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 —CH
2
SH substituent is the only side chain that
outranks —CO
2
H11002
according to the sequence rule. Remember, rank order is determined by
CH
2
SH
H
3
N CO
2
H11002
H11001
Clockwise; therefore R
HSCH
2
H
3
N
H11001
H11022 H11022 H11022CO
2
H11002
H
H11013H11013
L-Cysteine
CO
2
H11002
H
CH
2
SH
H
3
N
H11001
NH
3
H11001
CO
2
H11002
HSCH
2
H
C
H
3
N
H11001
CO
2
H11002
HSCH
2
H
C
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atomic number at the first point of difference, and —C—S outranks —C—O. In all the
other amino acids —CO
2
H11002
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 threo-
nine. 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 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:
In fact, the proton on nitrogen is slightly more acidic than the phenolic hydroxyl, as measured
by the pK
a
values of the following model compounds:
HO CH
2
CHCO
2
H11002
N(CH
3
)
3
CH
3
OCH
2
CHCO
2
H11002
NH
3
H11001H11001
pK
a
9.75
pK
a
9.27
HO andCH
2
CHCO
2
H11002
NH
2
H11002
OCH
2
CHCO
2
H11002
NH
3
H11001
HO CH
2
CHCO
2
H11002
NH
3
H11001
Isoleucine
CH
3
CH
2
CH
CH
3
CHCO
2
H11002
* *
H11001
NH
3
Threonine
CH
3
CH
OH
CHCO
2
H11002
**
H11001
NH
3
H11013
CH
2
CH
2
SCH
3
H
CO
2
H11002
H
3
N
H11001
CO
2
H11002
NH
3
H11001
H
CH
3
SCH
2
CH
2
C
CH
2
CH
2
SCH
3
H
3
NHH11022 CO
2
H11002
H11001
H11022H11022
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 753
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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 pK
a
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 pK
a
value for lysine is 8.95. This is a fairly typical value for the second pK
a
of amino
acids and likely corresponds to proton removal from the nitrogen on the H9251 carbon. The species that
results is the predominant one at pH 9.
The pK
a
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 H9251 carbon prior
to displacement by ammonia. This is best accomplished by bromination under the conditions of the
Hell–Volhard–Zelinsky reaction.
(CH
3
)
2
CHCH
2
CO
2
H
Br
2
, P
or Br
2
, PCl
3
NH
3
(CH
3
)
2
CHCHCO
2
H
Br
(CH
3
)
2
CHCHCO
2
H11002
NH
3
H11001
3-Methylbutanoic
acid
2-Bromo-3-methylbutanoic
acid
Valine
H
3
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H11002
H11001 HO
H11002
NH
2
H11001
H
2
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H11002
NH
2
(Principal form at pH 13)
H
3
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H11002
H11001 HO
H11002
NH
3
H11001
H11001
H
3
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H11002
H11001 H
2
O
NH
2
H11001
(Principal form at pH 9)
H
3
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H H11001 HO
H11002
NH
3
H11001
H11001
H
3
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H11002
H11001 H
2
O
NH
3
H11001
H11001
H
3
NCH
2
CH
2
CH
2
CH
2
CHCO
2
H
NH
3
H11001
H11001
(Principal form at pH 1)
H11002
OCH
2
CHCO
2
H11002
NH
2
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Valine has been prepared by this method. The Hell–Volhard–Zelinsky reaction was carried out in
88% yield, but reaction of the H9251-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 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% 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 S
N
2 type in-
volving 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% H11003 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.
H11001
O
O
O
Triketo form of
ninhydrin
O
NCHCO
2
H11002
R
O
ImineH9251-Amino acid
RCHCO
2
H11002
NH
3
H11001
HO
H11002
H
2
OH11001
O
O
O
Triketo form of
ninhydrin
Hydrated form of
ninhydrin
O
O
OH
OH
HBr, H
2
O
heat H11002CO
2
heat
2-Aminoisopropylmalonic
acid
Diethyl
acetamidoisopropylmalonate
CH(CH
3
)
2
CH
3
CNHC(CO
2
CH
2
CH
3
)
2
O
CH(CH
3
)
2
H
3
NC(CO
2
H)
2
H11001
Valine
CH(CH
3
)
2
H
3
NCHCO
2
H11002
H11001
NaOCH
2
CH
3
CH
3
CH
2
OH
H11001
Diethyl acetamidomalonate
CH
3
CNHCH(CO
2
CH
2
CH
3
)
2
O
Diethyl
acetamidoisopropylmalonate
CH(CH
3
)
2
CH
3
CNHC(CO
2
CH
2
CH
3
)
2
O
2-Bromopropane
(CH
3
)
2
CHBr
NH
3
HCN
1. H
3
O
H11001
, heat
2. HO
H11002
(CH
3
)
2
CHCHCO
2
H11002
NH
3
H11001
2-Methylpropanal Valine
(CH
3
)
2
CHCH
O
2-Amino-3-
methylbutanenitrile
(CH
3
)
2
CHCHC N
NH
2
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 755
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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 H9251 carbon of an
H9251-amino acid.
arises by decarboxylation ofCH
2
CH
2
CH
2
CO
2
H11002
NH
3
H11001
4-Aminobutanoic acid
H11002
O
2
CCHCH
2
CH
2
CO
2
H11002
NH
3
H11001
Glutamic acid
H11001 H
2
O
O
O H11002
N
H
O
O
OH
H11002
Violet dye
O
O
N
O
O
H11001
O
O
O
O
O
NH
2
H
O
O
N
H
O
O
H11001 H
2
O
O
O
NH
2
H
H11001 RCH
O
O
O
H
CHRN
H11001
O
NH
2
O
H11002
O
CHR
H11001
H11002
OH
O
O
H
CHRN
O
N H11001
O
CH C
R
O
H11002
O
CO
2
O
N
H11002
O
CHR
756 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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27.10 (b) Alanine is the N-terminal amino acid in Ala-Phe. Its carboxyl group is joined to the nitrogen
of phenylalanine by a peptide bond.
