Quizzes 4-5

Question 1

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.

Answer 1

True

Question 2

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.

Answer 2

False

Question 3

True or false: hydrophobicity plots are a good way to identify alpha helical transmembrane domain

Answer 3

True

Question 4

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.

Answer 4

False

Question 5

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.

Answer 5

True

Question 6

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.

Answer 6

False

Question 7

True or false: During one stage of a P-type pump’s pumping cycle, a serine on the pump itself is phosphorylated

Answer 7

False

Question 8

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.

Answer 8

False

Question 9

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.

Answer 9

True

Question 10

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

Answer 10

True

Question 11

How many amino acids are needed to span the membrane as a beta-strand?

Answer 11

10

Question 12

How many amino acids are needed to span the membrane as an alpha helix?

Answer 12

20-25

Question 13

How thick (in nanometers) is an average lipid bilayer?

Answer 13

5 nm

Question 14

How many carbons are in a typical fatty acid chain?

Answer 14

14-24

Question 15

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)

Answer 15

1. The membrane spanning regions of protein X might be strands of beta-barrel - as these regions are difficult to assess by a hydrophobicity plot
2. Protein X might post-translationally modified by the addition of a fatty acid tail
3. Protein X might be a peripheral membrane protein

Question 16

Can the amino acid serine serve as a hydrophilic head group for a phospholipid?

Answer 16

Yes

Question 17

Can the sugar alcohol inositol serve as a hydrophilic head group for a phospholipid?

Answer 17

Yes

Question 18

Can a farnesyl group serve as a hydrophilic head group for a phospholipid?

Answer 18

No

Question 19

Can a prenyl group serve as a hydrophilic head group for a phospholipid?

Answer 19

No

Question 20

Can choline serve as a hydrophilic head group for a phospholipid?

Answer 20

Yes

Question 21

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?

Answer 21

A non-ionic detergent

Question 22

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?

Answer 22

No

Question 23

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?

Answer 23

NO!

Question 24

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.

Answer 24

True

Question 25

4 ion gradients: K+, Cl-, Na+, Ca2+ Which has the steepest gradient by orders of magnitude?

Answer 25

Ca2+

Question 26

4 ion gradients: K+, Cl-, Na+, Ca2+ Which ion is normally more concentrated in the cytosol?

Answer 26

K+

Question 27

4 ion gradients: K+, Cl-, Na+, Ca2+ Which gradient is most commonly employed by animal cells to "power" symporters and antiporters

Answer 27

Na+

Question 28

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.

Answer 28

True

Question 29

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

Answer 29

Phosphatidylserine

Question 30

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.

Answer 30

True

Question 31

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?

Answer 31

100,000,000,000 10^10, 100 billion

Question 32

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.

Answer 32

True

Question 33

True or false: lipid rafts are typically devoid of cholesterol

Answer 33

False

Question 34

True or false: When plant-derived oils are hydrogenated, they become less fluid.

Answer 34

True

Question 35

True or false: Lipid rafts are rich in sphingolipids - which typically have longer fatty acid tails.

Answer 35

True

Question 36

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.

Answer 36

False

Question 37

Digoxin functions by partially impairing the function of the P-type pump, Na+ K+ ATPase. How is then that Digoxin raises cytosolic calcium levels?

Answer 37

With a less steep Na+ gradient, the ability of Na+Ca++ antiporters to move Ca++ out of cells is impaired.

Question 38

Could a membrane protein separating from a larger protein complex upon stimulus potentially increase it's mobility within the membrane?

Answer 38

Yes

Question 39

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?

Answer 39

No

Question 40

Could a membrane protein binding either directly or indirectly to intermediate filaments potentially increase it's mobility within the membrane?

Answer 40

No

Question 41

Could a membrane protein binding to a component of the extracellular matrix potentially increase it's mobility within the membrane?

Answer 41

No

Question 42

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.

Answer 42

True

Question 43

True or false: N-glycosylation occurs on what will ultimately be the cytosolic side of a transmembrane protein

Answer 43

False

Question 44

True or false: N-glycosylation involves the covalent addition of the oligosaccharide part of a prefabricated lipid-linked oligosaccharide known as a dolichol.

