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OLD "MBS 601" > Exam 5 > Flashcards

Exam 5 Flashcards

1
Q

What is the accepted proposed model of translation?

A

Adaptor Hypothesis (tRNA adaptors)

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2
Q

What 2 ways is the proper reading frame set?

A
  1. start codons
  2. ribosomes ensure the reading frame is maintained
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3
Q

How many possible codons are there?

A

64

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4
Q

What are the stop codons?

A

UAA
UAG
UGA

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5
Q

What is the start codon?

A

AUG

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6
Q

Multiple codons encode the _______ amino acid (synonyms)

A

same

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7
Q

_______ molecules serve as adaptors during translation

A

tRNA

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8
Q

Codon-anticodon pairing is ____________

A

anti-parallel

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9
Q

What position in the codon is NOT Watson-Crick pairing?

A

3

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10
Q

What benefit does the third wobble space in a codon have?

A

more base pairing options

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11
Q

What is responsible for stabilizing all tRNA tertiary structures?

A

nine long-range base pairs

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12
Q

_________ nucleotides are common in tRNA

A

unusual

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13
Q

What is amino acid activation (charging)?

A

attaching amino acid to tRNA

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14
Q

Does tRNA charging require ATP of GTP?

A

ATP

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15
Q

What are the 2 adaptors in translation?

A

tRNA synthetase
anticodon of tRNA

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16
Q

What does tRNA synthetase do?

A

attaches correct amino acid to each tRNA molecule

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17
Q

How is the accuracy of AA-tRNA synthetase maintained?

A

hydrolytic editing

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18
Q

How does hydrolytic editing work for AA-tRNA synthetase?

A

The incorrect amino acid is moved up to the editing site where it is proofread and removed

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19
Q

How does AA-tRNA synthetase recognize the correct tRNA?

A

unique identity elements on the anticodon region, 5’ and 3’ end

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20
Q

Translation in prokaryotes initiates with ____________ and ________

A

N-Formylmethionine
tRNA-fMET

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21
Q

How do N-Formylmethionine and tRNA-fMET initiate translation?

A

N-Formylmethionine is added to tRNA-fMET then cleaved away

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22
Q

What adds Met to tRNA(fMET)?

A

methionyl-tRNA synthetase

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23
Q

What adds Met-tRNA(fMET) to N-formyl?

A

methionyl-tRNA formyltransferase

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24
Q

What is the prokaryotic ribosome?

A

50S + 30S = 70S

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25
Q

What is the eukaryotic ribosome?

A

60S + 40S = 80S

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26
Q

Are prokaryotic ribosome made mainly of protein or rRNA?

A

rRNA

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27
Q

_____-protein facilitate ribosome function by transmitting information between different rRNA structures

A

R-proteins

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28
Q

What are the 3 binding sites of ribosomes?

A

A
P
E

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29
Q

The ____ and ____ site of a ribosome is base paired with their codons while the ____ site is not

A

A and P
E

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30
Q

What prokaryotic ribosome subunit is Peptidyl Transferase Center located?

A

50S (large)

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31
Q

Does the Peptidyl Transferase Center use proteins or rRNA to carry out its function?

A

rRNA

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32
Q

What is the job of the Peptidyl Transferase Center?

A

mediates peptide bond formation as the chain grows

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33
Q

What end of the growing peptide chain does new residues get added to?

A

C terminus

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34
Q

What is the job of the IF-1 in prokaryotes?

A

aids IF-3 in binding and blocks the A site

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35
Q

What is the job of the IF-2 in prokaryotes?

A

binds fMET-tRNA and GTP to 30S

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36
Q

What is the job of the IF-3 in prokaryotes?

A

prevents 50S binding and releases mRNA and tRNA

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37
Q

What does the 30S initiation complex consist of?

A

IF-3
IF-1
fMET-tRNA
GTP

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38
Q

What is the job of the EF-Tu in prokaryotes?

