Week 6

PollEV ALS 16: An absence of which protein in the "abnormal" population of cells could produce the result observed in the graph below? A B C D E

A

WEEKLY QUIZ: Which of the following might be expected to directly turn off calmodulin activity? A. Activating a plasma membrane calcium ion pump. B. Opening a plasma membrane voltage gated sodium ion channel. C. Turning off a plasma membrane potassium ion channel. D. A rapid increase in the concentration of GTP in the cytoplasm. E. Release of GDP from the activated calmodulin.

A. Activating a plasma membrane calcium ion pump.

Pre-ALS 16: Which of the following statements is true? A. An androgen receptor that lacks a DNA binding domain can still signal. B. Thyroid hormone receptors are located in the cytosol until they bind to a ligand. C. A retinoid hormone receptor lacking a ligand binding domain would be unable to regulate gene expression. D. Unlike the androgen receptor, the retinoic acid receptor (RAR) does not bind a co-activator protein.

A. An androgen receptor that lacks a DNA binding domain can still signal.

PollEV ALS 16: Describe three essential domains found in nuclear hormone receptors(and be able to explain their individual functions). A. DNA binding domain; ligand binding domain; transcriptional activation domain. B. Ligand binding domain; DNA binding domain, kinase domain. C. Ligand binding domain, transcriptional activation domain, kinase domain. D. DNA binding domain, transcriptional activation domain, kinase domain.

A. DNA binding domain; ligand binding domain; transcriptional activation domain.

PollEV ALS 15: Which type(s) of tubulin PTM might you predict to find enriched in axons and dendrites compared to the soma in a neuron? A. Polyglycylation B. Polyglutamylation C. Neither PTM D. Both PTMs

B. Polyglutamylation

PollEV ALS 15: Which of the indicated amino acids within the SH2 domain do you predictforms an electrostatic interaction with the phosphorylated-tyrosine residuein a target protein? A B C D E

D

PollEV ALS 16: Why is it contraindicated (could produce a risk) to use Viagra (sildenafil)and nitrates at the same time? A. The combination of these drugs can produce an unsafe increase in blood pressure. B. The combination of these drugs could produce an unsafe decrease in blood pressure. C. The combination of these drugs counteract each other's effect. D. The combination of these drugs produce an additive effect. E. B & D

E. B & D

WEEKLY QUIZ: A kinase modifies the side chain of two serine and three threonine amino acids in a protein. Which of the following statements are true or false regarding the non-phosphorylated protein and the phosphorylated protein ? (Select the correct response based on the correct combination of letters - e.g. TTFF would indicate statement 1 and 2 are true and statements 3 and 4 are false.) 1. The phosphorylated protein has a smaller molecular mass than the non-phosphorylated protein. 2. The overall (net) charge of the non-phosphorylated protein is more positive compared to the phosphorylated protein. 3. The phosphorylated protein might be more likely to interact with proteins containing a SH2 and a PTB domain. 4. The non-phosphorylated protein might be more likely to interact with proteins containing a SH2 and a PTB domain. A. FTFF B. TFTF C. FTTF D. FFTF E. TTTF

A. FTFF

PollEV ALS 16: Your friend has drunk a cocktail that suddenly inhibits guanylyl cyclase and is experiencing severe chest pains and shortness of breath. Which of the following theoretical treatments might providehim with some quick relief? A. Introduce cGMP into his smooth muscle cells. B. Introduce guanylyl cyclase into his endothelial cells. C. Allow him to breath oxygen mixed with nitric oxide. D. Increasing release of acetylcholine at the nerve terminals next toendothelial cells

A. Introduce cGMP into his smooth muscle cells.

WEEKLY QUIZ: Which of the following conclusions can you make from your results as to what causes there to be more normal human male tissue culture cells in a dish approximately 16 hours after treatment with testosterone? A. None of the above conclusions is fully supported by the results. B. Smooth cells divide more rapidly. C. Wrinkled cells divide more rapidly. D. A wrinkled appearance 15 min after exposure to testosterone is necessary for cells to divide more rapidly.