(c) The positions of the amino acids are reversed in Phe-Ala. Phenylalanine is the N terminus and
alanine is the C terminus.
(d) The carboxyl group of glycine is joined by a peptide bond to the amino group of glutamic
acid.
The dipeptide is written in its anionic form because the carboxyl group of the side chain is
ionized at pH 7. Alternatively, it could have been written as a neutral zwitterion with a
CH
2
CH
2
CO
2
H side chain.
(e) The peptide bond in Lys-Gly is between the carboxyl group of lysine and the amino group of
glycine.
The amino group of the lysine side chain is protonated at pH 7, and so the dipeptide is written
here in its cationic form. It could have also been written as a neutral zwitterion with the side
chain H
2
NCH
2
CH
2
CH
2
CH
2
.
( f ) Both amino acids are alanine in D-Ala-D-Ala. The fact that they have the D configuration has
no effect on the constitution of the dipeptide.
NHCHCO
2
H11002
d-A-d-A
CH
3
H
3
NCHC
CH
3
O
H11001
Alanine Alanine
H
3
NCHC KG
H
3
NCH
2
CH
2
CH
2
CH
2
O
H11001
H11001
Lysine
NHCH
2
CO
2
H11002
Glycine
H
3
NCH
2
C NHCHCO
2
H11002
GE
CH
2
CH
2
CO
2
H11002
O
H11001
Glycine Glutamic acid
FAH
3
NCHC
C
6
H
5
CH
2
O
H11001
Phenylalanine
NHCHCO
2
H11002
CH
3
Alanine
AFH
3
NCHC
CH
3
O
H11001
Alanine
NHCHCO
2
H11002
CH
2
C
6
H
5
Phenylalanine
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 757
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27.11 (b) When amino acid residues in a dipeptide are indicated without a prefix, it is assumed that the
configuration at the H9251 carbon atom is L. For all amino acids except cysteine, the L configura-
tion corresponds to S. The stereochemistry of Ala-Phe may therefore be indicated for the
zigzag conformation as shown.
The L configuration corresponds to S for each of the stereogenic centers in Ala-Phe.
(c) Similarly, Phe-Ala has its substituent at the N-terminal amino acid directed away from us,
whereas the C-terminal side chain is pointing toward us, and the L configuration corresponds
to S for each stereogenic center.
(d) There is only one stereogenic center in Gly-Glu. It has the L (or S) configuration.
(e) In order for the N-terminal amino acid in Lys-Gly to have the L (or S) configuration, its side
chain must be directed away from us in the conformation indicated.
( f ) The configuration at both H9251-carbon atoms in D-Ala-D-Ala is exactly the reverse of the config-
uration of the stereogenic centers in parts (a) through (e). Both stereogenic centers have the D
(or R) configuration.
27.12 Figure 27.7 in the text gives the structure of leucine enkephalin. Methionine enkephalin differs from
it only with respect to the C-terminal amino acid. The amino acid sequences of the two pentapep-
tides are
The peptide sequence of a polypeptide can also be expressed using the one-letter abbreviations
listed in text Table 27.1. Methionine enkephalin becomes YGGFM.
Tyr-Gly-Gly-Phe-Leu
Leucine enkephalin
Tyr-Gly-Gly-Phe-Met
Methionine enkephalin
H
3
N
H
O
N
H
H
CH
3
CH
3
H11001
CO
2
H11002
H
3
N
H
3
NCH
2
CH
2
CH
2
CH
2
O
N
H
H
H11001
H11001
CO
2
H11002
H
3
N
CH
2
CH
2
CO
2
H11002
O
N
H
H
H11001
CO
2
H11002
H
3
N
C
6
H
5
CH
2
H
3
C
O
N
H
H
H
H11001
CO
2
H11002
H
3
N
H
3
C
O
N
H
H
H
H11001
CO
2
H11002
CH
2
C
6
H
5
758 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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27.13 Twenty-four tetrapeptide combinations are possible for the four amino acids alanine (A), glycine
(G), phenylalanine (F), and valine (V). Remember that the order is important; AG is not the same
peptide as GA. Using the one-letter abbreviations for each amino acid the possibilities are
AGFV AGVF AFGV AFVG AVGF AVFG
GAFV GAVF GFAV GFVA GVFA GVAF
FAGV FAVG FVAG FVGA FGAF FGFA
VAGF VAFG VGAF VGFA VFAG VFGA
27.14 Chymotrypsin cleaves a peptide selectively at the carboxyl group of amino acids that have aromatic
side chains. The side chain of phenylalanine is a benzyl group, C
6
H
5
CH
2
—
. If the dipeptide isolated
after treatment with chymotrypsin contains valine (V) and phenylalanine (F), its sequence must
be VF.
The possible sequences for the unknown tetrapeptide are VFAG and VFGA.
