BioExam 1 Spring 2016 Key and Average.docx(3)

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AVERAGE = 71% Principles of Cell Biology Exam 1 March 1, 2016 Directions: There are 75 questions in this exam with only one correct answer for each. All answers are to be placed on the grid sheet. Make sure that you mark the version of your exam for question #76. The version is listed at the end of this exam. 1. You are working in a laboratory investigating how your newly developed nanoparticles that are approximately the size of mitochondria and lysosomes are able to deliver DNA into cells. You need to look at living cells that contain these nanoparticles over a long period of time to determine their intracellular distribution. Which microscope below would be best for this purpose given that it would generate the best contrast? a. Nomarski optics/differential interference contrast b. Phase microscope c. Darkfield microscope d. Transmission electron microscope e. Scanning electron microscope 2. The cell theory was proposed by Schleiden and Schwann in the mid 1800s but neurons were still not accepted as a part of the cell theory until much later. It was the Golgi stain that finally convinced cell biologists that which of the following theories about neurons was false and that brain tissue was actually cellular in nature? a. Labyrinth theory b. Continuity theory c. Fibrous theory d. Reticular theory e. Neuronal theory 3. CRISPR-Cas9 is a very exciting tool and was deemed the 2015 breakthrough of the year. Which phrase is most closely associated with this technique? a. Cell separation and sorting b. Telomerase - immortalized cell lines c. New type of column chromatography d. DNA sequencing using nanopores in artificial membranes e. DNA editing 4. Protein A immunoprecipitation a. Can be used to purify a protein from a mixed solution of proteins b. Uses Protein A which originates from S. aureus c. Commonly uses an antibody d. Typically requires a final centrifugation step to generate a pellet. e. All of the above 5. The use of decellularized organs such as kidney and liver seeded with stem cells may be important to the future field of a. Organ transplants b. Preventing inherited diseases c. Developing improved methods in disease detection d. Generating new methods of liquid biopsy e. DNA engineering/editing

6. EGTA is often used in cell biology applications and is almost always used when one is dissociating tissue into single cells. How does it work? a. It is a detergent and solubilizes cells b. It coats the cells so that they don't stick to each other c. EGTA is a protease and cleaves extracellular and other proteins that are responsible for cell to cell adhesion d. It is a calcium chelator and, as such, compromises the function of the calcium dependent cell adhesion molecules e. None of the above 7. JC-1 a. Is a vital dye b. Labels mitochondria c. Can fluoresce orange or green d. Can be analyzed in a Guava system e. All of the above 8. The VivaScope originally introduced by Lucid Technology of Rochester NY is an interesting system intended to be used for the non-invasive biopsy imaging of skin lesions and abnormalities such as skin cancer. Which type of microscope technology was used as the basis for this unique instrument? a. Confocal microscopy b. MRI microscopy c. Fluorescence microscopy d. Polarizing light microscopy e. X ray microscopy 9. Leonard Hayflick is well known to cell biologists given that he is most closely associated with which of the following? a. He was the first to isolate and propagate HeLa cells in culture b. He showed that cell strains exhibit a finite number of doublings that is inversely related to the age of the donor c. He developed photoaffinity analogs that can be used with a variety of techniques d. He started the development of "next-gen" sequencing e. He is regarded as the pioneer who launched tissue engineering 10. Which of the following about yeast is false ? a. Requires a feeder layer for cell culture b. Can be diploid c. Can be haploid d. Can be mated e. Can be budding or fission type 11. FACS is a device designed to a. Sequence DNA b. Locate mRNAs in cells c. Remove selected cells from a tissue section for subsequent molecular analysis d. Analyze proteins based on time of flight e. Separate cells based on fluorescent markers

