Amino Acids and Peptides - Lecture Notes | CH 332, Study notes of Organic Chemistry

Download Amino Acids and Peptides - Lecture Notes | CH 332 and more Study notes Organic Chemistry in PDF only on Docsity! Amino Acids & Peptides - Page 1 Chapter 20 Amino Acids and Peptides Amino Acids • α-amino carboxylic acids • The building blocks from which proteins are made CO2H CH2N R H • Except for GLYCINE (R = H), α-amino acids are chiral molecules. • Naturally occuring amino acids have the S- configuration at the α-carbon. • As it is with carbohydrates, it is traditional to use the D and L nomenclature with amino acids (again based upon the configuration of glyceraldehyde). • Naturally occurring amino acids have the same configuration as L-glyceraldehyde. C CH2OH HHO CHO C CH3 HH2N CO2H L-Glyceraldehyde L-Alanine Amino Acids & Peptides - Page 2 Since amino acids have both an acidic functionality and a basic functionality, we should expect the following equilibrium: CO2H CH2N R H CO2 CH3N R H In fact, the equilibrium lies to the right. Such species that are overall neutral molecules but contain charged ends are called
 or   Amino acids can react as either acids or bases: CO2H CH3N CH3 H CO2 CH3N CH3 H CO2 CH2N CH3 H H OH Alanine Amino Acids & Peptides - Page 5 • Gabriel Synthesis N K O O CO2Et CH CO2Et Br+ Potassium phthalimide Diethyl bromomalonate N O O CH CO2Et CO2Et 1) NaOEt 2) Br Br N O O C CO2Et CO2Et Br NaOH EtOH H2N C CO2 CO2 Br N H CO2 CO2 H3O (−CO2) N H CO2H H Proline Amino Acids & Peptides - Page 6 • Strecker Synthesis (Addition of ammonia and HCN to aldehydes) H3O NH3 HCN NH2 CH CH3 CO2H NH2 CH CH3 CN O C CH3 H Acetaldehyde Alanine Mechanism: O C CH3 H + NH3 (−H2O) NH C CH3 H imine HCN NH2 CH CH3 CN • Reductive Amination of α-Keto Acids O C CH3 CO2H NH2 CH CH3 CO2H NH3 H2 / cat Amino Acids & Peptides - Page 7 Peptides • Peptides are amino acid polymers containing from 2 to 50 individual units. • By convention, peptides of greater than 50 units are called proteins. • By convention, peptide structures are always written with the N-terminal amino acid on the left and the C-terminal amino acid on the right. H3N CH2 C NH CH CO2 O CH3 Glycylalanine = gly⋅ala H3N CH2 C NH CH C O CH2OH O NH CH C NH CH2 CO2 O CH2C6H5 Glycylserylphenylalanylglycine gly⋅ser⋅phe⋅gly Amino Acids & Peptides - Page 10 Structure Determination of Peptides 1. Disulfide Cleavage. Use oxidizing agent such as peroxyformic acid (HCO3H). Oxidatively cleaves disulfides to sulfonic acids: S S [O] SO3H HO3S Amino Acids & Peptides - Page 11 2. Amino Acid Analysis. Find out which amino acids and how many make up the peptide. Completely hydrolyze the peptide using acid. 3. Terminal Residue Analysis. Find out what's on the ends. a) N-Terminal Analysis • Edman Degradation: N C SC6H5 H2N CH R C O + Phenyl isothiocyanate Peptide base NH CH R C O C S NHC6H5 H3O CH NH N S O C6H5 R + rest of peptide Phenylthiohydantoin of N-terminal amino acid Amino Acids & Peptides - Page 12 • Sanger Method: H2N CH R C O Peptide H3O NO2 O2N F + 2,4-Dinitrofluorobenzene NO2 O2N O C R CHNH NO2 O2N CO2H R CHNH (yellow) b) C-Terminal Analysis Determined enzymatically using the enzyme    (specifically hydrolyzes the C- terminal amino acid. CO2H R CHNH + H2O carboxypeptidase CO2H R CHH2Nrest of peptide + Amino Acids & Peptides - Page 15 5. Cyanogen Bromide Cleavage (BrCN cleaves at carbonyl group of methionine) + H2N CH C O R N H CH O O BrCNN H CH C O N H CH C OCH2 R CH2 S CH3 + CH3SCN Homoserine lactone unit Amino Acids & Peptides - Page 16 Sample Problem: 20 amino acid polypeptide Composition: gly2ala4leu4phe3trp1lys2met2ser1arg1 End group analysis: N-terminus (Sanger method) = ala C-terminus (carboxypeptidase) = phe Trypsin hydrolysis gives four fragments: I. trp⋅phe⋅arg II. ala⋅leu⋅gly⋅met⋅lys III. leu⋅gly⋅leu⋅leu⋅phe IV. ala⋅ala⋅ser⋅met⋅ala⋅phe⋅lys Fragment III represents the last 5 amino acids (trypsin does  cleave at phenylalanine). Either fragment II or IV must be N-terminus (cannot know which). Cyanogen bromide cleavage gives three fragments: V. ala⋅leu⋅gly⋅met VI. ala⋅phe⋅lys⋅leu⋅gly(leu2phe1) VII. lys⋅trp⋅phe⋅arg⋅ala(ala1met1ser1) So: ala.leu.gly.met.lys.trp.phe.arg.ala.ala ser.met.ala.phe.lys.leu.gly.leu.leu.phe Amino Acids & Peptides - Page 17 Synthesis of Peptides The Problem: gly + ala → gly⋅ala + ala⋅gly + gly⋅gly + ala⋅ala To overcome this problem, use blocking groups. Example: block the amino group as a carbamate: O C C6H5CH2O Cl + NH2 CH CO2H R O C C6H5CH2O R CO2HCHNH Benzyl chlorocarbonate Carbobenzoxy chloride Benzyl chloroformate Now, activate the carboxylic acid: CO2H C O X Amino Acids & Peptides - Page 20 This blocking group (t-Boc) is removed with acid: + CO2 + O C CH R NHNH O CO CH3 CH3 C CH3 H CH2 C CH3 CH3 O C CH R NHNH2 Peptide bonds can also be formed by reacting N- protected amino acids with C-protected amino acids using   as a dehydrating/activating agent. (DCC) N C N + R CHNH2 C O CH2C6H5O CH3 CCH3 CH3 O C O R CO2HCHNH CH3 CCH3 CH3 O C O R CCHNH O O CH2C6H5 O CNH CH R Amino Acids & Peptides - Page 21 Solid-Phase Peptide Synthesis The most recent advance in peptide synthesis utilizes polymer support: Cl Styrene/chloromethylstyrene copolymer (~100:1) Amino Acids & Peptides - Page 22 + CH3 CCH3 CH3 O C O R CO2CHNH PClCH2 POCH2 O NH CH C R O CO CH3 CH3 C CH3 1) CF3CO2H 2) Et3N POCH2 O NH2 CH C R CH3 CCH3 CH3 O C O R' CO2HCHNH DCC OC NHCH C NHCH C OCH2 O O O RR' P POCH2C O HF CO2H PFCH2+