PROTEIN METABOLISM

Nada A.Abotemin

-Amino acid pool

- Protein turnover
- Nitrogen Balance

- Digestion of Dietary Proteins

- Removal of Nitrogen from Amino Acids

A. Transamination

B. oxidative deamination

- Transport of ammonia to the liver

- Urea Cycle

- Transport of ammonia in the circulation

- Hyperammonemia
- Amino Acid Degradation and Synthesis

- Metabolic Defects in Amino Acid Metabolism

- Other Nitrogen-Containing Compounds

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Protein metabolism
Amino acid catabolism is part of the larger process of the metabolism of nitrogen-containing molecules.
Nitrogen enters the body in a variety of compounds present in food, the most important being amino acids
contained in dietary protein. Nitrogen leaves the body as urea, ammonia, and other products derived from
amino acid metabolism. The role of body proteins in these transformations involves two important
concepts: the amino acid pool and protein turnover.

 A. Amino acid pool   

Free amino acids are present throughout the body, for example, in cells, blood, and the extracellular fluids.
For the purpose of this discussion, envision all these amino acids as if they belonged to a single entity,
called the amino acid pool. This pool is supplied by three sources:

1) amino acids provided by the degradation of body proteins,

2) amino acids derived from dietary protein, and

3) synthesis of nonessential amino acids from simple intermediates of metabolism (Figure 1).

Conversely, the amino pool is depleted by three routes:

1) synthesis of body protein,

2) amino acids consumed as precursors of essential nitrogen-containing small molecules, and

3) conversion of amino acids to glucose, glycogen, fatty acids or CO2 (Figure 1).

In healthy, well fed individuals, the input to the amino acid pool is balanced by the output, that is, the
amount of amino acids contained in the pool is constant. The amino acid pool is said to be in a steady state.
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Figure (1): Sources and fates of amino acids.

B. Protein turnover

Most proteins in the body are constantly being synthesized and then degraded, permitting the removal of
abnormal or unneeded proteins.

Rate of turnover: In healthy adults, the total amount of protein in the body remains constant,
because the rate of protein synthesis is just sufficient to replace the protein that is degraded. This
process, called protein turnover, leads to the hydrolysis and resynthesis of 300–400 g of body protein
each day. The rate of protein turnover varies widely for individual proteins. Short-lived proteins (for
example, many regulatory proteins and misfolded proteins) are rapidly degraded, having half-lives
measured in minutes or hours. Long-lived proteins, with half-lives of days to weeks, constitute the majority
of proteins in the cell. Structural proteins, such as collagen, are metabolically stable, and have half-lives
measured in months or years.

Protein degradation: There are two major enzyme systems responsible for degrading damaged or
unneeded proteins:
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1- the energy-dependent ubiquitin-proteasome mechanism : Proteasomes mainly degrade endogenous
proteins, that is, proteins that were synthesized within the cell.

2- the nonenergy-dependent degradative enzymes (acid hydrolases) of the lysosomes: Lysosomal

enzymes degrade primarily extracellular proteins, such as plasma proteins that are taken into the cell by
endocytosis, and cell-surface membrane proteins that are used in receptor-mediated endocytosis.

Ubiquitin-proteasome proteolytic pathway: Proteins selected for degradation by the ubiquitin-

proteasome mechanism are first covalently attached to ubiquitin, a small, globular protein. Ubiquitination
of the target substrate occurs through linkage of the α-carboxyl glycine of ubiquitin to a lysine ε-amino
group on the protein substrate by a three-step, enzyme-catalyzed process.

Proteins tagged with ubiquitin are then recognized by a large, barrel-shaped, macromolecular, proteolytic
complex called a proteasome, (Figure 2). The proteasome cuts the target protein into fragments that are
then further degraded to amino acids, which enter the amino acid pool. The degradation of proteins by the
ubiquitin-proteosome complex (unlike simple hydrolysis by proteolytic enzymes) requires adenosine
triphosphate (ATP)—that is, it is energy-dependent.

Figure (2): The ubiquitin-proteasome degradation pathway of proteins

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Nitrogen Balance

Catabolism of amino acids leads to a net loss of nitrogen from the body .This loss must be compensated by
the diet in order to maintain a constant amount of body protein ,Nitrogen balance studies evaluate the
relationship between the nitrogen intake ( in the form of protein ) and nitrogen excretion.

Three situations are possible as follows:

1- Nitrogen equilibrium:

●In normal adults nitrogen intake = nitrogen excretion. The subject is said to be in nitrogen equilibrium or
balance.

●In this situation ,the rate of protein synthesis is equal to the rate of the rate of degradation.

2- Positive nitrogen balance :

●In whish nitrogen intake ˃ nitrogen excretion

● It shows that nitrogen is retained in the body, which means that protein is laid down.

●This occurs in growing infants and pregnant women.

3- Negative nitrogen balance:

In which nitrogen intake ˂ nitrogen excretion .this occurs during serious illness and major injury and
trauma ,in advanced cancer and following failure to ingest adequate or sufficient high quality protein (
malnutrition).If the situation is prolonged, it will ultimately lead to death.

Digestion of Dietary Proteins

Proteins are generally too large to be absorbed by the intestine. Proteins must, therefore, be hydrolyzed to
yield their constituent amino acids, which can be absorbed. Proteolytic enzymes responsible for degrading
proteins are produced by three different organs: the stomach, the pancreas, and the small intestine (Figure
3).

