Problem set 3 - BIMM100 Problem set#3 Chapters 6 7 and 8 1...

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BIMM100 Problem set #3 Chapters 6, 7, and 8 1. You should know what the following experiments are useful for. Try to think really hard about all of their applications and uses in Molecular biology! Try to fill out this chart before asking the TAs (and me) about them!
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Experiment What does it do? DNA electrophoresis DNA cloning Plaque assay Northern blot In situ hybridization Southern blot Gene knockouts (know how to KO genes from the genome and also how to knockdown their expression postranscriptionally!) Microarray PCR Sanger dideoxy sequencing cDNA library Genetic complementation RNAi Genomic library DNase I foot printing EMSA 5' deletion assay Linker scanning mutations S1 endonuclease assay In vitro transcription assay Yeast 2 hybrid ChIP
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2. When you tried to identify a gene of interest from your cDNA library, you inadvertently created a probe that bound to every cDNA clone. What probe is it that you likely created? 3. When making your shuttle plasmid vector, you notice that your yeast cells are replicating the plasmid fine, but some daughter cells lack the plasmids. What did you likely forget in your vector design? 4. Would you use a cDNA or genomic library for the following scenarios? A. Studying the regulatory elements of a gene, such as its promoter and binding sites for transcription factors B. You want to express protein X in bacterial cells 5. For the following experimental questions, what techniques are likely to be the most effective to give you the answer you're looking for? A. Where is gene X expressed in a zebrafish embryo? B. What is the difference in gene expression between healthy liver cells and diseased liver cells? C. What is an assay you could do to see their multiple isoforms? D. What is the difference in expression of gene X in the brain compared to the testes? E. Is gene X present in different species of animals? F. Do different types of cancer cells have different gene expressions? G. Is gene X translocated to a different arm of chromosome 12 in patients that have a certain autosomal disease?
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6. When generating a disruption construct, what is a structural feature that facilitates the subsequent homologous recombination? What is the structural feature that will be used to prevent random integration? 7. You are investigating the function of gene X and it's role in liver formation. To address this issue, you make a mouse knockout. Unfortunately, you find that the mice are not viable. To get around this, what could you do? 8. What are three different ways that complex transcriptional units produce different gene products? Describe how they produce alternate products from the same gene. How is this different from a simple transcriptional unit? 9. What two things result from unequal crossing over? How are these things different?
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