Practice Final Exam Flashcards by Nick Tully

What process is used to create transgenic mice?
A. Particle bombardment
B. Nuclear microinjection
C. Nuclear fusion
D. Germ line transformation
E. None of the above

B. Nuclear microinjection

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Why are embryonic stem cells important? (5 pts)
A. They can be passed from one generation to the next.
B. These cells carry retroviral genes.
C. They can develop into any tissue in the body, including the germ line.
D. The cells are differentiated and can therefore be manipulated.
E. none of the above

C. They can develop into any tissue in the body, including the germ line.

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Why are Cre/loxP or Flp/FRT used in transgenic animals? (5 pts)
A. Activation of a transgene by removing blocking sequences flanked by the loxP or FRT sites
B. Large-scale deletions and rearrangements of the chromosomes
C. Removal of selectable markers that are no longer needed
D. Creation of conditional knockout mutants
E. all of the above

E. all of the above

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Which of the following was derived from bacteria and useful for generating transgenes of
modulating gene expression? (5 pts)
A. Cre recombinase
B. Flp recombinase
C. Flippase
D. phiC31 integrase
E. p element

D. phiC31 integrase

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A chimeric animal is (5 pts)
A. An offspring of the transgenic procedure that has stably acquired the transgene
B. An animal that has the transgene in some cells and not in others
C. A female animal of the species that has been implanted with the transgenic embryo
D. When two nuclei from two different eggs fuse rather than a sperm and an egg

B. An animal that has the transgene in some cells and not in others

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What is used by targeting vectors to insert transgenes at specific locations within the host
genome? (5 pts)
A. homologous recombination
B. transfection
C. transduction
D. conjugation
E. All of the above

A. homologous recombination

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What greenhouse gas does this bioreactor collect (give either the chemical name, structure, or
slang)? Up to 30L a day is collected. Some say livestock produces about 14% of greenhouse
gases. (7 pts)

Methane

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Dolly is the first animal to be cloned in 1996, a sheep, and was performed by nuclear transfer
from a germ cell to a single enucleated egg. Circle one (3 pts)
True False

False

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. Stem cell niche is where the stem cells reside and maintains stemness. Circle one (2 pts)
True False

True

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What causes cancer? (5 pts)
A. somatic mutations that disrupt normal cell division and death
B. germline mutations that result in cell death
C. somatic mutations that cause cells to die prematurely
D. germline mutations that disrupt normal cell division and death
E. none of the above

A. somatic mutations that disrupt normal cell division and death

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Which of the following is the main regulator for cellular reprograming to produce iPSCs? (5 pts)
A. OCT4
B. SOX2
C. NANOG
D. c-MYC
E. LIN28

A. OCT4

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Which of the following is required for cellular reprograming to produce iPSCs only in mice but
not humans? Choose one. (5 pts)
F. OCT4
G. SOX2
H. NANOG
I. c-MYC
J. LIN28

I. c-MYC

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Which of the following is (are) totipotent or pluripotent? Choose as many as needed (5 pts)
A. embryonic stem cells
B. cells of the blastula
C. cells of the inner cell mass
D. erythrocytes (red blood cells)
E. A and B
F. A-C
G. None of the above

F. A-C

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Stem cells that have lost the ability to divide are called ________. (5 pts)
A. totipotent
B. competent
C. undifferentiated
D. differentiated
E. transformed

D. differentiated

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When one daughter cell receives a signaling molecule that the other daughter cells does not
receive is called . (5 pts)
A. extrinsic asymmetry
B. intrinsic asymmetry
C. symmetrical renewal
D. symmetrical differentiation
E. differentiation

B. intrinsic asymmetry

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How are adult stem cells identified? (5 pts)
A. Lineage analysis of a marker within a labeled potential stem cell
B. Identification of organelle-like structures called spectrosomes
C. Genetic mosaic transplantation
D. Identification of signaling transduction molecules specific to stem cells.
E. All of the above

E. All of the above

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of piRNA (4 pts

A. Regulation of mRNA degradation
B. RNA nucleotide modification
C. Splicing of RNA
D. Transposon silencing in germ cells
E. X chromosome inactivation
F. RNA produced after snorting a white powder
G. Regulation of miRNA abundance
H. Defense against foreign RNA
I. Defense against foreign RNA and DNA
J. Regulation of the Krebs cycle

D. Transposon silencing in germ cells
PIWI-interacting RNA

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of siRNA (4 pts

H. Defense against foreign RNA.
small interfering RNA

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of crRNA (4 pts

I. Defense against foreign RNA and DNA
CRISPR RNA

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of miRNA (4 pts

A. Regulation of mRNA degradation

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of circRNA (4 pts

G. Regulation of miRNA abundance
Circular RNA

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of snRNA (4 pts

C. Splicing of RNA
Small nuclear RNA

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of snoRNA (4 pts

B. RNA nucleotide modification
Small nucleolar RNA

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Match the type of RNA with its overall role (From Table 5.1 C&P). There are two extra definitions.
Write the letter of the correct definition in front of the numbered type of RNA. (32 pts)
RNA TYPE

The class of XistRNA (4 pts

E. X chromosome inactivation

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What is the role of lncRNA?