27.15 The Edman degradation removes the N-terminal amino acid, which is identified as a phenylthiohy-
dantoin derivative. The first Edman degradation of Val-Phe-Gly-Ala gives the phenylthiohydantoin
derived from valine; the second gives the phenylthiohydantoin derived from phenylalanine.
27.16 Lysine has two amino groups. Both amino functions are converted to amides on reaction with
benzyloxycarbonyl chloride.
27.17 The peptide bond of Ala-Leu connects the carboxyl group of alanine and the amino group of leucine.
We therefore need to protect the amino group of alanine and the carboxyl group of leucine.
Protect the amino group of alanine as its benzyloxycarbonyl derivative.
H11001H
3
NCHCO
2
H11002
CH
3
H11001
Alanine
C
6
H
5
CH
2
OCCl
O
Benzyloxycarbonyl
chloride
C
6
H
5
CH
2
OCNHCHCO
2
H
CH
3
O
Z-Protected alanine
O
H
2
NCHCO
2
H11002
2C
6
H
5
CH
2
OCCl
O
O
C
6
H
5
CH
2
OCNHCHCO
2
H
C
6
H
5
CH
2
OCNHCH
2
CH
2
CH
2
CH
2
H11001
H
2
NCH
2
CH
2
CH
2
CH
2
Val-Phe-Gly-Ala Phe-Gly-Ala
first
Edman degradation
second
Edman degradation
H11001
S
HN
CH(CH
3
)
2
O
Gly-Ala H11001
S
HN
CH
2
C
6
H
5
O
N
C
6
H
5
N
C
6
H
5
CH
2
C
6
H
5
NHCHC
O
H
3
NCHC
H11001
O
(CH
3
)
2
CH
Valine Phenylalanine
CH
2
C
6
H
5
NHCHCO
H11002
O
H
3
NCHC
H11001
O
(CH
3
)
2
CH
Valinylphenylalanine (VF)
Rest of peptide Rest of peptide
chymotrypsin
H11001
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 759
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Protect the carboxyl group of leucine as its benzyl ester.
Coupling of the two amino acids is achieved by N,N′-dicyclohexylcarbodiimide (DCCI)-promoted
amide bond formation between the free amino group of leucine benzyl ester and the free carboxyl
group of Z-protected alanine.
Both the benzyloxycarbonyl protecting group and the benzyl ester protecting group may be removed
by hydrogenolysis over palladium. This step completes the synthesis of Ala-Leu.
27.18 As in the DCCI-promoted coupling of amino acids, the first step is the addition of the Z-protected
amino acid to DCCI to give an O-acylisourea.
This O-acylisourea is attacked by p-nitrophenol to give the p-nitrophenyl ester of the Z-protected
amino acid.
27.19 To add a leucine residue to the N terminus of the ethyl ester of Z-Phe-Gly, the benzyloxycarbonyl
protecting group must first be removed. This can be accomplished by hydrogenolysis.
C
6
H
5
CH
2
OCNHCHCNHCH
2
COCH
2
CH
3
H
2
NCHCNHCH
2
COCH
2
CH
3
C
6
H
5
CH
2
O O O O O
C
6
H
5
CH
2
H
2
, Pd
Z-Protected ethyl ester of Phe-Gly Phe-Gly ethyl ester
O
2
N O
2
NOH H11001H11001RH11032CO
O
C
NHC
6
H
11
NC
6
H
11
H
H11001
OCRH11032 C
6
H
11
NHCNHC
6
H
11
O O
H11001
Z-Protected
amino acid
R
ZNHCHCOH
O
DCCI
C
6
H
11
NCNC
6
H
11
O-Acylisourea
R
ZNHCHCO
O
C
NC
6
H
11
NHC
6
H
11
Ala-Leu
H11001
CH
3
CH
2
CH(CH
3
)
2
H
3
NCHCNHCHCO
2
H11002
O
H
2
, Pd
Protected dipeptide
CH
3
CH
2
CH(CH
3
)
2
C
6
H
5
CH
2
OCNHCHCNHCHCOCH
2
C
6
H
5
O O O
H11001
Z-Protected alanine
C
6
H
5
CH
2
OCNHCHCO
2
H
CH
3
O
Leucine benzyl ester
(CH
3
)
2
CHCH
2
H
2
NCHCOCH
2
C
6
H
5
O
DCCI
Protected dipeptide
CH
3
CH
2
CH(CH
3
)
2
C
6
H
5
CH
2
OCNHCHCNHCHCOCH
2
C
6
H
5
O O O
H11001H
3
NCHCO
2
H11002
(CH
3
)
2
CHCH
2
H11001
Leucine
C
6
H
5
CH
2
OH
Benzyl alcohol
(CH
3
)
2
CHCH
2
H
2
NCHCO
2
CH
2
C
6
H
5
Leucine benzyl ester
1. H
H11001
, heat
2. HO
H11002
760 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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The reaction shown has been carried out in 100% yield. Alternatively, the benzyloxycarbonyl
protecting group may be removed by treatment with hydrogen bromide in acetic acid. This latter
route has also been reported in the chemical literature and gives the hydrobromide salt of Phe-Gly
ethyl ester in 82% yield.
Once the protecting group has been removed, the ethyl ester of Phe-Gly is allowed to react with
the p-nitrophenyl ester of Z-protected leucine to form the protected tripeptide. Hydrogenolysis of
the Z-protected tripeptide gives Leu-Phe-Gly as its ethyl ester.
