MicroRNA Origin & Function PDF

Understand the origin of micro RNAs and be able to describe the mechanism that produces them in eukaryotic cell: 1. Where are primary miRNA (pri-miRNA) molecules produced in the eukaryotic cell? a) In the cytoplasm b) **In the nucleus** c) In the mitochondria d) In the endoplasmic reticulu...

Understand the origin of micro RNAs and be able to describe the mechanism that produces them in eukaryotic cell: 1. Where are primary miRNA (pri-miRNA) molecules produced in the eukaryotic cell? a) In the cytoplasm b) **In the nucleus** c) In the mitochondria d) In the endoplasmic reticulum 2. Which protein complex is responsible for cleaving the pri-miRNA to produce the precursor miRNA (pre-miRNA)? a) Exportin-5 and Ran-GTP b) Dicer and TRBP c) **Drosha and DGCR8** d) Argonaute and RISC 3. How is the pre-miRNA transported from the nucleus to the cytoplasm? a) Passive diffusion b) **Active transport by Exportin-5 and Ran-GTP** c) Vesicular transport d) Membrane fusion 4. What is the length of the pre-miRNA hairpin structure? a) 20-25 nucleotides b) 30-40 nucleotides c) 50-60 nucleotides d) **60-70 nucleotides** Describe how miRNA regulates gene expression in eukaryote cells: 1. What is the primary mechanism by which miRNAs regulate gene expression in mammals? a) Transcriptional activation b) Chromatin modification c) **mRNA degradation or translational inhibition** d) Protein stabilization 2. Which protein complex is responsible for loading the guide strand of the miRNA into the RNA-induced silencing complex (RISC)? a) Drosha and DGCR8 b) Dicer and TRBP c) Exportin-5 and Ran-GTP d) **Argonaute and RISC loading complex** 3. Where does the miRNA guide strand typically bind to its target mRNA? a) 5' untranslated region  b) Coding sequence c) Intron d) **3' untranslated region** 4. What are the two primary mechanisms by which miRNAs can regulate gene expression in mammals? a) Transcriptional activation and chromatin modification b) mRNA degradation and protein stabilization c) **Translational inhibition and mRNA deadenylation** d) Transcriptional repression and RNA editing Understand the domain structure of RNase III family members and how this relates to their function: 1. Which structural feature do all RNase III enzymes possess? a) RNase III domain b) Double-stranded RNA-binding domain (dsRBD) c) PAZ domain d) **Both a and b** 2. How many RNase III domains are present in the Class II RNase III enzyme, Drosha? a) 1 b) **2** c) 3 d) 4 3. Which structural feature of Dicer (Class III RNase III) allows it to bind and cleave the pre-miRNA substrate? a) RNase III domains b) Double-stranded RNA-binding domain (dsRBD) c) PAZ domain d) **All of the above** 4. How do the structural differences between the various classes of RNase III enzymes relate to their specific functions in the miRNA biogenesis pathway? a) They have no functional differences b) They cleave different types of RNA substrates c) They are involved in different cellular processes d) **They have variations in their domain organization and substrate binding** Understand how miRNAs can be identified using miRNA arrays and miRNA sequencing: 1. What is the main principle behind miRNA arrays for identifying and quantifying miRNAs? a) **Hybridization of labeled miRNAs to complementary oligonucleotides** b) Amplification of miRNAs by PCR  c) Sequencing of miRNA cDNA d) Immunoprecipitation of miRNA-protein complexes 2. What is the first step in the miRNA sequencing process? a) Ligation of 3' and 5' adapters to the miRNA b) Reverse transcription of the miRNA c) **Purification of the miRNA from total RNA** d) PCR amplification of the miRNA cDNA 3. Which technique allows for the identification of novel miRNAs in a sample? a) miRNA arrays b) **miRNA sequencing** c) Both a and b d) Neither a nor b 4. What is the typical length of the mature miRNA sequence identified by sequencing? a) 15-20 nucleotides b) **20-25 nucleotides** c) 25-30 nucleotides d) 30-35 nucleotides Know the number of miRNA expressed by eukaryote genomes, the % of gene predicted to be regulated by miRNA in the human genome: 1. Approximately how many microRNAs are thought to be encoded by the human genome? a) 500 b) 1,000 c) **2,000** d) 5,000 2. What percentage of human genes are predicted to be regulated by microRNAs? a) 20% b) 40% c) **60%** d) 80% 3. Where are most microRNA genes located in the eukaryotic genome? a) Within protein-coding genes b) **In intergenic regions** c) In the mitochondrial genome d) Both a and b 4. What is the primary evolutionary advantage of using microRNAs for gene regulation?  