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BIO311: Molecular Biology

Unit 6: Protein Synthesis and the Genetic Code   Protein synthesis is the translation of nucleic acid sequence to protein sequence.  The nucleic acid sequence is read in triplets; each triplet codes for only one amino acid.  The genetic code is said to be universal, since a mRNA is translated into the same protein in a variety of distantly related organisms.  Protein synthesis takes place in the cytosol on free ribosomes and on rough ER-bond ribosomes.   

Unit 6 Time Advisory
This unit should take you approximately 19 hours to complete.

☐    Subunit 6.1: 1.0 hours

☐    Subunit 6.2: 5.5 hours

☐    Subunit 6.2.1: 2.0 hours

☐    Subunit 6.2.2: 1.0 hours

☐    Subunit 6.2.3: 1.0 hour

☐    Subunit 6.2.4: 1.5 hours

☐    Subunit 6.3: 4.0 hours

☐    Subunit 6.4: 1.0 hour

☐    Subunit 6.5: 1.0 hour

☐    Subunit 6.6: 3.0 hours

☐    Subunit 6.7: 2.0 hours

☐    Subunit 6.8: 1.5 hours

Unit6 Learning Outcomes
Upon successful completion of this unit, students will be able to: - Compare mRNA, rRNA, and tRNA. - Discuss how the genetic code is interpreted by specific aminoacyl tRNA transferase enzymes. - Describe the ribosomal structure; compare and contrast free ribosomes and bound ribosomes.  - Compare and contrast the initiation of translation in prokaryotes and eukaryotes. - Describe the elongation and termination process.   - Discuss third-base degeneracy, codon bias, and variations of the universal genetic code.

6.1 Overview   - Reading: NHM: Access Excellence's "Protein Synthesis" Link:  NHM: Access Excellence's "Protein Synthesis" (HTML)
 
Instruction:  Please study this page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Assessment: University of Arizona: The Biology Project: "Problem 10: Protein Amino Acids from Translated mRNA" Link:  University of Arizona: The Biology Project: "Problem 10: Protein Amino Acids from Translated mRNA" (HTML)
     
    Instruction: Please complete this problem.  After answering the question, please click on and study the tutorial page as well.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.2 Main Translation Components   6.2.1 mRNA and Open Reading Frames (ORF)   - Reading: University of Wisconsin: Michael R. Brent's "Translation and Open Reading Frames" Link: University of Wisconsin:  Michael R. Brent's "Translation and Open Reading Frames" (HTML)
 
Instructions:  Please study this page.
 
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  • Reading: Washington University: Michael R. Brent's "Genome Annotation Past, Present, and Future: How to Define an ORF at Each Locus" Link: Washington University:  Michael R. Brent's "Genome Annotation Past, Present, and Future: How to Define an ORF at Each Locus" (HTML or PDF)
     
    Instructions:  Please study this page.
     
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  • Assessment: University of Arizona: The Biology Project: "Problem 15: DNA Template for mRNA Synthesis" Link:  University of Arizona: The Biology Project: "Problem 15: DNA Template for mRNA Synthesis" (HTML)
     
    Instruction: Please complete this problem.  After answering the question, please click on and study the tutorial page as well.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.2.2 Ribosomal RNA & Transfer RNA   - Reading: NCBI Bookshelf: Lodish et al.'s "Processing of rRNA and tRNA" Link: NCBI Bookshelf:  Lodish et al.'s "Processing of rRNA and tRNA" (HTML)
 
Instructions:  Please study this page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Assessment: University of Arizona: The Biology Project: "Problem 14: Codon-Anticodon Base Pairing" Link:  University of Arizona: The Biology Project: "Problem 14: Codon-Anticodon Base Pairing" (HTML)
     
    Instruction: Please complete this problem.  After answering the question, please click on and study the tutorial page as well.
     
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6.2.3 Aminoacyl tRNA Transferase   - Reading: NCBI Bookshelf: Berg et al.'s "Aminoacyl-Transfer RNA Synthetases Read the Genetic Code" Link: NCBI Bookshelf:  Berg et al.'s "Aminoacyl-Transfer RNA Synthetases Read the Genetic Code" (HTML)
 
Instructions: Please study this page.  Please note that Aminoacyl-Transfer RNA Synthetases interpret the anticodon when they charge specific tRNAs with appropriate amino acids.
 
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6.2.4 Ribosome   - Reading: John W. Kimball’s "Ribosomes" Link:  John W. Kimball’s "Ribosomes" (HTML)
 
Instruction:  Please study this page.
 
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6.3 Initiation of Translation   6.3.1 Prokaryotes: Shine-Delgarno Sequence, Initiator tRNA, and Start Codon   - Reading: University of California: Hartmut "Hudel" Luecke's "Initiation of Protein Synthesis" Link: University of California: Hartmut "Hudel" Luecke's "Initiation of Protein Synthesis" (HTML)
 
Instruction:  Please study this page.  Please follow the "Next: Schematic of Initiation" link at the bottom of the page.
 
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6.3.2 Eukaryotes: Kozak Sequence, Initiator tRNA, and Start Codon   - Reading: NCBI Bookshelf: Lodish et al.'s "Stepwise Formation of Proteins on Ribosomes" Link:  NCBI Bookshelf:  Lodish et al.'s "Stepwise Formation of Proteins on Ribosomes" (HTML)
 
Instruction:  Please study the "Eukaryotic Initiation of Protein Synthesis Occurs at the 5' End and Internal Sites in mRNA" section on this page.
 
