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Question 1

What does Sar1 do?

Answer 1

1. A protein involved in membrane trafficking.
2. GTPase found in COPII vesicles.
3. Regulates assembly and disassembly of COPII coats.

Question 2

Explain function of Sec12.

Answer 2

GDP-bound Sar1 interacts with membrane-bound exchange factor Sec12 and becomes Sar1-GTP.
2. Nterm of Sar1 then attaches to membrane and serves as binding site for Sec23/Sec24 protein coat complex.

Question 3

What does Sec23 do?

Answer 3

Once the coat is complete and released with vesicle, it promotes Sar1 GTPase activity which triggers the disassembly of COPII coat.

Question 4

What does calnexin do?

Answer 4

Retains unfolded or unassembled N-linked glycoproteins in the ER. (Is a chaperone)

Question 5

What does COP I do?

Answer 5

Transports cargo from Golgi to ER within Golgi stacks (retrograde).

Question 6

What does COP II do?

Answer 6

Transports cargo from ER to Golgi. (only assembled on cytosolic side, not ER)

Question 7

What does clathrin do?

Answer 7

Transports cargo from Trans Golgi to Endosome; PM to Endosome.

Question 8

Where do signal sequences belong?

Answer 8

N-terminus

Question 9

What can KDEL do?

Answer 9

Retrieval of receptor protein that accidentally escapes ER.

Question 10

Describe the steps of ERAD.

Answer 10

ER associated degradation:

1. Recognition of misfolded/mutated proteins in the ER.
2. Retro-translocation into the cytosol.
3. Ubiquitin-dependent degradation by proteasome.

Question 11

What is the purpose of N-linked glycosylation?

Answer 11

1. Helps proteins fold correctly.

2. Protects from degrading quickly.

Question 12

Which compartments are topologically equivalent to the extracellular space?

Answer 12

1. ER lumen
2. Interior of Golgi cisternae
3. Interior of lysosome

Question 13

What does KDEL do?

Answer 13

An amino acid structure of a protein that keeps it from secreting/leaving the ER. Targets things back to the ER. Proteins can only leave ER after this sequence is cut off.

Question 14

Type 1 membrane proteins have what in cytosol and what in lumen?

Answer 14

C terminus in cytosol. N terminus in lumen.

Question 15

On what side does signal sequence recognition occur?

Answer 15

Cytosolic, not lumen.

Question 16

Prion forming Prp adopts the _______.

Answer 16

Beta sheet confirmation.

Question 17

Wild type non-prion forming is _____.

Answer 17

Alpha-helical conformation.

Question 18

Transverse diffusion (flip-flop) is slow or rapid?

Answer 18

Very slow

Question 19

Lateral diffusion is slow or rapid?

Answer 19

Rapid

Question 20

What does fluorescent photobleaching recovery do?

Answer 20

Measures the rate at which diffusion takes place.

Question 21

What is the difference and similarity of simple diffusion and facilitated diffusion?

Answer 21

Both: Higher to Lower concentration and no energy input.
Difference: Simple diffusion uses no transporters, while facilitated does (for large substances such as glucose).

Question 22

How does the Na+/glucose co transporter work?

Answer 22

Na+/K+ pump creates conc. gradient for Na. Glucose transporter uses this energy/affinity to bring glucose into the cell against its concentration using the higher to lower conc gradient of the Na+.

Question 23

What does myosin II do?

Answer 23

Dimer with two light chains for each heavy chain. Produces muscle contraction.

Question 24

What does myosin V do?

Answer 24

Dimeric myosin with 36nm step size (total of 72nm length).

2. Walks towards barbed end (+)
3. May act as tether for vesicles and organelles.

Question 25

What's unique about myosin VI?

Answer 25

Minus end directed motor along with IX.

Question 26

What's unique about myosin VIII?

Answer 26

Plant-specific myosin involved in cell division.

Question 27

Myosin II leads to what formation?

Answer 27

Thick filament formation.

Question 28

What are the steps for when insulin is present (short version)?

Answer 28

1. Insulin -> IR -> IRS-1 -> P13K -> PDK1 -> PKB -> release of GLUT4 from cytoplasmic vesicle. 2. Glucose binds to GLUT4 and is transferred inside cell.

