Basic question regarding amino acid ammonia

[Lothric]

Hey,

What fundamental principle am I missing? In the context of ammonia transport in FA, it is stated in such a way that gives the reader the impression that amino acids always have NH3 in their structure.

More specifically, FA says: "Amino acids (NH3) are converted to alfa-ketoacids in a transamination reaction with concomitant conversion of alfa-ketoglutarate to glutamate (NH3)".

Why is there a NH3-group (ammonia) in the parentheses after amino acids? Amino acids have amino groups, NH2. What am I missing?

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[Pepe18]

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[Lothric]

The pKa of the N-terminus is around 9ish for most amino acids. pH of the body is around 7.4. When pH<pKa, the NH2 would exist in its protonated form (NH3+). Free amino acids would exist with the NH3+ form

I can understand that, definitely. But nh3+ is not nh3 after all or am I wrong?

 

[Pepe18]

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[Lothric]

I'm not sure what you are trying to ask. If you are saying that an amino acid's full structure isn't NH3+, then you are correct, but they are very obviously putting the NH3+ there to emphasize that it is the N that will attack the carboxyl group in the transamination reaction and not saying that NH3+ is the structure of an amino acid

They are not saying NH3+ though. They are saying "NH3", ammonia. I don't understand why they write ammonia after amino acids. Is every amino acid the source of ammonia maybe?

 

[Lothric]

Still don't understand. Let me upload a diagram where this is being shown.

As the diagram shows, I don't understand the parentheses around NH3 after amino acids. Ammonia is NOT in amino acids, there is an amino group however (NH2). What do they mean with NH3!?

Edit: I now understand what they mean. NH3 is obtainable from certain amino acids when they go through deamination (both oxidative/nonoxidative) where the amino group is released as ammonia.

However, urea does not have ammonia in it. Yet, FA says "Urea (NH3)". Is this just to remind the reader that the original ammonia from glutamate (when it got deaminated) got incorporated into urea in the form of an NH2-group?