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BIO311: Molecular Biology

Unit 5: Transcription   Transcription leads to the synthesis of a complementary RNA strand from a DNA template.  The process is less precise than DNA replication, since RNA polymerases do not have proofreading activity.  There are remarkable differences between prokaryotic and eukaryotic transcription, which we will discuss in detail in Unit 7 (Regulation of Gene Expression).  The turnover of RNA molecules is commonly regulated by P-bodies and miRNA in the cell.  This unit focuses on mRNA and miRNA; tRNA and rRNA are discussed in the next unit.      

Unit 5 Time Advisory
This unit should take you approximately 12.5 hours to complete.

☐    Subunit 5.1: 1.5 hours

☐    Subunit 5.2: 0.5 hours

☐    Subunit 5.3: 1.5 hours

☐    Subunit 5.4: 1.5 hours

☐    Subunit 5.5: 4.0 hours

☐    Subunit 5.6: 1.5 hour

☐    Subunit 5.7: 2.0 hour

Unit5 Learning Outcomes
Upon successful completion of this unit, students will be able to: - Describe the three stages of the transcriptional cycle. - Compare and contrast translation in prokaryotes and eukaryotes. - Compare the characteristics of RNA polymerases. - Compare and contrast RNA polymerases and DNA polymerases. - Discuss the consequence of RNA splicing and editing. - Predict the characteristics of differentially spliced RNA molecules. - Describe miRNA-regulated RNA turnover.

5.1 Basic Transcriptional Cycle   - Lecture: YouTube: Oregon State University: Kevin Ahern's "Transcription II" Link: YouTube: Oregon State University: Kevin Ahern's "Transcription II" (YouTube)
 
Instruction: Please watch this video (51 min).
 
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  • Reading: NCBI Bookshelf: Berg et al.'s "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites" Link: NCBI Bookshelf: Berg et al.'s "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites" (HTML)
     
    Instructions:  Please study the following sections: "An RNA Primer Synthesized by Primase Enables DNA Synthesis to Begin;" "One Strand of DNA Is Made Continuously, Whereas the Other Strand Is Synthesized in Fragments;" "DNA Ligase Joins Ends of DNA in Duplex Regions;" "DNA Replication Requires Highly Processive Polymerases;" "The Leading and Lagging Strands Are Synthesized in a Coordinated Fashion;" and "DNA Synthesis Is More Complex in Eukaryotes Than in Prokaryotes."
     
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5.2 Types of RNA Polymerase   - Reading: NCBI Bookself: Lodish et al.'s "Eukaryotic Gene Control: Purposes and General Principles" Link:  NCBI Bookself:  Lodish et al.'s "Eukaryotic Gene Control: Purposes and General Principles" (HTML)
 
Instruction:  Please study the introduction and "Three Eukaryotic Polymerases Catalyze Formation of Different RNAs" sections on this page.  Please note that these three RNA polymerases have different specificity, thus they cannot replace each other.
 
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5.3 Transcription in Prokaryotes   - Reading: NCBI Bookshelf: Brown's "Synthesis and Processing of RNA" Link: NCBI Bookshelf:  Brown's "Synthesis and Processing of RNA" (HTML)
 
Instructions:  Please study the "Synthesis of Bacterial mRNAs" section on this page.  Translation and transcription take place simultaneously in prokaryotes.  Please note that prokaryotic mRNAs are not processed.
 
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5.4 Transcription in Eukaryotes   - Reading: NCBI Bookshelf: Brown's "Synthesis and Processing of RNA" Link: NCBI Bookshelf:  Brown's "Synthesis and Processing of RNA" (HTML)
 
Instructions:  Please study the "Synthesis of Eukaryotic mRNAs by RNA Polymerase II" section on this page, including the "Capping of RNA Polymerase II Transcripts Occurs Immediately after Initiation," "Elongation of Eukaryotic mRNAs," and "Termination of mRNA Synthesis Is Combined with Polyadenylation" subsections.  In eukaryotes, transcription follows translation, and transcription and translation take place in different subcellular compartments.  Please note that eukaryotic mRNAs are processed with a 5'-cap and 3'-tail.  Capping and polyadenylation are post-translational modifications.
 
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5.5 RNA processing   5.5.1 RNA Splicing   - Reading: NCBI Bookshelf: Brown's "Synthesis and Processing of RNA" Link: NCBI Bookshelf:  Brown's "Synthesis and Processing of RNA" (HTML)
 
Instructions:  Please study the "Intron Splicing" section on this page, including the following subsections: "Conserved Sequence Motifs Indicate the Key Sites in GU-AG Introns," "Outline of the Splicing Pathway for GU-AG Introns," "snRNAs and Their Associated Proteins Are the Central Components of the Splicing Apparatus," "Alternative Splicing Is Common in Many Eukaryotes," and "AU-AC Introns Are Similar to GU-AG Introns but Require a Different Splicing Apparatus."  Differential splicing results in multiple RNA molecules from one gene.  In differentially spliced RNAs, different exon combinations are spliced together.  Exon(s) may correspond to protein domains, thus the characteristics of the encoded protein become predictable from the combination of the functional domains.
 
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  • Reading: Scitable: Dr. Suzanne Clancy's "RNA Splicing: Introns, Exons and Spliceosome" Link: Scitable:  Dr. Suzanne Clancy's "RNA Splicing: Introns, Exons and Spliceosome" (HTML)
     
    Instructions:  Please study this page.
     
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5.5.2 Trans-Splicing   - Reading: NCBI Bookshelf: Riddle et al.'s "Trans-Splicing" Link: NCBI Bookshelf:  Riddle et al.'s "Trans-Splicing" (HTML)
 
Instructions:  Please study this page.
 
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5.5.3 RNA Editing   - Reading: John W. Kimball’s "RNA Editing" Link:  John W. Kimball’s "RNA Editing" (HTML)
 
Instruction:  Please study this page.
 
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5.6 Riboswitches   - Reading: University of Colorado: Garst & Batey's "A Switch in Time: Detailing the Life of a Riboswitch" Link:  University of Colorado: Garst & Batey's "A Switch in Time: Detailing the Life of a Riboswitch" (HTML)
 
Instruction:  Please study this page, including the figures embedded into the publication.  Please note that binding of metabolites to riboswitches  regulates the expression of the mRNA wherein the riboswitch is located.
 
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5.7 RNA Degradation   5.7.1 MicroRNA (miRNA)   - Reading: Scitable: Suzanne Clancy's "RNA Functions" Link:  Scitable: Suzanne Clancy's "RNA Functions" (HTML)
 
Instructions:  Please study this page. 
 
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5.7.2 P-Bodies   - Lecture: YouTube: University of Arizona: Dr. Roy Parker's "P-bodies and the mRNA Cycle" Link:  University of Arizona: Dr. Roy Parker's "P-bodies and the mRNA Cycle" (YouTube)
 
Instructions: Please watch this video (35 min).  Please note that P-bodies serve as a scaffolding center for miRNA, and translationally repressed mRNAs are also stored in P-bodies.    
 
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