Biotech Final
Considering following conditions: (i) human genome has 25,000 genes, (ii) each gene is 10,000 nucleotide long, (iii) NGS can read reliably 500 nucleotide fragments. To read the entire sequence of all genes one needs to generate how many spots on the NGS chip? 25,000 250,000 500,000 10,000,000
10,000,000 (on similar questions on the exam, he will specify the amount of redundancy needed!)
After amplification of DNA fragment by PCR using 10 cycles the amount of target DNA will increase: 10x10=100 fold (10x10)x10=1000 fold 1x2x2x2x2x2x2x2x2x2x2=1024 fold (10+10)x10=200 fold 10 fold
1x2x2x2x2x2x2x2x2x2x2=1024 fold
If I sequenced 1 million clusters using NGS, how many lines are in the resulting FASTQ file? 20 1 million 4 million 10 million
4 million
If my chip for NGS sequencing contains one million spots, how many lines will the resulting FASTQ file have? the number of unique genes analyzed 50,000 1 million 4 million
4 million
The sequence that was amplified by PCR is ATTGCGTAGAGACTTTCAACACACGCGCTCTCA.....GCTCAAATTGGCCATACGTACCCTGAACCA (Realize that only one strand out of two is typed, and you need both strands to answer the question. Recall also that strands are antiparallel.) The sequence of primers that were used for PCR amplification are: 5'ATTGCGT and 5'CTGAACCA 5'TAACGCA and 5'CTGAACCA 5'TAACGCA and 5'TGGTTCA 5'ATTGCGT and 5'TGGTTCA 5'TAGAGAC and 5'ATACGTAC
5'ATTGCGT and 5'TGGTTCA
If mother is heterozygous for hemophilia mutation (does not have manifestation of hemophilia) and father does not have hemophilia, than the probability of their mail children to be affected by the disease is ... 100% 75% 50% 25% 0%
50%
The temperature steps for PCR that we discussed in the class are 95C, 60C, and 72C. What step and how will be affected by switching to more AT rich primers for PCR? 95C step needs to be performed at lower temperature. 60C step needs to be performed at higher temperature. 60C step needs to be performed at lower temperature. 95C step needs to be performed at higher temperature. 72C step needs to be performed at higher temperature.
60C step needs to be performed at lower temperature.
Alpha 1 anti-trypsin deficiency is an autosomal recessive genetic disorder. If both parents are genotype (Aa) what is the chance of the offspring not expressing the disease phenotype? 0 25% 50% 75% 100%
75%
The PNA (peptide nucleic acid) is ... A complex between a peptide and nucleic acid. Genetically modified DNA. Recombinant protein. A form of DNA backbone modification. A chimeric protein.
A form of DNA backbone modification.
In case of "three parent" situation associated with the mitochondrial pathology: Two egg cells are fertilized with one sperm cell. Mitochondria from a healthy individual are carried by a sperm cell. A nucleus from the egg cell of the unaffected individual is used to compensate for the mitochondrial mutation(s). A nucleus from the egg cell of the affected individual is transferred to the egg cell of a healthy individual whose nucleus has been removed, and resulting hybrid egg cell is fertilized. A mutation in the mitochondrial DNA is recessive and is compensated by dominant mitochondria from the egg cytoplasm of a healthy individual ("third parent").
A nucleus from the egg cell of the affected individual is transferred to the egg cell of a healthy individual whose nucleus has been removed, and resulting hybrid egg cell is fertilized.
Which of these is NOT a result of supervised learning? A neural network predicting which Netflix show you'd prefer to watch next A plot showing the likelihood that patients will respond to a treatment, based on their age A decision tree predicting which treatment is best for a patient with certain characteristics A plot demonstrating similarity between different patients based on gene expression levels
A plot demonstrating similarity between different patients based on gene expression levels
In what situation described below will a mutation certainly be dominant? A mutation completely destroys the gene promoter, shutting down gene expression. A frame-sift mutation in the early part of the gene's protein coding region. A mutation that completely inactivates the enzymatic activity of the expressed protein (mutation is in the active center). A nonsense mutation within the ORF. A silent mutation leading to a mild decrease of expression leading to an overall decrease of the corresponding enzymatic activity below the threshold for a disease.
A silent mutation leading to a mild decrease of expression leading to an overall decrease of the corresponding enzymatic activity below the threshold for a disease.
Which statement incorrectly describes euchromatin and heterochromatin? Both can exist in the same cell. Acetylation of histones is more prevalent in heterochromatin. The heterochromatin state of a gene can be switched to euchromatin. ON or OFF state of a gene can be inherited for several generations and then switched. A combination of histone modifications and DNA methylations can determine if gene is ON or OFF.
Acetylation of histones is more prevalent in heterochromatin.
DNA methylation usually: Affects translation. Affects activator binding to the major groove of DNA. Affects mutagenesis in the methylated regions. Is associated with eu-chromatin. Cannot be reversed.
Affects activator binding to the major groove of DNA.
Only one statement about viruses is correct. Which one is it? Virus is a form of bacteria. Similar to other biological microbial objects virus particles contain DNA and mRNA. Once the retrovirus penetrates the eukaryotic cell its DNA starts to amplify. After each single virus penetration of a single cell and virus propagation, the host cell dies and large quantity of new virus particles are released. After amplification virus uses eukaryotic proteins to create the coating. After virus particles are assembled they incorporate themselves into chromosomes.
After each single virus penetration of a single cell and virus propagation, the host cell dies and large quantity of new virus particles are released.
PCR is the "Xerox machine" of the molecular biology and modern medicine. Amplification of the target DNA in this reaction is achieved by synthesis of the amplicon (DNA) using small amount of initial source DNA, the DNA polymerase (Taq), and nucleotides. During PCR: Taq polymerase is added during each cycle. Nucleotides are added before each cycle. Source DNA is added before each cycle. The amount of DNA increases in arithmetical progression. All components are mixed before PCR and only temperature changes lead to the accumulation of the target amplicon.
All components are mixed before PCR and only temperature changes lead to the accumulation of the target amplicon.
Four restaurant customers were found to have contracted COVID-19, two to five days after a visit. Genetic sequencing found that the viral genomes of Customers #1 and #2 were nearly identical, while those of Customers #3 and #4 were each very different from the rest. Which interpretation of the data is the LEAST plausible? Customers #1 and #2 both contracted the virus at the restaurant, while the others did not. All four customers contracted the virus separately, at different locations. Customers #2 contracted the virus from Customer #1 (or vice versa).
All four customers contracted the virus separately, at different locations.
Which of these areas of pharmacy are affected by advances in data analytics? Drug development Clinical pharmacy Retail pharmacy All of the above
All of the above Literally everything lol :)
Considering a generic eukaryotic gene map, the nucleosome can be found: On the silencer, but not on the enhancer In the transcription termination region, but not transcription initiation region Never on the promoter region On introns but not on the exons All over the gene
All over the gene
Only one statement about PCR is wrong. Which one is it? During 95oC step of PCR all double stranded DNA fragments are separated (melted) into single stranded fragments. BDuring 60oC step of PCR primers anneal to target sequences. During 72oC step of PCR Taq polymerase starts to extend primers. All synthesized fragments after PCR have the same length. After 30 cycles of PCR the theoretical amplification rate is 230 = 1,073,741,824, however in reality it is lower simply because there is not enough building blocks (nucleotides) in the tube.
All synthesized fragments after PCR have the same length.
Which of these sentences is true about drug discovery using cheminformatics? Drug efficacy can only be predicted for molecules that have been synthesized in a lab. There is no need for analytics in this area, as high-throughput sequencing allows us to easily test any molecule on any disease. Almost any quantifiable molecular feature can be used as an input for drug efficacy predictions. Predictions using machine learning are so accurate that they do not need to be validated by experiments.