Answer 44

True

Question 45

True or false: flippases are members of the P-type pump superfamily

Answer 45

True

Question 46

True or false: one very important flippase uses ATP energy to ensure that phosphatidylserine exists exclusively in the cytosolic leaflet of the plasma membrane

Answer 46

True

Question 47

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.

Answer 47

False

Question 48

True or false: During the flipping process, only the hydrophilic head group is slotted within the inner region of the flippase.

Answer 48

True

Question 49

True or false: In a cell that has been induced to undergo programmed cell death (apoptosis), flippases become hyperactive.

Answer 49

False They become inactive (thank you caspases)

Question 50

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)?

Answer 50

Proteins that are normally secreted would only partially translated, and those mRNAs and protein fragments would be remain bound to ribosomes in the cytoplasm

Question 51

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?

Answer 51

No

Question 52

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?

Answer 52

No

Question 53

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?

Answer 53

No

Question 54

True or false: SRP is composed of both RNA and proteins

Answer 54

True

Question 55

True or false: SRP will halt protein translation upon binding to a ribosome

Answer 55

True

Question 56

True or false: SRP is found exclusively in eukaryotes as bacteria do not have ER

Answer 56

False

Question 57

True or false: SRP stands for "special reticulum protein"

Answer 57

False It stands for signal recognition particle

Question 58

Which of the following moves ions the fastest Channels, uniporters, or p-type pumps

Answer 58

Channels

Question 59

True or false: For ATP synthase to work, it is critical that the gamma shaft is physically asymmetric

Answer 59

True

Question 60

In ATP synthase, where does the electrochemical gradient convert to rotational energy?

Answer 60

The a and c subunit

Question 61

In ATP synthase, where does rotational energy convert to mechanical compression forces?

Answer 61

The gamma subunit

Question 62

In ATP synthase, where does the mechanical compression forces convert to chemical bond formation?

Answer 62

The beta subunit

Question 63

True or false: ABC transporters were first discovered in the context of multi-drug resistant cancer cells

Answer 63

True

Question 64

True or false: ABC transporters exist exclusively in vertebrates

Answer 64

False

Question 65

True or false: As a molecular superfamily, ABC transporters transport a wide variety of substances.

Answer 65

True

Question 66

True or false: In eukaryotes, some ABC transporters pumps substances out of cells whereas others pump substance into cells.

Answer 66

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.

Question 67

True or false: channels do not change during the transit of each ion

Answer 67

True

Question 68

True or false: channels can be gated by various mechanisms including ligand binding, voltage changes, and mechanical pressure.

Answer 68

True

Question 69

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"

Answer 69

False They move ions through single file

Question 70

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.

Answer 70

True

Question 71

How did scientists isolate "rough" ER for "in vitro" experiments which eventually lead to the discovery of the signal sequence and recognition particles?

Answer 71

By separating the cellular components via density gradient centrifugation

Question 72

Could scientists use column chromatography to isolate rough ER for use in in vitro experiments to learn more about signal sequences and recognition particles?

Answer 72

No

Question 73

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?

Answer 73

No

Question 74

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?

Answer 74

No

Question 75

What is the fate of a protein with no targeting sequences?

Answer 75

Remain in the cytosol

Question 76

What is the fate of a protein with an N-terminal signal sequence and nothing else?

Answer 76

It will be a secretory protein

Question 77

What is the fate of a protein with an N-terminal signal sequence and one TMD in the middle of the protein?

Answer 77

It will be a plasma membrane protein with the C-terminus in the cytosol

Question 78

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.

Answer 78

It will be a plasma membrane protein with its N-terminus in the cytosol

Question 79

What is the fate of a protein with an N-terminal signal sequence and one transmembrane at the C-terminus?

Answer 79

It could potentially be a GPI-anchored protein

Question 80

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?

Answer 80

Yes ATP synthases require 3 c subunits per proton for each ATP produced

Question 81

True or false: There is a higher percentage of the cell's membrane in the ER than in the plasma membrane

Answer 81

True

Question 82

True or false: Cells that produce a lot of lipids including steroid hormone are enriched in rough ER

Answer 82

False

Question 83

True or false: ER membranes are enriched in the P-type pump calcium ATPase - which maintains high concentrations of calcium within the ER lumen

Answer 83

True

Question 84

True or false: Within cells, the ER is restricted to small region between the nucleus and Golgi apparatus.

Answer 84

False

Question 85

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.

Answer 85

False