Unit 4

Question 1

Signal-mediated transport vs. Bulk flow

Answer 1

Signal-mediated: signal recognized by receptors which concentrate cargo near exit sites. Concentration in vesicle greater than in ER lumen.
Bulk flow: Default pathway without a signal sequence. Concentration of cargo in vesicles=concentration in ER lumen.

Question 2

Clathrin coat pathway

Answer 2

Endocytosis (also in trans golgi network vesicle)

Question 3

COPI pathway

Answer 3

Through golgi, golgi => ER

Question 4

COPII

Answer 4

ER => Golgi

Question 5

Describe COP assembly

Answer 5

Monomeric GTPase (ex SAR1) becomes activated by GEF, binds to donor membrane. Recruits adaptor proteins to form COP coat.

Question 6

Describe clathrin coat assembly

Answer 6

Adaptor proteins bind to clathrin triskelion, effect bud formation and shape membrane vesicle.

Question 7

List all proteins involved in vesicle coat assembly and transport

Answer 7

Clathrin, COPI, COPII, monomeric GTPases (ex SAR1), Rab, Rab effector, v- and t- SNAREs, dynamin

Question 8

Dynamin function

Answer 8

GTP hydrolysis leads to constriction of dimer => pinches off vesicle bud

Question 9

Describe nuclear pore complex structure

Answer 9

Like a “basket” between two membranes, FG nucleoporins

Question 10

Are all signal sequences described in lecture necessary and sufficient?

Answer 10

Yes for NLS and ER signal sequence - not sure re vesicle

Question 11

Ran GAP location and function

Answer 11

Located in cytosol, hydrolyzes GTP into GDP. “Activating” because activation of the Ran GTPase leads to increased hydrolysis, which then results in its “turning off.”

Question 12

Ran GEF location and function

Answer 12

Located in nucleus, replaces GDP with GTP

Question 13

When does Ran-GTP bind to the receptor? What is the impact of this?

Answer 13

In the nucleus, Ran-GTP binds to the receptor. This effects a conformational change which results in the release of the cargo into the nucleus.

Question 14

When does Ran dissociate from the receptor?

Answer 14

In the cytosol, after GTP is hydrolyzed (via GAP), the Ran-GDP dissociates from the receptor, leaving the receptor free to bind to new cargo.

Question 15

Describe nuclear export GTP cycle

Answer 15

Reverse process - cargo with export signal binds to receptor in nucleus, Ran-GTP also binds to receptor. Transported into cytosol with GTP is hydrolyzed and Ran-GDP dissociates from receptor. Dissociation promoted by GDP instead of GTP?

Question 16

Describe components of an intracellular signaling pathway.

Answer 16

Ligand, receptor, “second messenger” molecules, effector proteins, target molecule

Question 17

Signal transduction

Answer 17

Extracellular molecules elicit intracellular responses

Question 18

4 forms of intercellular signaling

Answer 18

Contact-dependent, autocrine, paracrine (ex synaptic), endocrine

Question 19

3 types of cell-surface receptors

Answer 19

G-Protein coupled receptors, receptor tyrosine kinases/enzyme-coupled receptors, ligand-gated ion channels

Question 20

Ion-channel coupled receptors

Answer 20

Binding of signal molecule causes channel to open, enabling ions to flow down concentration gradient

Question 21

What do G-protein coupled receptors bind to?

Answer 21

Heterotrimeric (3 domain) GTPases

Question 22

Enzyme coupled receptors either associate with an enzyme or…

Answer 22

Have a catalytic domain in the receptor

Question 23

Protein kinases and phosphatases

Answer 23

Protein kinases add phosphate group to specific amino acids, taking phosphate from ATP (“turn on”). Protein phosphates remove phosphate group from protein (“turn off”).

Question 24

List all “molecular switches” described in slides.

Answer 24

Kinases, phosphatases, GTPases (via GAPs and GEFs), binding of cAMP or calcium ions to proteins

Question 25

What happens upon ligand binding to G-protein coupled receptor?

Answer 25

Receptor activated, which activates nearby GTPase. The GDP in the alpha subunit is exchanged for a GTP. The G-protein is now activated and associates with nearby effector (ex adenylyl cyclase). Effector then produces cyclic AMP. Signaling stopped by hydrolysis of GTP back into inactive GDP.

Question 26

How is GPCR signaling stopped after pathway has been activated? How is this an example of negative feedback?

Answer 26

GTP is hydrolyzed into GDP and P. G protein reforms. GPCR is phosphorylated by a kinase. Arrestin binds to phosphorylated GPCR and inhibits it. Example of negative feedback! Activation of GPCR triggers kinase to phosphorylate it and arrestin to bind.

Question 27

How many domains in a GPCR?

Answer 27

7

Question 28

Receptor Tyrosine Kinases are an example of...

Answer 28

Enzyme-coupled receptor

Question 29

2 types of RTK dimerization

Answer 29

Ligand-mediated and receptor-mediated

Question 30

Trans-autophosphorylation

Answer 30

2 RTKs phosphorylate each other, this generates binding sites for signaling proteins

Question 31

What proteins bind to phosphorylated tyrosines on RTKs?

Answer 31

Proteins with SH2 domain

Question 32

What domains of the EGFR protein could be mutated that would result in constitutively active receptor?

Question 33

Describe monoclonal antibody treatment for breast cancer

Answer 33

Antibodies block cell signaling, prevent tumor from multiplying or "calling out" for help from blood vessels.

Question 34

What is cAMP?

Answer 34

Second messenger involved in cell signaling pathways

Question 35

How does ATP production enable the powering of cell processes?

Answer 35

When P bond proken, energy is released

Question 36

Function of ATP synthase

Answer 36

Protons flow back down EC gradient through ATP synthase, which uses this energy to produce ATP from ADP and Phosphate

Question 37

Compare and contrast mitochondrial and chloroplast systems

Answer 37

Similar processes with light reaction of photosynthesis and cellular respiration, but opposite equations.

Question 38

How does glucose enter cells? Describe whole process.

Answer 38

Food you eat is broken down into glucose, which is transported from intestinal lumen into blood space via asymmetrically distributed transporters. When blood glucose levels increase, pancreas starts releasing insulin, which binds to cell membranes and triggers the opening of channels for glucose to pass through.

Question 39

Cellular respiration equation

Answer 39

6 O2+ C6H12O6 => 6CO2+6H2O+ ATP (36 net gain)

Question 40

Photosynthesis equation

Answer 40

6 CO2+ 6H2O + Energy (light) =>6 O2+ C6H12O6

Question 41

Glycolysis: Location, NADH/ATP production, final result

Answer 41

Cytosol, 2 ATP and 2 NADH gained, 6-C glucose broken down into 3 2-C pyruvate and then 2 Acetyl CoA.

Question 42

Krebs Cycle

Answer 42

Mitochondrial matrix, 3 NADH and 1 FADH2 produced, 1 ATP/GDP produced, water waste product

Question 43

Oxidative phosphorylation

Answer 43

Using electrons from carriers (NADH and ATP) to generate ATP

Question 44

Electron transport chain

Answer 44

Cytochrome complex I-IV Electron carriers deposit electrons Flow creates electrochemical gradient ATP synthase

Question 45

Photosynthesis light reactions

Answer 45

Light photon knocks electron out of PSII chlorophyll, transferred to PSI which results in electrochemical gradient used by ATP synthase to generate ATP.

Question 46

Photosynthesis dark reactions

Answer 46

ATP and NADH produced in light reactions convert atmospheric CO2 to organic compounds (food)