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cell phys exam 2
Terms in this set (260)
A grad student discovers an inability of SRP receptors to recognize the SRP of a nascent protein being synthesized by a free ribosome. mRNA sequence shows this is a soluble resident ER protein. What might result from this problem?
Failure of the nascent protein to cross the ER membrane
G-proteins are a family of proteins necessary for various cell signalling processes. Analysis of a subtype of these proteins reveal an amino terminus on the cytosolic face of the cell membrane. It is unknown how many passes it makes within the membrane but it is widely known that the third transmembrane pass is responsible for binding to the alpha subunit and do not form channels. Which class of transmembrane proteins does this protein belong to?
During cell lysis, a protein was found without a signal sequence. Analysis of this protein shows a multimeric structure that is RanGAP-like. Where in the cell does this protein reside?
Bip is a resident soluble ER protein. It is trafficked into the cis golgi network (CGN) via COPII coat vesicles along with other proteins for golgi modfications. To return it back to the ER, what signal sequence does the receptor look for in this protein?
To study vesicular trafficking, a mutant KDEL receptor was created where the carboxy terminus is facing the lumen of the ER. The cell is then allowed to resume anterograde trafficking of vesicles. What can we expect to find in the Cis Golgi network?
An increased than normal in ER resident proteins
this is an extracellular protein that help other proteins form a lattice-like network in the extracellular membrane
where can we find laminins?
these are extra cellular proteins that acts as sieves, determining what can diffuse through the tissue. they also form gels.
cells attach to basement membrane via which structure ?
what is the function of integrin?
link cells to other proteins in the ecm
where are integrin proteins found?
on the cell membrane
the cytoplasmic side of integrins interact with?
extracellular side of integrins interacts with?
other ecxtracellular matrix proteins (collagen,laminins,fibronectin)
how do you die from scurvy?
hemorrhage via destruction of blood vessels
who are at risk for scurvy?
alcoholics and the elderly who barely get out to get groceries
what is the fxn of of fibronectin binding domain on fibronectin?
allow for polymerization of fibronectin dimer
enzymes that read DNA and create a new strand
enzyme that unwind dna
what is the fxn of single stranded binding proteins?
bind and stabilize single stranded DNA during replication
enzyme that relieves DNA supercoiling
DNA gyrase or topoisomerases
prokaryotic DNA pol III is what in eukaryotes?
DNA pol delta and epsilon
DNA gyrase is what in eukaryotes?
what is Ori in the DNA replication?
location of prokaryotic replication
how many origin of replications does eukaryotes and prokaryotes have?
eukaryotes- many; prokaryotes- 1
what are Orcs?
origin of replication complex proteins
this is the section of DNA with primase and helicase
why do we add an RNA primer before replication?
to allow attachment of first DNA nucleotide.
what is the direction of DNA synthesis?
5' to 3'
what are the fragments of DNA on lagging strand
which DNA pol does replication in eukaryotes and prokaryotes?
eukaryotes- delta ; prokaryotes- III
which DNA pol have a 3-5 (forward) exonuclease activity?
DNA pol III and I
what is the hayflick limit
the number of cell division a specific cell will undergo before eventually stopping
this is a type of integrin complex that are short lived complexes that form at the edge of cells?
a type of integrin complex that are mature focal contacts capable of resisting mechanical force?
a type of integrin receptor that are elongated structures found in cells exposed to sustain intracellular tension.
a part of the hemidesmosome that link that desmosome into the intermediate filament network of the cell
a disease with a presentation of:
bleeding from mucous membrane
loss of teeth
sign and symptoms of Ehlers-Danlos syndrome
unstable joints leading to arthritis
what is the usual life-threatening complication of Ehlers-Danlos Syndrome?
this is a disease resulting in a mutation in fibrillin gene
a type of cell jxn that serves to control what can move laterally between cells and act as a seal?
what is catenin for?
binds cadherins and cytoskeletons
cadherens are dependent on what ion?
cadherens are usually associted with what type of protein intracelullarly?
a type of cell jxn that provides a means of direct communication between cells
selectins are found on which cells?
what is the function of selectins?
allow extravasation of blood cells through endothelium
when is the expression of selectins increased?
what are the three parts of selectins?
what is the oligosaccharide of selectins?
sialyl lewis x
a disease where there are autoantibodies against desmogleins of desmosomes
what is the nikolsky presentation of pemphigus vulgaris?
the bullar will rupture and bleed when you press on it
a disease where we have autoantibodies against dystonin or collagen XVII
what is the nikolsky presentation of bullous pemphigoid?