A. None of the above conclusions is fully supported by the results.

PollEV ALS 15: What is the mnemonic that describes the rudimentary components of ageneric signaling pathway and what are the components? A. SR-TER B. SIR-TR C. LR-TUR D. SPR-TER E. SIR-TUR

A. SR-TER

PollEV ALS 15: Which of the following explains why different types of cells can respond tothe same extra-cellular signaling molecule in a different manner? A. Many different types of cells express the same transmembrane receptor B. Different types of cells can have different intracellular signal transduction machinery C. The generic signaling pathway is similar in all cell types D. Some cell types don't bind the extra-cellular signaling molecule

B. Different types of cells can have different intracellular signal transduction machinery

Pre-ALS 16: Compared to normal cells, which of the following signalling events would be altered in a human male tissue culture cell line in which the gene encoding the androgen receptor contained a missense mutation that abolishes the receptor's DNA binding activity? A. Non-genomic, but not genomic responses would be affected following addition of testosterone to a tissue culture dish containing the cells. B. Genomic, but not non-genomic responses would be affected following addition of testosterone to a tissue culture dish containing the cells. C. Both genomic and non-genomic responses would be affected following addition of testosterone to a tissue culture dish containing the cells. D. The mutated androgen receptor would be present in the nucleus in the absence of ligand.

B. Genomic, but not non-genomic responses would be affected following addition of testosterone to a tissue culture dish containing the cells.

Pre-ALS 15: You are working in a lab as a Bio199 student studying the function of a novel gene that encodes a cell surface transmembrane receptor in Drosophila (fruit-fly). Drosophila mutants that lose the function of this receptor show dramatic developmental defects involving loss of legs. Your boss asks you to start analyzing the mouse version of the gene encoding the related cell surface receptor. What might you discover when you undertake this task? A. The mouse genome doesn't appear to have a gene that can encode a protein related to the receptor found in Drosophila. B. The mouse genome has several genes whose exon coding sequence differ slightly from each other, but each gene is predicted to encode a receptor that is similar to the receptor found in Drosophila. C. The mouse genome appears to also have only one gene encoding the transmembrane receptor and its amino acid sequence is identical.

B. The mouse genome has several genes whose exon coding sequence differ slightly from each other, but each gene is predicted to encode a receptor that is similar to the receptor found in Drosophila.

PollEV ALS 15: Which parts of this generic signal transduction pathwaycorrespond to (1) Integration of a signal and (2)Amplification of a signal? A. 1 = d; 2 = e B. 1 = c, 2 = b C. 1 = d, 2 = b D. 1 = b, 2 = c

C. 1 = d, 2 = b

WEEKLY QUIZ: Which of the following molecules could best be categorized as functioning by "Transducing and Amplifying" a signal? A. E3 ligase in TNF-alpha signaling B. Retinoic Acid Receptor (RAR) without ligand in nuclear hormone receptor signaling. C. Guanylyl cyclase in NO signaling D. Hsp90 in androgen receptor signaling E. Citrulline in NO signaling

C. Guanylyl cyclase in NO signaling

WEEKLY QUIZ: Which of the following explanations would best explain why cells in some dishes became wrinkled 15 min after addition of testosterone? A. Transcription of target genes by an activated estrogen receptor caused a change in the actin cytoskeleton. B. Transcription of target genes by an activated androgen receptor caused a change in the actin cytoskeleton. C. Non-genomic responses by an activated androgen receptor caused a change in the actin cytoskeleton. D. Non-genomic responses by an activated estrogen receptor caused a change in the actin cytoskeleton. E. Non-genomic and genomic responses by an activated androgen receptor caused a change in the actin cytoskeleton.

C. Non-genomic responses by an activated androgen receptor caused a change in the actin cytoskeleton.

PollEV ALS 15: Which of the following molecular mechanisms is mostly responsible for generating proteins containing different combinations of modular domains during evolution? A. "Shuffling" of peptide modular domains by the activity of protein endopeptidases and protein ligases acting upon different proteins. B. Splicing between mRNAs encoding different proteins. C. Recombination of genes encoding different proteins.

