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BIO305: Genetics

Unit 6: The Internal Structure of Genes  

From the late 1950s to the 1980s, scientists were attempting to crack the genetic code and determine what base pair combinations made up what genes. Ultimately, this involved work by Matthew Meselson and Frank Stahl, who unraveled the mystery of DNA replication in the cell. By knowing how DNA is replicated, scientists can artificially mimic the process. Additional discoveries by Arthur Kornberg and Hamilton Smith of DNA replication and restriction enzymes – combined with the new technique of sequencing by Frederick Sanger – finally unlocked the secret of the genetic code. From this point on, scientists could determine the order of base pairs for selected DNA regions.
 
Once scientists could figure out what genes were located where, they could then begin to combine DNA from different organisms. This is the recombinant DNA technology, which is commonly used today, creating such interesting products as glowing bacteria, Bt corn, broccoflower, and other useful combinations. Many of these genetically modified organisms (GMOs) are designed with usefulness for humans in mind. GMOs have their dark side as well: due to their advantageous acquired trait(s), some GMOs contribute to the decrease of biodiversity and they may elicit adverse allergic reaction in uninformed individuals

Genetic analysis of organisms today is mainstream technology, and almost every university and college lab have the capability to either conduct genetic research or partner with someone who can. By the end of this unit, you should have a good understanding of the different techniques used today and what they can tell us about the organisms under study.

Unit 6 Time Advisory
This unit should take you approximately 17 hours to complete:
 
☐    Subunit 6.1: 2 hours
 
☐    Subunit 6.2: 7.25 hours
☐    Introduction: 1.75 hours
 
☐    Subunit 6.2.1: 3 hours
 
☐    Subunit 6.2.2: 2.5 hours

☐    Subunit 6.3: 1.5 hours
 
☐    Subunit 6.4: 3 hours
 
☐    Subunit 6.5: 1 hour
 
☐    Subunit 6.6: 2 hours
 
☐    Subunit 6.7: 0.25 hours

Unit6 Learning Outcomes
Upon successful completion of this unit, you will be able to: - describe processes of the polymarese chain reaction and DNA sequencing with dideoxynucleotides; - compare and contrast in vivo and in vitro DNA duplication; - describe mobile DNA elements; - compare and contrast nuclear and plasmid DNA; - describe recombinant DNA; - predict the effect of mutations on protein synthesis; and - identify and describe techniques for gene analyses.

6.1 Gene Structure and DNA Analysis   - Reading: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 10: Gene Structure and DNA Analysis” Link: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 10: Gene Structure and DNA Analysis” (PDF)
 
Instructions: Select the PDF link for “Lecture 10: Gene Structure and DNA Analysis,” and read these lecture notes. These lecture notes describe the bacterial gene structure. These lecture notes also explain DNA sequencing using dideoxynucleotides. DNA sequencing is most commonly used in vitro DNA amplification technique, the polymerase chain reaction. This text is technical, so please plan to read it several times for a full understanding.
 
Reading these lecture notes should take approximately 1 hour and 30 minutes.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: Dr. John W. Kimball’s Biology Pages: “DNA Replication” Link: Dr. John W. Kimball’s Biology Pages: “DNA Replication” (HTML)
     
    Instructions: Read this article to review the steps of DNA replication in the cell. Compare gene replication in prokaryotes and in eukaryotes.
     
    Reading this article should take approximately 30 minutes.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.2 Mutations   - Reading: National Institute of Health’s Genetics Home Reference: “What Is a Gene Mutation and How Do Mutations Occur?” Link: National Institute of Health’s Genetics Home Reference: “What Is a Gene Mutation and How Do Mutations Occur?” (HTML)
 
Instructions: Read this article. Make sure you understand the difference between hereditary mutations and acquired mutations.
 
Reading this article should take approximately 15 minutes.
 
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  • Reading: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 11: Mutations and Suppressors” Link: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 11: Mutations and Suppressors” (PDF)
     
    Instructions: Select the PDF link for “Lecture 11: Mutations and Suppressors,” and read these lecture notes. These lecture notes describe missense, nonsense, and frameshift mutations and discusses the mechanisms that can lead to these mutations. Finally, these lecture notes explain a commonly used genetic analysis tool: the generation of suppressor mutants. Suppressor mutations reverse the phenotypic effect of an investigated mutation. This text is technical, so please plan to read it several times for a full understanding.
     