no rupturing of the bulla
S&S of leukocyte adhesion deficiency?
failure of umbilicus to slough off
recurrent bacterial infection
no abscess formation
increased WBC count
what is wrong with LAD-1?
defect in integrin receptor found on WBCs
what is wrong with LAD-2?
defect in sialyl lewis X
what is wrong with LAD-3?
defect in another integrin receptor type. Also there is Glanzmann's thrombasthenia which is where fibrin cannot bind platelets
proteins associated with nuclear envelope that organize contents of nucleus?
a mutation in lamins that leads to weak condensation of DNA leading to advanced aging?
enzymes that read DNA and create a new strand using DNA?
an enzyme required to make RNA primer
seals DNA fragments
this is the sequence that recognizes the Ori
autonomously replicating sequence (ARS)
when do primosomes form?
when replication bubble is formed
when RNA primers are removed, which end of the parental DNA will be free?
what kind of template does telomerase have?
what are the two nucleotide excision repairs?
transcription-coupled pathway and global activation pathway
this is a major type of nucleotide excision repair where RNA pol reads DNA and they find error here and initiate this fix.
a major type nucleotide excision repair where there is a protein that is constantly turned on and floats around the nucleus and looks for errors
global activation pathway
what is the protein that is responsible for global activation pathway?
Xeroderma Pigmentosum Complex (XPC)
thymidine dimers that are induced by radiation are fixed in what way?
nucleotide excision repair
in nucleotide excision repair, what is the enzyme that cleaves out a large chunk of DNA that contains the error?
in the case of a mismatch repair, which nucleotide do we look at for methylation to indicate the parental strand?
what type of DNA repair is necessary when bases are deaminated or modified?
base excision repair because we are focusing on only one base.
what enzyme removes the altered base in base excision repair?
what gene is defective in xeroderma pigmentosum?
XPC gene, encodes for XPC protein for global activation pathway
which end of microtubules are connected to centrioles?
what pulls the microtubules toward the cell membrane and is anchored at the plasma mebrane?
Eg5 and HSET are what proteins?
kinesin related proteins
at what phase of mitosis do we have the astral microtubules emanating out of centrioles?
what part of the kinetichore organizes it in the centromere of the chromosome?
what part of a kinetichore binds to microtubules?
what is the checkpoint protein before anaphase?
how does Mad2 works?
Binds to exposed kinetichores where centromeres are supposed to be bound indicating that there is an improper alignment of chromosomes. This halts mitosis.
what holds together sister chromatids?
what breaks down cohesin?
what inhibits separase?
how do we activate degradation of cohesin in anaphase?
anaphase-promoting-complex tags securin via ubiquitin and degrades it in a proteasome. This then lets separase to be free and cleave cohesin
during initiation, RNA pol binds to what regio of DNA?
RNA pol I synthesizes which type of RNA?
RNA pol II synthesizes which type of RNA?
mRNA, miRNA, and snRNA
RNA pol III synthesizes which type of RNA?
tRNA and one type of rRNA
which Transcription factors fall under "basal transcription factors"?
TFIIA, IIB,IID,IIE,IIF ,IIH
a TF that recognizes the TATA box of the promotor region?
which TF recognizes the template strand?
which TF phosphorylates RNA pol II?
which end of the RNA do we add the poly A tail to?
3' end of the parent strand
what do we add to the 5' end of an mRNA?
what protein binds to the nuclear pore basket during mRNA export out of the nucleus
TAP=transporter associated with antigen processing
what is the sequence upstream of the translation start site for bacteria?
in eukaryotes, which sequence upstream of the start site does the ribosome look for?
proteins without any signal sequence will be sent to?
what is the target sequence for proteins necessary to be transported to peroxisome?
PTS1 and PTS2
what are the cytosolic receptors for PTS1 and PTS2 of peroxisomal targeting?
Pex5p and Pex7p
what are class I transmembrane proteins?
single pass transmembrane proteins that have their amino terminus in the ER lumen.
what are class II transmembrane proteins?
they are a single pass transmembrane protein with their amino terminus on the cytosolic side
a class of transmembrane proteins that are multi-pass and do not form a channel?
a class of transmembrane proteins that are multi-pass and form channels
what indicates that a protein needs N-glycosylation of asparagine ?
what is the lipid anchor of core oligosaccharides?
what makes up a core oligosaccharide?
what is the enzyme that adds the core oligosaccharide to ER transmembrane proteins?
oligosaccharyl transferase complex
explain GPI posttranslational modification process
1) an omega site must be present first in these proteins
2) transamidase complex recognizes omega site
3)This cleaves the new proteins at this site and attaches a GPI
what is the enzyme responsible for creating disulfide bonds between cysteine residues?
