MBI 485 FINAL EXAM REVIEW QUESTIONS WITH 100% DETAILED VERIFIED ANSWERS LATEST UPDATE 20, Exams of Business Administration

Download MBI 485 FINAL EXAM REVIEW QUESTIONS WITH 100% DETAILED VERIFIED ANSWERS LATEST UPDATE 20 and more Exams Business Administration in PDF only on Docsity! MBI 485 FINAL EXAM REVIEW QUESTIONS WITH 100% DETAILED VERIFIED ANSWERS LATEST UPDATE 2024/2025 In Linux system, which of the following commands can be used to generate a soft link to an existing file or folder? 1. ln 2. cp 3. ls 4. scp ln For the following Linux command ln -s /home/pub_data/w ./xyz which of the following statements is incorrect? 1. xyz is a new file or directory that has no connection to w. 2. ./ means being in the current folder. 3. The w is a file or a folder. 4. w is located within the folder pub_data 1. xyz is a new file or directory that has no connection to w. For the following Linux command in our tutorial time velvetg run_25 which of the following statements is incorrect? You can do the experiments by issue the command velvetg run_25 to understand what is going on. 1. There are two programs are running: one is time and the other is velvetg 2. run_25 is a folder name, which is used as input for velvetg 3. For genome assembly using velvet, both time and velvetg are mandatory 4. For genome assembly velvet, velvetg is the major program 3. For genome assembly using velvet, both time and velvetg are mandatory For an alphabet, we have four 2-mer nodes (GT, TG, GC, CT), which 3-mer can establish an directional edge from GT-TG? CGT GCG TGC GTG GTG For an alphabet, we have four 2-mer nodes (GT, TG, GC, CT), which 3-mer can establish an directional edge from CG-GT? TGC CGT GCG GTG CGT For an alphabet, we have four 2-mer nodes (GT, TG, GC, CT), which 3-mer can establish an directional edge from TG-GC? TGC CGT GCG GTG TGC For an alphabet, we have four 2-mer nodes (GT, TG, GC, CT), which 3-mer can establish an directional edge from GC-CG? GCG What is the length threshold that defines long non-coding RNAs? >= 200 bps >= 1000 bps >= 20 bps >= 2000 bps >= 200 bps What is the proper size range for small non-coding RNAs? 10-20 18-25 1-10 20-50 18-25 Which of the following is not a non-coding RNA (ncRNA)? miRNA mRNA tRNA rRNA mRNA Which of the following is shown to participate in translation repression, transcription repression and mRNA degradation? dsRNA (double-stranded RNA) ssRNA (single-stranded RNA) miRNA (micro-RNA) siRNA (small interfering RNA) and miRNA siRNA (small interfering RNA) and miRNA In total RNA that we sampled, __ has the highest abundance rRNA tRNA miRNA mRNA rRNA What defines gene expression? 1. the activation or "turning on" of a gene that results in production of proteins 2. the activation or "turning on" of a gene that results in production of RNA transcripts 3. the activation or "turning on" of a gene that results in production of mRNAs 4. the activation or "turning on" of a gene that results in transcription with or without production of proteins 4. the activation or "turning on" of a gene that results in transcription with or without production of proteins Which of the following statements is incorrect? 1. intron is a segment of a structural gene that is transcribed but not translated 2. regulator gene is defined as those that regulate or suppress the activity of one or more structural genes. 3. in eukaryotes, all introns will be spliced out from pre-mRNAs before mRNA maturation 4. structural gene is defined as those that code for a product, such as enzyme, protein, or RNA 3. in eukaryotes, all introns will be spliced out from pre-mRNAs before mRNA maturation RNA-Seq can be applied into __ 1. improvement in gene annotation by providing more expression evidence 2. transcriptome assembly 3. differential gene expression analysis 4. all of these applications 4. all of these applications About RNA-Seq, which of the following statements is incorrect? 1. Sequencing depths for both RNA-Seq and DNA assembly are similar 2. 3 replicates per treatments is the minimum requirement in RNA-Seq experimental design 3. RNA-Seq sequencing can be conducted for a single cell 4. RNA samples can be pooled from several individuals and used as one replicate or sample 1. Sequencing depths for both RNA-Seq and DNA assembly are similar The transcriptome assembly without using any genome sequence is known as Reference-based genome assembly Reference-based transcriptome assembly De novo genome assembly De novo transcriptome assembly De novo transcriptome assembly About de novo transcript assembly, what is its most important application? 