.

S E C T I O N
Metabolism of Proteins &
VI Amino Acids

Biosynthesis of the C H A P T E R

Nutritionally Nonessential
Amino Acids
Victor W. Rodwell, PhD
OBJEC TIVES
After studying this chapter,
you should be able to:
27
■ Explain why the absence from the diet of certain amino acids that are present
in most proteins is not deleterious to human health.
■ Appreciate the distinction between the terms “essential” and “nutritionally
essential” amino acids, and identify the amino acids that are nutritionally
nonessential.
■ Name the intermediates of the citric acid cycle and of glycolysis that are
precursors of aspartate, asparagine, glutamate, glutamine, glycine, and serine.
■ Illustrate the key role of transaminases in amino acid metabolism.
■ Explain the process by which the 4-hydroxyproline and 5-hydroxylysine of
proteins such as collagen are formed.
■ Describe the clinical presentation of scurvy, and provide a biochemical
explanation for why a severe deprivation of vitamin C (ascorbic acid) results in
this nutritional disorder.
■ Appreciate that, despite the toxicity of selenium, selenocysteine is an essential
component of several mammalian proteins.
■ Define and outline the reaction catalyzed by a mixed-function oxidase.
■ Identify the role of tetrahydrobiopterin in tyrosine biosynthesis.
■ Indicate the role of a modified tRNA in the cotranslational insertion of
selenocysteine into proteins.

BIOMEDICAL IMPORTANCE nutritional and metabolic abnormalities. Both the nutritional

Amino acid deficiency states can result if nutritionally essen-
tial amino acids are absent from the diet, or are present in inad-
equate amounts. Examples in certain regions of West Africa
include kwashiorkor, which results when a child is weaned
onto a starchy diet poor in protein, and marasmus, in which
both caloric intake and specific amino acids are deficient.
Patients with short bowel syndrome unable to absorb suffi-
cient quantities of calories and nutrients suffer from significant
disorder scurvy, a dietary deficiency of vitamin C, and specific
genetic disorders are associated with an impaired ability of
connective tissue to form hydroxyproline and hydroxylysine.
The resulting conformational instability of collagen results in
bleeding gums, swelling joints, poor wound healing, and ulti-
mately in death. Menkes syndrome, characterized by kinky
hair and growth retardation, results from a dietary deficiency
of copper, an essential cofactor for the enzyme lysyl oxidase
that functions in formation of the covalent cross-links that

281
282 SECTION VI Metabolism of Proteins & Amino Acids

strengthen collagen fibers. Genetic disorders of collagen bio- TABLE 272 Enzymes Required for the Synthesis
synthesis include several forms of osteogenesis imperfecta, of Amino Acids from Amphibolic Intermediates
characterized by fragile bones, and Ehlers-Danlos syndrome, Number of Enzymes Required to Synthesize
a group of connective tissue disorders that result in mobile
joints and skin abnormalities due to defects in the genes that Nutritionally Essential Nutritionally Nonessential
encode enzymes including lysyl hydroxylase. Arga 7 Ala 1

