bio exam 3
Which of the following best describes the series of steps necessary for RNA sequencing in a biological sample ? mapping reads to a genome > transcribe those regions > do next generation sequencing > transcribe the whole genome > reverse transcribe the RNAs produced > do RNA sequencing reverse transcribe the RNA present in a sample > translate the mRNAs > do proteomics analysis reverse transcribe the RNA present in a sample > do next generation sequencing > map reads to a genome fragment the genome into small portions > do next generation sequencing > assemble reads into a genome sequence
reverse transcribe the RNA present in a sample > do next generation sequencing > map reads to a genome
Which of the following processes needs to be performed in advance if PCR is used to figure out if a gene is expressed or not ? in vitro transcription of DNA reverse translation of RNA reverse translation of proteins direct transcription of RNA reverse transcription of RNA
reverse transcription of RNA
In trying to correct an immune disease through gene therapy, which of the following strikes you as a strategy that would NOT be part of a treatment ? infect T-cells with a modified retroviral vector that will insert itself randomly in the cell's genome stimulate T-cells to proliferate much more frequently than normal in the lab start a laboratory culture of T-cells from a patient re-inject genetically modified cells to the patient select isolated T-cells where the random retroviral injection interrupted the expression of a known tumor suppressor gene to move forward with the therapy
select isolated T-cells where the random retroviral injection interrupted the expression of a known tumor suppressor gene to move forward with the therapy
What is the process of inserting plasmids into bacteria called? polymerase chain reaction (PCR) translation transformation ligation colechior
transformation
If a restriction enzyme cuts a circular plasmid and a linear DNA molecules into three fragments, how many restriction sites are there in the plasmid and the linear DNA, respectively ? 4 and 3 3 and 4 3 and 2 2 and 3 2 and 2
3 and 2
A portion of one strand of DNA has the sequence 5' AATGGCTTA 3'. If this strand is used as a template for DNA replication, which of the following correctly depicts the sequence of the newly synthesized strand in the direction in which it will be synthesized? 3' TTACCGAAT 5' 0 3' AATGGCTTA 5' 5'AATGGCTTA 3' '5' TAAGCCATT 3'
3' TTACCGAAT 5'
Below is the template strand that corresponds to a coding region in which you'd like to mutate an ACG (Thr) to GCG (Ala). This template sequence is broken into codons for your convenience:5'- AAA ACA CGT ACG AGT TGA AGG -3'Which of the following primers would you use to introduce the desired mutation by PCR ? 3'- AAA ACA CGT GCG AGT TGA AGG -5' 5'- AAA ACA CGT GCG AGT TGA AGG -3' 5'- CCT TCA ACT CGT GCG TGT TTT -3' 3'- CCT TCA ACT CGT GCG TGT TTT -5' 3'- CCU UCA ACU CGU GCG UGU UUU -5'
5'- CCT TCA ACT CGT GCG TGT TTT -3'
What is the sequencing range of modern capillary sequencers ? 800-1000 bases 80K-1000K bases 80-100 bases 45-50 bases whole genome
800-1000 bases
More than 150 years after Gregor Mendel used the wrinkled pea trait to study genetics, researcher discovered the molecular cause of this mutation. R is the wild type allele and r is the mutant, recessive allele for wrinkled peas . While there is no protein detected for the gene responsible in the rr plant, mRNA analysis shows the RT-PCR product for the gene responsible from an rr plant is 800 bp longer than the corresponding RT-PCR product from a RR plant, what is the likely cause of the mutation? A 800 bp insertion in the 5' UTR of the R allele. A 800 bp insertion in the coding region of the r allele. A 800 bp deletion in a intron of the R allele. A 800 bp insertion in the coding region of the R allele. A 800 bp deletion in the promoter of the r allele.
A 800 bp insertion in the coding region of the r allele.
