Turnover of Biological Macromolecules

Question 1

RNA Turnover Enzymes

Answer 1

AKA nuclease/ribonuclease
-frequently require Mg cofactor
-hydrolase
-exonuclease vs endonuclease: cuts at 5' or 3' end 
Endo: has specific sequence to bind to

Question 2

-exonuclease vs endonuclease:

Answer 2

Exo: cuts at 5’ or 3’ end
Endo: has specific sequence to bind to

Question 3

RNA Exosome

Answer 3

Ringlike
Exo and endonuclease that hydrolizes via phosphate
acts on: mRNA, pre-tRNA, pre-rRNA

Question 4

Stalled Translation degredation of RNA

Answer 4

1. Endonuclease cuts mRNA
   - ->results in 2 unprotected ends
2. XRN1: chews up from 5’ end amd Exosome chews up from 3’ end

Question 5

Premature stop codon:

Answer 5

• typically occurs because of incorrect splicing
• Results in NonSense Mediated Decay:
  1. Cell senses if stop codon is too close to splice junction protein
  2. endonuclease, XRN, and Exosome action.
• ->would result in aggregation error.

Question 6

No stop codon

Answer 6

Nonstop mRNA Decay

XRN or Exosome will chew it up depending on what is exposed (3’ or 5’)

Question 7

Mi/Si RNA

Answer 7

Have basepairing complementary to some mRNA (usually at 3’ end)

2. when bound to mRNA, P bodies either concentrate in cytoplasm or degrade
   - ->If degration occurs, happens through stalled translation mechanism

Question 8

RNAi:

Answer 8

Like, SiRNA, but has weak complementation to mRNA and degrades in more slow methodical way
->takes of polyA tail, removes Cap, then degrades from 5’-end

Question 9

When is a protein gegraded by proteosome or lysosome?

Answer 9

Proteosome:

• short life
• abnormal/ damaged

Lysosome:

• long life
• membrane proteins

Question 10

Autophagy

Answer 10

lysosome degredation is slow and nonselective

Question 11

Chaperone-Mediated Autophagy

Answer 11

• selective:

* heat shock proteins bind to specific AA motif, unfold protein, and transport it into lysosome

Question 12

Cathepsin Proteasis

Answer 12

Acid tolerant Lysosmal enzymes that rip any protein to bits in no apparent order
NOT INVOLVED IN LYSOSOMAL STORAGE DISEASES

Question 13

Proteosome

Answer 13

• Located in Cytosol and nucleus
• Works in Neutral PH
• Recognizes Ubiquitin tag on its short-lived and/or damaged protein targets
• Requires ATP

Question 14

Proteosome pathway

Answer 14

(in cytosol).

1. Using ATP, ubiquitin (protein) binds to short lived protein
2. Proteasome then knows to shove it down.
3. This degrades the protein but not ubiquitin

Question 15

Ubiquitin Pathway:

Answer 15

• very precise*
  1. Ubiquitin binds to E1 activator protein
  2. E2 carrier isoform carries ubiquitin to target protein (many of these)
  3. E3 ligase protein binds target protein to Ubiquitin (very specific)
• ->poly ubiquitinylation must occur
• ->bind to each other using specific lysine
• ->Different #ubiquitins = different outcome
• ->Alternative Ubq positions on protein = alternative outcomes

Question 16

Ubiquitinylation chemistry:

Answer 16

Ubiquitin makes another Amide Polypeptide bond either on n-terminus or lysine of Protein

Question 17

3 specificities in Proteosome

Answer 17

1. Chymotripsin-like
2. Trypsin-like
3. Peptidyl-glutamyl

Question 18

In the proteosome, Chemotripsin-like cleaves what?

Answer 18

aromatic-like

Question 19

In the proteosome, trypsin-like cleaves:

Answer 19

-basic

Question 20

in the proteosome, peptidyl-glutamyl peptide-hydrolizing-like cleaves

Answer 20

acidic or branched

Question 21

Protein Turnover

Answer 21

1. Nitrogen is excreted as Urea
2. Carbs are used for energy
   “no storage”

Question 22

Proteosome as Cancer Target

Answer 22

Active site targeted. Works in cancer because all the cell cycle regulatory proteins cycled so fast

Question 23

Peptide N-glycanase

Answer 23

takes oligosaccharide off glycoprotein which goes to lysosome. Protein goes to proteosome though. INABILITY TO BREAK DOWN OLIGOSACCHARIDES = LYSOSOMAL DISEASES
–>SPECIFIC ORDER TO BREAKDOWN. ERROR IN 1 ENZYME STOPS CASCADE