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BIO311: Molecular Biology

Unit 11: Model Organisms   Many model organisms are used in molecular biology, both in research and in biotechnology.  They help to answer questions on the function of the genes, and they can be engineered to produce a variety of substances.  The simplest of all is E. coli, the working horse of any cloning protocol.  C. elegansand D. melanogaster taught us the function of many genes.  A. thaliana has been widely employed in GMO plan pilot experiments.  As a general rule, always the simplest possible model organism is employed for a certain task.  If post-translational modification is not essential, then proteins can be produced in E. coli, but a eukaryotic model organism is the right choice if post-translational modification is essential.  You can see an array of applications if you take the BIO403: Biotechnology course.

Unit 11 Time Advisory
This unit should take you approximately 9 hours to complete.

☐    Subunit 11.1: 1.0 hour

☐    Subunit 11.2: 0.5 hours

☐    Subunit 11.3: 5.0 hours

☐    Subunit 11.4: 2.5 hours

Unit11 Learning Outcomes
Upon successful completion of this unit, students will be able to: - Describe techniques to analyze, amplify, and modify DNA. - Outline a strategy for making recombinant DNA. - Describe techniques to purify and analyze proteins. - Compare and contrast the uses of model organisms; discuss the uses of model organisms in specific molecular biology applications. 

11.1 Prokaryote   - Reading: John W. Kimball’s “E. coli" Link:  John W. Kimball’s “E. coli" (HTML)
 
Instructions: Please study this page.  Please recall that E. coli is a prokaryote, thus it lacks membrane-bound subcellular organelles.
 
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  • Lecture: YouTube: Massspectrician's "Increasing Genome Information (Part Two): Conjugation" Links: YouTube: Massspectrician's "Increasing Genome Information (Part Two): Conjugation"  (YouTube)
     
    Instructions: Please watch the video (6 min) for an overview of plasmids
     
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  • Lecture: Khan Academy's "Viruses" Link:  Khan Academy's "Viruses" (Adobe Flash)
     
    Instructions: Please watch the video (24 min) for an overview of viruses.  Bacteriophages are viruses that infect only bacteria.  Viruses are in the grey zone between life and the non-living world.  A virus can multiple only in its specific host cell, while it takes over the host's metabolic activities.  The host range describes the cells that can be infected by a certain virus.  Viruses may destroy their host in a lytic cycle or incorporate themselves into the host's genome. Viruses are used in a broad range of biotechnology applications, including gene therapy and phage therapy.
     
    Terms of Use: This video is licensed under a Creative Commons Attribution-NonCommercial-NoDerives United States License 3.0.  It is attributed to the Khan Academy. 

11.2 Single-Celled Eukaryote   - Reading: MicrobiologyBytes: Dr Alan Cann’s “Saccharomyces cerevisiae” Link: MicrobiologyBytes: Dr Alan Cann’s “Saccharomyces cerevisiae” (HTML and Adobe Flash)
 
Instructions: Please study this page. Saccharomyces cerevisiae is a major eukaryotic model organism; its common name is baker's yeast.  Its genome is sequenced.
 
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  • Reading: John W. Kimball’s “Budding Yeast: Saccharomyces cerevisiae" Link:  John W. Kimball’s “Budding Yeast: Saccharomyces cerevisiae"(HTML)
     
    Instructions: Please study this page.
     
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11.3 Animal   11.3.1 Caenorhabditis elegans   - Reading: John W. Kimball’s “Caenorhabditis elegans” Link: John W. Kimball’s “Caenorhabditis elegans” (HTML)
 
Instructions:  Please study this page.  Note that C. elegans is the simplest multicellular model organism; all of its cells are mapped.
 
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  • Web Media: YouTube: The University of California: iBioMagazine's "Cynthia Kenyon: A Genetic Control Circuit for Aging” Link: YouTube: The University of California: iBioMagazine's "Cynthia Kenyon: A Genetic Control Circuit for Aging” (YouTube)
     
    Instructions:  Please watch this video (11 min).
     
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  • Web Media: YouTube: MIT: iBioMagazine's "H. Robert Horvitz: When Stockholm Called" and “H. Robert Horvitz: Discovering Programmed Cell Death” Link: YouTube: MIT: iBioMagazine's "H. Robert Horvitz: When Stockholm Called" "H. Robert Horvitz: Discovering Programmed Cell Death" (YouTube)
     
    Instructions:  Please watch these videos (25 min).
     
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11.3.2 Drosophila melanogaster   - Reading: John W. Kimball’s “Drosophila melanogaster” Link: John W. Kimball’s “Drosophila melanogaster” (HTML)
 
Instructions: Please study this page.  Please follow all links and study all pages in the "Follow these links to examples of things that Drosophila has taught us" section.
 
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  • Web Media: iBioMagazine's “Eric Wieschaus: Finding Genes that Control Development” Link: iBioMagazine's “Eric Wieschaus: Finding Genes that Control Development” (YouTube)
     
    Instructions:  Please watch this video (11 min).
     
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11.3.3 Mus musculus   - Reading: Yale School of Medicine: Dennis Jones's "Genetic Engineering of a Mouse: Dr. Frank Ruddle and Somatic Cell Genetics" Link: Yale School of Medicine: Dennis Jones's "Genetic Engineering of a Mouse: Dr. Frank Ruddle and Somatic Cell Genetics" (HTML)
 
Instructions: Please study this publication.
 
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  • Web Media: YouTube: The University of Utah, Howard Hughes Medical Institute: iBioMagazine's "Mario Capecchi: The Birth of Gene Targeting” (YouTube) Link: YouTube: The University of Utah, Howard Hughes Medical Institute: iBioMagazine's "Mario Capecchi: The Birth of Gene Targeting” (YouTube)
     
    Instructions:  Please watch this video (14 min).
     
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11.4 Plant   - Reading: John W. Kimball’s "Arabidopsis thaliana: Another ‘Model Organism’" Link: John W. Kimball’s “Arabidopsis thaliana: Another ‘Model Organism’"(HTML)
 
Instructions: Please study this page.
 
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  • Reading: NCBI Bookshelf: Alberts et al.’s “Plant Development” Link: NCBI Bookshelf: Alberts et al.’s “Plant Development” (HTML)
     
    Instructions: Please study this page.
     
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