Question 15 Which of the following could serve as a selectable marker in bacterial transformation? A gene coding for an enzyme that degrades a powerful eukaryotic antibiotic (Puromycin) This is wrong; selection markers apply only to constructs intended to make transgenic or knock- outs A gene that allows bacteria to extract energy from hydrocarbons that wild type bacteria can't metabolize A gene that specifically kills the bacteria that picked empty vectors (e.g. a vector with an MCS in the middle of the AmpR gene) but spares all other bacteria gene to produce a bacterial antibiotic
A gene that specifically kills the bacteria that picked empty vectors (e.g. a vector with an MCS in the middle of the AmpR gene) but spares all other bacteria
Which of the following does NOT describe the bond created by DNA ligase ? A hydrogen bond between nucleotides A covalent bond A phosphodiested bond A bond that fills strand nicks/gaps in a DNA molecule A bond between a 5' C and a 3' C between nucleotides on the same strand
A hydrogen bond between nucleotides
A labmate asks you to collect the reagents for an RT- PC reaction that she plans to run later. Which of the following would you NOT get from the lab freezer ? Two different single-stranded DNA primers An RNA reverse transcriptase A supply of the four DNA nucleotides A heat-stable DNA polymerase A restriction enzyme buffer
A restriction enzyme buffer
Which of the following is NOT needed in a bacterial expression vector ? A multiple cloning site (or MCS) to clone the DNA fragment to be expressed A strong poly-A signal downstream of the poly. An origin of replication (Ori) site for vector duplication A selection marker (such as an antibiotic resistance gene) A strong bacterial promoter and Shine-Dal sequence
A strong poly-A signal downstream of the poly.
Which of the following does PC require? A buffer solution A double-stranded DNA template containing the target sequence to be amplified A heat-stable DNA polymerase A supply of the four DNA nucleotides Actually, all of the components mentioned in the other options are necessary
Actually, all of the components mentioned in the other options are necessary
Which of the following is NOT a true step in Sanger or capillary DNA sequencing ? Add a restriction enzyme to fragment the template DNA sequence into smaller fragments to be sequenced Prepare a DNA sample to be sequence and make it as pure as possible Identify the last nucleotide in each DNA fragment obtained in the reaction Denature the DNA molecule to be sequenced to allow primer annealing Use ddNTPs to stop the DNA polymerization reaction at different positions of the DNA being sequenced
Add a restriction enzyme to fragment the template DNA sequence into smaller fragments to be sequenced
Which of the following is TRUE about Adenoviruses and Retroviruses? Neither retroviruses or adenoviruses need any associated proteins to complete a successful infection of their target cells Retroviruses inject their DNA through the plasma membrane, and adenoviruses inject their DNA through the nuclear membrane Adenoviruses inject their DNA through the plasma membrane, and retroviruses inject their DNA into the nucleus Adenoviruses are only used in vitro, and retro are only used in vivo Adenoviruses carry double stranded DNA, and retroviruses carry single stranded RNA
Adenoviruses carry double stranded DNA, and retroviruses carry single stranded RNA
If a disease is caused by the lack of an enzyme that degrades free cysteine in blood, which of the following does not appear like a viable treatment option ? Inject the patient with the missing enzyme Adenovital gene therapy to re express the ename in blood cells A fully cysteine-free diet Make transgenic hepatic cells that secrete the missing enzyme into circulation
Adenovital gene therapy to re express the ename in blood cells
Which of the following is the easiest approach to compare the size of two DNA molecules ? Northren Blotting PCR A diagnostic restiction digestion Western Blotting Agarose gel electrophoresis
Agarose gel electrophoresis
Suppose that you would like to investigate how the -10 consensus sequence works in a bacterial core promoter. A colleague recommends the following series of approaches. Which one seems most reasonable? Amplify any bacterial core promoter using primers that purposely introduce a point mutation in the -35 consensus, and clone the PCR amplicon upstream of Green Fluorescent Protein (GFP), so you can focus on how the -10 consensus sequence works. Clone a gene of interest without its promoter into a bacterial plasmid without a promoter, and study the expression of your gene of choice. Amplify a bacterial gene using primers that purposely introduce a point mutation in the -10 consensus sequence, clone the PCR amplicon into a vector without a promoter and introduce it into bacteria that do not express your gene of choice.
Amplify a bacterial gene using primers that purposely introduce a point mutation in the -10 consensus sequence, clone the PCR amplicon into a vector without a promoter and introduce it into bacteria that do not express your gene of choice.
Recombinant human proteins are often preferably produced in eukaryotic organisms (cows, sheep, etc) instead of bacteria, because Bacteria introduce post-translational modifications to their proteins that can be toxic to humans Alternative splicing is only possible in eukaryotic cells Humans generally don't like to drink bacteria with their cereal Bacteria cannot carry out post-translational modifications of eukaryotic proteins that are crucial for their production Bacteria cannot express human DNA
Bacteria cannot carry out post-translational modifications of eukaryotic proteins that are crucial for their production
are bacterial extra-chromosomal DNA elements that are circular, double stranded and replicate independently of the bacterial chromosome and can be present in high copy numbers within a cell. Nucleoli Plasmids Nucleosome Restriction enzymes Bacteriophages
Bacteriophages
Why aren't electroporations or liposomes used to transfect cells obtained from patients for ex vivo gene therapy ? Because DNA transfected into cells via liposomes or electroporation takes months to enter the cell Because electroporations and liposome-mediated transfection are less efficient than retroviral transformation, and specialists usually have very few cells that they obtained from a patient to work with. Because liposome-based transfections and electroporations are too expensive and difficult to implement, and that's why they are used routinely in basic research labs only Because the electric shock and the liposomes used when introducing DNA in cells while they are still in the patient can be toxic to the patient Because electroporation and liposome-based transfection can only be used with plant or fungal DNA
Because electroporations and liposome-mediated transfection are less efficient than retroviral transformation, and specialists usually have very few cells that they obtained from a patient to work with.
