M2MWeek6NotecardsSet8

Question 1

What are the three main types of autophagy?

Answer 1

macroautophagy and chaperone-mediated autophagy. And microautophagy

Question 2

Describe chaperone-mediated autophagy. What makes it unique?

Answer 2

Chaperone-mediated involves a chaperone protein (HSC70) that specifically targets certain proteins (must have KFERQ in them). Unique because of selectivity of proteins and direct shuttling of these proteins across the lysosomal membrane without the requirement for formation of additional vesicle.

Question 3

Compare chaperone-mediated to macroautophagy

Answer 3

Macroautophagy involves a double-membrane made around what is to be degraded. Thought to be more of a bulk/unregulated process; although this is probably not true

Question 4

Why do mice without Atg7 (autophagy gene) die right after birth?

Answer 4

Suggests that autophagy is a very important part in surviving nutrient starvation (autophagy keeps you alive between meals)

Question 5

What are functions of macroautophagy?

Answer 5

Recycle proteins et al during nutrient deprivation. Recycle mitochondira and peroxisomes. Allow cell suvival under stress conditions. Present antigens to MHC system. Neuro-protection. Remove intracellular pathogens. Involved in agin process (can extend life). Tumor suppression AND tumor promotion? Regulates apoptosis

Question 6

What are Atg genes?

Answer 6

Regulate autophagy but also do other things (Atg1 =protein kinase; Atg12 = ubiquitin-like Atg6 = “scaffold”). First identified in yeast- highly conserved. Because these are enzymes they are potentially “druggable.”

Question 7

What is Atg6 AKA? What does it form a part of?

Answer 7

AKA Beclin-1. Scaffold that forms part of Type III PI3 kinase complex

Question 8

What is the 7 step process for macroautophagy?

Answer 8

1. Induction 2. Vesicle Nucleation (phagophore) 3. Vesicle Expansion (omegasome) 4. Cargo Targeting (LC3II and p62) 5. Vesicle Closure (now an autophagosome) 6. Vesicle Fusion with endosome (now an amphisome) 7. vesicle fusion with lysososome (now autolysosome)

Question 9

What does activation of PI3K complex do?

Answer 9

allows nucleation of a membrane that will eventually form autophagosome

Question 10

Autophagy signaling often converges on which pathway?

Answer 10

mTOR

Question 11

What are some things that regulate autophagy?

Answer 11

Amino acids. Growth factors. Lipids. Everything that regulates the PI3 kinase pathway. Other protein kinases. Tumore suppresors like p53. Mutated oncogenes like RAS. Drugs

Question 12

What does rapamycin do with respect to autophagy? How does this show that autophagy is protective against neurodegeneration?

Answer 12

Rapamycin promotes autophagy and also protects against Huntington’s disease. Shows decreasing neurodegeneration is related to increased autophagy

Question 13

What specifically does autophagy do with respect to Huntington’s?

Answer 13

Autophagy will degrade the aggregate-prone proteins (the expanded stretches of glutamine residues) that cause neuronal cell death

Question 14

What do capsases do with respect to Beclin 1?

Answer 14

Cleave it

Question 15

What happens to autophagy and apoptosis when Beclin 1 is cleaved or bound to?

Answer 15

Inhibits autophagy; increases apoptosis

Question 16

What to Bcl2 and Bcl-xL do?

Answer 16

Bind to BH3 domains on Beclin 1. Inhibits autophagy

Question 17

What does cytochrome c do once it is released from the mitochondria?

Answer 17

Helps to activate capsases (proteolytic enzymes); which cleaves Beclin1. Autophagy is inhibited and apoptosis is induced

Question 18

What happens to autophagy and apoptosis after cytochrome c is released from mitochondria?

Answer 18

Autophagy is inhibited. Increases apoptosis

Question 19

Why can it be difficult to interpret results of therapeutic interventions that target Bcl-2 and other proteins?

Answer 19

Many of these proteins regulate apoptosis but also control autophagy. How do you tell which caused the results?

Question 20

Which organelle is stressed first in necrosis?

Answer 20

Mitochondria

Question 21

What happens to the mitochondria when it is starved for oxygen?

Answer 21

Begins to swell. At “high-amplitude swelling” it can no longer maintain its ionic gradients or oxidative phosphorylation and the cell runs out of energy.

Question 22

What happens to the rest of the cell once mitochondria are no longer producing ATP?

Answer 22

The plasma membrane’s ion pumps fail and water floods in. The cell swells and bursts. Lysis releases the cell�s intracellular contents into the extracellular space

Question 23

What happens to the body when after lysis of cells?

