Review Sheet for BIOC 460 at UA 2
Review Sheet for BIOC 460 at UA 2
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Date Created: 02/06/15
BIOC 460 General Chemistry Review Chemical E General Equilibrium M M gt cc m where a bl c and 1 me stolchlomemc numbals CeqcDeqd Equlllbnumcollsf l Ken ANNE 1 l eq Qq mm concennauon a equmbnm unns What are the UNITS 17 Example rezcuons A 77gt E units omeq 7 A 77gt E c units omeq 7 A E 77gt c units mg 7 AEgtCD unnsongq7 2A 77gt E units om 2A E 77gt c D unnsofKeq7 Units of Km depmd on due ma on Dimdz onofHZO H20 gt H OH quilibrium Ionization of H10 pH pKa mass action mno at equlllbnum mules mmoles M litel millmlel ln leallty pistons lEleased ale msmuy hydlated to hydlolllum ions 1H30 gt H30 DH but fol oul pulpom the mom dimple lomzzmon lcnchon suf ced Fol dlssoclauon of HQD the dlssoclauon equlllbnum consmnt IS HOH lt H201 gteq Keq Keq ofpule H30 can be measuled by measunng the conducuvlty ofpule watel Keg 18 x 1046 M at39liquot c What s the concennauon of undlssoclated waEl by weighing 1 11161 1000 gliter Divide by M w ls gluol H3017 Measule map 00 mollitei M H20 is a constant in biological solutions 555 vi Elm2MB Gene l Chemlsu39y me am pl Km H OH 1 H20 eq 13 X 1015 M z m 555 M eq HOH 1 X 10 14 M2 Kw the ion product of water a constant at a given temperature 25 C in this case In pure water H OH the square root of 10 14 N12 10 quotr M definition of a neutral solution L uses for Kw l lets us calculate H from OH and vice ve1sa 2 basis for de nition of pH pH longl 10310 can measure pH with a pH meter H Table 2 6 from Nelson amp Cox Lehninger Principles of Biochemistry 4th edition 2004 TABLE 2 6 The pH Scale H M PH OH J M DOH 100 1 O 10 3914 14 10 391 1 10 3913 13 10 392 2 10 3912 12 NOTE 103 3 1039 11 prHgt7 Hlt10 7M 10 4 4 10 3910 10 solution is quotbasicquot 105 5 109 9 1prlt7 Hgt10 7M 10 6 6 10 398 8 solution is quotacidicquot 10 7 7 10 7 7 1pr7 H10 7M 10 8 8 10 6 6 solution is quotneutralquot 10 9 9 10 5 5 pH scale is logarithmic 10 1O 10 10 4 4 If change in pH ApH 1 10 11 11 10 3 3 AH10110 f01d 10 12 12 10 2 2 If change i211 pH ApH 2 1013 13 101 1 AH 10 100 fold 103914 14 100 1 0 The expression pOH is sometimes used to describe the basicity or OH39 concen tration of a solution pOH is defined by the expression pOH og OH39 which is analogous to the expression for pH Note that in ail cases pH pOH 14 Bioc460 General Chemistry Review 2008 p 2 Ionization of weak acids and bases Bronsted definitions acid a proton donor base a proton acceptor Some of this material is reviewed on pp 147 17 of the textbook Btoehemtsw 6th ed by Berg Tymoczko amp Snyer cottiugateacitl 3 H conjugamaase neutral acid am ely Chalged base HA 2 H A positively cliai ged acid we HA 2 H A STRONG acids completely dissociated in dilute aqueous salmon example HNO 4 H N037 WEAK acids NOT complemy dissociated in dilute aqueous solution examples of weakly acidic gmups in blmnolecules a carboxylic acid Recooll 2 lt RCOO anaiuine R NHf W R NH The wealcei Lhe acid weaket tendency to donate its pinion ie y the coittugate base binds the pmlu ughuy the manger IE cumugate base sunnger tendency to ECGEL LEZE ZLaamr WWWASEHH q miuugate ACID Fox a mug acid Ka tacitl dlssoc equlllbnum constant is lrigll The M39Mkquot the aCKL the town it K3 acid dlssoc equilibnuin constant What are the units of K acid dissoc equilinnuin ceiistaiim Definition of pig conittme BASE Hgt coniqu ACID 1 We logl K logic f strong acid m high 1 low 19 low pKd high pKa Below is a table of some weak acids with their pig Values 25 C Explain the differences in sz within the 3 groups below Why does substitution of each successive H in the methyl group of acetic acid with a Cl decrease the pKa39Y Why does substitution of each additional methyl or methylene gloup for the H in formic acid or in methylamine 11021152 the pKa39Z Why does addition of the OH group to ethylamine to make ethanolamine decrease the pKa39Z BiDcA EI Genemlchemtstty RevieuZEIEIB p 3 Acid pKa acetic acid CH3COOH chloroacetic acid ClCHzCOOH dichloroacetic acid