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Cell & Molecular Biology > Chapter 7 > Flashcards

Chapter 7 Flashcards

1
Q

Why do cells depend on signals on proteins?

A

to ensure they arrive at their proper subcellular destination

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2
Q

Proteins with NO targeting signal will be translated entirely on and remain in?

A

free ribosomes and remain in cytosol

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3
Q

Which organelles receive proteins from the cytosol after their translation is complete?

A

mitochondria, nucleus, chloroplasts, and peroxisomes

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4
Q

What are translated by ribosomes attached to the ER and are translocated at the same time?

A

ER, Golgi, lysosomes, plasma membrane, and secreted proteins

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5
Q

ER, Golgi, lysosomes, and plasma membranes, and secreted proteins arrive at the other locations via

A

vesicle budding and fusing

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6
Q

Secretory pathway

A

transport of proteins through nucleus, ER, Golgi, and to the membrane

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7
Q

Lumen of organelles of the secretory pathway are topologically equivalent to

A

each other and to the exterior of the cell

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8
Q

Proteins targeting selectively recognizes

A

nascent proteins with signal sequences

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9
Q

The signal sequence binds to

A

signal recognition particle

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10
Q

Binding of signal sequence to the signal recognition particle causes

A

translation to temporarily halt

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11
Q

Which 3 arrive at the ER

A

ribosome, nascent polypeptide, SRP

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12
Q

What happens when the ribosome, nascent polypeptide, SRP interact with a receptor at the ER?

A

a channel (part of the translocon) opens and the nascent proteins begins to be co-translationally translocated

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13
Q

When was the signal hypothesis proposed?

A

1970

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14
Q

Why was the signal hypothesis proposed?

A

to explain how proteins got targeted to the RER

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15
Q

When is the ER targeting signal cut off?

A

after the protein begins its translcoation

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16
Q

Pre-protein

A

nascent protein prior to its signal sequence removal

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17
Q

Normally ER bound protein synthesized in an in vitro cell-free system for gel

A

larger, migrates more slowly

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18
Q

When translated in vitro in the presence of purified ER (microsomes) for gel

A

protein smaller, migrates faster, located in ER lumen (microsome lumen)

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19
Q

What particle is SRP?

A

ribonucleoprotein

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20
Q

SRP made up of

A

6 polypeptides and small (7S) RNA molecule

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21
Q

What of SRP has what activity?

A

GTPase activity

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22
Q

The part of SRP that binds to the nascent polypetide’s signal sequence has a

A

large number of Met residues (hydrophobic)

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23
Q

function of part of SRP that binds to the ribosome

A

slows translation until docking at the ER

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24
Q

Part of SRP bins to what? (2)

A

a. nascent polypeptide’s signal sequence
b. ribosome

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25
Q

SRP receptor structure

A

Dimer of two subunits: SRalpha and SRbeta

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26
Q

Where are SRalpha and SRbeta?

A

SRalpha - on cystol face
SRbeta - transmembrane

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27
Q

SRalpha and SRbeta are what proteins?

A

GTP-binding porteins (GTPases)

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28
Q

Coordinated GTP binding and hydrolysis by SRP and SR are required for

A

a. proper targeting of nascent chains to the ER
b. for their transfer to the translocation channel
c. for the recycling of SRP to the cytosol

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29
Q

What happens when SRP releases the ribosome?

A

Ribosome engages the translocon and the nascent polypeptide begins translocation

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30
Q

Transport of the polypeptide into the ER lumen through

A

an aqueous channel

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31
Q

Translocon comprised of

A

channel and other proteins closely associated with it

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32
Q

Ions cannot cross the membrane while

A

polypeptide is being translocated through a channel

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33
Q

After polypeptide is released and the ribosome is still attached, ions

A

permeate through the channel

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34
Q

Sec61 function

A

forms the channel through which the translocating protein passes

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35
Q

Sec61 structure

A

heterotrimeric complex, shaped like an hourglass in cross-section

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36
Q

What commits the chain to translocation?

A

Recognition and insertion of the signal sequence

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37
Q

What is displaced as translocation begins?

