● CHAPTER 27 AMINO ACIDS, PEPTIDES, AND PROTEINS NUCLEIC ACIDS SOLUTIONS TO TEXT PROBLEMS 27.1(b) L-Cysteine is the only amino acid in Table 27. 1 that has the r configuration at its stereogenic CO H CH, HN+H=—CO2= 一CO CH SH HSCH The order of decreasing sequence rule pre 一>HSCH When the molecule is oriented so that the lowest ranked substituent(H)is held away from us, the order of decreasing precedence traces a clockwise path Han CO2 Clockwise: therefore R The reason why L-cysteine has the R configu while all the other L-amino acids have the S configuration lies in the fact that the sH substituent is the only sic outranks-CO, according to the sequence rule. Remember, rank order is determined by 752 Back Forward Main Menu TOC Study Guide Toc Student OLC MHHE Website
752 CHAPTER 27 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS SOLUTIONS TO TEXT PROBLEMS 27.1 (b) L-Cysteine is the only amino acid in Table 27.1 that has the R configuration at its stereogenic center. The order of decreasing sequence rule precedence is When the molecule is oriented so that the lowest ranked substituent (H) is held away from us, the order of decreasing precedence traces a clockwise path. The reason why L-cysteine has the R configuration while all the other L-amino acids have the S configuration lies in the fact that the —CH2SH substituent is the only side chain that outranks —CO2 according to the sequence rule. Remember, rank order is determined by CH2SH H3N CO2 Clockwise; therefore R H3N HSCH2 CO2 H L-Cysteine CO2 H CH2SH H3N NH3 CO2 HSCH2 H C H3N CO2 HSCH2 H C Back Forward Main Menu TOC Study Guide TOC Student OLC MHHE Website
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 753 atomic number at the first point of difference, and-C-S outranks-C-O. In all the other amino acids-CO, outranks the substituent at the stereogenic center. The reversal in the Cahn-Ingold-Prelog descriptor comes not from any change in the spatial arrangement of substituents at the stereogenic center but rather from a reversal in the relative ranks of the carboxylate group and the side che (c) The order of decreasing sequence rule precedence in L-methionine is H,N->-CO.>>-CHCHSCH >H- Sulfur is one atom further removed from the stereogenic center, and so C-O outranks CO, H3N CH,,SCH CHSCHCH The absolute configuration is s 27. 2 The amino acids in Table 27. 1 that have more than one stereogenic center are isoleucine and threo- nine. The stereogenic centers are marked with an asterisk in the structural formulas shown. CH3CH,CH--CHCO CH NH OH NH Isoleucine Threonine 27.3(b The zwitterionic form of tyrosine is the one shown in Table 27.1 HO CHCHCO NH3 (c) As base is added to the zwitterion, a proton is removed from either of two positions, the am- monium group or the phenolic hydroxyl. The acidities of the two sites are so close that it is not possible to predict with certainty which one is deprotonated preferentially. Thus two struc- tures are plausible for the monoanion: HO -CH CHCO CH, CHCO, NH NH In fact, the proton on nitrogen is slightly more acidic than the phenolic hydroxyl, as measured by the pka values of the following model compounds pk,9.75 CHCHCO CHO -CH,CHCO, N(CH3)3 Back Forward Main Menu TOC Study Guide Toc Student OLC MHHE Website
atomic number at the first point of difference, and —C—S outranks —C—O. In all the other amino acids —CO2 outranks the substituent at the stereogenic center. The reversal in the Cahn–Ingold–Prelog descriptor comes not from any change in the spatial arrangement of substituents at the stereogenic center but rather from a reversal in the relative ranks of the carboxylate group and the side chain. (c) The order of decreasing sequence rule precedence in L-methionine is Sulfur is one atom further removed from the stereogenic center, and so C—O outranks C—C—S. The absolute configuration is S. 27.2 The amino acids in Table 27.1 that have more than one stereogenic center are isoleucine and threonine. The stereogenic centers are marked with an asterisk in the structural formulas shown. 27.3 (b) The zwitterionic form of tyrosine is the one shown in Table 27.1. (c) As base is added to the zwitterion, a proton is removed from either of two positions, the ammonium group or the phenolic hydroxyl. The acidities of the two sites are so close that it is not possible to predict with certainty which one is deprotonated preferentially. Thus two structures are plausible for the monoanion: In fact, the proton on nitrogen is slightly more acidic than the phenolic hydroxyl, as measured by the pKa values of the following model compounds: HO CH2CHCO2 N(CH3)3 CH3O CH2CHCO2 NH3 pKa 9.75 pKa 9.27 HO and CH2CHCO2 NH2 O CH2CHCO2 NH3 HO CH2CHCO2 NH3 Isoleucine CH3CH2CH CH3 CHCO2 * * NH3 Threonine CH3CH OH CHCO2 * * NH3 CH2CH2SCH3 H CO2 H3N CO2 NH3 H CH3SCH2CH2 C H3N H CO2 CH2CH2SCH3 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 753 Back Forward Main Menu TOC Study Guide TOC Student OLC MHHE Website