CDZCHCOOH trichloroacetic acid Cl3CCOOH formic acid HCOOH acetic acid CH3COOH propionic acid CH3CH2 COOH 476 285 148 070 375 476 487 Acid pKa ammonium ion 925 NH4 methylamine 106 CH3NH3 ethylamine 108 CH3CH2NH3 ethanolamine 95 HOCHzCHzNH3 Fig 216 Proton dissociation reactions of some mono di and triprotic acids with their pKas arranged on a pH scale from Nelson amp Cox Lehninger Principles afBiachemimy 4th edition 2004 Monoprotic acids Acetic acid Ka 174 x105 m Ammonium ion Ka 552 x10 10 11 Diproeic acids Carbonic acid Ka 17o gtlt 104111 Bicarbonate Ka 531gtlt1o11 m Glycine carboxyl Ka 457 x 103 m Glycine amino Ka 251 gtlt1o1O m Triprotic acids Phosphoric acid Ka 725 gtlt103 M Dihydrogen phosphate Ka 138 x107 m Monohydrogen phosphate Ka 398 x1013 11 U 1quotquot CH2C 3H phosphoric acid ionizations pKa2 lt H2P0439 q I H3P04 0 ll HOii OH OH H2C03 CH C0 3 0H 391 o CH2C pKa 234 H3PO4 H2PO H pKa 214 pKa Nos H H Bioc460 General Chemistry Review 2008 CH3C pKa 475 Hco H pKa 377 HPOqzquot 0 o H HZPOZ HPO pKa 686 pKa12 gt 4 H H pKa 9 25 Hco n Z 17 0 H 10 pH P043 391 CHC 2 NH NH H cog H pKa 102 0 o pKa 960 i HPog PC H pK39a 124 12 13 p4 Quantitative relationship between pK and pH Take log of both sides Base 1o 1o 1 11 gKa glAdd 0g Reaiiange 71ogH flogKn logLase Acid HendersonHayemalch Equation Base H 10 p PK g Add lets us calculate baseacid iauo noin pH and pKa oi calculate pKa nom pH and baseacid iauo W can calculate any one paiametei tom the othei two When base acid pH Kit 101 50 pH pK Conyeisely when pH 1JK base acitl Whean gt1K base gt acitl ie baseacitl ratio is greater than 11 When pH lt pK base lt acitl ie hamacid ratio is less than 11 When you do calculations alvmys stop at the end to think about whether your answer mam sense Look again atthe equilibrium dissociation reaction and remember LeChaLeller s Pnnclple HA lt2 H A The higher the ll i e the lower the pH the more the equilibrium shitts to the lett so the more coniugate acid will be present Conversely the lower the ll i e the higher the pH the more the equilibrium shitts to the right so the more con iu gate base will be present The exact ratio of base to acid depends on the pH and the ng HendersonrHasselbalch Equation Note that when pll pK A HA so base acid ratio 11 base acid When pll pKa the buffering capacityquot of the mixture will be the greatest Thatis a given change in concentration of base OI1 oracid lm will resultin the smallestchange in pH If the pH is ABOVEthe pit there will be more base than acidin the solution i e the base 4 acid ratio will be greater than 11 If the pH is BELOW the pig there will be more acid than base i e the baselacidlratio will be less than 11 When you do calculations always stop at the end to thnk about whetheryour answer nakes sense Work the posted practice problems at the end oi this review on pH pK and baseacid ratio and learn how to convert a baseacid ratio to the W oflhe tom base MMD that s in the iorm oi the conjugate base or the conjugate acid 306460 Generalcheiuistrypeyiewtzms p 5 Titration Curves add measured volume of solution of strong base NaOH of known concentration measure the pH eg with a pH meter can be used to determine oamount of acid in the solution from mols of OH required to completely deprotonate each acidic group which permits conversion of volume of standard OH added which was measured to equivalents OH added mols OH mol acidic group opKa values of acidic groups from pH at which an acidic group is exactly half titrated examplez titration of acetic acid CH3 COOH oinvolves 2 reversible equilibria H30 W OH Kw W OH1 1 x 1014 M2 I I II H A CH3COH n H CH3 COquot Ka 174 x 10 5 M acetic acid acetate anion Both equilibrilml constants must be satis ed at all times Fig 217 Titration curve of acetic acid from Nelson amp Cox Lehninger Principles of Biochemistry 4th edition 2004 When no OH has been added predominant form is HAc at the endpoint when 1 equivalent OH has been added all the HAc has been converted to Ac When exactly 05 equivalent of OH39 has been added exactly half the original HAc