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BIO311: Molecular Biology

Unit 2: Nucleic Acids and Proteins: Structure and Function   Nucleic acids and proteins are biopolymers. Nucleic acids are nucleotide polymers, while proteins are amino acid polymers. DNA is a polynucleotide, which typically has double helical 3D structure. RNA is a polynucleotide as well, but its 3D structure is more versatile. Some proteins and some RNA molecules act as biological catalysts and regulate cellular metabolism. 

Unit 2 Time Advisory
This unit should take you approximately 17 hours to complete.

☐    Subunit 2.1: 1.5 hours

☐    Subunit 2.2: 0.5 hours

☐    Subunit 2.3: 7.0 hours

☐    Subunit 2.3.1: 1.5 hours

☐    Subunit 2.3.2: 1.5 hours

☐    Subunit 2.3.3: 1.5 hours

☐    Subunit 2.3.4: 1.0 hour

☐    Subunit 2.3.5: 0.5 hours

☐    Subunit 2.3.6: 1.0 hour

☐    Subunit 2.4: 2.0 hour

☐    Subunit 2.5: 2.0 hours

☐    Subunit 2.5: 4.0 hours

Unit2 Learning Outcomes
Upon successful completion of this unit, students will be able to: - Discuss, compare, and contrast the structural differences of RNA and DNA. - Identify bases that can pair with each other. - Describe the general structural features of proteins.  - Discuss catalyzed reactions. - Compare and contrast enzyme and ribozyme catalyzed reactions. 

2.1 RNA and DNA are Polynucleotides   - Reading: NCBI Bookshelf: Strachan & Read's “DNA Structure and Gene Expression” Links: NCBI Bookshelf:  Strachan & Read's “DNA Structure and Gene Expression” (HTML)
 
Instructions: Please study the "DNA, RNA and Polypeptides are Large Polymers Defined by a Linear Sequence of Simple Repeating Units" section on this page.
 
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  • Lecture: MIT Open Courseware: Graham Walker's “Introduction to Nucleic Acids” Link: MIT Open Courseware: Graham Walker's “Introduction to Nucleic Acids” (Adobe Flash)
     
    Also available in:

    iTunes
     
    Instructions:  Please watch the first 7:20 of this video.
     
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2.2 Composition of DNA and RNA   - Reading: Diffen’s "DNA vs. RNA" Link:  Diffen’s "DNA vs. RNA" (HTML)
 
Instructions:  Please review the similarities and differences of the structure of DNA and RNA.
 
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2.3 Helical Forms of DNA   2.3.1 B-form: Right-Handed Double Helix   - Reading: NCBI Bookshelf: Lodish et al.'s “Structure of Nucleic Acids” Links: NCBI Bookshelf:  Lodish et al.'s “Structure of Nucleic Acids” (HTML)
 
Instructions: Please study the "Native DNA Is a Double Helix of Complementary Antiparallel Chains" and "DNA Can Undergo Reversible Strand Separation" sections on this page.  Please note that the B-form is the most common DNA structure.  If you read about DNA or dsDNA, then the structure is the B-form unless otherwise indicated. The B-form was discovered by Franklin and Gosling (see unit 1).  The DNA strands in the B-form are in antiparallel orientation.  A right-handed helix spirals away from the viewer in a clockwise manner.
 
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2.3.2 A-form: Right-Handed Double Helix and Z-form Left-Handed Double Helix   - Reading: Web-Books.com's "DNA's B Form, A Form and Z Form" Link:  Web-Books.com's "DNA's B Form, A Form and Z Form" (HTML)
 
Instructions:  Please study this page.  Please compare and contrast the A, B, and Z forms.  Note that all of the forms have antiparallel DNA strands.
 
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  • Reading: NCBI Bookshelf: Berg et al.'s “DNA Can Assume a Variety of Structural Forms” Links: NCBI Bookshelf:  Berg et al.'s “DNA Can Assume a Variety of Structural Forms” (HTML)
     
    Instructions: Please study this page.  Please note that A and Z forms have antiparallel strand s as well.
     
