BIO 2600 FINAL

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You are interested in how cyclic-AMP-dependent protein kinase A (PKA) functions to affect learning and memory, and you decide to study its function in the brain. It is known that, in the cells you are studying, PKA works via a signal transduction pathway like the one depicted in the figure below. Furthermore, it is also known that activated PKA phosphorylates the transcriptional regulator called Nerd that then activates transcription of the gene Brainy. Which situation described below will lead to an increase in Brainy transcription?

-A mutation in the gene that encodes cAMP phosphodiesterase that makes the enzyme inactive -The addition of a nonhydrolyzable form of GTP

Name three covalent modifications that can be made to an RNA molecule in eukaryotic cells before the RNA molecule becomes a mature mRNA.

-A poly-A tail is added -A 5' cap is added -Introns can be spliced out

Which of the following is triggered by Unfolded Protein Response (UPR)?

-Activation of chaperone genes -Inhibition of protein synthesis -Activation of genes that increase the protein-folding capacity of the ER

List three ways in which the process of eukaryotic transcription differs from the process of bacterial transcription.

-Bacterial cells contain a single RNA polymerase, whereas eukaryotic cells have three. -Bacterial RNA polymerase can initiate transcription without the help of additional proteins, whereas eukaryotic RNA polymerases need general transcription factors. -In eukaryotic cells, transcription regulators can influence transcriptional initiation thousands of nucleotides away from the promoter, whereas bacterial regulatory sequences are very close to the promoter.

Name the three main classes of cell-surface receptor.

-Ion-channel-coupled receptors -G-protein-coupled receptors -Enzyme-coupled receptors

Match the type of intermediate filament with its appropriate location. -Lamins -Neurofilaments -Vimentins -Keratins

-Lamins = nucleus -Neurofilaments = nerve cells -Vimentins = connective tissue -Keratins = epithelia

Name the membrane-enclosed compartments in a eukaryotic cell where each of the functions listed below takes place. -Photosynthesis -Transcription -Oxidative phosphorylation -Modification of secreted proteins -Steroid hormone synthesis -Degradation of worn-out organelles -New membrane synthesis -Breakdown of lipids and toxic molecules

-Photosynthesis = chloroplast -Transcription = nucleus -Oxidative phosphorylation = mitochondrion -Modification of secreted proteins = Golgi apparatus and rough ER -Steroid hormone synthesis = smooth ER -Degradation of worn-out organelles = lysosome -New membrane synthesis = ER -Breakdown of lipids and toxic molecules = peroxisome

Which of the following statements about molecular switches is true?

-Protein kinases transfer the terminal phosphate from ATP onto a protein -A G-protein exchanges its bound GDP for GTP to become activated

Receipt of extracellular signals can change cell behavior quickly (for example, in seconds or less) or much more slowly (for example, in hours). Which of the following molecular changes could cause quick changes in cell behavior?

-Protein phosphorylation -Protein dephosphorylation

Name two types of protein modification that can occur in the ER but not in the cytosol.

-Proteins in the ER can undergo disulfide bond formation -Proteins in the ER can undergo glycosylation

Name three possible fates for an endocytosed molecule that has reached the endosome.

-Recycled to the original membrane -Destroyed in the lysosome -Transcytosed across the cell to a different membrane

Which statement is true?

-Release factors bind to stop codons -Stop codons are not recognized by a tRNA -The genetic code contains three stop codons

Match the components involved with ER transport with the appropriate cellular location. Locations can be used more than once, or not at all. -Signal-recognition particle -Protein translocator -mRNA -SRP receptor -Active site of signal peptidase

-Signal-recognition particle = cytosol -Protein translocator = ER membrane -mRNA = cytosol -SRP receptor = ER membrane -Active site of signal peptidase = ER lumen

-Soluble secreted proteins -ER membrane proteins -Plasma membrane proteins

Which of the following organelles is not part of the endomembrane system?

-The nucleus -Mitochondria

Cell membranes are fluid, and thus proteins can diffuse laterally within the lipid bilayer. However, sometimes the cell needs to localize proteins to a particular membrane domain. Name three mechanisms that a cell can use to restrict a protein to a particular place in the cell membrane.

-The protein can be attached to the cell cortex inside the cell. -The protein can be attached to the extracellular matrix outside the cell. -The protein can be attached to other proteins on the surface of a different cell.

Cell membranes are fluid, and thus proteins can diffuse laterally within the lipid bilayer. However, sometimes the cell needs to localize proteins to a particular membrane domain. Which of the following is NOT used by cells to restrict a protein to a particular place in the cell membrane?

-The protein can be attached to the extracellular matrix outside the cell -The protein can be attached to other proteins on the surface of a different cell -The protein can be restricted by a diffusion barrier, such as that set up by specialized junctional proteins at a tight junction

Iron (Fe) is an essential trace metal that is needed by all cells. It is required, for example, for synthesis of the heme groups and iron-sulfur centers that are part of the active site of many proteins involved in electron-transfer reactions; it is also required in hemoglobin, the main protein in red blood cells. Iron is taken up by cells by receptor-mediated endocytosis. The iron-uptake system has two components: a soluble protein called transferrin, which circulates in the bloodstream; and a transferrin receptor—a transmembrane protein that, like the LDL receptor, is continually endocytosed and recycled to the plasma membrane. Fe ions bind to transferrin at neutral pH but not at acidic pH. Transferrin binds to the transferrin receptor at neutral pH only when it has an Fe ion bound, but it binds to the receptor at acidic pH even in the absence of bound iron. Which of the following is likely true of this system?

-Transferrin without Fe bound does not interact with its receptor and circulates in the bloodstream until it catches an Fe ion. -Once iron is bound, the iron-transferrin complex can bind to the transferrin receptor on the surface of a cell and be endocytosed. -Under the acidic conditions of the endosome, the transferrin releases its iron, but the transferrin remains bound to the transferrin receptor, which is recycled back to the cell surface, where it encounters the neutral pH environment of the blood -The neutral pH of the blood causes the receptor to release the transferrin into the circulation, where it can pick up another Fe ion to repeat the cycle.

One strand of a section of DNA isolated from the bacterium E. coli reads: 5'-GTAGCCTACCCATAGG-3' What are these peptides?

-VAYP -SLPIG

Diversity among the oligosaccharide chains found in the carbohydrate coating of the cell surface can be achieved in which of the following ways?

-Varying the types of sugar monomers used -Varying the types of linkages between sugars -Varying the number of branches in the chain

Match the numbered lines in the diagram with the following structures: -Nerve terminal -Cell body -Axon -Dendrite

1 = Cell body 2 = Dendrite 3 = Axon 4 = Nerve terminal

Rank the following cytoskeletal filaments from smallest to largest in diameter (1 = smallest in diameter, 4 = largest). -Intermediate filaments -Microtubules -Actin filaments -Myofibril

1-Actin filament 2-Intermediate filaments 3-Microtubules 4-Myofibril

Rank the following types of cell signaling from 1 to 4, with 1 representing the type of signaling in which the signal molecule travels the least distance and 4 the type of signaling in which the signal molecule travels the largest distance. -Paracrine signaling -Contact-dependent signaling -Neuronal signaling -Endocrine signaling

1-contact-dependent 2-neuronal signaling 3-paracrine signaling 4-endocrine signaling

Place the following in order of size, from the smallest to the largest. -Protofilament -Microtubule -α-tubulin -Tubulin dimer -Miotic spindle

1-α-tubulin 2-tubulin dimer 3-protofilament 4-microtubule 5-miotic spindle

There are two properties of phospholipids that affect how tightly they pack together: the length of the hydrocarbon chain and the number of double bonds. The degree of packing, in turn, influences the relative mobility of these molecules in the membrane. Which of the following would yield the most highly mobile phospholipid (listed as number of carbons and number of double bonds, respectively)?

15 carbon with 2 double bonds

How many replication forks are formed when an origin of replication is opened?

Glycolysis generates more stored energy than it expends. What is the net number of activated carrier molecules produced in this process (number and type of molecules produced minus the number of those molecules used as input)?

2 ATP, 2 NADH

Glycolysis generates more stored energy that it expands. ____ are invested in the first phase of glycolysis to generate ____, ____, and ____ in the third phase of glycolysis.

2 ATP; 2 NADH; 4 ATP; 2 pyruvate

Glycolysis generates more stored energy than it expends. ____ are invested in the first phase of glycolysis to generate: ____, ____, and ____ in the third phase of glycolysis.

2 ATP; 2 NADH; 4 ATP; 2 pyruvates

Modern eukaryotes depend on mitochondria to generate most of the cell's ATP. How many molecules of ATP can a single molecule of glucose generate?

DNA synthesis during replication always takes place in the ____ direction.

5' to 3'

Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5'-AGTCTAGGCACTGA-3' 3'-TCAGATCCGTGACT-5' What will be the sequence of that RNA?

5'-AGUCUAGGCACUGA-3'

The nucleotide sequence of one DNA strand in a DNA double helix is 5'-CATTGCCAGAAAAAT-3'. Which is the sequence of the complementary strand produced during replication?

5'-ATTTTTCTGGCAATG-3'

Below is the sequence from the 3' end of an mRNA. 5'-CCGUAUCCAUGCCUCAUUGAUAUUGGCGGAAAAAAAAAAAAAA-3' If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site?

5'-AUG-3'

You have a piece of DNA that includes the following sequence: 5'-ATAGGCATTCGATCCGGATAGCAT-3' 3'-TATCCGTAAGCTAGGCCTATCGTA-5' Which of the following RNA molecules could be transcribed from this piece of DNA?

5'-AUGCUAUCCGGAUCGAAUGCCUAU-3'

Below is the sequence from the 3' end of an mRNA. 5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site?

5'-CCA-3'

Below is the sequence from the 3′ end of an mRNA. 5′-CCGUUACCAGGCCUCAUUCAGUAGUGGCGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA being released from the P site of the ribosome when release factor binds to the A site?

5'-CUG-3'

One strand of a section of DNA isolated from the bacterium E. coli reads: 5'-GTAGCCTACCCATAGG-3' Suppose that an mRNA is transcribed from this DNA using the complementary strand as a template. What will be the sequence of the mRNA in this region (make sure you label the 5′ and 3′ ends of the mRNA)?

5'-GUAGCCUACCCAUAGG-3'

The nucleotide sequence of one DNA strand in a DNA double helix is 5'-GATTCGGAGTTTTTA-3'. Which is the sequence of the complementary strand produced during replication?

5'-TAAAAACTCCGAATC-3'

Which of the following molecules of RNA would you predict to be the most likely to fold into a specific structure as a result of intramolecular base-pairing?

5′-CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG-3′

An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the ____ site by forming base pairs with the exposed codon in the mRNA.

DNA polymerase

Describe how a standard flashlight battery can convert energy into useful work and explain how this is similar to the energy conversions in the mitochondria.

A battery contains chemicals that generate negatively charged ions at one pole, and it is able to cause the continuous transfer of electrons along a metal wire if that pole is connected to the other end of the battery. The energy released by the electron-transfer process driven by the battery can be harnessed to do useful work, as when it is used to run an electric motor. Likewise, the energy released by the electron transfers that occur between the protein complexes in the electron-transport chain does useful work when it drives the movement of protons to one side of the membrane, since the resulting proton gradient is then used to generate chemical energy in the form of ATP.

Which of the following is true?

A clamp loader is required to attach a sliding clamp each time a new Okazaki fragment is begun.

What is a polyribosome?

A cluster of ribosomes simultaneously translating the same mRNA, but positioned at different sites along the mRNA

Adrenaline stimulates glycogen breakdown in skeletal muscle cells by ultimately activating glycogen phosphorylase, the enzyme that breaks down glycogen, as depicted in Figure Q16-36.

A constitutively active mutant form of PKA in skeletal muscle cells would lead to an excess in the amount of glycogen available.

The rod photoreceptors in the eye are extremely sensitive to light. The cells sense light through a signal transduction cascade involving light activation of a GPCR that activates a G protein that activates cyclic GMP phosphodiesterase. How would you expect the addition of the following drugs to affect the light-sensing ability of the rod cells? Explain your answers. A drug that inhibits cyclic GMP phosphodiesterase.

A drug that inhibits cyclic GMP phosphodiesterase would decrease any light response in the rod cell. Normally, cyclic GMP is continuously being produced in the eye. The perception of light by a rod cell normally leads to the activation of cyclic GMP phosphodiesterase, which then hydrolyzes cyclic GMP molecules. This causes Na+ channels to close, which changes the membrane potential and alters the signal sent to the brain. If cyclic GMP phosphodiesterase were blocked, levels of cyclic GMP would remain high and there would be no cellular response to light.

A drug that is a nonhydrolyzable analog of GTP would lead to a prolonged response to light. This is because a nonhydrolyzable analog of GTP would prevent the G protein from turning itself off by hydrolyzing its bound GTP to GDP. Continued activation of the G protein would keep cyclic GMP phosphodiesterase levels higher than normal, leading to a prolonged period of lowered levels of cyclic GMP. This in turn would cause Na+ channels to be closed for longer than normal, leading to a prolonged change in the membrane potential and an extended light response.

Figure Q16-18 shows the pathway through which nitric oxide (NO) triggers smooth muscle relaxation in a blood-vessel wall. Which of the following situations would lead to relaxation of the smooth muscle cells in the absence of acetylcholine?

A muscle cell that has a defect in guanylyl cyclase such that it constitutively converts GTP to cyclic GMP.

The figure below shows the pathway through which nitric oxide (NO) triggers smooth muscle relaxation in a blood-vessel wall. Which of the following situations would lead to relaxation of the smooth muscle cells in the absence of acetylcholine?

A muscle cell that has a defect in guanylyl cyclase such that it constitutively converts GTP to cyclic GMP.

Activated protein kinase C (PKC) can lead to the modification of the membrane lipids in the vicinity of the active PKC. The figure below shows how G proteins can indirectly activate PKC. You have discovered the enzyme activated by PKC that mediates the lipid modification. You call the enzyme Rafty and demonstrate that activated PKC directly phosphorylates Rafty, activating it to modify the plasma membrane lipids in the vicinity of the cell where PKC is active; these lipid modifications can be detected by dyes that bind to the modified lipids. Cells lacking Rafty do not have these modifications, even when PKC is active. Which of the following conditions would inhibit Rafty-dependent membrane lipid modification even in the presence of the signaling molecule?

A mutation in the gene that encodes Rafty such that the enzyme can no longer be phosphorylated by PKC.

You are interested in how cyclic-AMP-dependent protein kinase A (PKA) functions to affect learning and memory, and you decide to study its function in the brain. It is known that, in the cells you are studying, PKA works via a signal transduction pathway like the one depicted in Figure Q16-35. Furthermore, it is also known that activated PKA phosphorylates the transcriptional regulator called Nerd that then activates transcription of the gene Brainy. Which situation described below will lead to an increase in Brainy transcription?

A mutation in the gene that encodes cAMP phosphodiesterase that makes the enzyme inactive.

A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in Figure Q7-45. What is the most likely cause of this variation in protein sequence?

A mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids.

A calmodulin-regulated kinase (CaM-kinase) is involved in spatial learning and memory. This kinase is able to phosphorylate itself such that its kinase activity is now independent of the intracellular concentration of Ca2+. Thus, the kinase stays active after Ca2+ levels have dropped. Mice completely lacking this CaM-kinase have severe spatial learning defects but are otherwise normal. Each of the following mutations also leads to similar learning defects. For each case explain why. A mutation that destroys the site of autophosphorylation.

A mutation that destroys the site of autophosphorylation will also impair the normal function of the kinase, because the kinase will become inactive as soon as Ca2+ levels decrease.

The growth factor Superchick stimulates the proliferation of cultured chicken cells. The receptor that binds Superchick is a receptor tyrosine kinase (RTK), and many chicken tumor cell lines have mutations in the gene that encodes this receptor. Which of the following types of mutation would be expected to promote uncontrolled cell proliferation?

A mutation that inactivates the protein tyrosine phosphatase that normally removes the phosphates from tyrosines on the activated receptor.

Which of the following might decrease the transcription of only one specific gene in a bacterial cell?

A mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site.

The growth factor RGF stimulates proliferation of cultured rat cells. The receptor that binds RGF is a receptor tyrosine kinase called RGFR. Which of the following types of alteration would be most likely to prevent receptor dimerization?

A mutation that prevents RGFR from binding to RGF.

Which of the following statements describes the phosphorylation event that occurs during the process known as oxidative phosphorylation?

A phosphate group is added to ADP.

Male cockroaches with mutations that strongly decrease the function of an RTK called RTKX are oblivious to the charms of their female comrades. This particular RTK binds to a small molecule secreted by sexually mature females. Most males carrying loss-of-function mutations in the gene for Ras protein are also unable to respond to females. You have just read a paper in which the authors describe how they have screened cockroaches that are mutant in RTKX for additional mutations that partly restore the ability of males to respond to females. These mutations decrease the function of a protein that the authors call Z. Which of the following types of protein could Z be?

A protein that stimulates hydrolysis of GTP by the Ras protein.

Human infants have a much larger portion of brown adipose tissue than adult humans. It was found that the mitochondria in brown adipocytes (brown fat cells) have a novel protein in the inner mitochondrial membrane. This protein, called the uncoupling protein (UCP), was found to transport protons from the intermembrane space into the matrix. What is the impact of UCP on oxidative phosphorylation in the mitochondria of brown fat?

A protein that transports protons into the mitochondrial matrix would diminish the proton gradient. Without the proton gradient, ATP will not be generated. However, the electron-transport chain can still work, as long as oxygen is present. The UCP, therefore, is a biological uncoupler of the oxidative phosphorylation process. The electron-transport chain will run in a futile cycle that does not convert the energy from redox reactions into chemical energy (ATP), but instead releases this energy as heat.

The figure below shows the pathway through which nitric oxide (NO) triggers smooth muscle relaxation in a blood-vessel wall. Which of the following situations would inhibit relaxation of the smooth muscle cells in the presence of acetylcholine?

A smooth muscle cell that has a defect in guanylyl cyclase such that it cannot bind NO.

What differentiates a stimulatory neuron from an inhibitory neuron?

A stimulatory neuron activates Na+ channels on the post-synaptic cell, while an inhibitory neuron opens Cl- channels.

If redox pair A has a higher redox potential than redox pair B, then:

A will accept and electron from B.

Identify the cytoskeletal structures (black lines) depicted in the epithelial cells shown in Figure Q17-1.

A-Microtubules B-Intermediate filaments C-Actin

Nucleation of new actin filaments at the side of an existing filament.

ARP proteins

Which of the following is not part of the process known as oxidative phosphorylation?

ATP molecules are produced in the cytosol as glucose is converted into pyruvate.

The thylakoid membrane becomes damaged, causing the inside of the thylakoid to mix with the stroma. Which of the following processes is likely to be most affected by this damage?

ATP synthesis

The carbon-fixation cycle requires energy in the form of ____ and reducing power in the form of ____.

ATP; NADPH

Which of the following is NOT a product of the citric acid cycle?

Acetyl-CoA

The stimulation of a motor neuron ultimately results in the release of a neurotransmitter at the synapse between the neuron and a muscle cell. What type of neurotransmitter is used at these neuromuscular junctions?

Acetylcholine

Abundant in filopodia.

Actin

Directly involved in muscle contraction.

Actin

Important for formation of the contractile ring during cytokinesis.

Actin

Monomer that binds ATP.

Actin

Which of the following statements about the cytoskeleton is true?

Actin filaments and microtubules have an inherent polarity, with a plus end that grows more quickly than the minus end.

Which of the following statements is false?

Actin filaments are usually excluded from the cell cortex.

Compared to the normal situation, in which actin monomers carry ATP, what do you predict would happen if actin monomers that bind a nonhydrolyzable form of ATP were incorporated into actin filaments?

Actin filaments would grow longer.

Which of the following is true of treadmilling?

Actin monomers added to the plus end of an actin filament are eventually removed from the minus end as the filament grows.

Figure Q12-55 illustrates changes in membrane potential during the formation of an action potential. What membrane characteristic or measurement used to study action potentials is indicated by the arrow?

Action potential

Which of the following is triggered by the unfolded protein response (UPR)?

Activation of genes that increase the protein-folding capacity of the ER.

Which of the following statements about the unfolded protein response (UPR) is false?