has dissociated so Ac 39 HAc base acid and pH pKa Shaded zone shows ie Fig 218 Titration curves of acetic acid H2P0439 and ammonium ion from Nelson amp Cox Lehninger Principles of Biochemistry 4th edition 2004 the pH range of useful buffering power from about 1 pH unit below to about 1 pH unit above the pKa ie between about 10 and 90 titration of the weak acid pH Bioo460 General Chemistry Review 2008 9 14 Midpoint 13 of 8 CH3COO titration l w 7 CH3COOI I CH3COO 11 9 925 3223 6 1o NH1INH31 T1025 pH 576 NH 9 Ham 3 5 Buffering L8 25 region 8 H2P031 HPOi39I T7285 4 L pH 376 7 Phosphate 3 PH PKla 475 P 6 pKa 686 L5 86 pKa 476 T5376 2 CH3COOH E 5 Acetate 4 1 CH3COOH CH3COO 33975 I 3 I I I I II I I I I 2 0 0 01 02 03 04 05 06 07 08 09 10 OH39 added equivalents I 50 Percent titrated I I I I I 0 01 02 03 04 05 06 07 08 09 10 0H39 added equivalents I 0 50 100 Percent titrated o 1 00 0 p6 Garrett at Grisham Biochemistry 21s Figure 21 4 imam i e e WM WW a No19 gt 04 Fig 213 from Garrett amp 1043 Grisharn Biochemistry 3rd ed 2004 For a polyprotic acid rnore than one acidic group so rnore than one pKa on titration curve it takes 1 equivalent of OH to titrate each acidic group so a tnprotic acid like phosphoric acid requires 3 equivalents The pK values are pH values at each hahf equivalent added 1 5 Equivalan OII added 0 10 20 25 30 Saunders Cunege Publishing Summary 1 2 3 4 H20 and acids in aqueous solution dissociate to yield protons H which in actuality would be hydrated to form H3 of The tendency of an acid to donate its proton to H20 dissociate the proton can be quantitatively described by its dissociation equilibriurn constant KB or its pKz which elong pKa values can be very accurately rneasured by titration curves as the pH at Mequjvalence points Relationship between pH pKz and ratio of baseacid can be described by the Hendersonr Hasselbalch Equation base pH pK log Buffers 39horneostasis the maintenance of constant conditions in internal environment lluids in living systerns have a characteristic alrnost constant pH How is pH controlled in living systems By buffer systems Buffer aqueous systern that tends to resist changes in pH when small amounts of acid or base are added Buffer system aqueous solution of a weak acid and its conjugate base Buffer range of a weak add new its pKa about 1 pH unit from the pKa Maximum buffering BIOMGD General Chemistry Review 2008 capacity is at the pKz Look again at the equilibrimn dissociation reaction and remember LeChatelier39s Principle HAzEHA39 The higher the H ie the lower the pH the more the equilibrium shifts to the left so the more conjugate acid will be present Conversely the lower the H ie the higher the pH the more the equilibrium shifts to the right so the more conjugate base will be present The exact ratio of base to acid depends on the pH and the pKa Henderson Hasselbalch Equation base H 39 1 p pk 0g acid Remember that when pH pKa A HA so base acid ratio 11 base acid When pH pKa the buffering capacity of the mixture will be the greatest That is a given change in concentration of base OH or acid H will result in the smallest change in pH 2 physiologically important buffer systems 1 INTRACELLULAR 2 inorganic phosphate ion H2PO4 lt gt HPO4 ZpKa 7 and organic phosphates eg phosphomonoesters ROP020H lt gt R OP03 pKa 7 2 EXTRACELLULAR blood plasma of mammals bicarbonate buffer system C02 H20 ltgt H2CO3 ltgt H HCO3 3 linked equilibria H Hco reaction 1 Aqueous phase 2503 blood in capillaries reactionz H20 J 9 H20 Cozld 1 reaction 3 Gas phase lung air space C029 0How can the HC03 H2C03 system effectively buffer the blood plasma at pH 74 with a pKa well below 7 clinical considerations of bicarbonate buffer system a What happens physiologically if the blood pH ie H acidosis You exhale excess C02 so C02 l so Le Chatelier39s Principle HJ ie pH goes back up b What happens physiologically if the blood pH l ie HJ alkalosis You exhale lei C02 so C02 I so Le Chatelier39s Principle H ie pH goes back down c What if you have difficulty exhaling respiratory failure