C. Recombination of genes encoding different proteins.

Pre-ALS 16: Indicate true (T) or false (F) for the statements below regarding cellular signaling mediated by nitric oxide (NO). Your final answer will be a four-letter string composed of letters T and F only, e.g. TTTF. ( ) Once produced, NO can diffuse to neighboring cells. ( ) The lifetime of NO is 5 - 10 minutes. ( ) NO normally decreases cGMP concentration by directly activating cGMP phosphodiesterase. ( ) The drug Viagra® counteracts the effects of NO on penile blood vessels. A. TTTT B. TTFF C. TFFF D. TFFT E. FTFF

C. TFFF

WEEKLY QUIZ: Which of the following conclusions about activity of the X-linked androgen receptor (AR) in the two new cell lines might best fit with your results? A. The gene encoding the AR in cell line Unk#2 has a mutation that affects the ability of the AR to bind to DNA. B. The gene encoding the AR in cell line Unk#2 is not being expressed at all. C. The gene encoding the AR in cell line Unk#1 has a mutation that affects the ability of the AR to bind to DNA. D. The gene encoding the AR in cell line Unk#1 is not being expressed at all. E. None of the above conclusions fits with the results obtained.

C. The gene encoding the AR in cell line Unk#1 has a mutation that affects the ability of the AR to bind to DNA.

PollEV ALS 15: Which amino acids can be commonly modifiedby phosphorylation in animal cells? A. Serine, Threonine and Glutamine B. Serine, Asparagine and Glutamine C. Threonine, Tyrosine and Serine D. Tyrosine, Arginine and Serine E. Tyrosine, Serine and Glutamine

C. Threonine, Tyrosine and Serine

WEEKLY QUIZ: Which of the following explanations would best fit your results concerning the appearance of the cells 15 min after addition of testosterone ? A. Unk#1 cells have not undergone a non-genomic response to testosterone, while Unk#2 cells have undergone a non-genomic response to testosterone. B. Unk#1 cells have not undergone a genomic response to testosterone, while Unk#2 cells have undergone a genomic response to testosterone. C. Unk#1 cells have undergone a non-genomic response to testosterone, while Unk#2 cells have not undergone a non-genomic response to testosterone. D. Unk#1 cells have undergone a genomic response to testosterone, while Unk#2 cells have not undergone a genomic response to testosterone. E. Both the Normal plus T cells and Unk#1 cells have undergone a genomic response to testosterone.

C. Unk#1 cells have undergone a non-genomic response to testosterone, while Unk#2 cells have not undergone a non-genomic response to testosterone.

PollEV ALS 15: Which of the following signals doesn't need a cell surface transmembrane receptor or channel to enter a cell? A. Glucose B. Sodium ions C. SARS-CoV-2 D. Dexamethasone (see figure below) E. ZincD103

D. Dexamethasone (see figure below)

PollEV ALS 16: Which of the following GFP-nuclear receptor fusion proteins might be present in the cells in this time-lapse animation? A. GFP-thyroid hormone receptor B. GFP-vitamin-D receptor C. GFP-retinoid receptor D. GFP-androgen receptor

D. GFP-androgen receptor

PollEV ALS 15: Which protein could inhibit this signaling pathway when present at a high concentration? A. Sos B. The "scaffold protein" C. A mutant form of Sos that is always active. D. IRS1 that has no tyrosine amino acids in its cytoplasmic "tail".

D. IRS1 that has no tyrosine amino acids in itscytoplasmic "tail".

Pre-ALS 15: A cell expresses a transmembrane protein that is cleaved at the plasma membrane to release an extracellular fragment. The fragment binds to receptor proteins on nearby cells and activates signaling pathways resulting in altered gene expression patterns in the cells. Which of the following best describes this form of intercellular signaling ? A. Contact-dependent signaling B. Endocrine signaling C. Synaptic signaling D. Paracrine signaling