A

channel plug

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38
Q

During translocation, some proteins are able to

A

transiently slip out of the gap between ribosome and translocon, positioning a loop of the protein in the cytosol

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39
Q

Some organisms (especially unicellular eukaryotes) are able to translate and translocate proteins in where?

A

translation in cytosol, keep them unfolded, and translocate them into ER

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40
Q

Protein is no longer associated with ribosome when

A

it is translocated

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41
Q

Chaperonins of the hsp70 family associate with

A

nascent polypeptides

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42
Q

Chaperonin of the hsp70 family function

A

prevent holding

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43
Q

What is most important for recognition by the channel?

A

hydrophobicity of the signal sequence

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44
Q

What is the main energy source driving posttranslational translocation and co-translational translocation?

A

ATP hydrolysis by the ER-lumenal hsp70 BiP protein

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45
Q

What does the active pulling model propose?

A

ATP hydrolysis causes a conformational change in BiP which causes the polypeptide to be actively pulled (or pushed with SecAp for prokaryotes) through the channel

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46
Q

Steps of polypeptide translocation using BiP

A
  1. BiP interacts with Sec63 and binds the polypeptide
  2. polypeptide can diffuse inwards (ER lumen), but BiP prevents backward diffusion
  3. when enough polypeptide is exposed, a second BiP binds
  4. diffusion occurs again
  5. process repeats, advancing the polypeptide incrementally
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47
Q

What side is the N-terminus on?

A

on the cytosol face or on the non cytosol face

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48
Q

What side is the C-terminus on?

A

on the opposite face from the N-terminus or may be on the same face

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49
Q

Steps of protein translocation (N-terminus)

A
  1. protein translocation begins with signal sequence at the N-terminus
  2. channel recognizes transmembrane domain
  3. transmembrane domain enters the lipid bilayer through side of the channel
  4. translation continues until termination
  5. integrated polypeptide
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50
Q

Signal anchor proteins target by using an

A

internal transmembrane domain (signal anchor)

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51
Q

Simplest situation of transmembrane orientation

A

proteins spans the membrane 1x, the N-terminus faces ER lumen, and C-terminus faces the cytosol

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52
Q

Two possible orientation?

A

N-terminus region translocated into the ER-lumen or the C-terminus translocated into the ER-lumen

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53
Q

Polytopic proteins

A

span the membrane multiples times; may have transmembrane regions integrate one-at-a-time or they may integrate in pairs

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54
Q

If the ER-signal peptide is ________, it is almost always..?

A

N-terminal; cleaved after it has served its purpose

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55
Q

Signal peptidase complex structure

A

5 subunits: 2 of which have proteolytic activity

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56
Q

Exact cleavage site is?

A

variable

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57
Q

Exact cleavage site is influenced by the

A

amino acid residues in the immediate vicinity of the cleavage sites

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58
Q

Following its removal, signal peptide is often processed by

A

signal peptide peptidase

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59
Q

GPI anchoring

A

lipid GPI added to some translocated proteins

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60
Q

GPI anchoring to proteins renders them attached to the membrane as

A

IMPs

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61
Q

IMPs

A

integral membrane proteins, non-removable from the membrane by salt extraction procedure

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62
Q

GPI anchoring always tethers a protein to the

A

non-c-face of a membrane (ER-lumenal face first)

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63
Q

GPI

A

glycosylphophatidylinositol

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64
Q

Where does GPI begin at and move to?

A

begins on the c-face of the ER membrane, then a flippase (translocase) moves it across to the lumenal side

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65
Q

What happens to GPI at the lumenal side

A

more sugars are added along with 3 phosphoethanolamines

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66
Q

Signal for GPI-anchoring

A

small C-terminal hydrophobic domain of variable length

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67
Q

What recognizes the signal for GPI anchoring?

A

integral membrane complex

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68
Q

Integral membrane complex function

A

cuts the signal off from the protein and transiently attached to new C-terminus (omega site) and attaches omega site to the terminal phosphoethanolamine residue of GPI and the enxyme complex liberates itself

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69
Q

3 reasons why GPI-anchoring occurs

A
  1. way of targeting proteins in polarized cells, lipid rafts…
  2. give an IMP more lateral mobility compared to transmembrane IMPs
  3. way to free a protein from membrane association by enzymatic cleavage of its attachment, thus passing along a message into the interior of a cell
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70
Q

More than half of secretory and membrane proteins in a cell are

A

glycosylated

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71
Q

Glycosylation in the ER is termed ____. Why?

