Protein Metabolism

I. Proteins:
Proteins are high molecular weight molecules; they are
polymers of amino acid. There are two types of proteins:

1. Simple proteins which contain only amino acids.

2. Complex proteins (Conjugated proteins): which contain
in addition to amino acids non-amino acids such as
heme, vitamin derivatives, or lipid (lipoproteins), or
carbohydrates (glycoproteins).

Amino acids contain both amino and carboxylic functional

groups.

Although about 300 amino acids occur in nature, only 20 of

these occur in proteins.

1. Source of proteins:
Exogenous: take with the diet.
Endogenous: synthesized inside the human body.

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

In healthy adults, the total amount of protein in the body

remains constant, because the rate of protein synthesis is
equal to that is degraded. So the protein turnover, leads to
the hydrolysis and resynthesis of 300 to 400 g of body
proteins each day.

1
Rate of turnover:
The rate of protein turnover varies widely for individual proteins.

Short-lived proteins, with half -lives of minutes or hours (rapidly

degraded), such as many regulatory proteins and misfolded
proteins.

Long-lived proteins, with half-lives of days to weeks, constitute the

majority of proteins in the cell, such as structural proteins, like
collagen.

3. Protein degradation:

Protein can be existing in the dietary and inside the body.

A.Digestion of dietary proteins:

To maintain a healthy steady state the average adult requires
30-
60g (100g in U.S) of protein diet per day with quality protein
(containing essential amino acids) to compensated the lost of
protein via the intestine and the kidneys.
There are two main classes of proteolytic digestive enzymes
(proteases). Endopeptidases hydrolyze peptide bonds between
specific amino acids throughout the molecule. Exopeptidases
catalyze the hydrolysis of peptide bonds, one at a time, from the
ends of peptides.
The digestion of proteins begins by the following:

1. Stomach:
Entry of dietary proteins into the stomach stimulates the gastric
mucosa of the gastric glands to secrete the hormone gastrin.
Gastrin, stimulates the secretion of gastric juice—a
unique
solution containing:
a. HCL (pH 1.0 to 2.5): by the parietal cells of the gastric glands
which act as antiseptic and denaturing agent.
Excessive secretion of gastric acid, associated with Helicobacter
pylori infection, can result in the development of gastric and
duodenal ulcers. 2
 b. Pepsinogen: by the chief cells of the gastric glands.
Pepsinogen, an inactive precursor, or zymogen, is
converted to active pepsin.
Pepsin hydrolyzes ingested proteins at peptide bonds on the
amino- side of the aromatic amino acid residues Phe, Trp, and Tyr,
cleaving long polypeptide chains into a mixture of smaller peptides.
2. Pancreas:
As the acidic stomach large polypeptides pass into the small
intestine, stimulate to secretion the two following hormones into
the blood.
a. Secretin: stimulates the pancreas to secrete bicarbonate
into the small intestine to neutralize the gastric HCl, abruptly
increasing the pH to about 7.
b. Cholecystokinin: which stimulates secretion (by the exocrine
cells of the pancreas), of several inactive pancreatic enzymes.
Trypsinogen, chymotrypsinogen, procarboxypeptidases A
and B, these zymogens was converted to the active enzymes by
enteropeptidase (a proteolytic enzyme secreted by intestinal
cells) to produce.
1. Trypsin: cleavage the carbonyl side of amino acids lysine &
arginine.
2. Chymotrypsin: cleavage the carbonyl side of amino acids
phenyl alanine, tyrosine, tryptophane, and leucine, but
not cleave theme if the amino acid proline come after them
in the sequence of polypeptide chain.
3. Carboxypeptidases A: cleavage the C-terminal of all the
amino acids except arginine, lysine, and proline.
4. Carboxypeptidases B: cleavage the C-terminal of the
amino acids arginine & lysine.

3
 3. 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 (di- and tripeptides, and oligopeptides)

4
 4. Absorption of amino acids and dipeptides:
 Free amino acids are taken up by the intestinal epithelial cells.
 Dipeptides and tripeptides enter the brush border of the
intestinal mucosal cells, where they are hydrolyzed to free amino
acids, which are then transported into the hepatic portal vein.
 Relatively large peptides may be absorbed intact, either by
uptake into mucosal epithelial cells (transcellular) or by passing
between epithelial cells (paracellular). Many such peptides are
large enough to stimulate antibody formation—this is the basis
of allergic reactions to foods.
 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.

