Turnover Mechanisms 9.8.08

Front 1

There are two regulated pathways that turnover mRNA - XRN1 and Exosome. Describe each.

Back 1

XRN1-- Cytosol (P-bodies)
1. Degradation signal is recognized.
2. Protein is de-adenylated (poly-AAA taken off)
3. Protein de-capped (irreversible)
4. XRN1 degrades 5' to 3'

Exosome - Cytosol (No P-Bodies)
1. Degradation signal recognized; may be AU rich signal & protein with short half life.
2. Protein de-adenylated (substrate can be mRNA, pre-tRNA, pre-rRNA, small RNAs, splicing leftovers)
3. Exosome degrades protein using activating proteins; phosphorylytic process; cytosolic and nuclear isozymes exist

Front 2

What are RNAi's?

Back 2

Interfering RNA's: mostly block translation but also degrade mRNA. The two main types are miRNA's and siRNA's.

Front 3

What is the difference in the degradation pathways between strong and weak complimentarity of siRNA/miRNA's?

Back 3

1. Strong Complementarity: endonuclease cuts at binding site and two fragments are sent to exosome or XRN1

2. Weak Complementarity: endonuclease cuts and sends to XRN1 only

Front 4

Describe "No Go" RNA Decay.

Back 4

1. translation is stalled due to "something"
2. Results in half a protein and a trapped ribosome
3. Endonuclease cuts at blocked site.
4. Ribosome can diffuse away.
5. Protein sent to exosome or XRN1.

Front 5

Describe the "Non-Sense Mediated" RNA Decay.

Back 5

1. premature stop codon exists (very common!)
2. sent to XRN1 without de-adenylation; or to exosome in one piece.

Front 6

Describe the "Non-Stop" RNA Decay.

Back 6

1. no stop codon
a. protein is too short - transcription terminated early
b. protein too long - adenylation too early

2. protein gets sent to the exosome

Front 7

Describe the proteosome mechanism for protein degradation.

Back 7

1. Protein that has a short half life or transient function are abnormal/damaged.

2. E1 activator protein uses ATP to put on "U"

3. "U" transferred to E2 Carrier Protein (many isoforms)

4. "U" place on protein @ N-termin/Lys.

5. At least 4 "U" needed.

6. Outcome is based on # of "U" and which lysines they are placed on.

7. Proteosome pushes protein through top ring that has unfoldase activity.

8. Two middle rings of proteosome have specific regions for aromatic, basic, acidic/branched amino acids, and a Asp-Thr-His sequence.

9. Protein degraded first in 4-25 AA fragments, then further to single AA's.

10. "U" is recycled.

Front 8

Describe lysosomal degradation of proteins.

Back 8

1. Proteins with long half life and housekeeping f(x) are sent to the lysosome via:

a. autophagy: random & slow
b. chaperone-mediated autophagy: selective (~30% proteins); unfolded protein taken into lysosome

2. In lysosome, Cathespins chew up protein. Constitutive proteases of many isoforms that exist as endo and exonucleases. Several cathespins can chew on one protein at same time.

Front 9

T/F: Deletion of cathespins do not cause a lysosomal storage disease.

Back 9

True; however, they do cause 4 other genetic diseases.

Front 10

T/F: Oligosaccharide turnover is an independent process.

Back 10

False; oligosaccharide turnover depends on glycoprotein turnover. Proteolysis precedes N-glycan breakdown.

Front 11

Two Mechanisms to Break Down Oligosaccharides:
1. Proteosome/DNGase
2. Lysosome

Describe each.

Back 11

1. DNGase, which lies close to proteosome, takes off oligosaccharide. The olig is then taken to the lysosome via a oligosaccharide transporter.

2. Some glycoproteins go straight to lysosome, where glycosidases break them down via hydrolysis. This is a highly ordered pathway, where if one enzyme is defected, then entire pathway is blocked.

Front 12

Gaucher Disease

Back 12

Glucocerebroside Deficiency; accumulation of the fatty substance glucocerebroside Fatty material collects in the spleen, liver, kidneys, lungs, brain and bone marrow.

Front 13

Sphingomyelinase Deficiency (or Niemann Pick Disease)

Back 13

sphingomyelin accummulates in the liver, spleen, nerve ganglion cells.

Only SOME symptoms:
mental retardation, spasticity, seizures, jerks, eye paralysis, wobbliness, retarded physical growth, hepatosplenomegaly, jaundice, liver failure, and fluid in the abdomen.

Front 14

What are some functions of phospholipid breakdown?

Back 14

1. FA used for fuel in mitochondria
2. Cholines, Ethanolamines, Serines, Inositols used for signal transduction.
3. Unsaturated FA's used for bioactive fuels, signaling, and inflammation.