Almost any quantifiable molecular feature can be used as an input for drug efficacy predictions.
What are transcription activation domains made of? Nucleic acids Amino acids Epitopes Carbohydrates
Amino acids
The SELEX process of aptamer selection is a multistep process. One of the statement below incorrectly describes the process. Which one is it? Target-interacting oligos are retained on the column containing the protein target Individual RNA molecules form multiple hairpins that interact with each other thus forming specific 3D structures The single-stranded DNA oligo pool is amplified and converted by (T7) RNA polymerase into the RNA oligo pool PCR amplification is necessary to increase the concentration of the oligo pool before selection. Amount and variety of individual oligo sequences is increased in the pool as a result of selection
Amount and variety of individual oligo sequences is increased in the pool as a result of selection
Drug leads based on aptamers are designed to interact with: Any protein chosen as a target. Intron/exon junction points of pre-mRNA Coding regions of mRNA Promoter regions of genes 5'UTRs
Any protein chosen as a target.
An oligo nucleotide that can be experimentally selected from a large pool of oligos so that it has a specific binding to a specific protein target is called: Antisense oligo Telomerase inhibitor Aptamer Triple-helix forming oligo Vitravene
Aptamer
The oligonucleotide that binds to a protein is ... Triple-Helix-Forming Oligo Antisense oligo Aptamer Anti-mRNA ribozyme Exon-skipping oligo Anti-telomerase oligo
Aptamer
The oligonucleotide that does not bind to mRNA is ... Antisense oligo Aptamer Anti-mRNA ribozyme Exon-skipping oligo Anti-telomerase oligo
Aptamer
Only one statement below is incorrect. Which one is it? CpG islands: Often appear in gene promoters. Are product of the unrepaired and inherited cytosine deamination. Can be found in coding parts of genes. If methylated, can affect gene expression. Do not normally occur in the intergenic regions.
Are product of the unrepaired and inherited cytosine deamination.
Only one statement about proteomics is incorrect. Which one is it? Each individual protein can be linked to a specific gene and identified by mass spec analysis of protein fragments. Individual proteins are often too big for the mass spec analysis and need to be fragmented (often by trypsin). DNA sequences of coding regions for all genes can be converted using genetic code into amino acid sequences of proteins of the cell. Because each human cell has the same set of genes, proteomes for different cells are also the same. Investigation of all proteins (proteome) in the cell became possible only after entire genome was sequenced.
Because each human cell has the same set of genes, proteomes for different cells are also the same.
Only one statement about proteomics is incorrect. Which one is it? Investigation of all proteins (proteome) in the cell became possible only after entire genome was sequenced. DNA sequences of coding regions for all genes can be converted using genetic code into amino acid sequences of proteins of the cell. Each individual protein can be linked to a specific gene and identified by mass spec analysis of protein fragments. Because each human cell has the same set of genes, proteomes for different cells are also the same. Individual proteins are often too big for the mass spec analysis and need to be fragmented (often by trypsin).
Because each human cell has the same set of genes, proteomes for different cells are also the same.
Only one statement below is correct. Which one is it? During production of a recombinant insulin ... If human cDNA (copy of mRNA) for insulin is used for expression in bacteria the product of expression would be proinsulin. Part A of insulin is expressed from the same plasmid as part B. Each plasmid for the recombinant insulin expression has three gens: beta-gal gene, insulin gene, and antibiotic resistance gene. Betta-gal and insulin coding parts (A or B) are fused in-frame forming a single coding region with one UAG and one stop codons. Two parts of insulin are fused together by hydrogen bonds.
Betta-gal and insulin coding parts (A or B) are fused in-frame forming a single coding region with one UAG and one stop codons.
Which tissue has the highest RNA expression of SP100? Blood Lung Kidney and urinary bladder Skin
Blood
Both RNAi and adenovirus based vectors affect gene expression. Only one statement correctly compares them. Which one is it? Both modify mutated gene Both require guiding DNA sequence Both are best if used ex-vivo Both affect the target gene expression temporarily. Both use viral delivery system.
Both affect the target gene expression temporarily.
Comparing the retroviral vectors and CRISPR-Cas9 system only one statement is correct. Which one is it? Both modify mutated gene Both require guiding DNA sequence Both are best if used ex-vivo Both affect the target gene expression temporarily. Both have viral origin.
Both are best if used ex-vivo
Comparing adenovirus and adeno-associated virus (not vectors) only one statement is incorrect. Which one is it? Both contain genetic material in the form of DNA Both cause immune response Both do not integrate their genome in the host chromosomes Have the different number of genes Both are used for transgene delivery vectors intended for the ex-vivo use.
Both are used for transgene delivery vectors intended for the ex-vivo use.
Only one statement comparing NGS and DNA microarray technologies is correct. Which one is it? Both use PCR for specific sequence spot generation. In both technologies the surface of the chip is prefabricated to have a set number of spots corresponding to each of ~25,000 genes. Both can be used for gene expression profiling (showing which genes are ON or OFF). In both cases coloring of the individual spot tells if the gene is ON or OFF. In only one technology cDNA can be used for the analysis.
Both can be used for gene expression profiling (showing which genes are ON or OFF).
Comparing retrovirus and adenovirus (not vectors) only one statement is correct. Which one is it? Both contain genetic material in the form of DNA Both cause immune response Both integrate their genome in the host chromosomes Both have the same number of genes Both are used for transgene delivery vectors intended for the in vivo use.
Both cause immune response
Comparing guiding oligo in CRISPR-Cas9 and in RNAi technologies only one statement is correct. Which one is it? Both target DNA Both have a 100% match to the target nucleic acid sequence Only one oligo is in complex with a nuclease Only one caries a desired mutation Both contain a desired mutation
Both have a 100% match to the target nucleic acid sequence
Which statement below correctly compares monoclonal and polyclonal antibodies? Production of monoclonal and polyclonal antibodies require creation of hybridoma. Transgenic animals are required for polyclonal antibody production. Embryonic cell lines are genetically modified in both cases. Both monoclonal and polyclonal antibodies are products of the expression of the same type of genes. Immortalizing a cell line is required for both mono- and poly-clonal antibody production.
Both monoclonal and polyclonal antibodies are products of the expression of the same type of genes.
Both old (Sanger) and new (NGS) sequencing techniques are used for diagnostic purposes. Consider the following statements which either correctly or incorrectly describe common points for these two sequencing approaches. Only one statement is incorrect. Which one is it? Both use DNA polymerase for synthesis of a new DNA strand. Both use one strand of DNA as a template. Both use dideoxynucleotides to terminate strand synthesis. Both use computer technology to register newly sequenced DNA fragment(s). Both use the nucleotide mix from which a correct nucleotide (based on complementarity rule) is used for addition of any single nucleotide of the growing DNA strand.
Both use dideoxynucleotides to terminate strand synthesis.
Only one approach creates the situation when the patient cells contain both healthy alleles of the disease causing gene. Which one is is it? RNAi technology. CRISPR-Cas9 technology. Retrovirus based vectors. Adenovirus based vectors Adeno-associated virus based vectors.
CRISPR-Cas9 technology.
Only one approach creates the situation when the patient cells contain both healthy alleles of the disease causing gene. Which one is it? RNAi technology. CRISPR-Cas9 technology. Retrovirus based vectors. Adenovirus based vectors Adeno-associated virus based vectors.
CRISPR-Cas9 technology.