If only had access to a DNA polymerase from humans, why couldn't you run a PCR reaction? Because human DNA polymerase cannot be used with any template DNA other than human DNA. Because the human DNA polymerase would not be able to work with synthetic primers Because human DNA polymerase cannot function outside of cells (in a test tube) Because the human DNA polymerase would denature and lose function with every cycle of DNA strand separation (melting) Because in the presence of human DNA polymerase, the newly synthesized DNA strands would degrade with every cycle of DNA melting
Because the human DNA polymerase would denature and lose function with every cycle of DNA strand separation (melting)
Which one of the following methods could you use to produce a transgenic plant using a species that CANNOT be infected by Argobacterium tumefaciens Electroporation Bioballistics Agrbacterium differensis-mediated transformation Transfecting mouse embryonic stem cells and adding them to the plant's soil Genome integration by RNAi
Bioballistics
Transgenic organisms contain foreign DNA that has been introduced using Gel Electrophoresis Translation Transcription Biotechnology PCR
Biotechnology
Which of the following is the true mechanism that makes gene editing via CRISP possible ? Homology-directed DNA repair Histone tail acetylation/de-acetylation DNA replication Cas9 nuclease activity Cell communication
Cas9 nuclease activity
Which of the following is NOT a necessary step for Illumina sequencing? Sequencing by synthesis Cluster generation Choose the primers for sequencing Sample prep Sequence reads mapping
Choose the primers for sequencing
Which of the following is the LEAST reasonable goal for a transgenic crop ? Creating a plant with reduced need for soil phosphorus and nitrogen Creating plants that are more resistant to intermittent but severe droughts Creating plants that require more frequent irrigation, facilitating the termination of crop growth at the end of a commercial season Creating a plant that is resistant to infection by Agrobacterium tumefaciens. Creating plants that are resistant to infection by a fungus due to the expression of a natural bacterial fungicide
Creating plants that require more frequent irrigation, facilitating the termination of crop growth at the end of a commercial season
Suppose that you would like to know if your Cre- mouse that allegedly expresses Cre only in muscle cells and only after streneous exercise is working as advertise. Which of the following approaches would you use? Cross it to a mouse that carries a Floxed GFP transgene, and look for fluorescence only in muscle cells of mice that spent more than 30 min in a training wheel Cross it to a mouse that carries a Floxed Cre transgene, and look for expression of the Cre mRNA by RT-PCR only in muscle cells of mice that spent more than 30 minutes in a training wheel. Clip a bit of the tail of the Cre-mouse, and run a PCR to detect the presence of the Cre transgene. Cross it to a mouse that carries a Floxed GFP transgene, and look for fluorescence in all cell types EXCEPT muscle cells of mice that spent more than 30 minutes in a training wheel.
