To determine if our protein unfolds or not is it sufficient to know the K a and K b Values of the functional groups? - O H

Transcription

1 A students work (without solutions mnul) ~ problems/night To determine if our protein unfolds or not is it sufficient to know the nd b Vlues of the functionl groups? Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions Ioniztion constnts for proteins 1 S - Zn + S - - O C O S- H RCOOH + H O RCOO + H O + q l q q D structure of ALAD directs Rectnts into proper orienttion D structure controlled by proper hydrogen nd ionic bonds, ph dependent!!!!!!! RSH + H O RS + H O + q l q q R refers to rest of protein Phosphoenolte crboylse, humn, cys Control of protein shpe is due to frction of sites chrged cysteine COOH, SH, 6 9 1

2 Protein folding due to FRACTION of sites chrged Vl,, NH 5 VlCOOH,, 501 tyrroh,, HA H O + A % Ionized (dissocited) + q q, from HA q mount dissocited ( M) % dissocition 0 initil concentrtion ( M) % dissocition 0 [ Aq [ HAq, initil This seems pretty stright forwrd Hemeglobin HA H O + A Clculting [A- This will require knowing [H O q + + q q, from HA q + [ Aq, [ HOq, [ HAeq, q AND new vocbulry for compring the solution cidity from eperiment to eperiment nd b tell us bout the possibility Of donting protons, not wht the solution Acidity is Define nother comprison number: ph A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions ph, poh, p

3 Chemists re LAZY To shorten clcultions use log ( ) ( ) ( ) log b log + log b log log( ) log( b) b log( ) log( ) ( ) [ [ p 1 log log log ( ) ( ) log + [ OH [ HO [ HO Assumption tht 555 molr is reltive unchnged + [ [ [ [ [ [ HO OH HO OH H O [ 14 W 5555 [ [ OH H O + W 14 eq eq [ [ + ( ) [ [ 14 + [ OHq log[ H Oq OH H O + W 14 q q log log log OH + log H O W q q 14 log + [ OH [ log H O + q q 14 log + [ [ p log 14 poh + ph scle runs from 0 to 14 ph Which is more Acidic? cid/bse ve [H + ph poh ve [OH - bse blood sliv 1-7 cid urine 51-7 cow s milk 54-7 cheese [ ph log # is slightly lrger thn -8, so I know it is 7 something [ OH You do the rest p [ log[ 14 ph + poh px

4 Wht re the two p s? ( )( ) p 1 log p ( ) ( 1) log ( 6 9 ) p ( 1)( 8 ) 8 - O C O S- H Wht is the of compound Whose p is 7? p RCOOH + H O RCOO + H O + q l q cysteine COOH, SH, 6 9 A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions HA H O + A Clculting [A- This will require n equilibrium clcultion + q q, from HA q + [ Aq, [ HOq, [ HAeq, q Generlized Strtegy involves compring s 1 Write down ALL possible rections involving proton Ecluding wter, identify ll the proton donors s 1 Strong cid Strong electrolyte: HNO, HCl, H SO 4 (No Clen Socks) b Give ll strong cid protons to wter or lph dog c Clculte hydronium conc d Clculte ph Wek Acid Identify strongest cid (omeg dog, cn not hold protons) b Hs lrgest ; smllest chrge density nion c Clculte how mny protons omeg gives up (equil) d Clculte ph e Use to determine wht lph gets 4

5 Emple Clcultions 1HCl Acetic cid (vinegr) HF B(OH) (Boric cid (eye wsh)) 4Miture (HF nd phenol) 5Miture (H SO 4, HSO 4- ) 6Triethylmine 7NAcette 8Our heme emple Clculte the ph of 0004 M HCl Generlized Strtegy involves compring s 1 Write down ALL possible rections involving proton + HCl H + Cl q q q HO H + OH + 14 l q q w Ecluding wter, identify ll the proton donors s 1 Strong cid Strong electrolyte: HNO, HCl, H SO 4 (No Clen Socks) Cl low ch rge density q b Give ll strong cid protons to wter or lph present give ll bone to wter HO l + HClq HO + Cl complete rection c Clculte hydronium conc d Clculte ph + q q Omeg dog + HO q 0004 M + HO q 0004 M Scientific nottion llows you to quickly check if Your nswer is in the right bllprk ph log 4 ph log ( ) ( 4) + log( ) ph log( 4) + ( ) ph ( 0 60) + ph 9 ph hs to be slightly less Thn Emple Clcultions 1HCl Acetic cid (vinegr) HF B(OH) (Boric cid (eye wsh)) 4Miture (HF nd phenol) 5Miture (H SO 4, HSO 4- ) 6Triethylmine 7NAcette 8Our heme emple 5

