Chapter 25 Amino Acids, Peptides, and Proteins

Transcription

1 Chapter 25 Amino Acids, Peptides, and Proteins eview of Concepts Fill in the blanks below. To verify that your answers are correct, look in your textbook at the end of Chapter 25. Each of the sentences below appears verbatim in the section entitled eview of Concepts and Vocabulary. Amino acids in which the two functional groups are separated by exactly one carbon atom are called amino acids. Amino acids are coupled together by amide linkages called bonds. elatively short chains of amino acids are called. nly twenty amino acids are abundantly found in proteins, all of which are amino acids, except for which lacks a chirality center. Amino acids exist primarily as at physiological p The of an amino acid is the p at which the concentration of the zwitterionic form reaches its maximum value. Peptides are comprised of amino acid joined by peptide bonds. Peptide bonds experience restricted rotation, giving rise to two possible conformations, called and. The conformation is more stable. Cysteine residues are uniquely capable of being joined to one another via bridges. is commonly used to form peptide bonds. In the Merrifield synthesis, a peptide chain is assembled while tethered to. The primary structure of a protein is the sequence of. The secondary structure of a protein refers to the of localized regions of the protein. Two particularly stable arrangements are the helix and pleated sheet. The tertiary structure of a protein refers to its. Under conditions of mild heating, a protein can unfold, a process called. Quaternary structure arises when a protein consists of two or more folded polypeptide chains, called, that aggregate to form one protein complex.

2 666 CAPTE 25 eview of Skills Fill in the blanks and empty boxes below. To verify that your answers are correct, look in your textbook at the end of Chapter 25. The answers appear in the section entitled SkillBuilder eview Determining the Predominant Form of an Amino Acid at a Specific p CSIDE TE FLLWIG AMI ACID, AD DAW TE FM TAT PEDMIATES AT PYSILGICAL p Using the Amidomalonate Synthesis IDETIFY EAGETS TAT WILL ACIEVE TE FLLWIG TASFMATI: 1) 2) Et Et 3) 4) Drawing a Peptide DAW A BD-LIE STUCTUE F TE TIPEPTIDE -Val-Trp Sequencing a Peptide via Enzymatic Cleavage IDETIFY TE FAGMETS BTAIED FM EZYMATIC CLEAVAGE F TE FLLWIG PEPTIDE: Ala--Lys-Pro-Met-Tyr-Gly-Arg-Ser-Trp-Leu-ist trypsin chymotrypsin

3 CAPTE Planning the Synthesis of a Dipeptide IDETIFY ALL EAGETS ECESSAY T PEPAE TE DIPEPTIDE Ala-Gly: Ala Gly Ala + Gly C 3 Ala Gly C 3 Ala Gly 25.6 Preparing a Peptide using the Merrifield Synthesis IDETIFY ALL EAGETS ECESSAY T PEPAE TE PETAPEPTIDE Ile-Gly-Leu-Ala-: PLYME Ile Gly Leu Ala PLYME Ile Gly Leu Ala PLYME PLYME Ala PLYME eview of eactions Identify the reagents necessary to achieve each of the following transformations. To verify that your answers are correct, look in your textbook at the end of Chapter 25. The answers appear in the section entitled eview of eactions. Analysis of Amino Acids 2 C C 2 C

4 668 CAPTE 25 Synthesis of Amino Acids Br 2 Et Et 2 C Et Et 2 C 2 ac Ac Ac 2 Analysis of Amino Acids PEPTIDE 2 PEPTIDE + Ph S Synthesis of Peptides [ + ] 2 2 a 2

5 CAPTE Solutions In each case, the chirality center has the configuration. C C 2 2 C 3 C(C 3 ) 2 D-Alanine D-Valine S 2 d) Pro,, Trp, Tyr, and is, Trp, Tyr, and is Arg, is, and Lys d) Met and Cys e) Asp and Glu f) Pro, Trp, Asn, Gln, Ser, Thr, Tyr, Cys, Asp, Glu, Arg, is, and Lys C d) 2 e) f) Arginine has a basic side chain, while asparagine does not. At a p of 11, arginine exists predominantly in a form in which the side chain is protonated. Therefore, it can serve as a proton donor Tyrosine possesses a phenolic proton which is more readily deprotonated because deprotonation forms a resonance-stabilized phenolate ion. In contrast, deprotonation of the group of serine gives an alkoxide ion that is not resonance-stabilized. As a result, the group of tyrosine is more acidic than the group of serine.

