p.38
Signal Transduction Pathways and Cellular Responses
What typically occurs at ligand concentrations where less than 100% of receptors are bound?
Near-maximal response of a cell to a particular ligand.
p.28
Signal Transduction Pathways and Cellular Responses
What is a GPI lipid anchor?
A type of exoplasmic anchor that attaches extracellular proteins to the exoplasmic surface of the plasma membrane.
p.29
Recombinant DNA Expression Vectors
What happens when the detergent concentration is higher than the CMC?
Detergent solubilizes lipids and integral membrane proteins, forming mixed micelles.
p.29
Recombinant DNA Expression Vectors
What are examples of non-ionic detergents mentioned?
Octylglucoside and Triton X-100.
p.28
Signal Transduction Pathways and Cellular Responses
How are plasma membrane proteins anchored to the phospholipid bilayer?
By covalently linked hydrocarbon groups.
p.11
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What system can introduce single-nucleotide mutations into the genome?
Engineered CRISPR-Cas9 system.
p.31
Signal Transduction Pathways and Cellular Responses
What do all cells respond to?
Extracellular signals/stimuli that activate plasma membrane or cytosolic receptors.
p.25
Signal Transduction Pathways and Cellular Responses
What does FRAP stand for?
Fluorescence Recovery After Photobleaching.
p.28
Signal Transduction Pathways and Cellular Responses
What is the significance of GPI-anchored proteins?
They can cluster in lipid rafts.
p.35
Protein Kinase Activation and Function
What activates Protein Kinase C (PKC)?
Calcium, DAG, and phosphatidylserine.
p.15
RNA Interference Mechanisms: siRNA and miRNA
What is the result of Drosha cleaving pri-miRNA?
It generates a ~70-nucleotide pre-miRNA.
p.6
Transient and Stable Transfection Methods
What is the purpose of using specially designed plasmid vectors in transfection?
To permit the expression of cloned genes in cultured animal cells.
p.35
Protein Kinase Activation and Function
Where does PKC move upon activation?
To the cytosolic face of the plasma membrane (PM).
p.22
Signal Transduction Pathways and Cellular Responses
What is the orientation of membrane-spanning proteins during vesicle budding and fusion?
They retain asymmetric orientation, with the same protein segment always facing the cytosol.
p.25
Signal Transduction Pathways and Cellular Responses
What does 50 percent fluorescence signal recovery mean?
50 percent of the receptor molecules in the illuminated membrane patch were mobile and 50 percent were immobile over 3 minutes.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What can DNA microarray analysis reveal?
Differences in gene expression in fibroblasts under different experimental conditions.
p.27
Recombinant DNA Expression Vectors
What accumulates within the hydrophobic core of the lipid bilayer during lipid droplet formation?
Cholesterol esters and triglycerides.
p.13
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What does Cre catalyze in the loxP-Cre system?
Recombination to delete the essential exon in the functional allele.
p.20
Recombinant DNA Expression Vectors
What occurs during the mechanical dispersal of the lipid extract in water?
Lipids spontaneously form liposomes.
p.17
RNA Interference Mechanisms: siRNA and miRNA
What happens to the mRNA-siRNA hybrid in the RNAi mechanism?
Specific nucleases in the RISC cleave the mRNA-siRNA hybrid.
p.19
Recombinant DNA Expression Vectors
What type of interactions provide membrane integrity and resilience?
Noncovalent interactions between phospholipids and between phospholipids and proteins.
p.19
Recombinant DNA Expression Vectors
What prevents unassisted movement of water-soluble substances across the membrane?
The hydrophobic core of the membrane.
p.1
Recombinant DNA Expression Vectors
What is the purpose of recombinant DNA expression vectors?
To enable regulated expression of exogenous genes and production of proteins in prokaryotic and eukaryotic cells.
p.9
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What can gene mutation reveal?
Clues to the function of its product.
p.29
Recombinant DNA Expression Vectors
What occurs at concentrations lower than the CMC with non-ionic detergents?
They dissolve membrane proteins without forming micelles by coating the protein membrane-spanning regions.
p.31
Signal Transduction Pathways and Cellular Responses
What do activated receptors function as?
Transcription factors or activate G protein switches.
p.22
Signal Transduction Pathways and Cellular Responses
What happens during endocytosis?
A segment of the plasma membrane buds inward toward the cytosol and pinches off to form a separate vesicle.
p.25
Signal Transduction Pathways and Cellular Responses
What was the fluorescent antibody used in the FRAP experiment?
Specific for the asialoglycoprotein receptor protein.
p.41
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What do G protein-coupled receptors (GPCRs) respond to?
A variety of extracellular signals.
p.6
Transient and Stable Transfection Methods
What characterizes transient transfection?
The plasmid vector contains a virus replication origin but is not faithfully segregated into daughter cells and is lost over time.
p.4
Recombinant DNA Expression Vectors
What happens after IPTG is added to the transformed E. coli?
