UREA CYCLE

M.Prasad Naidu
MSc Medical Biochemistry,
Ph.D,.

Urea Cycle
This tutorial will show you that the urea cycle, perhaps
the most important cycle in nitrogen metabolism, can be
mastered in 10 minutes. Follow the instructions and convince
yourself by the test at the end that you know this cycle.
Another important point of the tutorial is to show you that
learning structures are the key to developing a confidence in
biochemical pathways.

So, start your clock and click 1 for the first slide.
As with most biochemical pathways, the urea cycle should be mastered
by working backwards. Lets start by drawing the last component in the pathway
Arginine (click 1). As you study the structure of arginine try to imagine all of
the intermediates in the pathway built into this one molecule. Perhaps some color
will help. Arginine is the immediate source of urea. Can you see urea in
arginine. Oh, excuse me!. Click 1 to see urea. Now, can you see urea in arginine
(click 1). The oxygen is obtained from H
2
O when the urea molecule is
hydrolyzed free by the enzyme arginase.
H
2
N NH
2
C
O
COO
CH
2
CH
2
CH
2
H
3
N-C-H
NH
HN=C
NH
2

+
+
Urea
Ornithine
O
Citrulline
After the urea is removed
by hydrolysis, what
remains is ornithine (click
1). Ornithine reacts with
carbamoyl-PO
4
to form
citrulline (click 1). Now
that you know how three
compounds fit into the
arginine molecule, its time
to assemble arginine (click
1 to go on).
Arginine assembly starts with ornithine (click 1). First, you must make the
carbamoyl-PO
4
that condenses with ornithine (click 1). As you can see below,
carbamoyl-PO
4
is assembled from NH
4
+
and CO
2
using 2ATPs as an energy source and
the enzyme carbamoyl-PO
4
synthetase I .
NH
4
+
+ CO
2
+ 2ATP
H
2
N
C
O
OPO
3
=
+ 2ADP + P
i
Carbamoyl-PO
4
reacts with
ornithine to form citrulline
(click 1). Phosphate is liberated
in the reaction (click 1). Once
citrulline is formed , all you
have to do to make arginine is
to replace the oxygen on the
citrulline with a nitrogen group
(click 1).
COO
-
CH
2
CH
2
CH
2
H
3
N-C-H
NH
3
+
+
COO
-
CH
2
CH
2
CH
2
H
3
N-C-H
NH
NH
2
+
O=C
+ P
i
Ornithine
Citrulline
In the second step of the pathway the oxygen on the citrulline is replaced
with a NH
3
group from aspartate (click 1). A complex must be formed that allows
the transfer to occur smoothly (click 1). Forming the complex requires ATP, but no
phosphate group is transfered (click 1).
COO

CH
2
CH
2
CH
2
H
3
N-C-H
NH
NH
2
+
O=C
COO

CH
2
H
3
N-C-H
+
COO

COO

CH
2
CH
2
CH
2
H
3
N-C-H
NH
NH
2
+
=C
COO
CH
2
COO
H-C-N
+
ATP AMP + PP
i
Now you can see arginine in the product. The molecue that forms is called
argininosuccinate Wheres the succinate? Click 1 to see.
We now made urea, but there is still a little work left. Cyclic pathways,
as their name implies, return back to the starting compounds. When we split the
succinate from the argininosuccinate, a pair of electrons went with the NH
3
group
and we were left with oxidized succinate, better known as fumarate (click 1).
Sound familiar. It should. This is Krebs cycle stuff and we are in the
mitochondria. Our objective is turn fumarate back into aspartate (click 1). To do
this we must make OAA (click 1). To make OAA we need L-malate (click 1).
Bingo! Now all we need is to coenzymes and cofactors to connect all of these
intermediates as you can see it happen.
COO

CH
2
H
3
N-C-H
+
COO

COO

CH

COO

HC
COO

CH
2
COO

HO-C-H
COO

CH
2
COO

C=O
Glutamate -Kg NAD
+
NADH
Fumarate Aspartate
L-Malate
OAA
Check you watch. You just learned the urea cycle is less than 10 minutes.
Click 1 and see how well you can do on a short test.
H
2
O
answer after reading the question.
1. Name 5 -amino acids that are required in the urea cycle.
There are 3 traditional, arginine, aspartate, and glutamate, as well 2 non-
traditional: ornithine and citrulline. By traditional is meant amino acids
that appear in proteins.
2. What is the function of glutamate in the cycle?
Glutamate is needed to regenerate aspartate from OAA.
3. All told, how may ATPs are needed to make one molecule of urea?
Three are needed . Two to make carbamoyl-PO
4
and one to provide
energy for the aspartate condensation with citrulline.
4. Why is the urea cycle referred to as a bicycle?
There are actually 2 cycles going on. One takes ornithine to arginine
and returns arginine to ornithine. The second takes fumarate from
the argininosuccinate and returns it to aspartate.
THANK YOU