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216 Cards in this Set
- Front
- Back
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Which parts of the animal cell are specific to it compared to plant cells? |
The extracellular matrix and the lysosome |
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Which parts of the plant cell are specific to it compared to animal cells? |
Chloroplasts, vacuole, and cell wall |
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The aqueous part of the space outside the nucleus is called the _________ A. Cytoplasm B. Cytosol |
B. Cytosol |
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Protein synthesis is initiated on the _________ in the ___________. |
1. ribosomes
2. cytosol |
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True or false: large macromolecules all pass through nuclear pore complexes |
False. They go through selectively. |
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Transport between the nucleus and the cytosol is __________ and occurs in __________ direction(s) |
Gated and both |
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Molecules moving from the nucleus to the cytosol must pass __________ membrane(s) |
Two |
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True or false: nuclear localization signals can go anywhere in the cell |
False. They want to go to the nucleus |
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Nuclear import receptors bind NLSs and are rich in which amino acids? |
Lys and Arg |
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Name the steps for nuclear import |
1. NIR binds to NLS protein 2. Complex enters the nucleus 3. Ran-GTP attaches to NIR and the NLS protein is released 4. NIR goes back to the cytosol, where Ran-GTPase cuts Ran-GTP into Ran-GDP + P 5. Ran-GDP dissociates and the NIR can be used again |
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Name the steps for nuclear export |
1. NER enters nucleus 2. Binds Ran-GTP and protein with NES 3. Complex exits to the cytosol, where Ran-GTPase cuts Ran-GTP to Ran-GDP + P 4. The protein and Ran-GDP are released and the NER can be used again |
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How is Ran-GTPase regulated in the cytosol? |
Ran-GAP (GTPase Activating Protein) |
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How is Ran-GTPase regulated in the nucleus? |
Ran-GEF (Guanine Nucleotide Exchange Factor) |
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True or false: for proper direction of transport, Ran-GTP should be low in the cytosol but high in the nucleus |
True. |
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How is Ran-GDP taken to the nucleus? |
NTF2 (nuclear transport factor 2) |
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What does calcineurin do? |
Removes phosphate groups and attaches to NFAT to expose NIS |
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What happens in high calcium conditions in T-cells? |
The NIS on NFATs will be exposed; it will move to the nucleus where gene transcription will be activated
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What happens in low calcium conditions? |
NFAT is exported |
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_________ transport occurs in one direction from the cytosol to the _____, __________, ________, and ___________. |
Transmembrane; ER, mitochondria, plastids, and peroxisomes |
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True or false: most mitochondrial and chloroplast proteins are translated within the organelles |
False. They are translated in the cytosol and imported |
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Which chaperone helps the proteins stay unfolded? |
Hsp70 |
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In mitochondria, the protein goes through the _____ ________ in the outer membrane, the _____ _________ in the inner membrane, and is translocated to the matrix where the _______ ________ is cleaved |
TOM complex, TIM23 complex, signal peptide |
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What is on the N-terminal of these proteins? |
Amphipathic alpha-helix |
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How does chloroplast transport differ from mitochondrial |
The protein is targeted to the thylakoid and is signaled there once the signal peptide is cleaved |
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The peroxisome is targeted by the amino acids ______, _______, and ________ at the ___-terminus |
Serine, Lysine, Leucine, and C |
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In vesicular transport, which routes are only one-way? |
Golgi to cell exterior; secretory vesicles to cell exterior; early endosome to late endosome; late endosome to lysosome |
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When an SRP binds to a ribosome with a peptide that has an ER signal sequence, what happens? |
It binds to an SRP receptor on the ER |
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Which proteins bind the ER signal sequence? |
SRP and the translocator channel |
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What cuts off the signal peptide in the translocator? |
Signal peptidase |
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True or false: the side with the more negative amino acids around the signal peptide will go into the cytosol |
False. It will go into the ER lumen |
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True or false: both the start and stop transfer signals will be laterally diffused and degraded |
True |
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What happens to proteins with internal start-transfer sequences? |
They are not degraded; instead, they are laterally diffused |
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Where is the precursor to the N-linked oligosaccharide pre-formed? |
In the ER |
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Where is it processed? |
In the Golgi |