Transcription from the lac promoter occurs, producing G-CSF mRNA, which is translated into G-CSF protein.
p.40
Signal Transduction Pathways and Cellular Responses
What does a pull-down assay demonstrate regarding Rac?
It shows that the small GTP-binding protein Rac is activated by platelet-derived growth factor (PDGF).
p.13
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
How do loxP-Cre crossed mice produce Cre?
Cre is produced only in cells where the promoter is active.
p.14
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the purpose of somatic cell recombination?
To inactivate target genes in specific tissues or at specific development stages.
p.27
Recombinant DNA Expression Vectors
What happens to the lens as it grows?
It creates a spherical droplet, which is released by scission at the neck.
p.14
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What role does Cre play in the loxP system?
Cre catalyzes recombination between loxP site-specific sites.
p.14
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the function of the Cre mouse in the loxP-Cre system?
It has one target gene knockout allele and a cre gene linked to a cell-type-specific promoter.
p.38
Signal Transduction Pathways and Cellular Responses
Which experimental approaches are used to study receptors and signaling pathway intermediates?
Affinity chromatography, Western blotting, immunoprecipitation, and pull-down assays.
p.29
Recombinant DNA Expression Vectors
What is the critical micelle concentration (CMC)?
The detergent concentration at which micelles start forming.
p.15
RNA Interference Mechanisms: siRNA and miRNA
What proteins bind to the double-strand regions of pri-miRNA?
Drosha and DGCR8 (Pasha in Drosophila).
p.31
Signal Transduction Pathways and Cellular Responses
What do G protein switches regulate?
A variety of downstream pathways or induce generation of intracellular second messengers.
p.31
Signal Transduction Pathways and Cellular Responses
How do kinases and phosphatases regulate protein activity?
Through protein phosphorylation and dephosphorylation.
p.15
RNA Interference Mechanisms: siRNA and miRNA
What is the role of the RISC complex?
Binds one of the two strands of miRNA and incorporates mature miRNA with Argonaute proteins.
p.35
Protein Kinase Activation and Function
What is the dependency of PKC for its activation?
PKC is calcium dependent.
p.6
Transient and Stable Transfection Methods
What is the role of the selectable marker in stable transfection?
It allows for the selection of transfected cells that integrate the exogenous DNA into their genomes.
p.41
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
How do G proteins affect ion channels or effector enzymes?
By activating or inactivating them.
p.21
Signal Transduction Pathways and Cellular Responses
What is the structure of the plasma membrane?
A single bilayer that encloses the cell.
p.36
Protein Kinase Activation and Function
What effect does phosphorylation of PKA at threonine-197 have?
It leads to a marked conformational change in the activation loop.
p.6
Transient and Stable Transfection Methods
What happens to the cDNA-encoded protein in transient transfection?
It is produced only for a limited time.
p.32
Signal Transduction Pathways and Cellular Responses
What is the endocrine type of extracellular signaling?
Signaling molecules like epinephrine and insulin are synthesized and secreted by signaling cells, transported through the circulatory system, and affect distant target cells expressing the receptor.
p.21
Signal Transduction Pathways and Cellular Responses
What organelles are enclosed by two membranes?
Nucleus, mitochondrion, and chloroplast.
p.8
Lentivirus Vectors for Gene Delivery
What is the role of lentivirus retroviruses in gene modification?
They increase the efficiency of stable integration and expression of modified genes in animal cells.
p.40
Signal Transduction Pathways and Cellular Responses
What is the significance of Rac-GTP binding in the assay?
Only Rac-GTP will bind to the PBD, allowing for the assessment of Rac activation.
p.30
Signal Transduction Pathways and Cellular Responses
What types of proteins can signal transduction protein S1 be?
Often a GTP-binding protein or a protein kinase or phosphatase.
p.37
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What promotes binding to downstream signaling proteins in G proteins?
The active/ON state of the G protein when bound to GTP.
p.7
Lentivirus Vectors for Gene Delivery
What is VSV-G in the context of viral vectors?
A viral coat protein that enables hybrid virus particles to infect a variety of mammalian cell types.
p.1
Microarray and In Situ Hybridization for Gene Expression Analysis
What do microarray and in situ hybridization techniques reveal?
mRNA expression, co-regulation, and localization.
p.28
Signal Transduction Pathways and Cellular Responses
What components make up a phosphatidylinositol anchor?
Two fatty acyl chains inserted into the bilayer, a phosphoethanolamine unit linking the protein, and varying sugar units.
p.9
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What are some techniques for gene knockout?
Homologous recombination, CRISPR-Cas9 gene editing, or interfering RNA.
p.29
Recombinant DNA Expression Vectors
What determines the CMC of a detergent?
The hydrophobic and hydrophilic part structures of the detergent.
p.27
Recombinant DNA Expression Vectors
How do lipid droplets form?
By budding and scission from the ER membrane.
p.4
Recombinant DNA Expression Vectors
What is the function of G-CSF?
