15597.eh26.454-46810/20/0515:39Page45d EQA 26 Amino Acids,Peptides,Proteins,and Nucleic Acids: Nitrogen-Containing Polymers in Nature chemistry in particula mea molec of eviee the organic chemipoint of vThe nert s i drectn biochemistry. Outline of the Chapter 风 2Sucture nd Properieof Amino Acids 26-2,26-3 Preparation of Amino Acids Fancy footwork involving two very different functional groups. 26-4 Peptides and Proteins:Amino Acid Oligomers and Polymers The whole is greater than the sum of its parts. 265eamnienotPgibmrysmctre:5oqpencing 26,2678-DoeesAce29Cee0alknge 26-8 Polypeptides in Nature:The Proteins Myoglobin and Hemoglobin -1f Nucleic Acids w Nature appears to do 26-11 DNA Sequencing and Synthesis:Gene Technology The future is now! Keys to the Chapter 26-1.Structure and Properties of Amino Acids The th 454
26 Amino Acids, Peptides, Proteins, and Nucleic Acids: Nitrogen-Containing Polymers in Nature Here it is: the last chapter! It is, however, as much a beginning as an end. Chemistry in general, and organic chemistry in particular, are not isolated fields. Organic chemistry is the basic stuff of biology, and this chapter bridges the two. The basic principles that govern the behavior of organic molecules in general are shown here to be directly applicable to molecules of greater and greater complexity. You see here some of the most fundamental molecules of life viewed from the organic chemist’s point of view. The next step in this direction is biochemistry. Outline of the Chapter 26-1 Structure and Properties of Amino Acids Nature’s most versatile building blocks. 26-2, 26-3 Preparation of Amino Acids Fancy footwork involving two very different functional groups. 26-4 Peptides and Proteins: Amino Acid Oligomers and Polymers The whole is greater than the sum of its parts. 26-5 Determination of Polypeptide Primary Structure: Sequencing Exercises in logic, plus a lot of hard work. 26-6, 26-7 Synthesis of Polypeptides: A Protecting Group Challenge Even fancier footwork; how does Nature do it so easily??!! 26-8 Polypeptides in Nature: The Proteins Myoglobin and Hemoglobin 26-9, 26-10 Biosynthesis of Proteins: Nucleic Acids How Nature appears to do it so easily. 26-11 DNA Sequencing and Synthesis: Gene Technology The future is now! Keys to the Chapter 26-1. Structure and Properties of Amino Acids Read the introduction to the text chapter and this text section, and then come back here. All done? O.K., here’s the big picture. The chemistry of life is complicated. Structures have to be built to hold things together, and a lot of chemical reactions have to be going on to perform the various functions that maintain life, such as 454 1559T_ch26_454-468 10/20/05 15:39 Page 454
1559T_ch26_454-46810/20/0515:39Pa9e455 EQA Keys to the Chapter·455 R onstrained set of conditions:Water is the y very narrow ranges of temperature and pH are acceptable.Other The answer begn only in the polar groups.both small and large. capable of various egrees of There are uncharged bu polar hic will be eof this varicty. ofbe depoontod and negaivly chargodp lists pk valu s for all rele oups.Notice.for one thing.that the way the amino acids have been drawn up to no wrong.In so amino acids in fact never exi to pH.one or both of theseg oups is always charged.with the pH 7structure COOBe. gteeiectsofpHon ation of Amine acids 一2i子and子6r3eP时thrntinowr combinations aimed at solving the problem of introducing basic and acidic groups into the same molecule. 