Cross it to a mouse that carries a Floxed GFP transgene, and look for fluorescence only in muscle cells of mice that spent more than 30 min in a training wheel
Which of the following would you NOT expect from a DNA ligation reaction ? Blunt ended sequences will be joined together Molecules with non-complementary sticky ends will be joined together The same molecules that were separated by the restriction reaction will be re-joined together DNA fragments generated by restriction with different restriction enzymes that generate the same overhangs can be joined together Sticky ended molecules from different DNA sources will be joined together
DNA fragments generated by restriction with different restriction enzymes that generate the same overhangs can be joined together
Which of the following might be harder to study with transgenic mice ? Studying the intracellular distribution of the tyrosine kinase Src How beta-lactamase overexpression affects glycolysis in bacteria Effect of the deletion of glucose 6-phosphatase on cell proliferation Role of intracellular pH in protein folding Determining what cells express thymindine-kinase in response to oxidative stress
Determining what cells express thymindine-kinase in response to oxidative stress
A research hospital is trying to develop an ex vivo gene therapy treatment for a disease involving immune T-cells. Which of the following is NOT a likely step in their process? T-cells are infected with a retroviral vector T-cells are taken from a patient and placed in tissue culture Engineered T-cells are returned to the patient by iniection The T-cells in culture are stimulated to proliferate Engineered T-cells in culture are selected by treatment with ampicillin
Engineered T-cells in culture are selected by treatment with ampicillin
A research hospital is trying to develop an ex vivo gene therapy treatment for a disease involving immune T-cells. Which of the following is NOT a likely step in their process ? Engineered T-cells are returned to the patient by injection T-cells are taken from a patient and placed in tissue culture Engineered T-cells in culture are selected by treatment with ampicillin T-cells are infected with a retroviral vector The T-cells in culture are stimulated to proliferate
Engineered T-cells in culture are selected by treatment with ampicillin
For which of the following transgenic animals would you NOT have to carefully choose a promoter to clone upstream of your transgene of interest ? In a transgenic mouse for doxicyclin induced expression of a transgene of interest In a transgenic mouse for tissue-specific knockdown through expression of an RNA hairpin In a transgenic mouse for tissue-specific overexpression of a transgene In a transgenic Cre mouse that expresses Cre only in lung epithelial cells in adult individuals In a knock-in mouse designed to replace an endogenous gene with a GFP tagged version
In a knock-in mouse designed to replace an endogenous gene with a GFP tagged version
What does a capillary sequencer do when it detects two peaks of different fluorescence and comparable intensity in a given fragment ? It assigns a "Y" or "R", depending on whether the dual-fluorescence peak corresponds to purines or pyrimidines It assigns an adenine because the fluorescence associated to ddATP can often give rise to dual- fluorescence artifact It assigns an "N" to the position, to indicate that it could not accurately identify the corresponding nucleotide It assigns the corresponding nucleotides to two consecutive nucleotide positions (e.g. an A/G dual peak is converted into a ÉAGÉ call in the sequence) It assigns an "N" to the position, to indicate that any nucleotide can be present at that position in the species (i.e. to indicate a single-nucleotide polymorphism)
It assigns an "N" to the position, to indicate that it could not accurately identify the corresponding nucleotide
What do we understand by Gene Therapy? It is any form of therapy to treat a genetic disease It is any form of therapy in which the genome of the patient is altered to treat a disease It is any form of therapy to treat a disease using genetic engineering of cell cultures or bacteria It is any form of therapy in which the whole genome of a patient is sequenced to determine the most efficient course of action It is any form of therapy based on the introduction of a DNA sequence into the patient
It is any form of therapy based on the introduction of a DNA sequence into the patient
What is homologous recombination? It refers to expressing human genes in mice to replace the function of their homologous counterparts It refers to the exchange of DNA sequences between two different DNA molecules that occurs in random manner It refers to the exchange of very similar/identical DNA sequences between two different DNA molecules It refers to the recombination of alleles between different but homologous species
It refers to the exchange of very similar/identical DNA sequences between two different DNA molecules
What is the outcome of a Sanger sequencing reaction It results in the formation of DNA molecules with identical 3' ends and varying lengths at the 5' end It results in the formation of DNA molecules with identical 5' ends and different 3' ends It results in the formation of short DNA molecules that contain only one type of base (e.g. A) It results in the formation of DNA molecules that are missing one type of base (e.g. they are made of C.G and T only) It results in the formation of DNA molecules of idenhcal size hut difterent sequences
It results in the formation of DNA molecules with identical 5' ends and different 3' ends
A colleague of yours recently suggested that we could use a harmless version of SARS-CoV2 (the virus that causes COVID-19) for gene therapy, given its high infectious capacity. If such approach were to be developed, to which type of existing gene therapy approach would it be most similar, and why? It would be most similar to retroviral ex vivo gene therapy, because it would be impossible to create a non-replicative coronavirus that can infect a target cell. It would be most similar to retroviral ex vivo gene therapy, because both coronavirus and retroviruses are RNA-viruses It would be most similar to adenovirus-mediated in vivo gene therapy, because it could be used to express a protein that is not expressed by the patient due to a genetic mutation It would be most similar to adenoviral in vivo gene therapy, because coronaviruses do not reverse transcribe their RNA into cDNAs that insert themselves into the host cel
It would be most similar to adenoviral in vivo gene therapy, because coronaviruses do not reverse transcribe their RNA into cDNAs that insert themselves into the host cell's genome, and would need to be constantly re-applied throughout course of therapy.