B. Protein degradation inside the body:

There are two major forresponsible
enzyme systems degrading damaged or
unneeded proteins:
1. ubiquitin-proteasome mechanism (energy-dependent):
mainly degrade endogenous proteins, that is, proteins that
were synthesized within the cell.
Ubiquitin-proteasome proteolytic pathway: Proteins are first
covalently attached to ubiquitin, a small, globular protein.
Ubiquitination occurs through linkage of the α-carboxyl glycine of
ubiquitin to an ε-amino lysine of protein. The consecutive addition
of ubiquitin moieties generates a polyubiquitin chain. Proteins
tagged with ubiquitin are then recognized by a large, barrel-
shaped, proteolytic molecule called a proteasome, which
functions like a garbage disposal. The proteosome cuts the target

5
protein into fragments that are then further degraded to amino
acids, which enter the amino acid pool. It is noteworthy that the
selective degradation of proteins by the ubiquitin proteosome
complex (unlike simple hydrolysis by proteolytic enzymes) requires
. ATP, that is, it is energy-dependent

2. Degradative enzymes of the lysosomes (non- energy-

dependent): primarily degrade extracellular proteins, such as
plasma proteins and cell-surface membrane proteins.

6
 C. Chemical signals for protein degradation:
Protein degradation cannot be random, because proteins
have different half-lives, and influenced by:
a. Some structural aspect. For example, some proteins that
have been chemically altered by oxidation or tagged with
ubiquitin are preferentially degraded.
b. The nature of the N-terminal residue. For example,
1. Proteins that have serine as the N-terminal amino acid
are long-lived, with a half-life of more than twenty hours.
2. Proteins with aspartate as the N-terminal amino acid
have a half-life of only three minutes.
3. Proteins rich in sequences containing proline, glutamate,
serine, and threonine (called PEST sequences after the
one-letter designations for these amino acids) are rapidly
degraded and, therefore, exhibit short intracellular half-
lives.

II. Amino acids Catabolism:

1. Amino acid pool:

Amino acids released by hydrolysis of dietary or tissue protein,
or synthesized de novo, mix with other free amino acids distributed
throughout the body. Collectively, they constitute the amino acid
pool as shown in the figure below.
The amino acid pool, containing about 100g of amino acids, is
small in comparison with the amount of protein in the body (about
12kg in a 70 kg man).
If the only fate of the amino acid pool were to be used to re-
synthesize body proteins, adults would not have a significant need
for additional dietary protein. However, only about 75
percent of
7
the amino acids obtained

tahrough hydrolysis of body

protein are reutilized for new
protein synthesis.
The remainders are
metabolized or serve as
precursors for the compounds
nitrogen containing such as
porphyrins, creatine,
,neurotransmitters , purines
pyrimidines, and other
nitrogen containing
compounds, shown as
. Figure in
In well-fed individuals, this
metabolic loss of amino acids
is compensated for by dietary
protein, which contributes to
the amino pool.

2. Transport of amino
acids into cells:
The movement of free amino
acids from extracellular
fluids
to inside the cell is against the
concentration gradient using

8
active transport systems, which require energy, obtain
from hydrolysis of ATP
At least seven different transport systems are known that have
overlapping specificities for different amino acids.

Cystinuria:
 It is the inherited disorder resulting in the defective on the one of
the transport system that is responsible for reabsorption of the
amino acids cystine, ornithine, arginine, and lysine in kidney
tubules, resulting in the appearance of all four amino acids in the
urine.
 Cystinuria occur every 1 of 7000 individuals, making it one of the
most common inherited diseases, and the most common
genetic error of amino acid transport.
 The disease expresses itself clinically by the precipitation of
cystine to form kidney stones (calculi), which can block the
urinary tract.
 Oral hydration is an important part of treatment for this disorder.

3. Amino acids degradation:

 One important feature distinguishes amino acid degradation
from other catabolic processes, that is the amino groups and the
carbon skeleton take separate but interconnected pathways.
 Amino acids that are not immediately incorporated into new
protein are rapidly degraded; means that excess amino acids
are not stored also excess amino acids are not excreted as
such.

