Cell Biology Practice Problems

A single-pass transmembrane protein present in the plasma membrane of an animal cell has attached oligosaccharide chains and intrachain disulfide bonds. Are the oligosaccharide chains attached to both the cytosolic and the noncytosolic sides of this prote

Only one - the noncytosolic side

A single-pass transmembrane protein present in the plasma membrane of an animal cell has attached oligosaccharide chains and intrachain disulfide bonds. Where do you expect to find the disulfide bonds in this single-pass transmembrane protein? (cytosolic,

Noncytosolic

Explain why the polypeptide chain of transmembrane proteins crosses the lipid bilayer as an alpha helix or a Beta barrell

In both an a helix and a B barrel, the polar peptide bonds of the polypeptide backbone can be completely shielded from the hydrophobic environment of the lipid bilayer by the hydrophobic amino acid side chains. Hydrogen bonds formed between the atoms of t

Based on the amino acid sequence, it is relatively easy to identify the a helix forming segments of a transmembrane protein but it is not possible to identify the membrane spanning segments of a B barrel. Why?

Segments of the polypeptide chain that span the lipid bilayer as an a helix can be identified by estimating the degree of hydrophobicity of these segments. Using hydropathy plots, amino acid segments of 20-30 amino acids with a high degree of hydrophobici

T/F: Integral membrane proteins often precipitate (form insoluble aggregates) in aqueous solutions lacking detergents

True

T/F: Hydophilic amino acids in transmembrane regions of membrane proteins contact the lipid bilayer.

False.

T/F: Peripheral membrane proteins can only be dissociated from membranes with the use of a detergent.

False.

T/F: Strong detergents can completely unfold both membrane and nonmembrane proteins.

True.

T/F: In transmembrane proteins that form an aqueous pore through the membrane, the inside of the pore is lined with hydrophobic amino acid side chains.

False.

You are examining the mobility of transmembrane proteins using FRAP. Explain what FRAP stands for and how it is performed.

FRAP stands for Fluorescence Recovery After Photobleaching and is a technique that measures the rate of diffusion of a fluorescently labeled protein. To perform this technique, a protein of interest is fluorescently labeled. The fluorescent molecules in a

You have isolated plasma membranes and re-assembled the membranes into small vesicles. using a fluorescently labeled lectin, you see that some of the vesicles are fluorescently labeled and some are not. Lectins are proteins that bind to carbohydrates and

The population of vesicles labeled with fluorescent lectin is most likely to have a surface similar to that of the cell. Lectins bind carbohydrates and the cell adds polysaccharides to the noncytosolic portion of membrane proteins. Because the noncytosoli

How do you explain the other population of vesicles?

The population of vesicles that do not label with fluorescent lectin are probably "inside-out" vesicles. These vesicles have their cytoplasmic face on the outside of the vesicle and thus the glycosylated proteins and lipids are within the vesicles, where

Why do eukaryotic cells require a nucleus as a separate compartment when prokaryotic cells manage perfectly well without?

(i) The nuclear envelope separates the transcription and translation processes in a eukaryotic cell. A primary RNA transcript is held in the nucleus until it is properly processed to form an mRNA, and only then is it allowed to leave the nucleus so that r

What is the fate of a protein with no sorting signal?

It will remain in the cytosol

List the organelles in an animal cell that obtain their proteins via gated transport, via transmembrane transport, or via vesicular transport.

Gated transport - nucleus
ER, mitochondria, peroxisomes - transmembrane transport
Golgi apparatus, secretory vesicles, early and late endosomes, lysosome - vesicular transport

Imagine that you have engineered a set of genes, each encoding a protein with a pair of conflicting signal sequences that specify different compartments. If the genes were expressed in a cell, predict the location of the protein with the following signal

ER. The signal for import into the ER is located at the N-terminus of the protein and functions before the protein is fully synthesized, whereas the signal for nuclear import is internal and functions after the protein has been released from the ribosome.

What is responsible for the selectivity of active nuclear import?

Nuclear localization signals

What characterizes nclear localization signals for proteins to be imported into the nucleus?

