The document provides a detailed overview of the urea cycle, its enzymes, regulation, and associated disorders. It explains how ammonia, a toxic byproduct of amino acid breakdown, is converted into urea for safe excretion via the kidneys, highlighting the critical role of liver enzymes. Additionally, it discusses urea cycle disorders, their genetic basis, symptoms, and potential treatments, emphasizing the importance of timely intervention to prevent severe outcomes.

1. UREA CYCLE AND UREA
CYCLE DISORDERS
PREPARED BY : RABIA KHAN BABER
COURSE TITLE : BIOCHEMISTRY

2. AIMS AND OBJECTIVES OF CLASS
WHAT IS AMMONIAAND ITS ROLE
UREA CYCLE INTRODUCTION
IMPORTANT ENZYMES OF UREA CYCLE
REACTIONS OF UREA CYCLE
REGULATION OF UREA CYCLE
RELATED DISEASES OF UREA CYCLE
UREA CYCLE DISORDERS AND INHERITANCE

3. NITROGEN EXCRETION FROM AN AA
During fasting, muscle protein is cleaved to amino acids, some of which are
partially oxidized to produce energy. Portions of these amino acids are
converted to alanine and glutamine, which, along with other amino acids are
released into the blood. Glutamine is oxidized by various tissues, including
the gut and kidney, which convert some of its carbons and nitrogen to alanine.
Alanine and other amino acids travel to the liver, where the carbons are
converted to glucose and ketone bodies and the nitrogen is converted to urea,
which is excreted by the kidneys. Several enzymes are important in the
process of interconverting amino acids and in removing nitrogen so that the
carbon skeletons can be utilized. These include transaminases, glutamate
dehydrogenase and deaminases. Because reactions catalyzed by transaminases
and glutamate dehydrogenase are reversible, they can supply amino groups
for the synthesis of non-essential amino acids.

4. Transamination is the major process
for removing nitrogen from amino
acids. transfer of an amino group
from one amino acid to another α-
keto acid by Transaminase
(aminotransferase). The nitrogen from
one amino acid thus appears in
another amino acid.
Because transamination reactions are
reversible they can be used to remove
nitrogen from amino acids or to
transfer nitrogen to α-keto acids to
form amino acids. They participate in
both amino acid degradation and
amino acid synthesis.

5. AMMONIA
Ammonia (NH3) is a metabolite that results predominantly from protein
and amino acid degradation. Ammonia is an extremely toxic base and its
accumulation in the body would quickly be fatal so it is converted to
urea, which is nontoxic, very soluble, and readily excreted by the
kidneys through urine.

6. ROLE AND SIGNIFICANCE OF
AMMONIA
Ammonia does not have a physiologic function. However, it is
important clinically because it is highly toxic to the nervous system.
Because ammonia is being formed constantly from the deamination of
amino acids derived from proteins, it is important that mechanisms exist
to provide for the timely and efficient disposal of this molecule. The
liver is critical for ammonia catabolism because it is the only tissue in
which all elements of the urea cycle, providing for the conversion of
ammonia to urea. Ammonia is also consumed in the synthesis of
nonessential amino acids, and in various facets of intermediary
metabolism.

7. Ammonia in the circulation
originates in a number of different
sites. A diagram showing the
major contributors to ammonia
levels
AMMONIA IN THE CIRCULATION

8. UREA CYCLE
(KREBS–HENSELEIT CYCLE)
The urea cycle is the metabolic pathway that transforms nitrogen to
urea for excretion from the body. Liver cells play a critical role in
disposing of nitrogenous waste by forming urea hrough the action of
the urea cycle.
Nitrogenous excretory products are then removed from the body
through in the urine.
The urea excreted each day by a healthy adult (about 30 g) accounts
for about 90% of the nitrogenous excretory products.
The cycle occurs mainly in the liver.

9.  Location of Urea Cycle:
Cytosol and mitochondria of hepatocytes.
 Substrates:
NH3 (as derived from oxidative deamination of glutamate); CO2;
aspartate; three ATP.
 Products:
Urea; fumarate; H2O.
 Purpose of the Urea Cycle:
The urea cycle allows for the excretion of NH4
+ by transforming
ammonia into urea, which is then excreted by the kidneys.

