PS2

• (1a) How might the strongly acidic environment of stomach acid aid in dietary protein degradation by pepsin?

  Proteins need to be unfolded for degradation (I think because you need access to the peptide bonds in the primary structure). The acidic, low pH environment will denature the protein and disrupt its structure aid in unfolding.
• (1b) Two ways that random and indiscriminate degradation of cellular proteins by the proteasome is prevented?

  1. Must be marked for degradation by ubiquitin, often involves polyubiquitination. E3 is selective for specific proteins to get ubiquitinated.
  2. i don't know
• (1c) Proteasome req. ATP hydrolysis but pepsin does not. Why would proteasome req. ATP but pepsin not?

  Proteasome requires ATP to be used by its AAA+ parts to unfold the protein. But pepsin acts in an acidic environment (of the stomach) which already aids in the unfolding of the protein.
• (2b) How is ATP used in ubiquitination?

  ATP is used by E1 to adenylate Ub to activate it so that it may be attached to E1 and eventually passed down to the target protein.
• (3) What metabolic pathways use Schiff base linkages?

  1. transaminase of amino acid deamination: cofactor PLP is joined to either lysine of transaminase when inactive or to the substrate amino acid
  2. transaldolase in pentose phosphate pathway, enzyme joined to substrate
  3. aldolase of glycolysis or gluconeogenesis