Only one approach creates the situation when the patient's cells contain both healthy alleles of the disease causing gene. Which one is it? RNAi technology. CRISPR-Cas9 technology. Retrovirus based vectors. Adenovirus based vectors Adeno-associated bvirus based vectors.
CRISPR-Cas9 technology.
Analysis of small-molecule drug properties is an example of: Bioinformatics Cheminformatics Sports Analytics Business Analytics
Cheminformatics
Only one statement about NGS transcriptomics is incorrect. Which one is it? Considering we have 25,000 genes, using NGS we need one sequencing read per gene (25,000 total reads) to see the gene expression profile of the cell. Amount of NGS reads for each individual gene will be different for cells from different organs. To analyze the change of genes' transcription level in response to the administration of a drug one needs a computer, advanced software, and basic programing knowledge. Converting mRNA into cDNA is a necessary step to apply NGS for transcriptomic analysis. To see the expression level of a low activity gene one needs to increase the NGS redundancy (amount of reads per gene) several orders of magnitude.
Considering we have 25,00 genes, using NGS we need one sequencing read per gene (25,000 total reads) to see the gene expression profile of the cell.
The virus particles assembled for transgene delivery ... Contain all genes of the original virus Contain all envelop proteins of the original virus Contain only transgene in case of retrovirus based vectors Cause the immune response if used ex-vivo Are designed for the in-vivo treatment in case of retrovirus-based vector(s).
Contain all envelop proteins of the original virus
The bridge amplification during cluster generation of the Illumina NGS workflow has the same steps as: Sanger sequencing Conventional PCR DNA sticky ends generation Recombinant ligation Plasmid construction
Conventional PCR
All of the statements about restriction endonuclease (restrictase) are true, except one. Which one is wrong? Restriction endonuclease ... Is not a part of proofreading activity during DNA synthesis. Is part of the natural defense of the cell against viruses. Cuts DNA at the site of any palindrome. Recognizes a specific DNA sequence. Can be used for the detection of mutations.
Cuts DNA at the site of any palindrome.
Based on the Machine Learning analysis presented by Dr. Erkine's students, which of these sequences is most likely to be a functional TAD? Amino acid types: D = acidic, K = basic, W = aromatic, M = nonpolar MMMMK DDDWW KDKDK WWMMM
DDDWW
Only one statement below about epigenetics is incorrect. Which one is it? The inactive female X-chromosome will be in the heterochromatic region of the cell nucleus. The heterochromatin is depleted with acetylated histones. If the border line between eu-and hetero-chromatin on the chromosome is changed (migrated) and the gene is switched from euchromatin state to heterochromatin state, this gene's activity will be lower. There are numerous posttranslational modifications of histones in any cell. DNA methylation is generally associated with higher gene activity.
DNA methylation is generally associated with higher gene activity.
Only one description below regarding Sanger sequencing using Taq polymerase is incorrect. Which one is it? Adding individual dideoxynucleotides (ddG, or ddC, or ddT, or ddA) to four different reaction mixtures Heating the mixtures to 95C for DNA denaturation. Annealing the primer at 60C DNA synthesis at 72C Denaturation, annealing, and DNA synthesis steps are done only for PCR.
Denaturation, annealing, and DNA synthesis steps are done only for PCR.
Which mechanism of gene transcription is most consistent with the results of the research by the Erkine Lab? Initiation model Transcription model Recruitment model Detergent model
Detergent model (He may also ask a question about the Recruitment model, which they also experimented with)
Which of these cannot be accomplished with sequence alignment? Quantifying the expression levels of certain genes Identifying single-nucleotide variants in a patient's DNA Finding DNA insertions against the reference genome Determining the genome sequence of an unknown organism
Determining the genome sequence of an unknown organism
All of the statements about a cloning vector is true, except one. Which one is wrong? Bacterial plasmid or cloning vector ... Circular a DNA which does not have ends. Has origin of replication sequence. Has a marker for selection. Has to have sites for restriction digestion suitable for cloning. Does not have a gene with promoter containing UAS.
Does not have a gene with promoter containing UAS.
Which statement is correct? During a Sanger sequencing reaction two primers are used: one for the top strand and another for the bottom (complementary) strand. Primers are not used in sequencing reactions, they are necessary only for PCR. For a sequencing reaction using Taq polymerase, one needs to use two primers complementary to two different strands of DNA. Human DNA polymerase can be used for PCR the same way as Taq polymerase, if the primer extension step of PCR cycle is done at 37C. During bridge-amplification stage of Illumina NGS, individual DNA clusters are generated by PCR reaction.
During bridge-amplification stage of Illumina NGS, individual DNA clusters are generated by PCR reaction.
Illumina NGS technology (massive parallel sequencing) utilizes chips for the whole genome sequencing. Only one statement below incorrectly describes the NGS chip. Which one is it? Each spot on the chip has different sequence and no spots have identical DNA sequences. Each spot contains thousands of identical DNA strands Each spot is a result of PCR (bridge) amplification starting from a single DNA strand In each spot new DNA strand is synthesized in parallel with other spots during sequencing Occasionally different spots contain identical sequences.
Each spot on the chip has different sequence and no spots have identical DNA sequences.
A bacterial expression vector has all DNA sequence elements except one. Which one is absent? Transcription start site Translation start site AUG start codon. A stop codon -10 and -35 promoter sequences Transcription termination sequence Enhancer 5'UTR sequence
Enhancer
The CRISPR-Cas9 gene editing technology is most appropriately used ... Ex-vivo In-vivo In-vitro
Ex-vivo
Considering a generic gene map and sequences that are vital for gene expression, the antisense oligo will bind to what part of the gene: Transcription terminator Exon Promoter region (TATA box) Intron Promoter region (UAS)
Exon
Considering the generic map for eukaryotic gene the oligo designed to interfere with mRNA processing is likely to be complementary to: Promoter region Kozak sequence Stop codon Transcription start site Exon/intron junction
Exon/intron junction
Considering that there are ~25,000 genes in the human genome, each with its own promoter, and considering that DNA microarray technology is often utilized for gene expression profiling, the sequences of oligonucleotides in individual spots of the DNA microarray chip can contain sequences identical to: Promoters of genes Exons of genes Introns of genes Enhancers of genes Transcription termination sequence of genes
Exons of genes
Only one statement about monoclonal antibody is incorrect. Which one is it? For production of monoclonal antibody the lab animals are genetically modified. After injection of antigen the animal react by producing a polyclonal antibody response. The white blood cells producing antibody can be maintained outside of the animal's body only for several cell generations. Hybridizing the antibody-producing white blood cells and mice tumor cells allows to create the hybridoma cell culture that produces desired antibody and is immortal. The monoclonal antibody are call so because the entire hybridoma cell culture is the progeny of a single event of hybridization of one white blood cell and one tumor cell.
For production of monoclonal antibody the lab animals are genetically modified.
If there is a point mutation within the first exon of the gene, the effect on gene expression will likely be ... Likely no effect. Transcription rate will be affected. Translation will be slower. Alternative splicing. Frame-shift mutation that leads to expression of truncated protein.
Frame-shift mutation that leads to expression of truncated protein.
Only one statement about DNA microarrays is incorrect. Which one is it? DNA microarray chips are prepared by attaching gene specific DNA oligonucleotides into specific coordinates on the chip surface. The amount of spots on the DNA microarray chip is equal to the amount of genes necessary for analysis. Considering we have 25,000 genes one needs at least 25,000 individual synthetic oligos on the surface of the DNA microarray chip. Color labeled cDNA (or mRNA) forms double stranded hybrids with DNA microarray oligos on the surface of the chip. Gene expression profile for a specific type of cancer is the same for different patients.
