Quizzes 4-5 Flashcards
True or false: a hydrophobicity plot’s values reflect the free energy needed to move a segment from a non-polar solvent to an aqueous environment.
True
True or false: For a “peak” on a hydrophobicity plot to represent a transmembrane domain, it should span at least 50 units on the X axis.
False
True or false: hydrophobicity plots are a good way to identify alpha helical transmembrane domain
True
True or false: for a hydrophobicity plot, the X-axis is the position of the amino acid in the primary sequence whereas the Y axis is the relative hydrophobicity of each individual amino acid.
False
True or false: Just as in our cells, the membranes of thermophilic archaea are composed of lipid bilayers. However their phospholipids have exceedingly long fatty acid tails, and their membranes are much thicker than ours.
True
True or false: The difference between symporters and antiporters is that symporters move ions down a gradient whereas antiporters move ions up/against a gradient.
False
True or false: During one stage of a P-type pump’s pumping cycle, a serine on the pump itself is phosphorylated
False
True or false: During a P-type pump’s pumping cycle there are conformational changes in the cytosolic and extracellular domains, but the alpha helices that span the membrane do not change shape; the conformational changes are restricted to regions outside the membrane.
False
True or false: P-type pumps are part of a super-family of proteins; they are structurally related and are presumed to be derived from a common ancestor.
True
True or false: If a P-type pump is moving a particular ion out of the cell, then you should expect the pump to have a high affinity binding site for that ion when it is open to the cytosol
True
How many amino acids are needed to span the membrane as a beta-strand?
10
How many amino acids are needed to span the membrane as an alpha helix?
20-25
How thick (in nanometers) is an average lipid bilayer?
5 nm
How many carbons are in a typical fatty acid chain?
14-24
A hydrophobicity plot of protein X suggests that it lacks transmembrane domains. However, in a separate experiment, you find that protein X is present exclusively in the plasma membrane fraction of your cell preparation. How is this possible? (list 3 ways)
- The membrane spanning regions of protein X might be strands of beta-barrel - as these regions are difficult to assess by a hydrophobicity plot
- Protein X might post-translationally modified by the addition of a fatty acid tail
- Protein X might be a peripheral membrane protein
Can the amino acid serine serve as a hydrophilic head group for a phospholipid?
Yes
Can the sugar alcohol inositol serve as a hydrophilic head group for a phospholipid?
Yes
Can a farnesyl group serve as a hydrophilic head group for a phospholipid?
No
Can a prenyl group serve as a hydrophilic head group for a phospholipid?
No
Can choline serve as a hydrophilic head group for a phospholipid?
Yes
What should you use to remove an integral membrane protein complex from a biological membrane without disrupting the interactions between the various subunits or irreversibly destroying the function of complex?
A non-ionic detergent
Should you use high salt concentrations to remove an integral membrane protein complex from a biological membrane without disrupting the interactions between the various subunits or irreversibly destroying the function of complex?
No
Should you use an ionic detergent to remove an integral membrane protein complex from a biological membrane without disrupting the interactions between the various subunits or irreversibly destroying the function of complex?
NO!
True or false: By catalyzing the phosphorylation of glucose to yield glucose 6-phosphate, hexokinases maintain the downhill concentration gradient that favors the facilitated transport of glucose into cells.
True
4 ion gradients:
K+, Cl-, Na+, Ca2+
Which has the steepest gradient by orders of magnitude?
Ca2+
4 ion gradients:
K+, Cl-, Na+, Ca2+
Which ion is normally more concentrated in the cytosol?
K+
4 ion gradients:
K+, Cl-, Na+, Ca2+
Which gradient is most commonly employed by animal cells to “power” symporters and antiporters
Na+
True or false: In epithelial cells, tight junctions between cells often prevent membrane proteins in the apical membrane from intermixing with membrane proteins in the basal-lateral membrane.
True
In normal healthy cells, which of these is restricted to the CYTOSOLIC side and/or leaflet of a plasma membrane?