27.20 Amino acid residues are added by beginning at the C terminus in the Merrifield solid-phase
approach to peptide synthesis. Thus the synthesis of Phe-Gly requires glycine to be anchored to the
solid support. Begin by protecting glycine as its tert-butoxycarbonyl (Boc) derivative.
The protected glycine is attached via its carboxylate anion to the solid support.
(CH
3
)
3
COCNHCH
2
CO
2
H
O
(CH
3
)
3
COCNHCH
2
COCH
2
resin
O O
Boc-Protected glycine
1. HO
H11002
2. ClCH
2
resin
(CH
3
)
3
COCCl (CH
3
)
3
COCNHCH
2
CO
2
HH
3
NCH
2
CO
2
H11002
O
H11001
O
H11001
tert-Butoxycarbonyl
chloride
Glycine Boc-Protected glycine
Z-protected Leu-Phe-Gly ethyl ester
NO
2
H11001C
6
H
5
CH
2
OCNHCHCO
(CH
3
)
2
CHCH
2
O O
H
2
NCHCNHCH
2
COCH
2
CH
3
O O
C
6
H
5
CH
2
p-Nitrophenyl ester of
Z-protected leucine
Phe-Gly ethyl ester
C
6
H
5
CH
2
OCNHCHCNHCHCNHCH
2
COCH
2
CH
3
(CH
3
)
2
CHCH
2
O O
CH
2
C
6
H
5
O O
Leu-Phe-Gly ethyl ester
H
2
NCHCNHCHCNHCH
2
COCH
2
CH
3
(CH
3
)
2
CHCH
2
O O
CH
2
C
6
H
5
O
H
2
, Pd
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 761
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The amino group of glycine is then exposed by removal of the protecting group. Typical conditions
for this step involve treatment with hydrogen chloride in acetic acid.
To attach phenylalanine to resin-bound glycine, we must first protect the amino group of phenyl-
alanine. A Boc protecting group is appropriate.
Peptide bond formation occurs when the resin-bound glycine and Boc-protected phenylalanine are
combined in the presence of DCCI.
Remove the Boc group with HCl and then treat with HBr in trifluoroacetic acid to cleave Phe-Gly
from the solid support.
27.21 The numbering of the ring in uracil and its derivatives parallels that in pyrimidine.
Pyrimidine
1
2
3
4
5
6
N
N
Uracil
1
2
3
4
5
6
N
H
O
HN
O
5-Fluorouracil
5
N
H
F
O
HN
O
Boc-Protected, resin-bound Phe-Gly
(CH
3
)
3
COCNHCHCNHCH
2
COCH
2
O O O O
CH
2
C
6
H
5
resin
1. HCl, acetic acid
2. HBr, trifluoroacetic acid
H
3
NCHCNHCH
2
CO
2
H11002
H11001
CH
2
C
6
H
5
Phe-Gly
(CH
3
)
3
COCNHCHCO
2
H H11001
O
Boc-Protected phenylalanine Boc-Protected, resin-bound Phe-Gly
CH
2
C
6
H
5
(CH
3
)
3
COCNHCHCNHCH
2
COCH
2
O O O
CH
2
C
6
H
5
H
2
NCH
2
COCH
2
resin
O
resin
DCCI
Resin-bound glycine
(CH
3
)
3
COCCl (CH
3
)
3
COCNHCHCO
2
HH
3
NCHCO
2
H11002
O
H11001
O
H11001
tert-Butoxycarbonyl
chloride
Phenylalanine Boc-Protected phenylalanine
CH
2
C
6
H
5
CH
2
C
6
H
5
(CH
3
)
3
COCNHCH
2
COCH
2
resin
O O
H
2
NCH
2
COCH
2
resin
O
HCl
acetic acid
Boc-Protected, resin-bound glycine Resin-bound glycine
762 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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27.22 (b) Cytidine is present in RNA and so is a nucleoside of D-ribose. The base is cytosine.
(c) Guanosine is present in RNA and so is a guanine nucleoside of D-ribose.
27.23 Table 27.4 in the text lists the messenger RNA codons for the various amino acids. The codons for
valine and for glutamic acid are:
Valine: GUU GUA GUC GUG
Glutamic acid: GAA GAG
As can be seen, the codons for glutamic acid (GAA and GAG) are very similar to two of the codons
(GUA and GUG) for valine. Replacement of adenine in the glutamic acid codons by uracil causes
valine to be incorporated into hemoglobin instead of glutamic acid and is responsible for the sickle
cell trait.
27.24 The protonated form of imidazole represented by structure A is stabilized by delocalization of the
lone pair of one of the nitrogens. The positive charge is shared by both nitrogens.
The positive charge in structure B is localized on a single nitrogen. Resonance stabilization of the
type shown in structure A is not possible.
Structure A is the more stable protonated form.
B
N
HN
CH
2
CHC
NH
O
H11001
H
H
H
N
HN
CH
2
CHC
NH
O
H11001
H
N
HN
CH
2
CHC
NH
O
H11001
A
H
HOCH
2
H
HH
OH OH
O
N
N
N
H
2
N
HN
O
H
HOCH
2
H
HH
OH OH
O
N
NH
2
O
N
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 763
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27.25 The following outlines a synthesis of H9252-alanine in which conjugate addition to acrylonitrile plays a
key role.
Addition of ammonia to acrylonitrile has been carried out in modest yield (31–33%). Hydrolysis of
the nitrile group can be accomplished in the presence of either acids or bases. Hydrolysis in the pres-
ence of Ba(OH)
2
has been reported in the literature to give H9252-alanine in 85–90% yield.