A

N-linked because sugars are attached to asparagine residues

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72
Q

OST

A

oligosaccharyltransferase

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73
Q

Function of OST

A

transfers an oligosaccharide en bloc onto the translocating protein

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74
Q

Oligosaccharide presynthesized beginning in the

A

cytosol

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75
Q

Oligosaccharide presynthesized with the minor membrane ____.

A

phospholipid dolichol-phosphate

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76
Q

Sugars are added to ____.

A

dolichol-P

77
Q

dolichol-P moved to where and by what?

A

flippase moves it to the lumen-face of the membrane

78
Q

After oligosaccharide is added, what happens and where?

A

removal of some sugar residues and addition of others within the ER and Golgi

79
Q

Most abundant protein in the ER lumen

A

BiP (binding protein)

80
Q

BiP

A

Chaperonin

81
Q

BiP most abundant in

A

ER lumen

82
Q

BiP is a member of the

A

hsp70 family

83
Q

BiP binds to

A

exposed hydrophobic patches (buried within a globular protein, interacting with each other to drive protein folding)

84
Q

Why does BiP bind to exposed hydrophobic patches?

A

To help them get folded properly

85
Q

ER-lumenal chaperonins no longer associate when?

A

once the protein has achieved its proper folding?

86
Q

Cytosol has a __________ environment

A

reducing

87
Q

In the reducing environment of a cytosol, what is not formed?

A

disulfide bonds

88
Q

ER lumen and ECM have _________ environment

A

oxidizing

89
Q

In the oxidizing environment of the ER lumen and ECM, what is formed?

A

disulfide bonds

90
Q

The formation of the disulfide bonds in the oxidizing environment is catalyzed by

A

protein disulfide isomerases

91
Q

Where in the cell has oxidizing environment and reducing environment?

A

Reducing environment - cytosol
Oxidizing environment - ER lumen and ECM

92
Q

PDI

A

protein disulfide isomerase

93
Q

PDI catalyzes

A

disulfide bond rearrangement and formation

94
Q

PDI reduced when it

A

oxidizes the cysteines in a translocating protein

95
Q

Reduction of PDI helps

A

folding

96
Q

What oxidizes PDI by being itself reduced?

A

ER protein EroP1

97
Q

PDI is oxidized by

A

an ER protein EroP1

98
Q

EroP1 oxidized by

A

FAD

99
Q

What is calnexin and where is it?

A

IMP in the ER memebrane

100
Q

What is calreticulum and where is it?

A

protein in the ER lumen

101
Q

Calnexin and calreticulin binds to

A

sugar residues

102
Q

Binding of calnexin and calreticulin to the sugar residues indicate that they are

A

lectins

103
Q

The purpose of calnexin or calreticulin activity is in

A

protein quality control (QC)

104
Q

The calnexin or calreticulin activity is to

A

make certain that proteins are properly folded before they are allowed to leave the ER

105
Q

What is the ticket to enter the calnexin cycle?

A

To have been N-glycosylated

106
Q

After entering the calnexin cycle, the 2 distal glucose residues are removed by

A

glucosidase I and II

107
Q

Association of calnexin helps the

A

protein contact ERp57

108
Q

ERp57

A

a chaperonin and PDI family member

109
Q

ERp57 function

A

catalyzes the disulfide bond formation and rearrangement and allows folding/refolding

110
Q

What protein lets go of calnexin

A

unglycosylated protein

111
Q

If the protein is not folded properly, a glucose is re-added by

A

UDP-glucose-glycoprotein glucosyl transferase (UGGT)

112
Q

How does UGGT know that a protein is not folded properly?

A

it would be exposed clusters of hydrophobic residues

113
Q

Proteins in the secretory pathway are retained in

A

ER by chaperone-association until the assembly of its subunits are completed

114
Q

3 Retention mechanisms

A

a. associating a subunit with BiP
b. exposed cysteine binding to a PDI
c. exposed ER retention signal that will be masked later

115
Q

BCRs or secreted Ig depend upon the

A

association of 4 polypeptides, 2 H chains (transmembrane) and 2 L chains (free in ER-lumen)

116
Q

Retrograde translocation is used to

A

export misfolded proteins back into cytosol

117
Q

What happens to the misfolded proteins in the cytosol?