Blood C02 I so H acidosis and you can39t get rid of the excess C02 by exhaling Treatment inject bicarbonate HC03 to convert some of the excess H to H2C03 which would bring pH back up and get the person breathing again to get rid of the excess C02 For a little online quiz on acids bases pH amp pKa and buffers try the Biology Project website at httpWwwbiologyarizonaedubiochemistryproblem setsphphhtml Click on quottutorialquot at the bottom of each question for the tutorial that goes with that question Bioc460 General Chemistry Review 2008 p 8 For a little online quiz on clinical correlates of blood pH try the Biology Project website at httpwwwbiologyarizonaedubiochemistryproblem setsmedphmedphhtml Click on quottutorialquot at the bottom of each question for the tutorial that goes with that question PRACTICE PROBLEMS Work these without looking at the answers which are on the last page NOTE ESPECIALLY PROBLEM 2B how to go from the m of baseacid Henderson Hasselbalch calculation to the fraction of the total acid base that s in the form of the acid or What fraction is in the form of the base In fact anytime you calculate a RATIO and get a number STATE the understood quot1quot in the denominator If ratio is 04 state it as 04 1 Also start by writing chemical equations to describe acid dissociation reactions with CHARGE BALANCE 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 What fraction of the total is present in the form of the BASE COO at pH 5 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 in the amino acid sequence of that protein in the uncharged neutral form at pH 45 What is the pKa of that specific His residue in that protein You need to know the ionization properties of the functional group of His to answer this question look at the ionization equilibrium for His in Fig 2 15 p 32 and in Table 2 1 p 33 of Berg Tymoczko amp Stryer Biochemistry 6th ed All that concerns you is the ionization of the R group side chain the imidazole group The pKa of the imidazole group of the free amino acid histidine is about 60 but the exact pKa values of amino acid functional groups in proteins vary somewhat depending on the specific environment around that residue in that protein You39re being asked to calculate m specific His residue39s pKa Bioc460 General Chemistry Review 2008 p 9 SOLUTIONS TO PRACTICE PROBLEMS 1 pH logH Remember the log is the exponent If pH 60 H 10pr 10 0 M Use a calculator for this If H 5 x 10 7 m pH log5 x 10 7 63 2 acid dissocation reaction for a carboxyl group R COOH lt gt R COOT H A Use the Henderson Hasselbalch Equation whenever you see a problem involving the relationship of pH pKa and baseacid ratio or fraction of the total group that s in form of the base or of the acid pH pKa log baseacid logbaseacid 2 pH pKa 50 40 10 baseacid 101 101 There s 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 COOiCOOH ratio is 10 1 We can do this problem most simply by using proportions the total of the carboxyl group is COOH C007 2 1 10 11 The fraction of the total in the form of the M COOH is COOH total 2 COOH COOH C007 2 111 2 0091 91 of the molecules in solution have that carboxyl group in its acid form COO total 2 COO COOH C007 2 1011 0909 Alternatively if you ve already calculated that acidtotal 0091 then basetotal 1 acidtotal 1 0091 0909 Either way 909 of the molecules in solution have that carboxyl group in its base form 3 We39ll abbreviate the imidazole group in question as Im so neutral form is Im the conjugate base and charged form is Im the conjugate acid Im lt gt 1m H Use the Henderson Hasselbalch Equation again quotAbout 1 neutralquot means that base Im total 2 about 001 or 1 100 Thus baseacid ratio would be basetotal base 2 1 100 1 199 pH pKa log baseacid pKa 2 pH logbaseacid 45 log 199 2 45 20 45 20 65 The pKa of that specific His residue in that protein must be about 65 Note that this is slightly different from the pKa of the R group of the free amino acid histidine Bioc460 General Chemistry Review 2008 p 10
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