A

binds AA-tRNA and GTP to A site

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39
Q

What is the job of the EF-T in prokaryotes?

A

displaces GDP from EF-Tu

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40
Q

What is the job of the EF-G in prokaryotes?

A

promotes translocation through GTP hydrolysis

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41
Q

What prokaryotic elongation factor proofreads?

A

EF-Tu

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42
Q

What prokaryotic elongation factor does translocation from A to P site?

A

EF-G

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43
Q

How does the bottom of the A site in prokaryotes proofread?

A

checks to make sure there is no bulging in the codon-anticodon pairing

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44
Q

What does RF-1 do?

A

recognizes stop codons UAA and UAG

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45
Q

What does RF-2 do?

A

recognizes stop codons UAA and UGA

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46
Q

What does RF-3 do?

A

releases RF-1 and RF-2 via GTP hydrolysis

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47
Q

What does RFF do?

A

with EF-G induces ribosome dissociation

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48
Q

Do prokaryotic or eukaryotic mRNAs have 5’ or 3’ modifications?

A

eukaryotic

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49
Q

Do prokaryotic or eukaryotic mRNAs encode multiple different proteins?

A

prokaryotic

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50
Q

Do prokaryotic or eukaryotic mRNA contain their own independent ribosome binding sites as well and stop and start codons?

A

prokaryotic

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51
Q

Do prokaryotic or eukaryotic translation initiate independently at each gene?

A

prokaryotic

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52
Q

Do prokaryotic or eukaryotic translation usually initiate by a 40S subunit being recruited to the 5’ cap?

A

eukaryotic

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53
Q

Do prokaryotic or eukaryotic have sequences that regulate translation initiation at 5’ UTR?

A

eukaryotic

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54
Q

Do prokaryotic or eukaryotic have sequences that regulate mRNA stability at 3’ UTR?

A

eukaryotic

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55
Q

What are eukaryotic translation initiation factors called?

A

eIF

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56
Q

In eukaryotes translation initiation is tightly controlled by phosphorylation of _____

A

eIF2

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57
Q

What carries out the phosphorylation of eIF2 in eukaryotes translation initiation?

A

guanine nucleotide exchange factor (GEF)

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58
Q

What is the process of eIF2 phosphoryaltion in eukaryotes translation initiation regulation?

A

eIF2+GDP is phosphorylated to GTP which activates eIF2 allows protein synthesis

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59
Q

Multiple ribosome can translate an mRNA simultaneously in a ____________ complex

A

polysome

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60
Q

How is translation in eukaryotes in a circular configuration?

A

eIF4G at the 5’ end binds to poly-A at the 3’ end

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61
Q

What is the benefit of translation of eukaryotes in a circular configuration?

A

used to regulate the age of an mRNA

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62
Q

What is the only part of intracellular protein trafficking that is transmembrane and not vesicular?

A

cytosol to ER

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63
Q

________ is maintained during vesicular transport

A

topology

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64
Q

Does the ER have more membrane or more empty space?

A

more membrane

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65
Q

How many membranes does the ER have?

A

one

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66
Q

What is the purpose of the smooth ER?

A

lipid synthesis

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67
Q

What is the purpose of the rough ER?

A

entry point for proteins into the secretory pathway

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68
Q

What are translational elements?

A

(apart of the rough and smooth ER) sites where transport vesicles bud off to cary newly synthesized proteins and lipids to the golgi

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69
Q

Disrupted ER membranes form ________

A

microsomes

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70
Q

What are microsomes?

A

When ER membrane is disrupted and forms a circular vesicle with its membrane

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71
Q

Where is the SER and RER located in the sucrose concentration when separating them?

A

rough ER: high density sucrose
smooth ER: low density sucrose

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72
Q

What are the 2 types of ribosomes?

A

free (protein not translated into ER)
membrane bound

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73
Q

When separating free and membrane bound ribosomes, where are they each located in the sucrose concentration?

