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Rod Hori
1. Describe which molecules are important to the
assimilation and excretion of urea
A. contribute or transport nitrogen
B. steps of the urea cycle
2. Explain the cause and affects of ammonia,
Ornithine Transcarbamoylase deficiency and
3. Recall the diseases with corresponding symptoms
and enzymes in the Tyrosine Synthesis (Phe
Degradation) pathway
4. Recall the precursors in the synthesis of the
Serine family of amino acids
5. Recall the names and describe the roles of the
I. Introduction
II. Urea Cycle
III. Synthesis
A. Arginine
B. Phenylalanine/Tyrosine
C. Alanine, Serine, Glycine, Cysteine
Amino Acid Metabolism

(Amino Acids 1 - Tuesday) A

Absorption Transport

1 (Dr Albritton)

5Biosynthesis 2 (AA 4 - Thursday)

4Glycogen 3
and Fatty (3, 4, 5: AA 2 & 3-Tues and We
(Storage) 3
Amino Acids are also used in (Energy)
Metabolism Same slide in Amino Acids -2

In Fed state, glucose

and/or fatty acids (the
preferred fuels for
energy) are present. In
general, amino acids
are used in synthetic
In Fasting state,
proteins are degraded Figure 38.2
so the amino acids can
be used as fuel for
energy, for
gluconeogenesis and
modified to maintain
Fasting State
Same slide in Amino Acids -2



and Glutamine

and Kidney (not shown)

Chain Image not from Marks
#1. Transamination moves an amino group
from an amino acid-1 to a keto acid (of amino
acid-2) to generate amino acid-2 and the keto
acid of amino acid-1
Same slide in Amino Acids-2

Currency exchange Dr Nishimoto

Muscle and Peripheral tissues
generate Glutamine that can be
transported to the Liver
Similar to slide in Amino Acids

Figure 38.11
Glutamine is a major carrier of nitrogen to
the liver for disposal. (Urea cycle - next class
Glutamine can be deaminated and then used
Alanine can be transported from Muscle to
Liver, converted to Pyruvate and used for
(Glucose-Alanine Cycle)
Same slide in Amino Acids
Brain, Red Blood
Cells, Other tissues
and needs

Alanine amino group used in Urea Figure 42.12

In the liver, Glutamate has a key role in collecting
amino groups that will enter the Urea Cycle.
Glutamic acid can be deaminated or used in
transamination reactions to generate Aspartic
Alanine and
other amino

Figure 38.9
NH3 (ammonia) or NH4+
(ammonium ion)
NH4+ is predominant form b/c
pKa of dissociation = 9.3
However, NH3 is important b/c
it is the form that can cross
Limit to healthy level of
ammonia in blood
Normal level of ammonia in
blood = 30-60 M
Ammonia can pass across
blood-brain barrier
-KG > Glutamic Acid >
Affects Citric Acid Cycle
Affects neurotransmitter levels
Key points 1
Alanine and Glutamine transported
to liver are source of nitrogen that
needs to be disposed
Glutamic Acid collects amino groups
(nitrogens) that can enter the Urea
High levels of ammonia are toxic to
Amino Acid Metabolism

(Amino Acid 1) A


1 (Dr Albritton)

(5Biosynthesis) 2 (Amino Acids 4)

4Fatty Acids
(Storage) (3, 4, 5: Amino Acids 2 and 3

Most nitrogen disposal is
performed by Urea Cycle in the

Urea Cycle was worked out by Hans Krebs

same person who worked out the Citric Acid
Cycle (Citric Acid Cycle is also called the
Krebs Cycle, and also Tricarboxylic Acid Cycle)
What happens in the Urea
Generate urea which contains two
Uses ATP (high energy usage, esp for
person at rest)
Some steps occurs in the
Some steps occur in the cytoplasm.
Urea Cycle

Figure 38.12
Urea Cycle

Figure 38.12
Carbamoyl phosphate synthetase I
catalyzes the formation of carbamoyl

1. Incorporation of one nitrogen = first

2. ATP usage = Energy-requiring
Urea Cycle

Figure 38.12
In the mitochondria, Citrulline is generated from
Carbamoyl phosphate and Ornithine by Ornithine

Mitochondria Cytosol

Figure 38.12
Citrulline is transported from the
Mitochondria to the Cytoplasm

Mitochondria Cytosol

Figure 38.12
In the cytoplasm, Citrulline and Aspartic
Acid react.