12. Cynvenio has developed a device to detect very low levels of cells in circulating fluid. Given the type of cell detected, which phrase is best matched with the purpose of this instrument? a.Glucose levels in diabetic patients b.Blood in urine as an indication of kidney failure c.Circulating tumor cells as a means to determine a patient’s tumor burden d.Liver cirrhosis as evidenced by the sloughing of hepatocytes into the blood e.Inflammatory bowel disease 13. Calcein - AM and propidium iodide are commonly used together to assess which of the following? a. They are required for ELISA protocols b. They are colorimetric dyes commonly used by pathologists c. Cell membrane integrity d. Intracellular pH e. Intracellular calcium concentration 14. Which of the following is characteristic of a cell strain? a. Unlimited number of doublings b. Don't undergo senescence c. Telomeres shorten every cell division d. Are often isolated from tumors e. C3A cells are an example 15. GUAVA is best matched to a. Flow cytometry b. A blotting technique c. A gel electrophoresis technique d. An ion exchange chromatography technique e. The first imaging system used to visualize the major and minor grooves in DNA 16. Temperature sensitive yeast a. Grow well at 23 o C b. Don't grow at 36 o C c. Have been used by L.H. Hartwell to investigate cell cycle genes d. Can be used to determine if mutant alleles are in the same gene e. All of the above 17. Gel shift or band shift assays are used when analyzing which of the following? a. DNA binding proteins b. Post-translational modification c. The ability of insulin to bind to its receptor d. Analyzing the specificity and affinity of a monoclonal antibody e. None of the above 18. 23 and Me is a company that markets what type of product? a. Ion exchange chromatography beads b. Lab on a chip devices c. Stem cells d. Kit used for genetic testing/analysis e. Unique type of confocal microscope

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19. You are having lunch with a colleague and chat about the issues with your culture w ork that involve heterokaryons and hybridomas. Which area below best matches the nature of your conversation? a. Tissue engineering b. Stem cell therapy c. Generating monoclonal antibodies d. Isolating primary hepatocytes from an intact liver e. Using HeLa cells for generating proteins of pharmaceutical interest 20. You are a pathologist analyzing a hematoxylin and eosin stained paraffin embedded sections of liver from a patient who died of unknown reasons. What type of microscope would you be most likely using? a. Spinning disk confocal microscope b. Bright field microscope/compound light microscope c. Differential interference contrast/Nomarski d. Scanning tunneling microscope e. Darkfield microscope 21. A report was published last week (2/22/16) stating that the HPV (human papilloma virus) vaccine has made a substantial impact on the number of young women who are contracting cervical cancer through sexual contact by reducing the HPV incidence three fold compared to the time before the vaccine was available. Which cell type below is most associated with the HPV? a. CHO (chinese hamster ovary) cells b. HeLa cells c. NHEK (Normal Human Epidermal Keratinocytes) d. MDCK (Madin Darby Canine Kidney Cells) e. C3A cells 22. Many molecular biology techniques use hybridization in their protocols. Which of the following techniques does not use hybridization as part of the procedure? a. Reverse transcriptase PCR b. Southern blots c. Northern blots d. cDNA microarrays e. RNA antisense 23. Monoclonal antibodies were first generated for the sole purpose of immunocytochemistry and associated techniques. Now, however, they generate billions of dollars worldwide given that they are used to treat a myriad of diseases ranging from cancer to inflammatory diseases. What name is typically used when referring to this group of drugs? a. Secretomes b. Epigenomes c. Biologics d. Proteomics e. Only Dave Matthews knows for sure

24. Biological scaffolds can be either biodegradable or non-biodegradable. They are commonly used in which of the following areas? a. Tissue engineering b. Stem cell therapy c. Protein separation d. DNA sequencing e. Reverse transcriptase PCR 25. There are many hypotheses underlying the cellular basis of organismic aging. Which of the following is not considered to be one of the current possible players in either cellular and/or organismic aging? a. Telomeres b. Stem cell theory c. Sirtuin genes d. Epigenetic modifications such as methylation e. Retroviral infection 26. Variable number tandem repeats (VNTRs) a. Can be detected with Southern blots b. Are polymorphic markers c. Are used by the FBI through its CODIS (Combined DNA Index System) to match DNA samples to known individuals in their data base d. Can be used to determine if a bone marrow transplant was successful e. All of the above 27. You are visualizing a cell and select an excitation wavelength of 485 nm realizing that your probe will be excited by this wavelength and emit at a longer wavelength of approximately 535 nm. What type of technique are you probably most likely using? a. Ultrastructural autoradiography b. Ultrastructural immunocytochemistry c. Fluorescence immunocytochemistry d. Plastic thin section staining e. All of the above could be used with this type of probe 28. Methylation and phosphorylation of DNA bases and its resulting stable change in genotype is often referred to as a. Proteomics b. Metabolomics c. Xenolomics d. Epigenetics e. Secretomics 29. Autoradiography is designed to track which of the following? a. Radioisotopes b. Fluorescent dyes c. Gold particles d. Antibodies e. Nanoparticles 30. Like all science progress is made by brilliant ideas formulated by interesting people. Craig Venter fits this description. What is he best known for among those listed below?