Activation of the UPR occurs when receptors in the cytoplasm sense misfolded proteins.

Which of the following protein families are not involved in directing transport vesicles to the target membrane?

Adaptins

Figure Q16-63 shows how normal signaling works with a Ras protein acting downstream of an RTK. You examine a cell line with a constitutively active Ras protein that is always signaling. Which of the following conditions will turn off signaling in this cell line?

Addition of a drug that blocks protein Y from interacting with its target.

You are interested in cell-size regulation and discover that signaling through a GPCR called ERC1 is important in controlling cell size in embryonic rat cells. The G protein downstream of ERC1 activates adenylyl cyclase, which ultimately leads to the activation of PKA. You discover that cells that lack ERC1 are 15% smaller than normal cells, while cells that express a mutant, constitutively activated version of PKA are 15% larger than normal cells. Given these results, which of the following treatments to embryonic rat cells should lead to smaller cells?

Addition of a drug that causes cyclic AMP phosphodiesterase to be hyperactive.

Which of the situations below will enhance microtubule shrinkage?

Addition of a drug that inhibits GTP exchange on free tubulin dimers.

Addition of non-hydrolyzable GTP

Increase in cAMP levels.

Adenylyl cyclase

Which of the following statements about transport into mitochondria is NOT true?

After a protein moves through the protein translocator in the outer membrane of a mitochondrion, the protein diffuses in the lumen until it encounters a protein translocator in the inner membrane.

Which of the following statements about transport into mitochondria and chloroplasts is false?

After a protein moves through the protein translocator in the outer membrane of these organelles, the protein diffuses in the lumen until it encounters a protein translocator in the inner membrane.

When the neurotransmitter acetylcholine is applied to skeletal muscle cells, it binds the acetylcholine receptor and causes the muscle cells to contract. Succinylcholine, which is a chemical analog of acetylcholine, binds to the acetylcholine receptor on skeletal muscle cells but causes the muscle cells to relax; it is therefore often used by surgeons as a muscle relaxant. Propose a model for why succinylcholine causes muscle relaxation. What might be the mechanism to explain the different activities of acetylcholine and succinylcholine on the acetylcholine receptor?

Although succinylcholine can bind to the acetylcholine receptor, it does not activate the receptor and therefore does not cause the muscle cell to contract. Instead, succinylcholine blocks the ability of acetylcholine to bind to the receptor and thereby prevents acetylcholine from stimulating muscle contraction.

It is thought that the glucose transporter switches between two conformational states in a completely random fashion. How is it possible for such a system to move glucose across the membrane efficiently in a single direction?

Although the opening of the glucose transporter on one side of the membrane or the other is random, the binding of glucose into the binding site of the transporter is not a random event. The affinity between the glucose molecule and the transporter governs the binding event: transporter + glucose ↔ transporter-glucose At high glucose concentrations, the complex formation is favored; at low glucose concentrations, dissociation of glucose from the transporter is favored. So, as long as there is a large concentration gradient, efficient transport can occur by the simple rules of binding equilibria.

The citric acid cycle is a critical sequence of reactions for energy production, which take place in the matrix of the mitochondria. The reaction cycle requires materials from the cytosol to be converted into acetyl CoA, which represents the starting point of a new cycle. Which of the following statements about acetyl CoA is true?

Amino acids can be converted into acetyl CoA.

Membrane phospholipids, which form a bilayer in water, are labeled ____ because they contain a ____ head and a ____ tail.

Amphipathic; hydrophilic; hydrophobic

Myosin-I has a globular head which binds ____ and a single tail that binds ____. Myosin-I hydrolyzes ATP to move toward the ____ end of an actin filament.

An actin filament; cargo; plus

Which of the following channels would not be expected to generate a change in voltage by movement of its substrate across the membrane where it is found?

An aquaporin

Which organelle recycles some endocytosed proteins back to the plasma membrane?

An endosome

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a mutase?

An enzyme that catalyzes a change in the position of a specific chemical group within a single molecule.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a kinase?

An enzyme that catalyzes the addition of phosphate groups to other molecules.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a dehydrogenase?

An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of an isomerase?

An enzyme that catalyzes the rearrangement of bonds within a single molecule.

Which of the following cells rely exclusively on glycolysis to supply them with ATP?

Anaerobically growing yeast

Membrane proteins, like membrane lipids, can move laterally by exchanging positions with other membrane components. Which type of membrane proteins is expected to be the least mobile, based on their function?

Anchors

Single-strand binding protein

Experimental evidence supporting the chemiosmotic hypothesis was gathered by using artificial vesicles containing a protein that can pump protons in one direction across the vesicle membrane to create a proton gradient. Which protein was used to generate the gradient in a highly controlled manner?

Bacteriorhodopsin

Because binding to calmodulin in the presence of Ca2+ activates CaM-kinases, deletion of the calmodulin-binding portion would inactivate the kinase.

Can signaling via a steroid hormone receptor lead to amplification of the original signal? If so, how?

Because the interactions of the signal molecule with its receptor and of the activated receptor with its gene are both one-to-one, there is no amplification in this part of the signaling pathway. The signal can, however, be amplified when the target genes are transcribed, because each activated gene produces multiple copies of mRNA, each of which is used to make multiple copies of the protein that the gene encodes.

You are interested in cell-size regulation and discover that signaling through an enzyme-coupled receptor is important for the growth (enlargement) of mouse liver cells. Activation of the receptor activates adenylyl cyclase, which ultimately leads to the activation of PKA, which then phosphorylates a transcription factor called TFS on threonine 42. This phosphorylation is necessary for the binding of TFS to its specific sites on DNA, where it then activates the transcription of Sze2, a gene that encodes a protein important for liver cell growth. You find that liver cells lacking the receptor are 15% smaller than normal cells, whereas cells that express a constitutively activated version of PKA are 15% larger than normal liver cells. Given these results, predict whether you would expect the cell's size to be bigger or smaller than normal cells if cells were treated in the following fashion. You create a version of the receptor that is constitutively active.

Bigger

You are interested in cell-size regulation and discover that signaling through an enzyme-coupled receptor is important for the growth (enlargement) of mouse liver cells. Activation of the receptor activates adenylyl cyclase, which ultimately leads to the activation of PKA, which then phosphorylates a transcription factor called TFS on threonine 42. This phosphorylation is necessary for the binding of TFS to its specific sites on DNA, where it then activates the transcription of Sze2, a gene that encodes a protein important for liver cell growth. You find that liver cells lacking the receptor are 15% smaller than normal cells, whereas cells that express a constitutively activated version of PKA are 15% larger than normal liver cells. Given these results, predict whether you would expect the cell's size to be bigger or smaller than normal cells if cells were treated in the following fashion. You mutate the cAMP-binding sites in the regulatory subunits of PKA, so that the complex binds cAMP more tightly.

Bigger. Higher affinity of the PKA complex for cAMP will increase its activity, and thus cells will be bigger.

When activated by the binding of Ca2+, calmodulin relays the Ca2+ signal onward by:

Binding to Ca2+/calmodulin-dependent protein-kinases, which then phosphorylate other intracellular proteins.

It uses dynein motors.

Both microtubule of mitotic spindle and ciliary microtubules.

On a DNA strand that is being used as a template, where is the copying occurring relative to the replication origin-3' of the origin, 5', or both?

Both, as a result of the bidirectional nature of chromosomal replication.

In the reaction cycle involved in the oxidation of pyruvate, what are the advantages of having three enzyme activities contained in a single large complex instead of having three smaller and physically independent enzymes?

By co-localizing three enzyme activities in a large, layered complex, the substrates are already bound and properly positioned for rapid enzyme catalysis, and the free energy released by one reaction can be readily harnessed for the next.

Both excitatory and inhibitory neurons form junctions with muscles. By what mechanism do inhibitory neurotransmitters prevent the postsynaptic cell from firing an action potential?

By opening Cl- channels

Okazaki fragments

Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble?

CAC and CAU

Fatty acids can easily be used to generate energy for the cell. Which of the following fatty acids will yield more energy?

CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COOH

Which of the following fatty acids will yield more energy?

CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COOH

Carbon fixation converts ____ into sugars. The central reaction of this process is catalyzed by ____.

CO2; rubisco

Neurotransmitter release is stimulated by the opening of voltage-gated ____ in the nerve-terminal membrane.

Ca2+ channel

You have generated antibodies that recognize the extracellular domain of the Ca2+-pump. Adding these antibodies to animal cells blocks the active transport of Ca2+ from the cytosol into the extracellular environment. What do you expect to observe with respect to intracellular Ca2+?

Ca2+-pumps in the endoplasmic reticulum membrane keep cytosolic calcium levels low.

Figure Q16-61 shows that intracellular signaling pathways can be highly interconnected. From this information in Figure Q16-61, which of the following statements is incorrect?

CaM-kinase is only activated when the GPCR is active and not when the RTK is active.

The figure below shows that intracellular signaling pathways can be highly interconnected. Which of the following statements is incorrect?

CaM-kinase is only activated when the GPCR is active and not when the RTK is active.

Actin-binding proteins bind to actin and can modify its properties. You purify a protein, Cap1, that seems to bind and cap one end of an actin filament, although you do not know whether it binds the plus end or the minus end. To determine which end of the actin filament your protein binds to, you decide to examine the effect of Cap1 on actin polymerization by measuring the kinetics of actin filament formation in the presence and the absence of Cap1 protein. You obtain the results below.

Cap1 binds the plus end of actin.

Figure Q17-52 shows the leading edge of a lamellipodium. Which of the following statements is false?

Capping proteins bind to the minus end of actin filaments.

Which of the following statements is NOT true?

Carbon dioxide given off by chloroplasts may be used by mitochondria.

Which of the following statements is most likely to be true?

Cells carrying a Cdc42 mutation that makes Cdc42 act as if it is always bound to GTP will polymerize more unbranched actin filaments than normal cells.

You are examining a cell line in which activation of the Rho family member Rac promotes lamellipodia formation. Which of the following statements is most likely to be true?

Cells carrying a Rac mutation that makes Rac act as if it is always bound to GTP will polymerize more branched actin filaments than normal cells.

The size and charge of water-soluble molecules determine if they can pass through a ____, which carries out ____ transport.

Channel; passive

Which of the following statements is true?

Chaperone proteins in the mitochondria facilitate the movement of proteins across the outer and inner mitochondrial membranes.

Which of the following statements about vesicle budding from the Golgi apparatus is true?

Chathrin molecules act at the cytosolic surface of the Golgi membrane.

____ inhibits this activity of the α subunit, thereby keeping the subunit in an active state.

Cholera toxin

Which of the following membrane lipids does not contain a fatty acid tail?

Cholesterol

It is arranged in a "9 + 2" array.

Ciliary microtubules

It is involved in moving fluid over the surface of cells.

Ciliary microtubules

The basal body is the organizing center.

Ciliary microtubules

Although the extracellular environment has a high sodium ion concentration and the intracellular environment has a high potassium ion concentration, both must be neutralized by negatively charged molecules. In the extracellular case, what is the principal anion?

Cl-

Cells use membranes to help maintain set ranges of ion concentrations inside and outside the cell. Which of the following negatively charged ions is not primarily used to buffer positive charges inside the cell?

Cl-

Negatively charged ions are required to balance the net positive charge from metal ions such as K+, Na+, and Ca2+. Which of the following negatively charged ions is the most abundant outside the cell and which ion does most often neutralize (written in parentheses)?

Cl- (Na+)

Which of the following statements about vesicle budding from the Golgi is false?

Clathrin molecules are important for binding to and selecting cargoes.

Although the outer mitochondrial membrane is permeable to all small molecules, the inner mitochondrial membrane is essentially impermeable in the absence of specific transport proteins. Consider this information and what you have learned about the citric acid cycle to address the following questions. Present two types of benefits derived from separating the reactions of glycolysis in the cytosol from those that occur during the citric acid cycle in the mitochondrion.

Compartmentalization provides a basic mechanism for the regulation of independent sets of reactions, including the citric acid cycle, fatty acid oxidation, glycolysis, and gluconeogenesis. In some cases, metabolic reactions are physically compartmentalized to separate anabolic from catabolic reactions. For example, in the mitochondrial matrix, oxaloacetate is used in the citric acid cycle to help oxidize the acetyl carbons of acetyl CoA. However, oxaloacetate in the cytosol tends to be consumed by biosynthetic enzymes that use the molecule as a precursor for the production of amino acids such as aspartate. By keeping these reactions separate, the cell can control whether a molecule is used in an anabolic or catabolic reaction. A second advantage of compartmentalization is the co-localization and concentration of enzymes with their substrates, which can enhance reaction rates.

While many prokaryotic cells have a single membrane bilayer, all eukaryotic cells have a complex system of internal membrane-bound compartments. How might it be advantageous for the cell to have these additional compartments?

Compartmentalization using intracellular membranes allows eukaryotic cells to separate a variety of cell processes. Although this requires a higher degree of coordination, the cell also gains a more stringent degree of control over these processes.

The Meselson-Stahl experiment provided the necessary evidence to discover the mechanism by which DNA replicates. They accomplished this discovery by first culturing DNA with the heavy 15N nitrogen isotope. They then allowed the "heavy" DNA to replicate in "light" media with normal 14N nitrogen. The density of each generation of replicated DNA was recorded by marking its position in a test tube after centrifugation. The position of each generation was then compared to the positions of pure 15N DNA and pure 14N DNA. Suppose that the first generation after replication revealed two bands after being centrifuged: one at the pure14N mark, and one at the pure 15N mark. Which method of replication would this observation support?

Conservative replication

Which of the following steps or processes in aerobic respiration include the production of carbon dioxide?

Conversion of pyruvate to acetyl CoA

You make a mutation in a nuclear pore complex protein such that nuclear import is blocked. How will this alter the molecular mechanism of cortisol action?

Cortisol's target genes will not be transcribed.

Which of the following statements about the cytoskeleton is false?

Covalent bonds between protein monomers hold together cytoskeletal filaments.

Which of the following components of the electron-transport chain does not act as a proton pump?

Cytochrome c

____ is a small protein that acts as a mobile electron carrier in the respiratory chain.

Cytochrome c

Which component of the electron-transport chain is required to combine the pair of electrons with molecular oxygen?

Cytochrome c oxidase

____ transfers electrons to oxygen.

Cytochrome c oxidase

____ is a protein complex that receive electrons from cytochrome c and donates these electrons to ____.

Cytochrome c oxidase; O2

You are working in a biotech company that has discovered a small-molecule drug called H5434. H5434 binds to LDL receptors when they are bound to cholesterol. H5434 binding does not alter the conformation of the LDL receptor's intracellular domain. Interestingly, in vitro experiments demonstrate that addition of H5434 increases the affinity of LDL for cholesterol and prevents cholesterol from dissociating from the LDL receptor even in acidic conditions. Which of the following is a reasonable prediction of what may happen when you add H5434 to cells?

Cytosolic cholestrol levels will decrease relative to normal cells.

Primase

Which is NOT found in a cell membrane?

DNA

Researchers have isolated a mutant strain of E. coli that carries a temperature-sensitive variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just as well as the wild-type cells. At the nonpermissive temperature, all of the cells in the culture tube die within 2 hours. DNA from mutant cells grown at the nonpermissive temperature for 30 minutes is compared with the DNA isolated from cells grown at the permissive temperature. The results are shown in the figure below, where DNA molecules have been separated by size by means of electrophoresis (P, permissive; NP, nonpermissive). Explain the appearance of a distinct band with a size of 200 base pairs (bp) in the sample collected at the nonpermissive temperature.

DNA ligase has an important role in DNA replication. After Okazaki fragments are synthesized, they must be ligated (covalently connected) to each other so that they finally form one continuous strand. At the nonpermissive temperature this does not happen, and although there may be a range of fragments, the notable band at 200 base pairs is the typical size of an individual Okazaki fragments.

Compared to RNA polymerase, DNA polymerase has a much lower error rate for nucleotide incorporation. What structural difference between the two polymerases accounts for this?

DNA polymerase contains a proofreading domain that allows it to recognize incorrect base-pair insertion before moving on; RNA polymerase does not.

In a classic experiment that's sometimes referred to as "the most beautiful experiment in biology," Matt Meselson and Frank Stahl tested the three models for DNA replication: the semiconservative model, the dispersive model, and the conservative model. The researchers started by incubating E. coli in a nutrient medium containing a heavy isotope of nitrogen, 15N. The bacteria incorporate this heavy isotope into their nitrogen-containing molecules, including DNA. DNA purified from these bacteria could be analyzed by a technique called equilibrium density centrifugation, which separates molecules on the basis of their density. Next, Meselson and Stahl took bacteria that had been growing in the heavy, 15N-containing nutrient medium and placed them in medium containing the lighter 14N isotope. The bacteria then began incorporating this light isotope into their DNA. After one round of replication, the researchers found that DNA purified from these bacteria was intermediate in density—halfway between the heavy, 15N-containing DNA and the light, 14N-containing DNA (as shown in the figure above). From this observation alone, Meselson and Stahl could conclude that:

DNA replication is not conservative

Which of the following statements best explains the mechanism for DNA replication?

DNA replication is semi-conservative, because each DNA strand serves as a template during replication.

Which of the following is true?

DNA replication origins are typically rich in A-T base pairs.

The synthesis of DNA in living systems occurs in the 5′-to-3′ direction. However, scientists synthesize short DNA sequences needed for their experiments on an instrument dedicated to this task. Although 3′-to-5′ synthesis of DNA is chemically possible, it does not occur in living systems. Why not?

DNA synthesis from 3′ to 5′ does not allow proofreading. If the last nucleotide added is mispaired and is removed, the last nucleotide on the growing strand is a nucleoside monophosphate and the nucleotide coming in only has a hydroxyl group on the 3′ end. Thus, there is no favorable hydrolysis reaction to drive the addition of new nucleotides.

Acetylcholine acts at a GPCR on heart muscle to make the heart beat more slowly. It does so by ultimately opening K+ channels in the plasma membrane (as diagrammed in Figure Q16-32), which decreases the cell's excitability by making it harder to depolarize the plasma membrane. Indicate whether each of the following conditions would increase or decrease the effect of acetylcholine. Adding acetylcholinesterase to the external environment of the cell.

Decrease. Acetylcholinesterase degrades acetylcholine and thus will decrease the effect of acetylcholine.

Acetylcholine acts at a GPCR on heart muscle to make the heart beat more slowly. It does so by ultimately opening K+ channels in the plasma membrane (as diagrammed in Figure Q16-32), which decreases the cell's excitability by making it harder to depolarize the plasma membrane. Indicate whether each of the following conditions would increase or decrease the effect of acetylcholine. Addition of a drug that stimulates the GTPase activity of the Gα subunit.

Decrease. An increase in the GTPase activity of the Gα subunit will decrease the length of time that the G protein is active.

Acetylcholine acts at a GPCR on heart muscle to make the heart beat more slowly. It does so by ultimately opening K+ channels in the plasma membrane (as diagrammed in Figure Q16-32), which decreases the cell's excitability by making it harder to depolarize the plasma membrane. Indicate whether each of the following conditions would increase or decrease the effect of acetylcholine. Mutations in the K+ channel that keep it closed all the time.

Decrease. If the K+ channel remains closed, acetylcholine will not slow the heart.

Acetylcholine acts at a GPCR on heart muscle to make the heart beat more slowly. It does so by ultimately opening K+ channels in the plasma membrane (as diagrammed in Figure Q16-32), which decreases the cell's excitability by making it harder to depolarize the plasma membrane. Indicate whether each of the following conditions would increase or decrease the effect of acetylcholine. A mutation in the acetylcholine receptor that prevents its localization on the cell surface.

Decrease. If there is no receptor on the cell surface, cells will be unable to respond to acetylcholine.

Acetylcholine acts at a GPCR on heart muscle to make the heart beat more slowly. It does so by ultimately opening K+ channels in the plasma membrane (as diagrammed in Figure Q16-32), which decreases the cell's excitability by making it harder to depolarize the plasma membrane. Indicate whether each of the following conditions would increase or decrease the effect of acetylcholine. A mutation that decreases the affinity of the βγ complex of the G protein for the K+ channel.

Decrease. The activated βγ complex binds to and activates the K+ channel; decreasing their affinity for each other will decrease the time that the K+ channel is open, effectively decreasing the effect of acetylcholine.