Gene expression profile for a specific type of cancer is the same for different patients.
Which of these methods provides continuous values of gene expression? Gene expression profiling using microarrays Gene expression profiling using NGS Genome assembly
Gene expression profiling using microarrays
Mutation (deletion of one nucleotide) between UAS and TATA box will: Eliminate gene activator binding to the promoter Eliminate general transcription factors binding to the promoter Decrease transcription rate Eliminate nucleosome binding to the promoter Have no effect on gene expression
Have no effect on gene expression
Mutation (deletion of one nucleotide) between transcription initiation region and translation start site will: Eliminate transcription Have no effect on gene expression Be called a nonsense mutation Eliminate translation Create a frame shift
Have no effect on gene expression
Which of these is used to visualize the expression levels of genes within each sample? Volcano plot Genome assembly Manhattan plot Heatmap
Heatmap
Only one statement about data analytics and bioinformatics is incorrect. Which one is it? Due to rapid rise in the amount of digitized data in omics the role of computer based technologies (data analytics) is rapidly increasing. In order to accommodate the growing need in skills necessary to handle and to understand large datasets, the pharmacy curriculum has to include the programing (coding) literacy courses. While single gene mutation diseases can be handled by traditional medical approaches, more complex diseases such as cancer require individual transcriptomic gene profiling Her2 gene mutation is responsible for all breast cancer cases.
Her2 gene mutation is responsible for all breast cancer cases.
Only one statement about transgenic animals is incorrect. Which one is it? Embryonic stem cells can be modified using CRISPR-Cas9 technology. The initial injection of modified cells in the embryo leads to birth of the offsprings, which are also only partially modified. Only if modification (edited gene) gets into the part that includes germ cells, the second generation offspring will be fully transgenic. The second generation can be either fully transgenic or fully non-trasgenic. If the transgenic animal is not detected in the second generation, the breading has to continue with the hope to get the fully transgenic animal in third, fourth or following generations.
If the transgenic animal is not detected in the second generation, the breading has to continue with the hope to get the fully transgenic animal in third, fourth or following generations.
Only one statement about COVID PCR test is incorrect. Which one is it? For the COVID PCR test ... Swabs from areas most likely containing virus particles has to be obtained. Virus RNA has to be extracted and converted into DNA by reverse transcriptase. DNA has to be extracted and purified. Primers complementary to the virus DNA has to be used. If virus nucleic acid sequence is present it will block the amplification by PCR.
If virus nucleic acid sequence is present it will block the amplification by PCR.
Which antibody is produced in the process of innate immunity? IgG Antibodies are only produced in the adaptive immune response IgE IgM
IgM
Only one statement comparing NGS and DNA microarray technologies is incorrect. Which one is it? While for DNA microarray an individual gene spot has a specific coordinates on the chip surface, for the NGS coordinates of individual gene spots is random. While for NGS the chip surface is covered uniformly with only two oligos, the number of oligos for the DNA microarray technology is determined by the amount of genes to be analyzed. For DNA microarrays the chip can be used multiple times for the analysis of several samples, while NGS chip is for a single time usage. In both cases bioinformatics is used for reconstruction of the entire genome from the gene sequence of fragments. For DNA microarray one spot (fragment) per gene might be enough for analysis, while for the NGS the amount of spots per gene is uncertain.
In both cases bioinformatics is used for reconstruction of the entire genome from the gene sequence of fragments.
A patient almost dyed when administered a normal dose of the anesthetic drug during surgery. Later it was discovered that the person is the carrier of the recessive mutation in position 6 of the beta-globin gene. This hypersensitivity to the anesthetic drug is an example of ... Incomplete dominance Heterozygote advantage Co-dominance Multiple alleles phenotype Mitochondrial dysfunction
Incomplete dominance
Exondys 51 (Eteplirsen) is a newly approved drug. It corrects effects of only 1% of mutations causing DMD. This 1% is a particular frame-shift mutation in exon 51. Exonys 51 works via following mechanism: Restoring the reading frame by insertion of a nucleotide. Restoring the frame by excision of exon 51. Interfering with translation. Interfering with transcription. Increasing stability of mRNA
Interfering with translation. Restoring the frame by excision of exon 51. HE ACCEPTED TWO ANSWERS
SNURPs (U-particles) bind to: Poly adenylation site Intron/exon junction points Promoter Transcription termination sequence Enhancer
Intron/exon junction points
During the creation of a transgenic animal one needs to control if the desired gene is modified. To perform this control the most appropriate technique will be: Analyzing protein expression of the modified gene Isolating DNA from germ cells of the animal and performing real-time PCR analysis to determine the gene expression level. Testing the phenotype of the animal, especially if the mutation is recessive. Isolating DNA from germ cells of the animal, amplifying mutated region by simple conventional PCR, and use Sanger sequencing to read DNA of the amplicon. Performng Next Generation Sequencing (NGS) on DNA isolated from the germ cells.
Isolating DNA from germ cells of the animal, amplifying mutated region by simple conventional PCR, and use Sanger sequencing to read DNA of the amplicon.
Which of the following is true of Excel? It can hold many millions of data points without difficulty. It has many customizable tools, created by the community. Excel data sets cannot be used in coding analyses. It can make simple graphs using presets given by Microsoft.
It can make simple graphs using presets given by Microsoft.
Targets for new drug leads often become obvious by identification of proteins, which are under- or over-expressed in the affected tissue/organ. The protein identification can be done by electrophoresis in polyacryalamide gels or by mass-spec analysis. The advantages of the mass-spec analysis include .... Only one statement is INCORRECT, which one is it? Protein/peptide masses are determined with precision of several Daltons, while the threshold of resolution by electrophoresis is hundreds of Daltons. Utilization of proteomics databases with all possible protein sequences. Proteins with identical masses but different amino acid sequences are easily distinguished. It does not require computer bioinformatics analyses.
It does not require computer bioinformatics analyses.
Which of the following is true regarding coding and pharmacy? Pharmacists can just email data to an analyst and then forget about it. Learning how to code is a way to diversify your abilities as a pharmacist. Pharmacists will never find a use of coding in their jobs, especially if they don't go into drug discovery. Dedicated data analysts will do 100% of analytics work, because it's too hard for pharmacists to learn how to code.
Learning how to code is a way to diversify your abilities as a pharmacist.
If there is a point mutation between transcription and translation start points (5'UTR) within the gene, the effect on gene expression will likely be ... Likely no effect. Transcription rate will be affected. Translation will be slower. Promoter become non-functional. Frame-shift mutation that leads to expression of truncated protein.
Likely no effect.
If there is a point mutation within the first intron of the gene, the effect on gene expression will likely be ... Likely no effect. Transcription rate will be affected. Translation will be slower. Alternative splicing. Frame-shift mutation that leads to expression of truncated protein.
Likely no effect.
The Pfizer and Moderna anti-COVID vaccine contain the mRNA that codes for the COVID spike protein. The point mutation within the 3'UTR of this mRNA will lead to ... Likely no effect. Poly A tail will be shorter, thus mRNA will be less stable and the vaccine is less efficient. Translation will be slower and the vaccine will be less efficient. Alternative splicing and the vaccine will be less efficient. Frame-shift mutation that leads to expression of a truncated COVID spike protein, and the vaccine will be less efficient.
Likely no effect.
