Exam 5 Flashcards
(213 cards)
1
Q
What is the accepted proposed model of translation?
A
Adaptor Hypothesis (tRNA adaptors)
2
Q
What 2 ways is the proper reading frame set?
A
- start codons
- ribosomes ensure the reading frame is maintained
3
Q
How many possible codons are there?
A
64
4
Q
What are the stop codons?
A
UAA
UAG
UGA
5
Q
What is the start codon?
A
AUG
6
Q
Multiple codons encode the _______ amino acid (synonyms)
A
same
7
Q
_______ molecules serve as adaptors during translation
A
tRNA
8
Q
Codon-anticodon pairing is ____________
A
anti-parallel
9
Q
What position in the codon is NOT Watson-Crick pairing?
A
3
10
Q
What benefit does the third wobble space in a codon have?
A
more base pairing options
11
Q
What is responsible for stabilizing all tRNA tertiary structures?
A
nine long-range base pairs
12
Q
_________ nucleotides are common in tRNA
A
unusual
13
Q
What is amino acid activation (charging)?
A
attaching amino acid to tRNA
14
Q
Does tRNA charging require ATP of GTP?
A
ATP
15
Q
What are the 2 adaptors in translation?
A
tRNA synthetase
anticodon of tRNA
16
Q
What does tRNA synthetase do?
A
attaches correct amino acid to each tRNA molecule
17
Q
How is the accuracy of AA-tRNA synthetase maintained?
A
hydrolytic editing
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
19
Q
How does AA-tRNA synthetase recognize the correct tRNA?
A
unique identity elements on the anticodon region, 5’ and 3’ end
20
Q
Translation in prokaryotes initiates with ____________ and ________
A
N-Formylmethionine
tRNA-fMET
21
Q
How do N-Formylmethionine and tRNA-fMET initiate translation?
A
N-Formylmethionine is added to tRNA-fMET then cleaved away
22
Q
What adds Met to tRNA(fMET)?
A
methionyl-tRNA synthetase
23
Q
What adds Met-tRNA(fMET) to N-formyl?
A
methionyl-tRNA formyltransferase
24
Q
What is the prokaryotic ribosome?
A
50S + 30S = 70S
25
What is the eukaryotic ribosome?
60S + 40S = 80S
26
Are prokaryotic ribosome made mainly of protein or rRNA?
rRNA
27
_____-protein facilitate ribosome function by transmitting information between different rRNA structures
R-proteins
28
What are the 3 binding sites of ribosomes?
A
P
E
29
The ____ and ____ site of a ribosome is base paired with their codons while the ____ site is not
A and P
E
30
What prokaryotic ribosome subunit is Peptidyl Transferase Center located?
50S (large)
31
Does the Peptidyl Transferase Center use proteins or rRNA to carry out its function?
rRNA
32
What is the job of the Peptidyl Transferase Center?
mediates peptide bond formation as the chain grows
33
What end of the growing peptide chain does new residues get added to?
C terminus
34
What is the job of the IF-1 in prokaryotes?
aids IF-3 in binding and blocks the A site
35
What is the job of the IF-2 in prokaryotes?
binds fMET-tRNA and GTP to 30S
36
What is the job of the IF-3 in prokaryotes?
prevents 50S binding and releases mRNA and tRNA
37
What does the 30S initiation complex consist of?
IF-3
IF-1
fMET-tRNA
GTP
38
What is the job of the EF-Tu in prokaryotes?
binds AA-tRNA and GTP to A site
39
What is the job of the EF-T in prokaryotes?
displaces GDP from EF-Tu
40
What is the job of the EF-G in prokaryotes?
promotes translocation through GTP hydrolysis
41
What prokaryotic elongation factor proofreads?
EF-Tu
42
What prokaryotic elongation factor does translocation from A to P site?