10. IMPORTANT ENZYMES IN UREA CYCLE
Carbamoyl phosphate synthetase I: Converts ammonium and bicarbonate
into carbamoyl phosphate. This is the rate-limiting step in the urea cycle.
This reaction requires two ATP and occurs in the mitochondria.
Ornithine transcarbamoylase: Combines ornithine and carbamoyl
phosphate to form citrulline. Located in mitochondria.
Argininosuccinate synthetase: Condenses citrulline with aspartate to form
arginosuccinate. This reaction occurs in the cytosol and requires one ATP.
Argininosuccinate lyase: Splits argininosuccinate into arginine and
fumarate. Occurs in the cytosol.
Arginase: Cleaves arginine into one molecule of urea and ornithine in the
cytosol. The ornithine is then transported back into the mitochondria for
entry back into the cycle.

11. STAGES OF UREA CYCLE
THE MITOCHONDRIAL STAGE
• The first two steps of the urea
cycle occur in the mitochondria
of the cell. First, the enzyme
carbamoyl phosphate synthetase
(CPS) takes ammonia and
bicarbonate, and forms
carbamoyl phosphate with the
use of ATP.
THE CYTOSOLIC STAGE
• Argininosuccinate synthetase
(AS) takes the citrulline formed
in the mitochondrial stage, and
condenses it with aspartate to
form argininosuccinate. This
occurs by the formation of an
intermediate, citrulline-AMP.

12. REACTIONS OF THE
UREA CYCLE

13.  Step #1; Synthesis of Carbomyl phosphate
Carbamoyl phosphate is synthesized in the first reaction This is the rate-
limiting step in the urea cycle. This reaction requires two ATP and occurs in
the mitochondria.
Enzyme: carbamoyl phosphate synthetase I, which is located in mitochondria
and is activated by N-acetylglutamate.
NH3 + CO2 + 2ATP → carbamoyl phosphate + 2ADP + Pi
 Step#2:Synthesis of Citruline
Ornithine reacts with carbamoyl phosphate to form citrulline. Inorganic
phosphate is released.
Enzyme: ornithine transcarbamoylase, which is found in mitochondria. The
product, citrulline, is transported to the cytosol in exchange for cytoplasmic
ornithine.
Carbamoyl phosphate + ornithine → citrulline + Pi

14.  Step#3;Synthesis of Argininosuccinate
The third step is catalyzed by an enzyme called argininosuccinate
synthetase, which uses citrulline and ATP to form a citrullyl-AMP
intermediate, which reacts with an amino group from aspartate to produce
argininosuccinate
Enzyme: Argininosuccinate synthetase
Citrulline + ATP + aspartate → argininosuccinate + AMP + PPi
 Step#4;Cleavage of Argininosuccinate
Argininosuccinate is cleaved to form arginine and fumarate.
Enzyme: argininosuccinate lyase. This reaction occurs in the cytosol.
Argininosuccinate → arginine + fumarate

15.  Step#5; Cleavage of Arginine to Ornithine and Urea
Arginine is cleaved to form urea and regenerate ornithine.
Enzyme: arginase, which is located primarily in the liver and is inhibited
by ornithine.
Urea passes into the blood and is excreted by the kidneys.
Arginine → urea + ornithine
 Fate of Ornithine;
Ornithine is transported back into the mitochondrion (in exchange for
citrulline) where it can be used for another round of the cycle.
When the cell requires additional ornithine, it is synthesized from glucose
via glutamate.

16.  Regulation of Urea Cycle:
Carbamoyl phosphate synthetase I catalyzes the rate-limiting step of the
cycle and is stimulated by N -acetylglutamate.
Although the liver normally has a great capacity for urea synthesis, the
enzymes of the urea cycle are induced if a high-protein diet is consumed
for 4 days or more.
 Related Diseases of Urea Cycle:
Hyperammonemia occurs when there is a deficiency in one of more of the
urea cycle enzymes, causing insufficient removal of NH4
+.
Ammonia intoxication leads to CNS deterioration in the form of mental
retardation, seizure, coma, and death.