It stimulates the production of granulocytes.
p.15
RNA Interference Mechanisms: siRNA and miRNA
What is the effect of multiple RISC complexes binding to the 3′ UTR of an mRNA?
It leads to greater repression of translation.
p.13
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the purpose of the loxP-Cre recombination system?
To knock out genes in specific cell types.
p.6
Transient and Stable Transfection Methods
What is the significance of G-418 in stable transfection?
It is used to select cells that have integrated the plasmid vector carrying the selectable marker.
p.27
Recombinant DNA Expression Vectors
What forms a 'lens' during lipid droplet formation?
Delamination of the two lipid monolayers.
p.21
Signal Transduction Pathways and Cellular Responses
What are the two leaflets of the plasma membrane called?
Cytosolic and exoplasmic leaflets.
p.23
Signal Transduction Pathways and Cellular Responses
What is PE in membrane lipids?
Phosphatidyl ethanolamine.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What does a green spot indicate on a DNA microarray?
Higher expression in serum-starved cells.
p.13
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
How is the Cre gene linked to a cell-type-specific promoter in the Cre mouse?
Incorporated into the mouse genome by non-homologous recombination (NHEJ).
p.30
Signal Transduction Pathways and Cellular Responses
What is the first step in the generalized signal transduction pathway?
Receptor protein R binds ligand H.
p.14
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What happens when loxP-Cre crossed mice are produced?
Cre is expressed only in cells where the promoter is active, leading to deletion of the essential exon in those cells.
p.5
Recombinant DNA Expression Vectors
What substrate is used in Miller’s Assay for β-galactosidase activity?
o-nitrophenyl-β-D-galactopyranoside (ONPG).
p.16
RNA Interference Mechanisms: siRNA and miRNA
What is the initial form of siRNA?
Double-stranded RNA (dsRNA), either transcribed or artificially introduced.
p.26
Lipid Composition and Membrane Structure
What effect does cholesterol have on phosphoglyceride bilayer thickness?
Cholesterol increases the thickness of the phosphoglyceride bilayer.
p.1
Blotting Techniques for DNA Fragment Identification
What do blotting techniques identify?
Specific DNA fragments in complex mixtures.
p.28
Signal Transduction Pathways and Cellular Responses
What is acylation in the context of cytosolic anchors?
Anchoring of cytosolic proteins like v-Src to the plasma membrane through a single fatty acyl chain attached to the N-terminal glycine.
p.28
Signal Transduction Pathways and Cellular Responses
What is prenylation?
Anchoring of cytosolic proteins like Ras and Rab G-proteins to the membrane through a prenyl group thioether bond to C-terminal Cys-SH groups.
p.9
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
How can genes be mutated?
By introducing point mutations or using transient/stable gene knockout techniques.
p.11
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What does CRISPR stand for?
Clustered Regularly Interspaced Short Palindromic Repeats.
p.9
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What are the two types of mutations mentioned?
Chromosomal mutations and point mutations.
p.11
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What does NLS stand for in the context of CRISPR?
Nuclear Localization Signal.
p.4
Recombinant DNA Expression Vectors
What is the role of the lac promoter in E. coli expression systems?
It drives the transcription of the lacZ gene to produce β-galactosidase.
p.11
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is unique about each species regarding gene expression?
Every species has its own species-specific promoter.
p.25
Signal Transduction Pathways and Cellular Responses
What can FRAP experiments quantify?
The lateral movement of proteins and lipids within the plasma membrane.
p.22
Signal Transduction Pathways and Cellular Responses
What faces the cytosol after endocytosis?
The cytosolic face of the vesicle.
p.6
Transient and Stable Transfection Methods
What essential elements do plasmid vectors contain for functioning in both E. coli and animal cells?
Replication origin, selectable marker (e.g., amp^r), and polylinker (multiple cloning site).
p.25
Signal Transduction Pathways and Cellular Responses
What does the extent of fluorescence recovery indicate?
It is proportional to the fraction of labeled molecules that are mobile in the membrane.
p.15
RNA Interference Mechanisms: siRNA and miRNA
How do miRNA-RISC complexes inhibit mRNA translation?
By base pairing between the Argonaute-bound mature miRNA and complementary regions in the 3′ UTRs of target mRNAs.
p.36
Protein Kinase Activation and Function
What modification activates protein kinase A (PKA)?
Phosphorylation of a threonine residue in the activation loop.
p.31
Signal Transduction Pathways and Cellular Responses
What does G protein stand for?
Guanine nucleotide binding protein.
p.22
Signal Transduction Pathways and Cellular Responses
What occurs during exocytosis?
An intracellular vesicle fuses with the plasma membrane, connecting the vesicle lumen with the extracellular medium.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What is the purpose of a DNA microarray?
To evaluate the expression of thousands of genes at one time.
p.22
Signal Transduction Pathways and Cellular Responses
What is the exoplasmic face of a vesicle?
The face that faces the vesicle lumen.
p.40
Signal Transduction Pathways and Cellular Responses
What is the role of the PAK1 Rac-binding PBD domain in the assay?