What will the researcher in the passage most likely find after decreasing the extracellular concentration of calcium?

Decreased neurotransmitter release

Which of the following mutations would be predicted to have the greatest chance of harming an organism?

Deletion of four conservative nucleotides in the middle of the coding sequence.

Which of the following mechanisms is not directly involved in inactivating an activated RTK?

Dephosphorylation by serine/threonine phosphatases

Consider the mechanism by which actin and tubulin polymerize. Which of the items below does not describe something similar about the polymerization mechanisms of actin and microtubules?

Depolymerization initiates at the plus ends of filaments.

Unlike soluble, cytosolic proteins, membrane proteins are more difficult to purify. Which of the following substances is most commonly used to help purify a membrane protein?

Detergent

Which of the following statements is false?

Dissolved gases such as nitric oxide (NO) can act as signal molecules, but because they cannot interact with proteins they must act by affecting membrane lipids.

Which of the following statements about disulfide bond formation is false?

Disulfide bonds form spontaneously within the ER because the lumen of the ER is oxidizing.

If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can the genome of the fruit fly Drosophila be replicated in only 3 minutes?

Drosophila DNA contains more origins of replication than E. coli DNA

Although the outer mitochondrial membrane is permeable to all small molecules, the inner mitochondrial membrane is essentially impermeable in the absence of specific transport proteins. Consider this information and what you have learned about the citric acid cycle to address the following questions. If the inner mitochondrial membrane were rendered as permeable as the outer membrane, how would that affect oxidative phosphorylation? Which specific processes would stop and which remain?

During oxidative phosphorylation, the NADH and FADH2 generated by the citric acid cycle donate their electrons to an electron-transport chain in the inner mitochondrial membrane. As the electrons move along this chain, the energy released is used to drive protons across the inner mitochondrial membrane. This movement of protons produces a proton gradient across the membrane, which then serves as a source of energy for the generation of ATP. If the inner mitochondrial membrane were made "leaky," the proton gradient would dissipate. Thus, although acetyl CoA would continue to be oxidized by the citric acid cycle, and electrons donated to the electron-transport chain, these processes could no longer promote the production of ATP.

Your friend has just joined a lab that studies vesicle budding from the Golgi and has been given a cell line that does not form mature vesicles. He wants to start designing some experiments but wasn't listening carefully when he was told about the molecular defect of this cell line. He's too embarrassed to ask and comes to you for help. He does recall that this cell line forms coated pits but vesicle budding and the removal of coat proteins don't happen. Which of the following proteins might be lacking in this cell line?

Dynamin

Which of the following protein families are NOT involved in directing transport vesicles to the target membrane?

Dynamins

As a cell grows, which microtubule-associated protein pulls the Golgi apparatus inward, toward the nucleus?

Dynein

Sliding clamp

Using genetic engineering techniques, you have created a protein that contains 1.) a signal for import into the nucleus and 2.) a signal for import into the ER. Where would this protein end up in the cell?

Which of the following choices reflects the appropriate order of locations through which a protein destined for the plasma membrane travels?

ER --> Golgi --> plasma membrane

Which of the following statements below about intermediate filaments is false?

Each filament is about 10 μm in diameter.

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 on the inside of the vesicle and the portion of the molecule that normally faces the extracellular space is on the outside of the vesicle. Assume that each pump transports one Na+ ion in one direction and one K+ ion in the other direction during each pumping cycle (see the figure below for how the Na+-K+ pump normally functions in the plasma membrane). Predict what would happen if the solution outside contains ATP, while the solution inside contains Na+, K+ and ATP.

Each pump will transport a single Na+ out of the vesicle.

How do these standard redox potentials support our understanding of the stepwise electron transfers that occur in the electron-transport chain?

Each successive member of the electron-transport chain is a better electron acceptor, which permits a unidirectional series of electron transfers until reaching O2, which is the best electron acceptor and the final destination of the electrons, forming water as oxygen is consumed.

Figure Q12-56 illustrates changes in membrane potential during the formation of an action potential. What membrane characteristic or measurement used to study action potentials is indicated by the arrow?

Effect of a depolarizing stimulus

____ strands of tetramers come together and twist together to form the ____ nm filament.

Eight; ten

Identify the organelle that is bound by a single membrane.

Endoplasmic reticulum

Transport vesicles carry soluble proteins and membrane between compartments. The function of which cellular structure would be least affected by a malfunctioning Golgi apparatus?

Endoplasmic reticulum

Discovered for their role in responding to growth factors in animal cells.

Enzyme-coupled receptors

Pinocytosis occurs at a very high rate, and every time it occurs plasma membrane is removed from the cell surface. Which of the following processes prevents the plasma membrane from disappearing?

Exocytosis

Which of the following occur without coupling transport of the solute to the movement of a second solute?

Export of Ca2+ from the cytosol

Which of the following statements is true?

Extracellular signal molecules that are hydrophilic must bind to a cell-surface receptor so as to signal a target cell to change its behavior.

RNA primer

The mitochondrial ATP synthase consists of several different protein subunits. Which subunit binds to ADP + Pi and catalyzes the synthesis of ATP as a result of a conformational change?

F1 ATPase head

During oxidative phosphorylation, why does a single molecule of NADH result in the production of more ATP molecules than a single molecule of FADH2?

FADH2 and NADH feed their electrons to different carriers in the electron-transport chain.

We can estimate the relative mobility of a population of molecules along the surface of a living cell by fluorescently labeling the molecules of interest, bleaching the label in one small area, and then measuring the speed of signal recovery as molecules migrate back into the bleached area. What is this method called? What does the abbreviation stand for?

FRAP

T/F A polyribosome is a type of mutant ribosome that has three subunits.

False

T/F Acetyl CoA can only be generated from pyruvate.

False

T/F For a charged molecule, the direction of passive transport across a membrane is determined solely by its concentration gradient.

False

T/F Glycolipids are typically found in the cytosolic layer of the plasma membrane.

False

T/F Phosphorylation of a protein always results in the activation of that protein.

False

T/F The 5' to 3' sequence of nucleotides in a newly synthesized DNA strand is the same as the 3' to 5' sequence of the template strand used for its replication.

False

T/F The nuclear envelope is supported by a meshwork of lamin filaments outside the nuclear membranes.

False

T/F Action potentials are usually mediated by voltage-gated Ca2+ channels.

False -Action potentials are usually mediated by voltage-gated Na+ channels.

T/F Activated carrier molecules store heat energy for the cell to use later.

False -Activated carriers have high-energy bonds that can drive other reactions when broken. Heat may be released during these reactions and may increase the reaction rates but is not a form of energy that is stored in biological systems.

T/F When a mouse cell is fused with a human cell, the movement of the respective membrane proteins is restricted to their original locations at the time of fusion.

False -After about 1 hour, the mouse and human proteins present on the surface of the fused cell are found evenly dispersed throughout the plasma membrane.

T/F The driving force that pulls protons into the matrix is called the proton-motive force, which is a combination of the large force due to the pH gradient and the smaller force that results from the voltage gradient across the inner mitochondrial membrane.

False -Although it is true that both the pH gradient and the voltage gradient are components of the proton-motive force, it is the voltage gradient (also referred to as the membrane potential) that is the greater of the two.

T/F The only role of the carbohydrate layer on the cell surface is to absorb water, which creates a slimy surface and prevents cells from sticking to each other.

False -Although the absorption of water is an important role of the carbohydrates on the surface of the plasma membrane, a second critical role is that of cell-cell recognition, which is important in immune responses, wound healing, and other processes that rely on cell-type-specific interactions.

T/F The inner mitochondrial membrane is actually a series of discrete, flattened, membrane-enclosed compartments called cristae, similar to what is seen in the Golgi apparatus.

False -Although the cristae do look like individual compartments on the basis of the images of the inner structure of the mitochondria, the inner membrane is a single, albeit highly convoluted, membrane.

T/F A protein can be embedded on the cytosolic side of the membrane bilayer by employing a hydrophobic α helix.

False -An embedded protein employs an amphipathic helix. The hydrophobic side interacts with the fatty acid tails of the membrane lipids, and the hydrophilic portion interacts with the aqueous components of the cytosol.

T/F During glycolysis, glucose molecules are broken down to yield CO2 and H2O.

False -At the end of a series of the 10 different reactions involved in glycolysis, the final products are two molecules of pyruvate. Pyruvate will later be broken down into CO2 and H2O in the citric acid cycle.

T/F Cytosolic Ca2+ concentration is kept low by the use of chelators such as EDTA. (Calcium chelators bind free Ca2+).

False -Ca2+ concentration in the cytosol are kept low by the action of ATP-driven calcium pumps in the endoplasmic reticulum membrane and the plasma membrane.

T/F Catabolism is a general term that refers to the processes by which large molecules are synthesized from smaller molecules.

False -Catabolism comprises the metabolic reactions that are involved in breaking large molecules into smaller molecules. Anabolism encompasses the reverse types of reactions: synthesizing larger molecules from smaller molecules.

T/F Aquaporin channels are found in the plasma membrane and allow the rapid passage of water molecules and small ions in and out of cells.

False -Charged molecules (even protons, which are very small) are not able to pass through aquaporins.

T/F DNA replication origins are typically rich in G-C base pairs.

False -DNA replication origins are typically rich in A-T base pairs, which are held together by only two hydrogen bonds (instead of three for C-G base pairs), making it easier to separate the strands at these sites.

T/F Gap junctions are large pores that connect the cytosol to the extracellular space.

False -Gap junctions are used to connect the cytosol of adjacent cells, allowing the sharing of ions and small metabolites. Because gap junctions are large channels, if they were open while facing the extracellular environment, the ability of the plasma membrane to serve as a permeability barrier would be greatly reduced.

T/F The net negative charge on the cytosolic side of the membrane enhances the rate of glucose import into the cell by a uniporter.

False -Glucose is an uncharged molecule, and its import is not directly affected by the voltage differences across the membrane if glucose is being transported alone.

T/F Membrane proteins that pump ions in and out of the cell are classified as enzymes.

False -Membrane proteins that pump ions in either direction across the membrane are in the functional class of transporters.

T/F SDS is a mild detergent that is useful for the reconstitution of membrane components.

False -SDS is a strong, ionic detergent that will break up membrane bilayers and also denature proteins.

T/F The ion selectively of a channel depends solely on the charge of the amino acids lining the pore inside the channel.

False -Selectively depends on three parameters: the diameter, shape and charge of the ion trying to pass through the pore of the channel.

T/F FRAP is a method used to study the movement of individual proteins.

False -The FRAP method involves photobleaching of a small region of the membrane, which contains hundreds of target molecules, and follows the displacement of those molecules with neighboring molecules that have not been bleached.

T/F The dark reactions of photosynthesis occur only in the absence of light.

False -The dark reactions are those involved in carbon fixation and are named as such because they do not require light.

T/F The electron-transport proteins, utilized in stage 1 of photosynthesis, reside in the inner membrane of the chloroplast.

False -The electron-transport system in chloroplasts resides in the thylakoid membrane.

T/F Brown fat cells make less ATP because they have an inefficient ATP synthase.

False -The inner mitochondrial membranes in brown fat cells contain a transport protein that allows protons to move down their gradient without passing through the ATP synthase. As a result, less ATP is made and most of the energy from the proton gradient is released as heat.

T/F The inner mitochondrial membrane contains porins, which allow pyruvate to enter for use in the citric acid cycle.

False -The outer mitochondrial membrane contains porins, allowing the passage of all molecules with a mass of less than 5000 daltons. Although pyruvate must pass through the inner membrane, it does so in a highly regulated manner via specific transporter channels.

T/F The differences in permeability between artificial lipid bilayers and cell membranes arise from variations in phospholipid content.

False -The primary difference between cell membranes and artificial membranes is that cell membranes have proteins responsible for creating a selective permeability, which varies with the location and function of the membrane.

T/F Similar to oxidative phosphorylation, the electrons passed along the chloroplast electron-transport chain are ultimately passed on to a molecule of O2, to produce H2O.

False -The recipient of electrons is the chloroplast electron-transport chain is the NADP+ cofactor, which becomes reduced to NADPH.

T/F In order to study the activity of isolated transmembrane proteins, the membrane lipids must be completely stripped away.

False -The region of the protein that normally crosses the membrane must be stabilized by the presence of phospholipids for the purified protein to be active. For this reason, purified membrane proteins are often reconstituted into artificial lipid bilayers.

T/F The longest carbohydrates found on the surfaces of cells are linked to lipid molecules.

False -The very long, branched polysaccharides that are attached to integral membrane proteins are much longer than the oligosaccharides covalently attached to membrane lipids.

T/F Facilitated diffusion can be described as the favorable movement of one solute down its concentration gradient being coupled with the unfavorable movement of a second solute up its concentration gradient.

False -This describes coupled transport, which is one type of active transport. Facilitated diffusion can also be called passive transport, in which a solute always moves down its concentration gradient.

T/F Each round of the Calvin cycle uses five molecules of CO2 to produce one molecule of glyceraldehyde 3-phosphate and one of pyruvate.

False -Three molecules of CO2 are required for each round of the Calvin cycle, and the product is one molecule of glyceraldehyde 3-phosphate and the recycling of the ribulose 1,5-biphosphate molecule.

T/F Transporters are similar to channels except that they are larger, allowing folded proteins as well as smaller organic molecules to pass through them.

False -Transporters work by changing conformation after specific binding of the solute to be transported. Channels exclude molecules on the basis of size and charge, but do not depend on specific recognition of the molecules moving through.

T/F When subjected to anaerobic conditions, glycolysis in mammalian cells continue and causes a buildup of pyruvate in the cytosol.

False -Under anaerobic conditions, mammalian cells convert pyruvate to lactate in a fermentation process. The lactate is subsequently excreted from the cell.

T/F Voltage-gated K+ channels also open immediately in response to local depolarization, reducing the magnitude of the action potential.

False -Voltage-gated K+ channels respond more slowly than the voltage-gated Na+ channels. Because voltage-gated K+ channels do not open until the action potential reaches its peak, they do not affect its magnitude. Instead, they help to restore the local membrane potential quickly while the voltage-gated Na+ channels are in the inactivated conformation.

T/F The cleavage of fructose 1,6-biphosphate yields two molecules of glyceraldehyde 3-phosphate.

False -When fructose 1,6-biphosphate is cleaved, the products are dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Only after the subsequent isomerization of dihydroxyacetone phosphate is the second molecule of glyceraldehyde 3-phosphate produced.

T/F The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete.

False -although the sliding clamp is only loaded once on the leading strand, the lagging strand needs to unload the clamp once the polymerase reaches the RNA primer from the previous segment and then reload it where a new primer has been synthesized.

T/F Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.

False -primase does not have a proofreading function, nor does it need one because the RNA primers are not a permanent part of the DNA. The primers are removed an a DNA polymerase that does have a proofreading function fills in the remaining gaps.

T/F The repair polymerase is the enzyme that proofreads the newly synthesized strands to ensure the accuracy of DNA replication.

False -the repair polymerase is used to fill in the spaces left vacant after the RNA primers are degraded.

T/F There is a single enzyme that degrades the RNA primers and lays down the corresponding DNA sequence behind it.

False -this is a two-step process that requires two different enzymes. First, a nuclease removes the RNA primers. Then, the repair polymerase fills in the complementary DNA sequence.

T/F Lipid-linked proteins are classified as peripheral membrane proteins because the polypeptide chain does not pass through the bilayer.

False. -Lipid-linked proteins are classified as integral membrane proteins because although they are not transmembrane proteins, they are covalently bound to membrane lipids and cannot be dissociated without disrupting the membrane's integrity.

T/F When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate.

False. -the two strands do need to separate for replication to occur, but this is accomplished by the binding of initiator proteins at the origin of replication

Based on what you know about β oxidation, which is the process by which fatty acids are converted to acetyl-CoA, which would you expect to find most commonly in your cells?

Fatty acids with an even number of carbon atoms

Based upon what you know about metabolism, explain how electrons are stripped from food molecules and used to drive the electron-transport chain.

Food molecules are ultimately converted into acetyl CoA. Electrons removed during the generation of acetyl CoA are added to the cofactor NAD+ to generate the reduced cofactor NADH. The two carbon atoms in the acetyl group of acetyl CoA are then fed into the citric acid cycle, where they are oxidized to two molecules of CO2. The electrons removed during this oxidation are captured by the activated carriers NADH and FADH2. The high-energy electrons in all of these activated carriers, which are derived from carbons that were formerly part of food molecules, are now transferred to the proteins in the electron-transport chain.

Which of the following statements about RNA splicing is NOT true?

For a gene to be expressed properly, every exon must be removed from the pre-mRNA produced from that gene.

Which of the following statements about RNA splicing is false?

For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene.

Important for the growth of straight, unbranched actin filaments.

Formins

DNA helicase

All receptors of this class are polypeptides with seven transmembrane domains.

G-protein-coupled receptors

____-tubulin is found at the shrinkage ends of microtubules.

GDP

When unstimulated, the α subunit is bound to ____, which is exchanged for ____ on stimulation.

GDP; GTP

____ proteins can act as molecular switches, letting a cell know that a signal has been received.

GTP-binding

In a growing microtubule, the addition of ____-bound tubulin hereodimers to the GTP cap is ____ than the rate of GTP hydrolysis in the GTP cap.

GTP; faster

The intrinsic ____ activity of the α subunit is important for inactivating the G protein.

GTPase

We can test the relative permeability of a phospholipid bilayer by using a synthetic membrane that does not contain any protein components. Some uncharged, polar molecules are found to diffuse freely across these membranes, to varying degrees. Which of the following has the lowest rate of diffusion across an artificial membrane?

Glucose

A researcher is interested in uncovering mechanisms of synaptic transmission between two neurons. To do this, she is studying neurons cultured from embryonic mouse brain neural cells. The researcher is interested in several aspects of neurotransmission between neurons, but is particularly focused on the role of the synapse in transmitting neuronal signals. Using the cultured system, she is able to examine individual pairs of neurons that communicate through chemical synapses and modify different aspects of the synaptic environment. She can decrease the extracellular concentration of various ions and observe how this affects neurotransmitter release and target cell behavior. She can also apply a toxin that prevents synaptic vesicles from fusing with the presynaptic membrane of axon terminals. Prior to these manipulations, the researcher does a control experiment with two neurons where she stimulates the presynaptic neuron to fire an action potential and measures the response of the postsynaptic neuron. Consistently, the postsynaptic neuron depolarizes and propagates an excitatory potential. Which neurotransmitter is most likely released based on the results of the control experiment described in the passage?

Glutamate

Which of the following gated ion channels are involved in inhibitory synaptic signaling?

Glycine-gated Cl- channels

Which of the following processes do not take place in the mitochondria?

Glycogen breakdown

What catabolic process uses substrate-level phosphorylation, and how many ATP molecules are generated in this way in the reaction pathway?

Glycolysis uses substrate-level phosphorylation and generates two ATP molecules for each glucose molecule oxidized to pyruvate molecules (four total ATPs, but two of these are hydrolyzed in the first few steps of the pathway).

The ____ has a cis and trans face and receives proteins and lipids from the ____, a system of interconnected sacs and tubes of membranes that typically extends through the cell.

Golgi apparatus; endoplasmic reticulum

Describe the process by which gut epithelial cells use transporters to take up ingested glucose (against the concentration gradient) and to distribute glucose to other tissues by moving it back out of the cell (down the concentration gradient).

Gut epithelial cells use two different transporters to take glucose up from the gut and distribute it into the bloodstream and to other tissues. These transporters are located at opposite sides of the cell: the apical side of the cell (which faces the gut) contains a Na+-glucose symporter. This symporter couples the entry of Na+ down its electrochemical gradient to the active import of glucose against its concentration gradient. The Na+-glucose symporter is restricted to the apical side of the cell by tight-junction complexes in the plasma membrane, which link neighboring epithelial cells together. On the basolateral side of the cell, there is another transporter that facilitates movement of glucose down its concentration gradient, out of the cell. This transporter is a uniporter that transports glucose from the cytosol to the extracellular matrix (although transport from the extracellular matrix to the cytosol will occur if the concentration of glucose in the extracellular matrix is higher than that of the cytosol). The location of this uniporter is also restricted by the presence of the tight junctions, so that the epithelial cell will not transport glucose back into the lumen of the gut.

