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Cells: Form and Function > Midterm 2 > Flashcards

Midterm 2 Flashcards

1
Q

Ran is a ______ switch protein

A

GTPase

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2
Q

describe the secretory pathway of protein sorting

A

distribution of soluble and membrane proteins synthesized by the rough ER to final destinations at the cell surface

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3
Q

describe the endocytic pathway of protein sorting

A

vessicles budding from plasma membrane take up soluble extracellular proteins and deliver them to lysosomes via late endosomes

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4
Q

what are two techniques used for studying the secretory pathway?

A

sds page, analysis of yeast temperature sensitive secretory mutants, cell free asssays

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5
Q

protein transport through the secretory pathway can be visualized by____________ microscopy of cells producing a GFP tagged membrane protein

A

fluorescence

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6
Q

transport of a membrane glycoprotein from the ER to the golgi can be assayed based on sensitivity to cleavage by ___________

A

endoglycosidase D

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7
Q

what is a bradford assay used for ?

A

determine the protein concentration in biological samples

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8
Q

what are two advantages and two disadvantages of bradford assay?

A

accurate, widely used, simple, alternates are more expensive, requires irreversible dye binding, linear and short range, inhibited by detergents, time consuming

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9
Q

why are yeasts a good model organism for vesicular transport?

A

secretory pathway and molecular components similar in all eukaryotes

sec mutants in yeast were identified to secrete proteins at one temp but unable at higherq

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10
Q

the golgi apparatus outputs to the ______ ______ and inputs to the ____

A

plasma membrane, ER

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11
Q

how does vessicle budding work?

A

bud from the parent donor organelle and fuse with particular target organelle

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12
Q

what is budding initiated by?

A

recruitment of gtp binding proteins to a patch of donor membrane

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13
Q

how is vessicle budding driven?

A

by polymerization of soluble protein complexes on the cytosolic face of the membrane

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14
Q

after budding when the vessicle is released ____ proteins are shed

A

coat proteins

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15
Q

what are v snares?

A

v for vessicle, incorporated into vessicle membrane during assembly of coat, initially occluded by vessicle coat

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16
Q

t snares are?

A

for target, are embedded in target membrane and can join with cognate v snares

interaction brings membrane close together

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17
Q

all transport vessicles use v snares and t snares to fuse (t or f)

A

true

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18
Q

what are rab proteins?

A

small gtp binding proteins that regulate vesicle trafficking and fusion with the approprite membrane

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19
Q

_____ anchor allows rab proteins to be tethered to the vesicle membrane

A

isoprenoid

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20
Q

what is the two step process of the association of a Rab protein with a vessicle?

A
  1. cytosolic Rab GDP is targeted to vesicle membrane and held in place by isoprenoid anchor
  2. GEF in the membrane converts Rab GDP to Rab GTP which is enabled to bind Rab effectors
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21
Q

after vessicle fusion ______ hydrolysis releases Rab GDP

A

GTP hydrolysis

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22
Q

in order to expose both Rab and v snares, what must occur?

A

vessicle coat must be removed after it buds off parent membrane

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23
Q

rab mediated docking does what?

A

to cognate Rab effector occurs first

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24
Q

interaction of _______and ________ close enough to fuse

A

v snares and t snares

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25
Q

snares are ?

A

abundant proteins that are usually inserted into mebranes via c terminal transmembrane domain

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26
Q

cytosolic region of each snare protein contains what?

A

repeated heptad sequence of 60-70 amino acids that confer ability to form coiled coil structures

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27
Q

what are the 3 types of coated vesicles?

A

COPII - vesicles trnasport proteins from the ER to the golgi

COPI - vesicles mainly transport proteins in the retrogade direction between golgi cisternae and from the cis golgi back to the ER

Clathrin - coated vesicles transport proteins from the plasma membrane and the trans golgi network to late endosomes

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28
Q

what is the GTP binding protein that controls coat assembly in COPI and clathrin coated vessicles?

A

ARF protein

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29
Q

what is the GTP binding protein that controls coat assembly in COPII vessicles?