If a group of companies are trying to find a connection between patient's response to an experimental drug and a series of genetic markers across the genome, we would normally say that they are practicing Genetic engineering and therapeutics Medical Chemistry Rational Pharmacology Big Pharma research Pharmacogenomics
Pharmacogenomics
Which of the following techniques was commonly used as the only way to amplify specific DNA sequences before the invention of PCR ? Plasmid amplification in bacterial cultures Southern blotting Western blotting gel electrophesis PCR
Plasmid amplification in bacterial cultures
Which of the following explains how PCR can be used to make many copies of only a specific DNA sequence of interest ? The template DNA is pre-digested with specific combinations of restriction enzymes PC will amplify many different sequences; the selection of the amplicons of interest is carried out later, by gel electrophoresis Taq DNA polymerase can synthesize DNA only at higher temperatures, which makes DNA synthesis very specific Primers that are designed to target specific sequences in DNA allow of new DNA synthesis only at locations of interest
Primers that are designed to target specific sequences in DNA allow of new DNA synthesis only at locations of interest
When using miNA or siNA in trangenic cells or animals, the RNA molecules being transcribed are not mRNAs. Therefore, promoters for which RNA polymerase need to be used in the vector ? RNA polymerase Il RNA polymerase I TF Il H. instead of TF I D RNA polymerase Ill sigma factor
RNA polymerase Il
What is the most common transcriptomics tool used nowadays ? Microarrays Gel Electrophoresis Cloning RNA sequencing RT-qPCR
RNA sequencing
Which step in DNA replication normally carried out by cells is NOT necessary during PCR ? Separating the two strands of the template DNA molecule Making a primer to provide DNA polymerase with a free 3'OH to extend from Releasing DNA template overtorsion as a result of duplex unwinding Attaching new nucleotides to the growing DNA molecule based on complementarity to a template DNA strand Providing the right temperature, salts and pH for polymerase to work
Releasing DNA template overtorsion as a result of duplex unwinding
Which of the following is NOT a typical application of PCR ? To introduce small mutation in a DNA of interest Restore damaged DNA strands Paternity tests and forensic analyses To observe if a DNA sequence is present in a sample To find out if genes are expressed or not
Restore damaged DNA strands
Which of the following is NOT part of a typical bacterial plasmid vector? antibiotic resistance gene Ori site restriction enzyme sites MCS/polylinker TATA box
TATA box
Which of the following is NOT part of a typical bacterial plasmid vector? restriction enzyme sites TATA box Ori site antibiotic resistance gene MCS/polylinker
TATA box
Which of the following would you LEAST likely expect to find in the genome of a transgenic mouse ? A cDNA for Green Fluorescent Protein (GFP) expression A viral promoter The Ampicillin Resistance (AmpR) gene A gene from a different rodent species The Neomycin Resistance (NeoR) gene
The Ampicillin Resistance (AmpR) gene
Which of the following are NOT needed in a cell to package RNA into new retroviral particles ? The GAG protein The ENV protein The guide RNA (gRNA) The RNA packaging sequences The POL (reverse transcriptase) enzyme
The RNA packaging sequences
A stem cell line from rabbits was found to have a native, original DNA sequence containing resistance for neomycin. Scientists would like to know the natural function of this endogenous resistance to neomycin, so they plan to "knock-out" the neomycin resistance and replace it with resistance to another selection agent (puromycin), different from NeoR. What do you expect will happen if the transfected cell is plated in media containing neomycin and puromycin? The cells will likely die in culture, because they cannot resist more than one antibiotic treatment at a time. The cells will survive but will not be able to replicate because puromycin affects an important step in DNA replication. The cell will not survive if the media contains both the neomycin and puromycin antibiotics. The cell will survive and replicate, because transgenic cells are typically heterozygous for transgene and they will have retain one wild-type
The cell will survive and replicate, because transgenic cells are typically heterozygous for transgene and they will have retain one wild-type copy of the endogenous neomycin resistant resistant gene
Which statement best describes the first step of PCR, denaturation? The mixture is heated to speed up the rate of the reaction. The mixture is cooled enough so that the synthetic primers can bind to their target sequences The mixture is heated enough so DNA polymerase can be most active and start to synthesize new DNA. The mixture is heated enough to break the hydrogen bonds between the strands of DNA, producing two single stranded DNA molecules. The mixture is heated to produce DNA polymerase.
The mixture is heated enough to break the hydrogen bonds between the strands of DNA, producing two single stranded DNA molecules.
