Loading...

BIO301: Cell Biology

Unit 6: The Cell Nucleus and Gene Expression   As you learned in BIO101, the cell nucleus is the storage area for all genetic material and constantly full of activity. The nucleus, in fact, contains not only DNA, but RNA and protein as well. This unit will take a detailed look at chromosomes, the cell nucleus, gene expression, and expression regulation. When we refer to expression regulation, we are talking about the fact that not all genes are expressed in the cell at the same time. After all, though a liver cell and a nerve cell have the same genome (and thus the same DNA), they look and act completely differently. How does this happen? The answer is regulated gene expression!

Unit 6 Time Advisory
Completing this unit will take you approximately 21.5 hours.

☐    Subunit 6.1: 4.5 hours

☐    Subunit 6.2: 3 hours

☐    Subunit 6.3: 7.5 hours

☐    Subunit 6.4: 4.5 hours

☐    Assessment: 2 hours

Unit6 Learning Outcomes
Upon completion of this unit, you will be able to - distinguish between euchromatin and heterochromatin in terms of which is the active form of genes; - identify the components of the nuclear envelope and their functions; - describe the roles of enhancers and repressors in gene expression; and - describe gene regulation (pre- and post-transcription).

6.1 Chromosome Organization   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Chromosomes and Chromatin” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: Chromosomes and Chromatin (HTML)
 
Instructions: Read the introduction and subsection “Chromatin,” along with Table 4.3 and all associated figures (Figs. 4.8–4.10). This will cover the material in 6.1.1–6.1.6.

 Reading this text and taking 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.
  • Lecture: iTunes U: University of California, Berkeley: Professor David G. Drubin’s “Nuclear and Chromatin Structure” Link: iTunes U: University of California, Berkeley: Professor David G. Drubin’s Nuclear and Chromatin Structure (iTunes U)
     
    Instructions: Scroll down the webpage to item 18 titled Lecture 25: “Nuclear and Chromatin Structure,” and click on “View in iTunes.” Please note that the first few minutes of the video lecture deals with class administration issues and will not be necessary to watch. This material covers the topics outlined in 6.1, 6.2, and all inclusive subunits.

    Watching this lecture and taking notes should take approximately 2 hours.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.1.1 DNA and Histones   This subunit is covered by the reading assigned beneath subunit 6.1. Focus on the subsection “Chromatin” with associated table (Table 4.3).

6.1.2 Nucleosome   This subunit is covered by the reading assigned beneath subunit 6.1. Focus on the subsection “Chromatin” with associated figures (Figs. 4.8 and 4.9).

6.1.3 30-nm Fiber   This subunit is covered by the reading assigned beneath subunit 6.1. Focus on the subsection “Chromatin” with associated figure (Fig. 4.10).

6.1.4 Chromatin Loops and Scaffolding   - Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology: “Section 9.6: Morphology and Functional Elements of Eukaryotic Chromosomes” Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: H. Lodish, A. Berk, S.L. Zipursky, et al.’s Molecular Cell Biology: “Section 9.6: Morphology and Functional Elements of Eukaryotic Chromosomes”

 Instructions: Scroll down the webpage, and read the section titled
“Nonhistone Proteins Provide a Structural Scaffold for Long
Chromatin Loops” with associated figures (Figs. 9.35 and 9.36).  

 Reading this text and taking notes should take approximately 1
hour.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

6.1.5 Euchromatin and Heterochromatin   This subunit is covered by the reading assigned beneath subunit 6.1. Be sure to remember that euchromatin is for active gene use and heterochromatin is for genes that are inactivated or not in use. Focus on the subsection “Chromatin.”

6.2 Nuclear Organization   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Nuclear Envelope and the Traffic between the Nucleus and Cytoplasm” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: The Nuclear Envelope and the Traffic between the Nucleus and Cytoplasm (HTML)
 
Instructions: Read the introduction and subsections “Structure of the Nuclear Envelope”, “The Nuclear Pore Complex,” and “Selective Transport of Proteins to and from the Nucleus” along with all associated figures (Figs. 8.1, 8.4, 8.5, 8.78.11). These will cover the materials in 6.2.1–6.2.4.