It binds specifically to Rac-GTP, allowing for the quantification of Rac activation.
p.23
Signal Transduction Pathways and Cellular Responses
What are the three classes of membrane lipids?
Phosphoglycerides, Sphingolipids, Steroids.
p.29
Recombinant DNA Expression Vectors
What can be done with solubilized membrane proteins?
They can be further purified and characterized.
p.35
Protein Kinase Activation and Function
How does IP3 affect PKC?
IP3 induces a rise in Ca2+, which alters PKC.
p.4
Recombinant DNA Expression Vectors
How can granulocyte colony-stimulating factor (G-CSF) be synthesized in bacterial cells?
By replacing the lacZ gene in the plasmid with a cloned cDNA encoding G-CSF.
p.31
Signal Transduction Pathways and Cellular Responses
What is the role of protein phosphorylation in cellular pathways?
It can amplify intracellular signaling.
p.17
RNA Interference Mechanisms: siRNA and miRNA
What is RNA interference (RNAi) used for in C. elegans and other organisms?
To inhibit gene function.
p.27
Recombinant DNA Expression Vectors
What is the primary function of lipid droplets?
Storage compartments for triglycerides and cholesterol esters, and may also store proteins targeted for degradation.
p.20
Recombinant DNA Expression Vectors
What is the composition of the organic solvent used for membrane treatment?
A 3:1 mixture of chloroform and methanol.
p.41
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What do effector enzymes generate in GPCR signaling?
Second messenger molecules.
p.20
Recombinant DNA Expression Vectors
What happens to the solvent after the membrane treatment?
The solvent is removed by evaporation.
p.40
Signal Transduction Pathways and Cellular Responses
What happens to Rac during PDGF treatment?
PDGF treatment activates Rac.
p.19
Recombinant DNA Expression Vectors
What does the plasma membrane define?
It defines the cell and separates the cytosol from the extracellular environment.
p.14
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
How is a loxP site inserted into a target gene?
By homologous recombination in the introns on each side of an essential exon.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What does a red spot indicate on a DNA microarray?
Higher expression in serum(+) cells.
p.42
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What is the orientation of G protein-coupled receptors in the membrane?
N-terminus outside, C-terminus in cytosol.
p.19
Recombinant DNA Expression Vectors
What role do membrane proteins play?
They provide each cellular membrane its unique set of functions.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What is an example of using DNA microarray analysis?
Comparison of gene expression in fibroblasts starved for serum and after serum addition.
p.37
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What conformational changes occur during the ON-OFF transition of G proteins?
Involves switch I and switch II.
p.8
Lentivirus Vectors for Gene Delivery
What does the vector plasmid contain?
The cloned gene of interest next to a selectable marker, flanked by lentivirus LTR sequences.
p.39
Signal Transduction Pathways and Cellular Responses
What is the effect of activating fewer than 100% of receptors?
It usually elicits a near-maximal cellular response.
p.10
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the role of the kanMX G-418-resistance gene?
It enables the selection of kanamycin-resistant transformants in E. coli and G418-resistant transformants in yeast.
p.39
Signal Transduction Pathways and Cellular Responses
What does the dissociation constant (Kd) measure?
It measures receptor affinity for its ligand.
p.30
Signal Transduction Pathways and Cellular Responses
What is the role of signaling proteins S2, S3, S4, and S5?
They activate other signaling proteins in the pathway.
p.26
Lipid Composition and Membrane Structure
What shape do phosphatidylcholine (PC) molecules have?
PC has a cylindrical shape, forming essentially flat monolayers.
p.33
Signal Transduction Pathways and Cellular Responses
What are hydrophobic signaling molecules?
Steroids and related molecules.
p.16
RNA Interference Mechanisms: siRNA and miRNA
How does the guide strand of siRNA function?
It guides the active RISC to the target mRNA for cleavage.
p.33
Signal Transduction Pathways and Cellular Responses
What is the first step for hydrophobic signaling molecules in cell signaling?
Diffuse through the plasma membrane.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the purpose of including a single-stranded DNA segment in HDR?
To facilitate homologous recombination repair and introduce single base changes in the repaired genomic DNA.
p.26
Lipid Composition and Membrane Structure
How can proteins influence membrane curvature?
Several proteins can curve a membrane by binding to the phospholipid bilayer surface.
p.15
RNA Interference Mechanisms: siRNA and miRNA
What does Dicer do in the processing of pre-miRNA?
Processes pre-miRNA into a double-stranded miRNA with a two-base single-stranded 3′ end.
p.36
Protein Kinase Activation and Function
What is the form of protein kinase A (PKA) before activation?
Catalytically inactive, unphosphorylated form.
p.27
Recombinant DNA Expression Vectors
What do cells store in lipid droplets?
Excess lipids, including triglycerides and cholesterol esters.
p.20
Recombinant DNA Expression Vectors
What is the purpose of treating membranes with an organic solvent in the formation of phospholipid bilayers?