a. Si/shRNA b. Antisense RNA c. DNA sequencing/first artificial cell d. cDNA microarrays e. Developing the first hESC (human embryonic stem cell) line 31. Microfluidic devices are now being developed that can separate unlabeled cells based on size differences and their relative speed through a gravitational field. Which type of technique best matches this description? a. Dynabeads b. Velocity sedimentation c. Rate zonal centrifugation d. Panning e. Gel filtration 32. Which of the following is false concerning lucifer yellow? a. Membrane permeable b. Fluorescent c. Commonly used in intracellular injection d. Can trace neurons in intact neuronal tissue such as ganglia e. Doesn't compromise the viability of cells 33. SDS gel electrophoresis is designed to separate what type of molecule? a. Phospholipids b. mRNAs c. DNA fragments d. Proteins e. None of the above 34. BioLife and BioHeart worked together to address heart disease with the latter developing new, FDA-approved procedures for treating this disease. What type of procedure did BioHeart develop? a. Stem cell therapy for the heart using an autologous myoblast transplant b. Mechanical heart device c. New drug that regulates the calcium channel d. New medical device that thermally ablates an area of the heart that is causing atrial fibrillation e. New liquid biopsy test that can determine if you may have a heart attack within the next several hours 35. GFP, RFP, and BFP are all related to each other. Which of the following is false concerning these probes? a. They are commonly used in the freeze fracture technique b. They fluoresce c. They are often referred to as reporter molecules d. The DNA sequence for all three can be associated with a gene of interest and be used to determine if a particular protein of interest is being expressed in the cell e. The parent compound, GFP, was originally identified in jellyfish

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36. CellSearch is one of many new devices used to separate cells. What is the key phrase below that identifies the major mechanism that is the foundation for this Veridex instrument that can separate and enumerate circulating tumor cells (CTCs)? a. Nanoparticles endocytosed selectively by CTCs b. Selective protease activity on CTC- specific cell surface proteins c. Ligand receptor interactions of a specific hormone that binds only to CTCs d. Interaction of an iron-labeled anti-EpCAM antibody to the surface of CTCs e. Only Dave Matthews knows for sure 37. The ELAD or extracorporeal liver assist device a. Is designed to be used in the hospital b. Uses cartridges with porous fibers c. Has C3A cells as the active cell type d. Is a tissue engineered construct e. All of the above 38. Densitometry is a critical technique in the laboratory given that through imaging systems it can convert band densities to a bar graph that depicts the relative quantitative differences between bands. Of the following techniques below which one would not be amenable to densitometry performed in a typical imaging system? a. 2 D gel electrophoresis b. Gel filtration c. SDS gel electrophoresis d. Western blots e. Gel electrophoresis autoradiography 39. Which of the following protein separation techniques separates proteins on a gel that has a pH gradient? a. Isoelectric focusing b. SDS gel electrophoresis c. Native gel electrophoresis d. SELDI-TOF e. None of the above 40. Which type of microscope contains multiple lenses in a microlens array that is electronically coupled to a confocal array and can yield images of dynamic interactions within a millisecond span of time? a. Atomic force microscope b. Scanning tunneling microscope c. Two photon microscope d. Transmission electron microscope e. None of the above 41. Fetal bovine serum is commonly used in which type of application? a. Northern blots b. Cell culture of cell strains c. Ultrastructural autoradiography d. 2 photon microscopy e. PCR