Match each equation with the corresponding standard redox potential. -H2O ↔ ½O2 + 2H+ + 2 e- -reduced ubiquinone ↔ oxidized ubiquinone + 2H+ + 2 e- -NADH ↔ NAD+ + H+ + 2 e- -reduced cytochrome c ↔ oxidized cytochrome c + e-

H2O ↔ ½O2 + 2H+ + 2 e- = +30 mV reduced ubiquinone ↔ oxidized ubiquinone + 2H+ + 2 e- = +820 mV NADH ↔ NAD+ + H+ + 2 e- = +230 mV reduced cytochrome c ↔ oxidized cytochrome c + e- = -320 mV

When an electron moves from the reaction center to photosystem II, it leaves behind a positively charged special pair which must be reduced for photosynthesis to continue. The missing electron is replaced by an electron removed from ____. This process results in the release of ____ into the atmosphere.

H2O; O2

When adrenaline binds to adrenergic receptors on the surface of a muscle cell, it activates a G protein, initiating an intracellular signaling pathway in which the activated α subunit activates adenylyl cyclase, thereby increasing cAMP levels in the cell. The cAMP molecules then activate a cAMP-dependent kinase (PKA) that, in turn, activates enzymes that result in the breakdown of muscle glycogen, thus lowering glycogen levels. You obtain muscle cells that are defective in various components of the signaling pathway. Referring to Figure Q16-36, indicate how glycogen levels would be affected in the presence of adrenaline in the following cells. Would they be higher or lower than in normal cells treated with adrenaline? Cells that lack adenylyl cyclase

Higher

Which 3' functional group must be free in order to add the next nucleotide during DNA synthesis?

Hydroxyl

Why would it not be advantageous for living systems to evolve a mechanism for the direct transfer of electrons from NADH to O2?

If NADH directly donated electrons to O2, a large amount of energy would be released as heat and lost, rather than used as a way for the cell to generate chemical energy in the form of ATP.

You are curious about the dynamic instability of microtubules and decide to join a lab that works on microtubule polymerization. The people in the lab help you grow some microtubules in culture using conditions that allow you to watch individual microtubules under a microscope. You can see the microtubules growing and shrinking, as you expect. The professor who runs the lab gets in a new piece of equipment, a very fine laser beam that can be used to sever microtubules. She is very excited and wants to sever growing microtubules at their middle, using the laser beam. What do you expect would happen to the newly exposed plus ends if you were to grow the microtubules in the presence of an analog of GTP that cannot be hydrolyzed, and you then severed the microtubules in the middle with a laser beam?

If you were to polymerize the microtubules in the presence of a nonhydrolyzable analog of GTP and you then severed the microtubules with a laser, the newly exposed plus end would contain a GTP cap and so would probably continue to grow.

Which of the following statements is NOT true?

In a eukaryotic mRNA, the poly A tail promotes degradation of the molecule.

Which of the following statements about membrane-enclosed organelles is true?

In a typical cell, the area of the endoplasmic reticulum membrane far exceeds the area of plasma membrane.

Explain how scientists used artificial vesicles to prove that the generation of ATP by the ATP synthase was not powered by a single high-energy intermediate but rather by a proton gradient. Be sure to describe the two experiments that were negative controls (no ATP generated), the positive control (ATP generated as expected), and a fourth experiment proving that the gradient is the required energy source.

In all the experiments, artificial liposomes were generated and exposed to light, and the surrounding solution was checked for an increase in ATP. In the first experiment, the liposomal membranes contained only bacteriorhodopsin, a bacterial protein that pumps protons and is activated by light. In this negative control, ATP was not expected to be produced, and it was not. In the second experiment, also a negative control, the liposomes contained only ATP synthase. Again, if the chemiosmotic hypothesis was correct, ATP should not have been generated, which was what was observed. In the third experiment, both bacteriorhodopsin and ATP synthase were present in the liposomal membrane. When exposed to light, protons were pumped into the vesicle and ATP was generated. In the fourth experiment, to show that the ATP production was solely a result of the proton gradient, an uncoupling agent was added to the solution containing liposomes with bacteriorhodopsin and ATP synthase. In this case, even though the protons were being pumped into the liposomes, a gradient did not build up; this was because of the presence of the uncoupling agent, which made the membrane permeable to protons. No ATP was generated, proving that it was the proton gradient that was the energy source for ATP synthesis.

Where are proteins in the chloroplast synthesized?

In both the cytosol and the chloroplast

Intermediate filaments help protect animal cells from mechanical stress because the filaments ____.

In each cell are indirectly connected to the filaments of a neighboring cell through the desmosome, creating a continuous mechanical link between cells.

How does the generation of ATP by oxidative phosphorylation differ from ATP generation by substrate-level phosphorylation?

In oxidative phosphorylation, molecular oxygen is required to produce ATP, by means of a multistage, chemiosmotic process (see Chapter 14), while in substrate-level phosphorylation, the energy released by the enzyme-catalyzed oxidation of a substrate generates ATP directly.

Akt promotes the survival of many cells by affecting the activity of Bad and Bcl2, as diagrammed in Figure Q16-58. Which of the following statements is false?

In the absence of a survival signal, Bad is phosphorylated.

Some bacteria can live both aerobically and anaerobically. How does the ATP synthase in the plasma membrane of the bacterium help such bacteria to keep functioning in the absence of oxygen?

In the absence of oxygen, the respiratory chain no longer pumps protons, and thus no proton electrochemical gradient is generated across the bacterial membrane. In these conditions, the ATP synthase uses some of the ATP generated by glycolysis in the cytosol to pump protons out of the bacterium, thus forming the proton gradient across the membrane that the bacterium requires for importing vital nutrients by coupled transport.

In which cellular location would you expect to find ribosomes translating mRNAs that encode ribosomal proteins?

In the cytosol

Where does most new membrane synthesis take place in a eukaryotic cell?

In the endoplasmic reticulum

Provide a brief description of the process by which the body derives energy from food. Include in your description the three stages of catalysis, and delineate the input and output that connect each stage.

In the first stage of catabolism, polymers are broken down into smaller subunits in the digestive system, which stretches from the mouth to the gut. Proteins are converted to amino acids, fats to fatty acids and glycerol, and carbohydrates simple sugars, including the monosaccharide glucose. In the second stage of catabolism, these simple subunits are further broken down to generate the activated carrier acetyl CoA. Acetyl CoA is the molecular input for the third stage of metabolism. In the last stage of catabolism, the acetyl CoA is oxidized to CO2, coupled to the production of large amounts of ATP, which is used as chemical energy for the cell.

In an animal cell, where are the proteins of the electron-transport chain located?

In the inner mitochondrial membrane

Where in the cell does Ran-GTP bind to nuclear import receptors?

In the nucleus

A hungry yeast cell lands in a vat of grape juice and begins to feast on the sugars there, producing carbon dioxide and ethanol in the process: C6H12O6 + 2ADP + 2Pi + H+ 2CO2 + 2CH3CH2OH + 2ATP + 2H2O Unfortunately, the grape juice is contaminated with proteases that attack some of the transport proteins in the yeast cell membrane, and the yeast cell dies. Which of the following could account for the yeast cell's demise?

Inability to import sugar into the cell.

Pertussis toxin acts by:

Inactivating Gi, which leads to increased adenylyl cyclase activity.

Increase. Cholera toxin inhibits the GTPase activity of the Gα subunit, keeping the subunit in an active state for a longer time.

Which of the following is NOT true?

Inhibition of oxidative phosphorylation will not affect the citric acid cycle.

You decide to use different bacterial strains (each having one protein of the replication machinery mutated) in order to examine the role of individual proteins in the normal process of DNA replication. What part of the DNA replication process would be most directly affected if a strain of bacteria lacking primase were used to make the cell extracts?

Initiation of DNA synthesis

A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but fails to replicate with the yeast DNA. Where do you think the block to replication arises? Choose the protein or protein complex below that is most probably responsible for the failure to replicate bacterial DNA. Give an explanation for your answer.

Initiator proteins

Involvement in focal contacts.

Integrins

Can be connected through desmosomes.

Intermediate filaments

Includes keratin and neurofilaments.

Intermediate filaments

Supports and strengthens the nuclear envelope.

Intermediate filaments

Ricin is one of the most toxic substances known: less than 2 mg injected into the bloodstream will kill an adult human. Ricin is produced by the castor bean plant as a 65 kilodalton protein heterodimer composed of an A chain and a B chain. The B chain is a lectin that binds to carbohydrates on the cell surface. The A chain is an enzyme that modifies a highly conserved site in rRNA, leading to inhibition of translation. After entering the cell, ricin eventually ends up in the lumen of the endoplasmic reticulum (ER), and from there it moves into the cytosol, where it inactivates ribosomes. What is the most likely mechanism by which ricin enters the cell?

Internalization via endocytosis

Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why?

Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus.

You discover a fungus that contains a strange star-shaped organelle not found in any other eukaryotic cell you have seen. On further investigation, you find the following. i. The organelle is surrounded by a single membrane. ii. Vesicles pinch off from the organelle membrane. iii. The organelle does not contain DNA. How might this organelle have arisen?

Invagination of the plasma membrane in an ancient prokaryotic cell.

Changes in membrane potential.

Ion channels

Alter the membrane potential directly by changing the permeability of the plasma membrane.

Ion-channel-coupled receptors

Which of the following statements is true?

Ion-channel-coupled receptors can rapidly alter the membrane potential in response to signal binding.

For a voltage-gated channel, a change in the membrane potential can have what effect on the channel?

It alters the probability that the channel will be found in its open conformation.

If Na+ channels are opened in a cell that was previously at rest, how will the resting membrane potential be affected?

It becomes more positive

Many antibiotics work by inhibiting bacterial protein synthesis. Investigators have isolated a promising new compound and wish to determine its mechanism of action. Using a cell-free translation system similar to the ones originally used to deduce the genetic code, the researchers incubate their drug with the synthetic polynucleotide 5'-AUGUUUUUUUUU. In the absence of the drug, this polynucleotide directs the synthesis of the peptide Met-Phe-Phe-Phe. When the drug is added, only the peptide Met-Phe is produced. Based on this observation, which is most likely the mechanism of action of this potential new antibiotic?

It blocks translocation of the large ribosomal subunit, preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome.

Which of the following statements is not true about the possible fates of glyceraldehyde 3-phosphate?

It can be transported into the thylakoid space for use as a secondary electron acceptor downstream of the electron-transport chain.

Which of the following statements describes the mitochondrial matrix?

It contains enzymes required for the oxidation of fatty acids.

Which of the following statements describes the mitochondrial intermembrane space?

It contains proteins that are released during apoptosis.

Which of the following statements describes the mitochondrial inner membrane?

It contains transporters for ATP molecules.

Which is NOT true of the carbon-fixation (Calvin) cycle?

It directly requires oxygen.

Sanshool is a natural compound found in Sichuan pepper, which is commonly used in making spicy Asian food, and creates a numbing sensation in the mouth. It is known to inhibit a subset of potassium leak channels involved in maintaining the resting membrane potential in sensory neurons. How do you think sanshool affects these sensory neurons?

It elevates the resting membrane potential to less negative values and make it easier to excite the neuron.

Which of the following describes the structure of an actin filament?

It is a twisted chain of actin monomer.

What is the role of the nuclear localization sequence in a nuclear protein?

It is bound by cytoplasmic proteins that direct the nuclear protein to the nuclear pore.

What is the role of a nuclear import signal in a protein?

It is bound by cytoplasmic proteins that direct the protein to the nuclear pore and through it.

Which of the following statements describes the mitochondrial outer membrane?

It is permeable to molecules with molecular mass as high as 5000 daltons.

Which of the following explains what happens to oxygen produced by the light-dependent reactions?

It is released into the atmosphere.

RNA in cells differs from DNA in that ____.

It is single-stranded and can fold up into a variety of structures.

Which of the following best describes the behavior of a gated channel?

It opens more frequently in response to a given stimulus.

When the drug nigericin is added to mitochondria, their inner membranes become permeable to K+. How does this affect the electrochemical proton gradient?

It reduces the membrane potential but does not affect the pH gradient.

Which of the following statements about the newly synthesized strand of a human chromosome is true?

It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.

You have discovered an "Exo-" mutant form of DNA polymerase in which the 3′-to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have?

It will be more likely to generate mismatched pairs.

Cells use membranes to help maintain set ranges of ion concentrations inside and outside the cell. Which of the following ions is the most abundant inside a typical mammalian cell?

K+

Which of the following statements is true?

K+ is the most plentiful positively charged ion inside the cell, which Na+ is the most plentiful outside

Active transport requires the input of energy into a system so as to move solutes against their electrochemical and concentration gradients. Which of the following is NOT one of the common ways to perform active transport?

K+-coupled

Active transport requires the input of energy into a system so as to move solutes against their electrochemical and concentration gradients. Which of the following is not one of the common ways to perform active transport?

K+-coupled

____ leak channels are necessary to establishing a non-zero resting membrane potential. Concerning the movement of ions through these channels, the concentration gradient and voltage gradient work in ____.

K+; opposite directions

As a cell grows, which microtubule-associated protein pulls the ER membrane outward, stretching it like a net?

Kinesin

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking DNA ligase were used to make the cell extracts?

Lagging-strand completion

The 3rd reading frame of the RNA sequence 5'-AUUUGCCUCAGGGC-3' encodes which polypeptide?

Leu-Pro-Gln-Gly

Lower

Membrane channels and transporters are types of proteins that can let ions pass through the membrane, but the rate of this movement may vary depending on the type of protein. Which one of the following has a faster rate of ion transport?

Membrane channels

Which of the following statements is true?

Membrane lipids diffuse within the plane of the membrane.

Which of the following statements is NOT true?

Membrane lipids frequently flip-flop between their own monolayer and the other monolayer.

Although membrane proteins contribute roughly 50% of the total mass of the membrane, there are about 50 times more lipid molecules than there are protein molecules in cellular membranes. Explain this apparent discrepancy.

Membrane proteins are much larger molecules than the membrane lipids. Thus, fewer are required to represent the same total mass contributed by the lipid components of the membrane. By this estimation, the molecular weight of the average membrane protein is 50 times that of the average membrane lipid.

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine and added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs?

Methionine would be incorporated into proteins at some positions where leucine should be.

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine, and added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs?

Methionine would be incorporated into proteins at some positions where leucine should be.

A component of the mitotic spindle.

Microtubules

Their stability involves a GTP cap.

Microtubules

Used in the eukaryotic flagellum.

Microtubules

Which of the following statements about the function of the centrosome is false?

Microtubules emanating from the centrosome have alternating polarity such that some have their plus end attached to the centrosome while others have their minus end attached to the centrosome.

It is nucleated at the centrosome.

Microtubules of the mitotic spindle

Which of the following statements about the proteasome is false?

Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold.

Which of the following is NOT part of the endomembrane system?

Mitochondria

Which of the following statements about mitochondrial division is true?

Mitochondrial division is mechanistically similar to prokaryotic cell division.

The stimulation of a motor neuron ultimately results in the release of a neurotransmitter at the synapse between the neuron and a muscle cell. How is the chemical signal converted into an electrical signal in the postsynaptic muscle cell?

Most neurotransmitter receptors function as ligand-gated ion channels. These ion channels are similar to voltage-gated channels, except that they do not open in response to a change in voltage across the membrane, but to the binding of a neurotransmitter. In the neuromuscular junction, the neurotransmitter acetylcholine binds to the acetylcholine receptor, which allows Na+ to enter the muscle cell, altering its membrane potential. In this way, a chemical signal (acetylcholine) is converted back into an electrical signal (change in membrane potential).

When cells enter mitosis, their existing array of cytoplasmic microtubules has to be rapidly broken down and replaced with the mitotic spindle that forms to pull the chromosomes into the daughter cells. The enzyme katanin, named after Japanese samurai swords, is activated during the onset of mitosis and chops microtubules into short pieces. What do you suppose is the fate of the microtubule fragments created by katanin?

Most of the fragments depolymerize because both of their ends are composed of GDP-tubulin.

Which of the following statements about microtubules is true?

Motor proteins move in a directional fashion along microtubules by using the inherent structural polarity of a protofilament.

You discover a protein, MtA, and find that it binds to the plus ends of microtubules in cells. The hypothesis that best explains this localization is ____.

MtA binds to GTP-bound tubulin on microtubules.

Contracting the rear of the cell.

Myosin

Your friend works in a biotech company that has just discovered a drug that seems to promote lamellipodia formation in cells. Which of the following molecules is unlikely to be involved in the pathway that this drug affects?

Myosin

NADH contains a high-energy bond that, when cleaved, donates a pair of electrons to the electron-transport chain. What are the immediate products of this bond cleavage?

NAD+ + H+

____ produced in the citric acid cycle donates electrons to the electron-transport chain.

NADH

Anaerobically growing yeast further metabolizes the pyruvate produced by glycolysis to CO2 and ethanol as part of a series of fermentation reactions. What other important reaction occurs during this fermentation step?

NADH --> NAD+

NADH and FADH2 carry high-energy electrons that are used to power the production of ATP in the mitochondria. These cofactors are generated during glycolysis, the citric acid cycle, and the fatty acid oxidation cycle. Which molecule below can produce the most ATP?

NADH from the citric acid cycle

NADH and FADH2 carry high-energy electrons that are used to power the production of ATP in the mitochondria. These cofactors are generated during glycolysis in the cytosol and during the citric acid cycle and the fatty acid oxidation cycle (β oxidation) in the mitochondrial matrix. Which molecule below can produce the most ATP?

NADH from the fatty acid cycle (β oxidation)

It requires an electron-transport chain that operates on the high-energy electrons taken from the activated carrier molecules ____ and ____ that are produced by glycolysis and the citric acid cycle.

NADH; FADH2

Thus, oxidative phosphorylation refers to the oxidation of ____ and ____ molecules and the phosphorylation of ____.

NADH; FADH2; ADP

Stage 2 of photosynthesis, sometimes referred to as the dark reactions, involves the reduction of CO2 to produce organic compounds such as sucrose. What cofactor is the electron donor for carbon fixation?

NADPH

The light reactions of photosynthesis generate ATP and ____ that are in turn used ____.

NADPH; for carbon fixation

Cells use membranes to help maintain set ranges of ion concentrations inside and outside the cell. Which of the following ions is the most abundant outside a typical mammalian cell?

Na+

Cells make use of H+ electrochemical gradients in many ways. Which of the following proton transporters is used to regulate pH in animal cells?

Na+-H+ exchanger

It is involved in sperm mobility.

Neither microtubule of mitotic spindle nor ciliary microtubules.

The monomer is sequestered by profilin.

Neither microtubules of the mitotic spindle nor ciliary microtubules.

You know that: i. The signal-recognition-particle (SRP) is involved in protein import into the endoplasmic reticulum (ER). ii. ER proteins carry an ER-specific signal sequence. Does SRP itself have an ER-specific signal sequence?

Glycolysis is an anaerobic process used to catabolize glucose. What does it mean for this process to be anaerobic?

No oxygen is required

Thermal motion promotes lateral position exchanges between lipid molecules within a monolayer. In an artificial bilayer, this movement has been estimated to be ~2 μm/second. This represents the entire length of a bacterial cell. Do you expect the lateral movement of a lipid molecule within a biological membrane to be equally fast? Explain your answer.

No. Although the rate of movement may be similar, it will most likely be slower in a biological membrane. An artificial bilayer is primarily phospholipids. Biological membranes contain a large number of protein components and specialized membrane domains that could limit the rate of lateral diffusion.

Indicate by writing "yes" or "no" whether amplification of a signal could occur at the particular steps described below. Explain your answers. An extracellular signaling molecule binds and activates a GPCR.

No. Each signaling molecule activates only one receptor molecule.

Indicate by writing "yes" or "no" whether amplification of a signal could occur at the particular steps described below. Explain your answers. cAMP activates protein kinase A.

No. In unstimulated cells, protein kinase A is held inactive in a protein complex. Binding of cAMP to the complex induces a conformational change, releasing the active protein kinase A. Therefore, one cAMP cannot activate more than one molecule of protein kinase A.