Various roles long noncoding RNA

What is the role of snRNA

splicing of RNA small nuclear RNA

What is the role of gRNA

editing of mRNA Guide RNA

What is the role of aRNA

genetic regulation Antisense RNA

Circle the four mechanisms of epigenetic regulation? There should only 4 letters circled. (4 pts) A. Cytosine Methylation B. Histone modification C. Nucleosome remodeling D. snRNA, siRNA, and drosha can bind DNA causing methylation to occur E. aRNA, snoRNA, and dicer can bind DNA causing methylation to occur F. ncRNA, aRNA, and siRNA can bind DNA causing methylation to occur G. None of the above

A. Cytosine Methylation B. Histone modification C. Nucleosome remodeling F. ncRNA, aRNA, and siRNA can bind DNA causing methylation to occur

Which of the following statements about antisense RNA is true? (4 pts) A. Antisense RNA binds to form double-stranded regions on RNA to either block translation or intron splicing. B. Antisense RNA is transcribed using the sense strand of DNA as a template. C. The sequence of antisense RNA is complementary to mRNA. D. Antisense RNA is made naturally in cells and also artificially in the laboratory. E. All of the above statements about antisense RNA are true.

E. All of the above statements about antisense RNA are true.

. Liposomes, scrape-loading nd electroporation are methods for deliverying antisense oligonucleotides. (2 pts) True False

True

Describe the four steps of miRNA processing What does Drosha do?

an endonuclease that cleaves Pre-miRNA

Describe the four steps of miRNA processing What does Dicer do?

cleaves stem loop and makes dsRNA

Describe the four steps of miRNA processing What does the RISC/Argonaut complex do?

separates the two strands into single stranded miRNA, forming RISC/Argonaut/miRNA complex

Describe the four steps of miRNA processing. 4) What does miRNA do?

RISC/Argonaut/miRNA complex binds to mRNA and inhibits translation but does not degrade it

What is the sense strand

coding, nontemplate strand

What is the antisense strand

noncoding, template strand

What strand is mRNA made from

antisense RNA strand

mRNA is identical to which strand expect for what?

sense strand, except U for T

Antisense RNA uses which strand and is _____ to mRNA

sense strand, complementary

To construct an antisense gene: - The gene is cloned such that the sense (aka coding, nontemplate) strand of the gene is transcribed. - The gene is cloned such that the antisense (aka noncoding, template) strand of the gene is transcribed. - A terminator is placed on both sides of the gene. - The stop codon of the gene is removed.

The gene is cloned such that the sense (aka coding, nontemplate) strand of the gene is transcribed.

The anti-sense RNA will _____ to the mRNA and do what

the anti-sense RNA will anneal to the mRNA and block it from binding to ribosome or block the splice sites in the splicesome

6. The enzyme responsible for the production of siRNAs from dsRNA Dicer RISC RNA-dependent RNA polymerase streptolysin

Dicer

These RNA molecules are transcribed from an endogenous gene in the organism as longer precursor molecules before they are processed into small segments to trigger RNAi. shRNA siRNA dsRNA microRNA

dsRNA

CRISPR has been modified in genome editing to combine which two structures to form what

tracrRNA combined with crRNA to make gRNA

What are the steps to make transgenic mouse

Start with: 1. mouse embryonic stem cell line 2. Make a DNA construct with neomycin resistance inserted into gene of interest 3. Insert transgene into ES cells and generate transgenic ES cells 4. Microinject transgenic cells into blastocyst 5. Transgenic cells: incorporated into chimeras 6. Chimeras breed transgenic pups

CRISPR can target deletions to specific human sequences via

Non-homologous end joining (NHEJ)

What category of technology are these? - Using Adeno-Associated Virus Technology as Gene Therapy for Mucopolysaccharidosis IIIA (MPS IIIA) - Next-generaAon VRISPR Gene-driven Systems using CAS12a Nuclease - Transcriptional activation n of endogenous Oct4 via the CRISPR/dCas9 activator ameliorates Hutchinson-Gilford progeria syndrome in mice - CRISPR-Cas12a Therapeutics for Sickle Cell Anemia: Edit-301 - Utilizing Cell- SELEX for Targeted Therapies in Caner - ARCUS Gene Editing to Eliminate MELAS- associated m.3243A>G Mutant Mitochondrial DNA