27.26 (a) The first step involves alkylation of diethyl malonate by 2-bromobutane.
In the second step of the synthesis, compound A is subjected to ester saponification. Follow-
ing acidification, the corresponding diacid (compound B) is isolated.
Compound B is readily brominated at its H9251-carbon atom by way of the corresponding enol
form.
When compound C is heated, it undergoes decarboxylation to give an H9251-bromo carboxylic acid.
Treatment of compound D with ammonia converts it to isoleucine by nucleophilic substitution.
NH
3
H11001
CH
3
CH
3
CH
2
CH CHCO
2
H
Br
Compound D
CH
3
CH
2
CH CHCO
2
H11002
CH
3
NH
3
H11001
Isoleucine (racemic)
H11001CHCOOHCH
3
CH
2
CH
CH
3
Br
CH
3
CH
2
CH
Br
C(COOH)
2
CH
3
Compound C Compound D
CO
2
Carbon
dioxide
heat
OHCHO
CH
3
CH
2
CH
H
C
O
C
O
CH
3
Compound B
OH
H
CHO
O
CC
O
CH
3
CH
2
CH
CH
3
Enol form
OHC
Br
O
C
O
C
HO
CH
3
CH
2
CH
CH
3
Compound C
(C
7
H
11
BrO
4
)
Br
2
CH
3
CH
2
CHCH(COOCH
2
CH
3
)
2
CH
3
Compound A
CH
3
CH
2
CHCH(COOH)
2
CH
3
Compound B (C
7
H
12
O
4
)
1. KOH
2. HCl
H11001CH
3
CH
2
CHCH
3
Br
CH(COOCH
2
CH
3
)
2
H11002
CH
3
CH
2
CHCH(COOCH
2
CH
3
)
2
CH
3
2-Bromobutane Anion of diethyl malonate Compound A
NH
3
H
2
O, HO
H11002
heat
H
2
C CHC N
Acrylonitrile
H
2
NCH
2
CH
2
CN
3-Aminopropanenitrile
H
3
NCH
2
CH
2
CO
2
H11002
H11001
H9252-Alanine
764 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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(b) The procedure just described can be adapted to the synthesis of other amino acids. The group
attached to the H9251-carbon atom is derived from the alkyl halide used to alkylate diethyl
malonate. Benzyl bromide (or chloride or iodide) would be appropriate for the preparation of
phenylalanine.
27.27 Acid hydrolysis of the triester converts all its ester functions to free carboxyl groups and cleaves
both amide bonds.
The hydrolysis product is a substituted derivative of malonic acid and undergoes decarboxylation
on being heated. The product of this decarboxylation is aspartic acid (in its protonated form under
conditions of acid hydrolysis).
Aspartic acid is chiral, but is formed as a racemic mixture, so the product of this reaction is not
optically active. The starting triester is achiral and cannot give an optically active product when it
reacts with optically inactive reagents.
27.28 The amino acids leucine, phenylalanine, and serine each have one stereogenic center.
When prepared by the Strecker synthesis, each of these amino acids is obtained as a racemic mix-
ture containing 50% of the D enantiomer and 50% of the L enantiomer.
Thus, preparation of the tripeptide Leu-Phe-Ser will yield a mixture of 2
3
(eight) stereoisomers.
D-Leu-D-Phe-D-Ser L-Leu-L-Phe-L-Ser
D-Leu-D-Phe-L-Ser L-Leu-L-Phe-D-Ser
D-Leu-L-Phe-D-Ser L-Leu-D-Phe-L-Ser
D-Leu-L-Phe-L-Ser L-Leu-D-Phe-D-Ser
H
2
O, H
H11001
heat
H11001
RCHCO
2
H11002
NH
3
NH
2
NH
3
RCH HCN RCHC NH11001H11001
Chiral, but
racemic
O
H11001
RCHCO
2
H11002
Leucine:
Phenylalanine:
Serine:
NH
3
R H11005 (CH
3
)
2
CHCH
2
R H11005 C
6
H
5
CH
2
R H11005 HOCH
2
heat
H
3
N H11001
H11001
CH
2
COOH
C(COOH)
2
H
3
N
H11001
CH
2
COOH
CHCOOH
Aspartic acid
CO
2
Carbon
dioxide
O
O
CH
2
COOCH
2
CH
3
C(COOCH
2
CH
3
)
2
H
H11001
5H
2
OH
3
NH11001H11001
H11001
N
CH
2
COOH
C
O
OH
COH
O
C(COOH)
2
C
6
H
5
CH
2
Br
Benzyl bromide Phenylalanine
(racemic)
C
6
H
5
CH
2
CHCO
2
H11002
NH
3
H11001
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 765
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27.29 Bradykinin is a nonapeptide but contains only five different amino acids. Three of the amino acid
residues are proline, two are arginine, and two are phenylalanine. Five peaks will appear on the strip
chart after amino acid analysis of bradykinin.
27.30 Asparagine and glutamine each contain an amide function in their side chain. Under the conditions
of peptide bond hydrolysis that characterize amino acid analysis, the side-chain amide is also
hydrolyzed, giving ammonia.
27.31 (a) 1-Fluoro-2,4-dinitrobenzene reacts with the amino group of the N-terminal amino acid in a
nucleophilic aromatic substitution reaction of the addition–elimination type.