Answer 23

The body can tell when internal lipids and molecules are in the extracellular space and this induces an intense proinflammatory reaction. Many white cells (mostly macrophages) are drawn to the area of damage. This is usually good as it leads to debris removal and injury resolution

Question 24

What is the difference between necrosis and apoptosis?

Answer 24

Necrosis implies death of cells that are not supposed to die. Apoptosis is used in cells for whih death was normal and predictable.

Question 25

What is the general process of apoptosis?

Answer 25

Begins with collapse of the nucleus: chromatin is fragmented and supercondensed. Cells shrink and then tear themselves into smaller apoptotic bodies. These are recognized by macrophages and are soon phagocytosed

Question 26

What is phosphatidylserine (PS)?

Answer 26

A phospholipid that is normally confined to the inner surface of the membrane. When a cell commits to apoptosis PS is exposed on the outter surface and signals to macrophages and dendrites to consume the cell.

Question 27

What does the enzyme flippase do?

Answer 27

Ensures than any PS molecules that stray to the outer surface of the membrane are quickly returned

Question 28

What does the enzyme scramblase do?

Answer 28

Soon after apoptosis begins; scramblase makes sure PS is on both sides of the membrane via a "scrambling" mechanism

Question 29

Does apoptosis trigger an immune response?

Answer 29

No because the apoptotic cells are consumed before they lyse. This is a good thing

Question 30

What is morphogenetic death?

Answer 30

Determines the final shape of body parts and organs. EX in limbs the death by apoptosis of cells between the digits gives the final form to fingers and toes

Question 31

Describe the signaling of internal apoptosis pathway

Answer 31

Involves outer membrane of the mitohondria. Nomally; the membrane is guarded by anti-apoptotic proteins. When cell receives signal the pro-apoptotic proteins replace their anti-apoptotic family members. This allows other members of the family to act on the membrane so it is permeable and releases cytochrome C. Cty C activates a cytoplasmic protein that starts a signaling cascade.

Question 32

What are the anti-apoptotic members of the Bcl-2 protein family?

Answer 32

Bcl-2 and Bcl-XL

Question 33

What are the pro-apoptotic members of the Bcl-2 protein family?

Answer 33

Bim and PUMA

Question 34

What are the names of the proteins that act on the membrane of the mitochondria to make it permeable?

Answer 34

Bax and Bak

Question 35

What is the name of the cytoplasmic protein that is activated by cytochrome C?

Answer 35

Apaf-1

Question 36

What protein does Apaf-1 activate? What does it do?

Answer 36

Activates caspase-9 which is the signal caspase. Caspase-9 activates caspase-3 (the executioner)

Question 37

What does caspase-3 do?

Answer 37

Cleaves many substrates; eventually resulting in the classic appearance of apoptosis

Question 38

Describe the signaling of the external apoptosis pathway

Answer 38

Cytotoxic T cells (CTLs) survey surface of all body cells. If there is a mutation or infection the CTL expresses a surface molecule which binds to the abnormal cell's surface. This binding then sends a signal to the cell's interior; which activates a cascade of signaling to trigger apoptosis.

Question 39

What is the name of the surface molecule that CTL cells express when an abnormal cell is found? What do they bind to?

Answer 39

Could be one of two. Either Fas ligand (FasL) or CD95 ligand (CD95L). These ligands bind to either Fas or CD95 on the abnormal cell's surface

Question 40

What molecule is recruited to CD95 (or Fas?)? What does that molecule do?

Answer 40

CD95 sends a signal which recruits FADD. FADD activates caspase-8. Caspase-8 is a signaling caspase (like caspase-9 in the intrinsic pathway) and it activates caspase-3

Question 41

What is mutated in children with the condition called autoimmune lymphoproliferative syndrome (ALPS)?

Answer 41

Either Fas or FasL (their malignancy starts because not enough cells die; not because of uncontrolled proliferation)

Question 42

What is a FLIP? How does it relate to some pathogens?

Answer 42

FLIP is a competitor with caspase-8 for binding to FADD. When FLIP is bound to FADD it inhibits apoptosis signaling. There are viral FLIPs (v-FLIPs) which use anti-apoptotic genes to keep the cell alive until they can finish their replicative cycle

Question 43

What is another CTL mechanism?

Answer 43

The CTL secretes enzymes (granzymes) and a pore-making protein (perforin) that together deliver apoptosis-inducing molecules to its intended target