Molecular Cell Biology 7th edition Harvey Lodish, Arnold Berk, Chris A. Kaiser, Monty Krieger, Anthony Bretscher, Hidde Ploegh, Angelika Amon, Matthew P. Scott - Solutions

Even though GRB2 lacks intrinsic enzymatic activity, it is an essential component of the epidermal growth factor (EGF) signaling pathway that activates MAP kinase. What is the function of GRB2? What role do the SH2 and SH3 domains play in the function of GRB2? Many other signaling proteins pm~ess
Explain how expression of a dominant-negative mutant of JAK blocks the erythropoietin (Epo) cytokine signaling pathway.
Erythropoietin (Epo) is a hormone that is produced naturally in the body in response to low O2 levels in the blood. The intracellular events that occur in response to Epo binding to its cell surface receptor are well characterized. What molecule translocates from the cytosol to the nucleus after
Name three features common to the activation of cytokine receptors and receptor tyrosine kinases. Name one difference with respect to the enzymatic activity of these receptors.
cAMP is a second messenger that regulates many diverse cellular functions. In the intestinal lumen, cAMP is responsible for maintaining electrolyte and water balance. Certain bacterial toxins, including one produced by Vibrio cholera, can upset the levels of cAMP, leading to fatal dehydration.a.
The phosphorylation of a protein can influence its ability to interact with other proteins. These protein-protein interactions play a fundamental role in signal transduction pathways, and these interactions can be identified using numerous techniques, including fluorescence energy transfer (see
Mutations in .trimcric G proteins can cause many diseases in humans. Patients with acromegaly often have pituitary tumors that oversecrete growth hormone (GH). GH-releasing hormone (GHRH) stimulates GH release from the pituitary by binding to GHRH receptors and stimulating adenylyl cyclase.
Most of the short-term physiological responses of cells to cAMP are mediated by activation of PKA. cGMP is another common second messenger. What are the targets of cGMP in rod and smooth muscle cells?
In Chapter 3, the Kd of calmodulin's EF hands for binding Ca2+ is given as - 10 6 M. Many proteins have much higher affinities for their respective ligands. Why is the specific affinity of calmodulin important for Ca2+ signaling processes such as that initiated by production of IP3?
lnositoll,4,5-trisphosphate (IP1) and diacylglycerol (DAG) are second messenger molecules derived from the cleavage of the phosphatidylinositol 4,5-bisphosphate (PlP2) by activated phospholipase C. Describe the role of IP3 in causing a rise in cytosolic Ca2+ concentration. How do cells restore
What is the purpose of A kinase-associated proteins (AKAPs)? Describe how AKAPs work in heart muscle cells.
Continuous exposure of a G,., protein-coupled receptor to its ligand leads to a phenomenon known as desemitization. Describe several molecular mechanisms for receptor desensitization. How can a receptor be reset to its original sensitized state? What effect would a mutant receptor lacking serine or
In liver and muscle, epinephrine stimulation of the cAMP pathway activates glycogen breakdown and inhibits glycogen synthesis, whereas in adipose tissue, epinephrine activates hydrolysis of triglycerides and in other cells causes a diversity of other responses. What step in the cAMP signaling
Epinephrine binds to both β-adrenergic and a-adrenergic receptors. Describe the opposite actions on the effector protein, adcnylyl L) cyclase, elicited by the binding of epinephrine to these two types of receptors. Describe the effect of adding an agonist or antagonist to a β-adrenergic receptor
Both rhodopsin in vision and the muscarinic acetylcholine receptor system in cardiac muscle arc coupled to ion channels via G proteins. Describe the similarities and differences between these two systems.
The cholera toxin, produced by the bacterium Vibrio cholera, causes a watery diarrhea in infected individuals. What is the molecular basis for this effect of cholera toxin?