A

Sar1 protein

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30
Q

what are the 4 steps to vessicle coat assembly?

A
  1. sar 1 membrane binding gtp exchange
  2. COPII coat assembly
  3. GTP hydrolysis
  4. coat assembly
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31
Q

what are the 4 switch proteins?

A

ARF Sar1 Ran and Rab

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32
Q

how does the vesicle coat selects cargo proteins by?

A

directly binding specific sorting signals of cytosolic domains of transmembrane cargo proteins

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33
Q

what exposes Rab and SNARE proteins that target vessicles for fusion with specefic target mebranes?

A

coat shedding

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34
Q

how is the first step of the secretory pathway mediated?

A

by COPII vesicles

  • contain v snares
  • move in anterograde direction
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35
Q

v snare recycling and retrieval of missorted ER resident proteins from the cis golgi is via COPI coated vesicles in the _______ direction

A

retrograde

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36
Q

newly synthesized proteins travel in COPII vesicles from the ER to the cis golgi in which direction?

A

anteriograde

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37
Q

retrograde transport recycles what?

A

v snares in COPI vesicles form cis golgi to ER

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38
Q

yeast cells with mutations in genes for COPII proteins are class ___ sec mutants and accumulate proteins in the _____ ____.

A

B, rough ER

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39
Q

how is formation of the COPII vesicles triggered?

A

sec12 catylyzes activation of cytosolic Sar1

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40
Q

Sar1 GTP binds to ER membrane and recruits _____ and _____

A

sec 23, sec24

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41
Q

how does sec24 interact with the cytosolic domain of COPII ternary complex?

A

with di acidic targeting signals that recruits cargo protein into the vesicle membrane

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42
Q

the cytosolic domains of COPII contain what?

A

di acidic sorting signals, the signal binds to sec24 subunit of COPII coat

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43
Q

all sorting signals interact with Sec24 (t or f)

A

true

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44
Q

how do vessicles move?

A

by diffusion in the cytoplasm

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45
Q

how is the ER to golgi intermediate compartment formed?

A

several ER derived vesicles fused (aka cis golgi network)

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46
Q

retrograde tansport is?

A

between golgi cisternae and from cis golgi to rough ER

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47
Q

What proteins assist in folding and modification of newly synthesized secretory proteins?

A

chaperone BiP, protein disulfide isomerase, many soluble proteins

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48
Q

most ER resident proteins carry what?

A

a KDEL sorting sequence at the c terminus

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49
Q

what is the function of the KDEL receptor?

A

acts mainly to retrieve soluble proteins containing the KDEL sorting signal

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50
Q

KDEL receptor contains ___________ at the end of the c terminal segment

A

KKXX sorting signal

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51
Q

_________ _____ can also target certain proteins to COPI vesicles

A

Di arginine sequence

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52
Q

what is cisternal maturation responsible for ?

A

anterograde transport through the golgi

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53
Q

vesicle based transport visible by electron microscopy are all _____ transporters

A

COPI

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54
Q

as retrograde transport occurs the enzymatic makeup of the _______ _______ changes

A

cisternal lumen

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55
Q

how do COPII coated vesicles transport newly synthesized proteins containing golgi targeting sequences?

A

in their cytosolic domain or bound to such proteins from the rough er to the cis golgi

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56
Q

how do COPI coated vesicles transport vesicles carrying ER/golgi resident proteins?

A

in the retrograde direction which supports golgi cisternal maturation

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57
Q

facilitated transport is movement ____ the concentration gradient?

A

down

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58
Q

secondary active transport and primary active transport is movement _____ the concentration gradient?

A

up

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59
Q

p class Na /K ATPase moves ___ Na ions out of the cell and ____ K ions into the cell

A

3, 2

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60
Q

what is the E1 conformation of p class na/k atpase?

A

three high Na binding sites and two low affinity K binding sites accessible from the cytosolic surface of the protein

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61
Q

what is the E2 conformation ?