PDIs (protein disulfide isomerases)
what is the chaperone that proteins with core oligosaccharide use?
what removes terminal glucoses on core oligosaccharide?
glucosidase I and II
when ER protiens incorrectly fold, what enzyme reattaches a terminal glucose for re-binding to calnexin?
a protein that binds to hydrophobic regions of nascent proteins, indicating that this protein is misfolded.
for protein targeting to the mitochondrial outer membrane, what do we need to make this happen?
1. Hsp70 to stabilize unfolded protein
2. TOM complex to get it in there
for transmembrane protein transport to inner membrane of mitochondria what do we need?
1. Hsp70 to stabilize unfolded protein
2. TOM to get it through the OM
3. TIM22 to get it to the inner membrane
4. cleave signal sequence via peptidases
to target proteins into the mitochondrial matrix, what do we need?
1) Hsp70 to stabilize the unfolded proteins
2)TOM to get it through outer membrane
3) TIM23 to get inside the matrix
4. signal sequence peptidase to cleave signal
absence of hexosaminidase A
loss of vision, hearing, paralysis, death
cherry-red spot on the retina
spleen, liver, CNS accumulate sphingomyelin,
cherry-red spot.on macula
spleen,liver. white blood cells accumulate glucosylceramide
diagnosis: tissue macrophage
lysosome storage disease
absence of lysosomal enzymes
mainly affect Ashkenazi Jews (Germany/Europe)
mucopolysaccharidosis type I
Increased plasma lysosomal enzymes (I-cell) or increased urine heparan/dermatan sulfate.
does not have the enzyme that breaks down heparan.
Coarse facial features
I-Cell Disease (Mucolipidosis II)
No M6P production.
Lysosomal enzymes are not targeted to lysosomes.
Coarse facial features
breakdown nucleic acids
what gets majority of the cargo the lysosomes never received?
macrophages in the liver and spleen
•How to prevent breakdown of lysosomal membrane?
LIMPs and LAMPs are heavily glycosylated proteins on the lumen-side of lysosomal membrane
how are lysomal contents transported into the cytosol>
ph needed for lysosomal enzymes to turn on?
below ph 6
severe symptoms of i cell disease
enlargement of the liver and spleen. (hepatosplenomegaly)
•How were hydrolytic enzymes put into vesicles destined for lysosomes?
m6p(mannose 6 phosphate) and M6P-receptors
what part of the golgi sends out early endosomes that is later going to the lysosome?
TGN (Trans Golgi network)
is hydrolases active in a basics solution?
no, only acidic
what allows the cargo to separate from the m6p and the plasma membrane cargo receptors?
acidic environment provided by the atpase proton pump
protective barrier around lysosome
Early endosome is involved in?
•sorting/Separating cargo from their receptors
what proteins or enzymes help uncoated the vesicles?
Hsc70 and auxillin are involved in the uncoating process
what is clathrin used for?
to coat the membrane region that is going to endocytose. coating vesicles.
transport from the cis/ medial Golgi to the ER. designed to maintain a steady-state localization of proteins.
What protein is used for retrograde transport from-the-Golgi?
what is used to cleave vesicles from TGN?
•If a protein belongs in the Golgi, how does it maintain it?
a Golgi retention sequence
transport from rER to cgn?
COPII- MEDIATED PROCESS
what allows the fusion of target and vesicles when exocytosing from the rER?
V-snare with t-snare
Facing plasma membrane, shipping end
trans-Golgi network (TGN)
Facing nucleus, receiving end
cis-Golgi network (CGN)
Organelle receiving cargo is called
if you are created by a bound ribosome where do you go?
ER, GOLGI, Lysosome or Plasma membrane
if you are created by a free ribosome where do you go?
Nucleus, peroxisome or mitochondria
transmembrane sequence of related proteins recognize each other and stick together. medial Golgi
bilayer thickness model
a model, based on the varying thickness of the lipid bilayer, to explain how Golgi-resident proteins are sorted to their correct locations
if you do not fit in the golgi where do you go?
protein used to send cargo/vesicles to the ER?
protein used to send cargo/vesicles away from the ER?
What are the ER rentention signals?