6 670 CAPTE d) aspartic acid glutamic acid Leucine and isoleucine The pi of = 5.48, the pi of Trp = 6.11, and the pi of Leu = At p = 6.0, will travel the farthest distance. At p = 5.0, Trp will travel the farthest distance ) Br 2, PBr 3 2) 2 3) excess 3 2 (racemi 1) Br 2, PBr 3 2) 2 3) excess 3 2 (racemi 1) Br 2, PBr 3 2) 2 3) excess 3 2 (racemi

7 CAPTE C C C C Leucine Valine nylalanine d) Glycine ) aet Et Et 2) Br 2 3) 3 +, heat 1) aet Et Et 2) C 3 Br 3) 3 +, heat 2 1) aet Et Et 2) Br 2 3) 3 +, heat alanine valine leucine Leucine can be prepared via the amidomalonate synthesis with higher yields than isoleucine, because the former requires an S 2 reaction with a primary alkyl halide, while the latter requires an S 2 reaction with a secondary (more hindered) alkyl halide.

8 672 CAPTE S 1) 4 Cl, ac 2) 3 + S 2 1) 4 Cl, ac 2) ) 4 Cl, ac 2) ) 4 Cl, ac d) 2) C 1) 4 Cl, ac 2) C 2 alanine 1) 4 Cl, ac 2) leucine 1) 4 Cl, ac 2) valine C Ac Ac Ac d) Ac

9 CAPTE Glycine does not possess a chirality center, so the use of a chiral catalyst is unnecessary. Also, there is no alkene that would lead to glycine upon hydrogenation S 2 C S Leu-Ala--Cys-Asp or L-A-F-C-D Cys-Tyr-Leu Constitutional isomers C terminus terminus Steric hindrance results from the phenyl groups: 2

10 674 CAPTE S S C 2 C 2 C 2 C D-Glutamic acid ot naturally occurring L-Leucine L-Isoleucine L-Lysine S 2 ot naturally occurring 2 L-Isoleucine Bacitracin A L-asparagine 2 D-nylalanine D-Aspartic acid L-istidine

11 CAPTE An Edman degradation will remove the amino acid residue at the terminus, and Ala is the terminus in Ala--Val. Therefore, alanine is removed, giving the following PT derivative: Ph C 3 S Met--Val-Ala-Tyr-Lys-Pro-Val-Ile-Leu-Arg-Trp-is--Met-Cys-Arg-Gly-Pro- -Ala-Val Ala--Val-Lys Cleavage with trypsin will produce -Arg, while cleavage with chymotrypsin will produce Arg-. These dipeptides are not the same. They are constitutional isomers Trp () 2 Trp DCC 1) CF 3 C Trp Met C 3 2) a, 2 Trp Met [ + ] Met Met C 3 C 3 Ala () 2 Ala DCC 1) CF 3 C Ala Ile C 3 2) a, 2 Ala Ile [ + ] Ile Ile C 3 C 3

12 676 CAPTE 25 Leu () 2 Leu DCC 1) CF 3 C Leu Val C 3 2) a, 2 Leu Val [ + ] Val Val C 3 C Ile () 2 Ile DCC Ile C 3 [ + ] C 3 C 3 a, 2 Ile DCC Gly C 3 Ile Gly 1) CF 3 C 2) a, 2 Ile Gly C 3

13 CAPTE

14 678 CAPTE ) Cl PLYME 2) CF 3 C Ph -Leu-Val- 3), DCC 4) CF 3 C 5), DCC 6) CF 3 C 7), DCC 8) CF 3 C Ph 9) F 1) Cl PLYME Ala-Val-Leu-Ile 2) CF 3 C 3), DCC 4) CF 3 C 5), DCC 6) CF 3 C 7), DCC 8) CF 3 C 9) F

15 CAPTE ( terminus) Val-Ala- (C terminus) The regions that contain repeating glycine and/or alanine units are the most likely regions to form β sheets: Trp-is-Pro-Ala-Gly-Gly-Ala-Val-is-Cyst-Asp-Ser-Arg-Arg-Ala-Gly-Ala- 2 d) When applying the Cahn-Ingold-Prelog convention for assigning the configuration of a chirality center, the amino group generally receives the highest priority (1), followed by the carboxylic acid moiety (2), followed the side chain (3), and finally the (4). Accordingly, the S configuration is assigned to L amino acids. Cysteine is the one exception because the side chain has a higher priority than the carboxylic acid moiety. As a result, the configuration is assigned C C C C C 3 2 C 2 2 C 2 Ph d) 2 C 2 C Isoleucine and threonine Isoleucine = 2S,3S. Threonine = 2S, S S S S The protonated form below is highly stabilized by resonance, which spreads the positive charge over all three nitrogen atoms. 2 2 Acid 2 2