9
a. Amino group degradation:
1. Removal of nitrogen from amino acids:
 The presence of the α-amino group keeps amino acids safely
locked away from oxidative breakdown.
 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.
 Transamination & oxidative deamination reactions is the
most two reactions used for amino group removal.
a. Transamination reaction: Aminotransferases:
 Its transfer of an amino group from an amino acid to an α –
keto glutarate (a common amino group acceptor) to form
glutamate.

 Transamination is the tunneling of amino groups to

glutamate.
 Glutamate then can be oxadatively deaminated, or used
as an amino group donor in the synthesis of nonessential
amino acids.

10
  Aminotransferases: (transaminases):
enzymes found in Are a
familywhich, of
intestine, and muscle cells) the of cytosol
transfer amino
ofskeleton to
groups from one carbon the
another. liver,
 All amino acids are participating
kidney, in transamination, with the
exception of proline, hydroxyproline, lysine and threonine,
which lose their α-amino groups by deamination.
 The two most important aminotransferase reactions are
catalyzed by alanine aminotransferase (ALT), formerly
called glutamate pyruvate transaminase (GPT) and
aspartate aminotransferase (AST), formerly called
glutamate:oxaloacetate transaminase (GOT).

1. Mechanism of aminotransferases action:

 All aminotransferases require the coenzyme pyridoxal
phosphate (PLP 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.

11
  Aminotransferases act by transferring the amino group of an
amino acid to the pyridoxal part of the coenzyme to generate
pyridoxamine phosphate.
 The pyridoxamine form of the coenzyme then reacts with an
α-keto acid to form an amino acid at the same time
regenerating the original aldehyde form of the coenzyme.
 The figure below shows these two component reactions for
the reaction catalyzed by aspartate aminotransferase.

2. Equilibrium of transamination reactions:

For most transamination reactions, the equilibrium constant is near
one, which mean allowing the reaction to function in both amino
acid degradation through removal of α-amino groups (protein-rich
meal), and biosynthesis through addition of amino groups to the
carbon skeletons of α-keto acids (protein-poor meal).

12
 3. Diagnostic value of plasma aminotransferases:
 Aminotransferases are normally intracellular enzymes, with
the low levels found in the plasma.
 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.

Liver disease: Plasma AST and ALT are elevated in nearly all
liver diseases, particularly in conditions that cause extensive cell
necrosis, such as severe viral hepatitis, toxic injury. ALT is more
specific for liver disease than AST, but AST is more sensitive
because the liver contains larger amounts of AST.
The figure below shows the early release of ALT into the serum,
following ingestion of a liver toxin.

Note: Elevated serum bilirubin results from heptocellular damage

that decreases the hepatic conjugation and excretion of bilirubin.

Nonhepatic disease: Aminotransferases may be elevated in

nonhepatic disease, such as myocardial infarction and muscle

13
disorders. However, these disorders can usually be distinguished
clinically from liver disease.

b. Oxidative deamination: (Glutamate dehydrogenase):

An amino group is replaced by
a carbonyl(c = o)
group,
liberation as free ammonia
(NH4).
These reactions occur
primarily liver thein and
kidney.
They provide α-ketoacids that
can enter the central pathway
of energy metabolism, and
ammonia, which is a source of
nitrogen in urea synthesis.
Glutamate dehydrogenase:
is the enzyme that catalyzed
the deamination reaction.

1. Coenzymes: Glutamate
dehydrogenase is
unusual in that it can
use either NAD+ or
NADPH as a coenzyme.

NAD+ is used primarily in oxidative deamination (disposal of amino acids).

NADPH is used in reductive amination (synthesis of amino acids(.

14
 2. Direction of reactions:
 The direction of the reaction depends on the relative
concentrations of glutamate, α-ketoglutarate, and ammonia,
and the ratio of oxidized to reduced coenzymes.
 Protein-rich meal leads to elevated levels of glutamate in the
liver, and the reaction proceeds in the direction of amino acid
degradation and the formation of ammonia.
 Protein-poor meal leads to synthesis amino acids from the α-
ketoacids.
3. Allosteric regulators:
ATP and GTP are allosteric inhibitors of glutamate
dehydrogenase, whereas ADP and GDP are activators of the
enzyme.