Arginine and lysine; nuclear localization signals an be located almost anwhere in the AA sequence and are thought to form loops or patches on the proteins urface

Imagine that you have engineered a set of genes, each encoding a protein with a pair of conflicting signal sequences that specify different compartments. If the genes were expressed in a cell, predict the location of the protein with the following signal

ER. The signal for import into the ER is located at the N-terminus of the protein and functions before the protein is fully synthesized, whereas the signal for peroxisome import is at the C-terminus and functions after the protein has been released from t

Imagine that you have engineered a set of genes, each encoding a protein with a pair of conflicting signal sequences that specify different compartments. If the genes were expressed in a cell, predict the location of the protein with the following signal

Mitochondria. In order to be retained in the ER the protein must first be imported into the ER. Without a signal for ER import, the ER retention signal could not function.

Imagine that you have engineered a set of genes, each encoding a protein with a pair of conflicting signal sequences that specify different compartments. If the genes were expressed in a cell, predict the location of the protein with the following signal

A protein with signals for both nuclear import and nuclear export would shuttle between the cytosol and the nucleus.

Before nuclear pore complexes were well understood, it was unclear whether nuclear proteins diffused passively into the nucleus and accumulated there by binding to residents of the nucleus such as chromosomes, or were actively transported and accumulated

The portion of nucleoplasmin responsible for localization in the nucleus must reside in the tail. The nucleoplasmin head does not localize to the nucleus when injected into the cytoplasm, and it is the only injected component that is missing a tail.

(b) How do these experiments distinguish between active transport, in which a nuclear localization signal triggers transport by the nuclear pore complex, and passive diffusion, in which a binding site for a nuclear component allows accumulation in the nuc

These experiments suggest that the nucleoplasmin tail carries a nuclear localization signal and that accumulation in the nucleus is not the result of passive diffusion. The observations involving complete nucleoplasmin or fragments that retain the tail do

Nuclear localization signals are not cleaved off after transport into the nucleus, whereas the signal sequences for import into other organelles are often removed after import. Why do you suppose it is critical that nuclear localization signals remain att

At each mitosis, the contents of the nucleus and the cytosol mix when the nuclear envelope is disassembled. When the nucleus is then reassembled, the nuclear proteins must be selectively reimported. If the nuclear localization signals were removed upon im

Out of SD, FD, and AT, which processes are energy dependent?

Only AT (active transport)

Out of SD, FD, and AT, which processes need some kind of carrier protein?

FD and AT

Which processes can be saturated by substrate?

FD and AT

Which processes can establish a concentration gradient?

Only AT

Explain why nonpolar compounds are generally able to diffuse across biological membranes without the aid of a specific transport system.

A nonpolar compound is more soluble in nonpolar solutes, such as benzene or chloroform, than in polar solvents such as water. They generally pass through biological membranes unaided because it is energetically favorable for them to move from the aqueous

Compare the structure and activity of a membrane transport protein that transports a polar substance across a membrane with a typical soluble enzyme. How are these 2 types of proteins similar? How are they different?

-Both proteins have domains that specifically recognize and bind to their substrates via weak interactions; they both therefore mediate processes that are stereospecific and saturable.
-The membrane transporter usually spans the membrane, having one of se

Compare and contrast symport and antiport. Which term best describes the Na K ATPase?

-symport and antiport are both types of cotransport systems in which 2 solutes move through the membrane simultaneously. In symport, both move in the same direction; in antiport, one solute goes in one direction, the other in the opposite direction. The N

List 3 differences between ion channels and ion pumps.

1. The rate of ion movement through channels is much greater
2. Ion transporters exhibit saturation, whereas ion channels do not
3. Ion channels open and close in response to external stimuli or events such as ligand-binding or changes in electrical poten

T/F: Although lipid molecules are free to diffuse in the plane of the bilayer, they cannot flip-flop across the bilayer unless enzyme catalysts called phospholipid translocators are present in the membrane.

