Introduction to Molecular Biology Information Resources
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Exercises:
Sample User Questions and Answers
     
  Hands-On Exercises:  We use two genes (MLH1 and PER2) throughout the course to illustrate the use of the resources above to gather a wide range of information about a gene. The demonstrations and exercises pertaining to these genes are distributed throughout the modules. The pages below bring all of the exercises for each gene onto a single page, for your review.  
     
  Complete set of demonstration exercises on the MLH1 gene (colon cancer) from all modules.  
  Complete set of mastery exercises on the PER2 gene (circadian rhythms) from all modules.  
     
  The MLH1 and PER2 gene exercises are also listed by module, below. Additional exercises are interspersed through each module and will be added to this page in the future for reference and easy access. In many cases, there are several ways to arrive at an answer. The exercises generally demonstrate one method as an example.
     
Molecular Biology Review
Types of Databases
Format of Sequence Record
Entrez
BLAST
Structures
Genes
Genomes and Maps
User Questions Grab Bag
WWW Sites
  MOLECULAR BIOLOGY REVIEW back to top  
 
  • What is the central dogma of biology?
    		•  slide  
     
  • What is the difference between a prokaryotic and eukaryotic cell?
    		•  slide  
     
  • What is DNA?
    		•  slide1, slide2  
     
  • What is mRNA?
    		•  slide  
     
  • How is mRNA translated into protein? Does every organism use the same genetic code?
    		•  slide  
      TYPES OF DATABASES back to top  
     
  • What are some examples of comprehensive vs. specialized sequence databases?
    		•  slide  
     
  • What are the main differences between archival (primary) and curated sequence databases?
    		•  slide  
     
  • What is GenBank?
    		•  slide  
     
  • What is RefSeq? What is the difference between a provisional and reviewed record?
    		•  slide  
     
  • What types of sequences are in dbEST?
    		•  slide  
      FORMAT OF SEQUENCE RECORD back to top  
     
  • What is the difference between Accession, Version, and GI number?
    		•  strategy  
     
  • Compare primary (archival) vs. reference (curated) sequence records (MLH1 demo exercise)
    		•  strategy  
     
  • AB002345: salient parts of record (PER2 mastery exercise)
    		•  slide, answer  
     
  • BAA20804: salient parts of record (PER2 mastery exercise)
    		•  slide, answer  
     
  • NM_022817: salient parts of record (PER2 mastery exercise)
    		•  slide, answer  
     
  • NP_073728: salient parts of record (PER2 mastery exercise)
    		•  slide, answer  
      ENTREZ back to top  
     
  • Using Entrez "global query" (search across all Entrez databases):   advantages and caveats
    		•  slide  
     
  • Four ways to search individual Entrez databases
    		•  slide  
     
  • Find concise summary of genes pertaining to human colon cancer (MLH1 demo exercise)
    		•  strategy  
     
  • Find concise summary of genes pertaining to circadian rhythms (PER2 mastery exercise)
    		•  strategy  
     
  • Additional exercises are provided in the Information Hubs module of the 5-day Advanced Workshop
    		•     
      BLAST back to top  
     
  • Identify the possible function of an mRNA sequence (MLH1 demo exercise)
    		•  strategy  
     
  • Identify the gene involved in a sleep disorder (PER2 mastery exercise)
    		•  strategy  
      STRUCTURES back to top  
     
  • Find the 3-dimensional structure for a protein of interest or for similar protein sequences. View residues in active site. (MLH1 demo exercise)
    		•  strategy  
     
  • View a structure to examine the significance of a conserved domain (PER2 mastery exercise)
    		•  strategy  
      GENES back to top  
     
  • Gather sequence data and related information on a particular genetic locus (MLH1 demo exercise)
    		•  strategy  
     
  • Gather sequence data and related information on a particular genetic locus (PER2 mastery exercise)
    		•  strategy  
     
  • Additional exercises are provided in the Information Hubs module of the 5-day Advanced Workshop
    		•     
      GENOMES AND MAPS back to top  
     
  • View the genomic context a gene: find its chromosomal location and download the genomic sequence (MLH1 demo exercise)
    		•  strategy  
     
  • Find the location of a gene, and download the sequence for the gene plus the promoter region (PER2 mastery exercise)
    		•  strategy  
      USER QUESTIONS GRAB BAG - Reference Desk Simulation  (questions can pertain to any module in the course) back to top  
     
  • A number of user questions are provided in the module. In the future, they will be added to this page along with a strategy for each one.
    		•  slide (question list)  
      WWW SITES - Referral of users to directories of molecular biology databases and software back to top  
     
  • Find restriction map software
    		•  strategy  
     
  • What resources can be used to identify potential transcription factor binding sites in a DNA sequence?
    		•  strategy  
      (The strategy files for the two questions above are not contained within the materials for this introductory course. Instead, the strategy links lead to the In formation Hubs module of the 5-day Advanced Workshop.)    
      Revised March 3, 2005  
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