2. Nitrogen balance:

Refers to the difference between the total nitrogen intake of a

human (and other organism) and its total nitrogen loss.

a. Nitrogen equilibrium: when nitrogen intake equals nitrogen

loss. This is the condition of healthy adults.
b. Positive nitrogen balance: a condition that is characteristic
of growing children, pregnant women. Nitrogen intake
exceeds nitrogen loss.
c. Negative nitrogen balance: exists when an individual
cannot replace nitrogen losses with dietary sources.
3. Nitrogen compounds excretion:
 Ammonotelic excrete nitrogen compound as ammonia (fish).
 Uricotelic excrete nitrogen compound as uric acid (Bird).
 Ureotelic excrete nitrogen compound as urea (Mammals).

15
In healthy adult subject, 95% of nitrogen is eliminated by the
kidneys and the remaining 5% in the feces.
4. Ammonia toxicity:
 Since approximately 16% of the atomic mass of protein is
nitrogen (28N 20aa+additional 1N from Asn, Gln and Lys +3N Arg
+2N His the eq. is [28N X14atm/20aaXavaregeMW120]X100=
16.33%), means that 5-7g of nitrogen (mean 30g of protein) is
lost as ammonia per day.
 Ammonia is highly toxic; tissues convert ammonia to the
amide nitrogen of nontoxic glutamine.
 Subsequent deamination of glutamine in the liver releases
ammonia, which is then converted to nontoxic urea.
Terminal stages of ammonia intoxication:
 Ridding the cytosol of excess ammonia requires reductive
amination of α-ketoglutarate to glutamate, and conversion of
glutamate to glutamine for removal of ammonia.
 High levels of NH4+ lead to increased levels of glutamine,

which acts as an osmotically active solute (osmolyte) in brain

astrocytes (star-shaped cells of the nervous system that
provide nutrients, support, and insulation for neurons).
 This triggers an uptake of water into the astrocytes to
maintain osmotic balance, leading to swelling which leads to
comatose state accompanied by cerebral edema (an
increase in the brain’s water content) and increased cranial
pressure.
5. 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.

16
 a. Glutamine synthetase -
glutaminase mechanism:
Found in most tissues, uses
glutamine synthetase to combine
ammonia with glutamate to form
glutamine—a nontoxic transport
form of ammonia (Figure beside).
The glutamine is transported in the
blood to the liver where is cleaved
by glutaminase to produce
glutamate and free ammonia.

b.Glucose-alanine cycle:
This pathway used primarily
by muscle, involves
transamination
pyruvate )the of
end-product of
to glycolysis)anaerobic to form
alanine. (ALT or GPTreaction).
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.

17
 6. Urea cycle:
 Urea is the major disposal form of amino groups of amino
acids, and accounts for about 90% of the nitrogen-containing
components of urine.
 Urea molecule is supplied by;
 One nitrogen of the free NH3 and the other nitrogen by
aspartate.
 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.
Note: Glutamate is the immediate precursor of both ammonia
(through oxidative deamination by glutamate dehydrogenase) and
aspartate nitrogen (through transamination of oxaloacetate by
aspartate aminotransferase).

a. Reactions of the cycle:

Five enzymatic reactions leading to the synthesis of urea.
The first two reactions occur in the mitochondria, whereas the
three remaining are located in the cytosol, as shown in the figure
below.
1. Formation of carbamoyl phosphate:
 Condensation of 1 mole each of NH4+ (provided by the
oxidative deamination of glutamate), CO2 ( as HCO3
mitochondrialbyproduced respiration) and phosphate
(derived from ATP) to form carbamoyl phosphate.
 It is catalyzed by Carbamoyl phosphate synthetase I, an
enzyme present in liver mitochondria.
 The nitrogen atom derived from this ammonia becomes one
of the nitrogens of urea.
 The reaction is driven by cleavage of two molecules of ATP.

18
Note: Carbamoyl phosphate synthetase II participates in the
.biosynthesis of pyrimidines, and occurs in the cytosol

2. Formation of citrulline:
 Transfer of carbamoyl moiety from carbamoyl phosphate to
ornithine, forming citrulline + Pi, is catalyzed by ornithine
transcarbamoylase of liver mitochondria.
 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.