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True or false: most soluble membrane and transmembrane proteins are glycosylated |
True |
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N-linked oligosaccharide precursor is transferred to the _____ on the protein being synthesized |
Asn |
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Which sequence does the oligosaccharide precursor recognize to start transfer? |
Asn-X-Ser or Asn-X-Thr |
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True or false: the transfer of the oligosaccharide precursor will start when it recognizes the sequence Asn-Pro-Ser |
False. 'X' amino acid cannot be proline |
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The proteins are only glycosylated on the _____ _________ side |
ER lumen |
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Before the glycosylated protein can be transferred to the Golgi, what needs to be removed from the oligosaccharide? What removes them? |
1 glucose by glucosidase I; 2 glucose by glucosidase II (one at a time); 1 mannose by ER mannosidase |
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which Golgi network (cis or trans) faces the ER? |
Cis |
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Which of the following is not a purpose for protein glycosylation? A. Some g proteins are involved in cell adhesion B. Tag to mark state of protein folding C. Allow proper folding D. Some are involved in organelle packaging E. Protect them from proteases |
D. |
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What is the purpose of calnexin and when is it used? |
Calnexin is a chaperone used in tagging that helps the protein fold properly until glucosidase ii comes back to cut off the third glucose |
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What happens if the protein is still not folded properly? |
Transferase will recognize any hydrophobic amino acids sticking out and UDP-glucose will add a glucose back on and send the protein to calnexin |
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True or false: tagging to mark the state of protein folding takes place in the cytosol |
False. It takes place in the ER lumen |
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Which vesicular transport pathways go two ways? |
ER to Golgi; Golgi to secretory vesicles; Golgi to late endosomes; Golgi to early endosomes; early endosomes to cell exterior |
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Which of the following are not possible cargo proteins? A. Transmembrane proteins B. Soluble proteins bound by exterior cargo receptors C. Soluble proteins bound by transmembrane cargo receptors |
B. |
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True or false: after the vesicle forms, the protein coat remains to protect it |
False. It's purpose has been served, so it leaves |
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What do vesicle protein coats do? |
Select cargo, give curvature to vesicle, and promote budding |
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True or false: COPI and COPII proteins are used interchangeably between the ER and Golgi |
False. COPI is only from Golgi to ER or between Golgi cisternae while COPII is only between the ER to the Golgi |
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Which protein is used from the Golgi apparatus and plasma membrane to the endosome?
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Clathrin |
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When GTPase is bound by GDP, it is (ON/OFF) |
Off |
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What is monomeric GTPase regulated by? |
GEF and GAP |
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What is the first step in vesicle budding? |
GTPases recruit coat proteins |
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ArfGTPase recruits which coat proteins? |
COPI and clathrin |
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COPII is recruited by _______. |
Sar1GTPase |
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In the ER, where would Sar1-GEF be located? |
The ER membrane |
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Which part of Sar1-GTP interacts with the membrane once it's exposed? |
The amphipathic alpha-helix |
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What does the inner layer of the vesicle do? |
Selects cargo and binds to membrane |
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What do coat proteins need to select? |
Cargo, transmembrane cargo receptors, SNAREs |
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How many inner subunits does COPI have? How many outer? |
4 and 3 |
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How is a COPI vesicle uncoated? |
Gamma-cop binds to Arf-GTP, which is hydrolized to Arf-GDP and released along with the coat |
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How many inner and outer subunits does the COPII vesicle have? |
2 each |
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How is COPII uncoated? |
Sec23 is stimulated by Sec13/Sec31 and has GAP activity; Sar1-GTP is hydrolysed to Sar1-GDP and detaches from the membrane |
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How many outer subunits does clathrin have? What's on the inside? |
6 and different adaptor complexes |
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What helps to pinch off a clathrin vesicle? |
Dynamin |
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What helps to remove its protein coat? |
Hsp70 and auxilin |
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Which proteins are used for docking and tethering incoming vesicles? |
Rab GTPases and Rab effectors |
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SNAREs catalyze ___________ __________ to target membrane |
Vesicle fusion |
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What must attach to a vesicle before it can be tethered? |
Rab-GTP and a v-SNARE |