17. OVER ALL ENERGETICS OF THE
CYCLE

18. SIGNIFICANCE OF THE UREA CYCLE
The main purpose of the urea cycle is to eliminate toxic ammonia from
the body. About 10 to 20 g of ammonia is removed from the body of a
healthy adult every day. A dysfunctional urea cycle would mean excess
amount of ammonia in the body, which can lead to hyperammonemia
and related diseases. The deficiency of one or more of the key enzymes
catalyzing various reactions in the urea cycle can cause disorders related
to the cycle. Defects in the urea cycle can cause vomiting, coma and
convulsions in new born babies. This is often misdiagnosed as
septicemia and treated with antibiotics in vain. Even 1mm of excess
ammonia can cause severe and irreversible damages.

19. UREA CYCLE

21. UREA CYCLE DISORDERS (UCD)
A urea cycle disorder (UCD) is an inherited disease that affects how
the body removes the waste that is made from breaking down protein
When a person eats food that contains protein, the body breaks it
down into amino acids and uses only what it needs. It changes the rest
into nitrogen, which must then be removed by the body.

22. CAUSES OF UCD
The liver in a person with urea cycle disorder is missing an enzyme
necessary to convert nitrogen into urea. As a result, ammonia, a highly toxic
substance, builds up in the bloodstream and is not removed from the body.
Untreated, the high amounts of ammonia can cause brain damage, coma and
eventually death.
Urea cycle disorders are genetic. Genes give the body instructions on how
to break down protein. We usually have two copies of each gene, and most
UCD only occur when a person inherits a changed gene from both
parents. The exception is OTC deficiency, which is passed to the baby
through the mother who is most affected.

23. AUTOSOMAL RECESSIVE
INHERITANCE
 Autosomal recessive inheritance occurs when each parent carries
one abnormal gene. The disorder only becomes apparent when both
copies of the gene are abnormal.
 In order for an individual to have two abnormal copies of a gene, an
abnormal copy of the gene must be inherited from both parents.
 Even though both parents are carrying one abnormal gene they are
usually healthy.

24. Diagram showing hereditary passing of recessive gene

25. AUTOSOMAL DOMINANT
INHERITANCE
Autosomal dominant inheritance occurs when the abnormal gene that
is inherited overrides the normal gene in the pair.
Males and females pass on this type of disorder equally. Only one
parent has to have the affected gene to pass it on to the child, who then
has a 50 per cent chance of inheriting the gene and therefore the
disorder.
The same risk applies to each conception, regardless of the outcome
of previous conceptions.

26. Diagram showing hereditary passing of dominant gene

27. Urea cycle disorders are named based on the initials of the missing
enzyme. They are:
OTC – Ornithine transcarbamylase
ASD – Aargininosuccinic acid synthetase (citrullinemia)
AG – Arginase
ALD – Argininosuccinase acid lyase (argininosuccinic aciduria)
CPS – Carbamoyl phosphate synthetase
NAGS – N-acetylglutamate synthetase.

28. SIGN AND SYMPTOMS OF UCD
In children with severe UCD, the symptoms will develop within the
first 24 hours of life. While all of these symptoms may not be present,
usually the baby will become very sleepy and irritable and will have
feeding problems, including poor feeding and vomiting. Seizures,
trouble breathing and coma may appear later.
Symptoms in children with mild or moderate UCD, who do not show
symptoms until early childhood, may include:
Disliking meat or other foods rich in protein
Vomiting, nausea
Mental confusion or hyperactive behavior
Tired often and / or hard to awaken
Coma

29. UREA CYCLE DISORDERS
WITH DEFECTIVE ENZYME

30. Hyperinsulinism-hyperammonemia syndrome (Hyperactivity of
glutamate dehydrogenase)
Biochemical profile: Elevated urine alpha-ketoglutarate
Clinical features: Seizures, recurrent hypoglycemia, hyperinsulinism,
asymptomatic hyperammonemia