True. The hydrophobic interior of the lipid bilayer acts as a barrier to the passage of the hydrophilic lipid head groups that must occur during flip-flop. The energetic cost of this movement effectively prevents spontaneous flip flop of lipids, so that i

T/F: Whereas all the carbohydrate in the plasma membrane faces outward on the external surface of the cell, all the carbohydrate on internal membranes faces toward the cytosol.

False. The carbohydrate on internal membranes is directed away from the cytosol toward the lumen of an internal membrane bound compartment. Remember that the lumen of an internal compartment is topologically equivalent to the outside of the cell.

T/F: Although membrane domains with different protein compositions are well known, there are at present no examples of membrane domains that differ in lipid composition.

False. In addition to lipid rafts, which are microdomains with distinct lipid compositions, the apical and basolateral surfaces of epithelial cells, which are separated by intercellular tight junctions, also have different lipid compositions.

When a lipid bilayer is torn, why does it not seal itself by forming a "hemi-micelle" cap at the edges?

The same forces that dictate that certain lipids will form a bilayer, as opposed to micelles, operate in the repair of a tear in the bilayer. The tear will heal spontaneously because a bilayer is the most energetically favorable arrangement. The lipids th

Margarine is made from vegetable oil by a chemical process. Do you suppose this process converts saturated fatty acids to unsaturated ones or vice versa? Explain your answer

Vegetable oil is converted to margarine by reduction of double bonds (by hydrogenation), which converts unsaturated fatty acids to saturated ones. This change allows the fatty acids chains in the lipid molecules to pack more tightly against one another, i

Glycophorin, a protein in the plasma membrane of the red blood cell, normally exists as a homodimer that is held together entirely by interactions between its transmembrane domains. Since transmembrane domains are hydrophobic, how is it that they can asso

Transmembrane domains that are composed entirely of hydrophobic amino acid side chains obviously cannot interact with one another via hydrogen bonds or electrostatic attractions, to of the more important ways to link proteins together noncovalently. Never

You have prepared lipid vesicles (spherical lipid bilayers) that contain Na+-K+ pumps as the sole membrane protein. All of the Na+-K+ pumps are oriented in such a way that the portion of the molecule that normally faces the cytosol is in the inside of the

Without any ATP to provide energy for the Na+-K+ pumps, no ions will be pumped.

(ii) The solution outside contains Na+; the solution inside contains Na+ and ATP.

The pump will bind a molecule of Na+, causing the ATPase activity to hydrolyze ATP and transfer the phosphate group onto the pump. A conformational change will occur, leading to release of Na+ from the vesicle. However, since there is no K+ outside of the

(i) The Ca2+ pumps in the plasma membrane and endoplasmic reticulum are
examples of
(a) ATP-driven pumps.
(b) coupled transporters.
(c) passive carrier proteins.
(d) ion channels.
(e) symports.

A

Ca2+ pumps in the plasma membrane and endoplasmic reticulum are
imporportant for
(a) maintaining osmotic balance.
(b) preventing Ca2+ from altering the behavior of molecules in the cytosol.
(c) providing enzymes in the endoplasmic reticulum with Ca2+ ions

B

What is the basic structural organization of an ABC superfamily transport protein?

All members of the ABC superfamily of proteins contain two transmembrane domains and two cytosolic ATP-binding domains, which couple ATP-hydrolysis to solute movement. The transmembrane domains associate with each other. A transmembrane domain and associa

Action potentials move unidirectionally down the axon from the cell body to the axon terminus. When they reach the axon terminus they do not "bounce back' and move backwards up the axon. However, if you artificially induce an action potential in the middl

Normally, the action potential starts at the cell body and runs down the axon. This results in the sequential opening of voltage-gated sodium channels, which open to locally depolarize the membrane and close shortly afterwards upon inactivation. The chann

Acetylcholine-gated cation channels do not discriminate among Na+, K+ and Ca2+ ions, allowing all to pass through them freely. So why is it that when acetylcholine binds to this protein complex in muscle cells, the channel opens and there is a large net i

The membrane potential and the high extracellular Na+ concentration provide a large electrochemical driving force and a large reservoir of Na+ ions, so that mostly Na+ ions enter the cell as acetylcholine receptors open. Ca2+ ions will also enter the cell

