7

Question 1

what can be signalling molecules

Answer 1

ions hormones sugars

Question 2

what happens when signalling molecules bind

Answer 2

processes such as metabolic pathways and gene expression are initiated

Question 3

what type of molecule do you always need for cellular signalling

Answer 3

proteins

Question 4

signal transduction steps

Answer 4

signalling molecule binds in response to physiological stimulus, message is recieved by receptor (usually integral membrane protein), primary message is relayed to cell interior by generation of an intracellular secondary messenger (like g alpha), amplification, transduction, response then termination

Question 5

how many transmembrane segments in GPCRs

Answer 5

7

Question 6

what releases the g protein

Answer 6

conformational changes on the GPCRs

Question 7

natural ligands for GPCRs

Answer 7

serotonin, epinephrine, prostaglandins, dopamine, psilocin/psilocybin

Question 8

synthetic ligands for GPCRs

Answer 8

morphine, histamine, LSD

Question 9

GPCR specificity (how to tell GPCRs apart)

Answer 9

binding, they are otherwise structurally similar

Question 10

what is kd conceptually

Answer 10

a measure of binding affinity the lower it is, the stronger the binding

Question 11

kd formula

Answer 11

[A][B]/[AB]

Question 12

what determines binding affinity

Answer 12

noncovalent interactions between side chains, backbone, and molecule’s functional group

Question 13

what does it mean for binding to be saturatable on stoichiometry

Answer 13

upper limit due to specific ratio of ligand to protein

Question 14

is binding reversible for non covalent interactions

Answer 14

yes

Question 15

what happens to the beta adrenergic receptor when it is active

Answer 15

the tm5 on the extracellular side moves in, and the tm6 moves out, causing g alpha activation

Question 16

what happens after epinephrine binds

Answer 16

extracellular binding to receptor, which then breaks apart the g protein subunits, causing g alpha to activate adenyl cyclase, releasing cAMP. then GTP is hydrolyzed to GDP on g alpha. pKA is bound by cAMP, which phosphorylates other proteins to activate them

Question 17

what is PKA (protein kinase A)

Answer 17

transferase that can phosphorylate to activate or inactivate other enzymes

Question 18

how to regulate GPCR signalling

Answer 18

post translational modifications (like phosphorylation), disrupting binding interactions, metabolizing molecules, protein degradation

Question 19

most effective way of turning off epinephrine signalling

Answer 19

epinephrine binding (you need to turn off the start of the pathway)

Question 20

ras proteins are part of what family

Answer 20

small GTPases, and hence a type of G protein

Question 21

ras protein pathways

Answer 21

cell growth and apoptosis

Question 22

how does ras hydrolyze gtp

Answer 22

switch 1 and switch 2 motifs will have a conformational change

Question 23

what does defects in GTP hydrolysis cause

Answer 23

uncontrolled signalling and cancer

Question 24

at what point can signalling cause health complications

Answer 24

any point. post translational modifications, conformational changes play a key role especially

Question 25

mutations in receptor or effector proteins can cause what

Answer 25

prevent ligand-receptor or protein-protein interactions needed for activation or inactivation

Question 26

enzyme-linked receptors. how does it work

Answer 26

single transmembrane segment that dimerize with another upon ligand binding. activation leads to autophosphorylation or phosphorylation by tyrosine kinases

Question 27

example of enzyme linked receptors

Answer 27

insulin signalling pathway, epidermal growth factor, jak/stat pathways

Question 28

phospholipid mediated signalling

Answer 28

phospholipases hydrolyze phospholipids to make other second messengers like DAG or IP3, making calcium release from ER. basically cleave phospholipid head group and acyl chains

Question 29

IP3

Answer 29

result of phospholipase cleaving phospholipid. it's the head, and goes to ER membrane, binding to a membrane protein for signalling

Question 30

DAG

Answer 30

2 acyl chains from phospholipid being cleaved. it is left behind in the membrane where the cleaving happens and can activate protein kinase C