[Note: An example of an exception to this rule is that newborns can take up maternal antibodies in breast
milk ,e.g. immunoglobin IgA from colostrum of maternal milk are absorbed intact without loss of biologic
activity , so that they provide passive immunity to the infant. In contrast to the situation encountered in the
newborn infants , in some adult individuals ,small amount of intact proteins may be absorbed through the
intestinal mucosa. These proteins often cause undesirable immunological responses (formation of
antibodies against the foreign protein ) and are responsible for the symptoms of food allergies.

A. Digestion of proteins by gastric secretion

The digestion of proteins begins in the stomach, which secretes gastric juice—a unique solution containing
hydrochloric acid and the proenzyme, pepsinogen.
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1- Hydrochloric acid: Stomach acid is too dilute (pH 2–3) to hydrolyze proteins. The acid functions
instead to kill some bacteria and to denature proteins, thus making them more susceptible to subsequent
hydrolysis by proteases.

2- Pepsin: This acid-stable endopeptidase is secreted by the serous cells of the stomach as an inactive
zymogen (or proenzyme), pepsinogen. In general, zymogens contain extra amino acids in their sequences,
which prevent them from being catalytically active. [Note: Removal of these amino acids permits the
proper folding required for an active enzyme.] Pepsinogen is activated to pepsin, either by HCl, or
autocatalytically by other pepsin molecules that have already been activated. Pepsin releases peptides
and a few free amino acids from dietary proteins.

Figure (3): Digestion of dietary proteins by the proteolytic enzymes of the gastrointestinal tract.

B. Digestion of proteins by pancreatic enzymes

On entering the small intestine, large polypeptides produced in the stomach by the action of pepsin are
further cleaved to oligopeptides and amino acids by a group of pancreatic proteases

1- Specificity: Each of these enzymes has a different specificity for the amino acid R-groups adjacent to
the susceptible peptide bond. For example, trypsin cleaves only when the carbonyl group of the peptide
bond is contributed by arginine or lysine. These enzymes, like pepsin described above, are synthesized and
secreted as inactive zymogens.

2- Release of zymogens: The release and activation of the pancreatic zymogens is mediated by the
secretion of cholecystokinin and secretin, two polypeptide hormones of the digestive tract.

3- Activation of zymogens: (Enteropeptidase) an enzyme synthesized by and present on the luminal

surface of intestinal mucosal cells of the brush border membrane—converts the pancreatic zymogen
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trypsinogen to trypsin by removal of a hexapeptide from the NH2-terminus of trypsinogen. Trypsin
subsequently converts other trypsinogen molecules to trypsin by cleaving a limited number of specific
peptide bonds in the zymogen. Enteropeptidase thus unleashes a cascade of proteolytic activity, because
trypsin is the common activator of all the pancreatic zymogens.

4-Abnormalities in protein digestion: In individuals with a deficiency in pancreatic secretion (for

example, due to chronic pancreatitis, cystic fibrosis, or surgical removal of the pancreas), the digestion and
absorption of fat and protein is incomplete. This results in the abnormal appearance of lipids (called
steatorrhea,) and undigested protein in the feces.

C. Digestion of oligopeptides by enzymes of the small intestine

The luminal surface of the intestine contains aminopeptidase—an exopeptidase that repeatedly cleaves the
N-terminal residue from oligopeptides to produce free amino acids and smaller peptides.

D. Absorption of amino acids and dipeptides

Free amino acids are taken into the enterocytes up by a Na+-linked secondary transport system. Di- and
tripeptides, however, are taken up by a H+-linked transport system. There, the peptides are hydrolyzed in
the cytosol to amino acids before being released into the portal system. Thus, only free amino acids are
found in the portal vein after a meal containing protein. These amino acids are either metabolized by the
liver or released into the general circulation.

Transport of Amino Acids into Cells

The concentration of free amino acids in the extracellular fluids is significantly lower than that within the
cells of the body. This concentration gradient is maintained because active transport systems, driven by
the hydrolysis of ATP, are required for movement of amino acids from the extracellular space into cells.
At least seven different transport systems are known that have overlapping specificities for different amino
acids.

Removal of Nitrogen from Amino Acids

Removing the α-amino group is essential for producing energy from any amino acid, and is an obligatory
step in the catabolism of all amino acids. Once removed, this nitrogen can be incorporated into other
compounds or excreted, with the carbon skeletons being metabolized.

A. Transamination: the funneling of amino groups to glutamate

1-The first step in the catabolism of most amino acids is the transfer of their α-amino group to α-
ketoglutarate (Figure 4).

2- The products are an α-keto acid (derived from the original amino acid) and glutamate.

α-Ketoglutarate plays a pivotal role in amino acid metabolism by accepting the amino groups from other
amino acids, thus becoming glutamate.

Glutamate produced by transamination can be oxidatively deaminated (see below), or used as an amino
group donor in the synthesis of nonessential amino acids.
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This transfer of amino groups from one carbon skeleton to another is catalyzed by a family of enzymes
called aminotransferases (formerly called transaminases). These enzymes are found in the cytosol and
mitochondria of cells throughout the body—especially those of the liver, kidney, intestine, and muscle. All
amino acids, with the exception of lysine and threonine, participate in transamination at some point in their
catabolism. [Note: These two amino acids lose their α-amino groups by deamination].

Figure (4): Aminotransferase reaction using α-ketoglutarate as the amino-group acceptor

1- Substrate specificity of aminotransferases: Each aminotransferase is specific for one or, at most, a
few amino group donors. Aminotransferases are named after the specific amino group donor, because the
acceptor of the amino group is almost always α-ketoglutarate. The two most important aminotransferase
reactions are catalyzed by alanine aminotransferase (ALT) and aspartate aminotransferase (AST), Figure 5.