1. It can help quantify the expression of a given gene 2. It can help quantify the expression of a RNA transcript 3. It can help quantify the expression of a given isoform for a gene 4. It can help identification of novel transcript isoforms for the same genes 4. It can help identification of novel transcript isoforms for the same genes Which of the following is not caused by alternative splicing? 1. Intron retention 2. Alternative Transcription Start Sites (TSSs) 3. Exon skipping/inclusion 4. Alternative 3' or 5' splice site 2. Alternative Transcription Start Sites (TSSs) For two treatments (e.g., Lung cancer patients versus healthy people), a gene named A was found to have significantly higher expression levels (i.e., normalized counts), whereas a gene named B has significantly lower expression levels, in reference of healthy people. Which of the following statements is incorrect? 1. Gene B is down-regulated in healthy people in comparison with Lung cancer patients 2. Gene B is down-regulated in Lung cancer patients in comparison with healthy people 3. Both genes A and B have significant differential expression between healthy and Lung cancer people 4. Gene A is up-regulated in Lung cancer patients in comparison with healthy people 1. Gene B is down-regulated in healthy people in comparison with Lung cancer patients Taking the normalised read count data and performing statistical analysis to discover quantitative changes in expression levels between experimental groups is called __ 1. Differential transcriptome analysis 2. Differential genome expression analysis 3. Differential gene expression analysis 4. Differential allele analysis 3. Differential gene expression analysis In RNA-Seq, normalization of read count data is indispensable because __ 1 .Different samples might have different sequencing depths (or total read counts) 2. All of these answers 3. Different samples might have different low-quality reads 4. Different genes have different lengths 2. All of these answers In RNA-Seq analysis, currently, reverse transcription from __ to ___ is a critical step. DNA to RNA The first bacterial genome that was sequenced in 1995 is __ 1. Streptococcus pyogenes 2. bacteriophage MS2 3. Haemophilus influenza 4. Escherichia coli 3. Haemophilus influenza The Great Plate Count Anomaly suggests __ 1. most of the microbe seen in microscope cannot currently be grown under laboratory conditions 2. We do not have sufficient biological information to culture 'unculturable' microbe in vitro 3. All of these answers 4. There are a lot of 'unculturable' microbe that are not grown on artificial media 3. All of these answers Which of the following has a very different meaning than metagenome? Environmental genomics Genomics or Genome Ecogenomics Community genomics Genomics or Genome Which of the following statements is the proper definition of metagenome? (A) the genomes of a population within the same species (D) both (A) and (B) (B) the genomes of a community that contains different species (C) the genome of an individual organism (D) both (A) and (B) In microbial diversity study, __ are(is) used to indicate how similar they are when we compare two different microbial communities. Richness Both Richness and Evenness Evenness Fragmentation Both Richness and Evenness PCR sequencing of __ resulted in "The three domains of life" hypothesis. 16s rRNA 5s rRNA 18s rRNA 23s rRNA 16s rRNA Which of the following statements is incorrect about 16s RNA gene in bacteria? 1. Its product is an integral part of the large subunit of a ribosome 2. Its product has complex secondary structures with loops and stems 3. It is a fragment of DNA that will transcribe into ribosomal RNA (rRNA) 4. Its product will help match the mRNA (codon) to the tRNA (anticodon) 1. Its product is an integral part of the large subunit of a ribosome __ is thought to be the best phylogenetic marker in species diversity study in eukaryotes? 18s rRNA 5s rRNA 16s rRNA 23s rRNA 18s rRNA Which of the following statements about amplicon sequencing is incorrect? 1. It is highly targeted approach for analyzing genetic variations in specific genomic regions 2. For rRNA gene sequencing, the highly conserved regions are targeted for designing primers 3. Currently, it focuses on 16s rRNA gene for prokaryotes and 18s rRNA gene for eukaryotes 4. For rRNA gene sequencing, the highly variable regions are targeted for designing primers 4. For rRNA gene sequencing, the highly variable regions are targeted for designing primers Recently, the accuracy of using 16s/18s rRNA gene as a proxy for Optional Taxonomy Unit (OUT) identification and abundance counting is questioned due to __ 1. All of these answers 2. There are more changes in 16s RNA gene copies per genome in bacteria than previously thought 3. 