16. Aging and degradation of proteins.

Selective post-translational proteolysis is a crucial mechanism in cellular

regulation, allowing cells to control the levels of specific proteins based on
their functional requirements. The process involves the degradation of target
proteins in a selective and controlled manner. The Ubiquitin/Proteasome
system is a key player in this process, consisting of three main steps:
identification of the protein to be degraded, marking it by ubiquitination, and
delivering it to the proteasome for degradation.
1. Identification of Proteins for Degradation:
The cell identifies proteins for degradation based on various signals. These
signals can be intrinsic, such as specific hydrophobic sequences or motifs
within the protein, or acquired through processes like phosphorylation,
binding to adaptor proteins, or damage due to fragmentation, oxidation, or
aging. Proteins required at specific stages of the cell cycle are rapidly degraded
once they have completed their functions.
2. Ubiquitination Process:
Ubiquitin, a highly conserved 76 amino acid protein, is covalently attached to
lysine side chains of the target protein via an ATP-dependent pathway
involving three separate enzymes. The ubiquitin-activating enzyme (E1) uses
ATP hydrolysis energy to attach ubiquitin to itself through a high-energy
covalent bond (a thioester). E1 then passes this activated ubiquitin to one of a
set of ubiquitin-conjugating (E2) enzymes, each of which acts in conjunction
with a set of accessory (E3) proteins called ubiquitin ligases.

Ubiquitination can occur as monoubiquitination (one ubiquitin molecule

added to one substrate protein residue), multi-ubiquitination (one ubiquitin
molecule added to multiple substrate residues), or Polyubiquitination, which
involves attaching a chain of ubiquitin molecules to one or more lysine
residues. Chains linked via Lys48 (K48) target proteins for proteasomal
degradation, while those linked via Lys63 (K63) are implicated in DNA repair
and activation of protein kinases.
3. Proteasomes:
Ubiquitinated proteins are degraded by the 26S proteasome, a large complex
present in the cytoplasm and nucleus but not in the endoplasmic reticulum
(ER). It consists of two main subcomplexes: the 20S core particle and
regulatory particles on either end of the barrel. The 20S core particle contains
four rings, with three of the seven subunits in each ring having protease
activities, each with different substrate specificities. The regulatory particles
recognize ubiquitinated proteins, remove the ubiquitin chain, and unfold the
protein, allowing it to enter the core particle for degradation. The proteasome
plays a crucial role in maintaining cellular homeostasis by regulating the
turnover of specific proteins involved in various cellular processes, including
cell cycle progression, DNA repair, and immune response.

Misfolding of proteins in the endoplasmic reticulum (ER) is a common cellular

challenge that needs to be addressed to maintain proper cellular function.
When proteins fail to fold correctly in the ER, they can be targeted for
degradation through various cellular pathways, including ER-associated
degradation (ERAD) and lysosomal degradation.

1. ER-Associated Degradation (ERAD): ERAD is a quality control mechanism

that identifies and eliminates misfolded or unassembled proteins in the ER.
Initially, it was believed that the ER contained proteases capable of degrading
misfolded proteins locally. However, it is now understood that ERAD involves
retrograde translocation of misfolded proteins from the ER lumen to the
cytosol for subsequent degradation by the proteasome. Proteins selected for
ERAD are usually tagged with ubiquitin, marking them for recognition by the
proteasome.
2. Lysosomal degradation: Lysosomes contain a variety of hydrolytic enzymes,
including proteases, nucleases, lipases, and glycosidases. These enzymes
function optimally in the acidic environment of the lysosome. Lysosomes take
up cellular proteins by fusion with autophagosomes, which are formed by the
enclosure of areas of cytoplasm or organelles (e.g., a mitochondrion) in
fragments of the endoplasmic reticulum. This fusion yields a phagolysosome,
which digests the contents of the autophagosome.