Amino Acid Metabolism

Amino acid Metabolism
-Amino acids, in addition to their role as protein monomeric units, are energy metabolites and precursors
of many biologically important nitrogen-containing compounds, physiologically active amines, glutathione,
nucleotides, and nucleotide coenzymes. Amino acids are classified into two groups: essential and
nonessential. Mammals synthesize the nonessential amino acids from metabolic precursors but must
obtain the essential amino acids from their diet. Excess dietary amino acids are neither stored for future
use nor excreted. Rather, they are converted to common metabolic intermediates such as pyruvate,
oxaloacetate, acetyl-CoA, and -keto-glutarate. Consequently, amino acids are also precursors of glucose,
fatty acids, and ketone bodies and are therefore metabolic fuels.
three common stages of amino acid breakdown:

1. Deamination (amino group removal), whereby amino groups are converted either to ammonia or to the
amino group of aspartate.
2. Incorporation of ammonia and aspartate nitrogen atoms into urea for excretion.
3. Conversion of amino acid carbon skeletons (the -keto acids produced by deamination) to common
metabolic intermediates.
AMINO ACID DEAMINATION
The first reaction in the breakdown of an amino acid is almost always removal of its -amino group with the
object of excreting excess nitrogen and degrading the remaining carbon skeleton or converting it to
glucose. Urea, the predominant nitrogen excretion product in terrestrial mammals, is synthesized from
ammonia and aspartate. Both of these latter substances are derived mainly from glutamate, a product of
most deamination reactions.
Most amino acids are deaminated by transamination, the transfer of their amino group to an -keto acid to
yield the -keto acid of the original amino acid and a new amino acid, in reactions catalyzed by
aminotransferases (alternatively, transaminases). The predominant amino group acceptor is -ketoglutarate,
producing glutamate as the new amino acid:
Deamination occurs largely through the oxidative deamination of glutamate by
glutamate dehydrogenase (GDH), yielding ammonia. The reaction requires NAD or NADP
as an oxidizing agent and regenerates - ketoglutarate for use in additional transamination
reactions.
A. Transamination
B. a. Aminotransferase Reactions Occur in Two Stages
1. The amino group of an amino acid is transferred to the enzyme, producing the corresponding keto acid and
the aminated enzyme
2. The amino group is transferred to the keto acid acceptor (e.g., -ketoglutarate), forming the amino acid
product (e.g., glutamate) and regenerating the enzyme.
To carry the amino group, aminotransferases require participation of an aldehyde-containing coenzyme,
pyridoxal-5-phosphate (PLP), a derivative of pyridoxine (vitamin B6;). The amino group is accommodated
by conversion of this coenzyme to pyridoxamine-5- phosphate (PMP;). PLP is covalently attached to the
enzyme via a Schiff base (imine) linkage formed by the condensation of its aldehyde group with the ε-
amino group of an enzymatic Lys residue (Fig. 26-1d). This Schiff base, which is conjugated to the
coenzyme’s pyridinium ring, is the focus of the coenzyme’s activity.
Figure 26-1 Forms of pyridoxal-5-phosphate.

(a) Pyridoxine (vitamin B6). (b) Pyridoxal-5¿-
phosphate (PLP)
(c) Pyridoxamine-5¿-phosphate (PMP). (d) The

Schiff base that forms between PLP and an
enzyme ε-amino group.
Esmond Snell, Alexander Braunstein, and David Metzler demonstrated that the aminotransferase reaction
occurs via a Ping Pong Bi Bi mechanism whose two stages consist of three steps each
b. Stage I: Conversion of an Amino Acid to an -Keto Acid

Step 1. The amino acid’s nucleophilic amino group attacks the enzyme–PLP Schiff base carbon atom in a
transimination (trans-Schiffization) reaction to form an amino acid–PLP Schiff base (aldimine), with
concomitant release of the enzyme’s Lys amino group. This Lys is then free to act as a general base at the
active site.
Step 2The amino acid–PLP Schiff base tautomerizes to an -keto acid–PMP Schiff base by the active site Lys–
catalyzed removal of the amino acid hydrogen and protonation of PLP atom C4¿ via a resonance-stabilized
carbanion intermediate. This resonance stabilization facilitates the cleavage of the C¬H bond.
Step 3. The -keto acid–PMP Schiff base is hydrolyzed to PMP and an -keto acid.
c. Stage II: Conversion of an -Keto Acid to an Amino Acid To complete the aminotransferase’s catalytic
cycle, the coenzyme must be converted from PMP back to the enzyme–PLP Schiff base. This involves the
same three steps as above, but in reverse order:
Step 3. PMP reacts with an -keto acid to form a Schiff base.

