The 10-Minute 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. Let’s 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. H2NH2NNH 2 C O COO 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 CO 2 + 2ATP H2NH2N 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 H 3 N-C-H NH COO - 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 H 3 N-C-H NH NH 2 + O=C COO − CH 2 H 3 N-C-H + COO − 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” Where’s 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 – 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. C lick 1 and see how well you can do on a short test. H2OH2O

See what you learned. Click for the 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.