Class Note for BIOC 460 at UA 3
Class Note for BIOC 460 at UA 3
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Date Created: 02/06/15
REVIEW OF FRESHMAN CHEMISTRY pH pK buffers HendersonHasselbalch Equation see also Stryer pp 7374 Biological reactions occur in aqueous environments or in environments de ned by the active centers of enzymes which themselves eXist in aqueous environments The active centers of enzymes have functional groups that participate in the processes of catalysis and the chemical nature of those functional groups is often a function of the pH The importance of pH in the functional properties of proteins and enzymes is well known Dissociation of weak acids Consider the simple monoprotic acid HA or alternatively HA HA ak H A Example RCOOH ak H Rcoo OR HA ak H A Example RNH3 3 H RNH2 The form with the associated proton is the conjugate acid form The form after dissociation of the proton the form without the proton is the conjugate base The equilibrium dissociation constant is called Ka The higher the Ka the greater the tendency of the acid to DISSOCIATEDONATE its proton the stronger the acid Remember that pH 7 logH and pKa 7 logKa Thus the lower the pKa the stronger the acid a HA HA LA H Ka HA A pH pKa log HA The last equation is the Henderson Hasselbalch Equation pPUpKbuffer review amp practice problems page 1 of 3 HendersonHasselbalch Equation A7 H Ka 10 p p g HA Note that when pH pKa A HA At this condition the buffering capacity of the buffer will be the greatest That is a given change in concentration of base or acid will result in the smallest ApH pH titration 1O 9 E 7 6 a 5 I I I O I 02 04 06 08 1 Equwalents hvdroxnde Upon addition of 05 equivalents of base 12 of the acid will be converted to the conjugate acid such that A HA and pH pKa This condition will allow the largest concentration of both species and therefore the maximum buffering effect 39 0 quot 00 PRACTICE PROBLEMS Work these without looking at the answers which are on the last page 1 For a solution whose pH is 60 what is H If H is 5 x 10 7 M what is the pH Use a simple scientific calculator if necessary to do log problems 2 A For a weak acid such as the R group carboxyl group of Glu or Asp in a protein if the pKa of that specific residue39s carboxyl group is exactly 40 in an environment in which the pH 50 what would be the ratio of base to acid COOCOOH B For that same carboxyl group what fraction or what percentage of the total population of all the molecules in solution is present in the form of the ACID COOH at pH 50 3 Suppose that about 1 of the molecules of a particular protein in solution have the imidazole group of a specific His residue say it39s residue 20 of that protein in the uncharged neutral form at pH 45 What is the pKa of that specific His residue in that protein pPUpKbuffer review amp practice problems page 2 of 3 SOLUTIONS TO PRACTICE PROBLEMS 1 pH 7 logH Remember the log is the exponent prH 7 60 H 710 pH 7 10 0 M Use a calculator for this If H 5 x 10 7 M pH logS x 10 7 63 2 A Use the HendersonHasselbalch Equation whenever you see a problem involving the relationship of pH pK and baseacid ratio or fraction of the total group that s in form of the base or of the acid pH pKa logbaseacid logbaseacid pH 7 pKa 5040 10 baseacid 101 101 There39s 10 times as much of the carboxyl group in the form of the base as in the form of the acid when the pH is 1 unit above the pKa B At pH 50 the COOHC007 ratio is 101 We can do this problem most simply by using proportions the total of the carboxyl group is COOH COOT 10 1 11 The fraction of the total in the form of the Lid COOH is COOH total 7 COOH COOH 000 7 111 7 0091 91 of the molecules in solution have that carboxyl group in its acid form 3 You need to know the ionization properties of the functional group of His to answer this question Abbreviate the imidazole group in question as Im so neutral form is Im the conjugate base and charged form is Im the conjugate acid Use the HendersonHasselbalch Equation again quotAbout 1 neutralquot means that base Im total about 001 or 1100 Thus baseacid ratio would be basetotal 7 base 1 1001 199 pH pKa logbaseacid pKa pH logbaseacid 45 7 log 199 45 7 7 20 45 20 65 The pKa of that speci c His residue in that protein must be about 65 Note that this is slightly different from the quottypicalquot pKa for a quotgenericquot His imidazole group in proteins as given in Table 31 in Berg Timoczko amp Stryer pPUpKbuffer review amp practice problems page 3 of 3
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