KDEL Or KKXX
What microtubule mediated proteins allows the vesicle to get near the acceptor protein?
the protein has a specific receptor that tells it where to go, what is the selection?
anything in the are will get bud into a vesicle and pinched off, what is the selection?
if the cargo is the lumen or membrane where will it go ?
if the cargo is in the lumen of the vesicle it will end up in the lumen of the acceptor compartment.
if the cargo is in the membrane it will end up in the membrane.
pathway or anterograde that moves cargo forward
send stuff from in the cell to out..
pull cargo from outside the cell to inside the cell
dna polymerse III has which of the following types of exonuclease actvity?
3' to 5'
a cell maintained in a cell culture is found to have a mutations in the gene that encodes for mad2. this cell ultimately produces a series of daughter cells. which of the following types of cellular problems would these daughter cells most likely have?
which of the following regarding the poly-a-tail of mature mrna
increase the half-life of the mrna.
a pharmaceutical chemist has found a compound isolated from the plant in virtro studies has shown to act as an inhibitor of topoisomerase. which of the following types of cellular problems would develop in cells after exposure to this compound.
translation initiation factor that are used during mRNA export from the nucleus likely contain which of the following sequences.
NLS AND NES
a major distinction between a desmosome and adherens junction is that a desmosome associates with ? proteins whereas adherens junctions associate with ? proteins intracellularly.
intermediate filaments ; microfilaments
a patient with a disease characterized by increase para cellular movement of material is later confirmed to have a mutation in a gene that encodes for a protein that would normally prevent such movement. which of the following genes is likely affected in this patients?
a patient is found to have a mutation in the gene that encodes for plakoglobin. which of the following disease would this present most similar to?
in an eoerimental prcedure, a researcher knocked down the expression of heterotypic connexoncomposed of a homooligomer an heterooligomer in a cell line and observed the changes seen in the cells. which of the following changes would be expected?
decreased transcellular movement of calcium
a patient was recently discovered to have a mutation in the gene that encodes for elastin. based on this info, the disease would most likely have a similar presentation to which of the following disease?
characterization of a newly discovered protein in articular fluid finds that the protein contains multiple arginine-glycine-aspartate sequences. which of the following is most likely function of these sequence?
binds to integrin receptors
what sequence binds srp onto a translocon and does not get cleaved by signal peptidase?
signal anchor sequence
why can't signal peptidase cleave nascent proteins that contain signal anchor sequence?
it contains the transmembrane spanning region
how can you flip the n terminus and c terminus orientation on the endomembrane?
changing the charge of the translocon can put the c terminus in the ER lumen and the n terminus in the cytosol.
what sequence tell the oligosaccharyl to add a core olichosaccharide?
what transfers core oligosaccharide onto asparagine residue on protein?
Oligosaccharyltransferase complex transfer
what allows importin to undock its cargo ?
Oxidation of long chain fatty acids
to start nuclear targeting again what protein converts ran GDP tp Ran GTP?
cargo gong into the nucleus is bound to?
Importin with a NES and NLS signal or just a NLS
cargo going out of the nucleus is bound to?
Exportin with a NES and NLS signal
the hydrolysis from GTP to GDP, so ran can uncouple from exported or imported card is done by?
how is Ran-GDP transported back into he nucleus?
What are the stop codons?
UAA, UAG, UGA
•30S and 50S
Whole ribosome is 70
small and large ribosome subunit size in prokaryotes
•40S and 60S
Whole ribosome is 80S
small and large ribosome subunit size in eukaryotes
•Proteins that help complex assemble
•Proteins that help complex stay assembled
•Proteins that terminate complex
mrna that has a intron can leave the the nucleus?
Post-translational RNA modification process in which some exons are removed or joined in various combinations.
the 3' of the mrna is cleaved in the 3' to 5' direction by?
the non-coding sequence that is added because the RNA polymerase took too long to stop is called?
how does prokaryotes stop transcription?
prokaryotes have a protein called RHO that detects the end of the sequence and tells it to stop.
changing the shape stops transcription.
reverse the extra positive super coiling by inducing negative super coiling
relaxes the negative supercoiling behind the transcription bubble
when.how does transcription truly being?
TFIIH use a kinase enzyme to add a phosphate to rna poly II. everything dissociate and transcription begins.
DNA dependent RNA polymerase
enzyme that uses DNA as a model to build the mRNA chain
dna to rna
RNA to protein
rna to dna
What are the phases of mitosis?
interphase, prophase, metaphase, anaphase, telophase, and cytokinesis
when is mad2 activated?
when bound to exposed kinetochore
purpose of cap and tail?
prevent nucleases from breaking down the RNA
what is added to the 5' end of the nascent RNA at the 5' carbon
what removing excess 3'-end of RNA until it reaches polyadenylation sequence (5'AAUAAA3') ?
what is the name of this sequence(ACCAUGG)? who uses it?