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How does the vesicle tether? |
Rab-GTP tethers to a Rab effector |
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When the vesicle docks, what does the v-SNARE attach to? |
The t-SNARE |
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What does this promote? |
Vesicle fusion |
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True or false: there are only a few types of SNAREs which can be used interchangeably for vesicle fusion. |
False. There are many different types and a high level of specificity in the interactions between v- and t-SNAREs |
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How are SNARE complexes disassociated? |
NSF and adaptor proteins |
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True or false: the orientation of a vesicle stays the same depending on how it was inserted |
True. |
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A vesicle going from the ER will go to the ____ face of the __________ |
Cis face of the Golgi |
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What is formed after COPII vesicles shed their coats? |
A vesicular tubular cluster which moves to the GOlgi |
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What do vesicles returned to the ER from the Golgi contain? |
Escaped ER resident proteins and/or proteins involved in ER vesicle budding |
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True or false: retrieval vesicles returning to the ER are COPII |
False. They're COPI
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What is the signal for misplaced ER resident proteins (soluble or membrane)? |
KDEL |
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How are they retrieved?
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KDEL receptors and COPI packaging |
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True or false: the ER lumen is basic and has a high affinity for KDEL while the Golgi lumen is acidic and has a low affinity for KDEL |
False. The ER lumen has low affinity for KDEL while the Golgi lumen has high affinity |
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How are things transported in between Golgi cisternae in the Vesicular Transport Model? |
COPI vesicles for both cis-to-trans and retrograde |
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How about the cisternal maturation model? |
Everything gets promoted; each cisterna becomes the next and the trans Golgi network breaks off at the end; retrograde is still COPI |
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Which model is used in general (i.e. when speed is not an issue?) |
Cisternal maturation model |
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What is the cargo from the Golgi to late endosomes? |
Lysosomal hydrolases |
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How is the cell protected from these hydrolases? |
They only function at acidic pH within the lysosome and are isolated by a membrane |
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What is the signal to transport these hydrolases? |
Mannose-6-phosphate (M6P) |
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If a chemical is added to a cell that prevents the removal of N-acetylglucosamine from the N-linked oligosaccharide, what will happen to the lysosomal hydrolases? |
They'll never get moved to the lysosome since the M6P signal would remain covered |
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True or false: the sigma factor is part of the eukaryotic holoenzyme |
False. It's part of the prokaryotic |
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Where do transcription factors bind on DNA? |
Cis elements |
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How many genes are encoded in one RNA in the Trp operon? |
5 |
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Where is the operator located in the Trp operon? |
Within the promoter |
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When the Trp operon is bound by RNA polymerase, gene expression is (ON/OFF) |
On |
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Where does the Trp repressor bind |
The operator |
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In order for the repressor to bind, it must first bind ___ molecules of ______________. |
2, tryptophan |
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When does the repressor bind? |
In high levels of tryptophan |
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Which DNA-binding motif does the repressor contain, and where does the motif bind on the DNA? |
Helix-turn-helix; in the major grooves |
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True or false: E. coli's first choice is to use lactose |
False. It's first choice is glucose |
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What is the Lac activator called and when does it bind? |
CAP and in low glucose/high lactose |
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Where is the CAP binding site? |
Before the promoter |
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Where is the Lac operator? |
After the promoter
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What does the first gene of the Lac operon encode? |
Beta galactosidase |
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Why is the Lac operon never truly off? |
Need some beta galactosidase to convert lactose to allolactose, which binds to the Lac repressor when lactose levels go up |
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Why is the gene not turned on when both glucose and lactose are high? |
CAP is not bound |
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How is CAP similar to the Trp repressor? |
It contains a helix-turn-helix motif |
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What binds CAP in low glucose? |
cAMP |
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When both glucose and lactose are low, why is the gene still off? |
Allolactose is low so it doesn't bind the repressor |