Which of the following steps amplify the epinephrine signal response in cells: receptor activation of G protein, G protein activation of adenylyl cyclase (AC), cAMP activation of PKA, or PKA phosphorylation of glycogen phosphorylase kinase (GPK)? Which change will have a greater effect on
Explain how FRET could be used to monitor the association of G"' and adenylyl cyclase following activation of the epinephrine receptor.
Signal-transducing trimeric G proteins consist of three subunits designated α, β and 'γ· The Ga subunit is a GTPase switch protein that cycles between active and inactive states depending on whether it is bound to GTP or to GDP. Review the steps for ligand-induced activation of effector
How do seven trans-membrane domain G protein-coupled receptors transmit a signal across the plasma membrane? In your answer, include the conformational changes that occur in the receptor in response to ligand binding.
To understand how a signaling pathway works, it often is useful to isolate the cell-surface receptor and to measure the activity of downstream effector proteins under different conditions. How could you use affinity chromatography to isolate a cell-surface receptor? With what technique could you
A ligand binds two different receptors with a Kd value of 10-7 M for receptor l and a Kd value of 10-9 M for receptor 2. For which receptor does the ligand show the greater affinity? Calculate the fraction of receptors that have a bound ligand (IRL] / Rr) in the case of receptor 1 and receptor 2 if
Signaling by soluble extracellular molecules can be classified as endocrine, paracrine, or autocrine. Describe how these three types of cellular signaling differ. Growth hormone is secreted from the pituitary, which is located at the base of the brain and acts through growth hormone receptors
What common features are shared by most cell signaling systems?
A child appears to be suffering from I-cell disease, but when a sample of his proteins (lane 3* below), isolated from skin fibroblasts, is compared to protein samples from fibroblasts of his healthy parents (lanes 1 and 2) and siblings (lanes 4€“6) using Western blot analysis and
You have genetically engineered green fluorescent protein (GFP) containing a KDEL sequence. When the construct is transfected into normal human fibroblasts and examined using fluorescence microscopy, the fluorescence appears throughout the cytoplasm, as drawn below.a. How would you explain this $Nuclear fraction 90 kDa RER fraction 72 kDa 66 kDa 40 kDa 21 kDa Molecular weight ladder Cytoplasmic fraction Golgi frac$
In order to examine the specificity of membrane fusion conferred by specific v-SNAREs and t-SNAREs, researchers reconstituted liposomes (artificial lipid membranes) with specific t-SNARE complexes or with v-SNAREs (see McNew et al., 2000, Nature 407:153-159). To measure fusion, the v-SNARE
Explain the mechanism by which action potentials are prevented from being propagated to a postsynaptic cell if transmitted across an inhibitory synapse.
Neurons, particularly those in the brain, receive multiple excitatory and inhibitory signals. What is the name of the extension of the neuron at which such signals are received? How does the neuron integrate these signals to determine whether or not to generate an action potential?
Following the arrival of an action potential in stimulated cells, synaptic vesicles rapidly fuse with the presynaptic membrane. This happens in less than 1 ms. What mechanisms allow this process to take place at such great speed?
Describe the ion dynamics of the muscle-contraction process.
Acetylcholine is a common neurotransmitter released at the synapse. Predict the consequences for muscle activation of decreased acetylcholine esterase activity at nerve-muscle synapses.
Describe the mechanism of action for addictive drugs such as cocaine.
What is myelination? Myelination causes clustering of voltage-gated Na+ channels and Na+ IK+ pumps at nodes of Ran vier along the axon. Predict the consequences to action potential propagation of increasing the spacing between nodes of Ranvier by a factor of 10.
Why is the cell unable to initiate another action potential if stimulated during the refractory period?
What prevents a nerve signal from traveling "backwards" toward the cell body?
What does it mean to say that action potentials are "all or none"?
Explain why the membrane potential does not continue to increase, but rather, plateaus and then decreases during the course of an action potential.
Explain why the strength of an action potential doesn't decrease as it travels down an axon.
Explain how the crystal structures of potassium ion channels suggest the way in which the voltage-sensing domains interact with other parts of the proteins to open and close the ion channels. How does this structure-function relationship apply to other voltage-gated ion channels?