26-4 and 26-5.Peptides and Proteins:Amino Acid Oligomers and Polymers determining peptide and pro extremely well of fo 26-6an 26 Synth esis of Polypeptides:A Protecting Group Challenge ptide chains from condensations(Sections 18-6 and 23-1) e trick y nu y el at linkine two mol les of a.a.I to ther.two mo oh a.a to each er,or a.a. o a.a. in the wrong se tional gr will let you try them for yourself. 26-8 through 26-11.Proteins in Operation;Biosynthesis; DNA and Gene Technology units gives rise to structures of such highly elaborate function.This stuff is really neat.You might like to read more about it some time
energy storage and utilization. These all have to occur under a very constrained set of conditions: Water is the only available solvent, and in general only very narrow ranges of temperature and pH are acceptable. Otherwise everything falls apart. So how is it done? The answer begins with the amino acids. Look first at the structures of the 20 most common examples (Table 26-1). They differ only in the group attached to the -carbon. The variety in these groups establishes the versatility of amino acids. There are nonpolar groups, both small and large, capable of various degrees of steric interaction. There are uncharged but polar groups, capable of hydrogen bonding. There are nitrogen-containing groups of various base strengths, some of which will be protonated and positively charged at pH 7. There are oxygen and sulfur groups of various acid strengths, some of which will be deprotonated and negatively charged at pH 7. Because of this variety, Nature can choose from among these 20 compounds just the right one to fill any of a number of chemical needs. One feature that is emphasized in this section is the acid-base behavior of the amino acids. Table 26-1 lists pKa values for all relevant groups. Notice, for one thing, that the way the amino acids have been drawn up to now, H2NOCHROCOOH, is wrong. In solution, amino acids in fact never exist to any significant extent in this form, with neutral amino and carboxylic acid groups present at the same time. Depending on the pH, one or both of these groups is always charged, with the pH 7 structure being H3NOCHROCOO. Because of this feature, amino acids are very good buffers at a variety of different pH’s, depending on R. Obviously the effects of pH on amino acid structure are important, and Problem 28 will give you several examples to work on so you can get the feel for it. 26-2 and 26-3. Preparation of Amino Acids Although none of the individual reactions in these sections are new, the sequences present them in powerful combinations aimed at solving the problem of introducing basic and acidic groups into the same molecule. 26-4 and 26-5. Peptides and Proteins: Amino Acid Oligomers and Polymers Techniques for determining peptide and protein structure are extremely well worked out (and Problems 42–47 will give you plenty of chances to try them for yourself). The results, especially in the subtleties of folding of these polymeric chains, reveal the extent to which the characteristics of the different amino acids are combined and used in nature to generate large molecular assemblies perfectly suited for very specific biological roles. Problems 38–41 are intended to give you something to think about in this regard. 