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What is an example of negative regulation that requires a ligand? |
Trp repressor |
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What is an example of positive regulation that requires a ligand? |
CAP |
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True or false: in eukaryotes, RNA polymerase and repressors compete for promoter binding |
False. This only happens in prokaryotes |
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True or false: both eukaryotes and prokaryotes have introns |
False. Only eukaryotes do |
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How does the Lac repressor increase affinity for the operator? |
It's a tetramer so it can bind two at once |
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Under favourable conditions, the bacteriophage lambda follows the ___________ pathway |
Prophage |
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What can cause it to leap from the prophage to the lytic pathway? |
An induction event |
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Which two gene regulatory proteins are responsible for initiating this switch? |
Lambda repressor protein (cI) and Cro |
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True or false: Cro protein is made in the lytic stage |
True |
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Choose the incorrect statement: A. Lambda repressor activates its own synthesis and most of the bacteriophage is not transcribed B. Cro activates its own synthesis and most of the bacteriophage is transcribed |
B. Cro allows its own synthesis |
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Which type of transcriptional circuit does lambda repressor follow? |
Positive feedback loop |
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What type of circuit does the whole system follow? |
Flip-flop device |
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Which type of circuit can result in "cell memory"? |
Positive feedback |
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Which loop follows the "punch in the face metaphor? |
Feed-forward device |
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Why isn't a simple gene oscillator using a negative feedback presented as a simple sine wave? |
The real graph accounts for bacterial growth |
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In the circadian circuit, when is the Per and Tim dimer made? |
When it's dark |
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What kind of feedback loop is this? |
Negative feedback |
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In what conditions is Tim degraded? |
Light |
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What can also be used for gene regulation? |
Riboswitches |
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What is a riboswitch? |
A short RNA sequence that changes conformation when bound by a small molecule |
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In low guanine levels, a riboswitch would turn purine biosynthetic genes (ON/OFF) |
On
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What happens in high guanine conditions? |
Guanine binds to the riboswitch, causing it to change shape, pull off the ribosome, and tell RNA polymerase to end transcription |
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What TF do most eukaryotic promoters contain? |
A TATA box |
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Which five general transcription factors does eukaryotic transcription regulation require? |
TFIID, TFIIB, TFIIF, TFIIE, TFIIH |
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What acts as an intermediate between RNA polymerase and regulatory proteins? |
Mediator |
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What happens if there is no mediator present? |
The signal to start transcription won't be relayed from the activator |
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If there are two activators present but three repressors, what will happen? |
Transcription will not start |
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True or false: coactivators and corepressors bind DNA directly |
False.
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True or false: binding domains and activation domains can be mixed and matched |
True. |
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What subunits make up a histone octamer? |
Two each of H2A, H2B, H3, and H4 |
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What are the four ways that activator proteins can alter chromatin to increase binding affinity? |
Nucleosome sliding, histone removal, histone exchange, and specific patterns of histone modification |
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Which of these require ATP and a chromatin remodelling complex? |
Nucleosome sliding, histone removal, histone exchange |
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Where does histone modification occur? |
Specific amino acids on histone tails |
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What are the steps in regulating human interferon gene promoter? |
Attract acetyltransferase, which adds an acetyl group to both H3K9 and H4K8 tails; attract HK, which phosphorylates H3S10; serine signals tell acetyltransferase to acetylate both H3K14; TFIID and the chromatin remodeling complex bind to acetylated tails and initiate transcription |
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When DNA methylase is attracted by a Reader, it methylates nearby ___________ |
Cytosines |
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If a drug is designed to increase gene expression, the target's genes must normally have ____ expression |
Low |
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True or false: eukaryotic RNA processing is tightly coupled to transcription |
True |
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What is the function of the 5' cap on RNA? |