(a) The action potential is a wave of ___________________ that rapidly spreads along the neuronal plasma membrane. This wave is triggered by a local change in the membrane potential to a value that is ______________ negative than the resting membrane pote

(a) depolarization, less
(b) voltage
(c) negative
(d) cell body, axon
(e) dendrites

T/F: Transport by transporters can be either active or passive, whereas transport by channels is always passive

True. Transporters bind specific molecules and undergo a series of conformational changes to move the bound molecule across a membrane. They can transport passively down the electrochemical gradient, or the transporters can link the conformational changes

T/F: Transporters saturate at high concentrations of the transported molecule when all their binding sites are occupied; channels, on the other hand, do not bind the ions they transport and thus the flux of ions through a channel does not saturate

False. Transporters AND channels saturate. It is thought that permeating ions have to shed most of their associated water molecules in order to pass, in single file, through the narrowest part - the selectivity filter - of the channel. This requirement li

t/F: The membrane potential arises from movements of charge that leave ion concentrations practically unaffected, causing only a very slight discrepancy in the number of positive and negative ions on the two sides of the membrane.

True It takes a difference of only a minute number of ions to set up the membrane potential.

Order Ca2+, CO2, ethanol, glucose, RNA, and H2O according to their ability to diffuse through a lipid bilayer, beginning with the one that crosses the bilayer most readily. Explain your order.

CO2 (small and nonpolar)
ethanol (small and slightly polar)
H2O (small and polar)
glucose (large and polar)
Ca2+ (small and charged)
RNA (very large and highly charged)
2 properties that govern the capacity of molecules to diffuse through a lipid bilayer:

how is it possible for some molecules to be at equilibrium across a biological membrane and yetn ot be at the same concentration on both sides?

the equilibrium distribution of a molecule across a membrane depends on the chemical gradient (concentration) and on the electrical gradient (membrane potential). An uncharged molecule does not experience the electrical gradient and, thus, will be at equi

Ion transporters are "linked" together - not physically, but as a consequence of their actions. For example, cells can raise their intracellular pH, when it becomes too acidic, by exchanging external Na for internal H using a Na-H antiporter. The change i

Yes. They can normalize both the H and Na concentrations. For every 3 cycles of the Na-H antiporter, which imports one Na and exports one H, the Na-K pumps cycles once, exporting three Na ions with each operation.

Does the linked action of these 2 pumps cause imbalance in either the K concentration or the membrane potential? Why or why not?

The linked action of these 2 pumps moves 3H out for every 2K that are brought into the cell, thereby increasing both the internal K concentration and the membrane potential

T/F. Like the lumen of the ER, the interior of the nucleus is topologically equivalent to the outside of the cell.

False. The interior of the nucleus and the cytosol communicate through the nuclear pore complexes, which allow free passage of ions and small molecules. The cytoplasm and nucleus are said to be topologically equivalent because the outer and inner nuclear

T/F: membrane bound and free ribosomes, which are struturally and functionally identical, differ only in the proteins they happen to be making at a particular time.

True. Ribosomes all begin translating mRNAs in the cytosol. The mRNAs for tcertain proteins encode a signal sequence for the ER membrane. After this sequence has been synthesized, it directs the nascent protein, along with the ribosome and the mRNA to the

T/F: to avoid the inevitable congestion that would occur if two-way traffic through a single pore were allowed, nuclear pore complexes are specialied so that some mediate import while others mediate export.

False. Individual nuclear pores mediate transport in both directions. It is unclear how pores coordinate this two way traffic so as to avoid head on collisions and congestion.

T/F: peroxisomes are found in only a few specialized types of eucaryotic cell.

False. all eucaryotic cells contain peroxisomes

T/F: in multipass transmembrane proteins, the odd-numbered transmembrane segments (counting from the n-terminus) act as start-transfer signals and the even-numbered segments act as stop-transfer signals.

False. The first (most n-terminal) trans membrane segment that exits from the ribosome initiates translocation acts as a start-transfer signal). Its orientation in the ER membrane fixes the reading frame for the insertion of subsequent transmembrane segme