Name the three phases of an action potential. Describe for each the underlying molecular basis and the ion involved. Why is the term voltage-gated channel applied to Na channels involved in the generation of an action potential?
The resting potential of a neuron is -60 mV inside compared with outside the cell. How is the resting potential maintained in animal cells?
What is the role of glial cells in the brain and other parts of the nervous system?
An Analyze the Data question for this chapter can be found at the Molecular Cell Biology website: www.whfreeman.com/lodish7e
How do lAPs (inhibitor of apoptosis proteins) interact with caspases to prevent apoptosis? How do mitochondrial proteins interact with lAPs to prevent inhibition of apoptosis?
Predict the effects of the following mutations on the ability of a cell to undergo apoptosis:a. Mutation in Bad such that it cannot be phosphorylated by protein kinase B (PKB)b. Over expression of Bcl-2c. Mutation in Bax such that it cannot form homodimers One common characteristic of cancer cells
TNF and Fas ligand bind cell-surface receptors to trigger cell death. Although the death signal is generated external to the cell, why do we consider the death induced by these molecules to be apoptotic rather than necrotic?
Based on your understanding of the events surrounding cell death, predict the effect(s) of the following on the ability of a cell to undergo apoptosis:a. Functional CED-9; nonfunctional CED-3b. Active Bax and cytochrome c.,; nonfunctional caspase-9c. Inactive PI-3 kinase; active Bad
Identify and list the functions of the three general classes of proteins that control cell death.
Compare and contrast cell death by apoptosis and necrosis.
How do studies of brain development in knockout mice support the statement that apoptosis is a default pathway in neuronal cells?
Discuss the role of par genes in generating A-P polarity in the C. elegans embryo.
Asymmetric cell division often relies on cytoskeletal elements to generate or maintain the asymmetric distribution of cellular factors. In S. cerevisiae, what factor is localized to the bud by myosin motors? ln Drosophila neuroblasts, what factors are localized apically by microtubules?
The roundworm C. elegans has proved to be a valuable model organism for studies of cell birth, cell asymmetry, and cell death. What properties of C. elegans render it so well suited for these studies? Why is so much information from C. elegans experiments of use to investigators interested in
Explain how hematopoietic stem cells were shown experimentally to be both pluripotent and capable of self-renewal.
Explain how intestinal stem cells were first identified and then experimentally established to be multi potent stem cells.
True or false: Differentiated somatic cells have the capacity to become reprogrammed to become other cell types. Provide one line of evidence discussed in the chapter that corroborates your response.
Identify whether the following contain totipotent, pluripotent, or multipotent cells:(a) Inner cell mass(b) Morula,(c) Eight-cell embryo(d) Trophectoderm.
In 1997, Dolly the sheep was cloned by a technique called somatic-cell nuclear transfer (or nuclear-transfer cloning). A nucleus from an adult mammary cell was transferred into an egg from which the nucleus had been removed. The egg was allowed to divide several times in culture, then the embryo
Where are stem cells located in plants? Where are stem cells located in adult animals? How does the concept of stem cell differ between animal and plant systems?
What two properties define a stem cell? Distinguish between a totipotent stem cell, a pluripotent stem cell, and a precursor (progenitor) cell.
What do LDL receptor (LDLR) cytoplasmic domain mutations that cause familial hypercholesterolemia reveal about the receptor-mediated endocytosis (RME) pathway?
Compare and contrast the location and pH sensitivity of receptor-ligand interaction in the LDL and transferrin receptor-mediated endocytosis (RME) pathways?
The phagocytic and autophagic pathways serve two fundamental roles, but both deliver their vesicles to the lysosome. What arc the fundamental differences between the two pathways? Describe the three basic steps in the formation and fusion of autophagic vesicles.