26-6 and 26-7. Synthesis of Polypeptides: A Protecting Group Challenge Don’t ever lose sight of the fact that the linkage between amino acids is nothing more than a simple amide bond: OHNOCOO. Nonetheless, the construction of peptide chains from simple amino acids is a major challenge for the same reasons that, say, mixed aldol or Claisen condensations (Sections 18-6 and 23-1) are tricky things to do: Each amino acid involved has both a potentially nucleophilic atom (the N) and a potentially electrophilic one (the carboxy C). Thus, an attempt at linking, say, the amine of amino acid 1 with the carboxy group of amino acid 2 is going to be complicated by the need to prevent the simultaneous linkage of either two molecules of a.a.1 to each other, two molecules of a.a.2 to each other, or a.a.1 to a.a.2 in the wrong sense: carboxy of 1 to amine of 2. The solution to the problem lies in, again, a very well worked out array of functional group protection–deprotection procedures, the simplest of which are presented here. Problems 48 and 49 will let you try them for yourself. 26-8 through 26-11. Proteins in Operation; Biosynthesis; DNA and Gene Technology Obviously only a tiny taste of what’s involved with these topics can be presented in the space of four chapter sections. Nonetheless, you should be able to sense the remarkable way in which the linkage of relatively small units gives rise to structures of such highly elaborate function. This stuff is really neat. You might like to read more about it some time. Keys to the Chapter • 455 1559T_ch26_454-468 10/20/05 15:39 Page 455
1559r.ch26_454-46810/20/0515:39Pag0456 456.chapter 26 AMINO ACIDS,PEPTIDES,PROTEINS,AND NUCLEK ACIDS:NITROGEN-CONTAINING POLYMERS IN NATURE Solutions to Problems 26. COOH COOH HN- H.cH HN- CH2CHs CHs L-Isoleucine t-Threonine Systematic name for Lthreonine:()-2-amino-3-hydroxybutanoic acid. 27. COOH HN-H H-CHS Systematic name for allo-L-isoleucine:(2S.3R)-2-amino-3-methylpentanoic acid 28.Structures are presented in order of increasing pH(in parentheses). COOH C00- C00- aH衣H④HHm,N H(12) CH CH CH COOH C00 (b)HaN--H (1)HN-H (7) H2N--H (12) CH-OH CH2OH CH-OH COOH C00 C00 C00 (e)HN-H (1) HaN- H -H(9.5) N +H(12) (CH24-NH; (CH2)4-NHs (CH2)4-NH3 (CH2)4-NH2 COOH C00- C00 900 @HNH是a)HNH() HN十H() H.N- -H思(12 H COOH C00- C00- H (7)H-H (9)HN- H(12) CH-SH COOH C00- C00 C00 (f)HN-H (1)HN-H (3)HsN-H (7) HN-H(12) CH-COOH CH-COOH CH-COO CHCOO
Solutions to Problems 26. Systematic name for L-threonine: (2S, 3R)-2-amino-3-hydroxybutanoic acid. 27. Systematic name for allo-L-isoleucine: (2S, 3R)-2-amino-3-methylpentanoic acid. 28. Structures are presented in order of increasing pH (in parentheses). (a) (b) (c) (d) (e) (f) H3N (1) H COOH CH2COOH CH2COOH CH2COO CH2COO H3N (3) H COO H3N (7) H COO H2N H (12) COO H3N (1) H COOH CH2SH H3N (7) H COO CH2SH H3N (9) H COO CH2S H2N H (12) COO CH2S H3N (1) (5) (7) H H N NH COO COO COO CH2 H3N H H N NH COOH CH2 H2N H H N N CH2 H3N H H N N CH2 (12) H3N (1) NH3 H COOH (CH2)4 COO H2N H (9.5) COO H3N (7) NH3 H (CH2)4 NH3 (CH2)4 H2N H (12) COO (CH2)4 NH2 H3N (1) H COOH CH2OH CH2OH CH2OH H3N (7) H COO H2N H (12) COO H3N (1) H COOH CH3 H3N (7) H COO CH3 H2N H (12) COO CH3 H H2N S H COOH CH2CH3 CH3 Allo-L-isoleucine R H3C H2N S H H COOH CH2CH3 L-Isoleucine S H H2N S OH H COOH CH3 L-Threonine R 456 • Chapter 26 AMINO ACIDS, PEPTIDES, PROTEINS, AND NUCLEIC ACIDS: NITROGEN-CONTAINING POLYMERS IN NATURE 1559T_ch26_454-468 10/20/05 15:39 Page 456