EF-G
43
How does the bottom of the A site in prokaryotes proofread?
checks to make sure there is no bulging in the codon-anticodon pairing
44
What does RF-1 do?
recognizes stop codons UAA and UAG
45
What does RF-2 do?
recognizes stop codons UAA and UGA
46
What does RF-3 do?
releases RF-1 and RF-2 via GTP hydrolysis
47
What does RFF do?
with EF-G induces ribosome dissociation
48
Do prokaryotic or eukaryotic mRNAs have 5' or 3' modifications?
eukaryotic
49
Do prokaryotic or eukaryotic mRNAs encode multiple different proteins?
prokaryotic
50
Do prokaryotic or eukaryotic mRNA contain their own independent ribosome binding sites as well and stop and start codons?
prokaryotic
51
Do prokaryotic or eukaryotic translation initiate independently at each gene?
prokaryotic
52
Do prokaryotic or eukaryotic translation usually initiate by a 40S subunit being recruited to the 5' cap?
eukaryotic
53
Do prokaryotic or eukaryotic have sequences that regulate translation initiation at 5' UTR?
eukaryotic
54
Do prokaryotic or eukaryotic have sequences that regulate mRNA stability at 3' UTR?
eukaryotic
55
What are eukaryotic translation initiation factors called?
eIF
56
In eukaryotes translation initiation is tightly controlled by phosphorylation of _____
eIF2
57
What carries out the phosphorylation of eIF2 in eukaryotes translation initiation?
guanine nucleotide exchange factor (GEF)
58
What is the process of eIF2 phosphoryaltion in eukaryotes translation initiation regulation?
eIF2+GDP is phosphorylated to GTP which activates eIF2 allows protein synthesis
59
Multiple ribosome can translate an mRNA simultaneously in a ____________ complex
polysome
60
How is translation in eukaryotes in a circular configuration?
eIF4G at the 5' end binds to poly-A at the 3' end
61
What is the benefit of translation of eukaryotes in a circular configuration?
used to regulate the age of an mRNA
62
What is the only part of intracellular protein trafficking that is transmembrane and not vesicular?
cytosol to ER
63
________ is maintained during vesicular transport
topology
64
Does the ER have more membrane or more empty space?
more membrane
65
How many membranes does the ER have?
one
66
What is the purpose of the smooth ER?
lipid synthesis
67
What is the purpose of the rough ER?
entry point for proteins into the secretory pathway
68
What are translational elements?
(apart of the rough and smooth ER) sites where transport vesicles bud off to cary newly synthesized proteins and lipids to the golgi
69
Disrupted ER membranes form ________
microsomes
70
What are microsomes?
When ER membrane is disrupted and forms a circular vesicle with its membrane
71
Where is the SER and RER located in the sucrose concentration when separating them?
rough ER: high density sucrose
smooth ER: low density sucrose
72
What are the 2 types of ribosomes?
free (protein not translated into ER)
membrane bound
73
When separating free and membrane bound ribosomes, where are they each located in the sucrose concentration?
free: low density sucrose
bound: high density sucrose
74
What mRNAs are attached to membrane bound ribosomes?
secreted proteins going to ER
75
What mRNAs are attached to free ribosomes?
cytosolic proteins (not going to ER)
76
What are the 4 secretory signals that target protein to the ER?
1. positive amino terminal
2. alpha helix core
3. turn inducing residues (helix breaking)
4. specific cleavage site
77
Basic residues at the N terminus of signal anchors the signal to the cis (outside) face of membrane preventing ____________ causing a insertion loop
headfirst insertion
78
What is the evidence for proteinaceous channels for protein insertion instead of a lipid lined pore?
If there is a protein channel and you prematurely remove the protein you would be able to see ions flowing through
79
What is the Original Signal Hypothesis?
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
80
What are the 2 stages of ER translocation?
1. targeting of polypeptide to ER surface
2. translocation into the ER membrane (requires ATP)
81
What does SRP do in ER translocation?
recognizes the signal peptide coming out of the ribosome (tip of polypeptide) and brings to the SRP receptor on ER surface
82
What targets the signal peptide to the ER surface?