Figure (5): Reactions catalyzed during amino acid catabolism. A. Alanine aminotransferase (ALT).
  B. Aspartate aminotransferase (AST).

 
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a-Alanine aminotransferase (ALT): Formerly called glutamate-pyruvate transaminase, ALT is present
in many tissues. The enzyme catalyzes the transfer of the amino group of alanine to α-ketoglutarate,
resulting in the formation of pyruvate and glutamate.

b-Aspartate aminotransferase (AST): AST formerly called glutamate-oxaloacetate transaminase, AST

is an exception to the rule that aminotransferases funnel amino groups to form glutamate. During amino
acid catabolism, AST transfers amino groups from glutamate to oxaloacetate, forming aspartate, which is
used as a source of nitrogen in the urea cycle.

2-Mechanism of action of aminotransferases: All aminotransferases require the coenzyme pyridoxal

phosphate (a derivative of vitamin B6), which is covalently linked to the ε-amino group of a specific
lysine residue at the active site of the enzyme

3-Diagnostic value of plasma aminotransferases:

Aminotransferases are normally intracellular enzymes, with the low levels found in the plasma
representing the release of cellular contents during normal cell turnover. The presence of elevated plasma
levels of aminotransferases indicates damage to cells rich in these enzymes. For example, physical trauma
or a disease process can cause cell lysis, resulting in release of intracellular enzymes into the blood. Two
aminotransferases—AST and ALT—are of particular diagnostic value when they are found in the plasma.

a- Liver disease: Plasma AST and ALT are elevated in nearly all liver diseases, but are particularly high in
conditions that cause extensive cell necrosis, such as severe viral hepatitis, toxic injury, and prolonged
circulatory collapse. ALT is more specific than AST for liver disease, but the latter is more sensitive
because the liver contains larger amounts of AST. Serial enzyme measurements are often useful in
determining the course of liver damage.

b-Nonhepatic disease: Aminotransferases may be elevated in nonhepatic disease, such as myocardial

infarction and muscle disorders. However, these disorders can usually be distinguished clinically from liver
disease.

B. Glutamate dehydrogenase: the oxidative deamination of amino acids

In contrast to transamination reactions that transfer amino groups, oxidative deamination by glutamate
dehydrogenase results in the liberation of the amino group as free ammonia (Figure 6). These reactions
occur primarily in the liver and kidney. They provide α-keto acids that can enter the central pathway of
energy metabolism, and ammonia, which is a source of nitrogen in urea synthesis.

1- Glutamate dehydrogenase: As described above, the amino groups of most amino acids are ultimately
funneled to glutamate by means of transamination with α-ketoglutarate. Glutamate is unique in that it is
the only amino acid that undergoes rapid oxidative deamination—a reaction catalyzed by glutamate
dehydrogenase. Therefore, the sequential action of transamination (resulting in the collection of amino
groups from other amino acids onto α-ketoglutarate to produce glutamate) and the oxidative deamination of
that glutamate (regenerating α-ketoglutarate) provide a pathway whereby the amino groups of most amino
acids can be released as ammonia.
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 Figure (6): Oxidative deamination by glutamate dehydrogenase.

2- D-Amino acid oxidase: D-Amino acids are found in plants and in the cell walls of microorganisms, but
are not used in the synthesis of mammalian proteins. D-Amino acids are, however, present in the diet, and
are efficiently metabolized by the kidney and liver. D-Amino acid oxidase is an FAD-dependent
peroxisomal enzyme that catalyzes the oxidative deamination of these amino acid isomers. The resulting α-
keto acids can enter the general pathways of amino acid metabolism, and be re-aminated to L-isomers, or
catabolized for energy.

Transport of ammonia to the liver

Two mechanisms are available in humans for the transport of ammonia from the peripheral tissues to the
liver for its ultimate conversion to urea.

The first, found in most tissues, uses glutamine synthetase to combine ammonia with glutamate to form
glutamine—a nontoxic transport form of ammonia (Figure 7). The glutamine is transported in the blood to
the liver where it is cleaved by glutaminase to produce glutamate and free ammonia.

The second transport mechanism, used primarily by muscle, involves transamination of pyruvate (the end
product of aerobic glycolysis) to form alanine (see Figure 7). Alanine is transported by the blood to the
liver, where it is converted to pyruvate, again by transamination. In the liver, the pathway of
gluconeogenesis can use the pyruvate to synthesize glucose, which can enter the blood and be used by
muscle—a pathway called the glucose-alanine cycle.
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Figure (7): Transport of ammonia from peripheral tissues to the liver

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Urea Cycle
Urea is the major disposal form of amino groups derived from amino acids, and accounts for about 90% of
the nitrogen-containing components of urine. One nitrogen of the urea molecule is supplied by free NH3,
and the other nitrogen by aspartate. [Note: Glutamate is the immediate precursor of both ammonia (through
oxidative deamination by glutamate dehydrogenase) and aspartate nitrogen (through transamination of
oxaloacetate by AST).] The carbon and oxygen of urea are derived from CO2. Urea is produced by the
liver, and then is transported in the blood to the kidneys for excretion in the urine.

A. Sequence of reactions of the cycle

The sequence of reactions involved in the biosynthesis of urea , summarized in five steps as follows:

1- Formation of carbamoyl phosphate

2-Formation of citrulline

3- Formation of argininosuccinate

4- Formation of arginine and fumarate

5-Formation of urea and ornithine

The first two reactions leading to the synthesis of urea occur in the mitochondria, whereas the remaining
cycle enzymes are located in the cytosol (Figure 8).

