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BIO305: Genetics

Unit 8: Eukaryotic Genes and Genomes   Genome refers to the entire DNA content of an organism. There is no obvious correlation between the complexity of the organism and the size of the genome. Many genomes are much larger than the human genome. Some plants and fish have three billion DNA base pairs! About 5% of our genome codes for protein, while an amazing 95% seemingly does not have any known function (this 95% is called junk DNA). Genomics is a relatively new field with the bold aim of understanding the function of every single gene in a genome, including the human genome. This field took off with the completion of the first sequenced genome, and after the completion of the Human Genome Project, it has attracted ever increasing research. Decades from now, we might very well know not only which genes determine our phenotype but also an increasing number of alleles that are risk factors of diseases.

Unit 8 Time Advisory
This unit should take you approximately 41.75 hours to complete:
 
☐    Subunit 8.1: 7 hours
☐    Introduction: 2 hours
 
☐    Subunit 8.1.1: 2.5 hours
 
☐    Subunit 8.1.2: 2.5 hours

☐    Subunit 8.2: 2 hours
 
☐    Subunit 8.3: 3 hours
 
☐    Subunit 8.4: 1 hour
 
☐    Subunit 8.5: 3.5 hours
 
☐    Subunit 8.6: 8 hours
☐    Introduction: 3 hours
 
☐    Subunit 8.6.1: 2 hours
 
☐    Subunit 8.6.2: 3 hours

☐    Subunit 8.7: 1 hour
 
☐    Subunit 8.8: 6 hours
☐    Subunit 8.8.1: 3 hours
 
☐    Subunit 8.8.2: 3 hours

☐    Subunit 8.9: 2 hours
 
☐    Subunit 8.10: 3 hours
 
☐    Subunit 8.11: 3 hours
 
☐    Subunit 8.12: 2.25 hours

Unit8 Learning Outcomes
Upon successful completion of this unit, you will be able to: - compare and contrast as well as discuss nuclear and organellar genome organization; - compare and contrast prokaryotic and eukaryotic genomes; - describe and discuss genetically modified organisms; - compare and contrast as well as discuss eukaryotic model organisms; - explain the yeast two-hybrid system; - explain how to extract information from sequenced genomes; - describe the endosymbiotic theory; - discuss the genome size and organismal complexity; - compare and contrast as well as discuss genome sizes and the number of genes in the genomes; - describe junk DNA; and - explain the significance of molecular phylogeny.

8.1 Eukaryotic Genomes   - Reading: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 19: Eukaryotic Genes and Genomes I” Link: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 19: Eukaryotic Genes and Genomes I” (PDF)
 
Instructions: Select the PDF link for “Lecture 19: Eukaryotic Genes and Genomes I,” and read these lecture notes. These lecture notes give an introduction to eukaryotic genomics with examples of organismal genomes. These notes also highlight differences in eukaryotic and prokaryotic genomes. 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.

8.1.1 Animal Genomics   - Lecture: Lecture: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 11 – Animal Genomics & the Origin of Human Dogs” Link: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 11 – Animal Genomics & the Origin of Human Dogs” (Adobe Flash)
 
Instruction: Watch this lecture on animal genomics. This lecture is technical, so please plan to pause, take notes, and re-watch segments for a full understanding.
 
Watching this lecture and pausing to take notes should take approximately 2 hours and 30 minutes.
 
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8.1.2 Plant Genomics   - Reading: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 14 – Plant Genes and Genomes & Breeding” Link: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 14 – Plant Genes and Genomes & Breeding” (Adobe Flash)
 
Instruction: Watch this lecture on plant genes, genomes, and breeding. This lecture is technical, so please plan to pause, take notes, and re-watch segments for a full understanding.
 
Watchng this lecture and pausing to take notes should take approximately 2 hours and 30 minutes.
 
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8.2 Genetically Modified Organisms and Society   - Lecture: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 23 – GMOs and Society” Link: New York University: Professor Mark Siegal’s Genomes and Diversity: “Lecture 23 – GMOs and Society” (Adobe Flash)
 
Instruction: Watch this lecture on GMOs and society. This lecture is technical, so please plan to pause, take notes, and re-watch segments for a full understanding.
 
Watching this lecture and pausing to take notes should take approximately 2 hours.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

8.3 Genome Evolution   - Reading: PLOS One: Dr. Sheppard and Dr. Timmis’s “Instability of Plastid DNA in the Nuclear Genome” Link: PLOS One: Dr. Sheppard and Dr. Timmis’s “Instability of Plastid DNA in the Nuclear Genome” (HTML)
 
Instructions: Read this article, which provides some great examples of how genomes impact one another with some interesting results!
 
Reading this article should take approximately 3 hours.
 