16 680 CAPTE The protonated form below is aromatic. In contrast, protonation of the other nitrogen atom in the ring would result in loss of aromatic stabilization. 2 Acid d) d) d) Lysozyme is likely to be comprised primarily of amino acid residues that contain basic side chains (arginine, histindine, and lysine), while pepsin is comprised primarily of amino acid residues that contain acidic side chains (aspartic acid and glutamic acid) d)

17 CAPTE C C 2 (planar) 2 C + C 2 acemic mixture The pi of Gly = 5.97, the pi of Gln = 5.65, and the pi of Asn = At p = 6.0, Asn will travel the farthest distance. At p = 5.0, Gly will travel the farthest distance d) no reaction Methionine, valine, and glycine. The compound is highly conjugated and has a λ max that is greater than 400 nm (see Section 17.12) ) 4 Cl, ac 2) Alanine can be prepared via the amidomalonate synthesis with higher yields than valine, because the former requires an S 2 reaction with a primary alkyl halide, while the latter requires an S 2 reaction with a secondary (more hindered) alkyl halide The side chain () of glycine is a hydrogen atom (). Therefore, no alkyl group needs to be installed at the α position. Et Et 3 +, heat 2

18 682 CAPTE ) Br 2, PBr 3 2) 2 2 3) excess 3 1) 4 Cl, ac 2) Et Et 1) aet 2) C 3 I 3) 3 +, heat ) Br 2, PBr 3 2) 2 3) excess 3 2 (racemi 1) aet Et Et 2) Br 3) 3 +, heat 2 1) 4 Cl, ac 2) = 3,200, Ac

19 CAPTE ) Leu-Met-Val, 2) Leu-Val-Met, 3) Met-Val-Leu, 4) Met-Leu-Val, 5) Val-Met-Leu, 6) Val-Leu-Met Terminus C Terminus S S C S 2 cysteine valine

20 684 CAPTE tyrosine serine glycine It does not react with phenyl isothiocyanate so it must not have a free terminus. It must be a cyclic tripeptide: Gly Gly Ala Ala Arg + Pro-Pro-Gly--Ser-Pro--Arg Arg-Pro-Pro-Gly- + Ser-Pro- + Arg nylalanine = S Val-Ala-Gly: 2

21 CAPTE There cannot be any disulfide bridges in this peptide, because it has no cysteine residues, and only cysteine residues form disulfide bridges. is-ser-gln-gly-thr--thr-ser-asp-tyr-ser-lys-tyr-leu-asp-ser-arg-arg-ala-gln-asp--val- Gln-Trp-Leu-Met-Asn-Thr Prior to acylation, the nitrogen atom of the amino group is sufficiently nucleophilic to attack phenyl isothiocyanate. Acylation converts the amino group into an amide moiety, and the lone pair of the nitrogen atom is delocalized via resonance, rendering it much less nucleophilic d) () 2 DCC 1) CF 3 C Ala C 3 2) a, 2 Ala [ + ] Ala Ala C 3 C C 3 C C 3 C 3

22 686 CAPTE Ile () 2 Ile DCC Ile Val Leu C 3 [ + ] Val Leu C 3 Val Leu C 3 1) CF3 C 2) a, 2 Ile Val Leu ) Cl PLYME Leu-Val-Ala 2) CF 3 C 3), DCC 4) CF 3 C 5), DCC 6) CF 3 C 7) F A proline residue cannot be part of an α helix, because it lacks an - proton and does not participate in hydrogen bonding. (The amino acid proline does indeed have an - group, but when incorporated into a peptide, the proline residue does not have an - group)

23 CAPTE Br The stabilized enolate ion (formed in the first step) can function as a base, rather than a nucleophile, giving an E2 reaction: Et Br Et Et Et Et The lone pair on that nitrogen atom is highly delocalized via resonance and is participating in aromaticity. Accordingly, the lone pair is not free to function as a base.

24 688 CAPTE Br 2 Br Br At low temperature, the barrier to rotation keeps the two methyl groups in different electronic environments (one is cis to the C= bond and the other is trans to the C= bond), and they therefore give rise to separate signals. At high temperature, there is sufficient energy to overcome the energy barrier, and the protons change electronic environments on a timescale that is faster than the timescale of the M spectrometer. The result is an averaging effect which gives rise to only one signal The C group does not readily undergo nucleophilic acyl substitution because the group is not a good leaving group. By converting the C group into an activated ester, the compound can now undergo nucleophilic acyl substitution because it has a good leaving group. The nitro group stabilizes the leaving group via resonance. As described in Chapter 19, the nitro group serves as a reservoir for electron density. The nitro group must be in the ortho or para position in order to stabilize the negative charge via resonance. If the nitro group is in the meta position, the negative charge cannot be pushed onto the nitro group Cl, 2 2 heat 2 threonine