Amino Acids, Peptides, and Proteins - Lecture Slides | CHEM 239, Study notes of Organic Chemistry

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Chem 239: Chapter 27 Amino Acids, Peptides, and Proteins Representations: Classification 20 common amino acids Fisher projections and D-L notation Chemical Properties of Amino Acids: Acid-base behavior Synthesis Reactions of Amino Acids: Laboratory chemistry Biochemical reactions Peptides: Nature of peptides Analysis: Composition, end-group, sequence Synthesis: protection, bond-formation Synthesis: Solution vs solid-phase Proteins: Secondary structures Tesrtiary and quarternary structures Coenzymes Reading: Pg 1148-1199 Problems: 27.26, 27.28, 27.31, 27.34, 27.36 β Classification Amino Acids Contain —NH2 and —CO2H Actually —NH 3+ and —CO2– Classified as α, β, γ, etc. amino acids according the carbon that bears the nitrogen. + H3NCH2CH2CH2CO2 – C C O O– H H H3N + The only achiral aa Disrupts local protein structure C C O O– H H H3N + Glycine (Gly or G) Small achiral side chain Nonpolar side chain C C O O– CH3 H H3N + Alanine (Ala or A) C C O O– CH(CH3)2 H H3N + Valine (Val or V) C C O O– CH2CH(CH3)2 H H3N + Leucine (Leu or L) C C O O– CH3CHCH2CH3 H H3N + Isoleucine (Ile or I) Alkyl groups as side chains Nonpolar and hydrophobic Often found in core of soluble proteins Nonpolar side chain C C O O– CH3SCH2CH2 H H3N + Methionine (Met or M) Proline C C O O– CH2 H H2N + H2C C H2 (Pro or P) Only secondary amine Disrupts local protein structures AUG coded “start” amino acid Polar (non-ionizable) side chain Can form disulfides C C O O– CH2SH H H3N + Cysteine (Cys or C) C C O O– CH2S -H H3N + C C O O– H H3N + SCH2 Cystine Polar (non-ionizable) side chain Tyrosine C C O O– CH2 H H3N + OH (Tyr or Y) Asparagine C C O O– H H3N + H2NCCH2 O (Asn or N) Glutamine C C O O– H H3N + H2NCCH2CH2 O (Gln or Q) All can Form H-bonds Can be phosporylated Can be glycosylated Ionizable (acidic) side chains C C O O– H H3N + OCCH2 O – Aspartic Acid (Asp or D) C C O O– H H3N + OCCH2CH2 O – Glutamic Acid (Glu or E) All can form H-bonds All can form ionic bonds with (+) charged residues Configurations of α-Amino Acids H3N + H R CO2 – All common amino acids (except glycine) have at least one chiral center Properties of Glycine High melting point: When heated to 233°C, it decomposes before it melts Solubility: Soluble in water; Not soluble in nonpolar solvent O OHH2NCH2C •• •• •• •• •• –•• O OH3NCH2C •• •• •• •• + more consistent with this than this a zwitterion or dipolar ion Acid-Base Properties of Glycine –•• O OH3NCH2C •• •• •• •• + –•• O OH2NCH2C •• •• •• •• •• O OHH3NCH2C + •• •• •• •• pKa = 2.34 pKa = 9.60 The pI of glycine is 5.97. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 12 10 pK, = 9.60 Pg hss sta ans fd eed {) pI = 5.97 6 beeeeeode oe oo eo oe H,NCH,CO,H — > H,NCH,CO,- —~ H,NCH,CO> 0.5 1.0 1.5 Equivalents HO 2.0 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or displa A mixture of amino acids ~O,CCH,CHCO, ee H,N(CH;),CHCOs- Oo “NH, @ oun, aS “NH, is placed at the center of a sheet of cellulose acetate. The sheet is soaked with an aqueous solution buffere ata pH of 6.0. At this pH aspartic acid Mexists as its —1 ion, alanine @pas its zwitterion, and lysine @@Pas its +1 ion. (a) Application of an electric current causes the negatively charged ions to migrate to the + electrode, and th: positively charged ions to migrate to the — electrode. The zwitterion, with a net charge of zero, remains a its original position. | | {|i} + (5) Synthesis of Amino Acids From α-Halo Carboxylic Acids CH3CHCOH Br O 2NH3+ H2O CH3CHCO NH3 O + – (65-70%) + NH4Br HBr, H2O, heat O O HOCCCOH CH2C6H5H3N+ O O CH3CH2OCCCOCH2CH3 CH2C6H5CH3CNH O O HCCOH CH2C6H5H3N+ (65%) –CO2 Reactions of Amino Acids Acylation of Amino Group O H3NCH2CO –+ + CH3COCCH3 O O CH3CNHCH2COH O O (89-92%) Fisher Esterification of Carboxyl Group + CH3CH2OH HCl O H3NCHCO –+ CH3 (90-95%) O H3NCHCOCH2CH3 + CH3 –Cl Biosynthesis of L-Tyrosine CH2CHCO2 – NH3+ O2, enzyme CH2CHCO2 – NH3+ HO Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. OH OH H NH, HO. oO — — NH, 0. 