What mechanistic features are shared by(a) The formation of multivesicular endosomes by budding into the interior of the endosome and(b) The outward budding of HIV virus at the cell surface? You wish to design a peptide inhibitor/ competitor of HIV budding and decide to mimic in a synthetic peptide
Describe how pH plays a key role in regulating the interaction between mannose 6-phosphate and the mannose 6-phosphate receptor. Why does elevating endosomal pH lead to the secretion of newly synthesized lysosomal enzymes into the extracellular medium?
What does the budding of influenza virus and vesicular stomatitis virus (VSV) from polarized MDCK cells reveal about the sorting of newly synthesized cell plasma membrane proteins to the apical or basolateral domains? Now consider the following result: A peptide with a sequence identical to that of
The TGN, trans-Golgi network, is the site of multiple sorting processes as proteins and lipids exit the Golgi complex. Compare and contrast the sorting of proteins to lysosomes versus the packaging of proteins into regulated secretory granules such as those containing insulin. Compare and contrast
1-cell disease is a classic example of an inherited human defect in protein targeting that affects an entire class of proteins, soluble enzyme of the lysosome. What is the molecular defect in I-cell disease? Why does it affect the targeting of an entire class of proteins? What other types of
Clathrin adapter protein (AP) complexes bind directly to the cytosolic face of membrane proteins and also interact with clathrin. What are the four known adapter protein complexes? What observation regarding AP3 suggests that clathrin is an accessory protein to a core coat composed of adapter
Sorting signals that cause retrograde transport of a protein in the secretory pathway are sometimes known as retrieval sequences. List the two known examples of retrieval sequences for soluble and membrane proteins of the ER. How does the presence of a retrieval sequence on a soluble ER protein
What feature of procollagen synthesis provided early evidence for the Golgi cisternal maturation model?
Sec18 is a yeast gene that encodes NSF. It is a class C mutant in the yeast secretory pathway. What is the mechanistic role of NSF in membrane trafficking? As indicated by its class C phenotype, why does an NSF mutation produce accumulation of vesicles at what appears to be only one stage of the
Specificity in fusion between vesicles involves two discrete and sequential processes. Describe the first of the two processes and its regulation by GTPase switch proteins. What effect on the size of early endosomes might result from Over-expression of a mutant form of Rab5 that is stuck in the
Microinjection of an antibody known as EAGE, which reacts with the "hinge" region of the β subunit of COPI, causes accumulation of Golgi enzymes in transport vesicles and inhibits anterograde transport' of newly synthesized vesicles from the ER to the plasma membrane. What effect does the antibody
Treatment of cells with the drug brefeldin A (BfA) has the effect of decoating Golgi apparatus membranes, resulting in a cell in which the vast majority of Golgi proteins arc found in the ER. What inferences can be made from this observation regarding roles of coat proteins other than promoting
Vesicle budding is associated with coat proteins. What is the role of coat proteins in vesicle budding? How are coat proteins recruited to membranes? What kinds of molecules are likely to be included or excluded from newly formed vesicles? What is the best-known example of a protein likely to be
The studies of Palade and colleagues used pulse-chase labeling with radioactively labeled amino acids and autoradiography to visualize the location of newly synthesized proteins in pancreatic acinar cells. These early experiments provided invaluable information on protein synthesis and
Antibody labeling of proteins like that used in immune-fluorescence analysis can be applied to electron microscopy, but instead of using fluorescent labels attached to antibodies, investigators use gold particles that are electron dense and appear as uniform dots in an electron micrograph.
Recently, researchers discovered that treating mammalian cells with juniferdin, a plant-derived compound, affects protein secretion, and have reported that the target of this drug is protein disulfide isomerase (POI). In the following experiment, cultured pancreatic Î²-cells were treated
Imagine that you are evaluating the early steps in translocation and processing of the secretory protein prolactin. By using an experimental approach similar to that shown in Figure 13-7, you can use truncated prolactin mRNAs to control the length of nascent prolactin polypeptides that are
Why is localization of Ran-GAP in the nucleus and Ran-GEF in the cytoplasm necessary for unidirectional transport of cargo proteins containing an NES?