16s rRNA gene may exist in multiple different sequence copies in a single bacterium 4. Evidence shows that horizontal gene transfer involving rRNA gene may confound its reliability 1. All of these answers In taxonomic assignation of amplicon sequencing to get taxa or OUTs (Operational taxonomic units), __ is often adopted as the threshold for sequence identity in 16S rRNA genes to define different species. either 98% or 99% 98% 99% 97% either 98% or 99% __ is not part of the current bioinformatics analyses in metagenomics. 1. Assembly 2. Binning 3 .Marker gene analysis 4. Differential gene expression analysis by RNA-Seq 4. Differential gene expression analysis by RNA-Seq In bioinformatics analysis of metagenomics, the process of grouping reads and contigs and assigning them to OTUs (Operational taxonomic units) is known as __ read assembly binning marker gene analysis blast binning In bioinformatics analysis of metagnomics, __ aims to partition n observations into k clusters in which each observation belongs to the cluster with the nearest mean. GC content k-mer frequency k-means clustering Codon usage k-means clustering __ dose not belong to composition-based binning. K-mean clustering Binning using BLAST K-mer frequencies GC content and codon usage Binning using BLAST Which of the following is not in a matched pair? reads - contig clone - clony amplicon - polony PCR - polony PCR - polony How many naturally occurring amino acids are there? 20 18 135 Daltons 1.35 Daltons 1340 Daltons 13.5 Daltons 135 Daltons Which of the following is not a post-translational modification of proteins? Phosphorylation Alternative polyadenylation Ubiquitylation Glocosylation Alternative polyadenylation For cytoplasmic protein NcK, an adapter protein that can connect different other proteins or molecules, SH3 is an example of Protein family Protein domain Protein motif Protein subfamily Protein domain In peptide (protein) mass fingerprinting (PMF), X axis in mass spectrum results indicates __ (A) the mass measurement of a given peptide (c) the relationship between (A) and (B) (B) the number of elementary charge that the peptide carries (d) signal intensity of ions derived from peptides the relationship between (A) and (B) So far, which GO category has the most GO terms? Cellular Component (CC) Molecular Function (MF) None of these answers. Biological Process (BP) Biological Process (BP) About Gene Ontology (GO), which of the following statements is incorrect? 1. GO is structured as a hierarchical directed cyclic graph 2. There are only two relations between terms: either is-a or part-of 3. GO terms are represented as nodes 4. The relationship between terms are represented as edges GO is structured as a hierarchical directed cyclic graph Choosing parents with particular characteristics to breed together and produce offspring with more desirable traits is known as __ genome editing selective breeding genetic engineering natural selection selective breeding Current data shows that about __ sequenced genomes of bacteria use CRISPR as their innate immune system against phages. 90% 95% 40% 50% 50% Current data shows that about __ sequenced genomes of archaea have innate CRISPR as their innate immune system against foreign DNA invasion. 50% 95% 90% 40% 90% About the CRISPR locus, which of the following statements is incorrect? 1. It can be transcribed into crRNA 2. Cas genes are located within the CRISPR arrays 3. It is an array of short repeats interspersed with spacer sequences in many prokaryote genomes 4. It is also known as CRISPR array in many prokaryote genomes 2. Cas genes are located within the CRISPR arrays CRISPRs have three step defense mechanisms. The step where foreign invading DNAs are cleaved by the complex of Cas9 protein and crRNA is known as __. spacer acquisition CRISPR array transcription interference crRNA processing interference During spacer acquisition of CRISPRs, __ has been utilized mainly to cut and integrate viral DNA into spacer sequences of CRISPR arrays. Cas2 Cas1 Cas9 Cas6 Cas1 Among three types of CRISPR system, __ uses Cas9 to generate crRNA, which are attached with tracrRNA. Type I Type II All of Type I, II and III Type III Type II Which of the following statements is incorrect about PAM (Protospacer Adjacent Motif)?