1. Asp is the source of the second nitrogen

2. ATP usage (Energy-requiring)
3. You do NOT need to know the product or
Urea Cycle generates Arginine and

Figure 38.12
The Urea Cycle and Citric Acid Cycle
use common reactions

Also called Krebs Bi-cycle

Figure 38.13
Urea Cycle Urea is generated from

Figure 38.12
Blood Urea Nitrogen (BUN)
Blood Urea Nitrogen is a measure of blood
urea level
Patients with kidney (renal) failure have
high BUN.
Normal range = 250 700 M (8-20 mg/dl)
Disorders of the Urea Cycle
Ornithine Transcarbamoylase (OTC) deficiency
(Marks, p 718)
Most common urea cycle defect
X-linked disorder; 1 in 20,000 to 80,000
Major clinical problem increased blood
ammonia results in neuronal damage
and mental retardation
Hyperammonemia, Low to No Detectable
Citrulline and High Orotate (Orotic Acid)
Treatment: Need early intervention.
Generate low nitrogen levels by -
Low-protein diet
Drugs that conjugate (react with)
amino acids
-Benzoic acid and phenylbutyrate excretion
- Conjugated amino acids are lost by
resynthesize amino acids
All five enzymes of the urea cycle have
potential defects that lead to disease
Key points 2
Urea Cycle
In liver; Generates Urea; Consumes ATP (energy)
Majority of nitrogen disposal in cell
Carbamoyl phosphate
Catalyzed by Carbamoyl phosphate synthase I
Incorporate first nitrogen; energy requiring
Formed from Carbamoyl phosphate and Ornithine
Catalyzed by Ornithine Transcarbamoylase
Transported from Mitochondria into Cytoplasm
Citrulline and Aspartic Acid (Asp) react
Asp is source of second nitrogen
Energy required in reaction
Urea Cycle and Citric Acid Cycle use common reactions
Blood Urea Nitrogen is measure of Blood Urea Level
Ornithine Transcarbamoylase Deficiency
High ammonia in blood (hyperammonemia), low to no detectable
citrulline and high orotate
Amino Acid Synthesis
Emphasis on
Inborn errors of metabolism generating
Amino Acid Metabolism

(Amino Acids 1 - Tuesday) A

Absorption Transport

1 (Dr Albritton)

5Biosynthesis 2 (Amino Acids 4 - Thu

4 Glycoge
n and (3, 4, 5: Amino Acids 2 and 3
Acids 3
Essential and Non-Essential Amino

11 10 derived from glucose

Tyr derived from Phe

Some caveats:
Supplemental Arginine is sometimes required under conditions of
growth pregnancy and children.
Cysteine and Tyrosine synthesis depends on adequate amounts of
essential amino acids Met (i.e., sulfur) and Phe, respectively.
The 11 non-essential amino acids can be
The 11 non-essential amino acids can be
The 11 non-essential amino acids can be

Urea Cycle

*Precursor to ornithine
Synthesis of Tyrosine (Degradation of
Synthesis of Tyrosine (Degradation of

Phe and Tyr are

glucogenic and
Synthesis of Tyrosine (Degradation of
Phenylalanine Hydroxylase converts Phe
into Tyr

Phenylalanine is an essential
amino acid and obtained
through the diet

Figure 39.15

Phenylalanine Hydroxylase (PAH) uses the

cofactor Tetrahydrobiopterin or BH4.
Synthesis of Tyrosine (Degradation of
Phenylalanine Hydroxylase converts Phe
into Tyr

Phenylalanine is an essential
amino acid and obtained
through the diet

A block in Phenylalanine Hydroxylase (PAH) generates

increased levels of Phe and generates a disorder called
Phenylketonuria (PKU)
Phenylketonuria (PKU)
Dr. Ward will have a class on this
topic Thursday
Mental retardation can develop if not
treated early
eneral concept of deficient enzymatic pathwa

(Also, the product downstream of block

is decreased. This is less often a
problem. This issue can usually be
addressed by diet when it involves
amino acids.)
Image courtesy of Dr Nelson
Phenylketonuria (PKU)
If phenylalanine hydroxylase is
deficient, how would you treat?
Tetrahydrobiopterin (BH4) is synthesized
from GTP and deficiencies in its synthesis
can also cause PKU

Figure 39.16
A block in Tryosine Aminotransferase generates
increased levels of Tyr and results in a disorder
called Tyrosinemia II

Tyrosine aminotransferase uses the cofactor PLP,

just like other aminotransferases
Tyrosinemia II
Can lead to neurological problems (Marks,
p. 737)

Treat with diet:

foods with low tyrosine and low phenyalanine
A block in homogentisate oxidase generates
increased levels of homogentisate and results in a
disorder called Alcaptonuria
(alternative spelling: Alkaptonuria)
Homogentisic acid (homogentisate)
It forms a dark pigment when it oxidizes
Urine turns dark with exposure to air
Arthritis may develop later in life due to the
accumulation of this compound
Treatment: No specific treatment
High Vitamin C may decrease pigment accumulation
Low protein diet Phenylalanine eliminated from diet
A block in Fumarylacetoacetate Hydrolase results
in a disorder called Tyrosinemia I not on exam
Serine family and Alanine
Pyruvate is the precursor for Alanine
Next, Glycine and Cysteine are derived from
Glycine can be synthesized from Serine.
This reaction uses the cofactors PLP and Tetrahydrofolate
This reaction is reversible

