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BIO401: Biochemistry

Unit 3: Proteins   Proteins, as you know are the large, complex molecules that are made of amino acids, so this unit is a natural follow-up to the previous one. Protein is the equivalent of a strand of DNA to nucleotides, although protein structure is vastly more complex than a DNA structure. In fact, protein structure is an essential part of that protein’s function, and destroying its original structure will destroy its function as well. This process is known as denaturing, and it most commonly occurs from exposing proteins to high temperatures. This is why fevers are bad for people and why the albumen (clear liquid) in an egg turns white when cooked. Because structure is so important to function, a large part of this unit concerns the structural properties of proteins. The last part of this unit will also look at the life cycles of proteins, from synthesis to degradation.

Unit 3 Time Advisory
This unit should take you 13 hours to complete.

☐    Subunit 3.1: 2 hours

☐    Subunit 3.2: 1 hour

☐    Video: 30 minutes

☐    Review: 30 minutes

☐    Subunit 3.3: 2 hours

☐    Subunit 3.4: 2 hours

☐    Subunit 3.5: 2 hours

☐    Subunit 3.6: 2 hours

☐    Subunit 3.7: 1 hour

☐    Subunit 3.8: 1 hour

Unit3 Learning Outcomes
Upon successful completion of this unit, students will be able to:

  • Explain how a protein’s overall structure is determined.
  • Describe how proteins are formed and degraded.

3.1 Peptide Bond   3.1.1 Conformational Restraints   - Reading: WikiBooks: Biochemistry: "Proteins" Link: WikiBooks: Biochemistry: "Proteins" (PDF)
 
Instructions: Read the intoduction to protein structure focusing on the peptide bond.
 
Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikibooks version of this article here (HTML).

3.1.2 Ramachandran Diagram   Note: Ramachandran diagrams visually display the available configurations of the peptide bond. Secondary structures are clearly visible as defined areas on the graph. Be sure to know which area of the diagram represents which secondary structures. 

  • Reading: University of California San Diego: Bioinformatics I: "Lecture 1" Link: University of California San Diego: Bioinformatics I: "Lecture 1" (Microsoft PowerPoint)
     
    Instructions: Click on the link to go to the main page.  Download the lecture notes for "lecture 1."  These notes also cover section 3.1.3.
    Note: Ramachandran diagrams visually display the available configurations of the peptide bond.  Secondary structures are clearly visible as defined areas on the graph.  Be sure to know which area of the diagram represents which secondary structures.
     
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3.2 Primary Structure   Note: The primary structure of a protein is its amino acid sequence, and it also directly determines the structure of a protein.

  • Lecture: Appalachian State University: Dr. Eric Allain's "Proteins Primary Structure Part 1"  Link:  Appalachian State University: Dr. Eric Allain's "Proteins Primary Structure Part 1"

    Instructions: Take notes throughout the lecture.
     
    Note: The primary structure of a protein is its amino acid sequence, and it also directly determines the structure of a protein.
     
    Terms of Use: The material above has been reposted by the kind permission of Eric Allain from Appalachian State University, 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.

3.3 Secondary Structure   - Reading: The Open University: Proteins: "The Three-Dimensional Nature of Proteins" Link: The Open University: Proteins: "The Three-Dimensional Nature of Proteins" (HTML)
 
Instructions: Read through all the section under the heading "The Three-Dimensional Nature of Proteins" on the left of the page (1.1, 1.2, etc.)  This information covers 3.3.1-3.3.4, all of 3.4, and 3.5.1.
 
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3.3.1 Alpha Helix   3.3.2 Helical Orientation and Stabilization   3.3.3 Parallel Beta Sheet   3.3.4 Anti-Parallel Beta Sheet   3.4 Tertiary Structure   3.4.1 Hydrophobic Effect   3.4.2 Distribution of Amino Acids   3.5 Quaternary Structure   3.5.1 Subunit Binding   3.5.2 Hemoglobin and Myoglobin   - Reading: Indiana University: The Medical Biochemistry Page: "Myoglobin" Link: Indiana University: The Medical Biochemistry Page: "Myoglobin" (HTML)
 
Instructions: Compare and contrast the structure and mechanisms of myoglobin and hemoglobin.  Focus on how their structure affects their function.
 
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3.6 Folding   3.6.1 Cooperativity   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Protein Folding is a Highly Cooperative Process" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.:  "Protein Folding is a Highly Cooperative Process" (HTML)
 
Instructions: This webpage discusses protein folding.  This webpage also covers section 3.6.2.
 
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3.6.2 Folding Progression   3.6.3 Chaperonins   - Reading: The Open University: Proteins: "Chaperone Help Polypeptides to Fold" Link: The Open University: Proteins: "Chaperone Help Polypeptides to Fold" (HTML)
 
Instructions: Read about chaperones.  Perform the self assessment questions if you would like to test yourself.
 
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3.7 Protein Synthesis   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "A Ribosome Is a Ribonucleoprotein Particle Made of a Small and a Large Subunit" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.:  "A Ribosome Is a Ribonucleoprotein Particle Made of a Small and a Large Subunit"(HTML)
 
Instructions: This webpage discusses protein synthesis.  This webpage also covers sections 3.7.1-3.7.3.
 
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3.7.1 Ribosome 50S and 30S Subunits   3.7.2 Ribosomal Catalytic RNA   3.7.3 Formylmethionyl-tRNA Initiator   3.8 Protein Turnover   - Reading: Baldwin-Wallance College: Cell Biology: "The Ubiquitin System" Link: Baldwin-Wallance College: Cell Biology: "The Ubiquitin System" (HTML)
 
Instructions: Read through the information about ubiquitination of proteins.  This reading covers 3.8.1-3.8.2.
 
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3.8.1 Ubiquitin and Ubiquitination   3.8.2 Proteasome Degradation