To selectively solubilize phospholipids and cholesterol while leaving proteins and carbohydrates in an insoluble residue.
p.35
Protein Kinase Activation and Function
What does PKC do after activation?
PKC phosphorylates target proteins.
p.22
Signal Transduction Pathways and Cellular Responses
What remains facing the cytoplasm during exocytosis?
The cytoplasmic face of the vesicle.
p.6
Transient and Stable Transfection Methods
How long do stably transfected cells produce the cDNA-encoded protein?
As long as the culture is maintained.
p.41
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What range of cellular activities do GPCR signaling pathways regulate?
From metabolism to gene expression.
p.36
Protein Kinase Activation and Function
What does the conformational change in PKA promote?
Binding of both ATP and its substrate proteins.
p.7
Lentivirus Vectors for Gene Delivery
What is the primary use of retroviral vectors in gene delivery?
For the efficient integration of cloned genes into the mammalian genome.
p.34
Signal Transduction Pathways and Cellular Responses
What is cAMP and how is it generated?
cAMP is a second messenger generated from ATP by adenylyl cyclase.
p.20
Recombinant DNA Expression Vectors
What physical properties of bilayers can be studied using planar bilayers?
Their permeability to solutes.
p.34
Signal Transduction Pathways and Cellular Responses
What does cAMP activate?
cAMP activates Protein Kinase A (PKA).
p.5
Recombinant DNA Expression Vectors
What is a key advantage of using β-galactosidase in assays?
The enzyme is easily assayed.
p.14
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
How can different cell-specific promoters affect gene knockout?
They can cause gene knockout in other specific cell types.
p.26
Lipid Composition and Membrane Structure
How does sphingomyelin (SM) bilayer thickness compare to phosphatidylcholine (PC) bilayer?
The pure sphingomyelin bilayer is thicker than the phosphatidylcholine bilayer.
p.33
Signal Transduction Pathways and Cellular Responses
What type of cells respond to a signal?
Only target cells expressing receptor proteins that bind the signal.
p.23
Signal Transduction Pathways and Cellular Responses
What is the structure of phosphoglycerides?
One fatty acid chain attached to glycerol by an ester linkage.
p.19
Recombinant DNA Expression Vectors
What is the significance of the molecular model of the lipid bilayer?
It shows the embedded membrane proteins and their arrangement within the bilayer.
p.5
Recombinant DNA Expression Vectors
What is a benefit of the β-galactosidase assay regarding equipment?
It requires no expensive equipment.
p.2
Microarray and In Situ Hybridization for Gene Expression Analysis
What is used to hybridize with the mRNA of interest in in situ hybridization?
A probe specific for the mRNA, synthesized with nucleotide analogs recognized by antibodies.
p.18
RNA Interference Mechanisms: siRNA and miRNA
How is siRNA produced in vitro?
By using two plasmid vectors containing the target gene coding sequence in opposite orientations adjacent to a strong promoter.
p.16
RNA Interference Mechanisms: siRNA and miRNA
What is the first step in the biogenesis of miRNA?
Transcription of the miRNA gene by RNA polymerase II to form pri-miRNA.
p.33
Signal Transduction Pathways and Cellular Responses
What are hydrophilic signaling molecules?
Small molecules (like adrenaline, acetylcholine), peptides (like yeast mating factors, glucagon), and proteins (like insulin, growth hormone).
p.18
RNA Interference Mechanisms: siRNA and miRNA
How is RNAi inhibition of mex3 RNA expression assayed in C. elegans embryos?
By in situ hybridization to an enzyme-linked probe that produces a purple product.
p.17
RNA Interference Mechanisms: siRNA and miRNA
What role does RISC play in RNAi?
Mediates recognition and hybridization between one strand of the siRNA and its complementary target mRNA sequence.
p.40
Signal Transduction Pathways and Cellular Responses
How does Rac regulate molecular events?
By cycling between an inactive GDP-bound form and an active GTP-bound form.
p.5
Recombinant DNA Expression Vectors
Why is β-galactosidase considered a stable reporter gene?
Its protein product is stable and resistant to proteolytic degradation.
p.26
Lipid Composition and Membrane Structure
How does lipid composition affect bilayer thickness?
It influences membrane protein distribution and bilayer thickness.
p.34
Signal Transduction Pathways and Cellular Responses
How is cGMP generated?
cGMP is generated by guanylyl cyclase.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the primary function of Cas9 in gene editing?
To precisely modify a target gene by cleaving DNA.
p.10
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the purpose of PCR primer construction in generating a disruption construct?
To create a construct containing a selectable marker gene.
p.32
Signal Transduction Pathways and Cellular Responses
What happens to some paracrine signaling molecules in relation to the extracellular matrix (ECM)?
Some may bind to the ECM and are released only when the ECM is degraded.
p.18
RNA Interference Mechanisms: siRNA and miRNA
What is the role of double-stranded RNA in RNA interference (RNAi)?
It causes straightforward inhibition of specific gene function.
p.8
Lentivirus Vectors for Gene Delivery
How is the LTR-bearing RNA introduced into target cells?