His 6 Asp 1
NUTRITIONALLY ESSENTIAL & Thr 6 Asn b
1

NUTRITIONALLY NONESSENTIAL Met 5 (4 shared) Glu 1

AMINO ACIDS Lys 8 Gln a

1
c
Ile 8 (6 shared) Hyl 1
While often employed with reference to amino acids, the
terms “essential” and “nonessential” are misleading since all Val 6 (all shared) Hyp d
1
20 common amino acids are essential to ensure health. Of these Leu 7 (5 shared) Pro a
3
20 amino acids, 8 must be present in the human diet, and thus
Phe 10 Ser 3
are best termed “nutritionally essential.” The other 12 amino
acids are “nutritionally nonessential” since they need not be Trp 5 (8 shared) Glye 1
present in the diet (Table 27–1). The distinction between these 59 Cysf 2
two classes of amino acids was established in the 1930s by feed-
Tyrg 1
ing human subjects purified amino acids in place of protein.
Subsequent biochemical investigations revealed the reactions 17
and intermediates involved in the biosynthesis of all 20 amino a
From Glu, bFrom Asp, cFrom Lys, dFrom Pro, eFrom Ser, fFrom Ser plus S2-, gFrom Phe.
acids. Amino acid deficiency disorders are endemic in certain
regions of West Africa where diets rely heavily on grains that
are poor sources of tryptophan and lysine. These nutritional survival value than the ability to biosynthesize it. Why? If a
disorders include kwashiorkor, which results when a child is specific nutrient is present in the food, an organism that can
weaned onto a starchy diet poor in protein, and marasmus, in synthesize it will transfer to its progeny genetic information of
which both caloric intake and specific amino acids are deficient. negative survival value. The survival value is negative rather
than nil because ATP and nutrients are required to synthesize
Lengthy Metabolic Pathways Form the “unnecessary” DNA—even if specific encoded genes are no
longer expressed. The number of enzymes required by pro-
Nutritionally Essential Amino Acids
karyotic cells to synthesize the nutritionally essential amino
The existence of nutritional requirements suggests that depen- acids is large relative to the number of enzymes required
dence on an external supply of a given nutrient can be of greater to synthesize the nutritionally nonessential amino acids
(Table 27–2). This suggests a survival advantage in retaining
TABLE 271 Amino Acid Requirements of Humans the ability to manufacture “easy” amino acids while losing the
Nutritionally Essential Nutritionally Nonessential ability to make “difficult” amino acids. The metabolic path-
Argininea Alanine
ways that form the nutritionally essential amino acids occur
in plants and bacteria, but not in humans, and thus are not
Histidine Asparagine
discussed. This chapter addresses the reactions and interme-
Isoleucine Aspartate diates involved in the biosynthesis by human tissues of the
Leucine Cysteine 12 nutritionally nonessential amino acids and selected nutri-
Lysine Glutamate
tional and metabolic disorders associated with their metabolism.
Methionine Glutamine
Phenylalanine Glycine BIOSYNTHESIS OF THE
Threonine
Tryptophan
Hydroxyprolineb
Hydroxylysineb
NUTRITIONALLY NONESSENTIAL
Valine Proline AMINO ACIDS
Serine Glutamate
Tyrosine Glutamate, the precursor of the so-called “glutamate family” of
a
Nutritionally “semiessential.” Synthesized at rates inadequate to support growth amino acids, is formed by the reductive amidation of the citric
b
of children.
Not necessary for protein synthesis, but is formed during post-translational
acid cycle α-ketoglutarate, a reaction catalyzed by mitochon-
processing of collagen. drial glutamate dehydrogenase (Figure 27–1). The reaction
 CHAPTER 27 Biosynthesis of the Nutritionally Nonessential Amino Acids 283

–
O
O
O– –
O
NH3+
O–
Glutamate Dehydrogenase, Glutamine
Synthetase & Aminotransferases Play
O O O O
α-Ketoglutarate L-Glutamate
Central Roles in Amino Acid Biosynthesis
The combined action of the enzymes glutamate dehydro-
NH4+ H2O genase, glutamine synthetase, and the aminotransferases
(Figures 27–1, 27–2 and 27–4) converts inorganic ammonium
NAD(P)H+H+ NAD(P)+ ion into the α-amino nitrogen of amino acids.
FIGURE 271 The reaction catalyzed by glutamate
dehydrogenase (EC 1.4.1.3). Asparagine
The conversion of aspartate to asparagine, catalyzed by aspara-
NH3+ NH3+ gine synthetase, (Figure 27–5), resembles the glutamine syn-
–
O O– H2 N O–
thetase reaction (Figure 27–2), but glutamine, rather than
O O O O ammonium ion, provides the nitrogen. Bacterial asparagine
L-Glutamate L-Glutamine synthetases can, however, also use ammonium ion. The reac-
tion involves the intermediate formation of aspartyl phosphate
NH4+ (Figure 27–6). The coupled hydrolysis of PPi to Pi by pyrophos-
phatase, EC 3.6.1.1, ensures that the reaction is strongly favored.
Mg-ATP Mg-ADP + Pi