A

free: low density sucrose
bound: high density sucrose

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74
Q

What mRNAs are attached to membrane bound ribosomes?

A

secreted proteins going to ER

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75
Q

What mRNAs are attached to free ribosomes?

A

cytosolic proteins (not going to ER)

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76
Q

What are the 4 secretory signals that target protein to the ER?

A
  1. positive amino terminal
  2. alpha helix core
  3. turn inducing residues (helix breaking)
  4. specific cleavage site
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77
Q

Basic residues at the N terminus of signal anchors the signal to the cis (outside) face of membrane preventing ____________ causing a insertion loop

A

headfirst insertion

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78
Q

What is the evidence for proteinaceous channels for protein insertion instead of a lipid lined pore?

A

If there is a protein channel and you prematurely remove the protein you would be able to see ions flowing through

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79
Q

What is the Original Signal Hypothesis?

A

protein is fed into the ER with N terminus still on the outside forming a hairpin inside the ER and once all is inside signal peptidase cleaves the peptide

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80
Q

What are the 2 stages of ER translocation?

A
  1. targeting of polypeptide to ER surface
  2. translocation into the ER membrane (requires ATP)
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81
Q

What does SRP do in ER translocation?

A

recognizes the signal peptide coming out of the ribosome (tip of polypeptide) and brings to the SRP receptor on ER surface

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82
Q

What targets the signal peptide to the ER surface?

A

SRP

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83
Q

Once about 20 amino acids on the chain emerge from the ribosome bound to SRP what happens before SRP docking?

A

translational arrest

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84
Q

When is the translational arrest reversed in ER translocation?

A

When the SRP docks on the STP receptor on the ER membrane

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85
Q

ER translocation in vitro requires _________ since most proteins are inserted co-translationally

A

microsomes

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86
Q

What would happen to the protein if SRP is present but no SRP receptor?

A

It wont be made because the SRP doesn’t think its made it to the ER since the receptor isn’t present

87
Q

What are the 3 subunits of SRP?

A

p19/54
p68/72
p9/14

88
Q

What does the p19/54 subunit of SRP do?

A

binds to signal sequence

89
Q

What does the p9/14 subunit of SRP do?

A

binds to the A site of the ribosome and arrest translation

90
Q

What does the p68/72 subunit of SRP do?

A

helps initiate insertion of the signal sequence into the ER membrane by binding to SRP receptor

91
Q

SRP increases in binding affinity when the ____________ is present

A

signal sequence

92
Q

What subunit of SRP is a GTP binding domain (GTP hydrolysis)?

A

p54

93
Q

_______ receptor is much less abundant that ribosomes on the RER surface suggesting its not involved in the earlier stages

A

SRP receptor

94
Q

Is co-translational or post-translational ER translocation more common?

A

co-translation

95
Q

What does Sec61p do as an ER translocase?

A

helps anchor the ribosome to the ER membrane (interacts directly with translocating polypeptide)

96
Q

Crosslinking of Sec61p to translocating polypeptides requires _______

A

ATP

97
Q

What does Bip do as an ER translocase?

A

binds to misfolded protein and refolds them and crosslinks and pulls polypeptide through

98
Q

Are Sec62p and Sec63p required from ER translocation?

A

No

99
Q

_________ and _______ are sufficient alone for protein translocation into the ER

A

Sec61p and SRP receptor

100
Q

What does the signal peptidase do in ER translocation?

A

cleaves the signal sequence

101
Q

What does Oligosaccharyltransferase do in ER translocation?

A

glycosylation

102
Q

Is signal peptidase or oligosaccharyltransferase required for ER translocation?

A

No

103
Q

What 3 factors influence the protein topology during ER translocation?

A
  1. proteolytic processing
  2. location of signal
  3. charge around the signal
104
Q

What is Type I topology of integral membrane proteins?