19
Note: Ornithine and citrulline are basic amino acids that participate
in the urea cycle, but they are not incorporated into cellular
proteins, because there are no codons for these amino acids

3. Synthesis of argininosuccinate:
 Citrulline condenses with aspartate to form argininosuccinate,
is catalyzed by argininosuccinate synthase.
 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 AMP and pyrophosphate (PPi).
 This is the third and final molecule of ATP consumed in the
formation of urea.
4. Cleavage of argininosuccinate:
 Argininosuccinate is cleaved to yield arginine and fumarate,
is catalyzed by argininosuccinate lyase.
 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;

1. The malate can be transported into the mitochondria

via the malate shuttle and reenter the TCA cycle.
2. Alternatively, cytosolic malate can be oxidized to
oxaloacetate, which can be converted to aspartate. (By AST
or GOT enzymatic reaction).
3. Malate can be converted to pyruvate then to glucose.

20
.
 5. Cleavage of arginine to ornithine and urea:
Arginase cleaves arginine to ornithine and urea, and occurs almost
exclusively in the liver.

b. Overall stoichiometry of the urea cycle:

1. The overall equation is:
Aspartate + NH3 + CO2 + 3ATP —> Urea + fumarate + 2 ADP + AMP + 2 Pi +PPj + 3 H2O

2. Four high-energy phosphates are consumed in the synthesis

of each molecule of urea: two phosphates are needed to
restore two ADP to two ATP, plus two to restore AMP to ATP.
3. 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.
4. Glutamate is the immediate precursor of both ammonia
(through oxidative deamination by glutamate dehydrogenase)
and aspartate nitrogen (through transamination of
oxaloacetate by aspartate aminotransferase).

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).
 N-Acetylglutamate is synthesized from acetyl CoA and
glutamate, as shown in the figure below, 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.
21
 d. 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
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
hyperamonemia often seen in these patients.
 Oral administration of neomycin reduces the number of
intestinal bacteria responsible for this NH3 production.
e. General features of metabolic disorders associated with
urea cycle:
The comparatively rare, but medically devastating, illustrate
the
following important principles biosynthesis
1. Similar symptoms can characterize any enzyme defects
on
the cycle.
2. Rational therapy must be based on an understanding of
the
relevant enzymatic reactions in both normal and impaired
individuals.
3. The identification metabolites that accumulate prior to a
metabolic block provides the basis for metabolic screening
tests and can implicate the reaction that is impaired.
4. Precise diagnosis requires quantitative assay of the activity
of the enzyme suspected to be defective.
5. The DNA sequence of the gene that given mutant enzyme is
compared to that of the wild-type
22 gene to identify the specific
mutation(s) that cause the disease.
 7. Metabolism of Ammonia
 Ammonia is produced by all tissues are transported to the liver and
converted to the urea. Ammonia level 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, as mentioned previously
A. Sources of ammonia
 Amino acids are quantitatively the most important source of
ammonia, the linking of aminotransferase and glutamate
dehydrogenase reactions—producing ammonia.
 However, substantial amounts of ammonia can be obtained from
other sources.
1. From glutamine:
 The kidneys generate ammonia from glutamine by the actions of
renal glutaminase and glutamate dehydrogenase. Most of this
ammonia is excreted into the urine as NH4+, which provides an
important mechanism for maintaining the body’s acid-base balance
through the excretion of protons.
 Ammonia is also obtained from the hydrolysis of glutamine by
intestinal glutaminase. The intestinal mucosal cells obtain
glutamine either from the blood or from digestion of dietary
protein.
Note: Intestinal glutamine metabolism produces citrulline, which travels to the
kidney and is used to synthesize arginine.
2. From bacterial action in the intestine:
Ammonia is formed from urea by the action of bacterial urease in the
lumen of the intestine. This ammonia is absorbed from the intestine by
portal vein and removed by the liver via conversion to urea.
3. From amines: Amines obtained from the diet, and monoamines that
serve as hormones or neurotransmitters, give rise to ammonia by the
action of amine oxidase.
4. From purines and pyrimidines: In the catabolism of purines and
pyrimidines, amino groups attached to the rings are released as ammonia
(conversion of adenosine to inosine by adenosine deaminase and
conversion of guanine to xanthine by guanase).

23
B. Transport of ammonia in the circulation
Ammonia is constantly produced in the tissues, but it is present at
very
low levels in blood, because it released as amino acid nitrogen in the
form of glutamine or alanine, rather than as free ammonia.