Two protein kinases, PK1 and PK2, work sequentially in an intracellular signaling pathway. You create cells that contain inactivating mutations in the genes that encode either PK1 or PK2 and find that these cells no longer respond to a particular extracellular signal. You also create cells containing a version of PK1 that is permanently active and find that the cells behave as though they are receiving the signal even when the signal is not present. When you introduce the permanently active version of PK1 into cells that have an inactivating mutation in PK2, you find that these cells also behave as though they are receiving the signal even when no signal is present. From these results, does PK1 activate PK2, or does PK2 activate PK1?

Normally, PK2 activates PK1. We are told that PK1 and PK2 normally work sequentially in an intracellular signaling pathway. If PK1 is permanently activated, a response is seen independently of whether or not PK2 is present. If PK1 activated PK2, no response should be seen if PK1 were activated in the absence of PK2.

If a lysosome breaks open, what happens?

Not much will happen because the lysosomal hydrolases will not be very active.

Which of the following methods is not used by cells to regulate the amount of a protein in the cell?

Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

Which of the following statements about nuclear transport is true?

Nuclear pores have water-filled passages that small, water-soluble molecules can pass through in a nonselective fashion.

Your friend works in a biotechnology company and has discovered a drug that blocks the ability of Ran to exchange GDP for GTP. What is the most likely effect of this drug on nuclear transport.

Nuclear transport receptors would be unable to release their cargo in the nucleus.

In oxidative phosphorylation, ATP production is coupled to the events in the electron-transport chain. What is accomplished in the final electron-transfer event in the electron-transport chain?

O2 is reduced to H2O

Stage 1 of oxidative phosphorylation requires the movement of electrons along the electron-transport chain coupled to the pumping of protons into the intermembrane space. What is the final result of these electron transfers?

O2 is reduced to H2O

What is the final result of the electron transfers in oxidative phosphorylation?

O2 is reduced to H2O.

The endothelial cells found closest to the site of an infection express proteins called lectins. Each lectin binds to a particular ____ that is presented on the surface of a target cell.

Oligosaccharide

You are interested in Fuzzy, a soluble protein that functions within the ER lumen. Given that information, which of the following statements must be true?

Once the signal sequence from Fuzzy has been cleaved, the signal peptide will be ejected into the ER membrane and degraded.

Mitochondrial structure and the reaction products generated inside the matrix are critical for generating stores of energy. Answer the following questions based on what you know about mitochondrial structure and processes. The proton-motive force created by the electrochemical proton gradient is the source of free energy utilized in ATP formation. Describe the two components contributing to the total proton-motive force.

One component of the proton-motive force is the concentration gradient of protons (or pH gradient) across the membrane. This pH gradient makes it energetically favorable for protons to flow back into the matrix. A second component of the proton-motive force is a charge differential across the membrane, referred to as the membrane potential. Because the matrix side of the membrane has a net negative charge, and protons have a positive charge, this component of the proton-motive force also drives the movement of protons back into the matrix.

Steroid hormones such as testosterone and estrogen act on target cells by passing directly through the cell membrane. If steroid hormones can enter any cell, how do they only produce an effect in target cells?

Only target cells possess the proper intracellular receptor.

Which of the following statements about organellar movement in the cell is false?

Only the microtubule cytoskeleton is involved in organellar movement.

Which of the following stages in the breakdown of the piece of toast you had for breakfast generates the most ATP?

Oxidative phosphorylation

Where does oxidative phosphorylation take place, and what other processes are required for this to occur?

Oxidative phosphorylation takes place in mitochondria as part of a multistage oxidation process. First, the citric acid cycle generates NADH and FADH2, which donate their high-energy electrons to the electron-transport chain. These electrons ultimately reduce molecular oxygen to water, and the energy of their oxidation is used to pump protons across a membrane. The proton gradient thereby produced is in turn harnessed by the enzyme ATP synthase to drive the production of ATP from ADP and inorganic phosphate.

____ acts as the final electron acceptor in the electron-transport chain.

Oxygen

During the chain elongation process of translating an mRNA into protein, the growing polypeptide chain attached to a tRNA is bound to the ____ site of the ribosome.

When a cell releases a signal molecule into the environment and a number of cells in the immediate vicinity respond, this type of signaling is:

Paracrine signaling

____ membrane proteins are linked to the membrane through noncovalent interactions with other membrane-bound proteins.

Peripheral

You are viewing a sample of pond water under the microscope. The sample contains a variety of microorganisms, some moving faster than others. You spot a Paramecium that is being followed by a Didinium almost as large as itself; the Paramecium initially swims away and tries to escape, but Didinium, which moves in faster bursts, finally stops it and attaches firmly onto the side of the Paramecium and begins to eat it. What type of endocytosis will ensue?

Phagocytosis

Which of the following statements about phagocytic cells in animals is false?

Phagocytosis cells are important in the gut to take up large particles of food.

The 2nd reading frame of the RNA sequence 5'-AUUUGCCUCAGGGC-3' encodes which polypeptide?

Phe-Ala-Ser-Gly

Which of the following statements about molecular switches is false?

Phosphatases remove the phosphate from GTP on GTP-binding proteins, turning them off.

Cleavage of inositol phospholipids.

Phospholipase C

Which type of lipids are the most abundant in the plasma membrane?

Phospholipids

In an activated receptor tyrosine kinase (RTK) signaling pathway, multiple signaling proteins bind to ____ in the ____ domain of the RTK.

Phosphorylated tyrosines; cytoplasmic

When an electron moves from the reaction center of photosystem I, it leaves behind a positively charged special pair which must be reduced for photosynthesis to continue. The missing electron is donated by:

Plastocyanin

If you add a compound to illuminated chloroplasts that inhibits the NADP+ reductase, NADPH generation ceases, as expected. However, ferredoxin does not accumulate in the reduced form because it is able to donate its electrons not only to NADP+ (via NADP+ reductase) but also back to the cytochrome b6-f complex. Thus, in the presence of the compound, a "cyclic" form of photosynthesis occurs in which electrons flow in a circle from ferredoxin, to the cytochrome b6-f complex, to plastocyanin, to photosystem I, to ferredoxin. What will happen if you now also inhibit photosystem II?

Plastoquinone will accumulate in the oxidized form.

In which of the four compartments of a mitochondrion are each of the following located? -Porin -The mitochondrial genome -Citric acid cycle enzymes -Proteins of the electron-transport chain -ATP synthase -Membrane transport protein for pyruvate

Porin = the outer membrane Mitochondrial genome = matrix Citric acid cycle enzymes = matrix Proteins of the electron-transport chain = inner membrane ATP synthase = inner membrane Membrane transport protein for pyruvate = inner membrane

Glycolysis and the citric acid cycle comprise two different sets of oxidation reactions. The reaction sequence for glycolysis is linear, whereas the reaction sequence for the citric acid cycle forms a circle. How does this difference in the arrangement of reactions influence the rate of these processes when an excess amount of a single intermediate is added?

Primarily, what is seen is that the citric acid cycle occurs more rapidly after the addition of any one of the intermediates. This means that if one intermediate is added, levels of all of them increase. In glycolysis, only the intermediates downstream of the intermediate being added will be affected.

Which of the following is NOT true?

Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.

A bacterium is suddenly expelled from a warm human intestine into the cold world outside. Which of the following adjustments might the bacterium make to maintain the same level of membrane fluidity?

Produce lipids with hydrocarbon tails that are shorter and have more double bonds.

Regulation of the availability of actin monomers.

Profilin

To begin transcription, RNA polymerase recognizes nucleotide sequences in what region of the DNA?

Promoter region

Concerning bacterial transcription, which of the following is true?

Promoters orient the RNA polymerase and determine the direction of transcription.

Which of the following statements about the proteasome is NOT true?

Proteases reside on the external surface of a proteasome.

Protein kinases have a binding site for ATP, which is the source of the phosphate used for phosphorylating their target proteins; if the kinase cannot bind ATP, it will be inactive.

Which of the following statements is true?

Proteins destined for the ER are translated by cytosolic ribosomes and are targeted to the ER when a signal sequence emerges during translation.

Which of the following statements about the protein quality control system in the ER is NOT true?

Proteins that are misfolded are degraded in the ER lumen.

Which of the following statements about the protein quality control system in the ER is false?

Proteins that are misfolded are degraded in the ER lumen.

Which of the following statements about the endoplasmic reticulum (ER) is false?

Proteins to be delivered to the ER lumen are synthesized on smooth ER.

Mitochondria and peroxisomes do NOT have what in common?

Proteins translated in the cytosol are imported into them in an unfolded state.

Explain how the F0 complex of ATP synthase harnesses the proton-motive force to help synthesize ATP. What would happen if the proton gradient were reversed?

Protons flow through a channel that exists between the subunits of the transmembrane H+ carrier, which forms a ring (the rotor). The flow of protons through this carrier makes the rotor and its attached stalk rotate. As the stalk rotates, it rubs against proteins in the stationary F1 portion of the ATP synthase. The resulting mechanical deformation produces a conformational change in the subunits of the F1 ATPase that causes them to produce ATP. When the proton gradient is reversed, the F1 portion of the ATP synthase catalyzes the hydrolysis of ATP to ADP and Pi, rather than the reverse reaction of ATP synthesis; this causes protons to be pumped out of the matrix against their electrochemical gradient, as the rotor and its stalk rotate in the direction opposite to that involved in ATP synthesis.

____ from the mitochondrial ____ flow(s) through the rotor of ATP synthase and cause it to spin, which in turn alters the conformation of the ATP synthase head and prompts it to produce ____.

Protons; intermembrane space; ATP

In cells that cannot carry out fermentation, which products derived from glycolysis would accumulate under anaerobic conditions?

Pyruvate and NADH

The lab you work in has discovered a previously unidentified extracellular signal molecule called QGF, a 75,000-dalton protein. You add purified QGF to different types of cells to determine its effect on these cells. When you add QGF to heart muscle cells, you observe an increase in cell contraction. When you add it to fibroblasts, they undergo cell division. When you add it to nerve cells, they die. When you add it to glial cells, you do not see any effect on cell division or survival. Given these observations, which of the following statements is most likely to be true?

QGF activates different intracellular signaling pathways in heart muscle cells, fibroblasts, and nerve cells to produce the different responses observed.

Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because ____.

RNA is single-stranded

Transcription in bacteria differs from transcription in a eukaryotic cell because ____.

RNA polymerase (along with its sigma subunit) can initiate transcription on its own.

Transcription in bacteria differs from transcription in a eukaryotic cell because:

RNA polymerase (along with its sigma subunit) can initiate transcription on its own.

There are multiple RNA polymerases in a typical eukaryotic cell. Among them, ____ is directly involved in expressing protein-producing genes.

RNA polymerase II

mRNAs are synthesized by:

RNA polymerase II

Which of the following is NOT true of eukaryotic transcription initiation?

RNA polymerase binds the TATA box prior to TFIID and TFIIB.

Cell lines A and B both survive in tissue culture containing serum but do not proliferate. Factor F is known to stimulate proliferation in cell line A. Cell line A produces a receptor protein (R) that cell line B does not produce. To test the role of receptor R, you introduce this receptor protein into cell line B, using recombinant DNA techniques. You then test all of your various cell lines in the presence of serum for their response to factor F, with the results summarized in Table Q16-1.

Receptor R binds to factor F to induce cell proliferation in cell line A.

Given the generic signaling pathway in Figure Q16-12, write the number corresponding to the item on the line next to the descriptor below. -Recptor protein -Effector proteins -Intracellular signaling proteins -Ligand

Receptor protein = 2 Effector proteins = 4 Intracellular signaling proteins = 3 Ligand = 1

Which of the following would be inhibited by a drug that specifically blocks the addition of phosphate groups to proteins?

Receptor tyrosine kinase activity

Cell movement involves the coordination of many events in the cell. Which of the following phenomena is not required for cell motility?

Release of Ca2+ from the sarcoplasmic reticulum.

The respiratory chain is relatively inaccessible in the experimental manipulation of intact mitochondria. After disrupting mitochondria with ultrasound, however, it is possible to isolate functional submitochondrial particles, which consist of broken cristae that have resealed inside-out into small, closed vesicles. In these vesicles, the components that originally faced the matrix are now exposed to the surrounding medium. Consider an anaerobic preparation of such submitochondrial particles. If a small amount of oxygen is added, do you predict that the preparation will consume oxygen in respiration reactions? Will the medium outside the particles become more acidic or more basic? What, if anything, will change if the flow of protons through ATP synthase is blocked by an inhibitor? Explain your answer.

Respiration reactions will rapidly consume at least some of the added oxygen. During the anaerobic conditions, the electron carriers in the electron-transport chain were reduced; on the addition of oxygen, electrons will be transferred to oxygen, thereby reducing the oxygen and oxidizing the carriers. Concomitantly with the electron flow, protons will be pumped from the medium into the vesicles, thereby making the medium slightly more basic and the inside of the vesicles acidic. Inhibition of the ATP synthase will not have an immediate effect on oxygen consumption or proton pumping. However, the proton concentration inside the vesicles will quickly become too high to continue the activity of the electron-transport-coupled proton pumping, and thus electron transport and oxygen consumption will cease.

Figure Q12-54 illustrates changes in membrane potential during the formation of an action potential. What membrane characteristic or measurement used to study action potentials is indicated by the arrow?

Resting membrane potential

Which of the following is not an electron carrier that participates in the electron-transport chain?

Rhodospin

Which of the following statements about prokaryotic mRNA molecules are false?

Ribosomes must bind to the 5' cap before initiating translation.

Ricin is one of the most toxic substances known: less than 2 mg injected into the bloodstream will kill an adult human. Ricin is produced by the castor bean plant as a 65 kilodalton protein heterodimer composed of an A chain and a B chain. The B chain is a lectin that binds to carbohydrates on the cell surface. The A chain is an enzyme that modifies a highly conserved site in rRNA, leading to inhibition of translation. After entering the cell, ricin eventually ends up in the lumen of the endoplasmic reticulum (ER), and from there it moves into the cytosol, where it inactivates ribosomes. Which one of the following describes the most likely scenario for how ricin gets into the cytosol?

Ricin, by mimicking an unfolded protein, is tagged for transport across the ER membrane into the cytosol.

In a centrosome, which structures serve as nucleation sites for the formation of microtubules?

Rings of γ-tubulin

Sodium dodecyl sulfate (SDS) and Triton X-100 are both detergents that can be used to lyse cells. If the goal is to study the activity of membrane proteins after cell lysis, explain why SDS would not be a good choice.

SDS is a strong ionic detergent. When cells are exposed to SDS, membrane proteins are not only extracted from the membrane, they are completely unfolded. After denaturation, they cannot be studied as functional molecules.

Below is a segment of RNA from the middle of an mRNA. 5'-UAGUCUAGGCACUGA-3' If you were told that this segment of RNA was part of the coding region of an mRNA for a large protein, give the amino acid sequence for the protein that is encoded by this segment of mRNA. Write your answer using the one-letter amino acid code.

SLGT

It is possible to follow the movement of a single molecule or a small group of molecules. This requires the use of antibodies linked to small particles of gold, which appear as dark spots when tracked through video microscopy. What is this method called? What does the abbreviation stand for?

SPT

Which of the following items is not important for flagellar movement?

Sarcoplasmic reticulum

To maintain even ER membrane growth, the transfer of random phospholipids from one monolayer to the other is catalyzed by the ____.

Scramblase

The plasma membrane serves many functions, many of which depend on the presence of specialized membrane proteins. Which of the following roles of the plasma membrane could still occur if the bilayer were lacking these proteins?

Selective permeability

Foods are broken down into simple molecular subunits for distribution and use throughout the body. Which type of simple subunits, listed below, is used preferentially as an energy source?

Simply sugars

In a method called patch-clamping, a glass capillary can be converted into a microelectrode that measures the electrical currents across biological membranes. Which of the following is not true about the patch-clamp method?

Single-channel patch-clamp recordings have demonstrated that gated membrane channels will only open and close in response to specific stimuli.

DNA polymerases are processive, which means that they remain tightly associated with the template strand while moving rapidly and adding nucleotides to the growing daughter strand. Which piece of the replication machinery accounts for this characteristic?

Sliding clamp

Smaller

Smaller. This mutation will make a TFS that cannot be phosphorylated by PKA.

You are interested in cell-size regulation and discover that signaling through an enzyme-coupled receptor is important for the growth (enlargement) of mouse liver cells. Activation of the receptor activates adenylyl cyclase, which ultimately leads to the activation of PKA, which then phosphorylates a transcription factor called TFS on threonine 42. This phosphorylation is necessary for the binding of TFS to its specific sites on DNA, where it then activates the transcription of Sze2, a gene that encodes a protein important for liver cell growth. You find that liver cells lacking the receptor are 15% smaller than normal cells, whereas cells that express a constitutively activated version of PKA are 15% larger than normal liver cells. Given these results, predict whether you would expect the cell's size to be bigger or smaller than normal cells if cells were treated in the following fashion. You add a drug that increases the activity of cyclic AMP phosphodiesterase.

Smaller. cAMP phosphodiesterase is involved in converting cAMP to AMP and will down-regulate this signaling pathway.

Some cells have aquaporins—channels that facilitate the flow of water molecules through the plasma membrane. For these cells, what regulates the rate and direction of water diffusion across the membrane?

Solute concentrations on either side of the membrane.

Which of the following statements about the genetic code is correct?

Some amino acids are specified by more than one codon.

Voltage-gated channels contain charged protein domains, which are sensitive to changes in membrane potential. By responding to a threshold in the membrane potential, these voltage sensors trigger the opening of the channels. Which of the following best describes the behavior of a population of channels exposed to such a threshold?

Some channels remain closed and some open completely.

Which of the following statements about a protein in the lumen of the ER is false?

Some of the proteins in the lumen of the ER can end up in the plasma membrane.

Red blood cells have been very useful in the study of membranes and the protein components that provide structural support. Which of the following proteins is the principal fibrous protein in the cortex of the red blood cell?

Spectrin

Anemia, a condition that results in individuals with a low red blood cell count, can be caused by a number of factors. Why do individuals with defects in the spectrin protein often have this condition?

Spectrin is the primary protein in the cortex of red blood cells. A defect in the spectrin protein directly affects the strength and shape of the cortex. Red blood cells that contain mutated spectrin molecules have an irregular shape and are prone to lysis as a result of cortical fragility, leading to a smaller population of red blood cells.

The microtubules in a cell form a structural framework that can have all the following functions except which one?

Strengthening the plasma membrane

The stimulation of auditory nerves depends on the opening and closing of channels in the auditory hair cells. Which type of gating mechanism do these cells use?

Stress-gated

____ ion channels are found in the hair cells of the mammalian cochlea.

Stress-gated

A mutation in the anticodon sequence 5'-AUC3' of a tRNA results in the anticodon sequence 5'-CUC-3'. Which of the following aberrations in protein synthesis might this cause?

Substitution of aspartic acid (Asp) for glutamic acid (Glu)

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-GUU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause?

Substitution of lysine (Lys) for asparagine (Asn)

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause?

Substitution of lysine for isoleucine

Root cells in plants do not contain chloroplasts. How do these cells obtain the energy necessary for their survival? ____ produced in photosynthesizing tissues is/are transported to the root cells via phloem.

Sucrose

Membrane lipids are capable of many different types of movement. Which of these does not occur spontaneously in biological membranes?

Switching between lipid layers.

We learned about the enzyme DNA primase. Select the base that primase does NOT use.

On a DNA strand that is being synthesized, which end is growing-the 3' end, the 5' end, or both ends?

The 3' end. DNA polymerase can add nucleotides only to the 3'-OH end of a nucleic acid chain.

Which of the following statements about mRNA half-life is true?

The 5' and 3' untranslated regions of an mRNA often contain sequences that affect the lifetime of the mRNA molecule.

Although the outer mitochondrial membrane is permeable to all small molecules, the inner mitochondrial membrane is essentially impermeable in the absence of specific transport proteins. Consider this information and what you have learned about the citric acid cycle to address the following questions. The ATP generated by oxidative respiration is used throughout the cell. The majority of ATP production occurs in the mitochondrial matrix. How do you think ATP is made accessible to enzymes in the cytosol and other organelles?

The ATP must be transported across the inner mitochondrial membrane, after which it freely diffuses into the cytosol through the permeable outer membrane. Embedded in the inner membrane are dedicated ADP/ATP antiporters that serve the dual purpose of exporting ATP and bringing in new ADP, which can then be converted into ATP during oxidative phosphorylation.

You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription?

The Abd RNA from the mutant strain will be longer than normal.