A

N terminus on trans side (lumen)

105
Q

What is Type II topology of integral membrane proteins?

A

N terminus on cis side (cytosol)

106
Q

What is Type III topology of integral membrane proteins?

A

two or more membrane spanning segments

107
Q

Is the cis side located on the lumen or cytosol?

A

cytosol

108
Q

Is the trans side located on the lumen or cytosol?

A

lumen

109
Q

What 2 ways are different topological orientation obtained?

A

targeting signals on polypeptide
start and stop transfer sequences (polytopic)

110
Q

Orientation of proteins across the membrane is mediated by hydrophobic stretches of amino acids called _______________

A

start and stop transfer sequences

111
Q

Start and stop transfer sequences are _________ independent (they start with it then don’t need it again)

A

SRP-independent

112
Q

Start and stop transfer sequences have clearly defined _________ sections that stay inside the membrane

A

hydrophobic

113
Q

Normally, start transfer sequences have _______ residues before them that determine the orientation of the signal insertion (N towards cytoplasm)

A

basic

114
Q

In some cases, the direction of insertion of the start sequence can be reversed (N towards lumen) if the start transfer signal is followed by _______ residues

A

basic

115
Q

When integrating proteins in the ER membrane where does the negative charges typically point?

A

lumen

116
Q

When integrating proteins in the ER membrane where does the positive (basic) charges typically point?

A

cytosol

117
Q

Proteins that are not properly folded or modified in the ER are subject to __________

A

ERAD

118
Q

What happens during ERAD?

A

protein is transported retrograde from ER to cytoplasm to be degraded

119
Q

The ER lumen contains a lot of Bip why?

A

it binds to hydrophobic regions to make sure proteins are folding correctly

120
Q

___________ prevents disulfide bond formation in the cytosol and catalyzes them in the ER

A

Glutathione

121
Q

Are disulfide bonds preferred in the cytosol or ER?

A

ER

122
Q

In the cytosol what is the GSH:GSSG ratio?

A

50:1 DOES NOT promote disulfide bonds

123
Q

In the ER what is the GSH:GSSH ratio?

A

5:1 optimal for disulfide bonds

124
Q

What is Protein Disulfide Isomerase (PDI)?

A

make sure improper disulfide bonds are not created and creates correct bonding

125
Q

What is an example of an soluble protein ER retention signal?

A

KDEL

126
Q

What is an example of an transmembrane protein ER retention signal?

A

KKXX

127
Q

What is the Unfolded Protein Response (UPR)?

A

Decreases translation of the misfolded protein and increases gene expression of genes that help fix the unfolded proteins

128
Q

What are the 2 ER quality control mechanisms?

A

ERAD
UPR

129
Q

What are the 3 main players in the UPR in yeast?

A

Ire1p
HAC1 mRNA
Rlg1p tRNA ligase

130
Q

During the UPR in yeast, ER stress induced ____ to oligomerize and autophosphorylate which activates it

A

Ire1

131
Q

During the UPR in yeast once Ire1p is autophosphorylated and activated, _________ is made

A

Hac1

132
Q

What player in the UPR in yeast enters the nucleus and activates transcription of genes needed?

A

Hac1p

133
Q

What are the 3 main players in the UPR in mammals?

A

Ire1p
ATF6
PERK

134
Q

In the UPR in mammals _______ splices XBP1 then XBP1 can enter nucleus and activate transcription

A

Ire1p

135
Q

In the UPR in mammals, _______ is cleaved directly from cytoplasmic domain of ER and contains transcription factors

A

ATF6

136
Q

In the UPR in mammals, translational repression is mediated by ____________

A

PERK

137
Q

In the UPR in mammals, _______ is analogous to HAC1 in yeast

A

XBP1

138
Q

When _____ is bound to IRE1, PERK, and ATF6 in the mammalian UPR the response is off

A

Bip

139
Q

During the UPR, _____ usually cannot enter the nucleus because its bound to the ER membrane but when UPR is activated it can enter

A

ATF6

140
Q

During regulation of translation in the UPR, ______ phosphorylation inhibits bulk translation

A

elF2-alpha

141
Q

What is the molecular issue with cystic fibrosis?