By packaging it into viral particles and then using viral infection.
p.16
RNA Interference Mechanisms: siRNA and miRNA
What is the role of AGO2 in the RISC complex?
AGO2 cleaves the passenger strand of siRNA.
p.24
Recombinant DNA Expression Vectors
What are the four major head groups of phosphoglycerides?
Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylinositol (PI).
p.26
Lipid Composition and Membrane Structure
What is the natural curvature of a bilayer enriched with PC and PE?
PC is enriched in the exoplasmic leaflet and PE in the cytosolic face, leading to natural curvature.
p.8
Lentivirus Vectors for Gene Delivery
What is the efficiency of engineered lentiviruses in infecting cells?
They infect cells with such high efficiency that every cell in a population receives at least one copy of the lentivirus-borne plasmid.
p.33
Signal Transduction Pathways and Cellular Responses
Why can't hydrophilic signaling molecules diffuse across the cell membrane?
Because they are not hydrophobic.
p.18
RNA Interference Mechanisms: siRNA and miRNA
What does the transcription of the hairpin construct form?
An shRNA that is cleaved by Dicer to form siRNA.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What does a DNA microarray chip contain?
An organized array of thousands of individual, closely packed, known gene-specific sequences attached to a glass microscope slide.
p.27
Recombinant DNA Expression Vectors
What surrounds the newly formed lipid droplet?
A lipid monolayer derived from the cytosolic leaflet of the ER membrane.
p.20
Recombinant DNA Expression Vectors
How can planar bilayers be formed for study?
By creating a bilayer over a small hole in a partition separating two aqueous phases.
p.13
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the role of homologous recombination in the loxP-Cre system?
To insert loxP sites around the essential exon.
p.3
Microarray and In Situ Hybridization for Gene Expression Analysis
What does a yellow spot indicate on a DNA microarray?
Equal hybridization of green and red fluorescence, indicating no change in gene expression.
p.37
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What are the two states of monomeric G proteins?
Active/ON state (bound GTP) and Inactive/OFF state (bound GDP).
p.21
Signal Transduction Pathways and Cellular Responses
What separates the two membranes of certain organelles?
A small intermembrane space.
p.8
Lentivirus Vectors for Gene Delivery
What are the three different plasmids used in recombinant lentivirus particle production?
Vector plasmid, packaging plasmid, and viral coat plasmid.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What components are required for the gene editing protocol using Cas9?
A plasmid encoding Cas9 and a plasmid encoding the guide RNA.
p.24
Recombinant DNA Expression Vectors
What are the three classes of amphipathic lipids that compose a typical biomembrane?
Phosphoglycerides, sphingolipids, and sterols.
p.30
Signal Transduction Pathways and Cellular Responses
What does signal transduction protein S1 do?
It binds to and activates (or inhibits) other signal transduction proteins (S2).
p.19
Recombinant DNA Expression Vectors
How do peripheral proteins associate with the membrane?
They associate primarily with integral membrane proteins or membrane lipids through specific noncovalent interactions.
p.34
Signal Transduction Pathways and Cellular Responses
What is the role of IP3?
IP3 opens channels to release Ca2+ from the endoplasmic reticulum (ER).
p.2
Microarray and In Situ Hybridization for Gene Expression Analysis
What is the first step in the assay for in situ hybridization?
Permeabilize cells in the specimen using detergent and protease.
p.39
Signal Transduction Pathways and Cellular Responses
Why is incubation at low temperature (4 °C) used in ligand binding experiments?
To prevent endocytosis of the cell-surface receptors.
p.16
RNA Interference Mechanisms: siRNA and miRNA
What is the outcome of full complementary binding between siRNA and target mRNA?
Cleavage of the target mRNA.
p.33
Signal Transduction Pathways and Cellular Responses
What happens after the hydrophobic signaling molecules bind to cytosolic receptors?
The receptor-signal complex moves into the nucleus and binds transcription-control regions in DNA.
p.2
Microarray and In Situ Hybridization for Gene Expression Analysis
What does the substrate provided to the reporter enzyme produce?
A colored precipitate where the probe has hybridized to the target mRNA.
p.2
Microarray and In Situ Hybridization for Gene Expression Analysis
Which mRNA was probed in the Drosophila embryo example?
mRNA produced during trachea development.
p.33
Signal Transduction Pathways and Cellular Responses
What is the role of specific cell-surface receptor proteins in hydrophilic signaling?
They bind the signaling molecules and trigger a conformational change that activates the receptor.
p.16
RNA Interference Mechanisms: siRNA and miRNA
How does miRNA inhibit target mRNA?
Through translational repression, degradation, or cleavage.
p.7
Lentivirus Vectors for Gene Delivery
What is a key characteristic of lentivirus in terms of cell infection?
It can infect both dividing and postmitotic cells, such as neurons.
p.32
Signal Transduction Pathways and Cellular Responses
What distinguishes paracrine signaling?