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  • Reading: University of California: Hartmut "Hudel" Luecke's "Schematic of the Initiation of Protein Synthesis in Eukaryotes" Link: University of California: Hartmut "Hudel" Luecke's "Schematic of the Initiation of Protein Synthesis in Eukaryotes" (HTML)
     
    Instruction:  Please study the schema on this page.
     
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6.3.3 Translation Initiation Factors   - Reading: Nobelprize.org's "Initiation of Translation" Link:  Nobelprize.org's "Initiation of Translation" (HTML)
 
Instruction:  Please study the schema on this page.
 
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6.3.4 80S Initiation Complex   - Reading: NCBI Bookshelf: Poulin & Sonenberg's "Mechanism of Translation Initiation in Eukaryotes" Link:  NCBI Bookshelf: Poulin & Sonenberg's "Mechanism of Translation Initiation in Eukaryotes" (HTML)
 
Instruction:  Please study the schema on this page.
 
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6.4 Elongation of Translation   - Reading: NCBI Bookshelf: Brown's "Synthesis and Processing of the Proteome" Link:  NCBI Bookshelf: Brown's "Synthesis and Processing of the Proteome" (HTML)
 
Instruction:  Please study the "Elongation of Translation" section on this page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.5 Termination of Translation   - Reading: NCBI Bookshelf: Brown's "Synthesis and Processing of the Proteome" Link:  NCBI Bookshelf: Brown's "Synthesis and Processing of the Proteome" (HTML)
 
Instruction:  Please study the "Termination of Translation" section on this page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.6 Genetic Code   6.6.1 Genetic Codon Table   - Reading: John W. Kimball’s "The Genetic Code" Link:  John W. Kimball’s "The Genetic Code" (HTML)
 
Instruction:  Please study this page.  Please note that the genetic code is redundant, but it is not ambiguous.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Assessment: University of Arizona: The Biology Project: "Problem 11: Products after Protein Synthesis," "Problem 12: mRNA and Protein Coding," "Problem 13: mRNA Polypeptide Code" Link:  University of Arizona: The Biology Project: "Problem 11: Products after Protein Synthesis," (HTML) "Problem 12: mRNA and Protein Coding," (HTML)"Problem 13: mRNA Polypeptide Code" (HTML)
     
    Instruction: Please complete these problems.  After answering a question, please click on and study the tutorial page as well.
     
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6.6.2 Degeneracy and the Wobble Hypothesis   - Reading: NCBI Bookshelf: Griffiths et al.'s "Genetic Code" Link:  NCBI Bookshelf: Griffiths et al.'s "Genetic Code" (HTML)
 
Instruction:  Please study the "Multiple Codons for a Single Amino Acid" section on this page.
 
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6.6.3 Start and End Codons   - Reading: NCBI Bookshelf: Lodish et al.'s "Stepwise Formation of Proteins on Ribosomes" Link:  NCBI Bookshelf: Lodish et al.'s "Stepwise Formation of Proteins on Ribosomes" (HTML)
 
Instruction:  Please study "The AUG Start Codon Is Recognized by Methionyl-tRNAiMet" section on this page.
 
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  • Reading: NCBI Bookshelf: Griffiths et al.'s "Genetic Code" Link:  NCBI Bookshelf: Griffiths et al.'s "Genetic Code" (HTML)
     
    Instruction:  Please study the "Stop Codons" section on this page.
     
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6.6.4 Universality of the Genetic Code   - Reading: NCBI Bookshelf: Griffiths et al.'s "Universality of Genetic Information Transfer" Link:  NCBI Bookshelf: Griffiths et al.'s "Universality of Genetic Information Transfer" (HTML)
 
Instruction:  Please study this page.
 
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  • Reading: John W. Kimball 's "The Genetic Code" Link: John W. Kimball 's "The Genetic Code" (HTML)
     
    Instructions: Please scroll down to the "Exceptions to the Code" section and study the text until the end of the page. Please note that these are just a few examples when the standard genetic code is violated.
     
    Terms of Use: The linked material above has been reposted by the kind permission of Professor John W. Kimball, and can be viewed in its original form here.  Please note that this material is under copyright and cannot be reproduced in any capacity without explicit permission from the copyright holder. 

6.7 Protein Synthesis on Rough Endoplasmic Reticulum   - Reading: NCBI Bookshelf: Alberts et al.'s "The Endoplasmic Reticulum" Link:  NCBI Bookshelf: Alberts et al.'s "The Endoplasmic Reticulum" (HTML)
 
Instruction: Please study the "Membrane-Bound Ribosomes Define the Rough ER" section this page.  Please note that there are free ribosomes and bound ribosomes.  All ribosomes start as free ribosome.  A ribosome that translates a protein with an N-terminal ER signal peptide will move to the ER and will become a bound ribosome. 
 
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  • Reading: NCBI Bookshelf: Lodish et al.'s "Translocation of Secretory Proteins across the ER Membrane" Link:  NCBI Bookshelf: Lodish et al.'s "Translocation of Secretory Proteins across the ER Membrane" (HTML)
     
    Instruction:  Please study this page.
     
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6.8 Translation Defects   - Reading: Scitable: Nature Reviews Genetics: Scheper et al.’s "Translation Matters: Protein Synthesis Defects in Inherited Disease" Reading: Scitable: Nature Reviews Genetics: Scheper et al.’s "Translation Matters: Protein Synthesis Defects in Inherited Disease" (PDF)
 
Instruction: Please read this publication.
 
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