A

the three bound Na ions gain access to the expolasmic face and simultaneously, the affinity of the 3 Na binding sites drop

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62
Q

open/closing not affected by membrane potential or signaling molecules so called ____ ___________

A

non gated channels

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63
Q

simple diffusion rate of substance movement across the phospholipid part of a membrane is proportioal to its ______ ______, ______ and _______

A

concentration gradient, hydrophobicity and size

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64
Q

type 1 single pass transmembrane protein have N terminus on ______ face, and the C terminus on _______ face

A

exoplasmic, cytoplasmic

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65
Q

how is the signal anchor sequence bound in type III single pass transmembrane proteins?

A

SRP binds the terminal singal anchor sequence synthesized by a cytosolic and interacts with SRP receptor on the ER membrane ribosome

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66
Q

where are precursor proteins synthesized?

A

cytosolic ribosomes

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67
Q

polypeptide can be kept unfolded by ?

A

chaperones, cytosolic Hsp70

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68
Q

during protein import into the mitochondrial matrix ____ is inserted into the translocon of the outer membrane?

A

MTS

69
Q

MTS is removed by a matrix ______

A

protease

70
Q

a pure lipid bi layer is impermeable to ?

A

ions, amino acids, sugars, most water soluble molecules

71
Q

gases and small uncharged water soluble molecules use _______ as transport

A

diffusion

72
Q

would life be possible for a pure lipid bilayer without proteins?

A

no

73
Q

the higher the k value the more _________ and faster to cross a bilayer

A

hydrophobic

74
Q

all membrane transport proteins are ______ integral membrane proteins

A

multipass

75
Q

channels transport water, ions and hydrophobic small molecules ____ concentration gradient

A

down

76
Q

_____ is faster and more specific than ________

A

uniport, diffusion

77
Q

in uniport the molecules dont enter the bilayer directly ( t or f)

A

true

78
Q

the lower the km the more _____ the substrate binds to the transporter

A

tightly

79
Q

which transport is the fastest?

mannose or glucose

A

glucose transport 3.8 times faster

80
Q

galactose is the slowest transport (t or f)

A

true

81
Q

what is osmotic pressure?

A

the hydrostatic pressure required to stop the movement of water caused by concentration gradient

82
Q

aquaporins _____ water permeability of cellular membranes?

A

increase

83
Q

what type of transport is faster than simple diffusion?

A

protein mediated transport

84
Q

________ proteins convert between two conformational states to facilitate diffusion across a membrane

A

uniport

85
Q

what is f class ATPase used for ?

A

to synthesize ATP

86
Q

what does indebendent DNA encode?

A

rRNA trnas

87
Q

most proteins are encoded by?

A

nuclear genes

88
Q

N terminal targeting sequences specify binding to receptor proteins on the ______ organelle?

A

surface

89
Q

protein import requires ______

A

energy

90
Q

where does double membrane transport occur?

A

outer and inner membranes are in direct contact

91
Q

double membrane transport requires what?

A

two targeting sequences and two translocation systems

92
Q

where are matrix targetting seuqences are located?

A

at the N terminus

93
Q

how long are matrix targetting sequences ?

A

20 to 50 amino acids

94
Q

does transport to the mitochondria involve the ER or the golgi complex?

A

no

95
Q

what are the 3 energy inputs required for import?

A

cytosolic Hsp70, matrix has Hsp70 anchored to the Tim44 protein, H+ electrochemical gradient across inner membrane

96
Q

proteins must be ________ to translocate

A

unfolded

97
Q

what is the path A for mitochondrial intermembrane space?

A

analogous to type one membrane, protein are inserted into the ER

98
Q

many mitochondrial outer membrane proteins have ______ structure

A

b barrel

99
Q

what is tom44?

A

general import pore

100
Q

what is the SAM complex?

A

sorting and assembly machinery comlex, inserts b barrel proteins into the outer membrane

101
Q

the chloroplast lumen is called?

A

stroma

102
Q

enzymes of the calvin cycle fix ______

A

co2

103
Q

rubisco is encoded by?