Figure Q15-34 shows the organization of a protein that normally resides in the plasma membrane. The boxes labeled 1 and 2 represent membrane-spanning sequences and the arrow represents a site of action of signal peptidase. Given this diagram, which of the following statements must be true?

The C-terminus of this protein is cytoplasmic

The Calvin cycle is considered light-independent because it can occur in darkness. However, most often the Calvin cycle takes place in sunlight. Which of the following likely explains why?

The Calvin cycle requires ATP and NADPH, which require sunlight to be produced.

In the principle, a eukaryotic cell can regulate gene expression at any step in the pathway from DNA to the active protein. Transcriptional control occurs between:

The DNA and the RNA transcript

Meselson and Stahl grew cells in media that continued different isotopes of nitrogen (15N and 14N) so that the DNA molecules produced from these different isotopes could be distinguished by mass. Explain how "light" DNA was separated from "heavy" DNA in the Meselson and Stahl experiments.

The DNA samples collected were placed into centrifuge tubes containing cesium chloride. After high-speed centrifugation for 2 days, the heavy and light DNA products were separated by density.

The cholera toxin enters cells of the intestinal lining where it binds to the alpha subunit of a G-protein blocking its ability to hydrolyze GTP. The effect of the toxin on the alpha subunit will be:

The G-protein will remain permanently activated.

Which of the following statements about vesicular membrane fusion is false?

The GTP hydrolysis of the Rab proteins provides the energy for membrane fusion.

Briefly describe the mechanism by which an internal stoptransfer sequence in a protein causes the protein to become embedded in the lipid bilayer as a transmembrane protein with a single membranespanning region. Assume that the protein has an Nterminal signal sequence and just one internal hydrophobic stoptransfer sequence.

The N-terminal signal sequence initiates translocation and the protein chain starts to thread through the translocation channel. When the stop-transfer sequence enters the translocation channel, the channel discharges both the signal sequence and the stop-transfer sequence sideways into the lipid bilayer. The signal sequence is then cleaved, so that the protein remains held in the membrane by the hydrophobic stop-transfer sequence.

Which part of the protein is synthesized by a ribosome first?

The N-terminus

Antibodies are Y-shaped molecules that have two identical binding sites. Suppose that you have obtained an antibody that is specific for the extracellular domain of an RTK. When the antibody binds to the RTK, it brings together two RTK molecules. If cells containing the RTK were exposed to the antibody, would you expect the kinase to be activated, inactivated, or unaffected? Explain your reasoning.

The RTK will probably become activated on binding of the antibody molecule. This is because signal-induced dimerization usually activates RTKs. When RTK molecules are brought together, their cytoplasmic kinase domains become activated, and each receptor phosphorylates the other.

The synthesis of DNA in living systems occurs in the 5′-to-3′ direction. However, scientists synthesize short DNA sequences needed for their experiments on an instrument dedicated to this task. The chemical synthesis of DNA by this instrument proceeds in the 3′-to-5′ direction. Draw a diagram to show how this is possible and explain the process.

The actual chemical reaction in DNA synthesis is the same regardless of whether going in the 5′-to-3′ or in the 3′-to-5′ direction. The most important distinction between these two options is that if DNA is synthesized in the 3′-to-5′ direction, the 5′ end of the elongating strand, rather than the 3′ end, will have a nucleoside triphosphate.

What would happen in each of the following cases? Assume in each case that the protein involved is a soluble protein, not a membrane protein. You change the hydrophobic amino acids in an ER signal sequence into charged amino acids.

The altered signal sequence will not be recognized and the protein will remain in the cytosol.

Which of the following statements about the carbohydrate coating of the cell surface is false?

The arrangement of the oligosaccharide side chain is highly ordered, much like the peptide bonds of a polypeptide chain.

Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5'-AGTCTAGGCACTGA-3' 3'-TCAGATCCGTGACT-5' If the polymerase is transcribing from this segment of DNA from left to right, which strand (top or bottom) is the template?

The bottom strand

You have a segment of DNA that contains the following sequence: 5'-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3' 3'-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-3' You know that the RNA transcribed from this segment contains the following sequence: 5'-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3' Which of the following choices best describes how transcription occurs?

The bottom strand is the template strand; RNA polymerase moves along this strand from 3' to 5'

You have a segment of DNA that contains the following sequence: 5'-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3' 3'-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5' You know that the RNA transcribed from this segment contains the following sequence: 5'-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3' Which of the following choices best describes how transcription occurs?

The bottom strand is the template strand; RNA polymerase moves along this strand from 3' to 5'.

The ribosome is important for catalyzing the formation of peptide bonds. Which of the following statements is true?

The catalytic site for peptide bond formation is formed primarily from an rRNA.

The sliding clamp complex encircles the DNA template and binds to DNA polymerase. This helps the polymerase synthesize much longer stretches of DNA without dissociating. While the loading of the clamp only occurs once on the leading strand, it must happen each time a new Okazaki fragment is made on the lagging strand. How does the cell expedite this process?

The cell employs an additional protein in order to make the constant reloading of the sliding clamp on the lagging strand much more efficient. The protein, called the clamp loader, harnesses energy from ATP hydrolysis to lock a sliding clamp complex around the DNA for every successive round of DNA synthesis.

You are interested in cell-size regulation and discover that signaling through an enzyme-coupled receptor is important for the growth (enlargement) of mouse liver cells. Activation of the receptor activates adenylyl cyclase, which ultimately leads to the activation of PKA, which then phosphorylates a transcription factor called TFS on threonine 42. This phosphorylation is necessary for the binding of TFS to its specific sites on DNA, where it then activates the transcription of Sze2, a gene that encodes a protein important for liver cell growth. You find that liver cells lacking the receptor are 15% smaller than normal cells, whereas cells that express a constitutively activated version of PKA are 15% larger than normal liver cells. If you change threonine 42 on TFS to an alanine residue, what would you expect?

The cell's size to be smaller than normal cells.

How do the epithelial cells that line the gut actively take up glucose form the lumen of the gut after a meal?

The cells have glucose-Na+ symporters in their apical plasma membrane.

When Ras is activated, cells will divide. A dominant-negative form of Ras clings too tightly to GDP. You introduce a dominant-negative form of Ras into cells that also have a normal version of Ras. Which of the following statements is true?

The cells you create will divide less frequently than normal cells in response to the extracellular signals that typically activate Ras.

The following DNA sequence includes the beginning of a sequence coding for a protein. What would be the result of a mutation that changed the C marked by an asterisk to an A? 5'-AGGCTATGAATFFACACTGCGAGCCC... *

The change creates a stop codon (TGA, or UGA in the mRNA) very near the beginning of the protein-coding sequence and in the correct reading frame (the beginning of the coding sequence is indicated by the ATG). Thus, translation would terminate after only four amino acids had been joined together, and the complete protein would not be made.

The citric acid cycle generates NADH and FADH2, which are then used in the process of oxidative phosphorylation to make ATP. If the citric acid cycle (which does not use oxygen) and oxidative phosphorylation are separate processes, as they are, then why is it that the citric acid cycle stops almost immediately when O2 is removed?

The citric acid cycle stops almost immediately when oxygen is removed because several steps in the cycle require the oxidized forms of NAD+ and FAD. In the absence of oxygen, these electron carriers can be reduced by the reactions of the citric acid cycle but cannot be re-oxidized by the electron-transport chain that participates in oxidative phosphorylation.

The concentration of a particular protein, X, in a normal human cell rises gradually from a low point, immediately after cell division, to a high point, just before cell division, and then drops sharply. The level of its mRNA in the cell remains fairly constant throughout this time. Protein X is required for cell growth and survival, but the drop in its level just before cell division is essential for division to proceed. You have isolated a line of human cells that grow in size in culture but cannot divide, and on analyzing these mutants, you find that levels of X mRNA in the mutant cells are normal. Which of the following mutations in the gene for X could explain these results?

The deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein.

Which of the following statements about G-protein-coupled receptors (GPCRs) is false?

The different classes of GPCR ligands (protein, amino acid derivatives, or fatty acids) bind to receptors with different number of transmembrane domains.

Meselson and Stahl grew cells in media that continued different isotopes of nitrogen (15N and 14N) so that the DNA molecules produced from these different isotopes could be distinguished by mass. What experimental result eliminated the dispersive model of DNA replication?

The dispersive model was ruled out by using heat to denature the DNA duplexes and then comparing the densities of the single-stranded DNA. If the dispersive model had been correct, individual strands should have had an intermediate density. However, this was not the case; only heavy strands and light strands were observed, which convincingly supported the semiconservative model for DNA replication.

Which of the following statements about actin is false?

The dynamic instability of actin filaments is important for cell movement.

When the net charge on either side of the plasma membrane is zero, what else is true?

The electrochemical potential across the membrane is zero.

Steps 7 and 10 of glycolysis result in substrate-level phosphorylation. Which of the following best describes this process?

The energy derived from substrate oxidation is coupled to the conversion of ADP to ATP.

Which of the following statements about sequence proofreading during DNA replication is false?

The exonuclease activity cleaves DNA in the 5'-to-3' direction

Activated protein kinase C (PKC) can lead to the modification of the membrane lipids in the vicinity of the active PKC. Figure Q16-38 shows how G proteins can indirectly activate PKC. You have discovered the enzyme activated by PKC that mediates the lipid modification. You call the enzyme Rafty and demonstrate that activated PKC directly phosphorylates Rafty, activating it to modify the plasma membrane lipids in the vicinity of the cell where PKC is active; these lipid modifications can be detected by dyes that bind to the modified lipids. Cells lacking Rafty do not have these modifications, even when PKC is active. Which of the following conditions would lead to signal-independent modification of the membrane lipids by Rafty?

The expression of a constitutively active phospholipase C.

Activated protein kinase C (PKC) can lead to the modification of the membrane lipids in the vicinity of the active PKC. The figure below shows how G proteins can indirectly activate PKC. You have discovered the enzyme activated by PKC that mediates the lipid modification. You call the enzyme Rafty and demonstrate that activated PKC directly phosphorylates Rafty, activating it to modify the plasma membrane lipids in the vicinity of the cell where PKC is active; these lipid modifications can be detected by dyes that bind to the modified lipids. Cells lacking Rafty do not have these modifications, even when PKC is active. Which of the following conditions would lead to signal-independent modification of the membrane lipids by Rafty?

The expression of a constitutively-active phospholipase C

Intermediate filaments are made from elongated fibrous proteins that are assembled into a ropelike structure. You are interested in how intermediate filaments are formed, and you create a keratin subunit whose α-helical region is of normal length, but the globular heads at the N-terminus and C-terminus of the subunit are changed to those found in a neurofilament subunit. If you were to assemble intermediate filaments using this hybrid subunit, which of the following predictions describes the most likely outcome?

The filaments assembled will interact with different cytoskeletal components than keratin does.

The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 10,000 nucleotides, whereas the length of the mRNA produced from this gene is 4000 nucleotides. What is the most likely reason for this difference?

The gene contains one or more introns.

Why do phospholipids form bilayers in water?

The hydrophilic head is attracted to water while the hydrophobic tail shuns water.

A calmodulin-regulated kinase (CaM-kinase) is involved in spatial learning and memory. This kinase is able to phosphorylate itself such that its kinase activity is now independent of the intracellular concentration of Ca2+. Thus, the kinase stays active after Ca2+ levels have dropped. Mice completely lacking this CaM-kinase have severe spatial learning defects but are otherwise normal. What would be the effect on the activity of CaM-kinase if there were a mutation that reduced its interaction with the protein phosphatase responsible for inactivating the kinase?

The kinase would stay active for longer after a transient increase in intracellular Ca2+ concentration.

Which ribosomal subunit is responsible for catalyzing the formation of peptide bonds?

The large subunit

Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences?

The leading strand doubles back on itself to form a primer for the lagging strand.

In DNA replication, DNA "unwinds" to form two template strands: the leading strand and the lagging strand. Which of the following statements about these strands is true?

The leading strand of DNA is synthesized continuously.

If a lysosome breaks, what protects the rest of the cell from lysosomal enzymes?

The lysosomal enzymes are all acid hydrolases, which have optimal activity at the low pH (about 5.0) found in the interior of lysosomes. If a lysosome were to break, the acid hydrolases would find themselves at pH 7.2, the pH of the cytosol, and would therefore do little damage to cellular constituents.

Some lower vertebrates such as fish and amphibians can control their color by regulating specialized pigment cells called melanophores. These cells contain small, pigmented organelles, termed melanosomes, that can be dispersed throughout the cell, making the cell darker, or aggregated in the center of the cell to make the cell lighter. You purify the melanosomes from melanophores that have either aggregated or dispersed melanosomes and find that: 1. aggregated melanosomes co-purify with dynein 2. dispersed melanosomes co-purify with kinesin. Given this set of data, propose a mechanism for how the aggregation and dispersal of melanosomes occur.

The melanosomes are transported in the cell on microtubules. When it is advantageous for the animal to become lighter, a signal is sent to the pigment cell that causes the melanosomes to associate with dynein. Because dynein is a minus-end directed motor, it will transport the melanosomes toward the center of the cell, causing the melanosomes to aggregate in the center and the cell to take on a lighter appearance. When the animal wants to become darker, a signal is sent to the pigment cell that causes the melanosomes to associate with kinesin. Kinesin is usually a plus-end directed motor and will move the melanosomes away from the center of the cell so that they are more dispersed, making the cell look darker.

Which of the following statements about secretion is true?

The membrane of a secretory vesicle will fuse with the plasma membrane when it discharges its contents to the cell's exterior.

Which of the following phenomena will be observed if a cell's membrane is pierced?

The membrane reseals

Which end of a microtubule is embedded in the centrosome?

The minus end

Which of the following requires an input of energy to occur?

The movement of a solute from a region of lower concentration on one side of a membrane to a region of higher concentration on the other side.

Activated GPCRs activate G proteins by reducing the strength of binding of GDP to the α subunit of the G protein, allowing GDP to dissociate and GTP (which is present at much higher concentrations in the cell than GDP) to bind in its place. How would the activity of a G protein be affected by a mutation that reduces the affinity of the α subunit for GDP without significantly changing its affinity for GTP?

The mutant G protein would be constantly active. Each time the α subunit hydrolyzed GTP to GDP, the GDP would dissociate spontaneously, allowing GTP to bind and reactivate the α subunit, especially because the intracellular concentration of GTP is higher than that of GDP. Normally, GDP is tightly bound by the α subunit, which keeps the G protein in its inactive state until interaction with an appropriate activated GPCR stimulates the release of GDP.

Explain why the signal molecules used in neuronal signaling work at a longer range than those used in contact-dependent signaling.

The neurotransmitter released from a neuron in neuronal signaling must diffuse across the synaptic cleft to reach receptors on the target cell. In contrast, in contact-dependent signaling, the signal molecule is attached to the plasma membrane of the signaling cell and interacts with receptors located on the plasma membrane of the receiving cell; thus, the cells must be in direct contact for this type of signaling to occur.

You are curious about the dynamic instability of microtubules and decide to join a lab that works on microtubule polymerization. The people in the lab help you grow some microtubules in culture using conditions that allow you to watch individual microtubules under a microscope. You can see the microtubules growing and shrinking, as you expect. The professor who runs the lab gets in a new piece of equipment, a very fine laser beam that can be used to sever microtubules. She is very excited and wants to sever growing microtubules at their middle, using the laser beam. Do you predict that the newly exposed microtubule plus ends will grow or shrink?

The newly exposed microtubule plus ends will most probably shrink if you sever the microtubules in the middle. This is because a microtubule grows by adding GTP-carrying subunits to the plus end. The GTP is hydrolyzed over time, leaving only a cap of GTP-carrying subunits at the plus end, with the remainder of the tubulin protofilament containing GDP-carrying subunits. Therefore, if you sever a growing microtubule in its middle, you will most probably create a plus end that contains GDP-carrying subunits. The GDP-carrying subunits are less tightly bound than the GTP-carrying subunits and will peel away from each other, causing depolymerization of the microtubule and shrinkage.

Which of the following statements regarding dynamic instability is false?

The newly freed tubulin dimers from a shrinking microtubule can be immediately captured by growing microtubules and added to their plus end.

Which of the following statements is true?

The nuclear membrane is thought to have arisen from the plasma membrane invaginating around the DNA.

What structure is responsible for selecting and transporting into the cytoplasm only properly processed eukaryotic mRNAs?

The nuclear pore complex

Which of the following statements does not accurately describe the events involved in the propagation of an action potential?

The opening of transmitter-gated K+ channels helps to repolarize the membrane.

Mitochondrial structure and the reaction products generated inside the matrix are critical for generating stores of energy. Answer the following questions based on what you know about mitochondrial structure and processes. The gradients used to generate ATP are maintained across the inner mitochondrial membrane. Why don't we observe a similar gradient generation across the outer mitochondrial membrane?

The outer mitochondrial membrane contains large, channel-forming proteins called porins, which makes this membrane permeable to small molecules. Protons, other ions, nucleotides, and many other small molecules flow freely across this membrane, making it impossible to establish a gradient of any of these molecules on either side of this membrane.

Which of the following statements is true?

The pH in the mitochondrial matrix is higher than the pH in the intermembrane space.

Investigators have engineered a gene that encodes a protein bearing a mitochondrial signal sequence followed by an ER signal sequence. What would be the likely fate of that protein?

The protein will be recognized by an SRP and will eventually enter the ER.

What would happen in each of the following cases? Assume in each case that the protein involved is a soluble protein, not a membrane protein. You move the N-terminal ER signal sequence to the C-terminal end of the protein.

The protein will not enter the ER. Because the C-terminus of the protein is the last part to be made, the ribosomes synthesizing this protein will not be recognized by the signal-recognition particle (SRP) and hence not carried to the ER.

What would happen in each of the following cases? Assume in each case that the protein involved is a soluble protein, not a membrane protein. You add a signal sequence (for the ER) to the N-terminal end of a normally cytosolic protein.

The protein will now be transported into the ER lumen.

The protein will still be delivered into the ER. It is the distribution of hydrophobic amino acids that is important, not the actual sequence.

If you remove the ER retention signal from a protein that normally resides in the ER lumen, where do you predict the protein will ultimately end up? Explain your reasoning.

The protein would end up in the extracellular space. Normally, the protein would go from the ER to the Golgi apparatus, get captured because of its ER retention signal, and return to the ER. However, without the ER retention signal, the protein would evade capture, ultimately leave the Golgi via the default pathway, and become secreted into the extracellular space. The protein would not be retained anywhere else along the secretory pathway: it presumably has no signals to promote such localization because it normally resides in the ER lumen.

Using genetic engineering techniques, you have created a set of proteins that contain two (and only two) conflicting signal sequences that specify different compartments. Predict which signal would win out for the following combinations. Explain your answers. Signals for import into the nucleus and import into the ER.

The protein would enter the ER. The signal for a protein to enter the ER is recognized as the protein is being synthesized and the protein will end up either in the ER or on the ER membrane. Cytosolic nuclear transport proteins recognize proteins destined for the nucleus once those proteins are fully synthesized and fully folded.

The protein would enter the mitochondria. For a nuclear export signal to work, the protein would have to end up in the nucleus first and thus would need a nuclear import signal for the nuclear export signal to be used.

The protein would enter the mitochondria. To be retained in the ER, the protein needs to enter the ER. Because there is no signal for ER import, the ER retention signal would not function.

The Na+-K+ ATPase is also known as the Na+-K+ pump. It is responsible for maintaining the high extracellular sodium ion concentration and the high intracellular potassium ion concentration. What happens immediately after the pump hydrolyzes ATP?

The pump is phosphorylated

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 on the inside of the vesicle and the portion of the molecule that normally faces the extracellular space is on the outside of the vesicle. Assume that each pump transports one Na+ ion in one direction and one K+ ion in the other direction during each pumping cycle (see the figure below for how the Na+-K+ pump normally functions in the plasma membrane). Predict what would happen if the solution outside the vesicles contains both Na+ and K+ ions, while the solution inside contains both Na+ and K+ ions and ATP.

The pumps will transport Na+ out of the vesicles and K+ into the vesicles.

Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied. Which of the factors below does not contribute to the relative ease of strand separation by initiator proteins?

The reaction can occur at room temperature

Which of the following statements is true?

The regulation of inflammatory responses at the site of an infection is an example of paracrine signaling.