Question 31

examples of phospholipid mediated signalling

Answer 31

eicosanoid and akt signalling

Question 32

who would win, insulin and epinephrine

Answer 32

insulin is stronger and has priority in turning off epinephrine's pathway

Question 33

which is anabolic and which is catabolic out of insulin and epinephrine

Answer 33

insulin is anabolic and epinephrine catabolic

Question 34

insulin signalling pathway and terminatinv

Answer 34

insulin binds to insulin receptor, phosphorylating IRS-1, activating the pathway that leads to phosphorylation of beta adrenergic receptor by protein kinase B. then beta adrenergic receptor gets internalized and degraded, terminating GPCR signallign

Question 35

passive diffusing

Answer 35

small, uncharged can cross slowly and based on concentration

Question 36

facilitated diffusion saturation

Answer 36

water transporter protein is all occupied and therefore will slow if you have too water. depending on how many binding sites there are. a hyperbolic curve

Question 37

does passive diffusion saturate

Answer 37

no

Question 38

channel proteins. 3 main features?

Answer 38

facilitated diffusion, aka ion channel proteins. structure is key for function. selectivity, rapid conductance, can be gated due to stimuli

Question 39

potassium ion channel controls which cellular processes

Answer 39

regulating cell volume, secreting hormones, electrical impulse

Question 40

how are potassium ion channels selective

Answer 40

selectivity filter of 5 amino acids (TVGYG)

Question 41

how many transmembrane parts are in a potassium ion channel

Answer 41

4, it is a tetramer

Question 42

what binds the K+ ions as they go through the channel

Answer 42

4 backbone carbonyls and the Thr side chain hydroxyl form transient interactions, breaking quickly to let K+ move

Question 43

potassium channel gating mechanism

Answer 43

gly99 acts as a molecular hinge to open/close the channel, because glycine is a helical breaker. this is part of the regulatory domain

Question 44

what causes potassium channel gating

Answer 44

voltage or intracellular pH changes

Question 45

bata barrel protein physical properties

Answer 45

facing inside are hydrophilic and outside are hydrophobic. so alternating like DADADA

Question 46

which are more selective, beta or alpha channels

Answer 46

alpha

Question 47

how many amino acids to cross membrane for beta barrel

Answer 47

10 AA (you need less than alpha because they are more extended)

Question 48

can you use hydropathy plots for channel proteins

Answer 48

no because its averaged

Question 49

primary active transport needs what for energy

Answer 49

atp breakdown, light energy, or passing of electrons

Question 50

secondary transporters use what for energy

Answer 50

one must go down gradient and use that energy to move another

Question 51

how do conformational changes in a MsbA flippase make it open and closed

Answer 51

in the ATP bound closed form, lipid is attached, then ATP is hydrolyzed, and the lipid gets moved to interior side

Question 52

bacteriorhodopsin is found where

Answer 52

halobacterium salinarum in concentrated purple patches in membrane.

Question 53

what does bacteriorhodopsin do

Answer 53

light strikes the protein, cofactor absorbs light, induces conformational charge, moving protons out of the cell, creating a proton gradient that is then used to make ATP by ATP synthase

Question 54

what type of protein is bacteriorhodopsin

Answer 54

GPCR.

Question 55

structure of bacteriorhodopsin

Answer 55

7 TM protein with retinal prosthetic group

Question 56

prosthetic group in bacteriorhodopsin

Answer 56

all trans retinal group attached to a lysine via a Schiff base.

Question 57

how does light hitting bacteriorhodopsin change structure

Answer 57

conformational charge from all trans prosthetic group to 13-cis, causing pKa values of functional groups to change for protein transport (?)

Question 58

whats a chromaphore

Answer 58

protein that absorbs light, like bacteriorhodopsin

Question 59

protein hopping

Answer 59

protons are not directly pumped across membrane but passed from one functional group to another. much faster than true diffusion and explains fast H+ diffusion