(b) Hydrolysis of the product in part (a) cleaves the peptide bonds. Leucine is isolated as its 2,4-
dinitrophenyl (DNP) derivative, but glycine and serine are isolated as the free amino acids.
DNP-Leu-Gly-Ser
NHCHCNHCH
2
CNHCHCO
2
H
O O
CH
2
OH(CH
3
)
2
CHCH
2
O
2
N
NO
2
H11001H11001 H
3
NCH
2
CO
2
H11002
H11001
Gly
CH
2
OH
H
3
NCHCO
2
H11002
H11001
SerDNP-Leu
NHCHCOH
O
(CH
3
)
2
CHCH
2
O
2
N
NO
2
hydrolysis
H11001 H
3
NCHCNHCH
2
CNHCHCO
2
H11002
O O
CH
2
OH(CH
3
)
2
CHCH
2
H11001
Leu-Gly-Ser1-Fluoro-2,4-
dinitrobenzene
O
2
N F
NO
2
DNP-Leu-Gly-Ser
NHCHCNHCH
2
CNHCHCO
2
H
O O
CH
2
OH(CH
3
)
2
CHCH
2
O
2
N
NO
2
H11001H
2
NCCH
2
CH
2
CHCO
2
H11002
O
NH
3
H11001
Glutamine
H
2
O
Water
H11001NH
3
Ammonia
HOCCH
2
CH
2
CHCO
2
H11002
O
NH
3
H11001
Glutamic acid
H11001H
2
NCCH
2
CHCO
2
H11002
O
NH
3
H11001
Asparagine
H
2
O
Water
H11001NH
3
Ammonia
HOCCH
2
CHCO
2
H11002
O
NH
3
H11001
Aspartic acid
Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg 2Arg H11001 3Pro H11001 Gly H11001 2Phe H11001 Ser
766 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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(c) Phenyl isothiocyanate is a reagent used to identify the N-terminal amino acid of a peptide by
the Edman degradation. The N-terminal amino acid is cleaved as a phenylthiohydantoin
(PTH) derivative, the remainder of the peptide remaining intact.
(d) Benzyloxycarbonyl chloride reacts with amino groups to convert them to amides. The only
free amino group in Asn-Ser-Ala is the N terminus. The amide function of asparagine does not
react with benzyloxycarbonyl chloride.
(e) The Z-protected tripeptide formed in part (d) is converted to its C-terminal p-nitrophenyl
ester on reaction with p-nitrophenol and N,N′-dicyclohexylcarbodiimide (DCCI).
H11001
p-Nitrophenol
OHO
2
N
Z-Asn-Ser-Ala
C
6
H
5
CH
2
OCNHCHCNHCHCNHCHCO
2
H
CH
2
O O O
C
O NH
2
CH
2
OH
CH
3
DCCI
Z-Asn-Ser-Ala p-nitrophenyl ester
NO
2
C
6
H
5
CH
2
OCNHCHCNHCHCNHCHCO
CH
2
O O O
C
O NH
2
CH
2
OH
CH
3
O
H11001
Benzyloxycarbonyl
chloride
C
6
H
5
CH
2
OCCl
O
Asn-Ser-Ala
CH
2
CH
2
OH
CH
3
H
3
NCHCNHCHCNHCHCO
2
H11002
H11001
O O
Z-Asn-Ser-Ala
C
6
H
5
CH
2
OCNHCHCNHCHCNHCHCO
2
H
O O O
CH
2
CH
2
OH
CH
3
C
O NH
2
C
O NH
2
Ile-Glu-Phe
CH
3
CH
2
CH CH
2
CH
2
CO
2
HCH
3
CH
2
C
6
H
5
H
3
NCHCNHCHCNHCHCO
2
H11002
H11001
O O
1. C
6
H
5
N
2. HBr, nitromethane
C S
H11001
Glu-Phe
H
3
NCHCNHCHCO
2
H11002
H11001
CH
2
CH
2
CO
2
H
CH
2
C
6
H
5
O
PTH derivative of
isoleucine
CHCH
2
CH
3
CH
3
S O
N
C
6
H
5
HN
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 767
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( f ) The p-nitrophenyl ester prepared in part (e) is an “active” ester. The p-nitrophenyl group is a
good leaving group and can be displaced by the amino nitrogen of valine ethyl ester to form a
new peptide bond.
(g) Hydrogenolysis of the Z-protected tetrapeptide ester formed in part ( f ) removes the
Z protecting group.
27.32 Consider, for example, the reaction of hydrazine with a very simple dipeptide such as Gly-Ala.
Hydrazine cleaves the peptide by nucleophilic attack on the carbonyl group of glycine.
It is the C-terminal residue that is cleaved as the free amino acid and identified in the hydrazinoly-
sis of peptides.