6 Emple: Wht is the % ioniztion of commercil vinegr? The lbel reds 5% cidity (by weight) Vinegr is cetic cid which hs the formul HC H O (CH COOH) 18-5 Density of 5% cetic cid 0 g/ml 1 Write down ALL possible rections involving proton CH COOH + H O H O + CH COO q l q, q HO H + OH + 14 l q q w Ecluding wter, identify ll the proton donors s 1 Strong cid Strong electrolyte: HNO, HCl, H SO 4 (None) Wek Acid: CHCOOHq + HOl HOq, + CHCOOq 18 Clculte how mny protons omeg gives up (equil) + 5 Emple: Wht is the % ioniztion of commercil vinegr? The lbel reds 5% cidity (by weight) Vinegr is cetic cid which hs the formul HC H O (CH COOH) 18-5 Density of 5% cetic cid 0g/mL now Don t now ( 0 g solution ) % by wt gcetic cid 0gsolution 5gcetic cid 0gsolution 1mole 1mole cetic cid ( 5 g ) ( 5g cetic cid ) cetic cid ( ) ( ) ( ) g 1mL 1L L solution 0 g ml solution Need the initil molrity need the finl dissocition cetic cid cetic cid 008 mole 085 M L [ HC H O 0855 M Why complicte this sitution by dding in -7 When we get rid off it with n ssumption? Becuse it cretes hbit necessry of multiple r H O OH - H HC H O C H O - H + stoic conc init 5% 0-7 [Init Chnge Assume 0855>> + -7 << [Equil Wht is the % ioniztion of commercil vinegr? The lbel reds 5% cidity (by weight) Density of 5% cetic cid is 0 g/ml Vinegr is cetic cid which hs the formul HC H O (CH COOH) 18-5 ( )( + ) [ HAinit HA A H + Assume 0855>> + -7 << 0855( ) 0855( ) 5 ( 18 )( 0 855) Check: %? Sig figs error % % error ? % 0816 Originl sig figs were 08 So if we round to sig fig, hve Sme nswer [ [ ( )(( )() ) ph ( 1 ) ) log log ( 0 ( ) )

7 % dissocition 0 [ Aeq [ HAq, initil % 085 How does % dissocition or ioniztion vry with concentrtion? [Acetic Acid % ioniztion 0 M 04% 085M 046% 01 M 1% Observtions? % ioniztion increses with the lower molrity Why should this be so? Wht is the % ioniztion of commercil vinegr? The lbel reds 5% cidity (by weight) Density of 5% cetic cid is 0 g/ml Vinegr is cetic cid which hs the formul HC H O (CH COOH) 18-5 Wht is the % ioniztion of commercil vinegr? The lbel reds 5% cidity (by weight) Density of 5% cetic cid is 0 g/ml Vinegr is cetic cid which hs the formul HC H O (CH COOH) [ H [ A [ HA Dilute by (mke less concentrted): Q + [ H [ A [ HA + [ H [ A <,, >? [ HA Wht does this tell us, if nything? We hve too mny rectnts, need to shift to the right, or dissocite some more generl rule of thumb: dilution gives more dissocition Emple Clcultions 1HCl Acetic cid (vinegr) HF 4B(OH) (Boric cid (eye wsh)) (students Do this one yourself) 5Miture (HF nd phenol) 6Miture (H SO 4, HSO 4- ) 7Triethylmine 8NAcette 9Our heme emple 7

8 Clculte the F- of solution of 0 M HF Write down ALL possible rections involving proton + HF H + F 7 4 q q, F q + 14 HO l Hq + OHq w Ecluding wter, identify ll the proton donors s 1 Strong cid Strong electrolyte: HNO, HCl, H SO 4 (No Clen Socks) No Strong Acids (SA) Wek Acid Identify strongest cid (omeg dog, cn not hold protons) b Hs lrgest ; smllest chrge density nion + HFq Hq, F + Fq 7 4 c Clculte how mny protons omeg gives up (equil) H O H + OH HF (q) H + from HF F - stoic Init -7 0 Chnge Assum 1>> -7 << Equil 1 HF (q) H + from HF F - Init -7 0 Chnge Assum 1>> -7 << Equil 1 7 ( )( + ) 1 1 error Check ssumptions 1( ) ? % error 7 7 5% + 7? HF (q) H + from HF F - Init -7 0 Chnge Assum 1>> -7 << Equil 1 7 [ F 7 [ log ( )( ) 1 log 7 ( ) ( ) ph 1 log Clculte the ph of solution of 0 M HF Sig fig is here Clculte the F- of solution of 0 M HF

