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
1. Activate water to perform a nucleophilic attack on a peptide bond
2. Twist and thereby destabilize the peptide bond
3. 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
Angiotensin converting enzyme
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. . .
Membrane which expands to pinch off cyotplasm for autophagy
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
Ubiquitination occurs at. . .
The epsilon amino group of lysine sidechains
which reacts with the C-terminal glycine of ubiquitin
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.
Types of E3 ligase
Structure of an E3 Ligase
Where RING = Really Interesting New Gene
Receptors recognize targets and scaffolds position the E2 to transfer its ubiquitin. Once the ubiquitination has occurred, the E2 must dissociate in order to be reloaded by an E1 to continue polyubiquitination.
Ubiquitination continues until the target diffuses or the ubiquitin chain becomes too long to fit into the active site.
How is ubiquitination regulated?
By expression of E3 ligases and by having E3 receptors that only recognize phosphorylated proteins that have been "targeted" for ubiquitination and degradation.
Alpha chains on the core particle make up the proteasome gate
Beta chains on the core particle make up the catalytic threonine protease core
The 19S regulatory particle contains docking sites for ubiquitin that position the protein to be threaded through the regulatory particle's cannal with some aid from ATP hydrolysis for unfolding
"Coding genes", by definition, encode
NOT tRNA, rRNA, lncRNA, miRNA, etc etc etc
Only mRNA counts because only it is translated
The function of the mediator can best be described as a multi-protein complex that. . .
Helps recruit and stimulate the activity of RNA polymerase II
Levels of HIF1b vs HIF1a
HIF1b is constitutively expressed,
HIF1a varies in concentration in response to oxygen levels.
Receptor for the E3 complex that ubiquitinates HIF1a.
Requires HIF1a to be hydroxylated by prolyl hydroxylase in order to recognize. Thus, when oxygen levels are low and prolyl hydroxylase cannot bind oxygen to catalyze the reaction, HIF1a is not degraded, enabling its transcriptional activity.
Kd rate definition
What protein functions as the human body's oxygen sensor and initiates the respose to hypoxia?