Options: phosphatidylserine, cholesterol, glycosylated membrane protein, membrane protein with disulfide bonds
Phosphatidylserine
True or false: Cells can power the movement of an ion across a membrane and up/against a gradient IF that movement is coupled with the movement of a different ion across the membrane and down a gradient.
True
How much larger is the rate at which phosphoglyceride moves laterally within a leaflet that the rate at which it flip-flops to the other side of the lipid bilayer?
100,000,000,000
10^10, 100 billion
True or false: When chickpeas (a type of plant) are grown at lower than normal temperatures, the fatty acid composition of their membrane lipids shifts to having a higher level of unsaturated fatty acids.
True
True or false: lipid rafts are typically devoid of cholesterol
False
True or false: When plant-derived oils are hydrogenated, they become less fluid.
True
True or false: Lipid rafts are rich in sphingolipids - which typically have longer fatty acid tails.
True
True or false: In our biological membranes, the double bonds in our fatty acids exist in both cis configuration in the cytosolic leaflet and in the trans configuration in the non-cytosolic leaflet.
False
Digoxin functions by partially impairing the function of the P-type pump, Na+ K+ ATPase. How is then that Digoxin raises cytosolic calcium levels?
With a less steep Na+ gradient, the ability of Na+Ca++ antiporters to move Ca++ out of cells is impaired.
Could a membrane protein separating from a larger protein complex upon stimulus potentially increase it’s mobility within the membrane?
Yes
Could a membrane protein stably pairing with the extracellular domains of membrane proteins in an adjacent cell potentially increase it’s mobility within the membrane?
No
Could a membrane protein binding either directly or indirectly to intermediate filaments potentially increase it’s mobility within the membrane?
No
Could a membrane protein binding to a component of the extracellular matrix potentially increase it’s mobility within the membrane?
No
True or false: N-glycosylation occurs on regions of protein that are within the ER lumen and where there is an asparagine residue next to a random amino acid followed by either a serine or threonine.
True
True or false: N-glycosylation occurs on what will ultimately be the cytosolic side of a transmembrane protein
False
True or false: N-glycosylation involves the covalent addition of the oligosaccharide part of a prefabricated lipid-linked oligosaccharide known as a dolichol.
True
True or false: flippases are members of the P-type pump superfamily
True
True or false: one very important flippase uses ATP energy to ensure that phosphatidylserine exists exclusively in the cytosolic leaflet of the plasma membrane
True
True or false: Because new phospholipids are synthesized in the cytosolic leaflet of the ER membrane, flippases are required to distribute the excess to the lumenal leaflet.
False
True or false: During the flipping process, only the hydrophilic head group is slotted within the inner region of the flippase.
True
True or false: In a cell that has been induced to undergo programmed cell death (apoptosis), flippases become hyperactive.
False
They become inactive (thank you caspases)
In yeast cells with a temperature sensitive mutant in the SRP receptor, what would you expect to happen to protein synthesis if you shift the cells to the non-permissive temperature (where the receptor is non-functional)?
Proteins that are normally secreted would only partially translated, and those mRNAs and protein fragments would be remain bound to ribosomes in the cytoplasm
In yeast cells with a temperature sensitive mutant in the SRP receptor, if you were to shift the cells to the non-permissive temperature (where the receptor is non-functional), would all protein synthesis halt?
No
In yeast cells with a temperature sensitive mutant in the SRP receptor, if you were to shift the cells to the non-permissive temperature (where the receptor is non-functional), would proteins that are normally secreted accumulate in the cytoplasm as fully synthesized proteins?
No
In yeast cells with a temperature sensitive mutant in the SRP receptor, if you were to shift the cells to the non-permissive temperature (where the receptor is non-functional), would proteins that are normally secreted be stuck at the ER membrane?