Question 29

What are the steps for intrinsic apoptosis?

Answer 29

1. Internal cellular damage 2. Activation of proapoptotic BH3-only protein and subsequent activation of Bak or Bax 3. Bax channel/pore formed on surface of mitochondria 4. Release of cytochrome c through pore (electron transport and cell killer) 5. Apoptosome complex formed (Apaf-1 + cytochrome c + caspase 9) all recruited by cytochrome c. 6. Apoptosome cleaves executioner procaspases into caspase. 7. Apoptosis of targets.

Question 30

What are the steps for insulin signaling? (long version)

Answer 30

1. Blood glucose increases 2. Insulin released 3. Insulin binds to alpha chain receptors and triggers trans-autophophorylation (RTKs) beta chain 4. IRS (Insulin receptor substrate) has PTB domain that binds to phosphate on RTK. 5. IRS acts as docking station for Grb2 -> SOS -> Ras-GTP and PI3K (2 subunits with SH2 domains) 6. PI3K phosphorylates 3' OH from PI(4,5)P2 into PIP3 7. PDK1 has PH domain that binds to PIP3 8. Bound PDK1 activates PKB. 9. Activated PKB induces protein synthesis, glucose uptake, and glycogen synthesis.

Question 31

Explain the steps to the Epinephrine GPCR pathway.

Answer 31

1. Tyrosine binds to Epinephrine receptor. 2. Causes G-protein to bind to receptor. 3. GDP is exchanged for GTP. 4. G-alpha subunit with GTP now binds to effector protein. 5. Activated effector adenylyl cyclase makes cAMP (2nd messenger). 6. cAMP activates PKA (2 regulatory subunits and 2 catalytic subunits) by binding to 2 regulatory subunits causing catalytic subunits to dissociate. 7. Induces phosphorylation of enzymes (inhibits glycogen synthesis, and activates glycogen breakdown) 8. Also causes phosphorylation of transcription factors to increase glucose synthesis. 9. All of which increase [glucose]. (more glucose helps with stress response in brain/muscles)

Question 32

What are the steps for the Serum response factor (SRF) and TCF pathway?

Answer 32

1. After ERK is phosphorylated and enters the nucleus, it induces phosphorylation of TCF. 2. Phosphorylated TCF binds to SRF and this complex increases expression of early response genes such as C-Fos and C-Jun. 3. Bound together Fos and Jun are phosphorylated and form AP-1 complex, which leads to increased expression of delayed response genes. 4. These delayed response genes are things like cyclins and CDKs, which are the engine for driving cell growth and division.

Question 33

What are the steps for glucocorticoid signaling?

Answer 33

1. Steroid hormone (transcription factor) enters cytoplasm. 2. Binds to [receptor + Hsp90] chaperone complex causing Hsp90 to dissociate. 3. Receptor now has exposed NLS (nuclear localization signal) sending the signal/receptor into the nucleus. 4. Signal/Receptor complex dimerizes and attaches to a GRE sequence to regulate gene expression with the help of SWI/SNF BRG1 complex (DNA remodeling).

Question 34

What are the basics about glucocorticoid signaling?

Answer 34

1. Stress hormone 2. Nonpolar = hydrophobic 3. Localized in cytosol 4. Can cross membrane freely

Question 35

What are the steps for recognition of signal sequence on the ER?

Answer 35

1. Signal sequence on nascent polypeptide is recognized by SRP (signal recognition particle). 2. SRP attaches to signal and then binds to SRP receptor (arrests protein translation by blocking tRNA entry). 3. Upon binding, SRP dissociates from receptor following GTP hydrolysis. 4. Ribosome is now free to bind to Sec61 complex (translocon). 5. Peptide translocates into the ER lumen

Question 36

What is the purpose of disulfide bonds in ER proteins and are they common?

Answer 36

Disulfide bonds stabilize proteins and promote folding and are common among ER proteins. - PDI = protein disulfide isomerase

Question 37

The ER is the site for what?

Answer 37

1. Synthesis of all membrane proteins in the endomembrane system. 2. Membrane protein folding and modifications. 3. Lipid synthesis.