FIGURE 272 The reaction catalyzed by glutamine synthetase Serine

(EC 6.3.1.2).
Oxidation of the α-hydroxyl group of the glycolytic interme-
diate 3-phosphoglycerate, catalyzed by 3-phosphoglycerate
NH3+
–
dehydrogenase, converts it to 3-phosphohydroxypyruvate.
O3PO O–
Transamination and subsequent dephosphorylation then form
O O serine (Figure 27–7).
FIGURE 273 f-Glutamyl phosphate.
Glycine
strongly favors glutamate synthesis, which lowers the concen- Glycine aminotransferases can catalyze the synthesis of glycine
tration of cytotoxic ammonium ion. from glyoxylate and glutamate or alanine. Unlike most ami-
notransferase reactions, these strongly favor glycine synthesis.
Additional important mammalian routes for glycine formation
Glutamine are from choline (Figure 27–8) and from serine (Figure 27–9).
The amidation of glutamate to glutamine catalyzed by glu-
tamine synthetase, (Figure 27–2) involves the intermediate
formation of γ-glutamyl phosphate (Figure 27–3). Following
the ordered binding of glutamate and ATP, glutamate attacks
the γ-phosphorus of ATP, forming γ-glutamyl phosphate and + +
O NH 3 O NH 3
ADP. NH4+ then binds, and uncharged NH3 attacks γ-glutamyl O
–
O
–
phosphate. Release of Pi and of a proton from the γ-amino –
O H 2N
group of the tetrahedral intermediate then allows release of O O
the product, glutamine. L-Aspartate L-Asparagine

Alanine & Aspartate H2O + Gln Glu

Transamination of pyruvate forms alanine (Figure 27–4).

Similarly, transamination of oxaloacetate forms aspartate. Mg-ATP Mg-AMP + PPi

FIGURE 275 The reaction catalyzed by asparagine synthetase

O NH3+ (EC 6.3.5.4). Note similarities to and differences from the glutamine
– –
O O
synthetase reaction (Figure 27–2).
Pyruvate Alanine
O O

+
O NH 3
–
Glu or Asp α-Ketoglutarate or oxaloacetate O
–O PO
3
FIGURE 274 Formation of alanine by transamination of O
pyruvate. The amino donor may be glutamate or aspartate. The
other product thus is α-ketoglutarate or oxaloacetate. FIGURE 276 Aspartyl phosphate.
284 SECTION VI Metabolism of Proteins & Amino Acids

OH
O−
O Proline
NAD + O−
The initial reaction of proline biosynthesis converts the
O O O O
P P
γ-carboxyl group of glutamate to the mixed acid anhydride of
D-3-Phosphoglycerate Phosphohydroxy-
pyruvate
glutamate γ-phosphate (Figure 27-3). Subsequent reduction
forms glutamate γ-semialdehyde, which following spontaneous
α-AA
cyclization is reduced to l-proline (Figure 27–10).
α-KA

NH3+ NH3+
Cysteine
O − Pi H2O O− While not nutritionally essential, cysteine is formed from methi-
HO O P O O
onine, which is nutritionally essential. Following conversion of
O
L-Serine Phospho-L-serine

FIGURE 277 Serine biosynthesis. Oxidation of O−

3-phosphoglycerate is catalyzed by 3-phosphoglycerate dehydroge-
−O O +
nase (EC 1.1.1.95). Transamination converts phosphohydroxypyruvate NH3
to phosphoserine. Hydrolytic removal of the phosphoryl group cata- L-Glutamate
lyzed by phosphoserine hydrolase (EC 3.1.3.3) then forms L-serine. ATP

CH3 2H CH3 ADP

O
H3C N +
CH3 H3C N+ CH3
O−
−O P
Betaine aldehyde
NH3+
Choline 3 O
OH O O
Glutamate γ - phosphate
H 2O
NAD+ NADPH

H3C + CH3 CH3 Pi

[CH3]
N NADP+
H H3C N+ CH3
O−
O
O−
Dimethylglycine O Betaine O−
O
NH3+
O
[CH2O]
L-Glutamate
γ-semialdehyde

H + CH3 [CH2O] NH3+ H2O

N
H −
O− O O
Sarcosine Glycine O
O O−
FIGURE 278 Formation of glycine from choline. Catalysts NH+
include choline dehydrogenase (EC 1.1.91.1), betaine dehydrogenase 1− Pyrroline – 5 – carboxylate
(EC 1.2.1.8), betaine-homocysteine N-methyltransferase, sarcosine
NADPH
dehydrogenase (EC 1.5.8.3), and dimethylglycine dehydrogenase
(EC 1.5.99.2).