Step 2. The -keto acid–PMP Schiff base tautomerizes to form an amino acid–PLP Schiff base.
Step 1. The ε-amino group of the active site Lys residue attacks the amino acid–PLP Schiff base in a
transimination reaction to regenerate the active enzyme–PLP Schiff base, with release of the newly
formed amino acid.
The reaction’s overall stoichiometry therefore is

Aminotransferases differ in their specificity for amino acid substrates in the first stage of
the transamination reaction, thereby producing the correspondingly different -keto acid
products. Most aminotransferases, however, accept only -ketoglutarate or (to a lesser
extent) oxaloacetate as the -keto acid substrate in the second stage of the reaction,
thereby yielding glutamate or aspartate as their only amino acid products. The amino
groups of most amino acids are consequently funneled into the formation of glutamate or
aspartate, which are themselves interconverted by glutamate–aspartate
aminotransferase:
Oxidative Deamination:
Glutamate Dehydrogenase
Glutamate is oxidatively deaminated in the mitochondrial matrix by glutamate
dehydrogenase (GDH), the only known enzyme that, in at least some organisms, can
accept either NAD or NADP as its redox coenzyme. Oxidation is thought to occur with
transfer of a hydride ion from glutamate’s C to NAD(P), thereby forming alpha-
iminoglutarate, which is hydrolyzed to -ketoglutarate and ammonia (Fig. 26-4). GDH is
allosterically inhibited by GTP, NADH, and nonpolar compounds such as palmitoyl-CoA
and steroid hormones. It is activated by ADP, NAD, and leucine.
C. Other Deamination Mechanisms
Two nonspecific amino acid oxidases, L-amino acid oxidase and D-amino acid oxidase,
catalyze the oxidation of L- and D-amino acids, utilizing FAD as their redox coenzyme
[rather than NAD(P)].The resulting FADH2 is reoxidized by O2.
D-Amino acid oxidase occurs mainly in kidney. Its function is an enigma since D-
amino acids are associated mostly with bacterial cell walls. A few amino acids, such
as serine and histidine, are deaminated nonoxidatively.
2 THE UREA CYCLE
Living organisms excrete the excess nitrogen resulting from the metabolic breakdown of
amino acids in one of three ways. Many aquatic animals simply excrete ammonia. Where
water is less plentiful, however, processes have evolved that convert ammonia to less
toxic waste products that therefore require less water for excretion. One such product is
urea, which is excreted by most terrestrial vertebrates; another is uric acid, which is
excreted by birds and terrestrial reptiles
Accordingly, living organisms are classified as being either ammonotelic (ammonia excreting), ureotelic
(urea excreting), or uricotelic (uric acid excreting). Some animals can shift from ammonotelism to
ureotelism or uricotelism if their water supply becomes restricted. Here we focus our attention on urea
formation.
Urea is synthesized in the liver by the enzymes of the urea cycle. It is then secreted into the bloodstream
and sequestered by the kidneys for excretion in the urine. The overall urea cycle reaction is
Thus, the two urea nitrogen atoms are contributed by NH3 and aspartate, whereas the carbon atom
comes from HCO 3. Five enzymatic reactions are involved in the urea cycle, two of which are
mitochondrial and three cytosolic
Urea Is Produced from Ammonia in Five Enzymatic Steps
The urea cycle begins inside liver mitochondria, but three of the subsequent steps take place in the cytosol;
the cycle thus spans two cellular compartments (Fig. 18–10). The first amino group to enter the urea cycle is
derived from ammonia in the mitochondrial matrix—NH4 arising by the pathways described above. The liver
also receives some ammonia via the portal vein from the intestine, from the bacterial oxidation of amino
acids. Whatever its source, the NH4 generated in liver mitochondria is immediately used, together with CO2
(as HCO 3 ) produced by mitochondrial respiration, to form carbamoyl phosphate in the matrix. This ATP-
dependent reaction is catalyzed by carbamoyl phosphate synthetase I, a regulatory enzyme.
The carbamoyl phosphate, which functions as an activated carbamoyl group donor, now enters the urea
cycle.
The cycle has four enzymatic steps.
First, carbamoyl phosphate donates its carbamoyl group to ornithine to form citrulline, with the release of Pi
. The reaction is catalyzed by ornithine transcarbamoylase, and the citrulline passes from the mitochondrion
to the cytosol.
The second amino group now enters from aspartate (generated in mitochondria by
transamination and transported into the cytosol) by a condensation reaction between
the amino group of aspartate and the ureido (carbonyl) group of citrulline, forming
argininosuccinate. This cytosolic reaction, catalyzed by argininosuccinate synthetase,
requires ATP and proceeds through a citrullyl-AMP intermediate . The argininosuccinate
is then cleaved by argininosuccinase to form free arginine and fumarate, the latter
entering mitochondria to join the pool of citric acid cycle intermediates. This is the only
reversible step in the urea cycle. In the last reaction of the urea cycle (step 4 ), the
cytosolic enzyme arginase cleaves arginine to yield urea and ornithine. Ornithine is
transported into the mitochondrion to initiate another round of the urea cycle.

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Amino acid Metabolism

three common stages of amino acid breakdown:

Figure 26-1 Forms of pyridoxal-5-phosphate.

(c) Pyridoxamine-5¿-phosphate (PMP). (d) The

b. Stage I: Conversion of an Amino Acid to an -Keto Acid

Step 3. PMP reacts with an -keto acid to form a Schiff base.

The reaction’s overall stoichiometry therefore is

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