The delivery of the oligo (mRNA) in Pfizer and Moderna anti-COVID vaccine is done by ... Electroporation Injection of gold nanoparticles coated with the oligo Magnetofection Sonoporation Liposomes
Liposomes
What cell of the immune system secretes inflammatory cytokines in response to a bacterial infection? Macrophage Neutrophils Dendritic cell Memory B-cell
Macrophage
You are using Cas9/guiding oligo complex to target a frame-shift creating a point mutation in a specific gene. The action of this complex on the gene of your choice will be: Multiple unintended mutations instead of the original one Correction of mutation (conversion to WT) No action as you need to use a "patching" oligo. Substitution of a single nucleotide causing the mutation Deletion of a single nucleotide causing the mutation thus restoring the correct reading frame
Multiple unintended mutations instead of the original one
Delivery of a transgene using a virus-based vectors makes sense only if ... Transgene will be incorporated in the genome of the disease affected cells Vector does not cause an immune response Mutation causing the disease is dominant Mutation causing the disease is recessive
Mutation causing the disease is recessive
Using CRISPR-Cas9 technology you can relatively easy create or correct mutations. In a specific case the transgenic animal was created with a point mutation in a single (APC) gene. The National Institute of Health (NIH) raised concern that the procedure might have created multiple unintentional mutations in different loci. The technology that can alleviate (or confirm) this concern is: Cloning PCR NGS Sanger sequencing Gene editing using CRISP-Cas9
NGS
Recombining DNA fragments after restriction digestion ends of fragments has to be complementary to each other. To connect different pieces of DNA by ligase the ends of the DNA fragments ... Need to be created by digestion of the same restrictase. Need to be created by digestion of any restrictase. Need to be created by digestion of EcoR1 only. Need to be created by digestion of MstII only. Need not have complementarity to each other at the protrusion created by restrictase digestion.
Need to be created by digestion of the same restrictase.
Peptide nucleic acid (PNA) oligonucleotides are new emerging drugs. They are: Stabilized complexes of proteins and DNA Peptides with specific amino acid sequences recognizing specific DNA sequences Oligonucleotides with phosphodiester backbone substituted by peptide backbone Triple helix forming single stranded DNA oligonucleotides Mismatched DNA sequences binding to random DNA regions
Oligonucleotides with phosphodiester backbone substituted by peptide backbone
Only one statement about the in vitro oligomediated mutagenesis is incorrect. Which one is it? To create a mutation using a plasmid and an oligo ... One need an oligo that has full complementarity to a specific region of the plasmid. This oligo is annealed to one strand of the plasmid and serves as a primer for DNA polymerase. After the completion of the complementary strand synthesis by DNA polymerase the resulting double stranded DNA plasmid is cloned. The result of cloning is colonies containing either WT or mutant plasmid copies. At the final stage the colonies are screened and those containing mutation are selected.
One need an oligo that has full complementarity to a specific region of the plasmid.
Only one statement about NGS (Illumina) is incorrect. Which one is it? Only Sanger sequencing procedures require the DNA polymerase, while for NGS it is the chemical synthesis. During NGS hundreds of millions of DNA fragments are sequenced simultaneously. The amount of sequenced (read) letters will be the same for all DNA fragments. Each letter color for each fragment (hundreds of millions of fragments) is registered by the CCD camera attached to a computer during the synthesis. To assemble the whole genome sequence after NGS it is necessary to have overlaps between sequenced fragments.
Only Sanger sequencing procedures require the DNA polymerase, while for NGS it is the chemical synthesis.
Changing nucleotide sequence of the chromosomal DNA is an ultimate way to fight genetic disorders. Currently there are several protocols to modify genes both in vivo and in vitro. Comparing an in vitro site-directed oligo-mediated mutagenesis for plasmids and the in vivo CRISPR-Cas9 anti-viral bacterial defense system: In both cases the oligo is in physical complex with an enzyme. In both cases the oligo contains mutation Only in one case the oligo contains a desired mutation Only in one case the oligo is double stranded Only in one case the oligo forms specific and multiple hydrogen bonds with the target sequence on the plasmid or chromosome.
Only in one case the oligo contains a desired mutation
Which vaccine uses the in vivo virus-based antigen delivery system? Pfizer anti-COVID vaccine Moderna anti-COVID vaccine Oxford-AstraZeneca anti-COVID vaccine Pneumococcal conjugated vaccine Meningococcal vaccine
Oxford-AstraZeneca anti-COVID vaccine
Which anti-COVID vaccine is using the viral-based vector for immunization? Pfizer vaccine Moderna vaccine Correct! Oxford-AstraZeneca vaccine. Ely Lilly vaccine.
Oxford-AstraZeneca vaccine.
The patient's sample used for PCR amplification of the Huntigtin gene resulted in a single band corresponding to 40 CTG repeats. One of the interpretations of results and/or prognosis for this patient is/are INCORRECT. Which one is it? The patient is homozygous for the Huntington gene. PCR did not work correctly and did not produce second band. Both alleles of Huntington gene are identical. Symptoms of Huntington disorder will be mild and are likely to appear in second half of the lifespan. Parents of the patient were carriers of the Huntington mutation.
PCR did not work correctly and did not produce second band.
Only one statement about virus-based vectors is incorrect. Which one is it? Virus based Gene therapy vectors contain full set of virus envelop proteins, however the genes that code for these proteins are eliminated from the vector nucleic acid. Virus vectors can be used in vivo (directly delivered to the patient's body), or ex vivo (directly delivered to isolated cells of the patient). Pfizer anti-COVID vaccine is delivered using modified adeno virus based vector. The adenosine deaminase deficiency was treated ex vivo using retrovirus based vector. The patient's cells treated by virus based vector express both wild type and mutant variant of the disease associated enzyme.
Pfizer anti-COVID vaccine is delivered using modified adeno virus based vector.
Which of these sentences about data analytics is FALSE? Data analysis is a continuous process, as new data can be used to improve our understanding. As the cost of DNA sequencing has decreased, the amount of sequencing data available has skyrocketed. Data organization and storage is an important aspect of data analytics. Pharmacists must also get a CS degree to have any role in understanding data.
Pharmacists must also get a CS degree to have any role in understanding data.
Which of the following is FALSE about data analytics in pharmacy? Pharmacists no longer have to worry about doctors' handwriting, because computers can take care of everything. Neural networks can help read images, such as prescriptions or MRI scans Data analytics can help handle complicated insurance data Analytics can help improve pharmacy operations.
Pharmacists no longer have to worry about doctors' handwriting, because computers can take care of everything.
Which of these is not an example of data analysis using coding? Writing an R script to analyze hundreds of similar Excel files Using a Python library to conduct data analysis Plotting a bar graph in Excel Making an interactive scatterplot using Python
Plotting a bar graph in Excel
If you aplify by PCR the insulin coding region from the cDNA library, insert ii into the expression vector and express the protein from this vector in bacteria, than the resulting protein will be: The insulin protein with additional sequences correseponding to introns. Proinsulin Insulin partB fused to Gal Insulin partA fused to Gal Preproinsulin
Preproinsulin
The deletion of the TATA box will have following effect: Gene expression will be decreased but not fully eliminated Binding of the gene activator to promoter will be eliminated Interaction between proteins bound to promoter and enhancer will be impossible Promoter will be nucleosome free, but transcription will not start RNA transcribed from the gene will be processed as usual.