Reverse transcription of RNA is possible in eukaryotes but it is not common. However, during retroviral transformation, reverse transcription allows the retroviral RNA sequence to become a DNA that is inserted into the infected cell's genome. What makes reverse transcription during retroviral infection possible? The retrovirus triggers a powerful CRISP response in the infected cell, which includes the reverse transcription of viral RNA into gRNA The retroviral infection stimulates the expression of the infected cell's reverse transcriptase The retrovirus itself codes for a reverse transcriptase in its POL region
The retrovirus itself codes for a reverse transcriptase in its POL region
Which of the following is the best definition of Functional Genomics? The study of the functional relationship between genotypes and phenotypes The study of how genomic sequences function in different environments The study of ancestry based on genomic data The determination of whole genome sequences from diverse species The study of the expression and function of all the coding DNA sequences present in an organism
The study of the expression and function of all the coding DNA sequences present in an organism
Which of the following is NOT a necessary step to create a transgenic eukaryotic organism ? The transgenic DNA needs to enter the nucleus The transgenic DNA needs to be expressed into a new protein The transgenic DNA needs to enter a cell via electroporation, viral infection, microinjection or any other DNA delivery method A chromosome in the host organism must become mutated The transgenic DNA must be stably incorporated into a chromosome
The transgenic DNA needs to be expressed into a new protein
What is one thing that all transgenic organisms have in common ? Their DNA has been permanently changed through genetic engineering, and the genetic modifications will be inherited by their progeny in subsequent generations They are used in agriculture to increase profit or solve problems related to growing crops and stock They were created by microinjection of genetically engineered DNA into the nuclei of embryonic stem cells. They were created by infectious organisms (A. tumefaciens or retroviruses) that carry a genetically engineered DNA sequence of interest that we want to introduce into the transgenic organism. They are used to investigate the effect how expressing genes obtained from a different individual or species can affect the biology of the transgenic organism
Their DNA has been permanently changed through genetic engineering, and the genetic modifications will be inherited by their progeny in subsequent generations
What do modern Sanger sequencing and Illumina sequencing have in common ? They both require the generation of special DNA libraries before sequencing can take place They can both be used for rapid, parallel sequencing of hundreds of thousands of DNA fragments They both use special di-deoxy ribonucleotides (ddNTPs) to stop DNA synthesis They both use flourescently-labeled nucleotides that can detect for base calling
They both use flourescently-labeled nucleotides that can detect for base calling
During gel electrophoresis, how will large DNA fragments behave compared to small DNA fragments ? They will migrate at the same rate as small DNA fragments They will join the small DNA fragments through complementary, sticky ends They will degrade the small DNA fragments during the electrophoresis They will migrate faster than small DNA fragments They will migrate more slowly through the gel
They will migrate more slowly through the gel
Why does a typical bacterial cloning vector contain a bacterial origin of replication? To allow for expression of the antibiotic resistance due to enzymatic replication To allow for proper identification of the vector as an artificial plasmid created by scientists, which ensures that experiments can be replicated across different experimental conditions. To allow for vector integration into the bacterial To allow for replication of the vector in vitro by PCR To allow for vector replication during cell division, which ensures that both daughter cells can inb a copy of the plasmid as bacteria divide
To allow for vector replication during cell division, which ensures that both daughter cells can inb a copy of the plasmid as bacteria divide
Which of the following is a valid application of Polymerase Chain Reaction (PCR)? Term To create a new DNA sequence from scratch To create post-translational changes in a protein To introduce random mutations in a sequence of interest by inducing strand slippage To clone a portion of DNA into a different context To specifically delete a DNA sequence from cells or an organism
To clone a portion of DNA into a different context
What is CRE recombinase used for ? To cut out DNA sequences flanked by LoxP sites To mark the expression of a gene using fluorescence To direct homologous recombination To express the retroviral gag, env and pol genes To facilitate integration of the T-DNA during Agrobacterium infection
To cut out DNA sequences flanked by LoxP sites
Quantitative PCR (qPCR) is used for which of the following applications ...? To find out how many copies of a DNA template sequence are present in a sample To find out how much a given gene is expressed in a biological sample To find out the nucleotide sequence of a DNA amplicon To find out if how many mutations a DNA sequence has compared to a reference sequence To find out how large is the product of PCR amplification