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 (5–35 mol/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 mol/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 intoxication, which include tremors, slurring of speech,
somnolence, vomiting, cerebral edema, and blurring of vision.
 At high concentrations, ammonia can cause coma and death. The
two major types of hyperammonemia are:

1. Acquired hyperammonemia:
 Liver disease is a common cause of hyperammonemia in
adults, and may be due, for example, to viral hepatitis or to
hepatotoxins such as alcohol. Cirrhosis of the liver may result in
formation of collateral circulation around the liver.
 As a result, portal blood is shunted directly into the systemic
circulation and does not have access to the liver. The conversion of
ammonia to urea is, therefore, severely impaired, leading to
elevated levels of ammonia.
2. Congenital hyperammonemia:

 Genetic deficiencies of each of the five enzymes of the urea cycle

have been described, with an overall prevalence estimated to be
1:25,000 live births. Ornithine transcarbamoylase deficiency,
which is X-linked, is the most common of these disorders,
predominantly affecting males, although female carriers may
become symptomatic.
24
  All of the other urea cycle disorders follow an autosomal recessive
inheritance pattern. In each case, the failure to synthesize urea
leads to hyperammonemia during the first weeks following birth.
Note: The hyperammonemia seen with arginase deficiency is less severe
because arginine contains two waste nitrogens and can be excreted in
the
urine.
 Historically, urea cycle defects had high morbidity (neurological
manifestations) and mortality.
 Treatment included restriction of dietary protein in the presence of
sufficient calories to prevent catabolism. Administration of
compounds that bind covalently to amino acids, producing
nitrogen-containing molecules that are excreted in the urine, has
improved survival.
 For example, phenylbutyrate given orally is converted to
phenylacetate. This condenses with glutamine to form
phenylacetylglutamine, which is excreted (Figure below).

of administrationby defects cycle urea with patientsof Treatment

phenylbutyrate to aid in excretion of ammonia

25
Healthy note for urea:
a. Blood urea is elevated in:
1. Renal insufficiency.
2. Acute or chronic nephritis.
3. Acute renal failure.
4. Urinary tract obstruction.
5. Dehydration.
6. Shock.
7. Adrenal insufficiency.
8. Congestive heart failure.
9. Upper gastrointestinal bleeding due to:
a. Increase protein absorption from digestion of blood.
b. Decrease renal blood flow.
b. Blood urea is decreased in:
10.Hepatic failure.
11.Glomerulonephritis not complicated by renal insufficiency.
12.Cachexia.
c. Urea normal values:
 Normal blood urea level of adult (male & female) is: 20-40
mg/dl.
 Normal level for new born is: 9-36 mg/dl.
 Normal level in children: 15-40 mg/dl.

26
 f. Carbon skeletons of amino acids breakdowns:

 Removal of α-amino nitrogen by transamination is the first

catabolic reaction of amino acids except in the case of
proline, hydroxyproline, threonine, and lysine.
 The residual hydrocarbon skeleton of 20 amino acids is
then degraded to form seven intermediate products
pyruvate, oxaloacetate, α-ketoglutarate, succinyl CoA,
fumarate, acetyl CoA, and acetoacetyl CoA. As shown
in the figure below:

 Amino acids catabolism represents for 10 to 15% of the

human body’s energy production.
 The metabolic diseases or “inborn errors of metabolism”
associated with these processes.
 Left untreated, they can result in irreversible brain damage
and early mortality.
1. Glucogenic and ketogenic amino acids:
Amino acids can be classified according to its catabolism as:
a. Glucogenic amino acid: Amino acids whose catabolism
yields pyruvate or one of the intermediates of the citric acid
27
 cycle, which give rise to glucose through gluconeogenesis
pathway are termed glucogenic or glycogenic.

b. Ketogenic amino acid: Amino acids whose catabolism

yields either acetoacetate or one of its precursor, (acetyl
CoA or acetoacetyl CoA) are termed ketogenic.

c. Glucogenic & Ketogenic amino acid:

2. Enzyme cofactors of amino acid catabolism:

Several cofactors play important roles in chemical rearrangements

occur in the catabolic pathways of amino acids involves:
a. Transamination reactions: Requiring pyridoxal phosphate.
b. One-carbon transfers:
1. Biotin: Transfers carbon on its most oxidized state, CO2.

28
2. .S-adenosylmethionine (SAM(; ,Transfers methyl groups
the most reduced state of carbon.