RNA Technology Including CRISPR/CAS9 and Various Types of Gene Therapy

What category of technology are these? - Embryonic Stem Cells: Prospects for Gene/Cell Therapies - CAR-M and CAR-T Synergistic Relationship to Treat Solid Tumors - Chimeric Antigen Receptor T-Cell Therapy for Reduced Triple Negative Breast Cancer Tumor Growth - Parthenogenic Dopamine Neurons from Primate Stem Cells and Parkinson's Disease - Human Embryonic Stem Cell-Derived Midbrain Dopamine Progenitor Product: Stem Cell-Based Therapy for Parkinson's - Targeting Cardiac Fibrosis with Engineered T Cells - Unblocking the potential of allogenic VS2 T cells for ovarian cancer therapy through CD16 biomarker selection and CAR/IL-15 engineering - Protective effects of human iPS-derived retinal pigmented epithelial cells on retinal degenerative disease - In vivo reprogramming of murine cardiac fibroblasts into induced cardiomyocytes

Stem Cell and CAR-T Therapies

What category of technology are these? - The development of transgenic mice expressing human ACE2 for Coronavirus Modeling - Genetically Engineered Pigs as Efficient Bioreactors for hNGF

Transgenic Animals for Function Genomic Models of Disease or Protein Production

What category of technology are these? - Utilizing Photobioreactors for the Reduction of Carbon Emissions - Application of sodium triple-quantum coherence NMR spectroscopy for the study of growth dynamics in cartilage tissue engineering - Production of ULBIP1-KO pigs with human CD55 expression using CRISPR technology - Xenotransplantation of Galactosyl-Transferase Knockout, CD55, CD59, CD39, and Fucosyl-Transferase Transgenic Pig Kidneys into Baboons - Microfluidics for Angiogenesis Models: Functional angiogenesis requires microenvironmental cues balancing endothelial cell migration and proliferation - Multi-Organ chip Technology - Implementing the Scale-X Carbo Bioreactor to Produce Viral Vaccines - Biodegradable Microcarriers

Tissue Engineering & Regenerative Medicine from Bioreactor to Humanize Animal Organ transplants

What category of technology are these? - Programmable Ubiquibodies for Selected Degradation of Proteins - The antibody aducanumab reduces AB plaques in Alzheimer's disease - Anhrax Protective Antigen Retargeted with Single-Chain Variable Fragments Delivers Enzymes to Pancreatic Cancer Cells

Antibody or Protein Therapy

What category of techonology are these? - BRB-Sequencing: The Future of RNA Sequencing - Using NGS-sequencing to characterize non-culture Neisseria meningitidis

Genomics or Transcriptomics

What are the four epigenic mechanisms

- Most cases histone modifications increases transcription. Cytosine methylation silences genes. Nucleosome remodeling is a third mechanism. Noncoding (nc) RNA, antisense RNA, and small interfering (si) RNA can bind to DNA causing methylation to occur. Example of Xist RNA in X-inactivation. Down’s syndrome and trisomy - inactivation of Chromo. 21

What are the different types of antisense therapy delivery systems

Liposomes Peptides from viruses Streptolysin O pore electroporation

What are the different delivery of antisense to cell culture

microinjection scrape loading

CRISPR can be used to generate

site specific lesions in human DNA

Only ES cells express these two trancription factors

OCT4 and NANOG

Embryonic Stem and Embryonic Germ cells are which type of cell

totipotent cells

Describe the various steps of CRISPR/CAS9

1.) Design a guide RNA--> gRNA guides Cas9 protein to desired DNA sequence 2.) Delivery components to cell--> Cas9 and gRNA delivered to cell using viral vectors, nanoparticles, or electroporation, form complex scan genome for target sequence 3.) Cas9 cleaves DNA--> when target sequence is found, Cas9 makes double stranded break in DNA 4.) Gene editing occurs--> NHEJ occurs and leads to insertions, deletions, resulting in gene knockout Homology directed repair allows for insertion of new gene, knock in

Describe the use of chimeric guide RNA to knock out or knock in genes of interest.

cgRNAs have both DNA and RNA for gene knockout--> cgRNA designed to target specific coding sequence, leading to disruption through NHEJ for gene knock in--> donor DNA template can be incorporated into repaired site through HDR, introduction mutation

In CRISPR, the gRNA is designed to be _________ to a specific DNA sequence with the __________

complementary, target gene

What does crRNA do in CRISPR

recognizes target DNA

What does tracrRNA do in CRIPSR

binds Cas9 to gRNA

How does knockout occur in CRISPR

disruption or inactivation of target gene due to NHEJ induced mutations

How does knock in occur in CRISPR

introduction of specific sequences or modifications through HDR

Describe how chimeric antigen receptors (CARs) are integrated into a patients T cells to perform CAR-T therapy

1.) T cell collection--> T cell extracted from blood through leukapheresis 2.) CAR vector creation--> viral vector engineered to carry CAR gene, CAR gene encodes blueprint for chimeric antigen receptor 3.) T cell transduction--> T cells incubated with CAR vector, virus infects T cell and integrates CAR into DNA 4.) CAR expression and expansion--> T cells are cultured and CAR is expressed on surface and cells multiply 5.) T cell infusion--> expanded CAR-T cells are infused back into patients bloodstream

What does tissue mimicry mean in terms of designing bioreactors for tissue engineering?

tissue mimicry refers to the design of bioreactors that can replicate the microenvironment of a specific tissue or organ as closely as possible.