No
True or false: SRP is composed of both RNA and proteins
True
True or false: SRP will halt protein translation upon binding to a ribosome
True
True or false: SRP is found exclusively in eukaryotes as bacteria do not have ER
False
True or false: SRP stands for “special reticulum protein”
False
It stands for signal recognition particle
Which of the following moves ions the fastest
Channels, uniporters, or p-type pumps
Channels
True or false: For ATP synthase to work, it is critical that the gamma shaft is physically asymmetric
True
In ATP synthase, where does the electrochemical gradient convert to rotational energy?
The a and c subunit
In ATP synthase, where does rotational energy convert to mechanical compression forces?
The gamma subunit
In ATP synthase, where does the mechanical compression forces convert to chemical bond formation?
The beta subunit
True or false: ABC transporters were first discovered in the context of multi-drug resistant cancer cells
True
True or false: ABC transporters exist exclusively in vertebrates
False
True or false: As a molecular superfamily, ABC transporters transport a wide variety of substances.
True
True or false: In eukaryotes, some ABC transporters pumps substances out of cells whereas others pump substance into cells.
False
Note: this is just what the quiz answer was. However, I have found a recent paper (2021) on finding ABC importers in eukaryotic cells. This paper breaks the traditional dogma that eukaryotic ABC transporters pump things out, and only prokaryotic ABC transporters can pump things in.
True or false: channels do not change during the transit of each ion
True
True or false: channels can be gated by various mechanisms including ligand binding, voltage changes, and mechanical pressure.
True
True or false: One reason channels move ions so quickly is that they are “wide open”. The pore is sufficiently large to allow hundreds of ions to move through at exactly the same time “shoulder to shoulder”
False
They move ions through single file
True or false: As proteins are being co-translationally inserted through the Sec61 translocon, hydrophilic segment translocate through the center of the translocon whereas hydrophobic segments pass between Sec61’s own transmembrane domains into the hydrophobic core of the lipid bilayer.
True
How did scientists isolate “rough” ER for “in vitro” experiments which eventually lead to the discovery of the signal sequence and recognition particles?
By separating the cellular components via density gradient centrifugation
Could scientists use column chromatography to isolate rough ER for use in in vitro experiments to learn more about signal sequences and recognition particles?
No
Could scientists use isoelectric focusing gels to isolate rough ER for use in in vitro experiments to learn more about signal sequences and recognition particles?
No
Could scientists use SDS PAGE gels to isolate rough ER for use in in vitro experiments to learn more about signal sequences and recognition particles?
No
What is the fate of a protein with no targeting sequences?
Remain in the cytosol
What is the fate of a protein with an N-terminal signal sequence and nothing else?
It will be a secretory protein
What is the fate of a protein with an N-terminal signal sequence and one TMD in the middle of the protein?
It will be a plasma membrane protein with the C-terminus in the cytosol
What is the fate of a protein that lacks an N-terminal signal sequence, but has one SRP recognized TMD fairly close to the N-terminus which has positively charged amino acids on the adjacent N-terminal side of that TMD.
It will be a plasma membrane protein with its N-terminus in the cytosol
What is the fate of a protein with an N-terminal signal sequence and one transmembrane at the C-terminus?
It could potentially be a GPI-anchored protein
In a thought experiment, you predict that an ATP synthase with 15 c subunits would require 5 protons to move down their gradient for each ATP produced whereas an ATP synthase with 12 c subunits would require 4 protons to move down their gradient for each ATP produced.
Is your thinking correct?
Yes
ATP synthases require 3 c subunits per proton for each ATP produced
True or false: There is a higher percentage of the cell’s membrane in the ER than in the plasma membrane
True
True or false: Cells that produce a lot of lipids including steroid hormone are enriched in rough ER
False
True or false: ER membranes are enriched in the P-type pump calcium ATPase - which maintains high concentrations of calcium within the ER lumen
True
True or false: Within cells, the ER is restricted to small region between the nucleus and Golgi apparatus.
False
True or false: ATP synthase is oriented with the alpha and beta subunits of the F1 complex in the mitochondrial inner membrane space whereas the equivalent region of a lysosome’s V-type pump resides within the lumen of the lysosome.
False