A

chloroplast dna

104
Q

small subunit of rubisco and other calvin cycle enzymes contain _______ _______ sequence

A

N terminal stromal import sequece

105
Q

chlorplast stroma sequence is located at the _______

A

N terminus

106
Q

endoplasmic reticulum sequence is located at the ________

A

N terminus

107
Q

Mitochondrion sequence is located at the _______

A

N terminus

108
Q

Peroxisome sequence is loctaed at the?

A

C terminus for most

109
Q

import of chloroplast stromal proteins uses post _________ ______

A

translational translocation

110
Q

the stromal Hsp70 Chaperone is required for ?

A

import of proteins into the mitochondrial matrix

111
Q

Hsp 70 does what ?

A

hydrolyzes ATP

112
Q

Thylakoids are?

A

internal interconnected membranous sacs that contain all the enzymes for photosynthesis

113
Q

many thylakoid proteins are synthezised in the ?

A

cytosol

114
Q

what are the 4 pathways for transporting proteins from the stroma to the thylakoid?

A
  1. Sec1 like
  2. Oxa1 like
  3. SRP dependent
  4. pH dependent
115
Q

descripe the srp dependent pathway? **

A
  • used for transport of plastocyanin and related proteins
  • first imported in unfolded state into chloroplast stroma
  • n terminal stromal sequence cleaved off
  • unfolded protein translocated into thylakoid lumen
  • chaperones keep unfolded
  • thylakoid targetting seuqence removed then protein folds in thylakoid lumen
116
Q

descripe the ph dependent pathway? **

A
  • used by proteins that bind metal containing cofactors
  • first imported in unfolded state into chloroplast stroma
  • n terminal stromal sequence cleaved off
  • folded protein translocated into thylakoid lumen
  • Tat pathway
  • thylakoid targetting sequence must have two closely spaced arg residues
  • tat proteins oligomerize in membrane to create pores of variable size to accomidate folded protein
  • powered by electrochemical gradient across thylakoid membrane
  • thylakoid targetting sequence cleaved off
117
Q

mitochondrial and chloroplasts proteins encoded by nuclear genes are synthesized and maintained in an unfolded state by _______ this is _________ ________

A

chaperones, post translational translocation

118
Q

what do targetting sequences direct?

A

post translational transport of the unfolded proteins through translocons into the organelles

119
Q

name two characteristics of peroxisomes?

A

small organelles, bound by single membrane, divide when large enough, in mammals not abundant in liver, dont have dna and ribosomes

120
Q

what is the function of peroxisomes?

A

contain enzymes that oxidize amino acids and fatty acids breaking them down for biosynthetic pathways,

121
Q

All luminal proteins must be transported into _______

A

peroxisomes

122
Q

targetting of peroxisomal proteins requires a ________ _______ ________ sequence?

A

c terminal ser lys leu targetting sequence, called peroxisomal targetting sequence 1 (PSI1)

123
Q

PTS1 binds to ______

A

Pex5

124
Q

Peroxisome import machinery imports ______ proteins

A

folded

125
Q

ubiquitinylation controls ____ recycling back into monomeric soluble form in cytosol

A

Pex5

126
Q

peroxisomal membrane proteins are not targetted by PTS1 sequences ( t or f)

A

true

127
Q

luminal peroxisomal proteins are synthesized on free cytosolic ribosomes and contain a ______ targetting sequence

A

c terminal

128
Q

the nucleus is separated from the cytoplasm by what two membranes?

A

nuclear envolope and continuous with er

129
Q

what are nuclear pores used for?

A

allow movement of mrnas trnas, ribosomal subunits out of the nucleus

130
Q

import of nuclear proteins requires ?

A

nuclear localization signals

131
Q

structural nucleoporins form?

A

scaffold of nuclear pore including 16 copies of the y complex

132
Q

what are the 3 nucleoporins?

A

structural nucleoporins
membrane nucleoporins
FG nucleoporins

133
Q

what is the nuclear localization signal (NLS) ?

A

directs selective transport into the nucleus

134
Q

targetting of nuclear proteins requires?

A

Ran and nuclear transport receptor

135
Q

what ensures the direction of nuclear import ?

A

localization of GEF in the nucleus and GAP in cytoplasm

136
Q

do aquaporins have conformational change?