D. Paracrine signaling

WEEKLY QUIZ: You are a Bio199 student working in a lab that studies nuclear hormone receptors (yipee !). The clinical fellow working with you has taught you how to culture (grow and divide) human fibroblast cells in tissue culture dishes. She gives you two new cell lines developed from two new male patients seen by the clinic and asks you to investigate the response of each cell line to having testosterone added to the tissue culture media in their dishes. So that you can compare the results obtained to those expected from a normal male human cell line, she asks you to use an appropriate negative and positive control in your experiment. Your prepare four dishes of cultured human fibroblast cells. One dish contains cells from the first new male patient (Unk#1) while a second dish contains cells from the second new male patient (Unk#2). The two remaining dishes each contain cells from the same known normal human male. Your prepare all four dishes to contain the same number of cells. Next, you add testosterone (T) to each dish containing the two new cell lines (Unk#1 and Unk#2). You also add testosterone to one dish containing a known normal human cell line (Normal plus T), but you do not add testosterone to the second dish containing the normal human cell line (Normal without T). After adding the testosterone, you watch the cells in each dish using a microscope for 15 minutes and record their morphology. You then replace the dishes in the tissue culture incubator. The next day you re-examine each of the dishes and record some more results. You take a coffee break and review your results which include the following. Q2. Which dish is your positive control for a cellular response to testosterone, and which dish is your negative control ? A. Positive control is Normal without T; Negative control is Normal plus T B. Positive control is Unk#1; Negative control is Normal without T C. Positive control is Normal plus T; Negative control is Unk#2 D. Positive control is Normal plus T; Negative control is Normal without T E. Positive control is Normal plus T; Negative control is Unk#1

D. Positive control is Normal plus T; Negative control is Normal without T

Pre-ALS 15: Which statement best describes how molecular complementarity enables specificity during a signaling event? A. The molecular shape of two molecules should have a large amount of overall complementarity that involves strong interactions at multiple different sites. B. The molecular shape of two molecules should have a small amount of complementarity. C. The molecular shape of two molecules should have a large amount of overall complementarity that involves covalent interactions at multiple different sites. D. The molecular shape of two molecules should have a large amount of overall complementarity that involves weak interactions at multiple different sites.

D. The molecular shape of two molecules should have a large amount of overall complementarity that involves weak interactions at multiple different sites.

WEEKLY QUIZ: You are working in a biochemistry lab as a Bio199 student. After many days working in a cold room, you have managed to purify a single protein from extracts from human fibroblasts. You wish to find out the sub-cellular location of your protein in human fibroblasts, so you send your protein to a company that makes polyclonal antiserum by immunizing rabbits with your protein. About two months later, you receive a package from the company that contains two tubes shipped with ice-packs to keep the contents fresh. One tube (A) contains serum taken from the rabbit before it was immunized with your purified protein. The second tube (B) contains serum taken from the same rabbit 8 weeks after it had been immunized twice with your protein, with a gap of 4 weeks between injections. Using your knowledge from the first half of D103, you perform an immunofluorescence analysis of fixed human fibroblast cells using diluted serum from the two different tubes (A and B). You fix two identical samples of your fibroblasts that were grown on glass slides and then incubate one with serum from tube A and the other using serum from tube B. After rinsing the slides, you incubate both with the same fluorescently labeled anti-rabbit secondary antibody. You then examine your cells under a fluorescence microscope. Human fibroblast cells reacted using serum from tube A show weak fluorescence at the plasma membrane only, while the same human fibroblast cells reacted with serum from tube B show fluorescence in the nucleus as well as weak fluorescence at the plasma membrane. Based on these results, what do you predict is the more likely subcellular location of your purified protein in human fibroblasts? Also, why did the company also provide you with a sample of serum from the rabbit before it was immunized with your purified protein? A. The purified protein is more likely to be located in at the nucleus. The company sent a sample of the serum taken from the rabbit before immunization for use as a positive control in the immunofluorescence analysis. B. The purified protein is more likely to be located in at the plasma membrane. The company sent a sample of the serum taken from the rabbit before immunization for use as a negative control in the immunofluorescence analysis. C. The purified protein is more likely to be located in at the plasma membrane. The company sent a sample of the serum taken from the rabbit before immunization for use as a positive control in the immunofluorescence analysis. D. The purified protein is more likely to be located in the nucleus. The company sent a sample of the serum taken from the rabbit before immunization for use as a negative control in the immunofluorescence analysis.

D. The purified protein is more likely to be located in the nucleus. The company sent a sample of the serum taken from the rabbit before immunization for use as a negative control in the immunofluorescence analysis.

Pre-ALS 15: Evolutionary biology studies have identified the most invariant (conserved) aminoacids found within the SH2 domain family. Which of the following is true regardingthese invariant amino acids? A. The invariant amino acids generally have negatively charged side chains. B. The amino acids at these sites are generally hydrophobic. C. These sites evolve (change) relatively quickly because they have critical functions. D. These amino acids have an important function in allowing binding of the SH2 domain to a phosphorylated tyrosine. E. Mutation in these sites generally keeps the protein functional.

