BSCI410-Liu Spring 2009 List of Questions for exam#2Following list is aimed at helping you to study for the exam. It doesn't mean that myexam questions will be limited to the following. Anything I lectured (in lecture 9 through17) can be tested.1. Learn how to calculate genetic distance between a molecular marker and a mutant (likequestion #3 in homework#2).2. All types of molecular markers and ways to assay for them (like question #1 in homework#2)3. (a) What is the principal of positional cloning? (b) After narrowing (mapping) thecandidate gene to a small chromosomal region, how will you identify the specific generesponsible for the mutation (disease)? List all methods that are been utilized. what is theultimate proof a mutation corresponds to a gene?4. Explain following termsContigIntronExonAlternative splicingOpen reading framesSyntenyC-value paradox,BlastE-valueScorequeryFASTAAccession numberProtein domainHigh throughputOrthologParalogReverse transcriptionESTRNAidsRNAsiRNADicerRISCRDRPES cellspluripotent cells5. List a few genes that are specific to plants and a few genes specific to human (animal).BSCI410-Liu Spring 2009 List of Questions for exam#26. Learn to calculate percentage positive (%) and percentage identity (%) between twoproteins.7. Contrast and comparePhysical map vs. genetic mapParalog vs. ortholog,Southern blot vs. Northern blot vs. Westerne-value vs. score% positive vs. %identityShort gun sequencing vs hierarchical sequencing strategycDNA microarray vs. Affymetrix Gene ChipProteome vs. TranscriptomeIn situ RNA hybridization vs. Northern blot vs. qRT-PCRForward genetics vs Reverse geneticsHigh throughput DNA sequencing and MPSS to identify transcript abundance8. Be familiar with following methods and their application:a. Northern blotsb. RNA in situ hybridizationc. Western blotsd. Fluorescent in situ hybridization (FISH)e. Southern blotsf. cDNA microassay and Gene chip hybridizationg. Mass spec to identify the sequence of unknown proteinsh. ICATi. Yeast two hybrid interaction assays and library screenj. Chromatin Immunprecipitation (ChIP) and ChIP-chipk. EMSA l. Homologous recombination to knockout a mouse gene m. Protein chip n. Immunocoprecipitation9. What is a reporter gene? Give several examples of reporter genes. Which reporter(s)can be used for live imaging? What is the difference between promoter fusion and proteinfusion (ie. chimeric protein) in creating a reporter gene?10. What is "functional genomics"? How does one find out the function of a gene ifhe/she is given the gene sequence? What types of experiments should he/she perform(hint: from expression to protein interaction to generate mutants)?11. What types of information you are getting from following databases:PubmedBooksOMIMStructureProteinNucleotideENTREZ (All databases)BLASTBSCI410-Liu Spring 2009 List of Questions for exam#212. What is systems biology? Give examples of "elements" and "edges", and"perturbation to a system".13. What is RNA interference? What is its normal function in an organism? How couldwe apply it to identify gene function? Give examples of high throughput ways ofknocking out thousands of C. elegans
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