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2.3.3 Triple Helices and Quadruplexes   - Reading: NCBI Bookshelf: Michael W. Van Dyke's "Do DNA Triple Helices or Quadruplexes Have a Role in Transcription?" Link:  NCBI Bookshelf:  Michael W. Van Dyke's "Do DNA Triple Helices or Quadruplexes Have a Role in Transcription?" (HTML)
 
Instructions:  Please study this page.
 
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2.3.4 Major and Minor Grooves of DNA   - Reading: NCBI Bookshelf: Berg et al's "DNA Can Assume a Variety of Structural Forms"(HTML) Link: NCBI Bookshelf: Berg et al's "DNA Can Assume a Variety of Structural Forms" (HTML)
 
Instruction: Please study "The Major and Minor Grooves Are Lined by Sequence-Specific Hydrogen-Bonding Groups" section on this page.  Please note that the grooves are binding sites for proteins.
 
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2.3.5 Specificity of Base Pairing   - Reading: John W. Kimball’s "Base Pairing" Link:  John W. Kimball’s "Base Pairing" (HTML)
 
Instruction:  Please study this page.  Please review Chargaff's rules in Unit 1.
 
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  • Web Media: YouTube: Molvisions: Timothy Driscoll's "DNA Structure” Links: YouTube: Molvisions: Timothy Driscoll's "DNA Structure” (YouTube)
     
    Instructions: Please watch this video (3 min).
     
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  • Assessment: University of Arizona: The Biology Project: "Problem 8: Complementary Bases" Link:  University of Arizona: The Biology Project: "Problem 8: Complementary Bases" (HTML)
     
    Instruction: Please complete this problem. After answering the question, please click on and study the tutorial page as well.
     
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2.3.6 DNA Supercoils   - Reading: NCBI Bookshelf: Berg et al's "Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures" Links: NCBI Bookshelf: Berg et al's "Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures" (HTML)
 
Instructions: Please study this page.
 
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2.4 RNA Structure   - Reading: University of Illinois's "DNA Structure" Link:  University of Illinois's "DNA Structure" (HTML)
 
Instructions: Please study the "RNA structures," "Secondary and Tertiary Structures of tRNA Molecules," and "Ribosomal RNA" sections on this page.
 
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2.5 Protein Structure   - Reading: NCBI Bookshelf: Lodish et al.'s "Hierarchical Structure of Proteins" Link:  NCBI Bookshelf: Lodish et al.'s "Hierarchical Structure of Proteins" (HTML)
 
Instructions: Please study this page.
 
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  • Web Media: YouTube: Proneural’s "Protein Structure" Link: YouTube: Proneural’s "Protein Structure" (YouTube)
     
    Instructions: Please watch this video (1 min).
     
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  • Lecture: YouTube: Indian Institute of Technology: Prof. S. Dasgupta's "Lecture 4—Protein Structure II" Link: YouTube: Indian Institute of Technology: Prof. S. Dasgupta's "Lecture 4—Protein Structure II" (YouTube)
     
    Instruction: Please watch this video (50 min).
     
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2.6 Biological Catalysts   2.6.1 Enzymes   - Reading: NCBI Bookshelf: Cooper's "The Central Role of Enzymes as Biological Catalysts" Links: NCBI Bookshelf: Cooper's "The Central Role of Enzymes as Biological Catalysts" (HTML)
 
Instructions: Please study this page.
 
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  • Web Media: YouTube: Oregon State University: Kevin Ahern's "Enzymes II" Link: YouTube: Oregon State University: Kevin Ahern's "Enzymes II" (YouTube)
     
    Instruction: Please watch this video (50 min).
     
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2.6.2 Catalytic RNA   - Reading: NCBI Bookshelf: Berg et al.'s "The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution" Links: NCBI Bookshelf: Berg et al.'s "The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution" (HTML)
 
Instructions: Please study this page.
 
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