31. Hyperornithinemia, hyperammonemia, and homocitrullinemia
Biochemical profile: Elevated plasma ornithine, homocitrullinemia
Clinical features: Intellectual disability, progressive spastic
paraparesis, episodic confusion, hyperammonemia, dyspraxia,
seizures, vomiting, retinopathy, abnormal nerve conduction
Argininemia (Arginase I )
Biochemical profile: Elevated plasma arginine
Clinical features: Growth and developmental delay, anorexia,
vomiting, seizures, spasticity, irritability, hyperactivity, protein
intolerance, hyperammonemia

32. Ornithine-transcarbamoylase (OTC) deficiency
Biochemical profile: Elevated ornithine and glutamine, decreased citrulline
and arginine, markedly increased urine orotate
Clinical features: In males, recurrent vomiting, irritability, lethargy,
hyperammonemic coma, cerebral edema, spasticity, intellectual disability,
seizures, death
In female carriers, variable manifestations, ranging from growth delay, small
stature, protein aversion, and postpartum hyperammonemia to symptoms as
severe as those in males with the deficiency
N-acetylglutamate synthetase deficiency
Biochemical profile: Similar to OTC deficiency except for normal to low
urine orotate
Clinical features: Similar to OTC deficiency except carriers are
asymptomatic

33. Citrullinemia type I (Argininosuccinic acid synthetase deficiency)
Biochemical profile: High plasma citrulline and glutamine, citrullinuria,
orotic aciduria
Clinical features: Episodic hyperammonemia, growth failure, protein
aversion, lethargy, vomiting, coma, seizures, cerebral edema, developmental
delay
Citrullinemia type II
Biochemical profile: Elevated plasma citrulline, methionine, galactose, and
bilirubin
Clinical features: With neonatal onset, cholestasis resolved by 3 months
With adult onset, enuresis, delayed menarche, sleep reversal, vomiting,
delusions, hallucinations, psychosis, coma

34. Argininosuccinic aciduria (Argininosuccinate lyase deficiency)
Biochemical profile: Elevated plasma citrulline and glutamine, elevated
urine argininosuccinate
Clinical features: Episodic hyperammonemia, hepatic fibrosis, elevated
liver enzymes, hepatomegaly, protein aversion, vomiting, seizures,
intellectual disability, ataxia, lethargy, coma,
Ornithinemia
Biochemical profile: Elevated plasma ornithine and urine ornithine, lysine,
and arginine; low plasma lysine, glutamic acid, and glutamine
Clinical features: Myopia, night blindness, blindness, progressive loss of
peripheral vision, myopathy.

35. TREATMENT
 Treatment is a lifelong process that doesn't cure the condition, but it
can effectively manage the symptoms. Frequent blood tests are done to
continue to monitor ammonia levels. Doctors in the areas of pediatrics,
genetics and nutrition will work together to develop the child's
treatment plan.
1. Low protein, high-calorie diet: Protein in the diet is lowered by
avoiding protein-rich foods. Examples of foods that provide calories
without loading the body with protein are fruits, vegetables and
starches.

36. 2. Medications: Some children will need to take medicine to help take
extra ammonia out of the body. Oral medication is given that binds to
ammonia and carries it out in the urine.
3. Amino acid supplements: Depending on the type of UCD, amino
acid supplements such as arginine or citrulline may be added to the diet
to help give the body what it needs to make proteins that are important
for growth and tissue repair, since children with urea cycle disorder can't
make arginine on their own.
4. Liver transplantation: Because the production of urea cycle enzymes
takes place in the liver, a liver transplant can be an effective treatment
for urea cycle disorder.

37. REFERENCES
 Text book of medical biochemistry, MN Chatterjee
•Smith, C. M., Marks, A. D., Lieberman, M. A., Marks, D. B., & Marks,
D. B. (2005). Marks’ basic medical biochemistry: A clinical approach.
Philadelphia: Lippincott Williams & Wilkins.
•Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2000). Lehninger
principles of biochemistry. New York: Worth Publishers.