 Reading this text and taking notes should take approximately 2
hours.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

6.2.1 Inner and Outer Membrane   This subunit is covered by the reading assigned beneath subunit 6.2. Focus on figure 8.1.

6.2.2 Nuclear Pores   This subunit is covered by the reading assigned beneath subunit 6.2. Focus on figure 8.2.

6.2.3 Nucleoplasm   This subunit is covered by the reading assigned beneath subunit 6.2. Focus on figure 8.8.

6.2.4 Nuclear Lamina   This subunit is covered by the reading assigned beneath subunit 6.2. Focus on figure 8.4.

6.2.5 Nucleolus   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “The Nucleolus” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: The Nucleolus (HTML)
 
Instructions: Read the introduction and the subsection “Ribosomal RNA Genes and the Organization of the Nucleolus,” along with all associated figures (gigs. 8.22–8.24).

 Reading this text and taking notes should take approximately 1
hour.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

6.3 Gene Expression Transcription Unit   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Eukaryotic RNA Polymerases” and “General Transcription Factors” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: Eukaryotic RNA Polymerases and General Transcription Factors (HTML)
 
Instructions: Read the introduction and subsections “Eukaryotic RNA Polymerases” and “General Transcription Factors and the Initiation of Transcription by RNA Polymerase II,” along with all associated figures (Figs. 6.12 and 6.14). This will cover the material in 6.3.1–6.3.5.

 Reading this text and taking notes should take approximately 2
hours.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Lecture: Massachusetts Institute of Technology OpenCourseWare: Professor Graham Walker’s “Lecture 13: Gene Regulation I” Link: Massachusetts Institute of Technology OpenCourseWare: Professor Graham Walker’s Lecture 13: Gene Regulation I (YouTube)

    Also available in:
    MPEG4 (MP4) and OGG
    iTunes U Video, and Transcript

    Instructions: Watch this 50 minute-lecture on Massachusetts Institute of Technology’s OpenCourseWare website. You may also click on the tab titled “Transcript” to read the transcript in HTML or to click on “Download” to access the PDF file. This lecture will cover the topics outlined in subunits 6.3.1–6.3.3

    Watching this lecture and taking notes should take approximately 2 hours.
     
    Terms of Use: This resource is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0. It is attributed to Massachusetts Institute of Technology’s Professor Graham Walker and the original version can be found here.

6.3.1 RNA Polymerase II   This subunit is covered by the reading and video assigned beneath subunit 6.3. Focus on subsection “General Transcription Factors and Initiation of Transcription by RNA Polymerase II” with associated figures (Figs. 6.12 and 6.14).

6.3.2 General Transcription Factors   This subunit is covered by the reading and video assigned beneath subunit 6.3. Focus on “General Transcription Factors and Initiation of Transcription by RNA Polymerase II” section of the reading.

6.3.3 DNA Binding Domains   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Regulation of Transcription in Eukaryotes.” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Regulation of Transcription in Eukaryotes” (HTML)
 
Instructions: Read the introduction and subsections “Regulation of Transcription in Eukaryotes” and “Structure and Function of Transcriptional Activators,” along with all associated figures (Figs. 6.26–  6.27).

 Reading this text and taking notes should take approximately 1
hour.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

6.3.4 RNA Maturation   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Translation of mRNA” and “RNA Processing and Turnover” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: Translation of mRNA and RNA Processing and Turnover (HTML)
 
Instructions: From “Translation of RNA,” read the introduction and the subsections “The Ribosome,” “Organization of mRNAs” (first paragraph only), and “The Process of Translation,” along with associated figures (Figs. 7.4–7.6 and 7.8–7.14). Read the section “RNA Processing and Turnover”, along with all associated figures (Figs. 6.37–6.38). These will cover the material in 6.3.5–6.3.7.

 Reading this text and taking 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.

6.3.5 Ribosome   This subunit is covered by the reading assigned beneath subunit 6.3.4. Focus on “Translation of mRNA.”

6.3.6 Translation   This subunit is covered by the reading assigned beneath subunit 6.3.4. Focus on “Translation of mRNA.”