42. You are doing differential centrifugation and do a series of runs at a variety of speeds. Which below requires the highest gravitational force and/or the longest spin time to generate a pellet at the bottom of the test tube? a. Lysosomes/mitochondria b. Whole cells c. Whole nuclei d. Microsome fraction e. Can't predict 43. You are interested in determining if a particular integral membrane protein is able to diffuse laterally within the plane of the membrane. As such you use the direct technique and label this protein with a fluorochrome that is attached to the Fc end of a monoclonal antibody. You then apply this probe to a living cell and find that as expected the cell is now uniformly fluorescent around its exterior. Now you execute the experiment to determine this protein's lateral mobility characteristics. Which technique below would be best to use for this purpose? a. FACS b. FRET c. FISH d. FRAP e. DMB 44. A high 20% to 70% Ficoll or sucrose gradient is required for which of the following techniques? a. Ion exchange chromatography b. Gel filtration c. Affinity chromatography d. Protein A immunoprecipitation e. None of the above requires a Ficoll or sucrose gradient 45. Anthony Atala developed the first tissue engineered, implantable human organ in 2006. This organ was used to treat young children born with spina bifida. Which organ/tissue below was used for this purpose? a. Liver b. Bladder c. Spleen d. Tendon e. Spinal disks 46. You are visualizing platinum replicas that reveal the internal structure of cell membranes. Which of the following techniques are you using? a. Laser capture microscopy b. Two photon microscopy c. Transmission electron microscopy - plastic thin sections d. Transmission electron microscopy - freeze fracture e. X ray microscopy 47. There are groups such as one at the Wyss Institute at Harvard that are developing small devices that are about the size of a thumb drive that in the future will have several

interconnected and communicating “mini-organs” embedded in the same device. What type of technology does this best match? a. Lab on a chip b. Synthetic biology c. New medical device d. New type of DNA microarray e. Immuno-oncology 48. Abbe is best known for his work that describes which of the following? a. He was one of first to show that monoclonal antibodies can be used as agents to address diseases such as cancer b. He worked with Watt Webb at Cornell developing the 2 photon microscope c. He was critical in developing the early engineering plans for the spinning disk confocal microscope d. He was the first to show mathematically that the theoretical limit of resolution is limited by the diffraction characteristics of the illuminating source e. He developed FISH and FRET and as a result received a Nobel Prize in 1999. 49. A cryostat is an integral machine used in both research and clinical medicine. Which term below is the best match of this machine to its associated process? a. 2 photon microscopy b. cDNA microarrays c. Molecular beacons d. Bright field microscopy/microtome e. TIRF 50. Which of the following techniques is used to expand the amount of DNA by using a thermally stable DNA polymerase? a. Southern blots b. cDNA microarrays c. PCR d. FISH e. Molecular beacons 51. Which component below is not an advantage of a typical laser scanning confocal microscope compared to alternative conventional microscopy techniques? a. Can be used for triple labels b. Can be used to generate stereo images c. Can optically section cells better than most other microscope techniques d. Can determine if a cellular structure alters the plane of polarized light e. None of the above 52. FISH a. Is a fluorescent technique b. Relies on in situ hybridization c. Can be used to locate/image specific mRNAs in cells d. Can be used to label specific DNA sequences in the nucleus e. All of the above

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53. Which of the following techniques below would be best for purifying the insulin receptor assuming that you are able to tether the insulin molecule to an inert bead used in the column? a. CM ion exchange chromatography b. DEAE ion exchange chromatography c. Gel filtration d. Affinity chromatography e. Southern blots 54. ELISA is a technique that typically uses antibodies and is designed for which purpose? a. It is a type of microscope system like TIRF that can image the edges of cells b. It is designed to determine the amount of a selected protein in a sample c. It is a fluorescent technique that can locate specific mRNAs in cells d. It is a type of western blot application that can use photoaffinity analog amino acids e. None of the above 55. Which of the following uses antibodies as part of the protocol? a. Isoelectric focusing b. 2-D gel electrophoresis c. Western blots d. Southern blots e. Northern blots 56. Formaldehyde and glutaraldehyde are relatives of each other and used commonly in cell and molecular biology research. Which word or phrase below best matches the nature of these chemicals? a. Fixatives b. Stains for light microscopy c. Stains for electron microscopy d. Labels used for western blots e. Agents used to ionize proteins analyzed in SELDI-TOF and MALDI-TOF 57. Ricin is a toxin that is extremely potent. How does it work? a. It binds to and blocks the acetylcholine receptor b. It binds to and blocks the dopamine receptor c. It works similar to a restriction nuclease and cleaves endogenous mRNA molecules in neurons causing immediate death due to brain dysfunction d. It inhibits ribosome function e. Its function is not yet known 58. Which of the following protein separation techniques typically requires a sodium chloride (NaCl) gradient to elute the proteins from a substrate? a. DEAE Ion exchange chromatography b. Gel filtration c. Native gel electrophoresis d. SDS gel electrophoresis e. SELDI-TOF 59. Which of the following is false concerning SELDI-TOF/MALDI-TOF? a. Type of mass spectrometry