To find out how many copies of a DNA template sequence are present in a sample
What is GFP often used for in conditional knock-outs? It allows for selection of mice that successfully incorporated the "floxed" gene. It is used to select for successful transfectants in culture during the process of making the Cre-mouse It guides the Cre-recombinase to the right places in DNA It recombines the LoxP sites flanking the target gene, and allows it to be excised out of DNA To identify cells in which the "floxed" gene was successfully taken out
To identify cells in which the "floxed" gene was successfully taken out
For which of the following you would NOT use a transgenic mouse ? To express a protein specifically in neurons, purify it using biochemical tools and identify all the other proteins that interact with it inside the cells To determine if a human protein can replace its mouse homologue in a mouse that is mutant for that protein. To express plant genes and determine if it is at all possible for animals to photosynthesize To determine the intracellular localization of a protein of interest To produce a therapeutic protein for use in human patients
To produce a therapeutic protein for use in human patients
What does "dideoxy" refer to in "ddNTPs"? To the fact that ddNTPs stop a DNA synthesis reaction To the fact that ddNTPs are used in what used to be called "directed deterministic" sequencing To the fact that the missing hydroxyl group in ddNTPs is at the 3' position, instead of the 2' position To the fact that ddNTPs lack two hydroxyl groups (at carbons 2' and 3' of the ribose) To the fact that two nucleotides are linked together during each step of the sequencing reaction
To the fact that ddNTPs lack two hydroxyl groups (at carbons 2' and 3' of the ribose)
An engineered plasmid is successfully introduced into cultured cells placed in a rich medium with high proliferation rates. After 42 generations, and several expansions of the cells into a growing number of culture plates, you can no longer detect the effect of the transfected plasmid in the cells. This is best known as: Stable transfection Liposomal transfection Transient transfection Retroviral transfection Lentiviral transfection
Transient transfection
A researcher is interested in testing the role for a highly-conserved amino acid in the function of a mouse protein. She has been unable to locate any pre-existing variants in this codon among a large number of available mouse strains. What might be her approach to generating such mutants? Use RNAi to interfere with translation of the gene Use RNAi to knockdown the expression of the target gene. Use transposons to generate insertion alleles in the gene. Measure the expression of this gene in mice as they develop. Use CRISPR-cas to cause DNA cleavage at the codon encoding this amino acid.
Use CRISPR-cas to cause DNA cleavage at the codon encoding this amino acid.
How can we achieve high levels of overexpression in transgenic animals ? Using strong viral promoters By avoiding poly-adenylation (and thus avoiding delays during post-transcriptional processing) By taking out the promoter sequences, making transcription faster and more efficient. Using strong bacterial promoters By introducing a lot of CpG islands to be methylated upstream of the transgene.
Using strong viral promoters
What does a gene of interest do in a typical reverse genetics project? It is the gene that we have identified as responsible for a phenotype and that we would like to sequence to compare to its wild type counterpart. It allows us to select for transgenic cells in which we have successfully conducted a genetic manipulation We do not know: that's what we are trying to find out. It expresses a protein that doesn't exist in an animal, so we can study the effect of its expression. It allows us to know the DNA sequence of an organism or species
We do not know: that's what we are trying to find out.
Which of the following is CORRECT? Modern genome-wide RNA sequencing is the core of a discipline known as proteomics To do RNA sequencing, we need to have strong promoters to ensure robust transcription of the RNA molecules to be sequenced When doing RNA sequencing. we use ddUTP instead of ddTTP When doing RNA sequencing, we use RNA polymerase instead of DNA polymerase When doing RNA sequencing, we first need to reverse transcribe the RNA to cDNA
When doing RNA sequencing, we first need to reverse transcribe the RNA to cDNA
When trying to clone the coding sequence of a eukaryotic gene to express it in bacteria, you use RT- PC using an RNA sample from cells that express your sequence of interest. To your surprise, when you run the RT-PCR amplicons in an agarose gel, you see three different bands on your gel. How could you explain this observation? Your gene of interest was chopped by ubiquitin and proteasome-mediated degradation Your gene of interest was not transcribed in those cells. Your gene of interest must have undergone alternative splicing in these cells. Your mRNA of interest must have been targeted by miRNAs, which blocked translation and made reverse transcription very inefficient
Your gene of interest must have undergone alternative splicing in these cells.