a) Increased genome size b) **Faster response to environmental changes** c) Reduced energy expenditure d) Increased genetic diversity Understand that alterations in miRNA sequence and expression are linked to human disease: 1. Which human disease is caused by a mutation in the miR-96 microRNA? a) **Hereditary progressive hearing loss** b) Keratoconus and cataract c) Alzheimer's disease d) Breast cancer 2. Which human disease is caused by a mutation in the miR-184 microRNA? a) Hereditary progressive hearing loss b) **Keratoconus and cataract** c) Alzheimer's disease d) Breast cancer 3. Where can one find information on the known relationships between miRNA dysregulation and human disease? a) PubMed b) **miRBase** c) OMIM d) All of the above 4. What is the primary mechanism by which alterations in miRNA sequence and expression can contribute to human disease? a) Increased gene expression b) Chromatin modification c) **Disruption of normal gene regulation** d) Increased protein stability Be able to explain the reasons why it is thought RNAi mechanisms evolved: 1. What is one of the primary evolutionary advantages of RNAi mechanisms? a) Increased genome size b) **Defense against transposable genetic elements** c) Faster response to environmental changes d) Increased genetic diversity 2. How do RNAi mechanisms provide protection against viral infections? a) **By silencing viral mRNAs** b) By modifying viral genomes c) By enhancing the immune response d) Both a and b 3. What evidence supports the idea that RNAi evolved as a defense mechanism against viruses? a) **RNAi-deficient plants are more susceptible to viral infections** b) RNAi is only found in eukaryotic organisms c) RNAi mechanisms are highly conserved across species d) All of the above 4. Which cellular process do RNAi mechanisms help to regulate in order to maintain genome stability? a) Transcription b) Translation c) **Transposition of genetic elements** d) DNA repair Explain how RNAi has been used to create novel mutant phenotypes in C. elegans for research reasons: 1. What is the primary method used to induce RNAi-mediated gene silencing in C. elegans? a) Microinjection of dsRNA b) Feeding worms E. coli expressing dsRNA c) Soaking worms in dsRNA solution d) **All of the above** 2. What was the goal of the large-scale RNAi screen performed in C. elegans? a) **To identify genes involved in fat regulation** b) To create novel mutant phenotypes for all C. elegans genes c) To study the effects of RNAi on development d) To identify human disease genes 3. What percentage of C. elegans genes were successfully targeted using RNAi in the large-scale screen? a) 50% b) 70% c) **86%** d) 95% 4. How have the RNAi studies in C. elegans provided insights into human disease? a) **Many C. elegans genes have human homologs** b) C. elegans is a poor model for human disease c) RNAi is not effective in mammals d) The C. elegans genome is too different from humans Understand that RNAi could be used in therapeutic way to treat human disease and infection: 1. What type of RNAi-based therapeutic is being developed to silence target genes? a) Antisense oligonucleotides b) **Small interfering RNAs (siRNAs)** c) Plasmid-encoded shRNAs d) Both b and c 2. What is one of the main delivery methods for RNAi-based therapeutics? a) Oral administration b) Intravenous injection c) **Nanoparticle encapsulation** d) Topical application 3. Which human disease has an RNAi-based therapeutic (Bevasiranib) that has reached clinical trials? a) Cancer b) HIV infection c) **Wet age-related macular degeneration** d) Alzheimer's disease 4. What is the primary mechanism of action for RNAi-based therapeutics in treating human disease? a) Stimulating the immune system b) Inhibiting viral entry into cells c) **Silencing the expression of disease-causing genes** d) Promoting cell proliferation