NHCHCO
2
H11002
H11001H11001H
2
NNH
2
H
3
NCH
2
C
H11001
H
3
NCHCO
2
H11002
H11001
O
H
2
NCH
2
CNHNH
2
O
CH
3
CH
3
Gly-Ala Hydrazine Hydrazide of glycine Alanine
H
2
,
Pd
Z-Asn-Ser-Ala-Val ethyl ester
C
6
H
5
CH
2
OCNHCHCNHCHCNHCHCNHCHCOCH
2
CH
3
O
CH
2
O O O O
CH
2
CH
3
CH(CH
3
)
2
OHC
O NH
2
Asn-Ser-Ala-Val ethyl ester
H
2
NCHCNHCHCNHCHCNHCHCOCH
2
CH
3
CH
2
O O O O
CH
2
CH
3
CH(CH
3
)
2
OHC
O NH
2
H11001
Valine ethyl ester
H
2
NCHCOCH
2
CH
3
O
CH(CH
3
)
2
NO
2
Z-Asn-Ser-Ala p-nitrophenyl ester
C
6
H
5
CH
2
OCNHCHCNHCHCNHCHCO
CH
2
O O O
C
O NH
2
CH
2
OH
CH
3
O
Z-Asn-Ser-Ala-Val ethyl ester
C
6
H
5
CH
2
OCNHCHCNHCHCNHCHCNHCHCOCH
2
CH
3
CH
2
O O O O
C
O NH
2
CH
2
OH
CH
3
CH(CH
3
)
2
O
768 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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27.33 Somatostatin is a tetradecapeptide and so is composed of 14 amino acids. The fact that Edman
degradation gave the PTH derivative of alanine identifies this as the N-terminal amino acid.
A major piece of information is the amino acid sequence of a hexapeptide obtained by partial
hydrolysis:
Ala-Gly-Cys-Lys-Asn-Phe
Using this as a starting point and searching for overlaps with the other hydrolysis products gives the
entire sequence.
Ala-Gly-Cys-Lys-Asn-Phe
Asn-Phe-Phe-Trp-Lys
Phe-Trp
Lys-Thr-Phe
Thr-Phe-Thr-Ser-Cys
Thr-Ser-Cys
Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys
123456789101121314
The disulfide bridge in somatostatin is between cysteine 3 and cysteine 14. Thus, the primary struc-
ture is
27.34 It is the C-terminal amino acid that is anchored to the solid support in the preparation of peptides
by the Merrifield method. Refer to the structure of oxytocin in Figure 27.8 of the text and note that
oxytocin, in fact, has no free carboxyl groups; all the acyl groups of oxytocin appear as amide
functions. Thus, the carboxyl terminus of oxytocin has been modified by conversion to an amide.
There are three amide functions of the type , two of which belong to side chains of as-
paragine and glutamine, respectively. The third amide belongs to the C-terminal amino acid, glycine,
, which in oxytocin has been modified so that it appears as . There-
fore, attach glycine to the solid support in the first step of the Merrifield synthesis. The carboxyl
group can be modified to the required amide after all the amino acid residues have been added and
the completed peptide is removed from the solid support.
27.35 Purine and its numbering system are as shown:
N
N
N
N
H
1
2
3
4
5
6
7
8
9
NHCH
2
CNH
2
O
NHCH
2
COH
O
CNH
2
O
Ala-Gly-Cys
S-S-Cys-Ser-Thr-Phe-Thr
Lys-Asn-Phe-Phe-Trp-Lys
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 769
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In nebularine, D-ribose in its furanose form is attached to position 9 of purine. The stereochemistry
at the anomeric position is H9252.
27.36 The problem states that vidarabine is the arabinose analog of adenosine. Arabinose and ribose differ
only in their configuration at C-2.
27.37 Nucleophilic aromatic substitution occurs when 6-chloropurine reacts with hydroxide ion by an
addition–elimination pathway.
The enol tautomerizes to give hypoxanthine.
N
H
N
N
N
OH
Hypoxanthine
N
H
N
N
N
O
H
H
2
O
heat
H11001 HO
H11002
N
N
N
N
H
OHCl
H11002
N
N
N
N
H
OH
N
N
N
N
H
Cl
6-Chloropurine
Adenosine
H
HOCH
2
H
HH
OH OH
O
N
N
N
N
NH
2
Vidarabine
H
HOCH
2
H
HHO
OH H
O
N
N
N
N
NH
2
H
HOCH
2
H
HH
OH OH
O
N
N
N
N
9-H9252-d-Ribofuranosylpurine
(nebularine)
770 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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27.38 Nitrous acid reacts with aromatic primary amines to yield diazonium ions.
Treatment of the diazonium ion with water yields a phenol. Tautomerization gives inosine.
27.39 The carbon atoms of the ribose portion of a nucleoside are numbered as follows:
(a)A5′-nucleotide has a phosphate group attached to the C-5′ hydroxyl.
Inosinic acid
H
OCH
2
P
O
OH
HO
H
HH
OH OH
O
N
N
N
NH
O
H
HOCH
2
H
HH
OH OH
O
1H110324H11032
5H11032
2H110323H11032
H
HOCH
2
H
HH
OH OH
O
N
N
N
N
OH
H
2
O
Inosine
H
HOCH
2
H
HH
OH OH
O
N
N
N
N
N
2
H11001
H
HOCH
2
H
HH
OH OH
O
N
N
NH
N
O
H
HOCH
2
H
HH
OH OH
O
N
N
N
N
NH
2
Adenosine
HONO, H
H11001
H
HOCH
2
H
HH
OH OH
O
N
N
N
N
N
2
H11001
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 771
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(b) Deoxy nucleosides have hydrogens in place of hydroxyl groups at the positions indicated with
boldface.
27.40 All the bases in the synthetic messenger RNA prepared by Nirenberg were U; therefore, the codon
is UUU. By referring to the codons in Table 27.4, we see that the UUU codes for phenylalanine.
A polypeptide in which all the amino acid residues were phenylalanine was isolated in Nirenberg’s
experiment.