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8.4 Endosymbiotic Theory   - Reading: Dr. John W. Kimball’s Biology Pages: “Endosymbiosis and the Origin of Eukaryotes” Link: Dr. John W. Kimball’s Biology Pages: “Endosymbiosis and the Origin of Eukaryotes” (HTML)
 
Instructions: Read this article about endosymbiosis.
 
Reading this article should take approximately 1 hour.
 
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8.5 Genome Size and Gene Content   8.5.1 Nuclear Genome   - Reading: Dr. John W. Kimball’s Biology Pages:“Genome Sizes” Link: Dr. John W. Kimball’s Biology Pages: “Genome Sizes” (HTML)
 
Instructions: Read this webpage and click the organisms that interest you. Notice the different sizes of the genomes in the different organisms. Are these patterns that you would predict? What comes as a surprise to you? Who has the biggest genome? Is it humans?
 
Reading and answering the questions above should take approximately 1 hour.
 
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  • Reading: Dr. G.R. Kantharaj’s “DNA C-Value Paradox” Link: Dr. G.R. Kantharaj’s “DNA C-Value Paradox” (HTML)
     
    Instructions: Read this article, which focuses on the surprises behind genome size and organism size.
     
    Reading this article should take approximately 1 hour.
     
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8.5.2 HIV Virus   - Reading: Dan Stowell’s “The Molecules of HIV – A Hypertextbook” Link: Dan Stowell’s “The Molecules of HIV – A Hypertextbook” (HTML)
 
Instructions: Read the first seven links presented in navigation menu on the lefthand side of this page – from “Main Page” through “3D HIV” – for some great information on HIV and its genome. Please note that viruses are obligate parasites; they have no metabolism and their reproduction is fully dependent on the host’s metabolism. In general, viruses are considered to be in the grey zone between life and inorganic material. All viruses have nucleic acids, and it is interesting to compare the size and content of viral genomes to that of the bacterial and eukaryotic genomes.
 
Reading these sections should take approximately 1 hour and 30 minutes.
 
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8.6 Single-Celled Eukaryote: Yeast Genetics   - Reading: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 2: The Complementation Test and Gene Function” Link: Massachusetts Institute of Technology: Professor Chris Kaiser’s “Lecture 2: The Complementation Test and Gene Function” (PDF)
 
Instructions: Select the PDF link for “Lecture 2: The Complementation Test and Gene Function,” and read these lecture notes. Saccharomyces cerevisiaeis one of the more useful yeast species we have today. This species is the one used to make beer. This is also one of the first yeast species to be fully sequenced and it is also a model organism of system biology. These lecture notes discuss a genetic interaction test with Saccharomyces cerevisiae. Note that this type of genetic interaction is typical in diploid cells. 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.
 
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  • Reading: Saccharomyces Genome Database’s “Saccharomyces cerevisiae Genome Snapshot/Overview” Link: Saccharomyces Genome Database’s Saccharomyces cerevisiae Genome Snapshot/Overview” (HTML)
     
    Instructions: Read this optional webpage. Saccharomyces Genome Database aims to collect and organize genetic and derived information to facilitate information exchange in research. Similar databases are established for many other model organisms. Feel free to surf this website to read over any additional information that looks interesting to you.
     
    Reading this optional webpage should take approximately 2 hours.
     
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8.6.1 Metabolic Pathway Analysis in Yeast   - Reading: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 22: Eukaryotic Genes and Genomes II” Link: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 22: Eukaryotic Genes and Genomes II” (PDF)
 
Instructions: Select the PDF link for “Lecture 22: Eukaryotic Genes and Genomes II,” and read these lecture notes. It is relatively simple to study eukaryotic gene expression in yeast because yeast is unicellular. These lecture notes describe how the galactose metabolism pathway has been dissected in yeast with the help of yeast mutants. These notes explain the design of a gene expression investigation. 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.
 
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8.6.2 Protein – Protein Interaction Analysis in Yeast   - Reading: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 21: Eukaryotic Genes and Genomes III” Link: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 21: Eukaryotic Genes and Genomes III” (PDF)
 
Instructions: Select the PDF link for “Lecture 21: Eukaryotic Genes and Genomes III,” and read these lecture notes. These lecture notes describe the yeast two-hybrid assay. This assay is performed in yeast, but it is used to determine if two proteins of any origin interact or not. This text is technical, so please plan to read it several times for a full understanding.
 
Reading these lecture notes should take approximately 3 hours.
 
