Protein degradation and &

Molecular pathways controlling

protein degradation
The levels of proteins within cells are determined not only by rates of
synthesis, but also by rates of degradation.
The half-lives of proteins within cells vary widely, from minutes to
several days, and differential rates of protein degradation are an
important aspect of cell regulation.
Many rapidly degraded proteins function as regulatory molecules,
such as transcription factors.
The rapid turnover of these proteins is necessary to allow their levels
to change quickly in response to external stimuli.
Other proteins are rapidly degraded in response to specific signals,
providing another mechanism for the regulation of intracellular
enzyme activity.
In addition, faulty or damaged proteins are recognized and rapidly
degraded within cells, thereby eliminating the consequences of
mistakes made during protein synthesis.
In eukaryotic cells, two major pathways
the ubiquitin-proteasome pathway
lysosomal proteolysis—mediate protein degradation.
 Cellular Protein Degradative Routes

Lysosomal - a cellular compartment at ~pH 3.8 -4.9 containing

hydrolytic enzymes (cathepsins).
Degrade substances taken up by Endocytosis.
Recycle intracellular constituents enclosed within vacuoles.
In “well nourished cells” protein degradation is nonselective.
In starving cells a selective pathway is activated that imports and
degrades proteins that contain the pentapeptide (Lys-Phe-Glu-
Arg-Gln; KFERQ) e.g., in muscle and liver, but not brain.
Ubiquitin-Based – ATP-based process independent of lysosomes.
Proteins are marked for degradation by linking to ubiquitin.
 Distinguishing Protein Lifetimes
The N-end Rule:
N-terminal residues Asp,
Arg, Leu, Lys & Phe (half-life
~ 2-3 minutes)
 Ala, Gly, Met, Ser Thr, & Val
(half-life > 20 hrs in
eukaryotes ; >10
prokaryotes)
PEST proteins with segments
rich in Pro, Glu, Ser, & Thr
are rapidly degraded (these
AA have sites that can be
phosphorylated – thus
targeting them for
Voet, Voet & Pratt 2013 Table 21.1
ubiquitination).
 THE UBIQUITIN-PROTEASOME PATHWAY
Ubiquitin is a 76-amino-acid polypeptide that is highly conserved in
all eukaryotes (yeasts, animals, and plants).

It is utilized as a marker in selective protein degradation

in eukaryotic cells uses that targets cytosolic and
nuclear proteins for rapid proteolysis.

Protein: 76 amino acids; molecular mass 8.6 kDa.

Key features include its C-terminal tail and the 7 lysine residues. It is

highly conserved throughout eukaryote evolution; human and yeast
ubiquitin share 96% sequence identity.

Ubiquitylation is an enzymatic post-translational modification in

which a ubiquitin protein is attached to a substrate protein.
 Proteins are marked for rapid degradation by the covalent attachment of several
molecules of ubiquitin (the last amino acid of ubiquitin (glycine 76) to
a lysine residue on the substrate).

 Ubiquitin is first activated by the enzyme

E1. Activated ubiquitin is then transferred
to one of several different ubiquitin-
conjugating enzymes (E2).

 In most cases, the ubiquitin is then

transferred to a ubiquitin ligase (E3) and
then to a specific target protein.
 Multiple ubiquitin are then added, and
the polyubiquinated proteins are
degraded by a protease complex
(the proteasome).
 Ubiquitin is released in the process, so it
can be reused in another cycle.
 It is noteworthy that both the
attachment of ubiquitin and the
degradation of marked proteins require
energy in the form of ATP.
Ref:https://www.ncbi.nlm.nih.gov/books/NBK9957/#:~:text=In%20eukaryotic%20cells%2C%20two%20major,lysosomal%20proteolysis%E2%80%94mediate%20protein%20degradation.
A number of proteins that control
fundamental cellular processes, such
as gene expression and cell proliferation,
are targets for regulated ubiquitination
and proteolysis.

Ubiquitinylation and
proteolysis of cyclin B

Ref:https://www.ncbi.nlm.nih.gov/books/NBK9957/#:~:text=In%20eukaryotic%20cells%2C%20two%20major,lysosomal
%20proteolysis%E2%80%94mediate%20protein%20degradation.
 LYSOSOMAL PROTEOLYSIS
The other major pathway of protein degradation in eukaryotic
cells involves the uptake of proteins by Lysosomes.
Lysosomes are membrane-enclosed organelles that contain an array of
digestive enzymes, including several proteases.
They have several roles in cell metabolism, including the digestion of
extracellular proteins taken up by endocytosis as well as the gradual
turnover of cytoplasmic organelles and cytosolic proteins.
The containment of proteases and other digestive enzymes within
lysosomes prevents uncontrolled degradation of the contents of the
cell. 
 In order to be degraded by lysosomal proteolysis, cellular proteins must first be taken up by
Lysosomes.
 One pathway for this uptake of cellular proteins, Autophagy, involves the formation of vesicles
(autophagosomes) in which small areas of cytoplasm or cytoplasmic organelles are enclosed
in membranes derived from the endoplasmic reticulum .

 These vesicles then fuse

with lysosomes, and the
degradative lysosomal
enzymes digest their
contents.
 The uptake of proteins
into autophagosomes
appears to be
nonselective, so it
results in the eventual
slow degradation of
long-lived cytoplasmic
proteins.

Ref:https://www.ncbi.nlm.nih.gov/books/NBK9957/#:~:text=In%20eukaryotic%20cells%2C%20two%20major,lysosomal
%20proteolysis%E2%80%94mediate%20protein%20degradation.