A

single amino acid is mutated and the ER wont let the protein leave the ER

142
Q

What 3 places are ribosomes found?

A

ER
cytosol
mitochondria

143
Q

The ________ and ________ pathways are connected

A

secretory and endocytic

144
Q

Vesicle bud from _______ compartment and fuse with ______ compartment

A

donor
target

145
Q

_________ is the space within membrane enclosed compartments

A

lumen

146
Q

How does COP II coat proteins transport?

A

anterograde (ER to cis Golgi)

147
Q

How does COP I coat proteins transport?

A

retrograde (Golgi to ER)

148
Q

How does clatherin coat proteins transport?

A

between endosomes and golgi from plasma membrane

149
Q

What energy is required for coat proteins?

A

GTP

150
Q

What do inner adaptor proteins bind?

A

transmembrane cargo receptors (with exit signals)
outer coat proteins

151
Q

Inner coat proteins form __________ and outer coat proteins help with ________-

A

vesicles
budding

152
Q

What are the two GTP binding protein involved in phosphorylation of coat proteins?

A

GEF and GAP

153
Q

In coat protein phosphorylation, GEFs activate or inactivate?

A

activate (protein kinase)

154
Q

In coat protein phosphorylation, GAPs activate or inactivate?

A

inactivate (phosphatase)

155
Q

What is the GTP cascade of GEFs?

A

release of GDP and binding of GTP

156
Q

What is the GTP cascade of GAPs?

A

GTP hydrolysis to GDP

157
Q

Proteins leave the ER in _______ coated vesicles

A

COP II

158
Q

Inner coat adaptor proteins help recruit _____ coat proteins to help bud vesicles

A

outer

159
Q

Membrane _______ event pinches off vesicle

A

fusion

160
Q

What provides quick movement for vesicles between ER and Golgi?

A

microtubule networks

161
Q

COP___ coat dissembles as vesicles transport anterogradely to golgi

A

COP II

162
Q

COP ___ coat assembles as vesicles transport retrogradely to ER

A

COP I

163
Q

High affinity for KDEL sequence is present in ___________ and __________

A

vesicular tubular clusters
Golgi

164
Q

Low affinity for KDEL sequence is present in ________

A

ER

165
Q

Why is the KDEL affinity low in the ER?

A

because ER proteins aren’t suppose to leave the ER anyways so having a lower KDEL affinity means its less likely to leave the ER

166
Q

Why is the KDEL affinity high in the vesicles and golgi?

A

these proteins are meant to be secreted and higher affinity means transport

167
Q

High affinity of KDEL corresponds with COP ___ because…

A

COP I
retrograde transport

168
Q

Rab proteins are important for ______ vesicles to target membrane

A

tethers

169
Q

SNARE proteins are important for _____ vesicles to target membrane and ______- of opposing lipid bilayers

A

dock
fusion

170
Q

What are the 2 types of SNARES?

A

v and t

171
Q

______ ensure organelle specific targeting or vesicles not _____

A

Rabs
SNARES

172
Q

______ cascade is important for vesicle maturation

A

Rab

173
Q

The Rab cascade for vesicle maturation is regulated by ___ and ____

A

GEFs and GAPs

174
Q

What are the 3 steps of vesicles fusion using SNAREs?

A
  1. ATPase disassembles paired v and t SNAREs
  2. v and t SNARES from adjacent vesicles interact
  3. membranes fuse
175
Q

What part is the entry to the Golgi closest to the ER?

A

cis

176
Q

What part of golgi takes vesciles from the ER?

A

cis

177
Q

What is the stackable membrane enclosed compartments in Golgi?