Formation of carbamoyl phosphate: Formation of carbamoyl phosphate by carbamoyl phosphate

synthetase I is driven by cleavage of two molecules of ATP. Ammonia incorporated into carbamoyl
phosphate is provided primarily by the oxidative deamination of glutamate by mitochondrial glutamate
dehydrogenase (see Figure 8). Ultimately, the nitrogen atom derived from this ammonia becomes one of
the nitrogens of urea. Carbamoyl phosphate synthetase I requires N-acetylglutamate as a positive
  allosteric activator (see Figure 9).

 2-Formation of citrulline: Ornithine and citrulline are basic amino acids that participate in the urea cycle.
[Note: They are not incorporated into cellular proteins, because there are no codons for these amino acids
Ornithine is regenerated with each turn of the urea cycle, much in the same way that oxaloacetate is
regenerated by the reactions of the citric acid cycle. The release of the high-energy phosphate of carbamoyl
phosphate as inorganic phosphate drives the reaction in the forward direction. The reaction product,
citrulline, is transported to the cytosol.

3-Synthesis of argininosuccinate: Citrulline condenses with aspartate to form argininosuccinate. The α-

amino group of aspartate provides the second nitrogen that is ultimately incorporated into urea. The
formation of argininosuccinate is driven by the cleavage of ATP to adenosine monophosphate (AMP) and
pyrophosphate. This is the third and final molecule of ATP consumed in the formation of urea.
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Figure (8): Reactions of the urea cycle

4-Cleavage of argininosuccinate: Argininosuccinate is cleaved to yield arginine and fumarate. The

arginine formed by this reaction serves as the immediate precursor of urea. Fumarate produced in the urea
cycle is hydrated to malate, providing a link with several metabolic pathways. For example, the malate can
be transported into the mitochondria via the malate shuttle and reenter the tricarboxylic acid cycle.
Alternatively, cytosolic malate can be oxidized to oxaloacetate, which can be converted to aspartate or
glucose.

5-Cleavage of arginine to ornithine and urea: Arginase cleaves arginine to ornithine and urea, and
occurs almost exclusively in the liver. Thus, whereas other tissues, such as the kidney, can synthesize
arginine by these reactions, only the liver can cleave arginine and, thereby, synthesize urea.

6-Fate of urea: Urea diffuses from the liver, and is transported in the blood to the kidneys, where it is
filtered and excreted in the urine. A portion of the urea diffuses from the blood into the intestine, and is
cleaved to CO2 and NH3 by bacterial urease. This ammonia is partly lost in the feces, and is partly
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reabsorbed into the blood. In patients with kidney failure, plasma urea levels are elevated, promoting a
greater transfer of urea from blood into the gut. The intestinal action of urease on this urea becomes a
clinically important source of ammonia, contributing to the hyperammonemia often seen in these patients.

Four high-energy phosphates are consumed in the synthesis of each molecule of urea: two ATP are
needed to restore two ADP to two ATP, plus two to restore AMP to ATP. Therefore, the synthesis of urea
is irreversible, with a large, negative ΔG. One nitrogen of the urea molecule is supplied by free NH3, and
the other nitrogen by aspartate. Glutamate is the immediate precursor of both ammonia (through oxidative
deamination by glutamate dehydrogenase) and aspartate nitrogen (through transamination of oxaloacetate
by AST). In effect, both nitrogen atoms of urea arise from glutamate, which, in turn, gathers nitrogen from
other amino acids (Figure 7).

Figure( 9 ): Links between the urea cycle and citric acid cycle.

C. Regulation of the urea cycle

N-acetylglutamate is an essential activator for carbamoyl phosphate synthetase I—the rate-limiting step in
the urea cycle (see Figure 9). N-acetylglutamate is synthesized from acetyl coenzyme A and glutamate by
N-acetylglutamate synthase (Figure 10), in a reaction for which arginine is an activator. Therefore, the
intrahepatic concentration of N-acetylglutamate increases after ingestion of a protein-rich meal, which
provides both the substrate (glutamate) and the regulator of N-acetylglutamate synthesis. This leads to an
increased rate of urea synthesis.
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Figure (10): Formation and degradation of Nacetylglutamate, an allosteric activator of carbamoyl

phosphate synthetase I

Ammonia is produced by all tissues during the metabolism of a variety of compounds, and it is disposed of
primarily by formation of urea in the liver. However, the level of ammonia in the blood must be kept very
low, because even slightly elevated concentrations (hyperammonemia) are toxic to the central nervous
system (CNS). There must, therefore, be a metabolic mechanism by which nitrogen is moved from
peripheral tissues to the liver for ultimate disposal as urea, while at the same time low levels of circulating
ammonia must be maintained.

B. Transport of ammonia in the circulation

Although ammonia is constantly produced in the tissues, it is present at very low levels in blood. This is
due both to the rapid removal of blood ammonia by the liver, and the fact that many tissues, particularly
muscle, release amino acid nitrogen in the form of glutamine or alanine, rather than as free ammonia.

Urea: Formation of urea in the liver is quantitatively the most important disposal route for ammonia. Urea
travels in the blood from the liver to the kidneys, where it passes into the glomerular filtrate.

Glutamine: This amide of glutamic acid provides a nontoxic storage and transport form of ammonia .The
ATP-requiring formation of glutamine from glutamate and ammonia by glutamine synthetase occurs
primarily in the muscle and liver, but is also important in the nervous system, where it is the major
mechanism for the removal of ammonia in the brain. Glutamine is found in plasma at concentrations higher
than other amino acids—a finding consistent with its transport function. Circulating glutamine is removed
by the liver and the kidneys and deaminated by glutaminase.