1559T_ch26_454-46810/20/0515:53Pa9e457 EQA Solutionsto Problems457 COOH 900 (g)HN-H NH2 (1)HN-H NH2 (7) (CH)NHCNH> (CH2)3NHCNHz C00 C00 HaN--H NH2 (12) H2N-H NH (14) (CH2)NHCNHz 900 H (1)H. H (7)H2 H(9.5)H, H(12) 12 CH OH OH 0- 29.(a)Arg.Lys:(b)Ala.Ser.Tyr.His,Cys:(e)Asp single and a single roup.Their average is the pl. ()(9.0+10.5/2=9.7 (d(9.2+6.1)/2=7.6 (e(8.2+2.0/2=5.1 (0(6.7+1.92=2.8 (g(12.5+9.0M2=10.8 h)(9.1+2.2)/2=5.7 31.(a)Because the R group is secondary.alkylation routes should be avoided.Use the Strecker synthesis. NH3 CH(CO,CH,CH)
(g) (h) 29. (a) Arg, Lys; (b) Ala, Ser, Tyr, His, Cys; (c) Asp 30. First identify the net charge-neutral structure, which is always the one with a single and a single charge. Choose the two pKa values that bracket that structure. They are, repectively, the pKa for deprotonation of the most acidic group in that structure and the pKa for protonation of the most basic group. Their average is the pI. (c) (9.0 10.5)/2 9.7 (d) (9.2 6.1)/2 7.6 (e) (8.2 2.0)/2 5.1 (f) (3.7 1.9)/2 2.8 (g) (12.5 9.0)/2 10.8 (h) (9.1 2.2)/2 5.7 31. (a) Because the R group is secondary, alkylation routes should be avoided. Use the Strecker synthesis. (b) The R group is primary; now you have a choice. Either the Strecker synthesis starting with (CH3)2CHCH2CHO or a Gabriel-based method will do. 1. NaOCH2CH3, CH3CH2OH 2. BrCH2CH(CH3)2 3. H, H2O, NH3 N O O CH(CO2CH2CH3)2 (CH3)2CHCH2CHCOO H, H2O 1. NH3 2. HCN (CH3)2CHCHO (CH3)2CHCHCN NH2 (CH3)2CHCHCOO NH3 (1) COO COO COO O H3N H COOH CH2 OH H3N (7) H CH2 OH H2N H (9.5) CH2 OH H2N H (12) CH2 H3N NH2 (1) H COOH (CH2)3NHCNH2 H3N (7) H COO H2N H (12) COO H2N H (14) COO NH2 (CH2)3NHCNH2 NH2 (CH2)3NHCNH2 NH (CH2)3NHCNH2 Solutions to Problems • 457 1559T_ch26_454-468 10/20/05 15:53 Page 457
1559r.eh26.454-46810/20/0515:39Page458 458 chapter 26 AMINO ACIDS,PEPTIDES,PROTEINS,AND NUCLEK ACIDS:NITROGEN-CONTAINING POLYMERS IN NATURE Even the Hell-Volhardt-Zelinskyamination sequence works just fine here Br CH)CHCHCH-COOH(CH)CHCH-CHCOOH NHs (CH-CHCH CHCOO- (c)Several ways to go,but you have to first recognize the need for a three-carbon building block with leaving groups at 1.NaOCH.CH.CH.CH.OH -CH(COCH-CH COC.OCCH. NH3 Cone.HBr NH; BrCH,CH2CH-CHCOO- aving group raaawr"y 一N NCHCO.CH.CH HO NHs C(CO,CH,CH).H. CH:CHCHCOO- HOCHCH (e)The extra amine group must be present in protected form.irrespective of the method used.Here'sa Gabriel-type sequenc
Even the Hell-Volhardt-Zelinsky–amination sequence works just fine here. (c) Several ways to go, but you have to first recognize the need for a three-carbon building block with leaving groups at each end to allow linkage to both the -carbon and (later on) the amine nitrogen to form the ring. Start with a Gabriel-type sequence. (d) Use a Gabriel-based method. Instead of forming the necessary carbon–carbon bond by SN2 reaction with a haloalkane, use an aldol-type condensation with CH3CHO. (e) The extra amine group must be present in protected form, irrespective of the method used. Here’s a Gabriel-type sequence. H, H2O, NH3 HO CH3CHCHCOO N O O C(CO2CH2CH3)2 HOCHCH3 1. NaOCH2CH3 2. CH3CHO O O NCH(CO2CH2CH3)2 NH2 BrCH2CH2CH2CHCOO COO Br H2N H Conc. HBr (Converts OH to Br, a good leaving group) NH3 BrCH2CH2CH2CHCOO 1. NaOCH2CH3, CH3CH2OH 2. BrCH2CH2CH2OCCH3 O 3. H, H2O, N O O CH(CO2CH2CH3)2 NH3 HOCH2CH2CH2CHCOO NH3, H2O (CH3)2CHCH2CHCOO NH3 Br2, PBr3 (CH3)2CHCH2CH2COOH Br (CH3)2CHCH2CHCOOH 458 • Chapter 26 AMINO ACIDS, PEPTIDES, PROTEINS, AND NUCLEIC ACIDS: NITROGEN-CONTAINING POLYMERS IN NATURE 1559T_ch26_454-468 10/20/05 15:39 Page 458