Regulation of Protein Degradation

Question 1

how does protein degradation and synthesis change in states of anabolism and catabolism?

Answer 1

synthesis exceeds degradation in anabolic states

vice versa for catabolic states

Question 2

what are some reasons cells degrade their own proteins?

Answer 2

1. removal of regulatory or rate limiting proteins
2. quality control of mutated proteins (either mutated genetically or damaged by environment)
   3 usage for energy (AA for gluconeogenesis)
   4 angiten processing by the immune system

Question 3

how are extracellular antigens and intracellular antigens degraded differently?

Answer 3

intra- ubiquitin

extra- endo-lysosomes

Question 4

what are the 3 different ways to classify proteases?

Answer 4

active site nucleophile
-serine
-cysteine (lysosomal proteases)
-threonine (proteasome proteases)
- water (metalloproteases/acidic proteases)
these are the common residues found at active sites that enable them to act as enzymes

substrate specificity

• postively charged AA (trypsin)
• negatively charged AA
• hydrophobic AA

not every protease can cleave at every spot in the AA chain

cleavage location

• endoproteases- can cleave anywhere
• carboxypeptidase- can only cleave from carboxy end to amino
• aminopeptidase- can only cleave from amino end to carboxy

Question 5

what are the different mechanisms that cells use to regulate protein degradation?

Answer 5

natural protease inhibitors (serpins)
inactive enzyme precursors (zymogens)
compartmentalization (lysosomes)
specific “death signals” (ubiquitin)

Question 6

describe how lysosomes are formed

Answer 6

primary lysosomes are formed from the Golgi

secondary lysosomes formed via fusion with endosome or autophagosome

Question 7

how are lysosomal proteases regulated?

Answer 7

compartmentalization

requirement for acidic conditions

specific protease inhibitors (cystatins)

Question 8

what are lysosomal proteases called?

Answer 8

cathepsins

Question 9

cathepsin K deficiency causes what?

Answer 9

disorder of bone developement- pyncodysostosis

dysfunctional osteoclasts

Question 10

describe autophagy

Answer 10

non selective process of protein degradation activated by catabolic state

Question 11

where are extracellular proteases required?

Answer 11

tissue remodeling
complement cascade
thrombin cascade- clotting
plasmin cascade- fibrinolysis
pancreatic proteases- digestion

Question 12

serpins

Answer 12

natural serine protease inhibitors- inhibit proteases via irreversibly binding

Question 13

serpin deficiencies

Answer 13

a-antitrypsin deficiency- unbalanced neutrophil elastase in lung causes emphysema

misfolded a-antitrypsin in liver causes aggregation

C1INH deficiency- C1 inhibitor of complement causes massive complement activation- anaphylaxis and swelling

antithrombin deficiency- thrombin causes clots. w/o removal, inapporpriate clotting

Question 14

ubiquitin-protease pathway is selective

Answer 14

ok

Question 15

describe ubiquitination

Answer 15

carboxyl group of ubiquitin activated using ATP by ubiquitin activating enzyme E1. Activated ubiquitin is then transferred to a ubiquitin carrier E2. E2 binds to E3 to form a ubiquitin ligase. ubiquitin ligase can then give ubiquitin to lysine residues forming an isopeptide bond

Question 16

describe proteasome degradation

Answer 16

entry lid contains receptors that bind to ubiquitin tagged proteins, proteins to remove the ubiquitin (isopeptidases), and ATP dependent enzymes the unfold the substrate protein prior to entry into the cylindrical core (chaperones)

core contains multiple proteases w/ differing substrate specificities, which collectively degrade the protein. they only have threonine proteases

Question 17

describe how the ubiquitin pathway is involved in cervical cancer

Answer 17

HPV encodes a viral ubiquitin ligase (E6) capable of degrading p53, which would stop cell division

instead cervical cancer forms

Question 18

protein breakdown does not require energy. what does require energy?

Answer 18

preventing non-specific degradation

Question 19

how does a proteasome inhibitor kill multiple myeloma?

Answer 19

multiple myeloma- cancer of plasma cells causing excess Ab. these cells are more sensitive to proteasome inhibitors and exclusively kill plasma cells