9 Emple: Boric cid is commonly used in eyewsh solutions to neutrlize bses splshed in the eye It cts s monoprotic cid, but the dissocition rection looks different Clculte the ph of 075 M solution of boric cid, nd the concentrtion of B(OH) 4- BOH ( ) + HO BOH ( ) + HO 58 +, q l 4, q q 1 Write down ALL possible rections involving proton BOH ( ) + HO BOH ( ) + HO 58 +, q l 4, q q + 14 l q q w HO H + OH Identify proton donors 1 strong cids: No Clen Socks? Wek cids: No SA B(OH) Students do This on your own Set up ICAE chrt H O OH - H B(OH) + H O B(OH) 4- + H + stoic 1 n 1 1 [Init Chnge Assume 075>> -7 << Equil 075 ( ) 7 ( ) Students do This on your own [ HAinit [ HAinit 58 check?? two ssumptions B(OH) + H O B(OH) 4- + H Clculte the ph of 075 M solution of boric cid 5 B(OH) + H O B(OH) 4- + H + [Init Chnge Assume 075>> -7 << Equil 075 ( ) % error ? [ B( OH) 4 1 yes error [ H %? ph ( 1) log ( 1 ) Students do This on your own check?? two ssumptions Sig fig B(OH) + H O B(OH) 4- + H Clculte the ph of 075 M solution of boric cid Emple Clcultions 1HCl Acetic cid (vinegr) HF 4B(OH) (Boric cid (eye wsh)) (students Do this one yourself) 5Miture (HF nd phenol) 6Miture (H SO 4, HSO 4- ) 7Triethylmine 8NAcette 9Our heme emple 9

10 Mitures of Acids Clculte the ph of solution tht contins M HF nd M HOC 6 H 5 Clculte the conc of -OC 6 H 5 t this concentrtion 1 Write down ALL possible rections involving proton + HF H + F 7 4 q q, F q l q q HO l Hq + OHq w CHOH H CHO Ecluding wter, identify ll the proton donors s 1 Strong cid NONE Wek Acid Identify strongest cid (omeg dog, cn not hold protons) Hs lrgest ; smllest chrge density nion Clculte how mny protons omeg gives up (equil) Clculte ph (Use to determine wht lph gets) HF will control the proton concentrtion, but Should include ll possible sources to remind ourselves H O OH - H HF + H O F - + H + stoic 1 n 1 1 [Init 0-7 Chnge Assume >> -7 << Equil ( + ) 7 7 [ HAinit [ HAinit 4 check?? two ssumptions HF H + + F HOC 6 H 5 H + + -OC 6 H ( ) Clculte the ph of solution tht contins M HF nd M HOC 6 H 5 Clculte the conc of -OC 6 H 5 t this concentrtion HF + H O F - + H + stoic 1 n 1 1 [Init 0-7 Chnge Assume >> -7 << Equil ( ) Check ssumptions: 5% error 1 7 1? Sig fig error 7 7 5% + 7? Sig fig 007 HF + H O F - + H + stoic 1 n 1 1 [Init 0-7 Chnge Assume >> -7 << Equil ( ) [ H + 7 Clculte the ph of solution tht contins M HF nd M HOC 6 H 5 Clculte the conc of -OC 6 H 5 t this concentrtion

11 HF + H O F - + H + stoic 1 n 1 1 [Init 0-7 Chnge Assume >> -7 << Equil C 6 H 5 OH+ H O C 6 H 5 O - + H + stoic 1 n 1 1 [Init Chnge Assume >> <<7 - Equil 7 - C 6 H 5 OH+ H O C 6 H 5 O - + H + stoic 1 n 1 1 [Init Chnge Assume >> <<7 - Equil 7 - CHOH + HO HO + CHO l q 6 5 q + [ HOq, [ CHOq, [ CHOH [ 7 ( 7 ) ( 7 ) 4 [ 7 5% error + [ 7? % 7 7 [ 6 5 q C H O 666, 4 Clculte the ph of solution tht contins M HF nd M HOC 6 H 5 Clculte the conc of -OC 6 H 5 t this concentrtion Emple Clcultions 1HCl Acetic cid (vinegr) HF 4B(OH) (Boric cid (eye wsh)) (students Do this one yourself) 5Miture (HF nd phenol) 6Miture (H SO 4, HSO 4- ) 7Triethylmine 8NAcette 9Our heme emple Emple: clculte the ph of 000 M sulfuric cid 1 Write down ALL possible rections involving proton + HSO 4, q + HO HSO4q, F + HO q lrge HSO + H O H O + SO 1 + 4, q q 4 q l + 14 HO l Hq + OHq w Ecluding wter, identify ll the proton donors s 1 Strong cid Strong electrolyte: HNO, HCl, H SO 4 (No Clen Socks) + HSO 4, q + HO HSO4q, F + HO q lrge b Give ll strong cid protons to wter or lph dog 11