Plays a role in translation, protects it from degradation, and helps in processing and export from the nucleus |
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What percentage of human genes produce multiple proteins through alternative splicing? |
~75% |
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Which enzyme splices RNA? |
Splicosome |
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What serves as a marker for properly spliced RNA? |
Exon junction complexes (EJC) |
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What is negative control of splicing? |
When the default is splicing and the sequence requires a repressor to stop the splicing |
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What is positive control? |
When there is usually no splicing; splicing requires an activator |
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What is the ratio of X:A chromosomes in Drosophila males? Females? |
Male 1:2, female 1:1
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What are the three genes involved in Drosophila sex determination? |
Sex lethal (Sxl), a splicing repressor; Transformer (Tra), a splicing activator; Doublesex (Dsx), a sex gene regulator
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Is there regulated splicing in Drosophila males? |
No |
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Which is the only functional protein in the sex determinant genes? |
Dsx |
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If a transient Sxl protein is produced, what happens? |
It blocks the splice site of Sxl and Tra so Tra is produced and activates the splice site of Dsx, and then a Dsx that represses male differentiation genes is produced (female fly) |
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Which factors must attach to RNA polymerase to create the poly-A tail? |
Cleavage stimulating factor (CstF) and cleavage and polyadenylation specificity factor (CPSF) |
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True or false: the poly-A tail can be added while transcription is still occurring |
False. It must be terminated |
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What does the tail help with? |
Stability, export, and translation |
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True or false: eukaryotic RNA processing is initiated after transcription is complete |
False. It's initiated before
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Which part of RNA polymerase binds RNA processing proteins? |
The C-terminal domain
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How are these proteins regulated? |
Phosphorylation of RNA polymerase |
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Which of the following markers would not be a marker of mature RNA? A. Cap binding complex B. snRNPs C. Exon junction complex D. Poly-A tail |
B. |
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What fraction of RNA actually leaves the nucleus? |
1/20 |
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What happens to improperly processed mRNA? |
It is degraded in the nucleus by the exosome |
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What is the problem with HIV using a host for replication? |
Some of its RNA retains introns so it's not exported to the cytosol |
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How is this problem solved? |
Some spliced mRNAs produce Rev protein whcih goes back to the nucleus to bind unspliced mRNAs and direct their export to the cytosol where they're translated |
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True or false: amino acids are added to the N-terminal of the growing polypeptide chain |
False. Added to the C-terminal |
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When translation is to begin, what must the 5' cap and poly-A tail be bound by? |
eIF4E (5') and eIF4G (poly-A) |
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True or false: both the small and large ribosomal subunits will travel along the RNA looking for AUG |
False. Only the small subunit will
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What is nonsense-mediated RNA decay? |
A method for mRNA quality control |
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How does it work and where does it take place?
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The ribosome will bulldoze off the EJCs; takes place in cytosol |
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What happens when splicing is abnormal? |
The stop codon will be premature and the EJCs will remain on the mRNA |
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How will this mRNA be degraded? |
Upf proteins |
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What kind of RNA is used when there is a ribosome stuck on a broken mRNA? |
tmRNA |
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What does tmRNA do? |
Attaches to A site and adds alanine to the peptide chain; 10 codons are then translated from the tmRNA; proteases recognize the 11 amino acid tag and degrade the protein |
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What degrades mRNAs in prokaryotes? |
Exonucleases |
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What do both mechanisms of mRNA degradation in eukaryotes involve? |
Gradual poly-A shortening |
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What are the two mechanisms? |
Decapping followed by rapid 5'-->3' degradation or rapid 3'-->5' degradation with no decapping
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What does cytosolic aconitase do? |
Stabilizes mRNA and prevents degradation |
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True or false: transferrin receptors are made only when iron levels are high. |
False. Only when iron is low. |
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When iron levels are high, iron binds ___________ and mRNA is _____________. |
Aconitase, degraded |
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Why does deadenylase cause competition between degradation and translation? |
