chapter 13

Question 1

pumps

Answer 1

use a source of ree energy such as atp or light to drive thermodynamically uphill transport of ions or molecules (active transport

Question 2

channels

Answer 2

enable ions to flow rapidly through membranes in a downhil direction (passive/faciliatited transport)

Question 3

3 type of pumps

Answer 3

1. p-type ATPase
2. atp binding casette (abc) transporters
3. secondary transporters

Question 4

2 energy sources for pumps

Answer 4

atp or concentration gradient

Question 5

p-type atpases

Answer 5

use atp to drive active transport of a specific ion

Question 6

3 p-type atpases

Answer 6

ca2+ atpase: transports calcium from cytoplasm to sarcoplasmic reticulum of muscle cells
2. H+ K+ atpase enzyme responseible for pumping sufficient protons into the stomach to lower the pH below 1.0

2. na+ k+ atpase - pumps na+ out of the cell and k+ into the cell

Question 7

structure of sarcoplasmic reticulum ca2+ ATPase (SERCA)

Answer 7

110-kd polypeptide with a transmembrane domain consisting of 10
ALPHA helices. transmembrane domaine includes sites for binding 2 calcium ions. each calcium ion is coordinated to 7 oxygen atoms

3 domains: N binds atp nucleotide, P accepts phosphoryl group on aspartate residue, and A serves as an actuator for N domain

Question 8

what does SERCA do?

Answer 8

maintains a calcium ion concentration of about .1 mM in the cytosol compared with 1.5 mM in the sarcoplasmic reticulum

Question 9

what is muscle contraction and relaxation triggered by?

Answer 9

contraction: Abrupt rise in cytosolic calcium level. relaxation depends on rapid removal of ca2+ from cytosol into sarcoplasmic reticulum

Question 10

sarcoplasmic reticulum:

Answer 10

contains large stores of calcium

Question 11

what happens to SERCA after atp hydrolysis

Answer 11

N and P domains move toward one another during catalytic clycle. closure is facilitated by atp binding and binding of ca2+ to the membrane spanning helices

Question 12

what happens when a phosphoryl analog binds, but no calcium

Answer 12

very different compared to structure without atp but with calcium

Question 13

simple pump action mechanism

Answer 13

pump interconverts between 2 conformational states, each with a binding site acccessible to a different side of the membrane

Question 14

serca mechanism

Answer 14

1. atp binds into n domain, atp cleaved to adp, clacium is released

finally calcium goes back in

Question 15

digitalis

Answer 15

plants that inhibit na+ K+ pump. 
digitoxigenin and ouabain are membres of this class as inhibitors

they inhibit dephosphorylation of ep-2 form of the atpase when applied on the extracellular face of the membrane.

Question 16

digitoxigenin and ouabain are known as?

Answer 16

cardiotonic streoids becasue of their strong effects on the heart

Question 17

how is digitalis used for congestive heart failure

Answer 17

increases force of contraction of heart muscle. inihibition of the na k+ pump leads to higher Na+ inside the cell. this risults in slower extrusion of CA2+ by sodium calcium exchanger. increase in intracellular level of ca2+ enhances contractility of cardiac muscle

Question 18

multidrug resistance

Answer 18

tumor cells in culture often becoem resistant to drugs that were intialy quite toxic to the cells. development of resistance to one drug also makes the cells less sensitive to a range of other compounds

Question 19

what causes multidrug resistance

Answer 19

multidrug resistance protein acts as an atp dependent pump that extrudes a wide range of small molecules from cells that express it. when cells are xposed to the drug, the MDR pumps the drug out of the cell before the drug can exerti ts effects

Question 20

common architecture of MDR and homologous proteins

Answer 20

each protein has 4 domains: 2 membrane binding domains and 2 atp binding domains (abc transporters atp binding casettes). they are members of the p-loop NTPase super family

Question 21

bacterial abc transporters are usually what compared to eukaryotic ones?

Answer 21

Bacterial ABC transporters are usually multimeric whereas

eukaryotic ones are monomeric

Question 22

Mechanism of abc transporter mechanism

Answer 22

1. opening of channel toward inside of teh cell
2. substrate binding and conformational changes in the atp-binding casettes
3. atp binding and further conformational changes
4. speapartion of the membrane binding domains and relase of the substrate to the other side of the membrane
5. atp hydrolysis to reset the transporter to its intitial state

Question 23

how do abc transporters differ from p-type atpases?

Answer 23

different mechanism

Question 24

what is a secondary transporter

Answer 24

membrane proteins that pump ions or moelcules uphill by coupling with the dowhill flow of a different species

Question 25

2 types of secondary transporters/cotransporters

Answer 25

antiporters or symporters

Question 26

what are antiporters

Answer 26

couple the downhill flow of one species to the uphill flow | of another in the opposite direction across the membrane

Question 27

what are symporters

Answer 27

Symporters use the flow of one species to drive the flow of a different species in the same direction across the membrane

Question 28

what are uniporters

Answer 28

Uniporters are governed by the concentration of a single species

Question 29

lactose permease

Answer 29

symporter uses the h+ gradient across e.coli membrane generated by oxidation of fuel molecules to drive uptake of lactose and other sugatrs against a concentration gradient. has a proton binding site and al actose binding site