D. These amino acids have an important function in allowing binding of the SH2 domain to a phosphorylated tyrosine.

Pre-ALS 15: Which of the following is NOT a common mechanism used to regulate activity of signaling proteins? A. Binding of another molecule to the signaling protein B. Masking of a NLS signal in the signaling protein by another protein C. Degradation of the signaling molecule by proteolysis D. Uptake of the signaling protein by the ER E. Covalent modification of a protein involved in a signaling pathway (e.g. phosphorylation)

D. Uptake of the signaling protein by the ER

Pre-ALS 16: Select the correct phrase to complete the following sentence. "All nuclear hormone receptors ..." A. are transcriptional activators when bound to their ligand. B. are transcriptional repressors in the absence of their ligand. C. are cytosolic proteins that enter the nucleus upon ligand binding. D. have ligand-binding and DNA-binding domains, and can directly bind to DNA. E. bind to steroid hormones.

D. have ligand-binding and DNA-binding domains, and can directly bind to DNA.

PollEV ALS 16: What would happen to signaling if an amino acid was changed within the DNA binding domain of the androgen receptor that prevented the NHR from binding to DNA? A. The receptor would bind its ligand, but not bind DNA, therefore it would be unable to directly stimulatetranscription in the nucleus. B. The receptor would bind to DNA in the absence of ligand. C. The variable region can still activate DNA transcription, so signaling could continue. D. Signaling could continue at the inner leaflet of the plasma membrane. E. A and D are likely to occur

E. A and D are likely to occur

Pre-ALS 15: Which domains would you expect to find in an adaptor signaling protein capable ofsimultaneously binding to (i) a phospho-tyrosine; (ii) a phosphatidyl-inositol (3,4,5)tri-phosphate (PI(3,4,5)P ) and (iii) a di-acyl glycerol (DAG)? A. A protein containing a FYVE, a 14-3-3, and a SH2 domain. B. A protein containing a C1, a FYVE and a WW domain. C. A protein containing a SH2, a FYVE and a PH domain. D. A protein containing a SH3, a Tubby and a C1 domain. E. A protein containing a SH2, a C1 and a PH domain.

E. A protein containing a SH2, a C1 and a PH domain.

Pre-ALS 16: What is the receptor for nitric oxide (NO) in blood vessels? A. Calmodulin in endothelial cells. B. Nitric oxide synthase in endothelial cells. C. Cyclic GMP in smooth muscle cells. D. Guanylyl cyclase in endothelial cells. E. Guanylyl cyclase in smooth muscle cells.

E. Guanylyl cyclase in smooth muscle cells.

WEEKLY QUIZ: Which protein in the TNF-alpha signaling pathway serves a similar function to Hsp90 in the steroid hormone signaling pathway? A. p50 B. p65 C. I-kB kinase D. E3 ligase E. I-kB alpha

E. I-kB alpha

Pre-ALS 16: n your molecular biology class you make two different cDNAs. The first cDNA expresses a green fluorescence protein (GFP) fused to the retinoid hormone receptor. The second cDNA expresses a red fluorescent protein (RFP) fused to the glucocorticoid receptor. You express both cDNA's in the same mammalian cell in a dish and you examine their appearance using a microscope equipped with fluorescence optics. You then add retinoid and glucocorticoid ligands to the dish and wait for 30 min before re-examining the cells. Which colors would be seen in the nucleus and the cytosol before and after addition of the ligands ? A. Green fluorescence in cytoplasm and red fluorescence in nucleus before addition of ligands; red and green fluorescence in nucleus after addition of ligands. B. Red and green fluorescence in cytoplasm, but not nucleus before addition of ligands; red and green fluorescence in nucleus after addition of ligands. C. Red and green fluorescence in nucleus before and after addition of ligands. D. Red and green fluorescence in cytoplasm before and after addition of ligands. E. Red fluorescence in cytoplasm and green fluorescence in nucleus before addition of ligands; red and green fluorescence in nucleus after addition of ligands.

E. Red fluorescence in cytoplasm and green fluorescence in nucleus before addition of ligands; red and green fluorescence in nucleus after addition of ligands.