Protein Catabolism

What two types of reactions are used to remove nitrogen from an amino acid so its carbon skeleton can be catabolized?,

"1. Transamination (movement of the amino group to an α-keto acid) 2. Deamination (removal of the amino group as free ammonium, NH4+)"

What defines a 'glucogenic' amino acid?,

It is an amino acid whose carbon skeleton is catabolized into a pathway that yields a precursor (like pyruvate or oxaloacetate) that can be used to form glucose via gluconeogenesis.

What defines a 'ketogenic' amino acid?,

It is an amino acid whose carbon skeleton is catabolized into Acetyl-CoA or Acetoacetyl-CoA, which cannot be used to make glucose but can be used to form ketone bodies or enter lipogenesis.

Which two amino acids are STRICTLY ketogenic?

Leucine and Lysine.

Which amino acids are BOTH glucogenic and ketogenic?,

Phenylalanine, Tyrosine, Tryptophan, and Isoleucine.

Why can't an amino acid that degrades ONLY into Acetyl-CoA (ketogenic) be used to make glucose?,

Acetyl-CoA requires a ≥4 carbon intermediate (like oxaloacetate) to enter the TCA cycle. Two carbons are oxidized to CO2 during the cycle, resulting in no net gain of carbons that could be drawn off for gluconeogenesis.

How does the body store excess dietary amino acids?,

Excess amino acids cannot be stored as proteins/amino acids in tissues. They are deaminated and their carbon skeletons are converted into FAT for storage.

Why must ammonia (NH3) be converted into urea in mammals?,

Ammonia is a weak base. High levels buffer protons (forming NH4+), leading to metabolic alkalosis. High NH4+ also depletes α-ketoglutarate from the TCA cycle (lowering energy production) and increases glutamine, causing cellular swelling/edema.

How do different organisms excrete nitrogen?,

Mammals excrete Urea. Aquatic animals excrete Ammonia. Birds and reptiles excrete Uric Acid.

Where do the two nitrogen atoms in a molecule of urea come from?,

"1. The first nitrogen comes from free ammonium (from deamination) via Carbamoyl-Phosphate in the mitochondria. 2. The second nitrogen comes from Aspartate in the cytosol."

How much ATP does the Urea Cycle consume directly?,

It consumes 4 ATP equivalents: 2 ATP to form Carbamoyl-Phosphate and 2 ATP equivalents (ATP -> AMP + PPi) to form Argininosuccinate.

How does the Urea Cycle partially 'pay for itself' energetically through its connection to the TCA cycle?,

The Urea Cycle produces Fumarate in the cytosol, which enters the mitochondria as Malate. The TCA cycle oxidizes Malate to Oxaloacetate, producing 1 NADH. That NADH generates ~2.5 ATP in the electron transport chain, reducing the net cost of the Urea cycle from 4 ATP to 1.5 ATP.

What is the role of Aspartate Aminotransferase (AST) in linking the TCA and Urea cycles?,

AST transaminates Oxaloacetate (generated from Malate in the TCA cycle) with Glutamate to produce α-Ketoglutarate and Aspartate. This new Aspartate is then shuttled out to the cytosol to provide the second nitrogen for the Urea Cycle.