Figure 39.5
Tetrahydrofolate (FH4) is the reduced
form of Folic Acid (Folate)
FH4 is a cofactor
involved in transferring
one-carbon groups
One carbon groups
(~methyl) attached to
folate are called the one-
carbon pool
Folate is involved in
glycine synthesis,
nucleotide metabolism
and transfer of carbon
to vitamin B12.
Tetrahydrofolate (FH4) is the reduced
form of Folic Acid (Folate)
Folate and derivatives
are obtained from
green leafy vegetables,
fruits and legumes
Reduced form (FH4) is
most common form in
Dietary folate is
So FH4 or FH2
Supplemental folate is
Folate and Fetal Neural Tube
Folate deficiency during pregnancy has been
associated with an increased risk of neural tube
defect in the developing fetus and spina bifida.
Folate deficiency causes inhibition of DNA
synthesis leads to neural tube defects.
First observed in women with variant enzyme in
folate metabolism
Recommendation is that women considering
getting pregnant begin taking folate
supplements before conception and during at
least 1 month after conception
USDA has mandated that folate be added to
flour-containing products
Cysteine can be made from Serine and
Methionine (via S-Adenosylmethionine;
Cysteine can be made from Serine and
Methionine (via S-Adenosylmethionine;
Vitamin B12
Also called cobalamin
Coordinates cobalt
Vitamin B12 is obtained
from meat, eggs, dairy,
fish, poultry and seafood
Cofactor for two
Transfer of methyl group
from FH4 to Homocysteine
to form Methionine
[Rearrangement of
methylmalonyl-CoA to
generate succinyl-CoA]
FH4, Vitamin B12 and S-
Adenosylmethionine are methyl donors.
S-Adenosylmethionine (SAM) is
generated from Met and ATP
Note: Methionine is essential and obtained from diet.
SAM donates a methyl group (similar to FH 4)
which produces SAH, then Homocysteine
Note: Methionine is essential and obtained from diet.
FH4 can transfer a methyl group to Vitamin
Homocysteine can accept a methyl group
from Vitamin B12 to regenerate Methionine
Alternatively: Homocysteine (derived from Met)
and Serine react to generate an intermediate,
which is cleaved to generate Cysteine

Metabolic Disorder of Cysteine
Homocysteinemia = High
homocysteine in blood
Homocysteinemia describes a biochemical
Can result from deficiency of several
results when
Cystathionine -synthase (CBS) is
CBS is the enzyme that produces the
You do not
intermediate. need to
know this
name for


can form

Homocysteine level is also a diagnostic

High correlation between Homocysteinelevel
Biochemical Characteristics
Elevated homocysteine in blood
High levels of homocysteine will lead to
elevated levels of homocystine
Elevated homocystine in blood
Homocystinuria observed
Homocysteinuria NOT observed
Classical Homocysteinemia also exhibits
elevated Methionine in blood but not urine
due to efficient absorption

Pathology is highly variable but can
Mental retardation (50%)
Dislocated optic lenses (80%), usually
High levels of Homocysteine and Met interfere
with collagen function
Differs from that observed in Marfans syndrome
Abnormal blood clotting
Tissues have infarcts (lack of oxygen)
Osteoporosis, lengthening of long bones
1. Diet low in Methionine
2. Oral Vitamin B6 (precursor to PLP; cofactor
of CBS)
unknown mechanism; works in 50% of
CBS mutants

The 11 non-essential amino acids can be

Not covered yet: Asp/Asn and Glu/Gln/Pro

The 11 non-essential amino acids can be

Glu: transamination of -KG

Gln: Glu + NH4
Pro: derived from Glu
Not covered yet: Asp/Asn and Glu/Gln/Pro
The 11 non-essential amino acids can be

Asp: transamination of OAA

Asn: amine added to Asp

Not covered yet: Asp/Asn and Glu/Gln/Pro

Key points
Arginine is made in Urea Cycle
Tyrosine and Phenylalanine metabolism
Three disease names, associated enzymes,
cofactors such as BH4 and PLP, symptoms and
treatment were discussed
General concept of deficient enzymatic
Ser family and Alanine
Key steps in synthesis of Ala, Ser, Gly and Cys
were described including cofactors
(tetrahydrofolate and vitamin B12, S-
Clinical consequence of low folate