NADP+
Methylene O
H4 folate H4 folate

NH3+ O−
NH3+
NH2+
–
O O–

HO O L-Proline
O
Serine H2O Glycine FIGURE 2710 Biosynthesis of proline from glutamate.
Catalysts for these reactions are glutamate 5-kinase (EC 2.7.2.11),
FIGURE 279 Interconversion of serine and glycine, catalyzed glutamate semialdehyde dehydrogenase (EC 1.2.1.41), and pyrroline
by serine hydroxymethyltransferase (EC 2.1.2.1). The reaction is 5-carboxylate reductase (EC 1.5.1.2). Ring closure of glutamate semi-
freely reversible. (H4 folate, tetrahydrofolate.) aldehyde is spontaneous.
 CHAPTER 27 Biosynthesis of the Nutritionally Nonessential Amino Acids 285

NH3+ quantities of the nutritionally essential amino acid phenyl-

O− alanine, tyrosine is nutritionally nonessential. However,
HO O since the phenylalanine hydroxylase reaction is irreversible,
+ L-Serine dietary tyrosine cannot replace phenylalanine. Catalysis by
H3N+ S H
−O this mixed-function oxidase incorporates one atom of O2 into
H2O
NH3+
the para position of phenylalanine and reduces the other atom
O−
O to water. Reducing power, provided as tetrahydrobiopterin
L-Homocysteine derives ultimately from NADPH (Figure 27–12).
H3N+ S O
−O
H2O
O Hydroxyproline & Hydroxylysine
Cystathionine Hydroxyproline and hydroxylysine occur principally in col-
NH3+ lagen. Since there is no tRNA for either hydroxylated amino
O− acid, neither dietary hydroxyproline nor dietary hydroxy-
HS O lysine is incorporated during protein synthesis. Peptidyl
H3N+ OH hydroxyproline and hydroxylysine arise from proline and
−O L-Cysteine
lysine, but only after these amino acids have been incorpo-
+
O rated into peptides. Hydroxylation of peptidyl prolyl and pep-
L-Homoserine tidyl lysyl residues, catalyzed by prolyl hydroxylase and lysyl
hydroxylase of skin, skeletal muscle, and granulating wounds
FIGURE 2711 Conversion of homocysteine and serine to
homoserine and cysteine. The sulfur of cysteine derives from methi- requires, in addition to the substrate, molecular O2, ascorbate,
onine and the carbon skeleton from serine. The catalysts are cystathi- Fe2+, and α-ketoglutarate (Figure 27–13). For every mole of
onine ß-synthetase (EC 4.2.1.22) and cystathionine lyase (EC 4.4.1.1). proline or lysine hydroxylated, one mole of α-ketoglutarate
is decarboxylated to succinate. The hydroxylases are mixed-
methionine to homocysteine (see Figure 29–19), homocysteine function oxidases. One atom of O2 is incorporated into proline
and serine form cystathionine, whose hydrolysis forms cysteine or lysine, the other into succinate (Figure 27–13). A deficiency
and homoserine (Figure 27–11). of the vitamin C required for these two hydroxylases results in
scurvy, in which bleeding gums, swelling joints, and impaired
Tyrosine wound healing result from the impaired stability of collagen
Phenylalanine hydroxylase (EC 1.14.16.1) converts phenylala- (see Chapters 5 and 50).
nine to tyrosine (Figure 27–12). If the diet contains adequate
Valine, Leucine, & Isoleucine
NADP+ NADPH + H+
While leucine, valine, and isoleucine are all nutritionally
essential amino acids, tissue aminotransferases reversibly
Tetrahydro- Dihydro-
interconvert all three amino acids and their corresponding
biopterin biopterin α-keto acids. These α-keto acids thus can replace their amino
acids in the diet.
O2 H 2O