    Reading these lecture notes should take approximately 1 hour and 30 minutes.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.2.1 Transposable Elements   - Reading: Dr. John W. Kimball’s Biology Pages: “Transposons: Mobile DNA” Link: Dr. John W. Kimball’s Biology Pages: “Transposons: Mobile DNA” (HTML)
 
Instructions: Read this article, which should give you a good review on transposons, retrotransposons, MITEs, and mutations.
 
Reading this article should take you approximately 1 hour and 30 minutes.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 12: Bacterial Genetics: Transposition” Link: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 12: Bacterial Genetics: Transposition” (PDF)
     
    Instructions: Select the PDF link for “Lecture 12: Bacterial Genetics: Transposition,” and read these lecture notes. These lecture notes describe the structure and function of bacterial transposons. Transposons are mobile genetic elements that cause loss-of-function mutation if they insert into genes. This text is technical, so please plan to read it several times for a full understanding.
     
    Reading these lecture notes should take approximately 1 hour and 30 minutes.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: PLOS One: Marybeth Langer, et al.’s “Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements” Link: PLOS One: Marybeth Langer, et al.’s “Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements” (HTML)
     
    Instructions: Read this optional article, which will allow you to see what the more recent research is focusing on regarding transposons and the excision process. This text is technical, so you may need to read it several times for a full understanding.
     
    Reading this optional article should take approximately 2 hours and 30 minutes.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.2.2 Human Genome Mutation   - Lecture: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 17 – Genetics of Human Disease” Link: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 17 – Genetics of Human Disease” (Adobe Flash)
 
Instruction: Watch this lecture, which provides an overview of Mendelian and complex human genetic diseases and genetic testing. This lecture is technical, so please plan to pause, take notes, and re-watch segments several times for a full understanding.
 
Watching this lecture and pausing to take notes should take approximately 2 hours and 30 minutes.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.3 Neurospora: One Gene, One Protein   - Reading: Dr. John W. Kimball’s Biology Pages: “Neurospora crassa and the One Gene – One Enzyme Theory” Link: Dr. John W. Kimball’s Biology Pages: Neurospora crassa and the One Gene – One Enzyme Theory” (HTML)
 
Instructions: Read this article on the One Gene, One Enzyme theory. You should already be familiar with the Neurospora system, and after reading this information, you should realize how it was used to discover this theory.
 
Reading this article should take approximately 1 hour and 30 minutes.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.4 Recombinant DNA   - Reading: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 14: Complementation in Bacteria: Plasmids” Link: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 14: Complementation in Bacteria: Plasmids” (PDF)
 
Instructions: Select the PDF link for “Lecture 14: Complementation in Bacteria: Plasmids,” and read these lecture notes. Plasmids are extra chromosomal dsDNAs. This text is technical, so please plan to read it several times for a full understanding.
 
Reading these lecture notes should take approximately 1 hour and 30 minutes.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 15: Complementation in Bacteria: Recombinant DNA” Link: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 15: Complementation in Bacteria: Recombinant DNA” (PDF)
     
    Instructions: Select the PDF link “Lecture 15: Complementation in Bacteria: Recombinant DNA,” and read these lecture notes. Recombinant DNA combines DNA elements from at least two different sources, e.g., zebrafish DNA and the green fluorescent protein encoding gene from jellyfish to make GloFish. These lecture notes describe how to construct a transformation vector in bacteria. This text is technical, so please plan to read it several times for a full understanding.
     
    Reading these lecture notes should take approximately 1 hour and 30 minutes.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.5 Cloning   - Reading: Team Heidelberg: “Technical Background Information: Molecular Cloning” Link: Team Heidelberg: “Technical Background Information: Molecular Cloning” (HTML)
 
Instructions: Read this article for an introduction to molecular cloning.
 
Reading this article should take approximately 1 hour.
 
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6.6 Microarrays and Gene Expression   - Reading: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 22: Eukaryotic Genes and Genomes IV” Link: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 22: Eukaryotic Genes and Genomes IV” (PDF)
 
Instructions: Select the PDF link for “Lecture 22: Eukaryotic Genes and Genomes IV,” and read these lecture notes. These lecture notes describe genome-wide gene expression analysis with microarrays and compare microarrays to Southern blot technique. Transposons are mobile genetic elements that cause loss-of-function mutation if they insert into genes. This text is technical, so please plan to read it several times for a full understanding.
 
Reading these lecture notes should take approximately 2 hours.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.7 Data Interpretation and Assumptions   - Assessment: The Saylor Foundation’s “Unit 6 Assessment” Link: The Saylor Foundation’s “Unit 6 Assessment” (HTML)
 
Instruction: Complete this multiple choice and true/false Unit 6 Assessment.
 
Completing this assessment should take approximately 15 minutes.