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8.7 Drosophila Genetics   - Reading: National Center for Biotechnology Information’s “Drosophila melanogaster (Fruit Fly) Genome View” Link: National Center for Biotechnology Information’s Drosophila melanogaster (Fruit Fly) Genome View” (HTML)
 
Instructions: Read this article and feel free to surf this website to learn more about the fruit fly, which is a common model organism in research using eukaryotic mutants. Please note the link to “Flybase”; this website aims to collect and organize genetic and derived information to facilitate information exchange in research. Genes that are homologous to the fruit fly genes are present in humans as well. Research shows that homologous fruit fly and human genes often has similar functions. Similar databases are established for many other model organisms.
 
Reading this article should take approximately 1 hour.
 
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8.8 A Model for Human Disease: Mouse Genetics   8.8.1 Introducing Sickle Cell Anemia Gene into the Mouse Genome   - Reading: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 23: Transgenes and Gene Targeting in Mice I” Link: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 23: Transgenes and Gene Targeting in Mice I” (PDF)
 
Instructions: Select the PDF link for “Lecture 23: Transgenes and Gene Targeting in Mice I,” and read these lecture notes. These lecture notes describe the genetics of human sickle cell anemia and the making of a transgenic mouse that carries human β-globin gene with sickle cell mutation. This text is technical, so please plan to read it several times for a full understanding.
 
Reading these lecture notes should take approximately 3 hours.
 
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8.8.2 Knock-Out Mice   - Reading: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 24: Transgenes and Gene Targeting in Mice II” Link: Massachusetts Institute of Technology: Professor Leona Samson’s “Lecture 24: Transgenes and Gene Targeting in Mice II” (PDF)
 
Instructions: Select the PDF link for “Lecture 24: Transgenes and Gene Targeting in Mice II,” and read these lecture notes. These lecture notes describe the making of a knock-out mouse, and the construction of mouse that has sickling red blood cells. The mouse model can be used to investigate approaches to treating the disease. This text is technical, so please plan to read it several times for a full understanding.
 
Reading these lecture notes should take approximately 3 hours.
 
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8.9 Human Genetics   - Reading: Massachusetts Institute of Technology: Professor Gerry Fink’s “Lecture 28: Human Polymorphisms” Link: Massachusetts Institute of Technology: Professor Gerry Fink’s “Lecture 28: Human Polymorphisms” (PDF)
 
Instructions: Select the PDF link for “Lecture 28: Human Polymorphisms,” and read these lecture notes. These lecture notes explain and list polymorphism examples in human 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.
 
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8.10 Coding DNA and Non-Coding DNA   - Reading: PLOS One: Utah State University: Kenneth J. Locey and Ethan P. White’s “Simple Structural Differences between Coding and Noncoding DNA” Link: PLOS One: Utah State University: Kenneth J. Locey and Ethan P. White’s “Simple Structural Differences between Coding and Non-coding DNA” (HTML)
 
Instructions: Read this article, which focuses on the structural differences between coding and junk DNA. In genomics, coding DNA is used to make proteins. This is what gives us our characteristics and every trait we have. However, as researchers have found, we seem to have a lot of extra genes, non-coding DNA, which does not seem to serve any particular function. Whether this junk DNA does serve a purpose will likely not be determined until the structure of coding and junk DNA are closely analyzed. (How can you tell if you have extra car parts until you take an inventory?) Although there are many technical terms, you should still be able to understand the main points and the importance of the study.
 
Reading this article should take approximately 3 hours.
 
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8.11 Understanding a Genome Sequence   - Reading: National Institute of Health: National Human Genome Research Institute’s “Bioinformatics” Link: National Institute of Health: National Human Genome Research Institute’s “Bioinformatics” (HTML)
 
Instructions: Read the following sections: “1. Introduction,” “2. Finding Genes,” “3. Finding Functions” and “4. Examining Variations.” When a genome is sequenced, there is a sequence made from the A, C, G, and T bases for each chromosome. This reading aims to explain how to find meaning within the sequence of bases.
 
Reading these sections should take approximately 3 hours.
 
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8.12 Molecular Phylogenetics   - Reading: National Center for Biotechnology Information: Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources: “Systematics and Molecular Phylogenetics” Link: National Center for Biotechnology Information: Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources: “Systematics and Molecular Phylogenetics” (HTML)
 
Instructions: Read this webpage from the heading “The Origins of Molecular Phylogenetics” through the end of this page. Optionally, you may want to study the first half of this webpage. Note that the first half of the page provides very useful information on how phylogenetic trees are used to present evolutionary relationships.
 
Reading this webpage should take approximately 2 hours.
 
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  • Assessment: The Saylor Foundation’s “Unit 8 Assessment” Link: The Saylor Foundation’s “Unit 8 Assessment” (HTML)
     
    Instruction: Complete the multiple choice and true/false Unit 8 Assessment.
     
    Completing this assessment should take approximately 15 minutes.