SRP
83
Once about 20 amino acids on the chain emerge from the ribosome bound to SRP what happens before SRP docking?
translational arrest
84
When is the translational arrest reversed in ER translocation?
When the SRP docks on the STP receptor on the ER membrane
85
ER translocation in vitro requires _________ since most proteins are inserted co-translationally
microsomes
86
What would happen to the protein if SRP is present but no SRP receptor?
It wont be made because the SRP doesn't think its made it to the ER since the receptor isn't present
87
What are the 3 subunits of SRP?
p19/54
p68/72
p9/14
88
What does the p19/54 subunit of SRP do?
binds to signal sequence
89
What does the p9/14 subunit of SRP do?
binds to the A site of the ribosome and arrest translation
90
What does the p68/72 subunit of SRP do?
helps initiate insertion of the signal sequence into the ER membrane by binding to SRP receptor
91
SRP increases in binding affinity when the ____________ is present
signal sequence
92
What subunit of SRP is a GTP binding domain (GTP hydrolysis)?
p54
93
_______ receptor is much less abundant that ribosomes on the RER surface suggesting its not involved in the earlier stages
SRP receptor
94
Is co-translational or post-translational ER translocation more common?
co-translation
95
What does Sec61p do as an ER translocase?
helps anchor the ribosome to the ER membrane (interacts directly with translocating polypeptide)
96
Crosslinking of Sec61p to translocating polypeptides requires _______
ATP
97
What does Bip do as an ER translocase?
binds to misfolded protein and refolds them and crosslinks and pulls polypeptide through
98
Are Sec62p and Sec63p required from ER translocation?
No
99
_________ and _______ are sufficient alone for protein translocation into the ER
Sec61p and SRP receptor
100
What does the signal peptidase do in ER translocation?
cleaves the signal sequence
101
What does Oligosaccharyltransferase do in ER translocation?
glycosylation
102
Is signal peptidase or oligosaccharyltransferase required for ER translocation?
No
103
What 3 factors influence the protein topology during ER translocation?
1. proteolytic processing
2. location of signal
3. charge around the signal
104
What is Type I topology of integral membrane proteins?
N terminus on trans side (lumen)
105
What is Type II topology of integral membrane proteins?
N terminus on cis side (cytosol)
106
What is Type III topology of integral membrane proteins?
two or more membrane spanning segments
107
Is the cis side located on the lumen or cytosol?
cytosol
108
Is the trans side located on the lumen or cytosol?
lumen
109
What 2 ways are different topological orientation obtained?
targeting signals on polypeptide
start and stop transfer sequences (polytopic)
110
Orientation of proteins across the membrane is mediated by hydrophobic stretches of amino acids called _______________
start and stop transfer sequences
111
Start and stop transfer sequences are _________ independent (they start with it then don't need it again)
SRP-independent
112
Start and stop transfer sequences have clearly defined _________ sections that stay inside the membrane
hydrophobic
113
Normally, start transfer sequences have _______ residues before them that determine the orientation of the signal insertion (N towards cytoplasm)
basic
114
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
basic
115
When integrating proteins in the ER membrane where does the negative charges typically point?
lumen
116
When integrating proteins in the ER membrane where does the positive (basic) charges typically point?
cytosol
117
Proteins that are not properly folded or modified in the ER are subject to __________
ERAD
118
What happens during ERAD?
protein is transported retrograde from ER to cytoplasm to be degraded
119
The ER lumen contains a lot of Bip why?
it binds to hydrophobic regions to make sure proteins are folding correctly
120
___________ prevents disulfide bond formation in the cytosol and catalyzes them in the ER
Glutathione
121
Are disulfide bonds preferred in the cytosol or ER?
ER
122
In the cytosol what is the GSH:GSSG ratio?
50:1 DOES NOT promote disulfide bonds
123
In the ER what is the GSH:GSSH ratio?