12 1 Pure Wter H O OH - H Control/complete H SO 4 HSO - 4 H + stoic [init complete stoic HSO - 4 H + SO [Init Chnge Assume? 000> 000> + [Equil [ HO q, [ SO4 q, [ [ 5% error [ HSO4, q, [ [ SO4, q Emple: clculte the ph of 000 5% error M sulfuric cid; ? + NO! ? Here is our first emple in which we cn not mke ssumptions stoic HSO - 4 H + SO [Init Chnge Assume? 0001> 0001> + [Equil % error [ [ [ 0001 Emple: clculte the ph of 000 M sulfuric cid; % error! ( 1 )( ) ( ) ( ) ( )( ) ± ( ) ± ± [SO b + c 0 b b 4c ± -Solution gives neg Number which is not llowed [H ph-log( )7 Successive Approimtions (itertions) Alterntive Strtegy to going to ect equil Epression ITERATIVE SOLUTIONS Why? becuse the rel body or rel world Is much too comple to lwys be ble to Find n ect equilibrium epression 1

13 Clculte proton concentrtion of 00 M HNO using the itertive method ( 60-4 ) 1 4 [ HAeq Pure Wter H O OH - H HNO NO H + stoic [Init Chnge Assume 00>> >> -7 [Equil 00 Clc New Equil Clc New New Equil Clc [ HA ( 60 4 )( 01 ) 77 4 ( 60 4)( ) ( 6 0 4)( 0 09) '' '' Converging, plusible nswer for itertive method: 00 M HNO, 60-4 A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions Wek Bses Emple Clcultions 1HCl Acetic cid (vinegr) HF 4B(OH) (Boric cid (eye wsh)) (students Do this one yourself) 5Miture (HF nd phenol) 6Miture (H SO 4, HSO 4- ) 7Triethylmine 8NAcette 9Our heme emple 1

14 1 Clcultion with Wek Bse Clc the [OH, [H, nd ph of 00 M solns of triethylmine, b 40-4 H O H + OH B H O BH + OHstoic [Init Chnge Assum 00>> -7 < Equil 00 Clc the [OH, [H, nd ph of 00 M solns of triethylmine, b H O H + OH B H O BH + OHstoic [Init Chnge Assum 00>> -7 < Equil 00 7 ( + ) 00 4 b 40 4 ( ) error % + 894? 5% error ? Clc the [OH, [H, nd ph of 00 M solns of triethylmine, b Rounds to Rounds to 00 [ OH 894 poh ( 1) [ log ( ) 048 ph A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions Slts Emple Clcultions 1HCl Acetic cid (vinegr) HF 4B(OH) (Boric cid (eye wsh)) (students Do this one yourself) 5Miture (HF nd phenol) 6Miture (H SO 4, HSO 4- ) 7Triethylmine 8NAcette 9Our heme emple 14

15 Write ll rections involving protons, hydroides ( ) N CH COO + H O N + CH COO + l q q CH COO + H O OH + CH COOH q l q q HO + + no rection l N q HO H + OH + 14 l q q w Determine who is omeg nd will donte CH COO + H O OH + CH COOH q l q q Hmm, slight problem we don t know b If we plce N cette in solution (to mke 01 M solution) wht re the min species present? Wht will be the ph of the solution? 18-5 CH COOH + H O CH COO + H O q l q q + CH COO q + H O q CH COOH q + H O l HO + HO HO + OH + 14 l l q q w CH COO + H O CH COOH + OH q l q q w b If we plce N cette in solution (to mke 01 M solution) wht re the min species present? Wht will be the ph of the solution? 18-5 b b 1 1 w b CH COO - + H O CH COOH + OH - 1 H O H + OH CH COO - + H O CH COOH + OH - stoich [Init Chnge Sum Assume <<<01 >>> -7 [Equil 01 If we plce N cette in solution (to mke 01 M solution) wht re the min species present? Wht will be the ph of the solution? b stoich [Init Chnge Sum Assume <<<01 >>> -7 [Equil 01 [ OH q, eq [ CH COOH q, eq [ CH COOq, eq ( ) % error ? yes 7 ( + ) error % ? If we plce N cette in solution (to mke 01 M solution) wht re the min species present? Wht will be the ph of the solution? 18-5 No