C. Hyperammonemia

The capacity of the hepatic urea cycle exceeds the normal rates of ammonia generation, and the levels of
serum ammonia are normally low (5–50 µmol/L). However, when liver function is compromised, due
either to genetic defects of the urea cycle, or liver disease, blood levels can rise above 1,000 µmol/L. Such
hyperammonemia is a medical emergency, because ammonia has a direct neurotoxic effect on the CNS.
For example, elevated concentrations of ammonia in the blood cause the symptoms of ammonia
   - 15 -
 
intoxication, which include tremors, slurring of speech, somnolence, vomiting, cerebral edema, and
blurring of vision. At high concentrations, ammonia can cause coma and death .

Why are high levels of ammonia toxic?

The toxic effect of ammonia may be due to :

●A decrease in the formation of ATP by citric acid cycle because of diversion of excessive amounts of
-ketoglutarate from citric acid cycle intermediates to form glutamate and glutamine in the brain and thus
lowering the rate of oxidation of glucose , the major fuel of the brain or

●By increased formation of GABA(gamma amino butyric acid) from glutamate ,figure (10) leads to
impaired neural transmission process .

●One more possibility is that elevated levels of glutamine ,formed from NH4+ and glutamate which
produce osmotic effect that lead directly to swelling of brain .

Decarboxylase

Glutamate---------------------------------→ Gamma aminobutyric acid ( GABA)

PLP CO2

Figure (11): Decarboxylation of glutamate

Amino Acid Degradation and Synthesis

The catabolism of the amino acids found in proteins involves the removal of α-amino groups, followed by
the breakdown of the resulting carbon skeletons. These pathways converge to form seven intermediate
products: oxaloacetate, α-ketoglutarate, pyruvate, fumarate, succinyl coenzyme A (CoA), acetyl
CoA, and acetoacetate.

These products directly enter the pathways of intermediary metabolism, resulting either in the synthesis of
glucose or lipid or in the production of energy through their oxidation to CO2 and water by the citric acid
cycle.

Glucogenic and Ketogenic Amino Acids

Amino acids can be classified as glucogenic, ketogenic, or both based on which of the seven intermediates are
produced during their catabolism (see Figure 12).

A. Glucogenic amino acids

Amino acids whose catabolism yields pyruvate or one of the intermediates of the citric acid cycle are
termed glucogenic or glycogenic. These intermediates are substrates for gluconeogenesis and, therefore,
can give rise to the net formation of glucose or glycogen in the liver and glycogen in the muscle.
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B. Ketogenic amino acids

Amino acids whose catabolism yields either acetoacetate or one of its precursors (acetyl CoA or
acetoacetyl CoA) are termed ketogenic (see Figure 20.2). Acetoacetate is one of the “ketone bodies,”
which also include 3-hydroxybutyrate and acetone. Leucine and lysine are the only exclusively ketogenic
amino acids found in proteins. Their carbon skeletons are not substrates for gluconeogenesis and, therefore,
  cannot give rise to the net formation of glucose or glycogen in the liver, or glycogen in the muscle.

Figure (12):Classification of amino acids

Catabolism of the Carbon Skeletons of Amino Acids

The pathways by which amino acids are catabolized are conveniently organized according to which one (or
more) of the seven intermediates listed above is produced from a particular amino acid.

A. Amino acids that form oxaloacetate

Figure (12): Metabolism of asparagine and aspartate

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Asparagine is hydrolyzed by asparaginase, liberating ammonia and aspartate Figure (13). Aspartate loses
its amino group by transamination to form oxaloacetate .

B. Amino acids that form α-ketoglutarate

Glutamine is converted to glutamate and ammonia by the enzyme glutaminase. Glutamate is converted to
α-ketoglutarate by transamination, or through oxidative deamination by glutamate dehydrogenase.
Figure(14)

- Ketoglutarate

Transamination

NH4 + L-Glutamate  NH4+

Mg-ATP

Glutamine synthetase Glutaminase

Mg-ADP + Pi

Glutamine

Figure (14): Synthesis and degradation of glutamine

Proline: This amino acid is oxidized to glutamate. Glutamate is transaminated or oxidatively deaminated
to form α-ketoglutarate.

Arginine: This amino acid is cleaved by arginase to produce ornithine and urea . [Note: This reaction
occurs primarily in the liver as part of the urea cycle. Ornithine is subsequently converted to α-
ketoglutarate.

C. Amino acids that form pyruvate

Alanine: This amino acid loses its amino group by transamination to form pyruvate (Figure 4)

Serine: This amino acid can be converted to glycine and N5,N10-methylenetetrahydrofolate. Serine can also
be converted to pyruvate by serine dehydratase (15).

Glycine: This amino acid can either be converted to serine by addition of a methylene group from N5,N10-
methylenetetrahydrofolic acid (see Figure 15), or oxidized to CO2 and NH3.

Cystine: This amino acid is reduced to cysteine, using NADH + H+ as a reductant. Cysteine undergoes
desulfuration to yield pyruvate.

Threonine: This amino acid is converted to pyruvate or to α-ketobutyrate, which forms succinyl CoA.
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Figure (15): A. Interconversion of serine and glycine, and oxidation of glycine.

B. Dehydration of serine to form pyruvate

D. Amino acids that form fumarate

Phenylalanine and tyrosine: Hydroxylation of phenylalanine leads to the formation of tyrosine (Figure
16). This reaction, catalyzed by phenylalanine hydroxylase, is the first reaction in the catabolism of
phenylalanine. Thus, the metabolism of phenylalanine and tyrosine merge, leading ultimately to the
formation of fumarate and acetoacetate. Phenylalanine and tyrosine are, therefore, both glucogenic and
ketogenic.