Kozak sequence; eukaryotes
what is the name of this sequence (AGGAGG)? who uses it?
where is the DNA polymerase found on the chromosome after initiation?
a genetic test shows mutation on one of the lysomal enzymes that has an increase in glucosylceramide?
Lack glucocerebrosidase in gaucher disease
proteins that enters the nucleus and can also leave the nucleus?
transcription, translation factors and poly a binding protein.
Docking/RING Complex that bring proteins in the peroxisomal matrix
importomer in the peroxisomal membrane
what binds the docking/RING complex (importomer)
An organic salt transporter (OST) in enterocytes is located on the basolateral membrane and is responsible for transport of absorbed bile acids out of the cell and into the bloodstream. In a certain disease, it was found that this transporter fails to localize into the cell membrane. Moreover, clathrin coated vesicles filled with this transporter are found free in the cytosol near the membrane in the affected cells. What could a cell biologist conclude from this finding?
Inability of SNARE proteins to mediate vesicular fusion into the cell membrane
In peroxisomal targeting, proteins are transported into the interior of the organelle in its functional shape as opposed to protein targeting in any of the mitochondrial membranes. What could account for this difference between the two pathways?
Mitochondrial proteins are transported into the TOM complex translationally with the help of Hsp70 to stabilize its unfolded state as it goes into the complex.
Replication of DNA is halted because the strands kept re-annealing. What protein is not doing its job?
single stranded binding protein
Telomerase adds DNA nucleotides on which strand?"
reverse transcriptase on parental strand on 5'
a 6 month old child comes in with skin cancer. What DNA repair isn't working?
Nucleotide Excision repair
in cancerous cells, cells are still dividing despite exposed kinetochores. What protein is not functioning right?
RNA pol can't dissociate from transcription factors. what protein is malfunctioning?
A ribosome has a defective P site, what can't the protein not do?
peptide bond between the aa sequence and the new aa.
"A nuclear protein got its NLS removed, what would happen to this protein?"
cannot go into the nucleus
an ER protein has a negatively charged amino acid towards the amino terminus. How does this protein localize in the ER membrane?"
amino terminus on the lumen
A cell loses its inability to have dolichol phosphate. what post translational modification can the protein not undergo?"
addition of Oligosaccharide
what enzyme is involved in improperly folded protein and re-folds it?
A nascent protein was made by a ribosome but fails to produce the initial signal sequence. where would be the final destination of this protein?"
transport from the ER to the CGN includes what proteins in the vesicle?"
COPII and vSNARE
A cell bio researcher is wishing to isolate a vesicle from the golgi containing his protein of interest but ended up isolating an endosome from the TGN. What proteins here identifies it as an endosome from TGN?"
proton pumps and hydrolytic enzyme
a grad student wishes to target a non-lysosomal enzyme to the lysosome. what post translational modification should the protein undergo?"
Mannose to mannose-6-phosphate
What would happen if there was a defect in these LIMPS and LAMPS
the lysosome will start to digest itself
A genetic test shows mutation on one of the lysosomal enzymes but not sure which type. There is an increase in glucosylceramide"
Prior to leaving the nucleus, Exonuclease activity will cleave until it reaches what sequence?
what is the top priority for all cels?
what is the importance of the nucleus double membrane?
helps keep the dna instruction from escaping and keep things out.
pull two old strands apart and add two new daughter cells to each strand.
directs DNA replication throughout the genome and is required for its initiation.
dna ORC (origin recognition complex)
will be synthesized continuously
will be synthesized discontinuously
which strand drags the polymerase forward in the fork?
elongation and making dna on both strands are done by?
dna polymerase 3
what is a good way to kill of cancer cells?
which polymerase is doing this replication
dna polymerase 3
which cells surpass the halflik limit?
embryological cells, bone marrow and spleen cells.
add the wrong base pairs together and do not catch it to fix it. what kind of error is this? what do you use to fix it?
mismatch error; TCP or GAP
•Common cause of pyrimidine dimers
•Multiple types of damage
•Deamination of C to U
nh2 fall off
Addition of large alkyl groups to DNA.
can be caused by bbq meat
heterochromatin provides for chromatid cohesion
tell the rna polymerase to change shape and stop transcription in prokaryotes?
push microtubules apart from the center of the cell
eg5 and hset
what can inhibit transcription and translation?
partially unzips DNA
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