Promoter will be nucleosome free, but transcription will not start
Which of these types of information cannot be found at pharmgkb.org? Prescribing information based on genetic mutations Protein expression levels in various tissues Pathway information for drug pharmacokinetics and pharmacodynamics Pharmacogenetic drug label annotations
Protein expression levels in various tissues
Which of these types of information cannot be found at pharmgkb.org? Protein expression levels in various tissues Pharmacogenetic drug label annotations Pathway information for drug pharmacokinetics and pharmacodynamics Prescribing information based on genetic mutations
Protein expression levels in various tissues
Transcription termination hairpin binds to: RNA polymerase Ribosome polyA tail TATA binding protein (TBP) Nucleosome
RNA polymerase
Only one statement about Sanger DNA sequencing is incorrect. Which one is it? For Sanger sequencing... To read the sequence of one DNA fragment one needs to do four separate DNA polymerase reactions. In each reaction the synthesis is terminated by a specific dideoxynucleotide. The amount of fragments generated in each sequencing reaction is proportional to the amount of letters causing termination. Each reaction mix contains deoxy and dideoxy nucleotides. Reading on the sequencing gel goes top to bottom, because bands on the top correspond to letters closest to the sequencing primer.
Reading on the sequencing gel goes top to bottom, because bands on the top correspond to letters closest to the sequencing primer.
What is a characteristic of innate immunity? high level of specificity Slow response Same level of response at every encounter with pathogen Necessary for the activation of the adaptive immunity
Same level of response at every encounter with pathogen Necessary for the activation of the adaptive immunity HE ACCEPTED TWO CORRECT ANSWERS
Lac operon has the following elements: Kozak sequence Introns Nucleosome binding site Sequences coding for three stop codons Enhancer
Sequences coding for three stop codons
Relatively rare X-linked "lionization" (alternating skin pigmentation) in females is a result of: Several consecutive alternative inactivation events between two X-chromosomes in different cells early in embryogenesis. An expression of the pigment-producing gene from either one or two X-chromosomes. Early embryonic mutation on one of the X-chromosomes. Two of the statements are correct. Three of the statements are correct.
Several consecutive alternative inactivation events between two X-chromosomes in different cells early in embryogenesis.
RNAi are used as a component of new drugs. These oligonucleotides can affect the: Translation rate of specific mRNA Binding of the small subunit of ribosome to the 5' cap of specific mRNA Two of the above are possible affects Poly adenylation of specific mRNA Stability of specific mRNA in the cell.
Stability of specific mRNA in the cell.
Lac operon does not have the following element: Regions coding for UTRs TATA box Transcription terminator Single promoter Transcription start site
TATA box
Only one statement about NGS (Illumina) is incorrect. Which one is it? For Illumina NGS ... Long DNA has to be fragmented in short overlapping fragments. The identical left and right side adaptor DNA sequences has to be appended to each individual fragment. The adaptor sequences are used to form hydrogen bonds with complementary oligos attached to the surface of the chip. Once individual fragments are attached, they are amplified on the surface of the chip by PCR (bridge amplification). During the sequencing step one out of four added colored nucleotides is added and registered for each fragments according to the nucleotide complementarity rule. The DNA synthesis reaction is terminated by dideoxynucleotides.
The DNA synthesis reaction is terminated by dideoxynucleotides.
After differential expression analysis, a researcher found that leukemia patients have much higher expression of a certain protein than healthy controls. She wants to determine whether this protein is specific to a certain tissue type, to see whether it may be a good drug target. Which database would be most useful? The Human Protein Atlas (proteinatlas.org) The Pharmacogenomics Knowledge Base (pharmgkb.org) Gene Expression Omnibus (ncbi.nlm.nih.gov/geo/) Electronic Health Records
The Human Protein Atlas (proteinatlas.org)
You would like to determine whether genetic testing is required for a patient who has been prescribed a certain medicine. Which database would be most useful? The Human Protein Atlas (proteinatlas.org) The Pharmacogenomics Knowledge Base (pharmgkb.org) Electronic Health Records Gene Expression Omnibus (ncbi.nlm.nih.gov/geo/)
The Pharmacogenomics Knowledge Base (pharmgkb.org)
You would like to determine whether genetic testing is required for a patient who has been prescribed a certain medicine. Which database would be most useful? The Pharmacogenomics Knowledge Base (pharmgkb.org) Electronic Health Records Gene Expression Omnibus (ncbi.nlm.nih.gov/geo/) The Human Protein Atlas (proteinatlas.org)
The Pharmacogenomics Knowledge Base (pharmgkb.org)
Only one statement about viruses is correct. Which one is it? Retrovirus contains two genes: gag and env. Adenovirus nucleic acid is usually incorporates into host chromosomes. The adeno associated virus and its vector derivatives do not produce a long lasting immune response after treatment. The anti-COVID Oxford vaccine is the mRNA coated into lipids. The patient's cells treated by virus based vector express both wild type and mutant variant of the disease associated enzyme.
The adeno associated virus and its vector derivatives do not produce a long lasting immune response after treatment.
If during the COVID PCR test the threshold amplification level is reached on 28th cycle instead of 23th cycle, than... The individual has 5 times higher COVID titer (amount of COVID DNA). The individual has 5 times lower COVID titer (amount of COVID DNA). The individual has 32 times higher COVID titer (amount of COVID DNA). The individual has 32 times lower COVID titer (amount of COVID DNA). The individual does not have COVID.
The individual has 32 times lower COVID titer (amount of COVID DNA).
A previously healthy 8-year-old boy is infected with an upper respiratory tract virus for the first time. During the first few hours of the infection, which one of the following events occurs? Memory B-cells are activated and express high affinity antibodies B and T lymphocytes recognize the virus and stimulate the innate immune response The adaptive immune system responds rapidly to the virus and keeps the viral infection under control. The innate immune system responds rapidly to the viral infection
The innate immune system responds rapidly to the viral infection
A previously healthy 8-year-old boy is infected with an upper respiratory tract virus for the first time. During the first few hours of the infection, which one of the following events occurs? The adaptive immune system responds rapidly to the virus and keeps the viral infection under control The innate immune system responds rapidly to the viral infection and keeps the viral infection under control. Passive immunity mediated by maternal antibodies limits the spread of infection B and T lymphocytes recognize the virus and stimulate the innate immune response
The innate immune system responds rapidly to the viral infection and keeps the viral infection under control.
The quantitation of DNA using real-time PCR approach showed that for the investigated sample it takes 25 cycles to reach the same level of amplicon generation as a control (reference) sample. For the control sample it takes only 22 cycles. The interpretation of this result is: The investigated sample has 3 times less DNA than reference The investigated sample has 3 times more DNA than reference The investigated sample has 8 times more DNA than reference The reactions have to be done in the same tube to be compared. The investigated sample has 8 times less DNA than reference
The investigated sample has 8 times less DNA than reference
Which statement(s) correctly describes the Sanger sequencing reaction? Two primers can be used as in PCR. The mixture for each sequencing reaction contains all four unmodified nucleotides. All four dideoxynucleotides together are used as part of the mixture in each sequencing reaction. DNA fragment size is registered after addition of each consecutive nucleotide. One set of sequencing reactions (four) with a single primer is enough to read the whole chromosome.
The mixture for each sequencing reaction contains all four unmodified nucleotides.
Only one statement is INCORRECT. Which one is it? During utilization of NGS for gene profiling... mRNA has to be converted into cDNA All cDNA variants has to be sequenced (read) multiple times individually The more reads any specific gene has the less active it is. Analyzing transcription datasets is impossible without computer software. The redundancy of individual gene sequencing is a necessary requirement for gene expression analysis.
The more reads any specific gene has the less active it is.
The spread of the recessive mutations associated with such diseases as cystic fibrosis and sickle cell anemia happened in the past because The mutation is recessive and thus there is no selective pressure against this mutation. The mutation is a single letter change in the unimportant part of the gene. The mutation in case of the heterozygote only leads to an increased survivability (relative to the WT homozygote) associated with a disease not caused by any mutation. The mutation displays incomplete dominance. The mutation co-dominates with another mutation.
The mutation in case of the heterozygote only leads to an increased survivability (relative to the WT homozygote) associated with a disease not caused by any mutation.