It binds both the 5' cap like an initiation factor and chews up the poly-A tail |
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What kind of non-coding RNAs also help with stability? |
miRNA
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Which protein helps miRNA bind to mRNA? |
Argonaute |
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What are the two outcomes of binding? |
REduction in translation or degradation |
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Which of the following do siRNA and miRNA not have in common? A. Interacts with Argonaute and RITS B. Interacts with RISC C. Initiated by Dicer |
A. Only siRNA interacts with RITS
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Shine-Dalgarno sequence |
A six-nucleotide sequence in prokaryotes upstream of the AUG start codon that helps position the ribosome |
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What happens when an RNA binding protein attaches to the SD sequence? |
Translation will not occur as the ribosome won't be able to find the AUG |
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Why can temperature-regulated RNA structures only allow translation in high temperatures? |
The structure would block the SD sequence but the H-bonds holding the structure together would be broken in high temperatures, and thus the protein would be made |
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What are the 4 mechanisms of prokaryotic translational regulation? |
RNA binding proteins, temperature regulated structures, riboswitches, and antisense RNA |
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How do riboswitches block translation? |
Small molecule causes structural rearrangement to block SD |
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How does the antisense method differ from what miRNA does? |
miRNA binds to mRNA to stabilize it in order to reduce translation or to degrade the mRNA while an antisense RNA binds to block the SD sequence and halt translation entirely; also, antisense is prokaryote-specific while miRNA is only for eukaryotes |
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What is made in high iron conditions when aconitase is not bound? |
Ferritin |
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What structure needs to be formed between the cap and tail of the mRNA before translation can start? |
A loop |
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Which initiation factor and molecule must bind to the small ribosomal subunit to start translation? |
eIF2 and GTP |
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What happens when there is not enough eIF2B present? |
eIF2 remains inactive and bound to GDP since it can't get phosphorylated and protein synthesis decreases |
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If there is enough eIF2B but translation is supposed to be off, what happens? |
eIF2 sequesters all eIF2B as an inactive complex |
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What three things must proteins do in order to become functional? |
Fold properly, be covalently modified, and interact with cofactors |
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What do both Hsp60 and Hsp70 interact with and use? |
Interact with hydrophobic misfolded proteins and use ATP hydrolysis to help proteins fold properly |
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What degrades improperly folded proteins? |
The proteasome |
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What is the tag that tells the proteasome that a protein is to be destroyed? |
Ubiquitin |
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True or false: E3 is ubiquitin ligase |
False. The E2:E3 complex is ubiquitin ligase |
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Name the steps for priming ubiquitin ligase with ubiquitin. |
E1 binds ubiquitin, then the E2:E3 complex binds E1; ubiquitin is transferred to E2:E3 and E1 is released |
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Which amino acid residue on the target protein does ubiquitin bind to? |
Lysine |
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Mono-ubiquitylation causes ___________ regulation. |
Histone |
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Polyubiquitination linkage on ______ of ubiquitin causes proteasomal degradation. |
Lys48 |
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What three methods can activate ubiquitin ligase? |
Phosphorylation, allosteric transition caused by protein subunit addition, or allosteric transition caused by ligand binding |
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How are degradation signals activated? |
Phosphorylation by kinase, unmasking by protein dissociation, or destabilizing N-terminus |
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What happens to PKA when cAMP levels increase in the cell? |
It undergoes a conformational change and releases its two catalytic subunits |
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When activated, PKA does what to glycogen? |
Promotes its breakdown and inhibits its formation |
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True or false: inactive PKA is located in the nucleus |
False. It's in the cytosol
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Choose the incorrect statement: A. CRE activates target genes B. CREB recruits CBP C. Activated PKA is phosphorylated by CREB D. CBP activates transcription of target genes |
C. PKA phosphorylates CREB |
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Choose the statement that is MOST correct. A. PP2C phosphotases inhibit SnrK2 kinases in the presence of ABA B. In the absence of ABA, ABF transcription factors are inactive C. In the presence of ABA, gene expression is on D. In the absence of ABA, SnrK2 kinases can't activate ABF TFs |
A. They inhibit in the absence of ABA |
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In the presence of ABA, the ABA receptor ___________ PP2C phosphotases |
Inhibit |