Inherited deficiencies: Inherited deficiencies in the enzymes of phenylalanine and tyrosine metabolism
lead to the diseases phenylketonuria, and alkaptonuria, and the condition of albinism.

Figure (16):Degradation of phenylalanine

E. Amino acids that form succinyl CoA:

Methionine : Methionine is one of four amino acids that form succinyl CoA. This sulfur-containing amino
acid deserves special attention because it is converted to S-adenosylmethionine (SAM), the major methyl-
group donor in one-carbon metabolism (Figure 17).
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Synthesis of SAM: Methionine condenses with adenosine triphosphate (ATP), forming SAM—a high-
energy compound that is unusual in that it contains no phosphate. The formation of SAM is driven, in
effect, by hydrolysis of all three phosphate bonds in ATP

Activated methyl group: The methyl group attached to the tertiary sulfur in SAM is “activated,” and can
be transferred to a variety of acceptor molecules, such as norepinephrine in the synthesis of epinephrine.
The methyl group is usually transferred to oxygen or nitrogen atoms, but sometimes to carbon atoms.

Hydrolysis of SAM: After donation of the methyl group, S-adenosylhomocysteine is hydrolyzed to

homocysteine and adenosine. Homocysteine has two fates: If there is a deficiency of methionine,
homocysteine may be remethylated to methionine (17). If methionine stores are adequate, homocysteine
may enter the transsulfuration pathway, where it is converted to cysteine

Resynthesis of methionine: Homocysteine accepts a methyl group from N5-methyltetrahydrofolate (N5-

methyl-THF) in a reaction requiring methylcobalamin, a coenzyme derived from vitamin Bl2. The methyl
group is transferred from the B12 derivative to homocysteine, and cobalamin is recharged from N5-methyl-
THF.

 Synthesis of cysteine: Homocysteine condenses with serine, forming cystathionine, which is hydrolyzed
to α-ketobutyrate and cysteine (see Figure 17). This vitamin B6–requiring sequence has the net effect of
converting serine to cysteine, and homocysteine to α-ketobutyrate, which is oxidatively decarboxylated to
form propionyl CoA. Propionyl CoA is converted to succinyl CoA. Because homocysteine is synthesized
from the essential amino acid methionine, cysteine is not an essential amino acid as long as sufficient
methionine is available.

Figure( 16): Formation of S-adenosylmethionine. ~CH3 represents the high group transfer potential
of “active methionine.”
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Figure (17): Degradation and resynthesis of methionine.

F. Other amino acids that form succinyl CoA

Degradation of valine, isoleucine, and threonine also results in the production of succinyl CoA a
tricarboxylic acid (TCA) cycle intermediate and glucogenic compound
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Valine and isoleucine: These amino acids are branched-chain amino acids that generate propionyl CoA,
which is converted to succinyl CoA by biotin- and vitamin B12–requiring reactions [Note: Propionyl CoA,
then, is generated by the catabolism of certain amino acids and odd-numbered fatty acids]. 

Threonine: This amino acid is dehydrated to α-ketobutyrate, which is converted to propionyl CoA and
then to succinyl CoA. [Note: Threonine can also be converted to pyruvate].

Threonine

Threonine dehydratase  PLP

NH4+

-Ketobutyrate

 Oxidativedecarboxylation

Prpionyl-CoA

Biotin

Methyl malonyl –CoA

Vitamin B

Succinyl –CoA

TCA cycle

Figure (18):Degradation of Thrionine

G. Amino acids that form acetyl CoA or acetoacetyl CoA

Leucine, isoleucine, lysine, and tryptophan form acetyl CoA or acetoacetyl CoA directly

Leucine: This amino acid is exclusively ketogenic in its catabolism, forming acetyl CoA and acetoacetate.

Isoleucine: This amino acid is both ketogenic and glucogenic, because its metabolism yields acetyl CoA
and propionyl CoA.

Lysine: An exclusively ketogenic amino acid, this amino acid is unusual in that neither of its amino groups
undergoes transamination as the first step in catabolism. Lysine is ultimately converted to acetoacetyl CoA.

Tryptophan: This amino acid is both glucogenic and ketogenic because its metabolism yields alanine and
acetoacetyl CoA.

Catabolism of the branched-chain amino acids

The branched-chain amino acids, isoleucine, leucine, and valine, are essential amino acids. In contrast to
other amino acids, they are metabolized primarily by the peripheral tissues (particularly muscle), rather
   - 22 -
 
than by the liver. Because these three amino acids have a similar route of catabolism, it is convenient to
describe them as a group (see Figure 19).

  Figure(19): Degrada on of branched chain amino acids

Role of Folic Acid in Amino Acid Metabolism

Some synthetic pathways require the addition of single carbon groups. These “one-carbon units” can exist
in a variety of oxidation states. These include methane, methanol, formaldehyde, formic acid, and carbonic
acid. It is possible to incorporate carbon units at each of these oxidation states, except methane, into other
organic compounds. These single carbon units can be transferred from carrier compounds such as
tetrahydrofolic( THF ) acid and S-adenosylmethionine to specific structures that are being synthesized
or modified.