5:1 optimal for disulfide bonds
124
What is Protein Disulfide Isomerase (PDI)?
make sure improper disulfide bonds are not created and creates correct bonding
125
What is an example of an soluble protein ER retention signal?
KDEL
126
What is an example of an transmembrane protein ER retention signal?
KKXX
127
What is the Unfolded Protein Response (UPR)?
Decreases translation of the misfolded protein and increases gene expression of genes that help fix the unfolded proteins
128
What are the 2 ER quality control mechanisms?
ERAD
UPR
129
What are the 3 main players in the UPR in yeast?
Ire1p
HAC1 mRNA
Rlg1p tRNA ligase
130
During the UPR in yeast, ER stress induced ____ to oligomerize and autophosphorylate which activates it
Ire1
131
During the UPR in yeast once Ire1p is autophosphorylated and activated, _________ is made
Hac1
132
What player in the UPR in yeast enters the nucleus and activates transcription of genes needed?
Hac1p
133
What are the 3 main players in the UPR in mammals?
Ire1p
ATF6
PERK
134
In the UPR in mammals _______ splices XBP1 then XBP1 can enter nucleus and activate transcription
Ire1p
135
In the UPR in mammals, _______ is cleaved directly from cytoplasmic domain of ER and contains transcription factors
ATF6
136
In the UPR in mammals, translational repression is mediated by ____________
PERK
137
In the UPR in mammals, _______ is analogous to HAC1 in yeast
XBP1
138
When _____ is bound to IRE1, PERK, and ATF6 in the mammalian UPR the response is off
Bip
139
During the UPR, _____ usually cannot enter the nucleus because its bound to the ER membrane but when UPR is activated it can enter
ATF6
140
During regulation of translation in the UPR, ______ phosphorylation inhibits bulk translation
elF2-alpha
141
What is the molecular issue with cystic fibrosis?
single amino acid is mutated and the ER wont let the protein leave the ER
142
What 3 places are ribosomes found?
ER
cytosol
mitochondria
143
The ________ and ________ pathways are connected
secretory and endocytic
144
Vesicle bud from _______ compartment and fuse with ______ compartment
donor
target
145
_________ is the space within membrane enclosed compartments
lumen
146
How does COP II coat proteins transport?
anterograde (ER to cis Golgi)
147
How does COP I coat proteins transport?
retrograde (Golgi to ER)
148
How does clatherin coat proteins transport?
between endosomes and golgi from plasma membrane
149
What energy is required for coat proteins?
GTP
150
What do inner adaptor proteins bind?
transmembrane cargo receptors (with exit signals)
outer coat proteins
151
Inner coat proteins form __________ and outer coat proteins help with ________-
vesicles
budding
152
What are the two GTP binding protein involved in phosphorylation of coat proteins?
GEF and GAP
153
In coat protein phosphorylation, GEFs activate or inactivate?
activate (protein kinase)
154
In coat protein phosphorylation, GAPs activate or inactivate?
inactivate (phosphatase)
155
What is the GTP cascade of GEFs?
release of GDP and binding of GTP
156
What is the GTP cascade of GAPs?
GTP hydrolysis to GDP
157
Proteins leave the ER in _______ coated vesicles
COP II
158
Inner coat adaptor proteins help recruit _____ coat proteins to help bud vesicles
outer
159
Membrane _______ event pinches off vesicle
fusion
160
What provides quick movement for vesicles between ER and Golgi?
microtubule networks
161
COP___ coat dissembles as vesicles transport anterogradely to golgi
COP II
162
COP ___ coat assembles as vesicles transport retrogradely to ER
COP I
163
High affinity for KDEL sequence is present in ___________ and __________
vesicular tubular clusters
Golgi
164
Low affinity for KDEL sequence is present in ________
ER
165
Why is the KDEL affinity low in the ER?
