PowerPoint PresentationSlide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Slide 45Slide 46Slide 47Slide 48Slide 49Slide 50Slide 51Slide 52Slide 53Slide 54Slide 55Slide 56Slide 57MCB 450Lecture 3Amino Acids & Their PropertiesIonization of Amino AcidsPeptidesSecondary Structure of Proteins3-1General structure of an amino acidexcept proline...COOCHCH2CH2H2CH2N+-2° amine(imino acid)3-21° amine19 differentR-groupscarboxylcarbonaminoAmino acids in proteins are all L-stereoisomersWhere R ≠ H, the carbon is a chiral center3-3RGly AlaAmino acids with non-polar R groups: small3-43-letter abbreviation:G AG has a small side chain (just H)- permits adoption of many different conformations,hence found in bends in protein chainNOT CHIRAL!Val, V Leu, L Ile, I3-5 with non-polar R groups: branched, aliphaticV, L, I (and A): Side chains non-polar, uncharged, hydrophobic:- found inside folded proteinsPro, P Met, M3-6 with non-polar aliphatic R groupsnon-polarthioetherLimited rotation about bondbetween 2° amine & carbonreduces structural flexibility ofpolypeptide regions containing P:- found in bends in protein chain.Phe, F Tyr, Y Trp, WTyrosine's –OH…- can form H-bonds- is functional group in some enzymes.Phosphoryl group can be transferred to OH.3-7Y & W are more polar than F(OH of Y, N of W) with non-polar aromatic (hydrophobic) R groupsTrp and Tyr absorb UV light3-8W>Y, F to a lesser extent.This accounts for the strongabsorbance of UV lightby most proteins at 280 nm.The more W & Y in apeptide, the more theabsorbanceSer, S Thr, T Cys, CPolar -OH can serve as H-bonddonors and acceptors, andphosphoryl and sugar groups canbe transferred to the OHPolarity contributed by –SH.3-9 with polar uncharged R groupsSIDE CHAINS CONTAIN ANELECTRONEGATIVE ATOMReversible formation of a disulfide bondbetween two Cys3-10Disulfide bonds areimportant in determiningprotein structure.Disulfide bond within and betweenthe two chains of bovine insulin3-11N can be linked to sugar in"glycoproteins":Asn, N Gln, Q with polar, uncharged R groups, cont....3-12-CH2-CN or Q: can serve as H-acceptor ONcan serve as H-donorH H WHAT'S THEFUNCTIONALGROUP?Asp, D Glu, E3-13 with negatively charged R groupsAcidic, hydrophilic:Second carboxylic acid group onside chain is deprotonated atneutral pH, so net charge is -ve Ability of Asp & Glu side chains to accept protonscan be important in enzyme catalysis COOHH+H+COOHH+H+Lys, K Arg, R His, Hbasic, hydrophilicK:Second 1° amine at position onaliphatic side chain is+vely charged at neutral pH.R:guanidino group is+vely charged at neutral pH.N+H3-14Positively charged R groupsN+HHis side chain = imidazoleOnly standard with an ionizableside chain with pKa near neutrality.H is often found in active sites ofenzymes, where its imidazole ringcan switch between uncharged and+vely charged (protonated) statesto catalyze making and breakingof bonds.3-15 with positively charged R groups…HistidineHis, HGrouping by structural relationships (of R-group)3-16Simple: Gly, AlaBranched chain hydrophobic: Leu, Ile, ValImino acid: ProAromatic: Phe, Tyr, TrpAmide: Asn, GlnHydroxyl group: Ser, ThrCarboxyl group: Asp, GluBasic: Arg, Lys, HisContain S: CysMetNON-POLARPOLAR,UNCHARGEDPOLAR, UNCHARGEDNON-POLAR-vely CHARGED+vely CHARGEDNet charge +1 Net charge 0 Net charge -13-18 Ionization state of the -amino and -carboxyl groupsof amino acids as a function of pHIs there a pH at which the -carboxyl is protonated and the -amino is unprotonated?H+H+fully protonated:net charge: +1 0 -1Titration of glycine3-19ISOELECTRIC POINT net charge = 0Removal of COOH proton essentially complete,Removal of NH3+ protonhas just begunTHE pI IS THE AVERAGEOF pKa1 and pKa2! 9.0 2.1 5.55Titrations of free amino acids3-20Generalization:Amino acids with and an R-group that does not ionize….…..have similar titration curves to Gly(just the -NH2 and -COOH titrate)net charge:+1 0 -1 -2H+H+H+Titration of glutamic acid3-21 pKR=4.1 pK2=9.0 pK1=2.1 pKas governing formationof the +1 and -1 formsgovern formation ofuncharged glutamate, andpI =2.1 + 4.12= 3.1H+net charge:+2 +1 0 -1H+H+Titration of histidine3-22pI =6.0 + 9.02= 7.5 pK1=2.1 pKR=6.0 0in free in free 2.1~9Typical pKas of the -NH2 and -COOH groupsin free amino acids3-23Typical pKas of the-NH2 groups-COOH groupsionizable side chainsin peptides & proteins3-24• Isolation/characterization of amino acids or proteins often utilizes charge.• Only one charge isomer may undergo metabolism.• Structure of proteins is stabilized by charge interactions.• Binding of small molecules by enzymes may depend on charge interactions.• Many enzymes catalyze reactions utilizing acid-base catalysis.Why are charge isomers important?3-25peptide bond3-26 Formation of a peptide bondCondensationHydrolysis“N-terminus” “C-terminus”3-27 Peptide sequences have directionalityS G Y A LNote: SGYAL and LAYGS are different molecules!WRITTEN STARTINGFROM THE N-TERMINALAMINO ACID-amino and -carboxylgroups of non-terminal are covalently joined in peptidebonds, and do not ionize: donot contribute to acid-baseproperties of the peptideIonization of peptides3-28pKa ~3.1pKa for the terminal COO-groups is shifted ~1 unittoward neutralitypKa ~8In general, pKa of amino gp decreases from 9 in free to ~8 in peptide:Peptides have one free amino groupand one free carboxyl group ateither end of the chain.R-groups can ionize, and contributeto the acid-base behavior of thepeptide.3-291. straightforward if the pKa's of the ionizable groups are well-separatedDetermining the isoelectric point of a simple peptide2. identify the two ionization steps that govern formation of the form ofthe peptide with no net charge (i.e. the neutral form with 0 charge)3. = ionization steps in which…the +1 charged form of the peptide is converted to the 0 charge form, and…the 0 charge form is converted to the –1 charged form.4. the pI is the average of the pKas that govern these two ionization steps5. a simple way to do this is to start with the form of the peptide with all
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