SELF-TEST
PART A
A-1. Give the structure of the reactant, reagent, or product omitted from each of the following:
A-2. Give the structure of the derivative that would be obtained by treatment of Phe-Ala with
Sanger’s reagent followed by hydrolysis.
A-3. Outline a sequence of steps that would allow the following synthetic conversions to be car-
ried out:
Leu-Val from leucine and (CH
3
)
2
CHCHCO
2
H11002
(valine)(b)
NH
3
H11001
(CH
3
)
2
CHCH
2
CHCO
2
H11002
(leucine) from CH
3
CNHCH(CO
2
CH
2
CH
3
)
2
(a)
ONH
3
H11001
Boc-Phe H
2
NCH
2
CO
2
CH
2
CH
3
H11001(c)
?
Boc NHCHCNHCH
2
CO
2
CH
2
CH
3
CH
2
C
6
H
5
O
C
6
H
5
CH
2
OCCl ?valineH11001(b)
1. HO
H11002
, H
2
O
2. H
H11001
O
C
6
H
5
CH
2
CHCO
2
H11002
?(a)
1. NH
4
Cl, NaCN
2. H
3
O
H11001
, heat
3. neutralize
NH
3
H11001
2H11032,3H11032-Dideoxyinosine
H
HOCH
2
H
HH
HH
O
N
N
N
NH
O
772 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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A-4. The carboxypeptidase-catalyzed hydrolysis of a pentapeptide yielded phenylalanine (Phe).
One cycle of an Edman degradation gave a derivative of leucine (Leu). Partial hydrolysis
yielded the fragments Leu-Val-Gly and Gly-Ala among others. Deduce the structure of the
peptide.
A-5. Consider the following compound:
(a) What kind of peptide does this structure represent? (For example, dipeptide)
(b) How many peptide bonds are present?
(c) Give the name for the N-terminal amino acid.
(d ) Give the name for the C-terminal amino acid.
(e) Using three-letter abbreviations, write the sequence.
A-6. Consider the tetrapeptide Ala-Gly-Phe-Leu. What are the products obtained from each of the
following? Be sure to account for all the amino acids of the peptide.
(a) Treatment with 1-fluoro-2,4-dinitrobenzene followed by hydrolysis in concentrated
HCl at 100°C.
(b) Treatment with chymotrypsin.
(c) Treatment with carboxypeptidase
(d ) Reaction with benzyloxycarbonyl chloride
PART B
B-1. Which phrase correctly completes the statement?
Except for glycine, which is achiral, all the amino acids present in proteins …
(a) are chiral, but racemic
(b) are meso forms
(c) have the L configuration at their H9251 carbon
(d) have the R configuration at their H9251 carbon
(e) have the S configuration at their H9251 carbon
B-2. Which statement correctly describes the difference in the otherwise similar chemical con-
stituents of DNA and RNA?
(a) DNA contains uracil; RNA contains thymine.
(b) DNA contains guanine but not adenine; RNA contains both.
(c) DNA contains thymine; RNA contains uracil.
(d) None of these applies—the chemical constitution is the same.
B-3. Assume that a particular amino acid has an isoelectric point of 6.0. In a solution of pH 1.0,
which of the following species will predominate?
(a)(c)
(b)
(d) H
2
NCHCO
2
H11002
R
H
2
NCHCO
2
H
R
H
3
NCHCO
2
H11002
R
H11001
H
3
NCHCO
2
H
R
H11001
H
HOCH
2
CH
3
CH
2
H HH
CH(CH
3
)
2
H
3
N
CO
2
H11002
H
H CH
2
H
N
H
N
N
H
N
H
O
OO
O
H11001
AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS 773
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B-4. Choose the response which provides the best match of terms.
Purine Pyrimidine
(a) Adenine Guanine
(b) Thymine Cytosine
(c) Cytosine Adenine
(d) Guanine Cytosine
B-5. Which of the following reagents would be combined in the synthesis of Phe-Ala?
H20841
R
[In phenylalanine (Phe), R in the generalized amino acid formula H
2
NCHCO
2
H is CH
2
C
6
H
5
,
and in alanine (Ala) it is CH
3
.]
1. 2.
3. 4.
(a) 1 and 2 (b) 1 and 4 (c) 2 and 3 (d) 3 and 4
B-6. A nucleoside is a
(a) Phosphate ester of a nucleotide
(b) Unit having a sugar bonded to a purine or pyrimidine base
(c) Chain whose backbone consists of sugar units connected by phosphate groups
(d) Phosphate salt of a purine or pyrimidine base
B-7. What are the products obtained following treatment of Ser-Tyr-Val-Ala with chymotrypsin?
(a) Serine H11001 Tyr-Val-Ala (d) Ser-Tyr-Val H11001 Alanine
(b) Ser-Tyr H11001 Valine H11001 Alanine (e) Serine H11001 Tyrosine H11001 Val-Ala
(c) Ser-Tyr H11001 Val-Ala
B-8. The first cycle of the Edman degradation of the tetrapeptide Gly-Ala-Ile-Leu would give a
PTH derivative of
(a) Glycine (c) Isoleucine
(b) Alanine (d) Leucine
H
2
NCHCO
2
CH
2
C
6
H
5
CH
2
C
6
H
5
ZNHCHCO
2
H
CH
2
C
6
H
5
H
2
NCHCO
2
CH
2
C
6
H
5
CH
3
ZNHCHCO
2
H
CH
3
774 AMINO ACIDS, PEPTIDES, AND PROTEINS. NUCLEIC ACIDS
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