Forward genetics starts with _______________; and reverse genetics starts with _____________ a known genotype and phenotype ; unknown genotype and phenotype an unknown phenotype ; a well described phenotype a known genotype but unknown phenotype ; a known phenotype of unknown genotype a known phenotype but unknown genotype ; a known gene of unknown function polygenic diseases ; monogenic diseases
a known phenotype but unknown genotype ; a known gene of unknown function
Which of the following does your transgene of interest need to have in order to be properly assembled into viral particles used for transfection ? a restriction enzyme site a CRISPR gRNA target site a strong viral promoter sequence enhancers for cell type-specific expression once in the target cell a packaging sequence
a packaging sequence
PCR does NOT require ___________ a restriction enzyme a double-stranded DNA template containing the target sequence to be amplified a heat-stable DNA polymerase a supply of the four DNA nucleotides two different single-stranded DNA primers
a restriction enzyme
Roughly how often would you expect the restriction enzyme EcoRI (recognition site GAATTC) to cut within: a) a ds DNA genome that is 50% AT (50% GC)? b) a ds DNA genome that is 60% AT (40% GC)? a) about 1/4000 b) about 1/3000 a) about 1/250 b) about 1/1000 a) about 1/4000 b) about 1/7000 a) about 1/1000 b) about 1/250
a) a ds DNA genome that is 50% AT (50% GC)?
Which of the following is a mutagenic agent that could be used at the start of a mutant screen ? actually, all of the other options are mutagenic agents chemical mutagens transposable elements X-radiation UV-radiation
actually, all of the other options are mutagenic agents
In ex vivo gene therapy, which of the following is normally a necessary step ? amplify the successful transfectant clones in culture, before re-introducing them into the patient inject the successfully transfected cells into experimental animals to rule out toxicity place the patient in a sterile environment and under a very strict diet purify the proteins produced in the lab by successful transfectants to later inject them into the patient inject the successfully transfected cells into surrogate volunteers, to rule out toxicity
amplify the successful transfectant clones in culture, before re-introducing them into the patient
In order to sequence the genomes of multicellular eukaryotes by shotgun sequencing, various fragments of DNA must be sequenced and their overlapping sequences used to make... restriction maps open reading frames (ORFs) gene annotations copy number variants assembly "contigs" (contiguous sequences)
assembly "contigs" (contiguous sequences)
In order to insert a human genetic into a bacterial plasmid, both must ..... . be able to confer the bacterial host resistance to an antibiotic ....... (this is actually wrong: you can't insert a eukaryotic gene into a bacterial plasmid - you need to use a eukaryotic vector). code for the same genetic sequences ....be cut by restriction enzymes that produce complementary "sticky" ends. .... be able to be expressed in both cacteria and eukaryotic cells
be cut by restriction enzymes that produce complementary "sticky" ends.
Why are adenoviruses used as the vector of choice for in vivo gene therapy ? because they do not randomly integrate into the target cell's genome because they cannot infect cells because they do not trigger an immune reaction by the patient because they are much more effcient at inserting themselves into the host genome because they achieve much higher levels of expression than other transgenes
because they do not randomly integrate into the target cell's genome
What is one of the modern ways to ensure that an insert of interest was cloned into a vector? re-digestion Annealing the insert to the vector heating and denaturing the vector blue-white selection unwinding the vector DNA at the Ori
blue-white selection
To produce a multicellular eukaryotic organism in which all cells are transgenic, you need to obtain transgenic DNA enucleated eggs gametes wild type bacteria
gametes
Which of the following is not a method for transfecting DNA into cells ? liposomes and other chemical carriers infectious viruses and bacteria gel electrophoresis microinjection electroporation
gel electrophoresis
In one of the methods for making transgenic mice, a transgene of interest is ....... directly into the one of the pro-nuclei of a mouse zygote, which is then implanted in a female mouse. About 3-4 weeks later, you may find......... among the progeny. microinjected; transgene heterozygous coated in liposomes and exposed; transgenic homozygous microinjected ; transgenic chimeras electroporated ; transgenic heterozygous cloned directly with restriction enzymes; transgenic chimeras
microinjected; transgene heterozygous
The typical diseases that are candidates for gene therapy are and infectious: enzymatic polygenic : dominat polygenic; recessive monogenic: recessive monogenic; dominant
monogenic: recessive
"Metagenomics" is evaluating potential drug effectiveness based on genomic data the bioinformatic annotation of a genomic sequence that follows its sequencing the study of collective genomes of multiple species that grow and interact in an environmental niche a set of genes necessary for methane production by methanogenic bacteria a complete set of metabolites that are produced by an organism or group of organisms
the study of collective genomes of multiple species that grow and interact in an environmental niche
What do we normally call a mouse that carries a completely new sequence that doesn't naturally exist in mice ? clonal transfected knock-in transgenic knock-out
transgenic
To jump around the genome of a host cell, transposons need a _________________ and ________________ ENV protein ; GAG protein Cre recombinase ; LoxP sequences selection marker (e.g. antibiotic resistance) ; recombination signals transposase ; repeat sequences reverse transcriptase ; proviral sequences
transposase ; repeat sequences