Question 30

lactose permease structure

Answer 30

2 halves each with 6 membrane spanning alpha helices. 2 halves surround sugar and are linked to each other by a single polypeptide. the sugar lies in a pocket in the center of the protein and is accesible from a path that leads from the interior of the cell

Question 31

mechanism of lactose permease

Answer 31

1. h+ from outside binds to coo-, 2. lactose binds between two halves at the active site. 3. eversion 4. lactose pumped in 5. h+ pumped in 5. eversion

Question 32

properties of ion channels

Answer 32

1. ion channels can be highly selective for particular ions 2. ion channels exist in open and closed states 3. transitions between the open and closed states are regulated 4. open states of channels often spontaneously convert into inactive state

Question 33

ligand gated channels

Answer 33

channels open and close in response to the bding of specific chemicals

Question 34

voltage gated channels

Answer 34

open and close in resposne to the elctrical potential across the membrane in which they are found

Question 35

patch clamp technique

Answer 35

enables measurment of the activity of asingle ion channel to be measured.

Question 36

how do you do the patch clamp technique

Answer 36

a clea glass pipette with a tip diameter of about 1mm is preast against an intact cell to form a seal. slight suction ldeads to the formation of a very tight seal. (gigaseal) ensures that an electric current flowing through pipette is identical to current flowing through membrane covered by pipette

Question 37

cell attached

Answer 37

high resistance gigaseal formed

Question 38

whole cell mode

Answer 38

breaking of the membrane patch by increased suction produces low resistance pathway between pipette and interior of the cell

Question 39

excised patch mode

Answer 39

pieptte is pulled away from the cell

Question 40

acetylcholine receptor channel

Answer 40

ligand-gated channel which communicates the nerve impuse between certain neurons

Question 41

voltage gated na+ and k+ channels

Answer 41

conduct the nerve impuse down the axon of a neuron

Question 42

potassium ion channel | structure

Answer 42

both sodium and potassium channels contain 4 repeats, each repeat has 5 hydrophobic segments and one positively charged segment. hydrophobic segments wer thought to be membrane spanning while positively charged segment was a voltage sensor. it is tetrameric with 2 membrane spanning alpha helices. the subunits come together to form a pore in the same of a cone that runs through center of structure. opening to the outside and central cavity of the pore are filled with water so that k+ ion can fit in the pore without losing solvation shell of water

Question 43

stucture of potassium ion channel pore

Answer 43

inside of the cell diameter is about 10 angstroms, constricts to 8 angstroms and finally down to 3 angstroms where the k+ ions must give up water molecules and interact with carbonyl groups of the protein

Question 44

what must happen for potassium ions to relinquish their water molecules?

Answer 44

other polar interactions must replace those with water

Question 45

what functions as a selectivity filter that determines preference for k+ over other ions?

Answer 45

5 amino acid stretch within region including thr, val, gly, tyr, gly which is observed in all k+ channels

Question 46

how is selectivity of potassium ion channel achieved

Answer 46

narrow diameter 3 angstomrs rpevents having ions with a radius greater than 1.4 angstroms. but na+ is small enough to fit. it does not pass through, however because it is energetically unfavorable to become unsolvated because it is too small. protein only compensates for k+ losing its solvation shell

Question 47

how does the potassium ion channel manage to have tight binding but quick transport rate?

Answer 47

4 k+ binding sites present in the constristed region of the k+ channel. one hydrated k+ ion proceeds into the channel and through the relatively unrestriscted part of the channel

Question 48

potassium ion channel mechanism

Answer 48

1. 1 hydrated k+ ion proceeds into the channel and through the relatively unrestrsicted part of the channel 2. it gives up most or all of its coordinated water molecules and binds to the first site of the slectivity filter region 3. the binding energy of the second site presents a free energy barrier or trap preventing the ion from completing its journey 4. if a second ion moves through the channel into the first site, the electrostatic repulsion betwee 2i ons will stabilize initially bound ion and push it into solution

Question 49

what are s1 and s4 in voltage gated channels

Answer 49

paddles that extend from core of the channel. s4 is the voltage sensor. s1 5o s4 lie within the membrane. positively charged s4 region lies on the outside of the structure at the bottom of the pore

Question 50

mechanism of voltage gated channel

Answer 50

voltage sensing paddles lie in the down position below the closed channel. membrane depolarization pulls these paddles through the membrane. this motion pulls the base of the channel apart, opening the channel

Question 51

what happens when exposing cytoplasm side of potassium or sodium channel to trypsin?

Answer 51

cleavage of trypsin produced a trimmed channel that stayed persistently open after depoalrization

Question 52

what happens when mutant potassium channel lacked 42 amino acids near amino terminus?

Answer 52

opened in response to depolarization, but did not inactivate. inactivation was restored by adding a syntehtic peptide corresponding to the first 20 resideus of the native channel

Question 53

ball and chain model of inactivation

Answer 53

first 2 residues of potassium channel form a cytoplasmic unit (ball) that is atached to a flexible segment of the polypeptid (chain). when channel is closed, ball rotates freely in the aqueous solution, when the channel opens, the ball quickly finds a complemetnary site in the pore and occludes it

Question 54

where is the ball located in the inactivated state?

Answer 54

located in the cytosol

Question 55

what happens during depolarziation that affects the ball?

Answer 55

channel opens and creates a negatively charged binding site for the positively charged ball near the mouth of the pore. movement of the ball into this site inactivates channel