Chem 109 C Bioorganic Compounds Fall 2019 HFH1104 Armen Zakarian Office: Chemistry Bldn 2217 http://labs.chem.ucsb.edu/~zakariangroup/courses.html CLAS Instructor: Dhillon Bhavan [email protected] Amino acids, Peptides, Proteins: Introduction Chapter 21 O R OH NH2 α-amino acid O O + H N R R R OH 2 R N - H2O H peptide bond = amide bond Proteins: Function 21.1 3 Proteins: Structural Histone Protein Structure: DNA packaging 4 Proteins: Protective botulinum toxin (botox) structure most toxic substance known LD50 = 10 ng/kg Amino acids, Peptides, Proteins: Introduction O O R O R O H R R OH R N OH N N OH H NH2 H NH2 O NH2 O R α-amino acid dipeptide tripeptide ! oligopeptide: 3 - 10 amino acids ! polypeptide, or protein: many amino acids Proteins: Amino Acids, Configuration NH2 HO O phenylalanine O + - NH3 natural amino acids C O +H N H same as - have the L configuration (S) 3 O2C R R Amino acids: Classification • Hydrophobic: “water-fearing”, nonpolar side chains – Alkyl side chain • Hydrophilic: “water-loving” side chains – Polar, neutral side chains – Anionic – Cationic - Table 21.1 lists 20 most common natural occurring amino acids - The structures of amino acids will be provided on the tests nonpolar side chains polar neutral (uncharged) side chains Amino acids: Classification polar acidic (anionic) side chains Amino acids: Classification polar basic (cationic) side chains Amino acids: Classification PROBLEM 1 Explain why when the imidazole ring of histidine is protonated, the double-bonded nitrogen is the nitrogen atom that accepts the proton. same for guanidine group in arginine. H NH N CO2H CO2H H2N N H NH2 N NH2 Amino acids: Zwitterions NH2 ! contain the amino group HO2C R NH2 ! contain the carboxylic acid group: HO2C R + + NH3 NH3 NH2 - - HO2C R O2C R O2C R a zwitterion pH = 0 pH = 7 pH = 11 Amino acids: Zwitterions pKa of amino acids: NH2 α HO2C R -amino: 8.84 - 10.60 pKa of the α-amino group is 9 NH2 carboxylic acid: 1.82 - 2.63 HO2C R pKa of the CO2H group is 2 Amino acids: Zwitterions pKa of side-chains: H NH O NH NH2 2 2 NH2 N HO HO OH HO HO SH OH N+ O O O O H O aspartic acid glutamic acid histidine cysteine pKa 3.86 pKa 4.25 pKa 6.04 pKa 8.35 OH NH NH2 NH2 2 H HO N NH HO HO + 2 NH3 O NH + O O 2 tyrosine lysine arginine pKa 10.07 pKa 10.79 pKa 12.48 Amino acids: Zwitterions Amino acids: Zwitterions PROBLEM 8 Draw the predominant form of glutamic acid in a solution with the following pH: a. 0 NH2 HO OH 4.25 O O b. 3 glutamic acid c. 6 d. 11 Amino acids: Zwitterions PROBLEM 8 Draw the predominant form of glutamic acid in a solution with the following pH: 9.67 a. 0 NH2 2.19 HO OH 4.25 O O b. 3 glutamic acid c. 6 d. 11 Amino acids: Isoelectric Point (pI) pI of amino acid is pH at which it has no net charge case 1: non-ionizing side chain Amino acids: Isoelectric Point (pI) pI of amino acid is pH at which it has no net charge 9.17 H + NH3 N 1.82 HO 6.04 N+ O H case 2: ionizable side chain (acidic or basic) average of pKa’s of similarly ionizing groups Amino acids: Separation/Purification " electrophoresis based on pI values of amino acids O OH visualized with ninhydrin: OH O buffer paper or gel arginine, alanine, and aspartate separated at pH = 5 Amino acids: Separation/Purification " paper/thin layer chromatography based on polarity O OH visualized with ninhydrin: OH O glutamate, alanine, and leucine Amino acids: Separation/Purification " ion-exchange chromatography based on ions/charge used on preparative scale washed with buffers of increasing pH packed with insoluble resin beads Amino acids: Separation/Purification Ion-exchange chromatography can be used to perform preparative separation of amino acids: Negatively charged resin binds selectively to positively charged amino acids Amino acids: Separation/Purification " ion-exchange chromatography A typical chromatogram obtained from separation of amino acids using an automated analyzer Amino acid synthesis: HVZ reaction Hell-Volhardt-Zelinski reaction, see Sections 17.5 and 9.2 1. Br2, PBr3 O 2. H O O 2 excess NH3 R R OH OH Br O R + NH4Br OH + NH3 note the source of side-chains.... Amino acid synthesis: reductive amination review Section 16.4 1. excess NH3 O O 2. H2, Pd/C R R OH O- + O NH3 O R OH NH intermediate note the source of side-chains.... Amino acid synthesis: N-phthalimidomalonic O O O O O H EtO EtO OEt N K EtO OEt Br O N O O α-bromomalonic ester potassium phthalimide N-phthalimidomalonic ester O O O O R HCl, H2O O R Br CO2H EtO OEt EtO OEt heat R OH CO2 N N O O O O + NH3 CO2H phthalic acid review Sections 15.4, 17.1, and 17.17 Amino acid synthesis: Strecker synthesis NH3 NaCN, HCl N R R R C + O NH NH3 -amino nitrile an imine α HCl, H2O O heat R OH + NH4Cl + NH3 review Section 15.15 for nitrile hydrolysis .