Which of the following statements correctly explains what it means for DNA replication to be bidirectional?

The replication forks formed at the origin move in opposite directions.

Which of the following does NOT occur before a eukaryotic mRNA is exported from the nucleus?

The ribosome binds to the mRNA.

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus?

The ribosome binds to the mRNA.

Intracellular steroid hormone receptors have binding sites for a signaling molecule and a DNA sequence. How is it that the same steroid hormone receptor, which binds to a specific DNA sequence, can regulate different genes in different cell types?

The specific genes regulated in response to an activated steroid hormone receptor depends not only on the genes having the appropriate DNA sequence for binding the receptor but also on a variety of other nuclear proteins that influence gene expression, some of which vary between different cell types.

Which of the following statements concerning propagation of an action potential across the synaptic cleft is NOT true?

The synaptic vesicles cross the synaptic cleft and fuse with the postsynaptic cell membrane and release their neurotransmitters.

Human infants have a much larger portion of brown adipose tissue than adult humans. It was found that the mitochondria in brown adipocytes (brown fat cells) have a novel protein in the inner mitochondrial membrane. This protein, called the uncoupling protein (UCP), was found to transport protons from the intermembrane space into the matrix. Propose an explanation for the higher proportion of brown fat cells in infants compared to adults.

The thermogenesis resulting from the action of UCP is important for helping infants maintain a constant body temperature. As our body mass increases with age, our body temperatures are probably less susceptible to fluctuations, and therefore adults do not require the same amount of brown fat as infants.

In a cell capable of regulated secretion, what are the three main classes of proteins that must be separated before they leave the trans Golgi network?

The three main classes of protein that must be sorted before they leave the trans Golgi network in a cell capable of regulated secretion are (1) those destined for lysosomes, (2) those destined for secretory vesicles, and (3) those destined for immediate delivery to the cell surface.

Meselson and Stahl grew cells in media that continued different isotopes of nitrogen (15N and 14N) so that the DNA molecules produced from these different isotopes could be distinguished by mass. Describe the three existing models for DNA replication when these studies were begun, and explain how one of them was ruled out definitively.

The three models were conservative, semiconservative, and dispersive. The conservative model suggested a mechanism by which the original parental strands stayed together after replication and the daughter duplex was made entirely of newly synthesized DNA. The semiconservative model proposed that the two DNA duplexes produced during replication were hybrid molecules, each having one of the parental strands and one of the newly synthesized strands. The dispersive model predicted that the new DNA duplexes each contained segments of parental and daughter strands all along the molecule. The conservative model was ruled out by the density-gradient experiments.

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon?

The transcription of a eukaryotic gene is more likely to be influenced by proteins that bind far from the promoter.

Why is the old dogma "one gene-one protein" not always true for eukaryotic genes?

The transcripts from some genes can be spliced in more than one way to give mRNAs containing different sequences thus encoding different proteins. A single eukaryotic gene may therefore encode more than one protein.

In bacteria, the transport of many nutrients, including sugars and amino acids, is driven by the electrochemical H+ gradient across the plasma membrane. In E. coli, for example, a H+-lactose symporter mediates the active transport of the sugar lactose into the cell. Given what you know about coupled transport, which is likely true of the H+-lactose symporter?

The transporter oscillates randomly between states in which it is open to either the extracellular space or the cytosol.

The following happens when a G-protein-coupled receptor activates a G protein.

The α subunit exchanges its bound GDP for GTP.

Which of the following happens when a G-protein-coupled receptor activates a trimeric G protein?

The α subunit exchanges its bound GDP for GTP.

The figure below shows the leading edge of a lamellipodium. Which of the following statements is NOT true?

There is more ADP-bound actin at the leading edge than in the actin filaments away from the leading edge.

Use your knowledge of how a new strand of DNA is synthesized to explain why DNA replication must occur in the 5′-to-3′ direction. In other words, what would be the consequences of 3′-to-5′ strand elongation?

There would be several detrimental consequences to 3'-to-5' strand elongation. One of those most directly linked to the processes of DNA replication involves synthesis of the lagging strand. After the RNA primers are degraded, the DNA segments remaining will have 5' ends with a single phosphate group. The incoming nucleotide will have a 3'-OH group. Without the energy provided by the release of PPi from the 5' end, the process of elongation would no longer be energetically favorable.

Cytochalasin is a drug that caps actin filament plus ends, thus preventing actin polymerization. Phalloidin is a drug that binds to and stabilizes actin filaments, preventing actin depolymerization. Even though these drugs have opposite effects on actin polymerization, the addition of either of these drugs instantaneously freezes the cell movements that depends on actin filaments. Explain why drugs that have opposite effects on actin filaments can have a similar effect on cell movements.

These drugs both stop cell movements because actin polymerization and depolymerization are both required for this process. As cells move forward, the growth of actin filaments near the plasma membrane helps push out the membrane. As this occurs, continuous depolymerization of actin filaments occurs at the actin filaments away from the plasma membrane.

Your friend is studying mouse fur color and has isolated the GPCR responsible for determining its color, as well as the extracellular signal that activates the receptor. She finds that, on addition of the signal to pigment cells (cells that produce the pigment determining fur color), cAMP levels rise in the cell. She starts a biotech company, and the company isolates more components of the signaling pathway responsible for fur color. Using transgenic mouse technology, the company genetically engineers mice that are defective in various proteins involved in determining fur color. The company obtains the following results. Normal mice have beige (very light brown) fur color.Mice lacking the extracellular signal have white fur.Mice lacking the GPCR have white fur.Mice lacking cAMP phosphodiesterase have dark brown fur. Your friend has also made mice that are defective in the α subunit of the G protein in this signaling pathway. The defective α subunit works normally except that, once it binds GTP, it cannot hydrolyze GTP to GDP. What color do you predict that the fur of these mice will be? Why?

These mice will have dark brown fur. The inability to hydrolyze GTP to GDP will lead to inappropriate activation of the signaling pathway that makes pigment. Too much pigment will be produced, as seen in the mice lacking cAMP phosphodiesterase (which lack the ability to damp the signal), and the mice will end up with dark brown fur.

Which of the following is NOT true of mitochondria?

They are replaced by chloroplasts in plants.

Which of the following is true about sugar side chains present on the cell membrane?

They can help cells identify each other.

Which of the following is true of mitochondria?

They have their own prokaryotic-like biosynthetic machinery for making RNA and protein.

What is NOT true of ion channels?

They hydrolyze ATP.

K+ leak channels are found in the plasma membrane. These channels open and close in an unregulated, random fashion. What do they accomplish in a resting cell?

They keep the electrochemical gradient for K+ at zero.

Which of the following statements about GABA receptors is not true?

They promote neuronal uptake of Na+.

This arrangement of components within the vesicles allows the experimental manipulation of the medium surrounding the vesicles, which permits the consequences of different conditions in the mitochondrial matrix to be examined. The medium can be altered by changing pH, adding electron carriers and oxygen, and providing ADP and Pi, for example. The oxidation of electron carriers, the consumption of oxygen, and the production of ATP can be measured in the medium. By changing the composition of the medium, it should be possible, for example, to identify the electron carriers that can donate electrons from the matrix to the transport chain (the side of the membrane that normally faces the matrix is now on the outside), to assess the redox potentials of various components of the transport chain, and to determine the dependence of ATP synthesis on the pH gradient across the membrane and on the ATP/ADP ratio.

The pyruvate dehydrogenase complex contains ____ enzymes which work together to convert pyruvate into ____.

Three; acetyl CoA

Figure Q12-53 illustrates changes in membrane potential during the formation of an action potential. What membrane characteristic or measurement used to study action potentials is indicated by the arrow?

Threshold potential

Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electron-transport chain. Where are the proteins of the electron-transport chain located in chloroplasts?

Thylakoid membrane

In stage 1 of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast?

Thylakoid space

What is the purpose of the two ATP molecules used in glycolysis?

To phosphorylate sugar molecules

The DNA duplex consists of two long covalent polymers wrapped around each other many times over their entire length. The separation of the DNA strands for replication causes the strands to be "overwound" in front of the replication fork. How does the cell relieve the torsional stress created along the DNA duplex during replication?

Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork.

____ are highly selective in the solutes they transport, binding the solute at a specific site and changing conformation so as to transport the solute across the membrane.

Transporter proteins

Sodium dodecyl sulfate (SDS) and Triton X-100 are both detergents that can be used to lyse cells. How does Triton X-100 work in cell lysis, and why is it a better choice of detergent to help you extract proteins?

Triton X-100 has a smaller nonpolar portion and a polar but uncharged end, allowing it to mimic more closely the type of solvation effect of the membrane lipids. Triton X-100 forms a shell around the hydrophobic portion of the protein without disrupting the existing structure. This makes it possible to then place the protein into a new, synthetic membrane bilayer for study.

T/F A protein that relies on protein-protein interactions to stabilize its membrane association is classified as a peripheral membrane protein because it can be dissociated without the use of detergents.

True

T/F ATP is moved out of the matrix, across the inner mitochondrial membrane, in a co-transporter that also brings ADP into the matrix.

True

T/F Amino acids can be transported into the mitochondria and converted into acetyl CoA.

True

T/F Anaerobic respiration is not the same as fermentation, as only the former requires an electron-transport chain.

True

T/F As a replication fork moves away from the origin of replication, a single RNA primer is used to initiate synthesis of the leading strand, while multiple RNA primers are needed to synthesize the lagging strand.

True

T/F CO2 and H2O are generated during the oxidation of food molecules.

True

T/F CO2 and O2 are water-soluble molecules that diffuse freely across cell membranes.

True

T/F Ca2+ pumps in the endoplasmic reticulum membrane help keep the cytosolic Ca2+ concentration low.

True

T/F Carbon fixation can be described as a process by which gaseous carbon-containing molecules are captured and incorporated into biological hydrocarbon molecules.

True

T/F Cells expand energy in the form of ATP hydrolysis so as to maintain ion concentrations that differ from those found outside the cell.

True

T/F DNA ligase is required to seal the sugar-phosphate backbone between all the DNA fragments on the lagging strand.

True

T/F DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells.

True

T/F Epithelial cell membranes are asymmetric, and proteins from the apical side of the cell membrane cannot diffuse into the basal side of the membrane.

True

T/F For Ca2+, the direction of passive transport across a cell membrane is determined by both its concentration gradient and its voltage gradient.

True

T/F In response to binding extracellular signaling molecules, ion-channel-coupled receptors open and cause a change in the permeability of the plasma membrane to selected ions.

True

T/F In the lysosome, acid hydrolases degrade many different types of organic matter. For example, nucleases and proteases in the lysosome degrade nucleic acids and proteins, respectively. The resulting products of digestion, such as nucleotides and amino acids, are transported into the cytosol for re-use.

True

T/F Meselson and Stahl ruled out the dispersive model for DNA replication.

True

T/F Most ion channels are gated, which allows them to open and close in response to a specific stimulus, rather than allowing the constant, unregulated flow of ions.

True

T/F Much of glyceraldehyde 3-phosphate made in the chloroplast ends up producing the molecules needed by the mitochondria to produce ATP.

True

T/F Neurotransmitters are small molecules released into the synaptic cleft after the fusion of synaptic vesicles with the presynaptic membrane.

True

T/F Primase is needed to initiate DNA replication on both the leading strand and the lagging strand.

True

T/F Ribulose 1,5-biphosphate is similar to oxaloacetate in the Krebs cycle in that they are both regenerated at the end of their respective cycles.

True

T/F Stage 2 of photosynthesis involves a cycle of reactions that does not directly depend on energy derived from sunlight.

True

T/F Telomerase is a DNA polymerase that carries its own RNA molecule to use as a primer at the end of the lagging strand.

True

T/F The Golgi apparatus sorts materials destined to be exocytosed.

True

T/F The electrochemical gradient for K+ across the plasma membrane is small. Therefore, any movement of K+ from the inside to the outside of the cell is driven solely by its concentration gradient.

True

T/F The electron-transport proteins, utilized in stage 1 of photosynthesis, reside in the thylakoid membrane of the chloroplast.

True

T/F The error-correcting proofreading activity of DNA polymerase occurs in a 3' to 5' direction.

True

T/F The extracellular concentration of Ca2+ is approximately 10^4-fold higher than the concentration of Ca2+ in the cytosol.

True

T/F The intermembrane space of the mitochondria is chemically equivalent to the cytosol with respect to pH and the small molecules present.

True

T/F The low cytosolic Ca2+ concentration sensitizes the cell to an influx of Ca2+, ensuring a rapid response to environmental stimuli.

True

T/F The number and location of mitochondria within a cell can change, depending on both the cell type and the amount fo energy required.

True

T/F The oxidation of sugar is an energetically favorable process.

True

T/F The pyruvate dehydrogenase complex catalyzes three different, but linked, enzymatic reactions.

True

T/F The repair polymerase does not require the aid of the sliding clamp, because it is only synthesizing DNA over very short stretches.

True

T/F The speed of fluorescent signal recovery during a FRAP assay is a measure of lateral mobility for the molecule of interest.

True

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

True

T/F Under anaerobic conditions, the ATP synthase can hydrolyze ATP instead of synthesizing it.

True

T/F Voltage-gated Na+ channels become automatically inactivated shortly after opening, which ensures that the action potential cannot move backward along the axon.

True

T/F When Na+ channels in the plasma membrane open, the movement of Na+ from the outside to the inside of the cell is driven by both its concentration gradient and its voltage gradient.

True

One strand of a section of DNA isolated from the bacterium E. coli reads: 5'-GTAGCCTACCCATAGG-3' How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence?

Two

____ dimers will line up to form a staggered tetramer.

Two

____ of the G-protein subunits are tethered to the plasma membrane by short lipid tails.

Two

Electron-transfer reactions occur rapidly. Which of the following statements best describes how the diffusion of ubiquinone is controlled in order to ensure its proximity to the other enzyme complexes?

Ubiquinone is anchored directly in the inner mitochondrial membrane via its hydrocarbon tail and can only diffuse laterally.

Anaerobically growing yeast further metabolizes the pyruvate produced by glycolysis to CO2 and ethanol as part of a series of fermentation reactions. Why is this reaction (that is, the answer to part A) essential for the anaerobically growing cell?

Under anaerobic conditions, it is the only means of regenerating the NAD+ required for glycolysis, the main energy-generating pathway of an anaerobically growing yeast cell.

Which of the following statements is false?

Unlike DNA, RNA uses a uracil base and a deoxyribose sugar -RNA nucleotides contain the sugar ribose

Most animal fats form a solid at room temperature, while plant fats remain liquid at room temperature. Which of the following is a feature of lipids in plant membranes that best explains this difference?

Unsaturated hydrocarbons

Vegetable oil is liquid at room temperature, whereas lard (animal fat) is solid at room temperature. Based on this information and your knowledge of hydrocarbon tails, you might predict that plants lipids are generally ____, while animal lipids are generally ____.

Unsaturated; saturated

Membranes undergo spontaneous rearrangement if torn. Which of the following would happen if a cell membrane had a large tear?

Vesicles form

____ ion channels in the mimosa plant propagate the leaf-closing response.

Voltage-gated

____ ion channels respond to changes in membrane potential.

Voltage-gated

Which of the following is required for the secretion of neurotransmitters in response to an action potential?

Voltage-gated Ca2+ channels

Which of the following is true?

Voltage-gated Na+ channels become automatically inactivated shortly after opening, which ensures that the action potential cannot move backward along the axon.

An animal cell has a 2% salt concentration. It is placed into a solution with a 0.05% salt concentration. What will happen to the animal cell?

Water will move into the animal cell cauing it to swell and burst.

You have the following two proteins: i. X, with an N-terminal ER signal sequence followed by a peptidase cleavage site ii. Y, with an internal ER signal sequence Both X and Y also contain an ER stop transfer sequence. Which one is a multi-pass transmembrane ER protein?

Indicate by writing "yes" or "no" whether amplification of a signal could occur at the particular steps described below. Explain your answers. The activated GPCRs cause Gα to separate from Gβ and Gγ.

Yes. Each activated GPCR activates many G-protein molecules.

Indicate by writing "yes" or "no" whether amplification of a signal could occur at the particular steps described below. Explain your answers. Adenylyl cyclase produces cyclic AMP.

Yes. Each activated adenylyl cyclase molecule can generate many molecules of cAMP.

Indicate by writing "yes" or "no" whether amplification of a signal could occur at the particular steps described below. Explain your answers. Protein kinase A phosphorylates target proteins.

Yes. Each activated protein kinase A molecule can phosphorylate many molecules of each type of target protein.

You would predict that Cap1 binds the plus end of actin, because it seems to inhibit actin polymerization. Actin filaments grow through the addition of monomers to the plus end of the actin filament. A capping protein that binds the plus end of actin can block monomer addition to the actin filament. Thus, less actin polymerization will be seen in the presence of the Cap1 protein.

Two protein kinases, PK1 and PK2, work sequentially in an intracellular signaling pathway. You create cells that contain inactivating mutations in the genes that encode either PK1 or PK2 and find that these cells no longer respond to a particular extracellular signal. You also create cells containing a version of PK1 that is permanently active and find that the cells behave as though they are receiving the signal even when the signal is not present. When you introduce the permanently active version of PK1 into cells that have an inactivating mutation in PK2, you find that these cells also behave as though they are receiving the signal even when no signal is present. You now create a permanently active version of PK2 and find that cells containing this version behave as though they are receiving the signal even when the signal is not present. What do you predict will happen if you introduce the permanently active version of PK2 into cells that have an inactivating mutation in PK1?

You would predict that no response to the signal would be observed. This is because PK2 normally needs to activate PK1 for the cells to respond to the signal. When PK2 is permanently activated in the absence of PK1, PK1 is not there to relay the signal.

The citric acid cycle oxidizes ____ and produces ____ as a waste product.

acetyl groups; carbon dioxide

The interiro of the trans Golgi network is ____.

acidic

In the ____ environment of the endosome, LDL dissociates from its receptor. The LDL receptors are then ____.

acidic; returned to the plasma membrane

Protein phosphorylation is commonly involved with all of the following except:

activation of G-protein-coupled receptors.

Intestinal cells can take up glucose from the extracellular environment even when there is a higher concentration of intracellular glucose. This must be an act of:

active transport

Pumps are transporters that are able to harness energy provided by other components in the cells to drive the movement of solutes across membranes, against their concentration gradient. This type of transport is called ____.

active transport

Molecules to be packaged into vesicles for transport are selected by ____.

adaptins

Alternative splicing can produce multiple mature mRNAs from one single pre-mRNA. This is because in alternative splicing:

all introns and some exons are removed.

The hydrolysis of GTP to GDP carried out by tubulin molecules ____.

allows the behavior of microtubules called dynamic instability.

The address information for protein sorting in a eukaryotic cell is contained in the ____ of the proteins.

amino acid sequence

Amino acids are attached to their tRNA molecules by:

aminoacyl-tRNA synthetases

Membrane lipids are ____ molecules, composed of a hydrophilic portion and a hydrophobic portion.

amphipathic

On the other hand, membrane-associated proteins do not span the bilayer and instead associate with the membrane through an α helix that is ____.

amphipathic

Membrane proteins can be solubilized by a detergent. Detergents are small ____ molecules.

amphipathic, lipid-like

Detergents are small ____ molecules. When cells are exposed to SDS detergent, membrane proteins are extracted from their membranes and ____.

amphipathic; unfold

Intracellular signaling proteins can ____ the signal received to evoke a strong response from just a few extracellular signal molecules.

amplify

Fermentation is an ____ process that converts ____ into carbon dioxide and ____.

anaerobic; pyruvate; ethanol

After the absorption of sunlight, chlorophyll molecules in a(n) ____ become excited and will seek to get rid of excess ____, which will jump randomly from one chlorophyll molecule to the next and will eventually be captured by a special pair in a(n) ____.

antenna complex; energy; reaction center

The piece of RNA below includes the region that codes for the binding site for the initiator tRNA needed in translation. 5'-GUUUCCCGUAUACAUGCGUGCCGGGGG-3' Which amino acid will be on the tRNA that is the first to bind to the A site of the ribosome?

arginine

The action potential travels along the neuron's ____ to the nerve terminals.

axon

Most proteins destined to enter the endoplasmic reticulum ____.

begin to cross the membrane while still being synthesized.

snRNAs ____.

can bind to specific sequences at intron-exon boundaries through complementary base-pairing.