CH2 CH COO– CH2 CH COO−

+
Selenocysteine, the 21st Amino Acid
NH3 NH3+
HO While the occurrence of selenocysteine (Figure 27–14) in
L-Phenylalanine L-Tyrosine
proteins is uncommon, at least 25 human selenoproteins are
known. Selenocysteine is present at the active site of several
O OH
H H
N
N α-Ketoglutarate [18O] Succinate
OH
H 2N N N Fe2+
H H 18O
2
Ascorbate 18OH
Tetrahydrobiopterin
Pro Pro
FIGURE 2712 Conversion of phenylalanine to tyrosine by
phenylalanine hydroxylase (EC 1.14.16.1). Two distinct enzymatic FIGURE 2713 Hydroxylation of a proline-rich peptide.
activities are involved. Activity II catalyzes reduction of dihydrobiop- Molecular oxygen is incorporated into both succinate and proline.
terin by NADPH, and activity I the reduction of O2 to H2O and of phe- Peptidyl prolyl 4-hydroxylase (EC 1.14.11.2) thus is a mixed function
nylalanine to tyrosine. This reaction is associated with several defects oxidase. Lysyl 5-hydroxylase (EC 1.14.11.4) catalyzes an analogous
of phenylalanine metabolism discussed in Chapter 29. reaction.
286 SECTION VI Metabolism of Proteins & Amino Acids
H
H Se CH2 C COO–
NH3+
O intermediates and the amino acids to which they give rise are
Se + ATP + H2O AMP + Pi + H Se P O–
O–
FIGURE 2714 Selenocysteine (top) and the reaction cata-
lyzed by selenophosphate synthetase (EC 2.7.9.3) (bottom).
human enzymes that catalyze redox reactions. Examples
include thioredoxin reductase, glutathione peroxidase, and
the deiodinase that converts thyroxine to triiodothyronine.
Where present, selenocysteine participates in the catalytic
mechanism of these enzymes. Significantly, the replace-
ment of selenocysteine by cysteine can actually impair cata-
lytic activity. Impairments in human selenoproteins have
been implicated in tumorigenesis and atherosclerosis, and
are associated with selenium deficiency cardiomyopathy
(Keshan disease).
Biosynthesis of selenocysteine requires cysteine, selenate
(SeO42−), ATP, a specific tRNA, and several enzymes. Serine
provides the carbon skeleton of selenocysteine. Selenophos-
phate, formed from ATP and selenate (Figure 27–14), serves
as the selenium donor. Unlike hydroxyproline or hydroxy-
lysine, selenocysteine arises cotranslationally during its incor-
poration into peptides. The UGA anticodon of the unusual
tRNA called tRNASec normally signals STOP. The ability of
the protein synthetic apparatus to identify a selenocysteine-
specific UGA codon involves the selenocysteine insertion
element, a stem-loop structure in the untranslated region
of the mRNA. tRNASec is first charged with serine by the
ligase that charges tRNASer. Subsequent replacement of the
serine oxygen by selenium involves selenophosphate formed
by selenophosphate synthetase (Figure 27–14). Successive
enzyme-catalyzed reactions convert cysteyl-tRNASec to
aminoacrylyl-tRNASec and then to selenocysteyl-tRNASec. In
the presence of a specific elongation factor that recognizes
selenocysteyl-tRNASec, selenocysteine can then be incorpo-
rated into proteins.
SUMMARY
■ All vertebrates can form certain amino acids from amphibolic
intermediates or from other dietary amino acids. The
α-ketoglutarate (Glu, Gln, Pro, Hyp), oxaloacetate (Asp, Asn),
and 3-phosphoglycerate (Ser, Gly).
■ Cysteine, tyrosine, and hydroxylysine are formed from
nutritionally essential amino acids. Serine provides the carbon
skeleton and homocysteine the sulfur for cysteine biosynthesis.
■ In Scurvy, a nutritional disease that results from a deficiency
of vitamin C, impaired hydroxylation of peptidyl proline and
peptidyl lysine results in a failure to provide the substrates for
cross-linking of maturing collagens.
■ Phenylalanine hydroxylase converts phenylalanine to tyrosine.
Since the reaction catalyzed by this mixed function oxidase is
irreversible, tyrosine cannot give rise to phenylalanine.
■ Neither dietary hydroxyproline nor hydroxylysine is
incorporated into proteins because no codon or tRNA dictates
their insertion into peptides.
■ Peptidyl hydroxyproline and hydroxylysine are formed by
hydroxylation of peptidyl proline or lysine in reactions catalyzed
by mixed-function oxidases that require vitamin C as cofactor.
■ Selenocysteine, an essential active site residue in several
mammalian enzymes, arises by cotranslational insertion from
a previously modified tRNA.
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