3 1 MCB 450 Lecture 3 Amino Acids Their Properties Ionization of Amino Acids Peptides Secondary Structure of Proteins 3 2 General structure of an amino acid carboxyl amino 1 amine 19 different R groups carbon except proline 2 amine imino acid COO H C H2N CH2 H2C CH2 3 3 Amino acids in proteins are all L stereoisomers Where R H the carbon is a chiral center R 3 4 Amino acids with non polar R groups small G has a small side chain just H permits adoption of many different conformations hence found in bends in protein chain NOT CHIRAL 3 letter abbreviation Gly Ala G A 3 5 with non polar R groups branched aliphatic Val V Leu L Ile I V L I and A Side chains non polar uncharged hydrophobic found inside folded proteins 3 6 with non polar aliphatic R groups Limited rotation about bond between 2 amine carbon reduces structural flexibility of polypeptide regions containing P found in bends in protein chain non polar thioether Pro P Met M 3 7 with non polar aromatic hydrophobic R groups Phe F Tyr Y Trp W Y W are more polar than F OH of Y N of W Tyrosine s OH can form H bonds is functional group in some enzymes Phosphoryl group can be transferred to OH 3 8 Trp and Tyr absorb UV light W Y F to a lesser extent This accounts for the strong absorbance of UV light by most proteins at 280 nm The more W Y in a peptide the more the absorbance 3 9 with polar uncharged R groups SIDE CHAINS CONTAIN AN ELECTRONEGATIVE ATOM Ser S Thr T Polar OH can serve as H bond donors and acceptors and phosphoryl and sugar groups can be transferred to the OH Cys C Polarity contributed by SH 3 10 Reversible formation of a disulfide bond between two Cys Disulfide bonds are important in determining protein structure 3 11 Disulfide bond within and between the two chains of bovine insulin with polar uncharged R groups cont 3 12 WHAT S THE FUNCTIONAL GROUP N can be linked to sugar in glycoproteins Asn N Gln Q can serve as H acceptor O N or Q CH2 C N H H can serve as H donor 3 13 with negatively charged R groups Acidic hydrophilic Second carboxylic acid group on side chain is deprotonated at neutral pH so net charge is ve H COOH H H COOH H Asp D Glu E Ability of Asp Glu side chains to accept protons can be important in enzyme catalysis 3 14 Positively charged R groups basic hydrophilic K Second 1 amine at position on aliphatic side chain is vely charged at neutral pH N H R guanidino group is vely charged at neutral pH Lys K Arg R His H 3 15 with positively charged R groups His side chain imidazole Only standard with an ionizable side chain with pKa near neutrality Histidine His H N H H is often found in active sites of enzymes where its imidazole ring can switch between uncharged and vely charged protonated states to catalyze making and breaking of bonds 3 16 Grouping by structural relationships of R group Simple Gly Ala Branched chain hydrophobic Leu Ile Val Imino acid Pro Aromatic Phe Tyr Trp Amide Asn Gln Hydroxyl group Ser Thr Carboxyl group Asp Glu vely CHARGED Basic Arg Lys His vely CHARGED Contain S Cys Met NON POLAR POLAR UNCHARGED POLAR UNCHARGED NON POLAR 3 18 Ionization state of the amino and carboxyl groups of amino acids as a function of pH Net charge 1 Net charge 0 Net charge 1 Is there a pH at which the carboxyl is protonated and the amino is unprotonated 3 19 Titration of glycine net charge 1 0 H 1 H fully protonated THE pI IS THE AVERAGE OF pKa1 and pKa2 ISOELECTRIC POINT net charge 0 9 0 Removal of COOH proton essentially complete Removal of NH3 proton has just begun 5 55 2 1 3 20 Titrations of free amino acids Generalization Amino acids with and an R group that does not ionize have similar titration curves to Gly just the NH2 and COOH titrate 3 21 Titration of glutamic acid net charge 1 H 2 1 4 1 3 1 2 H 1 pK2 9 0 pKas governing formation of the 1 and 1 forms govern formation of uncharged glutamate and pI 0 pKR 4 1 pK1 2 1 H 2 3 22 Titration of histidine net charge 2 H 1 H 0 H 0 pKR 6 0 pI 6 0 9 0 7 5 2 pK1 2 1 1 3 23 Typical pKas of the NH2 and COOH groups in free amino acids in free in free 9 2 1 3 24 Typical pKas of the NH2 groups COOH groups ionizable side chains in peptides proteins 3 25 Why are charge isomers important 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 3 26 Formation of a peptide bond Hydrolysis Condensation peptide bond 3 27 Peptide sequences have directionality S G Y A L WRITTEN STARTING FROM THE N TERMINAL AMINO ACID N terminus C terminus Note SGYAL and LAYGS are different molecules 3 28 Ionization of peptides In general pKa of amino gp decreases from 9 in free to 8 in peptide pKa 8 amino and carboxyl groups of non terminal are covalently joined in peptide bonds and do not ionize do not contribute to acid base properties of the peptide Peptides have one free amino group and one free carboxyl group at either end of the chain R groups can ionize and contribute to the acid base behavior of the peptide pKa for the terminal COO groups is shifted 1 unit pKa 3 1 3 29 Determining the isoelectric point of a simple peptide 1 straightforward if the pKa s of the ionizable groups are well separated 2 identify the two ionization steps that govern formation of the form of the 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 steps 5 a simple way to do this is to start with the form of the peptide with all its ionizable groups protonated i e most vely charged form 6 then see what happens as the pH is raised the ionizable groups will become deprotonated in the order of ascending pKa 3 30 What s the pI of Met Asp Gly His Met Gly side chains don t ionize so ignore His pKa 6 0 Asp pKa 4 1 H H H N N N O O O start with the form of the peptide with all its …
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