A

multi-ubiquitinated and degraded by a proteasome

118
Q

Ubiquitin

A

ubiquitous small protein used as a tag for protein degradation

119
Q

Proteasome

A

cytoplasmic recycling barrel, a large protease complex

120
Q

Degradative pathway (ubiquitinated protein degraded by proteasome) is known as

A

ER-associated degradation (ERAD)

121
Q

ER-associated degradation (ERAD)

A

Misfolded proteins that cannot get refolded properly moves into the cytosol, and they are tagged with ubiquitin, marking them for degradation by proteasome

122
Q

One of the retrograde translocation channels

A

Sec61

123
Q

Unfolded protein response (UPR)

A

signaling pathway from the ER lumen to the nucleus

124
Q

UPR function

A

a. allows the cell to monitor folding conditions
b. increase the expression of ER chaperonins when necessary

125
Q

Protein that senses folding conditions in the ER and transmits the info

A

ER-membrane protein Ire1p

126
Q

Ire1p has the ability to

A

dimerize by self-association of its lumenal domain

127
Q

Under normal conditions, _______ bound to the lumenal domain of _______ resulting in?

A

BiP; Ire1p; inhibition of dimerization

128
Q

Under stress, BiP is

A

too busy with misfolded proteins, so it leaves Ire1p to dimerize and send a signal

129
Q

Cytosolic domain of Ire1p contains

A

a serine-threonine kinase

130
Q

Serine-threonine kinase

A

it phosphorylates proteins on serine and threonine residues

131
Q

When Ire1p dimerizes, it does what two things?

A

autophosphorylates and activates a second cytosolic domain

132
Q

Dimerization of Ire1p catalyzes what?

A

the removal of an intron from the mRNA of a specific gene, HAC1

133
Q

After Ire1p has removed HAC1, tRNA ligase does what and resulting in?

A

tRNA ligase joins the axon, allowing Hac1p (mRNA) to be translated

134
Q

What happens if HAC1 (intron) is left in?

A

causes ribosomes to stall on the mRNA, causing no Hac1p to be translated

135
Q

What is Hac1p?

A

transcription factor

136
Q

What does Hac1p bind to?

A

a regulatory sequence called the unfolded protein response element (UPRE)

137
Q

What does binding of Hac1p to UPRE stimulate?

A

transcription of several chaperonin genes
ex) BiP

138
Q

Making the additional chaperonins help

A

QC with unfolded proteins during stressful conditions

139
Q

Unfolded protein response (UPR) influences

A

transcription of a much broader collection of genes beyond those for chaperonins

140
Q

What process is altered as a consequence of the cell’s UPR?

A

increased lipid synthesis for ER expansion

141
Q

Primary site of sythesis of the cell’s phospholipids

A

ER

142
Q

Where is the cell’s phospholipid made in?

A

cytosolic leaflet of the ER membrane

143
Q

Kennedy pathway

A

two fatty acyl CoAs are attached to glycerol 3-P to form diacylglycerol (DAG), which is hydrophobic enough to insert into the c-face of the ER membrane

144
Q

From the membrane-associated DAG, what group can be added to form a complete phospholipid?

A

polar head groups

145
Q

How is the polar group added? (STEPS)

A
  1. head group phosphorylated
  2. attached to CDP
  3. Head group + a P is transferred to DAG
  4. Releases CMP
146
Q

What is the most abundant membrane phospholipid?

A

Phosphatidylcholine

147
Q

What 4 membrane phospholipid is made by Kennedy pathway?

A

Phosphatidylcholine (PC), phosphatidylserine (PS), phosphatidylethanolamine (PL), phosphatidylinositol (PI)

148
Q

The 4 membrane phospholipid (PS,PE, PC, PL) is made by the Kennedy pathway in the ?

A

cytosol-face of the ER

149
Q

Where can PE be made other than ER?