b. Can detect proteins that differ by as little as one amino acid c. Can use protein chips with chromatographic-like surfaces d. Analyzes proteins based on their speed once accelerated by a laser e. None of the above because all are true 60. There are a number of substrates used in cell culture. Which type of device or substrate listed below is one of the most commonly used substrates for large cell bioreactors given that they favor very high cell density designed to work in a closed loop system? a. Roller bottles b. Microporous membranes c. Microcarrier beads d. Cell culture plates e. DMB manifolds 61. Which cell type below is the most commonly used cell line to generate proteins that are used to treat diseases? a. CHO cells b. NHEK cells c. MDCK cells d. C3A cells e. Pancreatic islets 62. Reverse transcriptase PCR is a useful technique given that it is designed to measure the abundance of the same molecule that is analyzed by which of the following? a. Northern blots b. Western blots c. Southern blots d. Eastern blots e. None of the above 63. You are working with a cell strain and determine that while the cells appear viable their cytochrome p450 function has declined over a week's time in culture. What type of cell are you culturing? a. Beating cardiomyocytes b. Adipose- derived mesenchymal stem cells c. NHEK d. Primary human hepatocytes e. HeLa cells 64. Which of the following types of microscopes is not diffraction limited? a. Super resolution fluorescence microscopy b. Transmission electron microscopy c. Phase microscopy d. Fluorescence microscopy e. None of the above because they are all diffraction limited 65. Triggering the differentiation of NHEK so that these cells would multilayer is critical to the process of developing a tissue engineered human skin construct. How was this accomplished? a. Insulin was added to the medium

b. The calcium was removed from the medium c. Very low levels of detergent were added d. The microporous membrane was delicately removed from the developing tissue engineered construct e. None of the above 66. Sodium dodecyl sulfate and Triton X-100 are a. Commonly used in conjunction with micropipette intracellular injections b. Detergents c. Proteases used to dissociate cells d. Used to denature DNA so that it can be hybridized e. All of the above 67. You are working in a tissue engineering laboratory and execute a stage of the protocol where you move your multilayered culture to the air/liquid interface. What type of tissue are you probably developing? a. Liver b. Cartilage c. Vaginal tissue d. Skin e. Skeletal muscle 68. Which of the following about restriction enzymes (nucleases) is false ? a. Can result in sticky ends b. Cleave DNA c. Are produced by bacteria d. Are required for PCR e. Discovery was so important that it resulted in a Nobel Prize awarded in 1978 69. The final output of this type of technique could be described as "a set of up to 8000+ spots that have either a red, green, yellow or no color". a. cDNA microarrays b. High voltage electron microscopy c. Fluorescent immunocytochemistry d. Genomic cloning e. None of the above 70. Humulin was the first recombinant DNA product used clinically. It was generated from which type of cell? a. Yeast b. CHO cells c. HeLa cells d. Prokaryotic cells e. Hybridomas 71. SiRNA and shRNA are useful in the research laboratory and are currently being tested clinically. What do they do? a. They generate small pores in target cells and cause them to lyse. b. They bind to cDNA molecules inside cells c. They target and degrade mRNAs

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d. They can edit genes base by base so that you can change the function of genes e. None of the above 72. Which of the following is not a current transfection technique? a. Lipid mediated (liposomes) b. Optoperforation c. Viral transduction d. Polymers such as calcium phosphate e. None of the above because all are currently being used as trasfection techniques. 73. Cameleon is discussed in your book that consists of a CFP and YFP at the two ends of calmodulin. As such it can measure the same parameter as which of the following fluorescent dyes? a. BCECF-AM b. Fluo3-AM and Fura-2 c. Annexin V d. Hoescht e. AlamarBlue 74. IPTG a. Can turn on the lac operon b. Is used in prokaryotic expression systems c. Is a lactose analog d. When present can cause the expression of β -galactosidase e. All of the above 75. The term “liquid biopsy” has been on the news recently given that many companies that distribute these tests have not had them rigorously tested by the research or clinical community and often make unsubstantiated claims about their efficacy. What is the advantage(s) of a liquid biopsy? a. They are typically non/less invasive than an alternative test b. Often use a small sample of blood c. Can be designed to detect “biomarkers” in the liquid that indicates a pending disease state d. In some cases can be used with disposable microfluidic devices e. All of the above YOUR EXAM VERSION IS “D”. Blacken “D” for question #76

BioExam 1 Spring 2016 Key and Average.docx(3)

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