3. Tetrahydrofolate (THF ):
 Carry and transfers one-carbon groups in an intermediate
oxidation states and sometimes as methyl groups. such
as methyl group CH3 (most reduced form), methylene
group CH2 (more oxidized form), and methenyl CH, formyl,
HC=O or formimino group HC=NH (most oxidized forms).
 THF are reduced form of folic acid (oxidized form).
 Folic acid is a vitamin can be converted in two steps to
THF by the enzyme dihydrofolate reductase (DHFR).

29
 The one-carbon group undergoing transfer, in any of 
.three oxidation states, is bonded to N-5 or N-10 or both
The most reduced form of the cofactor carries a methyl 
group, a more oxidized form carries a methylene group,
and the most oxidized forms carry a methenyl, formyl, or
. formimino group

c. Tetrahydrobiopterin (BH4): another cofactor of amino acid

catabolism, is similar to the pterin moiety of tetrahydrofolate,
but it is not involved in one-carbon transfers; instead it
participates in oxidation reactions.

30
 3. Catabolism of the carbon skeletons of amino acids
The pathways by which amino acids are catabolized they are
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 pyruvate:

 The three carbon atoms of Ser, Ala, and Cys are converted
to pyruvate.
 Six amino acids form pyruvate are Thr, Gly, Trp, Ser, Ala,
and Cys and subsequently acetyl-CoA.

31
Glycinuria:
 An inherited disease.
 Increased urinary excretion of glycine.
 Plasma glycine levels are normal so the condition may results
from a defect in renal tubular reabsorption.

Primary hyperoxaluria:

 An inherited disease.
 The defect in primary hyperoxaluria is the failure to catabolize
glyoxylate formed by deamination of glycine.
 Subsequent oxidation of glyoxylate to oxalate results in
urolithiasis, nephrocalcinosis, and early mortality from renal
failure or hypertension.
 Crystals of calcium oxalate account for up to 75% of all kidney
stones.

Nonketotic hyperglycinemia:

 Autosomal recessive disorder

 Result of defects in glycine cleavage enzyme activity.
 The condition is characterized by elevated serum levels of
glycine, leading to severe mental deficiencies and death in very
early childhood.
 At high levels, glycine is an inhibitory neurotransmitter, perhaps
explaining the neurological effects of the disease.

Cystinosis (cystine storage disease):

 Caused by a defective cystine transporter of
lysosomal membrane from lysosomal vesicles to the cytosol
 Stored cystine forms crystals with deposition in tissue cells
and early mortality from acute renal failure.

32
 b. Amino acids that form oxaloacetate:
The four carbon atoms of Asparagine & Aspartate are
converted to oxaloacetate.

Asparagenase and acute lymphoplastic leukemia (ALL):

Some rapidly dividing leukemic cells cannot synthesize sufficient

asparagine to their growth. This makes require asparagine from
the blood. Asparaginase, which hydrolyzes asparagine to
aspartate, can be administered systemically to treat leukemic
patients. Asparaginase lowers the level of asparagine in the
plasma and, therefore, deprives cancer cells of a required nutrient.

c. Amino acids that form α-ketoglutarate:

 The five carbon atoms of Glu converted to α-ketoglutarate.
 Five amino acids form α-ketoglutarate are His, Gln, Arg and Pro
are converted to Glu, and subsequently α-ketoglutarate.

33
Diagnostic of folic acid defifiency
Individuals deficient in folic acid excrete increased amounts of N-
forminino-glutamate (FiGlu) in the urine, particularly after ingestion
of a large dose of histidine. The FiGlu excretion test has been
used in diagnosing a deficiency of folic acid.
Benign disorders of histidine catabolism include histidinemia and
urocanic aciduria associated with impaired histidase.
Gyrate atrophy of the retina:
 Mutations in ornithine δ -aminotransferase elevate plasma
and urinary ornithine.
 Treatment involves restricting dietary arginine.
Type I hyperprolinemia & Type II hyperprolinemia:
 Both are autosomal recessive traits, and are consistent with a
normal adult life.
 The metabolic block in type I hyperprolinemia is at proline
dehydrogenase. There is no associated impairment of
hydroxyproline catabolism.
 The metabolic block in type II hyperprolinemia is at glutamate-γ -
semialdehyde dehydrogenase, an enzyme that also functions in
hydroxyproline catabolism.

34
d. Amino acids that form succinyl CoA:
Four amino acids form succinyl CoA
1. Valine & 2. isoleucine: branched-chain amino acids.
3. Threonine.
4. Methionine.

