Oxygen Sensing Part II Flashcards
Common functions of proteases
Protein digestion: typsin, chymotrypsin, pepsin
Clotting cascade: thrombin
Blood pressure control: angiotensin converting enzyme
Regulation of cell death: caspases
Viral life cycle: HIV protease, Hepatitis C protease
Protein quality control and turnover: proteasome
Lysosomal pathway: cathepsin
Primary chemical functions of proteases
- Activate water to perform a nucleophilic attack on a peptide bond
- Twist and thereby destabilize the peptide bond
- Directly attack the peptide bond in order to form a less stable intermediate for water to attack
In summary, to fix the problem that water is a bad nucleophile and amide carbonyls are bad electrophiles
Serine proteases
Trypsin
Chymotrypsin
Thrombin
Aspartyl proteases
HIV protease
pepsin
presenilin
Cysteine protease
Caspases
Cathepsins
Deubiquitinases
Metallo proteases
Angiotensin converting enzyme
Threonine protease
Proteasome
HIV protease contortion of peptide bond

Autophagy of cytoplasm outline

Critical Parameters of Proteolytic Control
Access - How does the protease access an unfolded peptide sequence?
Specificity - Where does the protease cleave?
Regulation - What regulates the activity of this protease?
A highly dynamic protein is. . .
synthesized and degraded at a high rate
One example of a highly dynamic protein would be. . .
a regulatory transcription factor
One example of a non-dynamic protein would be. . .
cytoskeletal elements
Phagophore
Membrane which expands to pinch off cyotplasm for autophagy
Mitophagy
Autophagy of mitochondria
Modes of autophagy

Lysosomal storage disorders
Disorders resulting in a deficiency of a lysosomal enzyme, leading to a buildup of the associated substrate in lysosomes.
Non-degradation roles of ubiquitination
Epigenetic marker for readers
Protein trafficking
Ubiquitination occurs at. . .
The epsilon amino group of lysine sidechains
which reacts with the C-terminal glycine of ubiquitin
K48 Ubiquitination

K63 Ubiquitination

K11 Ubiquitination

Linear Ubiquitination

Where does the energy for ubiquitination come from?
E1 enzymes utilize energy from ATP hydrolysis to form a thioester bond with ubiquitin, transfering the ATP’s hydrolysis energy to this thioester.
This thioester transfered to E2 and its energy is preserved, and finally it is utilized in an irreversible attachment of the ubiquitin to its target protein via the formation of an amide bond.
Some specialized E3 ligases also form a thioester with ubiquitin and then transfer this ubiquitin to the target protein.