Only one statement about Sanger sequencing is correct. Which one is it? The amount of bands in each sequencing line (individual letter reaction) for all four reaction is the same. If the DNA fragment is GC rich you will see more bands in the A and T lines. The mutation that is a deletion of one nucleotide will be seen as an alternative band (peak) in the sequencing lines. The mutation that is a deletion of one nucleotide will be seen as a shift of bands in all four lines starting at the mutation point. Two primers can be used for sequencing similar to PCR.
The mutation that is a deletion of one nucleotide will be seen as a shift of bands in all four lines starting at the mutation point.
Only one statement about CRISPR-Cas9 is correct. Which one is it? Cas9 is the DNA polymerase. Eukaryotic cells contain Cas9 as a part of their defense system against viruses. The guiding oligo has complementarity to chromosomal region to be edited and also the desired sequence modification. When Cas9 is guided to a specific chromosome locus, it cuts it and creates a desired mutation. The patching oligo has complementarity to the specific chromosome site and caries the desired sequence modification.
The patching oligo has complementarity to the specific chromosome site and caries the desired sequence modification.
Only one statement about the RNAi technology is incorrect. Which one is it? RISC complex is the RNAase. Eukaryotic cells contain RISC complex as a part of their gene regulation sytem. The guiding oligo has complementarity to specific mRNA. When RISC complex is guided to a specific mRNA, it cuts it, which leads to the mRNA degradation. The patching oligo helps to save the mRNA from degradation.
The patching oligo helps to save the mRNA from degradation.
The CRISPR-Cas9 and RNAi technologies are recent breakthroughs more and more often applied in medicine and drug development. Only one statement incorrectly compares them. Which one is it? Both use a nuclease to cut a nucleic acid Both are used in vivo (in the living cell) Only one can be used to eliminate mutations Both use guiding oligo The result of using both technologies can be observed by DNA sequencing.
The result of using both technologies can be observed by DNA sequencing.
The mutation will be certainly dominant if... The activator binding sequence (UAS) of gene promoter is eliminated by this mutation. There is a nonsense mutation in the first exon of the gene. This mutation eliminates key junction points between exons and introns. The Kozak sequence and first ATG codon of the first exon is changed. The second parental wild type allele cannot fully compensate the lost function of the protein expressed from the mutant allele.
The second parental wild type allele cannot fully compensate the lost function of the protein expressed from the mutant allele.
Only one statement about NGS (Illumina) is incorrect. Which one is it? Our individual genome sequence determines most of the traits we have in our life including predispositions to specific diseases. The price tag for genome sequencing dropped a million fold during last two decades and is ~$1000 now. Knowing you own genome sequence can have both positive and negative consequences, as the traits can be actionable or not. It is highly beneficial for an insurance company to know the genome sequences of its clients. This knowledge can be obtained for a fraction of the annual premium the individual pays. The size of Human genome is such that you cannot store this information one the hard drive of an individual computer.
The size of Human genome is such that you cannot store this information one the hard drive of an individual computer.
Only one statement about omics is correct. Which one is it? Genome of modern human and ancient Egyptian are drastically different because in 5,000 years human changed. All proteins and protein variants from a human cell represent the human proteome. If you convert all mRNAs of the human cell into cDNA than the library of these molecules will represent entire transcriptome of that cell The total DNA isolated from a human cell represents the human genome. Knowing all 25,000 human genes means we know all coding regions of these genes, and thus using the genetic code we can convert coding region sequences into protein amino acid sequences, which constitute entire human proteome.
The total DNA isolated from a human cell represents the human genome.
Only one statement about omics is correct. Which one is it? If you convert all mRNAs of the human cell into cDNA than the library of these molecules will represent entire transcriptome of that cell. All proteins and protein variants from a human cell represent the human proteome. The total DNA isolated from a human cell represents the human genome. Knowing all 25,000 human genes means we know all coding regions of these genes, and thus using the genetic code we can convert coding region sequences into protein amino acid sequences, which constitute entire human proteome. Genome of modern human and ancient Egyptian are drastically different because in 5,000 years human changed.
The total DNA isolated from a human cell represents the human genome.
What is the incorrect (only one) statement? During allele-discriminating Real-time PCR... Three oligonucleotides are used. Both 5' to 3' and 3' to 5' exonuclease activities of Taq polymerase are being utilized. One oligonucleotide is destroyed for each amplicon molecule synthesized. Reporter and quencher are separated by Taq polymerase during amplicon synthesis. The yield of the PCR amplicon is measured after 30 cycles of PCR.
The yield of the PCR amplicon is measured after 30 cycles of PCR.
Prior to thiopurine prescription, a patient underwent genetic sequencing. A mutation was detected at position 238 of the TPMT gene, with 98% VAF. Which of these statements is correct? This patient has the TPMT*1 (normal) genotype in both alleles. This patient has the TPMT*3A in one allele, with moderate risk of toxicity at normal thiopurine dosage. This patient has the TPMT*2 genotype in both alleles, and thiopurines can be prescribed at normal dosage. This patient has the TPMT*2 genotype in both alleles, and thiopurines may cause fatal toxicity at normal dosage.
This patient has the TPMT*2 genotype in both alleles, and thiopurines may cause fatal toxicity at normal dosage.
How do B-cells recognize antigens? Through Toll like receptors Through B-cell receptors Through MHC II Through MHC I
Through B-cell receptors
For polyclonal antibody production one needs: To edit the antibody producing gene so that the resulting antibody has higher affinity for antigen. A transgenic animal that is created for antibody production. To collect B-cells from the immunized animal and cultivate them in cell culture. To immunize an animal with the antigen and after while collect blood from this animal. A hybridoma cell line that can be maintained indefinitely producing the specific antibody.
To immunize an animal with the antigen and after while collect blood from this animal.
Out of five synthetic oligos listed below only one directly interacts with a protein. Which one is it? Antisense oligo Transcription factor decoy Triple-helix forming oligo Fomivirsen Telomerase inhibitors
Transcription factor decoy
If there is a point mutation within the UAS of the gene, the effect on gene expression will likely be ... Likely no effect. Transcription rate will be affected. Translation will be slower. Promoter become non-functional. Frame-shift mutation that leads to expression of truncated protein.
Transcription rate will be affected.
Considering a generic eukaryotic gene map, RNA polymerase binds to: TATA box Transcription start site Silencer Enhancer UAS
Transcription start site
The oligonucleotide that binds to DNA is ... Transcription factor decoy Triple-Helix-Forming Oligo Antisense oligo Aptamer Anti-mRNA ribozyme Exon-skipping oligo Anti-telomerase oligo
Triple-Helix-Forming Oligo
Out of five synthetic oligos listed below only one directly interacts with DNA. Which one is it? Transcription factor decoy Telomerase inhibitors Antisense oligo Triple-helix forming oligo Riboswitch
Triple-helix forming oligo
New data can help us improve a machine learning model. True False
True
What is the correct (only one) statement about Huntington's disease PCR test? The Huntington's PCR amplicons from a particular patient have always the same size. The test is positive if PCR product is detected. Huntington's disease is recessive. The amount of CTG repeats detected by PCR is above 37 for the unaffected person. Two amplicons often detected during the Huntington's disease PCR test are the result of human sexual reproduction.
Two amplicons often detected during the Huntington's disease PCR test are the result of human sexual reproduction.
Tay-Sachs disease shows autosomal recessive inheritance. The parents of a newly diagnosed, affected child are referred for genetic counseling. It would be correct to tell them that: the probability that their next child will be affected is 1 in 2 the probability that the older but unaffected sister of the affected child is a carrier of Tay-Sachs is 2 in 3. the fact that this child is affected means that their next three children will not be affected. There is 100% probability that each parent is a carrier of Tay-Sachs. Two of the responses are correct.