Biosynthesis of Nonessential Amino Acids

Nonessential amino acids are synthesized from intermediates of metabolism or, as in the case of tyrosine
.and cysteine, from the essential amino acids phenylalanine and methionine, respectively

A. Synthesis from α-keto acids

Alanine, aspartate, and glutamate are synthesized by transfer of an amino group to the α-keto acids
pyruvate, oxaloacetate, and α-ketoglutarate, respectively. These transamination reactions (Figure 5) are the
   - 23 -
 
most direct of the biosynthetic pathways. Glutamate is unusual in that it can also be synthesized by the
reverse of oxidative deamination, catalyzed by glutamate dehydrogenase.

Figure( 20): Formation of alanine, aspartate, and glutamate from the corresponding α-keto acids.

  B. Synthesis by amidation

Glutamine: This amino acid, which contains an amide linkage with ammonia at the γ-carboxyl, is formed
from glutamate by glutamine synthetase (see Figure 14). The reaction is driven by the hydrolysis of ATP.
In addition to producing glutamine for protein synthesis, the reaction also serves as a major mechanism for
the detoxification of ammonia in brain and liver.

Asparagine: This amino acid, which contains an amide linkage with ammonia at the β-carboxyl, is formed
from aspartate by asparagine synthetase, using glutamine as the amide donor. The reaction requires ATP,
and, like the synthesis of glutamine, has an equilibrium far in the direction of asparagine synthesis.

D. Serine, glycine, and cysteine

Serine: This amino acid arises from 3-phosphoglycerate, an intermediate in glycolysis , which is first
oxidized to 3-phosphopyruvate, and then transaminated to 3-phosphoserine. Serine is formed by hydrolysis
of the phosphate ester (figure 21). Serine can also be formed from glycine through transfer of a
hydroxymethyl group by serine hydroxymethyl transferase (see Figure 15).
   - 24 -
 

Glucose

3-Phosphoglycerate

 NAD+

NADH+H+

3- Phosphpo-hydroxy-pyruvate

 L-Glutamate

-Ketoglutarate

3-Phospho-L-serine

 H 2O

Pi

L-Serine

Figure(21): Synthesis of serine from a glucose molecule

Glycine: This amino acid is synthesized from serine by removal of a hydroxymethyl group, also by serine
hydroxymethyl transferase (see Figure 15).

Cysteine: This amino acid is synthesized by two consecutive reactions in which homocysteine combines
with serine, forming cystathionine, which, in turn, is hydrolyzed to α-ketobutyrate and cysteine (see Figure
17). Homocysteine is derived from methionine. Because methionine is an essential amino acid, cysteine
synthesis can be sustained only if the dietary intake of methionine is adequate.

E. Tyrosine

Tyrosine is formed from phenylalanine by phenylalanine hydroxylase. The reaction requires molecular
oxygen and the coenzyme tetrahydrobiopterin (BH4), which can be synthesized from guanosine
triphosphate (GTP) by the body. One atom of molecular oxygen becomes the hydroxyl group of tyrosine,
and the other atom is reduced to water. During the reaction, tetrahydrobiopterin is oxidized to
dihydrobiopterin. Tetrahydrobiopterin is regenerated from dihydrobiopterin in a separate reaction requiring
NADH. Tyrosine, like cysteine, is formed from an essential amino acid and is, therefore, nonessential only
in the presence of adequate dietary phenylalanine (figure 16).
   - 25 -
 
VI. Metabolic Defects in Amino Acid Metabolism

Inborn errors of metabolism are commonly caused by mutant genes that generally result in abnormal
proteins, most often enzymes. The inherited defects may be expressed as a total loss of enzyme activity or,
more frequently, as a partial deficiency in catalytic activity. Without treatment, the inherited defects of
amino acid metabolism almost invariably result in mental retardation or other developmental abnormalities
as a result of harmful accumulation of metabolites. Although more than 50 of these disorders have been
described, many are rare, occurring in less than 1 per 250,000 in most populations. Phenylketonuria is the
most important disease of amino acid metabolism because it is relatively common and responds to dietary
treatment.

Figure (22): A deficiency in phenylalanine hydroxylase results in the disease phenylketonuria (PKU).

Phenylketonuria

Phenylketonuria (PKU), caused by a deficiency of phenylalanine hydroxylase (Figure 20.15), PKU is the
most common clinically encountered inborn error of amino acid metabolism (prevalence 1:15,000).
Biochemically, it is characterized by accumulation of phenylalanine (and a deficiency of tyrosine).
Hyperphenylalaninemia may also be caused by deficiencies in any of the several enzymes required to
synthesize BH4, or in dihydropteridine (BH2) reductase, which regenerates BH4 from BH2 (Figure 20.16).
Such deficiencies indirectly raise phenylalanine concentrations, because phenylalanine hydroxylase
requires BH4 as a coenzyme. BH4 is also required for tyrosine hydroxylase and tryptophan hydroxylase,
which catalyze reactions leading to the synthesis of neurotransmitters, such as serotonin and
catecholamines. Simply restricting dietary phenylalanine does not reverse the central nervous system
(CNS) effects due to deficiencies in neurotransmitters. Replacement therapy with BH4 or L-DOPA and 5-
hydroxytryptophan (products of the affected tyrosine hydroxylase– and tryptophan hydroxylase–catalyzed
reactions) improves the clinical outcome in these variant forms of hyperphenylalaninemia, although the
response is unpredictable.

Characteristics of classic PKU

   - 26 -
 
Elevated phenylalanine: Phenylalanine is present in elevated concentrations in tissues, plasma, and urine.
Since patients can not convert phenylalanine to tyrosine by normal pathway ,some minor pathway of
phenylalanine becomes prominent in phenylketonurics and accumulation of toxic derivatives of
phenylalanine such as Phenyl lactate, phenyl acetate, and phenyl pyruvate, which are not normally
produced in significant amounts in the presence of functional phenylalanine hydroxylase (Figure 20.17).
The disease acquired its name (PKU) from the high levels of the keto acid , phenyl pyruvate in urine .