A

no

137
Q

what are the 4 classes of atp powered pumps?

A

P Class
V class
Fclass
ABC superfamily

138
Q

describe p class

A

combined action of p class atp powered pumps generates usual ionic milieu of animal cells

139
Q

v class and f class transport what?

A

most transport H+

140
Q

abc superfamily transports?

A

transports substrates, drugs, toxins, peptides, phospholipids

141
Q

name two characteristics of P class pumps

A

two catalytic a subunits, smaller beta subunits, generate ions across membranes

142
Q

describe V and F class pumps?

A

v class - function to generate low ph of plant vacuoles and of lysosomes and other acidic vesicles in animal cells by pumping protons from the cytoplasmic to exolasmic face

f class- reverse proton pumps also called atp synthases

143
Q

describe atp superfamily pumps

A

atp binding casssete superfamily

most diverse class, multidrug resistance proteins

144
Q

what are the 4 core domains of abc superfamily ?

A

two transmembrane t domains, two cytosolic atp binding domains bind and hydrolyze atp

145
Q

muscle relaxation requires?

A

Ca2+ ATPases

146
Q

what is stored in the sarcoplasmic reticulum?

A

ca 2+ ions are concentrated and stored here

147
Q

_______ ca atpase located in the SR membrane pumps ca from the cytosol back into the lumen of the SR

A

p class

148
Q

what makes up more than 80 % of intergral membrane protein in muscle sr membranes

A

p class ca 2+ atpase

149
Q

what is the difference between the e1 and e2 states of pclass ca2+ atpase?

A

e1 - binding site facing the cytosol

e2 - have binding sites facing the exoplasmic face of the membrane

150
Q

what has a higher affinity, the e1 or e2 state?

A

e1 high affinity

e2 low affinity

151
Q

where are p class pumps phosphorylated?

A

on an Asp residue

152
Q

why are v class H+ atpases called electrogenic pumps?

A

because a net movement of electric charge occurs during transport

153
Q

what are two ABC proteins ?

A

ABCB1 multidrug export

ABCB4 flips phosphatidylcholine from cytosolic to exoplasmic leaflet

154
Q

what is ABC CFTR?

A

cl channel
has a and t domains
cl flows down concentration gradient

155
Q

resting membrane potential results from?

A

charge separation across the membrane, -70mv cytosolic face negative with respect to exoplasmic face

156
Q

nongated ion channel transports Na+ and K+ Ca 2+ and Cl - ________ concentration gradient

A

down

157
Q

the animal cell plasma membrane is generated by ?

A

ATP powered na/k pump and nongated K channels

158
Q

what two forces constitute an electrochemical gradient across a membrane?

A

electric potential and ion concentration gradient

159
Q

what is the Na/ glucose symporter?

A

GLUT transport glucose down concentration gradient, facilitated transport, cyclic mechanism

160
Q

what is symport mechanism best studied for?

A

bacterial Na/ amino aicd symport

161
Q

_____ ion bound to carboxyl group of transported leucine in the symport mechanism

A

Na+

162
Q

polarized cells are ________

A

asymetric

163
Q

what is the two stage movement of molecules through a cell?

A

import through apical membrane

export though the basolateral membrane

164
Q

what are three transport processes involved with apical and basolateral plasma membrane regions of epithelial cells transport proteins?

A

transport of amino acids and glucose from intestinal lumen to the blood

stomach acid secretion

bone resorption

165
Q

what begins on cytosolic ribosomes?

A

synthesis of secreted proteins, integral plasma membrane proteins, proteins destined for lysosomes, golgi, er or plasma membrane

166
Q

membrane bound ribosomes are recruited to the ER during synthesis of a polypeptide containing an ________

A

er signal sequence

167
Q

when cells are homogenized the plasma membrane shears the rough er into small vessicles called __________

A

microsomes

168
Q

what is cotranslational insertion?

A

cell free expierments demonstrate that translocation of secretory proteins into microsomes is coupled to translation

169
Q

what are two key componants of targetting ribosomes to the RER or SRP?

A

signal recognition particle and its receptor

Cells: Form and Function (6 decks)

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