6.3.7 Protein Folding   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Protein Folding and Processing”

Link: National Center for Biotechnology Information’s Bookshelf:
Sinauer Associates, Inc.: Professor Geoffrey Cooper’s *The Cell*: *A
Molecular Approach, *2e: [“Protein Folding and
Processing”](http://www.ncbi.nlm.nih.gov/books/NBK9839/) (HTML)  
    
 Instructions: Read the introduction and subsection “Chaperones and
Protein Folding,” along with all associated figures (Figs. 7.17,
7.18, and 7.20) regulation.


 Reading this text and taking notes should take approximately 1
hour.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

6.4 Regulation of Gene Expression   - Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Regulation of Transcription in Eukaryotes” Link: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates, Inc.: Professor Geoffrey Cooper’s The CellA Molecular Approach, 2e: Regulation of Transcription in Eukaryotes (HTML)
 
Instructions: Read this section, along with all associated figures (Figs. 6.18–6.27 and 6.29, 6.30, 6.32–6.36). This will cover the material in 6.4.1–6.4.4. Please note that, although they are not described as such, the “Relationship of Chromatin Structure to Transcription” and “DNA Methylation” are examples of epigenetic regulation.

 Reading this text and taking notes should take approximately 2
hours.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Lecture: Massachusetts Institute of Technology OpenCourseWare: Professor Graham Walker’s “Lecture 14: Gene Regulation II” Link: Massachusetts Institute of Technology OpenCourseWare: Professor Graham Walker’s Lecture 14: Gene Regulation II (YouTube)

    Also available in:
    MPEG4 (MP4) and OGG
    iTunes U Video, and Transcript

    Instructions: Watch this 50-minute lecture on Massachusetts Institute of Technology’s OpenCourseWare website. You may also click on the tab titled “Transcript” to read the transcript in HTML or to click on “Download” to access the PDF file. Please note that this lecture also covers the topics outlined in subunits 6.4.1–6.4.4.

    Watching this lecture and taking notes should take approximately 2 hours.
     
    Terms of Use: This resource is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0. It is attributed to Massachusetts Institute of Technology’s Professor Graham Walker and the original version can be found here.

6.4.1 Epigenetic Regulation   This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on the “Relationship of Chromatin Structure to Transcription” and “DNA Methylation” sections of the reading.

6.4.2 Post-transcriptional Modifications   This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on the subsections “RNA Editing” and “RNA Degradation” with associated figures (Figs. 6.47 and 6.48).

6.4.3 Repressors and Enhancers   This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on “Eukaryotic Repressors” and cis-Acting Regulatory Sequences: Promoters and Enhancers” sections of the reading.

6.4.4 Inducible Systems   This subunit is covered by the reading and video assigned beneath subunit 6.4. Focus on “Structure and Function of Transcriptional Activators” section.

  • Assessment: National Center for Biotechnology Information’s Bookshelf: SinauerAssociates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: “Questions - The Nucleus” and “Questions – RNA Synthesis and Processing” Link: National Center for Biotechnology Information’s Bookshelf: SinauerAssociates, Inc.: Professor Geoffrey Cooper’s The Cell: A Molecular Approach, 2e: Questions - The Nucleus and Questions – RNA Synthesis and Processing (HTML)

    Instructions: Answer all questions (1–5). Please note that answers areposted directly below the questions asked; try to cover them while youanswer the questions yourself.

    Completing this assessment should take approximately 1 hour.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Web Media: Studio Daily: XVIVO and Harvard University’s “The Inner Life of a Cell” Link: Studio Daily: XVIVO and Harvard University’s The Inner Life of a Cell (Flash)

    Instructions: Please note that this resource is optional. Watch this short (eight-minute), un-narrated video to visualize the processes occurring daily within a eukaryotic cell. This video was created by animators as XVIVO after consultation with cell and molecular biologists at Harvard University, in order to illustrate the workings of a cell.

    Watching this optional video should take approximately 30 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Assessment: The Saylor Foundation’s “Unit 6 Quiz” Link: The Saylor Foundation’s “Unit 6 Quiz” (HTML)

    Instructions: Please complete the linked quiz to test your knowledge of the material covered in Unit 6.

    Completing this assessment should take approximately 1 hour.