16 CH COO - + H O CH COOH + OH - stoich [Init Chnge Sum Assume <<<01 >>> -7 [Equil 01 Equil new [ [ + b 555 [ 01 ( 555 )[ 01 [ [ ( 7 ) If we plce N cette in solution (to mke 01 M solution) wht re the min species present? Wht will be the ph of the solution? 18-5 ( 555 )[ 01 [ [ ( 7 ) 11 7 ( ) + ( ) ( ) ( ) ( ) ( ) ( )( ) 0555 ± ( ) ± ± ± Before we got b + c 0 b b 4c ± A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions Biologicl Chemistry Emple Clcultions 1HCl Acetic cid (vinegr) HF 4B(OH) (Boric cid (eye wsh)) (students Do this one yourself) 5Miture (HF nd phenol) 6Miture (H SO 4, HSO 4- ) 7Triethylmine 8NAcette 9Our heme emple 16

17 tyrroh,, Which ph (, 7, 11) is most fvorble for the formtion of hydrogen bond between Vl nd tyr in hemoglobin ssuming tht we define fvorble s hving the most possible H bonds VlCOOH,, HA + H O H O A 501 q l q, + from HA q VlCOOH,, Hemeglobin % dissocited 0 Mss blnce [ Aq, [ HAinit [ HAinit [ HAeq, q + [ Aq, % dissocited 0[ Aq, [ HAeqt + [ Aq, tyrroh,, + [ Aq, [ HOq, [ HAeq, q + [ Aq, [ HOq, [ HAeq, q % dissocited 0[ Aq, + [ Aq, [ HOq, + [ Aq, Which ph (, 47, 7, 11) is most fvorble for the formtion of hydrogen bond between Vl nd tyr in hemoglobin ssuming tht we define fvorble hs hving the most possible H bonds VlCOOH,, 501 % dissocited % dissocited [ 0[ Aq, + [ Aq, [ HOq, + [ Aq, + [ HO q, ph; H 0 dissocitedcooh 0 % dissocitedcooh [ [ tyrroh,, vlnine tyrosine ^(-ph) ^(-ph) COOH OH ph ph ph [H+ [H+ 500E-0 0E- %ionized %ionized E E E E-0 1E- 1E E+01 Repet procedure With tyrosine tyrroh,, VlCOOH,, vlnine tyrosine ^(-ph) COOH OH ph [H+ 500E-0 0E- %ionized %ionized 001 0E E E E-0 1E E+01 Which ph is best? Hint: Wnt Vl ionized Tyr not ionized

18 A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions When should we Be mking ssumptions? Emple on Using Simplifictions If mol NOCl is plced in 0 L flsk wht re the equilibrium concentrtions of NO nd Cl given tht t 5 o C the equilibrium constnt, c, is 16-5 mol/l? Red herrings: 5 o C is red herring Clues? is smll compred to others (<<< 1) we hve worked with!!!!! Emple CO + H CO + H O, g, g g g Module 17A c is 064 EXAMPLE : NO 4 NO ( g) c 06M Emple 4: H, g + I, g HI( g) p is 1 - We will define Smll in the Net chpter! We wnt to know when ssumptions re vlid HA (q) H + from HA A - Init HA INIT -7 0 Chnge Equil HA INIT ( )( + ) [ HAINIT [ HAINIT 7 [ HA init 0 < 5%??? %ionized % dissocited Mss blnce + [ Aq, [ HOq, [ HAeq, q The issue is smll with respect To the initil concentrtion!! [ Aq, [ HAeq + [ Aq, + [, [, [, A H O HA Considering simple system [ HAinit [ HAeq, q + [ Aq, q eq q eq eq q HA A + H eq eq eq 0 %dissocited [, [, A HA q eq eq q [, [, A HA q eq eq q [ HAeq [ HA + [ HAeq 0 O this is not nice eqution Do you need to know it? 18

19 50E+01 Rule of Thumb % ioniztion 00E E+01 0E+01 Error too lrge Smll ~ < -6 Sort of smll -6 << -4 Lrge ~> - 500E E Conc Never mke Sfe to mke ssumption iffy ssumption Error O A A students work (without solutions mnul) ~ problems/night Dr Alnh Fitch Flnner Hll fitch@lucedu Office Hours Th&F -:0 pm Module #17B: Acid Bse Ioniztion Computtions 19