Two of the responses are correct. There is 100% probability that each parent is a carrier of Tay-Sachs. the probability that their next child will be affected is 1 in 2
In the ABO blood group system in humans, if a person of type-B blood has children with a person of type-AB blood, what blood types could their children have? Type-AB, type-A, and type-B Type-A and Type-B Type-B and Type AB Type-AB, Type-A, type-B, and Type-O None of answers is correct.
Type-AB, type-A, and type-B
Clustering patients by gene expression, to determine which ones are similar, is an example of: Supervised analysis Unsupervised analysis Excel data analysis None of these
Unsupervised analysis
DNA microarrays are a tool used in analyzing genomes and transcriptomes. They are also actively used in drug design. DNA microarrays work: Via hybridization of synthetic nucleic acid sequences attached to the surface of the chip with a variety of nucleic acid sequences isolated from the cell. By mimicking the 3D structure of proteins. Via a shotgun approach, fragmenting genomic DNA and attaching individual pieces to the surface of the chip. By aligning known and unknown DNA sequences using computer software.
Via hybridization of synthetic nucleic acid sequences attached to the surface of the chip with a variety of nucleic acid sequences isolated from the cell.
RNAi technology affects gene expression. The outcome of specific RNAi action in the cell is most appropriately observed using: NGS Western blotting Southern blotting PCR Sanger sequencing
Western blotting
PCR amplicon of insulin gene from a human chromosomal DNA: Can be used for the proinsulin expression in bacterial cells Can be used for the insulin part A expression in bacterial cells Can be used for the preproinsulin expression in bacterial cells Will contain intron sequences Can be used for the insulin part B expression in bacterial cells
Will contain intron sequences
The mutation will be certainly lethal if it completely eliminates ... a gene activator a general transcription factor an enhancer the activity of one allele. The active center of an enzyme.
a general transcription factor
Why are soe people protected against infection for a virus they were never exposed to? common epitopes common B-cell receptors common T-cell receptors Common MHC genes
common epitopes
What effector cell of the adaptive immunity is important for viral infections? macrophages cytotoxic T-cells plasma cells T-helper cells
cytotoxic T-cells
What cell is directly involved in antigen presentation and activation of T-cells based on an infection at various parts of the body? macrophages neutrophils dendritic cells complement
dendritic cells
A read with poor quality scores across the entire sequence should be retained as-is, since the low quality across the sequence is consistent. discarded entirely, as the data from this read will not be reliable. cut, to remove only the lowest-quality letters from the sequence. cut, to remove the beginning and end of the sequence.
discarded entirely, as the data from this read will not be reliable.
What is the key function of Toll like receptors in dendritic cells that is essential for the activation of naive T-cells? expression of B7 that provides the second signal expression of MHC II that provides the first signal expression of B-cell receptor that provides thefirst signal expression of MHC I that provides thesecond signal
expression of B7 that provides the second signal
Mutation (deletion of one nucleotide) in last exon will be called a: frame-shift mutation truncation (shortening of the expressed protein) nonsense mutation missense mutation silent mutation
frame-shift mutation
How does vaccination protect us from infectious disease? generating memory antigen generating memory lymphocytes generating memory macrophages generating memory toll like receptors
generating memory lymphocytes
What type of immunity will subunit vaccine generate? generation of high affinity antibody generation of cytotoxic T-cells generation of neutrophils generation of macrophages
generation of high affinity antibody
What is the reason that vaccines against influenza must be administered annually? the antigens that stimulate protection against influenza virus are inside the virion and not on the surface influenza stimulates T-independent responses that fail to generate memory cells the polysaccharide antigens of influenza stimulate poor immune responses influenza is an RNA virus with a higher mutation rate
influenza is an RNA virus with a higher mutation rate
What vaccine type would you recommend to young healthy people that run the risk to be exposed to a virulent form of a virus? subunit vaccine live attenuated vaccine killed vaccine
live attenuated vaccine
What type of vaccine is more likely to stimulate a cell mediate immune response (production of effector cytotoxic T-cells)? subunit vaccines live attenuated vaccines killed viral vaccine adjuvants
live attenuated vaccines
Both mRNA vaccine and subunit vaccine focus on spike protein. Why would mRNA vaccine be more effective? mRNA better mimics the viral RNA mRNA better designed to stimulateTLR mRNA is a better target for dendritic cells mRNA is a better antigen for T-cell activation
mRNA better designed to stimulate TLR
Which of the following characteristics distinguishes dendritic cells from macrophages? phagocytosis migration pathogen degradation antigen presentation
migration
Which typhoid fever vaccine would you recommend the students get before going off to Nepal? modified live vaccine subunit vaccine killed vaccine DNA vaccine
modified live vaccine
What is the key function of the antibody isotype IgG that is important in vaccine development? neutralization complement activation Transport across the epithelium sensitization of mast cells
neutralization
What statement is true regarding clonal selection? occurs for macrophages occurs for dendritic cells occurs for self antigens occurs for naive B-cells
occurs for naive B-cells
All of the following are descriptive of inactivated virus vaccines except _____. grown in cells of another animal heat treated irradiated pathogenic virus required
pathogenic virus required
Out of 5 statements below, one is false. Which one is it? Conventional PCR and real-time PCR both: rely on measurement of amplified DNA after each PCR cycle. have limitation for the size of the amplified fragment. have amplification of the target DNA in geometrical progression. require at least two primers. utilize Taq polymerase.
rely on measurement of amplified DNA after each PCR cycle.
What is the function of adjuvant? stimulate activation of neutrophils stimulate the activation of TLR receptors Stimulate complement expression stimulate interferon secretion
stimulate the activation of TLR receptors
What is an advantage of the live attenuated vaccine ? they are non virulent but induce immune response they are virulent and able to induce an immune response they have no risk to immune compromised they have no risk to revert to a virulent form
they are non virulent but induce immune response
Why does subunit vaccine require adjuvants? they induce strong inflammatory response that needs to be diminished they induce weak inflammatory response that needs to be stimulated they induce strong clonal selection that needs to be diminished they induce weak clonal selection that needs to be stimulated
they induce weak inflammatory response that needs to be stimulated
For the catalytic function of a ribozyme it is critically for the RNA component : to adopt a specific 3D structure. to be in complex with proteins. to be in the PNA form. to be flexible so that large number of 3D structures can be adopted. to be able to form large number of specific hydrogen bonds with other nucleic acid molecules..
to adopt a specific 3D structure.
To determine a DNA sequence using the Sanger method one needs ... to perform four independent chemical reactions with the same DNA fragment, in each case cleaving DNA at one of four nucleotides (G,A, T ,and C). to design a DNA primer which will block DNA polymerase at one of four nucleotides (G,A, T ,and C). to use the same single primer in four different letter specific sequencing reactions. to fragment chromosomal DNA into pieces so that the enormous chromosomal DNA size does not interfere with the sequencing reaction. To take images of the running electrophoresis gel after addition of each nucleotide.
to use the same single primer in four different letter specific sequencing reactions.
How do T-cells recognize antigens? via complement via T-cell receptor via MHC Via Toll like receptors
via MHC
Mass spectrometry usually CANNOT identify proteins: which are not separated on 2D gels or chromatographically which are not previously digested after isolation by a protease (usually trypsin) into specific peptides which can form crystals which are over-expressed in specific cells (e.g. tumor cells) which are the products of alternative splicing
which are not previously digested after isolation by a protease (usually trypsin) into specific peptides