2 Tyrosi apes 3,4-Dihydroxyphenylalanine Dopamine (L-Dopa) OH OH HO HO , NHCH, 7 NH, H OH H OH Epinephrine Norepinephrine (Adrenaline) (Noradrenaline) Decarboxylation CH2CHCO2 – NH3+ –CO2, enzymes CH2CH2 NH2 N N H N N H Peptides CH3 O C + H C O–H3N O C H H CH3N + O– CH3 O CH3N + H C O CN H H C O– H Two α-amino acids are joined by a peptide bond in alanylglycine. It is a dipeptide. Alanylglycine CH3 O CH3N + H C O CN H H C O– H H O CH3N + H C O CN H CH3 C O– H Alanylglycine Ala—Gly AG Glycylalanine Gly—Ala GA CH3 O CH3N + H C O CN H H C O– H The peptide bond is characterized by a planar geometry. Introduction to Peptide Structure Determination peptideH3NCHC O R + NHC6H5N C S + C6H5NHCNHCHC O R NH S peptide HCl H3N + + C6H5NH C S C N CH R O peptide + H3N + peptide CC N HN CH R OS C6H5 phenylthiohydantoin (PTH) derivative. phenyl isothiocyanate Introduction to Peptide Structure Determination Introduction to Peptide Structure Determination Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ‘The reaction is carried out by mixing the peptide and 1-fluoro-2,4-dinitrobenzene in the presence of a weak base such as sodium carbonate. In the first step the base abstracts a proton from the terminal H,N group to give a free amino function. The nucleophilic amino group attacks 1-fluoro-2,4-dinitrobenzene, displacing fluoride. NO, 9 ° 9 ON Fo+ HANCHC—NHCHC—NHCH,C—NHTHCO; (CH,),CH CH,C,H, ‘Coy mF ¢ * O.N: Aen — NH PHC“ NHCH,C-NHCHCO S| CH(CH,), CH,C,Hs CH, Acid hydrolysis cleaves the amide bonds of the 2,4-dinitrophenyl-labeled peptide, giving the 2,4-dinitrophenyl-labeled N-terminal amino acid and a mixture of unlabeled amino acids. 6, |Ho ON NHCHCO.H + H,NCHCO,H) + H,NCH,CO,H + HNCHCO,H CH(CH,): CHC, CH, DNP-Val Phe ay Ala Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. MECHANISM 27.3. The Edman Degradation ‘A peptide is treated with phenyl isothiocyanate to give a phenylthiocarbamoyl (PTC) derivative, Step ° 9 CoH: So+ uiticHl—Ne = candice —va R i PTC derivative Phenyl isothiocyanate Step 2: On reaction with hydrogen chloride in an anhydrous solvent, the thiocarbonyl sulfur of the PTC derivative attacks the carbonyl carbon of the N-terminal amino acid. The N-terminal amino acid is cleaved as a thiazolone derivative from the remainder of the peptide Ss oO #~\ net BS CoHsNHC *C--NH- —> CéHsNH—C ‘C=O + HN fea. —[reeive | SY N—CH N—CH pS \ H R R PTC derivative ‘Thiazolone Remainder of peptide Step 3: Once formed, the thiazolone derivative isomerizes to a more stable phenylthiohydantoin (PTH) derivative, ated and characterized, thereby providing identification of the N-terminal amino acid. The whic remainder of the peptide (formed in step 2) can be isolated and subjected to a second Edman degradation. Boos CoH s PR IN ‘ CHNH—C*>*c=0 *cl — caun—G se “ ~c=0 (N—cH N—cu HN—cu Cl HN—CH cisH \ ff N \ R HOR R R PTH derivative ‘Thiazolone Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 123 45 67 8 9 ON Phe-Val-Asn-Gin-His-Leu-Cys-Gly-Ser-His-Leu Ser-His-Leu-Val Leu-Val-Glu-Ala RB MIs Val-Glu-Ala-Leu Ala-Lew-Tyr 16 17 ‘Tyr-Leu-Val-Cys 18 19 20 21 2 23 2% ‘Val-Cys-Gly-Glu-Arg-Gly-Phe 2s Gly-Phe-Phe-Tyr-Thr-Pro-Lys 26 27 28 2 30 ‘Tyr-Thr-Pro-Lys-Ala 1 5 0 1s 20 25 30 Phe-Val-Asn-Gin-His-Leu-Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys-Ala Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. N terminus S——S | of A chain 5 af \ 15 C terminus | Valu} Gin} >s) cys)Ser)Leu} Tyr] Gin} of A chain I ea) Cys) val) 10 Asn) 20 $7 Fala) Ser AID) \ NA “ cys] As) Y ‘ s nO oy \ 10 15 O29 N terminus y) 20 of B chain of B chain Glu C terminus Thr) Tyr, Pree) Gly) 8 SD oe 30 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (a) (b) (©) @ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Disulfide bond N terminus C terminus @ (b) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H,C=CH CH, H;C CH=CH, HC CH, HO,CCH,CH, CH,CH,CO,H (a) (b) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. C terminus N terminus Y (a) (b)