The nuclear import of proteins larger than 40 kDa requires the presence of what amino acid sequence? Describe the mechanism of nuclear import. How are nuclear transport receptors able to get through the nuclear pore complex?
Suppose that you have identified a new mutant cell line that lacks functional peroxisomes. Describe how you could determine experimentally whether the mutant is primarily defective for insertion/assembly of peroxisomal membrane proteins or matrix proteins.
Peroxisomes contain enzymes that use molecular oxygen to oxidize various substrates, but in the process hydrogen peroxide––a compound that can damage DNA and proteins––is formed. What is the name of the enzyme responsible for the breakdown of hydrogen peroxide to water? What is the
Design a set of experiments using chimeric proteins, composed of a mitochondrial precursor protein fused to dihydrofolate reductase (DHFR), that could be used to determine how much of the precursor protein must protrude into the mitochondrial matrix in order for the matrix-targeting sequence to be
Describe the similarities and differences between the mechanism of import into the mitochondrial matrix and the chloroplast stroma.
Describe what would happen to the precursor of a mitochondrial matrix protein in the following types of mitochondrial mutants: (a) A mutation in the Tom22 signal receptor; (b) A mutation in the Tom70 signal receptor; (c) A mutation in the matrix Hsc70; and (d) A mutation in the
Name four different proteins that facilitate the modification and/or folding of secretory proteins within the lumen of the ER. Indicate which of these proteins covalently modifies substrate proteins and which brings about only conformational changes in substrate proteins.
Temperature-sensitive yeast mutants have been isolated that block each of the enzymatic steps in the synthesis of the dolichol-oligosaccharide precursor for N-linked glycosylation. Propose an explanation for why mutations that block synthesis of the intermediate with the structure
An abundance of misfolded proteins in the ER can result in the activation of the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways. UPR decreases the amount of unfolded proteins by altering gene expression of what type of genes? What is one manner in which ERAD may
Describe the typical principles used to identify topogenic sequences within proteins and how these can be used to develop computer algorithms. How does the identification of topogenic sequences lead to prediction of the membrane arrangement of a multipass protein? What is the importance of the
Translocation into most organelles usually requires the activity of one or more cytosolic proteins. Describe the basic function of three different cytosolic factors required for translocation into the ER, mitochondria, and peroxisomes, respectively.
Describe the source or sources of energy needed for unidirectional translocation across the membrane in (a) Cotranslational translocation into the endoplasmic reticulum (ER);(b) Post-translational translocation into the ER; (c) Translocation into the mitochondrial matrix.
The following results were obtained in early studies on the translation of secretory proteins. Based on what we now know of this process, explain the reason why each result was observed. (a) An in vitro translation system consisting only of mRNA and ribosomes resulted in secretory proteins
A proton gradient can be analyzed with fluorescent dyes whose emission-intensity profiles depend on pH. One of the most useful dyes for measuring the pH gradient across mitochondrial membranes is the membrane-impermeant, water-soluble fluorophore 2', 7'-bis-(2-carboxyethyl )-5(6)-carboxyfluorescein
Rubisco, which may be the most abundant protein on earth, plays a key role in the synthesis of carbohydrates in organisms that use photosynthesis. What is rubisco, where is It located, and what function does it serve?
The Calvin cycle reactions that fix CO2 do not function in the dark. What are the likely reasons for this? How are these reactions regulated by light?
Chloroplasts contain two photosystems. What is the function of each? For linear electron flow, diagram the flow of electrons from photon absorption to NADPH formation. What does the energy stored in the form of NADPH synthesize?
Photosynthesis in green and purple bacteria does not produce O2. Why? How can these organisms still use photosynthesis to produce ATP? What molecules serve as electron donors in these organisms?

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Molecular Cell Biology 7th edition Harvey Lodish, Arnold Berk, Chris A. Kaiser, Monty Krieger, Anthony Bretscher, Hidde Ploegh, Angelika Amon, Matthew P. Scott - Solutions

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