Signaling molecules like neurotransmitters and growth factors are secreted by a cell and affect only nearby target cells expressing the receptor.
p.10
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What technique can inactivate specific target genes in yeast?
Homologous recombination with transfected disruption constructs.
p.7
Lentivirus Vectors for Gene Delivery
Why does lentivirus delivery lead to long-term expression?
Because the DNA integrates into the genome.
p.34
Signal Transduction Pathways and Cellular Responses
What does cGMP activate?
cGMP activates Protein Kinase G (PKG) and specific cation channels.
p.8
Lentivirus Vectors for Gene Delivery
What is the function of the left LTR sequence in the vector plasmid?
It directs the synthesis of an RNA molecule carrying lentiviral LTR sequences at either end.
p.23
Signal Transduction Pathways and Cellular Responses
What is a characteristic structure of steroids?
Amphiphatic structure with a conjugated 4-ring hydrocarbon.
p.2
Microarray and In Situ Hybridization for Gene Expression Analysis
What does in situ hybridization retain and reveal?
Gene expression positional information in an organism.
p.24
Recombinant DNA Expression Vectors
What is the structure of phosphoglycerides?
They have a glycerol backbone with two esterified hydrophobic fatty acyl chains.
p.7
Lentivirus Vectors for Gene Delivery
How are recombinant lentivirus particles produced?
By introducing three different plasmids into cells via transient transfection.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
How does NHEJ affect gene function after cleavage?
It usually removes a few bases at the cleavage site, potentially producing a frameshift mutation that inactivates gene function.
p.5
Recombinant DNA Expression Vectors
What is monitored to measure β-galactosidase activity in the assay?
The accumulation of yellow color (increase in 420 nm absorbance) per minute.
p.2
Microarray and In Situ Hybridization for Gene Expression Analysis
What is the purpose of the antibody in the in situ hybridization assay?
To bind to the probe and is covalently linked to a reporter enzyme.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is a potential outcome of using HDR in gene editing?
It allows for the introduction of single base changes without base loss.
p.26
Lipid Composition and Membrane Structure
Why is membrane curvature important?
It is important in the formation of transport vesicles that bud from a donor membrane.
p.16
RNA Interference Mechanisms: siRNA and miRNA
What happens to pre-miRNA in the cytoplasm?
It is processed by Dicer into miRNA.
p.33
Signal Transduction Pathways and Cellular Responses
What do activated receptors do in the signaling pathway?
They activate one or more downstream signal transduction proteins or small-molecule second messengers.
p.40
Signal Transduction Pathways and Cellular Responses
What type of cells were used in the pull-down assay?
Hematopoietic stem cells.
p.30
Signal Transduction Pathways and Cellular Responses
What happens after receptor R binds to ligand H?
It triggers a conformational change in the receptor (R*) that enables it to bind to and activate signal transduction protein S1.
p.32
Signal Transduction Pathways and Cellular Responses
How do autocrine signals function?
Cells respond to signals they secrete, such as growth factors; tumor cells may overproduce and respond to these factors.
p.26
Lipid Composition and Membrane Structure
What is the difference in lipid composition between the exoplasmic and cytosolic leaflets?
They differ in the types of lipids present, affecting bilayer properties.
p.32
Signal Transduction Pathways and Cellular Responses
What is the role of membrane protein signals?
They signal neighboring cells by direct contact with surface receptors.
p.19
Recombinant DNA Expression Vectors
What characterizes lipid-anchored proteins?
They are tethered to one leaflet by a covalently attached hydrocarbon chain.
p.34
Signal Transduction Pathways and Cellular Responses
What are IP3 and DAG derived from?
IP3 and DAG are made from PIP2 by phospholipase C.
p.7
Lentivirus Vectors for Gene Delivery
Which types of cells can VSV-G-coated hybrid virus particles infect?
Hematopoietic stem cells, neurons, muscle, and liver cells.
p.37
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What happens to switch I and switch II during the OFF state of G proteins?
They relax into an off conformation, inhibiting interaction with downstream effectors.
p.10
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the significance of G-418 in the selection process?
Only recombinant diploid cells will grow on a medium containing G-418.
p.26
Lipid Composition and Membrane Structure
What shape do phosphatidylethanolamine (PE) molecules have?
PE has a conical shape, forming curved monolayers.
p.8
Lentivirus Vectors for Gene Delivery
What is the purpose of the viral coat plasmid?
It encodes the expression of a viral coat protein that allows hybrid virus particles to infect a wide variety of mammalian target cell types.
p.37
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
How does the mechanism of monomeric G proteins compare to heterotrimeric G proteins?
Both use a spring-loaded mechanism to switch between active and inactive conformations.
p.39
Signal Transduction Pathways and Cellular Responses
What is observed at relatively high ligand concentrations in receptor binding?
The number of receptor-bound ligand molecules approaches the total number of cell-surface receptors.
p.18
RNA Interference Mechanisms: siRNA and miRNA
What is the function of RISC in RNAi?
