Protein Degradation and the Amino Acid Pool

22 vocabulary flashcards covering key terms related to protein degradation and the amino acid pool.

Ubiquitin

A small 76-residue protein that covalently attaches to target proteins to mark them for proteasomal degradation.

Ubiquitination Pathway

Using ATP, Ub attaches to E1 (activation of ubiquitin), then E2 (carries activated Ub from E1 to E3 ligases). Then, E3 (ligation) attaches Ub to target protein, creating a polyubiquinated protein. This attaches the protein to a proteosome. Finally, the protein is de-ubiquinated, breaking the protein down to peptides and AAs, and free ubiquitin subunits are released.

Endosome-Lysosomal Pathway

The process by which extracellular proteins are endocytosed and delivered to lysosomes, where they are degraded by lysosomal enzymes into amino acids and other peptides for recycling.

Autophagy

Cytoplasmic proteins and damaged organelles are brought into the lysosome and broken up with cathepsins (protease)

Source of AA pools

Diet; from existing cellular protein AAs; de novo amino acid synthesis

Transamination reactions

Transfer of a-amino groups to a-KG using a “ping-pong” reaction with cofactor PLP and aminotransferase. The a-amino group is transferred to AKG, which becomes glutamate, and the AA is deaminated into a-keto acid.

Pyridoxal Phosphate (PLP)

Vitamin B6-derived cofactor essential for transamination and other amino acid metabolic reactions.

Reasons for protein degradation

Eliminate damaged proteins, eliminate unneeded proteins (i.e. don’t need the enzyme), eliminate misfolded proteins

Studying protein half-lives

Using a Western Plot/ immunoblot, measure amount (in pixels) of POI at time zero, and see how long it stays. Add CHX to stop new translation. Protein amount over time is graphed with normalized expression. Can also test and graph with different conditions

Amino acid catabolism

AAs are broken down into carbon skeletons and NH4+. C skeletons turn into a-keto acids, which go through the CAC. NH4+ is converted into carbamoyl phosphate for the urea cycle, or are used in AA, nucleotide, and amine synthesis. The CAC and urea cycles are connected by the aspartate-arginino-succinate shunt

Fate of excess amino acids

If possible, AAs are reused, but there is no storage for excess AAs. They are broken down for energy production, synthesis of glucose/ fatty acids, or synthesis of N-containing non-protein molecules

Glucogenic amino acid catabolism

AAs converted into glucose via gluconeogenesis (Arg, Glu, His, Pro, Iso, Met, Thr, Val, Phe, Tyr, Asp, Ala, Cys, Gly, Ser). These AAs are converted into Glutamate and then a-KG, Succinyl-CoA, Fumarate, Pyruvate, and OAA

Ketogenic AA catabolism

AAs are converted into ketone bodies via ketogenesis (Leu, Lys, Phe, Try, Tyr, Iso, Leu, Thr). These AAs are converted into Acetoacetyl-CoA or Acetyl-CoA. This acetyl-CoA cannot be used to make glucose.