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
Why is the KDEL affinity high in the vesicles and golgi?
these proteins are meant to be secreted and higher affinity means transport
167
High affinity of KDEL corresponds with COP ___ because...
COP I
retrograde transport
168
Rab proteins are important for ______ vesicles to target membrane
tethers
169
SNARE proteins are important for _____ vesicles to target membrane and ______- of opposing lipid bilayers
dock
fusion
170
What are the 2 types of SNARES?
v and t
171
______ ensure organelle specific targeting or vesicles not _____
Rabs
SNARES
172
______ cascade is important for vesicle maturation
Rab
173
The Rab cascade for vesicle maturation is regulated by ___ and ____
GEFs and GAPs
174
What are the 3 steps of vesicles fusion using SNAREs?
1. ATPase disassembles paired v and t SNAREs
2. v and t SNARES from adjacent vesicles interact
3. membranes fuse
175
What part is the entry to the Golgi closest to the ER?
cis
176
What part of golgi takes vesciles from the ER?
cis
177
What is the stackable membrane enclosed compartments in Golgi?
cisterna
178
What is the exit point for proteins in the Golgi?
trans
179
What starts N-linked glycosylation in ER?
GlcNac
180
What is the purpose of ER glycosylation?
proper protein folding
removal of misfolded proteins
181
What starts O linked glycosylation in Golgi?
GalNac
182
What are the steps of Oligosaccharide processing?
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
What is cause of Congenital Disorders of Glycosylation (CDG)?
deficiencies in genes related to N-linked glycosylation
184
T/F? ST6Gal1 is upregulated in certain cancers
true
185
What is Triskelion?
shape of one clatherin that comes together to form pits
186
_______ protein bind to membrane bound proteins and the triskelion in clatherin coated vesicles
adaptor
187
Coat assembly of clatherin induces membrane _________
curvature
188
__________ proteins are recruited to neck of budding clatherin vesicles
fission
189
What energy is required for clatherin coating?
GTP
190
Are all coat protein GTP binding mediated?
yes
191
During protein sorting in the trans golgi networks, __________ tags proteins for delivery to lysosomes
M6P
192
What is the difference between regulated and constitutive secretory pathway?
regulated: proteins guided to secretory vesicles in specialized cells
constitutive: common proteins delivered to plasma membrane
193
Where is P-GlcNAc added to proteins?
cis golgi
194
Where is GlcNAc removed exposing M6P?
trans golgi
195
What cleaves GlcNAc exposing M6P on lysosomal hydrolase?
alpha-N-acetylglucosamidinase
196
What is the most basic in the secretory pathway?
ER
197
What maintains the low pH in lysosomes?
ATPase H+ pump
198
What is Neuronal Ceroid Lipofuscinoses (NCL)?
mutations in proteins that compromise lysosome function
199
What is the most common movement disorder related to lysosome disfunction?
Parkinsons
200
Is the constitutive or regulated secretory pathway happening all the time?
constitutive
201
What are the steps of exocytosis of synaptic vesicles?
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
Is endocytosis clatherin dependent?
yes
203
What are the 3 possible fates of endocytosed cargo?
1. recycled
2. transcytosis
3. degradation
204
Endocytosis of clathrin coated vesicles form clathrin coated ________
pits
205
What are MVB? (multivesicular bodies)
endosomes with multiple vesicles in them
206
Diabetes affects the ________ of glucose
endocytosis
207
Is macropinocytosis clathrin dependent or independent?
independent
208
What is macropinocytosis?
When cell membrane protrudes and swallows up things outside of cell
209
What is caveolae?
pits formed in cell membrane and are swallowed by cell and pinched off
210
Is caveolae clatherin dependent or independent?
independent
211
_________ coated vesicles are responsible for delivering cargo from the TGB to endosomes; from endosomes to TGN; and from the plasma membrane to endosomes
clathrin
212
The _______ pathway is critical for delivery of hydrolases to lysosomes
M6P
213
o
MVB (multivesicular bodies)