A

cisterna

178
Q

What is the exit point for proteins in the Golgi?

A

trans

179
Q

What starts N-linked glycosylation in ER?

A

GlcNac

180
Q

What is the purpose of ER glycosylation?

A

proper protein folding
removal of misfolded proteins

181
Q

What starts O linked glycosylation in Golgi?

A

GalNac

182
Q

What are the steps of Oligosaccharide processing?

A
  1. ER: removal of glucose and mannose
  2. Golgi: removal of 3 mannose
  3. Golgi: addition of GlcNac
  4. Golgi: removal of 2 mannose
  5. Golgi: addition of sugars
183
Q

What is cause of Congenital Disorders of Glycosylation (CDG)?

A

deficiencies in genes related to N-linked glycosylation

184
Q

T/F? ST6Gal1 is upregulated in certain cancers

A

true

185
Q

What is Triskelion?

A

shape of one clatherin that comes together to form pits

186
Q

_______ protein bind to membrane bound proteins and the triskelion in clatherin coated vesicles

A

adaptor

187
Q

Coat assembly of clatherin induces membrane _________

A

curvature

188
Q

__________ proteins are recruited to neck of budding clatherin vesicles

A

fission

189
Q

What energy is required for clatherin coating?

A

GTP

190
Q

Are all coat protein GTP binding mediated?

A

yes

191
Q

During protein sorting in the trans golgi networks, __________ tags proteins for delivery to lysosomes

A

M6P

192
Q

What is the difference between regulated and constitutive secretory pathway?

A

regulated: proteins guided to secretory vesicles in specialized cells
constitutive: common proteins delivered to plasma membrane

193
Q

Where is P-GlcNAc added to proteins?

A

cis golgi

194
Q

Where is GlcNAc removed exposing M6P?

A

trans golgi

195
Q

What cleaves GlcNAc exposing M6P on lysosomal hydrolase?

A

alpha-N-acetylglucosamidinase

196
Q

What is the most basic in the secretory pathway?

A

ER

197
Q

What maintains the low pH in lysosomes?

A

ATPase H+ pump

198
Q

What is Neuronal Ceroid Lipofuscinoses (NCL)?

A

mutations in proteins that compromise lysosome function

199
Q

What is the most common movement disorder related to lysosome disfunction?

A

Parkinsons

200
Q

Is the constitutive or regulated secretory pathway happening all the time?

A

constitutive

201
Q

What are the steps of exocytosis of synaptic vesicles?

A
  1. vesicles dock to plasma membrane
  2. t-SNARE assembles
  3. SNARE bundle assembles blocking complexin protein
  4. action potential triggers Ca2+ entry
  5. Fusion block released, fusion pore opens
202
Q

Is endocytosis clatherin dependent?

A

yes

203
Q

What are the 3 possible fates of endocytosed cargo?

A
  1. recycled
  2. transcytosis
  3. degradation
204
Q

Endocytosis of clathrin coated vesicles form clathrin coated ________

A

pits

205
Q

What are MVB? (multivesicular bodies)

A

endosomes with multiple vesicles in them

206
Q

Diabetes affects the ________ of glucose

A

endocytosis

207
Q

Is macropinocytosis clathrin dependent or independent?

A

independent

208
Q

What is macropinocytosis?

A

When cell membrane protrudes and swallows up things outside of cell

209
Q

What is caveolae?

A

pits formed in cell membrane and are swallowed by cell and pinched off

210
Q

Is caveolae clatherin dependent or independent?

A

independent

211
Q

_________ coated vesicles are responsible for delivering cargo from the TGB to endosomes; from endosomes to TGN; and from the plasma membrane to endosomes

A

clathrin

212
Q

The _______ pathway is critical for delivery of hydrolases to lysosomes

A

M6P

213
Q

o

A

MVB (multivesicular bodies)

OLD "MBS 601" (8 decks)

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