754 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS (d) On further treatment with base, both the monoanions in part (c) yield the same dianion CHCHCO 27.4 At pH I the carboxylate oxygen and both nitrogens of lysine are protonated H3NCH, CH,CH,CH,CHCO,H Principal form at pH As the ph is raised, the carboxyl proton is removed first. H3 NCH,CH,CH CH, CHCO H HO HNCH..CHCO+ HO The pk value for the first ionization of lysine is 2. 18(from Table 27.3), and so this process is virtually complete when the pH is greater than this value The second pKa value for lysine is 8.95. This is a fairly typical value for the second pKa of amino acids and likely corresponds to proton removal from the nitrogen on the a carbon. The species that results is the predominant one at pH 9 H3NCH, CH, CH, CH,CHCO, HO H3NCH, CH,CH, CH- CHCO, H,O Principal form at pH 9) The pKa value for the third ionization of lysine is 10.53. This value is fairly high compared with those of most of the amino acids in Tables 27. 1 to 27.3 and suggests that this proton is removed from the nitrogen of the side chain. The species that results is the major species present at pH values greater than 10.53 H3NCH,CH,CH, CH,CHCO, HO H,NCH, CH,CH,CH,CHCO, N (Principal form at pH 13) 27.5 To convert 3-methylbutanoic acid to valine, a leaving group must be introduced at the a carbon prior to displacement by ammonia. This is best accomplished by bromination under the conditions of the Hell-Volhard-Zelinsky reaction Br2- P H3 (CH3)2CHCH2 CO2H or Br. PC(CH3)2CHCHCO2H (CH3)2CHCHCO 3-Methylbutanoi 2-Bromo-3-methylbutanoic Back Forward Main Menu TOC Study Guide Toc Student OLC MHHE Website
754 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS (d) On further treatment with base, both the monoanions in part (c) yield the same dianion. 27.4 At pH 1 the carboxylate oxygen and both nitrogens of lysine are protonated. As the pH is raised, the carboxyl proton is removed first. The pKa value for the first ionization of lysine is 2.18 (from Table 27.3), and so this process is virtually complete when the pH is greater than this value. The second pKa value for lysine is 8.95. This is a fairly typical value for the second pKa of amino acids and likely corresponds to proton removal from the nitrogen on the carbon. The species that results is the predominant one at pH 9. The pKa value for the third ionization of lysine is 10.53. This value is fairly high compared with those of most of the amino acids in Tables 27.1 to 27.3 and suggests that this proton is removed from the nitrogen of the side chain. The species that results is the major species present at pH values greater than 10.53. 27.5 To convert 3-methylbutanoic acid to valine, a leaving group must be introduced at the carbon prior to displacement by ammonia. This is best accomplished by bromination under the conditions of the Hell–Volhard–Zelinsky reaction. (CH3)2CHCH2CO2H Br2, P or Br2, PCl3 NH3 (CH3)2CHCHCO2H Br (CH3)2CHCHCO2 NH3 3-Methylbutanoic acid 2-Bromo-3-methylbutanoic acid Valine H3NCH2CH2CH2CH2CHCO2 HO NH2 H2NCH2CH2CH2CH2CHCO2 NH2 (Principal form at pH 13) H3NCH2CH2CH2CH2CHCO2 HO NH3 H3NCH2CH2CH2CH2CHCO2 H2O NH2 (Principal form at pH 9) H3NCH2CH2CH2CH2CHCO2H HO NH3 H3NCH2CH2CH2CH2CHCO2 H2O NH3 H3NCH2CH2CH2CH2CHCO2H NH3 (Principal form at pH 1) O CH2CHCO2 NH2 Back Forward Main Menu TOC Study Guide TOC Student OLC MHHE Website
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 755 Valine has been prepared by this method. The Hell-Volhard-Zelinsky reaction was carried out in 889 yield, but reaction of the a-bromo acid with ammonia was not very efficient, valine being nly 48% yield in this step 27.6 In the Strecker synthesis an aldehyde is treated with ammonia and a source of cyanide ion. The resulting amino nitrile is hydrolyzed to an amino acid L.H. O heat (CH3),CHCH (CH3)2 CHCHO≡N 2. HO (CH,), CHCHCO, NH NH3 valine As actually carried out, the aldehyde was converted to the amino nitrile by treatment with an aque ous solution containing ammonium chloride and potassium cyanide. Hydrolysis was achieved in aqueous hydrochloric acid and gave valine as its hydrochloride salt in 65%o overall yield 27.7 The alkyl halide with which the anion of diethyl acetamidomalonate is treated is 2-bromopropane NaOCH, CH, CHa CNHCH(CO, CH, CH3)2+( CH3), CHBr CH.CHAOH CH, CNHC(CO, CH, CH3)2 CH(CH3) Diethyl acetamidomalonate 2-Bromopropane Diethyl acetamidoisopropylmalonate This