Figure (23): Pathways of phenylalanine metabolism in normal individuals and in patients with
phenylketonuria.

CNS symptoms: Mental retardation, failure to walk or talk, seizures, hyperactivity, tremor, microcephaly,
and failure to grow are characteristic findings in PKU. The patient with untreated PKU typically shows
symptoms of mental retardation by the age of one year.

B. Maple syrup urine disease

Maple syrup urine disease (MSUD) is a rare (1:185,000), autosomal recessive disorder in which there is a
partial or complete deficiency in branched-chain α-keto acid dehydrogenase, an enzyme complex that
decarboxylates leucine, isoleucine, and valine (see Figure 20.10). These amino acids and their
corresponding α-keto acids accumulate in the blood, causing a toxic effect that interferes with brain
functions. The disease is characterized by feeding problems, vomiting, dehydration, severe metabolic
   - 27 -
 
acidosis, and a characteristic maple syrup odor to the urine. If untreated, the disease leads to mental
retardation, physical disabilities, and even death.

C. Albinism

Albinism refers to a group of conditions in which a defect in tyrosine metabolism results in a deficiency in
the production of melanin. These defects result in the partial or full absence of pigment from the skin, hair,
and eyes. In addition to hypopigmentation, affected individuals have vision defects and photophobia
(sunlight hurts their eyes). They are at increased risk for skin cancer.

Hypopigmentation: Patients with phenylketonuria often show a deficiency of pigmentation (fair hair, light
skin color, and blue eyes). The hydroxylation of tyrosine by tyrosinase, which is the first step in the
formation of the pigment melanin, is competitively inhibited by the high levels of phenylalanine present in
PKU.

tyrosinase

Dopa Tyrosine → Dopa

  

Dopamine Tyroxine Dopaquinone

Neurotransmitter  

Norepinphrine Chaticholamines 

 

Epinpherine Melanine pigmint

Figure(24): : Biosynthesis of biologically important compounds from tyrosine

E. Alkaptonuria

Alkaptonuria is a rare metabolic disease involving a deficiency in homogentisic acid oxidase, resulting in
the accumulation of homogentisic acid. [Note: This reaction occurs in the degradative pathway of
tyrosine] , The illness has three characteristic symptoms: homogentisic aciduria (the patient's urine contains
elevated levels of homogentisic acid, which is oxidized to a dark pigment on standing), large joint arthritis,
and black ochronotic pigmentation of cartilage and collagenous tissue. Patients with alkaptonuria are
usually asymptomatic until about age 40. Diets low in protein—especially in phenylalanine and tyrosine—
help reduce the levels of homogentisic acid, and decrease the amount of pigment deposited in body tissues.
Although alkaptonuria is not life-threatening, the associated arthritis may be severely crippling.

Biologically important compounds derived from Tryptophan

1- Vitamin niacin ( vitamin B3)

2- Neurotransmitter serotonin
   - 28 -
 
3- Hormone melatonin : is a hormone produced by the pineal gland which has effects on the hypothalamic
pituitary system .Synthesis of melatonin is regulated by light –dark cycle and blood levels of melatonin rise
at night.

Parkinson, s disease :

in Parkinson, s disease , dopamine levels in the CNS are decreased because of a deficiency of cells that
produce dopamine and depression is associated with low levels of serotonin.

Other Nitrogen-Containing Compounds

A. Histamine

Histamine is a chemical messenger that mediates a wide range of cellular responses, including allergic and
inflammatory reactions, gastric acid secretion, and possibly neurotransmission in parts of the brain. A
powerful vasodilator, histamine is formed by decarboxylation of histidine in a reaction requiring pyridoxal
phosphate. It is secreted by mast cells as a result of allergic reactions or trauma. Histamine has no clinical
applications, but agents that interfere with the action of histamine have important therapeutic applications.

Figure (25): Biosynthesis of histamine

C. Serotonin

Serotonin, also called 5-hydroxytryptamine, is synthesized and stored at several sites in the body (Figure
21.18). By far the largest amount of serotonin is found in cells of the intestinal mucosa. Smaller amounts
occur in the central nervous system, where it functions as a neurotransmitter, and in platelets. Serotonin is
synthesized from tryptophan, which is hydroxylated in a reaction analogous to that catalyzed by
phenylalanine hydroxylase. The product, 5-hydroxytryptophan, is decarboxylated to serotonin. Serotonin
has multiple physiologic roles, including pain perception, affective disorders, and regulation of sleep,
temperature, and blood pressure.
   - 29 -
 

Figure (26):Synthesis of serotonin.

Serotinin

Acetyl –CoA Acetyl transferase

CoA-SH

N-Acetyl serotonin

S-Adenosylmethionine Methyl transferase

N-Acetyl -5-methoxyserotonin(Melatonin)

Figure(27) : Formation of melatonin from serotonin

D. Creatine

Creatine phosphate (also called phosphocreatine), the phosphorylated derivative of creatine found in
muscle, is a high-energy compound that can reversibly donate a phosphate group to adenosine diphosphate
to form ATP (Figure 21.19). Creatine phosphate provides a small but rapidly mobilized reserve of high-
energy phosphates that can be used to maintain the intracellular level of adenosine triphosphate (ATP)
during the first few minutes of intense muscular contraction. [Note: The amount of creatine phosphate in
the body is proportional to the muscle mass.
   - 30 -
 

Figure (28):Synthesis of creatine