A

MItochondria by modifying PS

150
Q

A specialized ER region that is responsible for transport of PS from ER

A

mitochondrial-associated membrane

151
Q

What is mitochondrial-associated membrane (MAM)?

A

specialized ER that is very close to a mitochondria, making very close contact with its membrane

152
Q

What synthesis also occur in the ER?

A

Sterol (most cholesterol)

153
Q

Following their synthesis in the ER, some phospholipids must be transferred to where?

A

all the other membranes in the cell and NOT randomly

154
Q

Transferring phospholipid to other membranes may occur in which regions?

A

where ER makes direct contact with other organelles of the cell

155
Q

Phospholipid transfer proteins thout to move lipids from one bilayer to another but they cannot?

A

account for membrane growing because after they bring a lipid to membrane, they leave with a different one

156
Q

Flippases neceessary to?

A

flip half of the newly-synthesized lipids from ER c-face to the non-c-face

157
Q

Flipping of the lipid occurs randomly, but?

A

other phospholipid translocators must be more selective because memrbanes in cells are varied in their lipid composition from each other and within any membrane the two faces are varied

158
Q

Where are PC, PS, PE, and PI enriched?

A

PC in non-c-face of the plasma membrane
PS and PE in the c-face
PI in c-face (EXCEPT GPI-anchored proteins)

159
Q

ER form morphologically and in other regions

A

Morphologically, ER forms large, flat sheets (cisternae)
In other regions, it is in form of long, curving tubules

160
Q

The flat sheets are generally found next to the

A

nuclear envelope

161
Q

Tubules extend as a

A

network throughout the cell, contracting other organelles and the plasma membrane

162
Q

RER is abundant in cells which secrete ?

A

proteins like Ig (plasma B cell), hormones,,

163
Q

SER responsible for

A

lipid metabolism steroid synthesis, glycogen metabolism, and drug detoxification

164
Q

SER is abundant in cells which secrete

A

steroid hormones (testes’ leydig cells, ovary follicular cells) or liver hepatocytes

165
Q

SER amount goes up with an?

A

increase in drug use

166
Q

SR in skeletal muscle cells, cntain

A

calsequestrin

167
Q

What is calsequestrin?

A

protein that has several Ca2+ binding sites

168
Q

SR stores

A

intracellular Ca2+

169
Q

SR in other cell types enables?

A

rapid Ca2+ regulation

170
Q

What is calreticulin?

A

glycoprotein chaperone and a Ca2+ binding protein

171
Q

When does BIP, calnexin, and calreticulin functio less efficiently?

A

when ER Ca2+ stores are depleted

172
Q

Prolonged calcium depletion can induce?

A

UPR

173
Q

Ca2+ release from the ER is implicated in?

A

triggering apoptosis

174
Q

Tubular elements of the ER are in

A

continual flux, aligned to the cytoskeleton

175
Q

Cytoskeleton is not required for the

A

formation of tubules or networks in vitro

176
Q

Role of cytoskeleton ensures that

A

after the ER network forms, it is properly distributed throughout the cell

177
Q

In response to increase in what drug expands SER?

A

phenobarbital

178
Q

Removal of phenobarbital causes

A

rapid return of the SER to its normal size

179
Q

The plasma B cells proliferate their RER in order to

A

meet the need for the cell to secrete large amounts of Ig proteins

180
Q

Nucleus uses

A

internal signal patches

181
Q

Internal signal patches are comprised of

A

non-contiguous aa residues that are brought together by tertiary and quaternary structure

182
Q

What is not removed after import into the nucleus through the nuclear pore complexes?

A

nuclear localization signals (NLSs)

183
Q

Why are NLSs not removed after import into the nucleus through the NPCs?

A

because many of the proteins might need their signal if they are outside after telophase and it is difficult to remove internal signals

184
Q

Nucleus is able to import proteins in what form dues to what?

A

folded form due to size of the NPCs

185
Q

Mitochondria and chloroplasts must import proteins in what form?

A

unfolded form

186
Q

Peroxisome import proteins in what form?

A

folded form

187
Q

Organelle targeting signals are

A

N-terminal or C-terminal

188
Q

When are organelle targeting signals removed?

A

post-translocation

Cell & Molecular Biology (3 decks)

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