: Do not forget to consider the N- or C-termini) 5