Ligand-gated ion channels in nerve cell membranes convert ____ signals into ____ ones.

chemical; electrical

The link between bond-forming reactions and membrane transport processes in the mitochondria is called ____.

chemiosmotic coupling

Vesicles from the ER enter the Golgi at the ____.

cis Golgi network

The α-helical region of the rod interacts with the α-helical region of another monomer in a ____ configuration to form a dimer.

coiled-coil

For an uncharged molecule, the direction of passive transport across a membrane is determined solely by its ____ gradient.

concentration

New plasma membrane proteins reach the plasma membrane by the ____ exocytosis pathway.

constitutive

New plasma membrane reaches the plasma membrane by the ____ exocytosis pathway.

constitutive

During nervous-system development in Drosophila, the membrane-bound proteins Delta acts as an inhibitory signal to prevent neighboring cells from developing into neuronal cells. Delta is involved in ____ signaling.

contact-dependent

On the other hand, ____ methods of cell signaling do not require the release of a secreted molecule and are used for very localized signaling events.

contact-dependent

Plasma membranes are extremely thin and fragile, requiring an extensive support network of fibrous proteins. This network is called the ____.

cortex

Plasma membranes are extremely thin and fragile, requiring an extensive support network of fibrous proteins. This network is called the ____ and is located on the ____ side of the plasma membrane.

cortex; cytosolic

The transporter proteins called ____ transporters use the movement of one solute down its gradient to provide energy to drive the uphill transport of a second solute.

coupled

Other proteins are ____ attached to the lipid molecules that are inserted in the membrane.

covalently

The activation of the serine/threonine protein kinase Akt requires phosphoinositide 3-kinase (PI 3-kinase) to ____.

create phosphorylated lipids that serve as docking sites that localize Akt to the plasma membrane.

The ____ makes up about half of the total cell volume of a typical eukaryotic cell.

cytosol

New membrane phospholipids are synthesized by enzymes bound to the ____ side of the ____ membrane.

cytosolic; endoplasmic reticulum

In the phospholipid inositol signaling pathway, phophatidylinositol 4,5-biphosphate is the plasma membrane is cleaved by cytosolic phospholipase C. Thus, one might predict that phosphatidylinositol 4,5,-biphosphate is primarily concentrated in the ____ layer of the plasma membrane. This asymmetric distribution is likely established by ____ activity.

cytosolic; flippase

For both actin and microtubule polymerization, nucleotide hydrolysis is important for:

decreasing the binding strength between subunits in filaments.

For both actin and microtubule polymerization, nucleotide hydrolysis is important for ____.

decreasing the binding strength between subunits on filaments.

Neurons chiefly receive signals at their highly branched ____.

dendrites

The action potential is a wave of ____ that spreads rapidly along the neuronal plasma membrane.

depolarization

These filaments are usually connected from cell to cell through junctions called ____.

desmosomes

The local mediator nitric oxide stimulates the intracellular enzyme guanylyl cyclase by ____.

diffusing into cells and stimulating the cyclase directly.

The formation of ____ in the endoplasmic reticulum stabilizes protein structure.

disulfide bonds

Proteins that are constitutively secreted ____ in the trans Golgi network.

do not aggregate

DNA replication is considered semiconservative because ____.

each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand

These intracellular signaling proteins ultimately change the activity of ____ proteins that bring about cell responses.

effector

The net driving force for a charged molecule across a membrane therefore has two components and is referred to as the ____ gradient. Active transport allows the movement of solutes against this gradient

electrochemical

Signal sequences that direct proteins to the correct compartment are ____.

encoded in the amino acid sequence and sufficient for targeting a protein to its correct destination.

Cells can signal to each other in various ways. A signal that must be relayed to the entire body is most efficiently sent by ____ cells, which produce hormones that are carried throughout the body through the bloodstream.

endocrine

Fluid and marcomolecules are transported into the cell via the ____ pathway.

endocytic

Transport vesicles link organelles of the ____ system.

endomembrane

Plasma membrane proteins are inserted into the membrane in the ____.

endoplasmic reticulum

All proteins being transported out of the cell pass through the ____ and the ____.

endoplasmic reticulum; Golgi apparatus

After these vesicles have pinched off from the plasma membrane, they will fuse with the ____, where materials that are taken into the vesicle are sorted.

endosome

Ingested materials within the cell will pass through a series of compartments called ____ on their way to the ____, which contains digestive enzymes and will ultimately degrade the particles and marcomolecules taken into the cell and will also degrade worn-out organelles.

endosomes; lysosome

The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO2 and H2O in a single step is that ____.

energy can be extracted in usable amounts

Below is a list of molecules with different chemical characteristics. Knowing that all molecules will eventually diffuse across a phospholipid bilayer, select the option below that most accurately predicts the relative rates of diffusion of these molecules (fastest to slowest). -alanine -estrogen -propanol -sodium

estrogen > propanol > alanine > sodium

Intermediate filaments help protect animal cells from mechanical stress because ____.

filaments in each cell are indirectly connected to the filaments of a neighboring cell through desmosome, creating a continuous mechanical link between cells.

NADH donates electrons to the ____ of the three respiratory enzyme complexes in the mitochondrial electron-transport chain.

first

Proteins enter the nucleus in their ____ form.

folded

The electron-transport chain pumps protons:

from the mitochondrial matrix to the mitochondrial intermembrane space.

The ____ domains are exposed on the surface of the intermediate filament, allowing for interaction with cytoplasmic components.

globular

The final product of carbon fixation in chloroplasts is the three-carbon compound ____.

glyceraldehyde 3-phosphate

Ras proteins are important in signal transduction pathways. An inactive Ras protein would:

have a GDP bound to it.

Intermediate filaments are elongated fibrous proteins with an N-terminal globular ____ region and a C-terminal globular ____ region; these regions flank the elongated rod domain.

head; tail

Ras-GEF:

helps Ras exchange GDP for GTP.

Because their concentration is much ____ outside than inside the mitochondria, the flow of ____, or ____, down the concentration gradient is energetically very ____ and can thus be coupled to the production of ATP from ADP.

higher; protons; H+

When a signal needs to be sent to most cells throughout a multicellular organism, the signal most suited for this is a ____.

hormone

Transporter proteins and ion channels function in membrane transport by providing a ____ pathway through the membrane for specific polar solutes or inorganic ions.

hydrophilic

A product of glycolysis consumed during fermentation in yeast is: i. NADH ii. ATP iii. Pyruvate iv. CO2 v. Ethanol

i and iii

Transcription is an essential step of gene regulation. During transcription, mRNA is produced. Besides mRNA, which of the following is also produced by transcription? i. rRNA ii. snRNA iii. tRNA

i, ii, and iii

Which of the following processes occur in the nucleus? i. mRNA capping ii. mRNA polyadenylation iii. mRNA splicing iv. Translation

i, ii, and iii

Transcription produces: i. mRNA ii. rRNA iii. snRNA iv. tRNA

i, ii, iii, and iv

Which of the following is NOT involved in splicing? i. mRNA ii. rRNA iii. snRNA iv. tRNA

ii and iv

After isolating the rough endoplasmic reticulum from the rest of the cytoplasm, you purify the RNAs attached to it. Which of the following proteins do you expect the RNA from the rough endoplasmic reticulum to encode? i. Mitochondrial membrane proteins ii. Soluble secreted proteins iii. Plasma membrane proteins iv. ER membrane proteins v. Ribosomal proteins

ii, iii, and iv

Oxidative phosphorylation is a process that occurs in the ____ of mitochondria.

inner membrane

A cell that receives more than one extracellular signal at the same time can ____ this information using intracellular signaling proteins.

integrate

All members of the steroid hormone receptor family ____.

interact with signal molecules that diffuse through the plasma membrane.

Foreign substances like nicotine, morphine, and menthol exert their initial effects by ____.

interacting with cell-surface receptors, causing the receptors to transduce signal inappropriately in the absence of the normal stimulus.

On the other hand, ____ discriminate between solutes mainly on the basis of size and electrical charge.

ion channels

A protein kinase can act as an integrating device in signaling if it ____.

is activated by two or more proteins in different signaling pathways.

Which of the following processes occur in the cytosol? i. Transcription initiation ii. mRNA capping iii. mRNA splicing iv. Translation initiation v. Translation elongation

iv and v

Intermediate filaments are found mainly in cells that are subject to mechanical stress. Gene mutations that disrupt intermediate filaments cause some rare human genetic diseases. For example, the skin of people with epidermolysis bullosa simplex is very susceptible to mechanical injury; people with this disorder have mutations in their _____ genes, the intermediate filament found in epithelial cells.

kertain

In anaerobic conditions, skeletal muscle produces ____.

lactate only

Humans with progeria, a disease that causes premature aging, carry mutations in a nuclear _____.

lamin

The nuclear envelope is supported by a meshwork of ____ filaments inside the inner nuclear membrane. A mutation of the monomer that makes up these filaments causes ____.

lamin; progeria

Once an mRNA is produced, its message can be decoded by ribosomes. The ribosome is composed of two subunits: the ____ subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the ____ subunit, which matches the tRNAs to the codons of the mRNA.

large; small

This wave is triggered by a local change in the membrane potential to a value that is ____ negative than the resting membrane potential.

less

Which amino acid would you expect a tRNA with the anticodon 5'-CAG-3' to carry?

leucine (Leu)

Many receptors for neurotransmitters are ____ ion channels.

ligand-gated

The acetylcholine receptor in skeletal muscle cells is a ____ ion channel.

ligand-gated

The initiation of an action potential might fail if not enough:

ligand-gated sodium channels open.

All cell membranes have the same ____ structure, with the ____ of the phospholipids facing into the interior of the membrane and the ____ on the outside.

lipid bilayer; fatty acid tails; hydrophilic head groups

In the electron-transport chain in chloroplasts, ____-energy electrons are taken from ____.

low; H2O

Ca2+ can trigger biological effects in cells because an unstimulated cell has an extremely ____ concentration of free Ca2+ in the cytosol, compared with its concentration in the ____ space and in the ____, creating a steep electrochemical gradient.

low; extracellular; endoplasmic reticulum

Which amino acid would you expect a tRNA with the anticodon 5'-CUU-3' to carry?

lysine

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5′-TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant?

mRNA

____ molecules code for proteins, ____ molecules act as adaptors for protein synthesis, ____ molecules are integral components of the ribosome, and ____ molecules are important in the splicing of RNA transcripts.

mRNA; tRNA; rRNA; snRNA

On the other hand, for a charged molecule, the ____ must also be considered.

membrane potential

In the cytosol, thymosin proteins bind actin ____ and by doing so, ____ actin filament growth.

monomers; inhibit

During an action potential, the membrane potential changes from ____ to ____.

negative; positive

In the nervous system, _____ helps strengthen the extremely long extensions often present in nerve cell axons; disruptions in these intermediate filaments can lead to neurodegeneration.

neurofilaments

Finally, ____ signaling involves the conversion of electrical impulses into a chemical signal.

neuronal

If heart muscle cells are supplied with nonhydrolyzable GTP, this will result in:

no effect on K+ channels

Which of the following statements is correct? Kinesins and dyneins _____.

often move in opposite directions to each other.

Electron transfer in the chain occurs in a series of ____ reactions.

oxidation-reduction

The synthesis of ATP in mitochondria is also known as ____.

oxidative phosphorylation

During ____ signaling, the signal remains in the neighborhood of the secreting cell and thus acts as a local mediator on nearby cells.

paracrine

A molecule moves down its concentration gradient by ____ transport, but requires ____ transport to move up its concentration gradient.

passive; active

The ____ enzyme catalyzes the formation of a new peptide bond between the growing polypeptide chain and the newly arriving amino acid.

peptidyl transferase

A second type of endocytosis is ____, which is used to take up large vesicles that contain microorganisms and cellular debris.

phagocytosis

You want to truncate an RNA strand. In other words, you want to make fragments out of a longer stretch of RNA. To do so, you must disrupt its:

phosphodiester bonds

The most common lipids in most cell membranes are the ____.

phospholipids

Eukaryotic cells are continually taking up materials from the extracellular space by the process of endocytosis. One type of endocytosis is ____, which uses ____ proteins to form small vesicles containing fluids and molecules.

pinocytosis; clathrin

People who carry mutations in the gene for ____, an important protein for cross-linkng intermediate filaments, have a disease that combines symptoms of epidermolysis bullosa simplex, muscular dystrophy, and neurodegeneration.

plectin

Many neurotransmitter receptors are ligand-gated ion channels that open transiently in the ____ cell membrane in response to neurotransmitters released by the ____ cell.

postsynaptic; presynaptic

When growing at high temperatures, bacteria and yeast maintain an optimal membrane fluidity by:

producing membrane lipids with tails that are longer and contain fewer double bonds.

When grown at high temperatures, bacteria and yeast maintain an optimal membrane fluidity by:

producing membrane lipids with tails that are longer and contain fewer double bonds.

Eventually, most proteins will be degraded by a large complex of proteolytic enzymes called the ____.

proteasome

The end of a protein-coding message is signaled by the presence of a stop codon, which binds the ____ called release factors.

protein

When Ca2+ enters the cytosol, it interacts with Ca2+-responsive proteins such as ____, which also binds diacylclycerol, and ____, which activates CaM-kinases.

protein kinase C; calmodulin

Enzymes that phosphorylate proteins, termed ____, can also serve as molecular switches; the actions of these enzymes are countered by the activity of ____.

protein kinases; protein phosphates

The proteins transported into the endoplasmic reticulum by ____ are in their ____ form.

protein translocators; unfolded

It is possible for membrane proteins to form attachments with membrane lipids or other membrane proteins. If you are looking at a protein that attaches to the membrane via weak noncovalent interactions, it is likely a ____ membrane protein.

protein-attached, peripheral

The specialized functions of different membranes are largely determined by the ____ they contain.

proteins

These electrons are transferred through a series of molecules, and the energy released during these transfers is used to generate a gradient of ____, or ____.

protons; H+

Osmosis describes the movement of water across a biological membrane and down its concentration gradient. In chemiosmosis, useful energy is harnessed by the cell from the movement of ____ across the inner mitochondrial membrane into the matrix ____ a concentration gradient.

protons; down

The three respiratory enzyme complexes in the electron transport chain pump ____ across the inner mitochondrial membrane and into the mitochondrial ____.

protons; intermembrane space

Macrophages are especially suited for this process, as they extend ____ (sheetlike projections of their plasma membrane) to surround the invading microorganisms.

pseudopods

The final metabolite produced by glycolysis is ____.

pyruvate

Mitochondria can use both ____ and ____ directly as fuel.

pyruvate; fatty acids

This is converted into ____ (which can be used directly by the mitochondria), into ____ (which is exported to other cells), and into ____ (which is stored in the stroma).

pyruvate; sucrose; starch

Which of the following statements is true?

rRNA contains the catalytic activity that joins amino acids together.

Cells receive signals through a ____, which can be an integral membrane protein or can reside inside the cell.

receptor

An extracellular signal molecule can act to change a cell's behavior by acting through cell-surface ____ that control intracellular signaling proteins.

receptors

The sigma subunit of bacterial RNA polymerase ____.

recognize promoter sites in the DNA

If no O2 is available, all components of the mitochondrial electron-transport chain will accumulate in their ____ form. If O2 is suddenly added again, the electron carriers in cytochrome c reductase will become ____ those in cytochrome c oxidase.

reduced; oxidized after

Insulin is secreted from pancreatic cells by the ____ exocytosis pathway.

regulated

DNA makes DNA via ____. DNA makes RNA via ____. RNA instructs the synthesis of proteins via ____.

replication; transcription; translation

In the carbon fixation process in chloroplasts, carbon dioxide is initially added to the sugar ____.

ribulose 1,5-biphosphate

Proteins are transported out of a cell via the ____ or ____ pathway.

secretory; exocytic

The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ____ mechanism.

semiconservative

The piece of RNA below includes the region that codes for the binding site for the initiator tRNA needed in translation. 5'-GUAUCCCCAAGGUAUAAUGCAUCCGUCCCGGGGGC-3' Which amino acid will be on the tRNA that is the third to bind to the A site of the ribosome?

serine (Ser)

G-protein-coupled receptors (GPCRs) all have a similar structure with ____ transmembrane domains.

seven

Without this process, the yield of ATP from each glucose molecule would be ____ decreased.

severely

In simple diffusion, the molecule that would diffuse that fastest across the plasma membrane is the one that is:

smallest and hydrophobic.

A large protein that passes through the nuclear pore must have an appropriate ____.

sorting sequence, which typically contains the positively charged amino acids lysine and arginine.

Proteins that remain in the cytosol do not contain a ____.

sorting signal

Transporters, in contrast to channels, work by ____.

specific binding to solutes.

Transporters:

specifically bind molecules and change shape during the transport of those molecules.

The head group of a glycolipid is composed of ____.

sugars

When this transporter moves both ions in the same direction across the membrane, it is considered a ____; if the ions move in opposite directions, the transporter is considered an ____.

symport; antiport

Neurons communicate with each other through specialized sites called ____.

synapses

The enzyme that replicates the ends of linear chromosomes is called:

telomerase

The process of DNA replication requires that each of the parental DNA strands be used as a ____ to produce a duplicate of the opposing strand.

template

The length of time a G protein will signal is determined by ____.

the GTPase activity of Gα.

The photosystems in chloroplasts contain hundreds of chlorophyll molecules, most of which are part of ____.

the antenna complex

Bacteria and fungi often occupy the same ecological niche. Thus, as a result of "biological warfare" between the two, bacteria have produced many antifungal toxins, and fungi have produced many antibacterial toxins. Given that bacteria are prokaryotes and fungi are eukaryotes, which of the following is likely less toxic to humans?

the antibacterial agents produced by fungi

In the α helices of a transmembrane channel, hydrophilic amino acid side chains are typically in contact with:

the aqueous channel

N-linked oligosaccharides on secreted glycoproteins are attached to ____.

the asparagine in the sequence Asn-X-Ser/Thr

All intermediate filaments are of similar diameter because ____.

the central rod domains are similar in size and amino acid sequence.

Proteins that are fully translated in the cytosol and lacking a sorting signal will end up in ____.

the cytosol

In the β sheets of a transmembrane porin channel, the hydrophobic amino acid side chains are typically in contact with:

the lipid bilayer.

In principle, a eukaryotic cell can regulate gene expression at any step in the pathway from DNA to the active protein. Post-translational control occurs between:

the protein and the inactive protein

If a protein lacks a signal sequence:

the protein will remain in the cytosol.

A target cell will respond slowly to an extracellular signal if:

the response requires changes in gene expression.

An important feature of unstimulated ion channels is that:

they can open briefly and then close again.

When a GPCR binds an extracellular signal, a intracellular G protein, composed of ____ subunits, becomes activated.

three

For a cell's genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called ____.

transcription

The plasma membrane is NOT directly involved in:

transcription

There are several ways that membrane proteins can associate with the cell membrane. Membrane proteins that extend through the lipid bilayer are called ____ proteins and have ____ regions that are exposed to the interior of the bilayer.

transmembrane; hydrophobic

Transport across a membrane is said to be "coupled" when:

transport of one molecule down its gradient provides the energy to transport another molecule against its gradient.

Proteins that are fully translated in the cytosol do NOT end up in ____.

transport vesicles

Proteins that are fully translated in the cytosol do not end up in ____.

transport vesicles

Proteins are transported into the Golgi apparatus via ____.

transport vesicles.

The first mobile electron carrier in the respiratory chain is ____.

ubiquinone

Which amino acid would you expect a tRNA with the anticodon 5'-GAC-3' to carry?

valine (Val)

The main filaments found in muscle cells belong to the ____ family; people with disruptions in these intermediate filaments can have muscular dystrophy.

vimentin

The action potential is propagated by the opening of ____-gated channels.

voltage

An individual transport vesicle ____.

will fuse with only one type of membrane

Which of the following statements about the structure of microtubules is NOT true?

α-Tubulin and β-tubulin are covalently bound to make the tubulin dimer that then assembles into protofilaments.

Which of the following statements about the structure of microtubules is false?

α-Tubulin and β-tubulin are covalently bound to make the tubulin dimer that then assembles into protofilaments.

BIO 2600 FINAL

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