It mediates recognition and hybridization between one strand of the siRNA and its complementary target mRNA sequence.
p.39
Signal Transduction Pathways and Cellular Responses
How can drug binding to ligands be beneficial?
It can decrease overactive physiological responses that cause diseases.
p.24
Recombinant DNA Expression Vectors
What is the amphipathic structure of sterols?
They have a single polar hydroxyl head group and a tail consisting of a conjugated four-ring hydrocarbon and a short hydrocarbon chain.
p.33
Signal Transduction Pathways and Cellular Responses
What is the final step in the termination of the cellular response?
Destruction of the extracellular signal.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What is the role of the guide RNA in the Cas9 mechanism?
It base pairs with the complementary genomic DNA sequence to direct the Cas9 complex to the target region.
p.10
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What happens during homologous recombination in diploid Saccharomyces cells?
The target sequence is replaced with the marker gene.
p.12
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What are the two repair mechanisms following Cas9-induced cleavage?
Nonhomologous end joining (NHEJ) and homology-directed repair (HDR).
p.8
Lentivirus Vectors for Gene Delivery
What does the packaging plasmid carry?
Viral genes necessary for packaging LTR-containing viral RNA into a functional lentivirus particle, excluding the major viral coat protein.
p.34
Signal Transduction Pathways and Cellular Responses
How are calcium ions (Ca2+) involved in cellular signaling?
Calcium ions are released from intracellular stores or transported into the cell and activate calmodulin, specific kinases (PKC), and other regulatory proteins.
p.30
Signal Transduction Pathways and Cellular Responses
What is a key feature of most signal transduction pathways?
They have feedback controls whereby a protein in the pathway modifies either the receptor or an early protein.
p.39
Signal Transduction Pathways and Cellular Responses
What is the significance of the Kd value in ligand binding?
Kd (half maximal) ligand binding = 1 nM ligand indicates receptor affinity.
p.18
RNA Interference Mechanisms: siRNA and miRNA
What happens during the transcription of constructs in vitro?
It yields many RNA copies in both sense and complementary antisense orientations, which hybridize to form dsRNA.
p.8
Lentivirus Vectors for Gene Delivery
What happens to the cloned gene after it is reverse-transcribed into DNA?
It is transported into the nucleus and integrated into the host genome for expression.
p.18
RNA Interference Mechanisms: siRNA and miRNA
What is the outcome of the mRNA-siRNA hybrid in RNAi?
Specific nucleases in the RISC cleave the mRNA-siRNA hybrid.
p.39
Signal Transduction Pathways and Cellular Responses
What does a binding assay determine?
It determines the Kd and the number of receptors per cell.
p.33
Signal Transduction Pathways and Cellular Responses
How is the cellular response terminated?
Through negative feedback/feedback repression from intracellular signaling molecules.
p.37
G Protein-Coupled Receptors (GPCRs) and Their Mechanisms
What is the role of intrinsic GTPase activity in G proteins?
It hydrolyzes GTP to GDP, removing the GTP γ phosphate.
p.5
Recombinant DNA Expression Vectors
What type of linkage is formed by the condensation of galactose and glucose?
A β-1→4 glycosidic linkage.
p.39
Signal Transduction Pathways and Cellular Responses
What is the purpose of using labeled ligand in receptor affinity experiments?
To determine the affinity of a receptor for a ligand by measuring binding.
p.30
Signal Transduction Pathways and Cellular Responses
What is an effector protein in the context of signal transduction?
It can be an enzyme, transcription factor, transport protein, ion channel, or other type of protein.
p.10
Gene Editing Techniques: CRISPR-Cas9 and Homologous Recombination
What occurs if the target gene is essential for viability?
50 percent of the haploid spores formed by recombinant diploid cell sporulation will be nonviable.
p.24
Recombinant DNA Expression Vectors
What distinguishes plasmalogens from other phosphoglycerides?
One fatty acyl chain is attached by an ester linkage and one by an ether linkage.
p.24
Recombinant DNA Expression Vectors
What are sphingolipids derived from?
Sphingosine, an amino alcohol with a long hydrocarbon chain.
p.24
Recombinant DNA Expression Vectors
What is a characteristic feature of sphingomyelins?
They contain a phosphocholine head group.
p.24
Recombinant DNA Expression Vectors
What are sterols and their role in membranes?
Sterols are membrane components such as cholesterol in animals, ergosterol in fungi, and stigmasterol in plants.
p.18
RNA Interference Mechanisms: siRNA and miRNA
What is the structure of the hairpin construct used for shRNA production in vivo?
It contains a tandem arrangement of both sense and antisense sequences of the target gene.
p.39
Signal Transduction Pathways and Cellular Responses
What is the relationship between receptor binding and physiological response?
The relative physiological response is greater than ligand binding.
p.33
Signal Transduction Pathways and Cellular Responses
What is the function of effector proteins in cell signaling?
They stimulate modification of specific cytosolic proteins for short-term changes or move into the nucleus for long-term changes in gene expression.