is the difficult step in the synthesis; it requires a nucleophilic substitution of the Sn2 type volving a secondary alkyl halide Competition of elimination with substitution results in only a 37%0 observed yield of alkylated diethyl acetamidomalonate. Hydrolysis and decarboxylation of the alkylated derivative are straightforward and proceed in 85% yield to give valine HBr. Ho CH_CNHC(CO, CH,CH3)2 H3 NC(CO,H) H,NCHCO CH(CH3) CH(CH3h2 Diethyl 2.Aminoisopropylmalonic valine The overall yield of valine(31%)is the product of 37%X 85%0 27.8 Ninhydrin is the hydrate of a triketone and is in equilibrium with it. OH Hydrated form of Triketo form of An amino acid reacts with this triketone to form an imine -O RCHCO2 ≥ NCHCO2 Triketo form of Imine Back Forward Main Menu TOC Study Guide Toc Student OLC MHHE Website
Valine has been prepared by this method. The Hell–Volhard–Zelinsky reaction was carried out in 88% yield, but reaction of the -bromo acid with ammonia was not very efficient, valine being isolated in only 48% yield in this step. 27.6 In the Strecker synthesis an aldehyde is treated with ammonia and a source of cyanide ion. The resulting amino nitrile is hydrolyzed to an amino acid. As actually carried out, the aldehyde was converted to the amino nitrile by treatment with an aqueous solution containing ammonium chloride and potassium cyanide. Hydrolysis was achieved in aqueous hydrochloric acid and gave valine as its hydrochloride salt in 65% overall yield. 27.7 The alkyl halide with which the anion of diethyl acetamidomalonate is treated is 2-bromopropane. This is the difficult step in the synthesis; it requires a nucleophilic substitution of the SN2 type involving a secondary alkyl halide. Competition of elimination with substitution results in only a 37% observed yield of alkylated diethyl acetamidomalonate. Hydrolysis and decarboxylation of the alkylated derivative are straightforward and proceed in 85% yield to give valine. The overall yield of valine (31%) is the product of 37% 85%. 27.8 Ninhydrin is the hydrate of a triketone and is in equilibrium with it. An amino acid reacts with this triketone to form an imine. O O O Triketo form of ninhydrin O NCHCO2 R O -Amino acid Imine RCHCO2 NH3 HO H2O O O O Triketo form of ninhydrin Hydrated form of ninhydrin O O OH OH HBr, H2O heat CO2 heat 2-Aminoisopropylmalonic acid Diethyl acetamidoisopropylmalonate CH(CH3)2 CH3CNHC(CO2CH2CH3)2 O CH(CH3)2 H3NC(CO2H)2 Valine CH(CH3)2 H3NCHCO2 NaOCH2CH3 CH3CH2OH Diethyl acetamidomalonate CH3CNHCH(CO2CH2CH3)2 O Diethyl acetamidoisopropylmalonate CH(CH3)2 CH3CNHC(CO2CH2CH3)2 O 2-Bromopropane (CH3)2CHBr NH3 HCN 1. H3O, heat 2. HO (CH3)2CHCHCO2 NH3 2-Methylpropanal Valine (CH3)2CHCH O 2-Amino-3- methylbutanenitrile (CH3)2CHCHC N NH2 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 755 Back Forward Main Menu TOC Study Guide TOC Student OLC MHHE Website
756 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS This imine then undergoes decarboxylation R CHR The anion that results from the decarboxylation step is then protonated. The product is shown as its diketo form but probably exists as an enol x+-0 NECHR Hydrolysis of the imine function gives an aldehyde and a compound having a free amino group N=CHR H,O t RCH This amine then reacts with a second molecule of the triketo form of ninhydrin to give an imine Proton abstraction from the neutral imine gives its conjugate base, which is a violet dye violet dye 27.9 The carbon that bears the amino group of 4-aminobutanoic acid corresponds to the a carbon of an a-amino acid CH,CH, CH,CO, arises by decarboxylation of O, CCHCH,CH, CO tNH 4-Aminobutanoic acid Glutamic acid Back Forward Main Menu TOC Study Guide Toc Student OLC MHHE Website
This imine then undergoes decarboxylation. The anion that results from the decarboxylation step is then protonated. The product is shown as its diketo form but probably exists as an enol. Hydrolysis of the imine function gives an aldehyde and a compound having a free amino group. This amine then reacts with a second molecule of the triketo form of ninhydrin to give an imine. Proton abstraction from the neutral imine gives its conjugate base, which is a violet dye. 27.9 The carbon that bears the amino group of 4-aminobutanoic acid corresponds to the carbon of an -amino acid. CH arises by decarboxylation of 2CH2CH2CO2 NH3 4-Aminobutanoic acid O2CCHCH2CH2CO2 NH3 Glutamic acid H2O O O N H O O OH Violet dye O O N O O O O O O O NH2 H O O N H O O H2O O O NH2 H RCH O O O H N CHR O N H2O O CHR OH O O H N CHR O N O CH C R O O CO2 O N O CHR 756 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS Back Forward Main Menu TOC Study Guide TOC Student OLC MHHE Website