35
L o w concentration of folate , vitamin B12, or B6 may be
increase the level of homocysteine.
 Elevated homocysteine level is an independent risk factor for
heart disease and stroke.

Maple Syrup Urine Disease (MSUD) (branched-chain ketonuria).

 Partial or complete deficiency in branched-chain α-ketoacid

decarboxylase.
 Symptoms: Neurological problems, mental
retardation, Physical disabilities and death.
 Treatment: limited leucine, isoleucine and valine.

e. Amino acids that form fumarate:

Phenylalanine & Tyrosine.

Type II tyrosinemia (Richner-Hanhart syndrome): increasing

excretion of tyrosine (reaction 1).
Neonatal tyrosinemia, due to lowered p -hydroxyphenylpyruvate
hydroxylase activity (reaction 2). Therapy employs a diet low in
protein.
Alkaptonuria: An inherited disease. The defect is lack
of
homogentisate oxidase (reaction 3).
The urine darkens on exposure to air due to oxidation of excreted
homogentisate. Late in the disease, there is arthritis
and 36
connective tissue pigmentation (ochronosis) due to oxidation of
homogentisate to benzoquinone acetate, which polymerizes and
binds to connective tissue.
Type I tyrosinemia (tyrosinosis): A defect in
fumarylacetoacetate hydrolase (reaction 4). Therapy employs a
diet low in tyrosine and phenylalanine. Untreated acute and
chronic tyrosinosis leads to death from liver failure.
Phenylketonuria (PKU):
• Hyperphenylalaninemia
• Defect in the conversion of Phenylalanine to Tyrosine
• Deficiency in any of the following enzymes:
1. phenylalanine hydroxylase (majority).
2. Dihydrobiopterin (BH2) synthetase.
3. Dihydrobiopterin (BH2) reductase.

 Characteristics of PKU:
1. Symptoms associated with PKU: Elevated phenylalanine
and low level of Tyrosine.
2. CNS Symptoms: Mental retardation, failure to walk or talk,
seizure, and failure to grow.
3. Hypopigmentation: fair hair, light skin color and blue eyes,
no melanin, as a result in the deficiency for produced
tyrosine which is responsible for these symptoms.

37
Treatment:
1. Deficiency in phenylalanie hydroxylase (PAH):
 special diet low in phenylalanine for the rest of their life.
 injectable PAH.
2. Deficit in tetrahydrobiopterin BH4: administration of BH4.
f. Amino acids that form acetyl CoA.
Seven amino acids form acetyl CoA, divided in the following;
3. Two amino acids (Ile & Thr) forming acetyl CoA.
4. Three amino acids (Phe, Tyr & Lys) forming acetoacetyl-
CoA then acetyl CoA.
5. Two amino acids (Leu & Trp) are participating in forming
both 1& 2 above.

38
III. Biosynthesis of nonessential amino acids:
 Twelve nonessential amino acids are synthesized from
intermediates of metabolism.
 Tyrosine and cysteine, are nonessential amino acids, but
they are synthesized from essential amino acids.
 Histidine and arginine, are generally classified as
nonessential. However, their normal concentrations are limit
in, and, during periods of tissue growth as in children, so
they are needed to be supplemented in the diet.
 hydroxyproline and hydroxylysine are modified after their
incorporation into the protein (posttranslational modification).

1. Synthesis from α- ketoacids:

A. Alanine.
B. Aspartate.
C. Glutamate.
Are synthesized by transfer of an amino group to the α-
keto
acids.

39
2. Synthesis by amidation:
A. Glutamine.

B. Asparagine.

3. Proline:
From glutamate by cyclization and reduction reactions.

4. Serine, glycine and cysteine:

40
Homocystinuria:

 Defect in cystathionine β-synthase.

 Symptoms: Ectopic lentis, skeletal abnormalities, premature

arterial disease, osteoporosis, and mental retardation.

 Treatment: restriction of methionine intake, administration of

Vitamins 6, B12 and folate.

5. Tyrosine:

Albinism: caused by
a
deficiency ofconsequently,
enzyme, a tyrosinase black
melanin,
found in skin, hair, & eyes, is
. not produced
pigment

Affected individuals
albinos) (called are
extremely
to sunlight. In
sensitiveto their susceptibility
addition
to skin cancer & sunburn,
the eyesight is often
.affected
41