Oxygen Sensing Part II Flashcards Preview

HMS Chemical Biology and Biochemistry > Oxygen Sensing Part II > Flashcards

Flashcards in Oxygen Sensing Part II Deck (34)
1

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

2

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

3

Serine proteases

Trypsin

Chymotrypsin

Thrombin

4

Aspartyl proteases

HIV protease

pepsin

presenilin

 

5

Cysteine protease

Caspases

Cathepsins

Deubiquitinases

6

Metallo proteases

Angiotensin converting enzyme

7

Threonine protease

Proteasome

8

HIV protease contortion of peptide bond

9

Autophagy of cytoplasm outline

10

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?

11

A highly dynamic protein is. . .

synthesized and degraded at a high rate

12

One example of a highly dynamic protein would be. . .

a regulatory transcription factor

13

One example of a non-dynamic protein would be. . .

cytoskeletal elements

14

Phagophore

Membrane which expands to pinch off cyotplasm for autophagy

15

Mitophagy

Autophagy of mitochondria

16

Modes of autophagy

17

Lysosomal storage disorders

Disorders resulting in a deficiency of a lysosomal enzyme, leading to a buildup of the associated substrate in lysosomes.

18

Non-degradation roles of ubiquitination

Epigenetic marker for readers

Protein trafficking

19

Ubiquitination occurs at. . .

The epsilon amino group of lysine sidechains

 

which reacts with the C-terminal glycine of ubiquitin

20

K48 Ubiquitination

21

K63 Ubiquitination

22

K11 Ubiquitination

23

Linear Ubiquitination

24

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.

25

Types of E3 ligase

26

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.

27

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.

28

Proteasome structure

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

 

29

"Coding genes", by definition, encode

mRNA/protein

NOT tRNA, rRNA, lncRNA, miRNA, etc etc etc

Only mRNA counts because only it is translated

30

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

 

31

Levels of HIF1b vs HIF1a

HIF1b is constitutively expressed,

 

HIF1a varies in concentration in response to oxygen levels.

32

VHL

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.

33

Kd rate definition

koff/kon

34

What protein functions as the human body's oxygen sensor and initiates the respose to hypoxia?

Prolyl hydroxylase