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CHEM204: Bioorganic Chemistry

Unit 1: Common Mechanisms in Bioorganic Chemistry   The reaction mechanism is the step-by-step sequence of events in a chemical reaction.  It includes breaking chemical bonds, producingtransition state intermediates, and making chemical bonds.  In this unit, you will start with an overview of the functional groups of organic molecules.  Next, you will study the mechanisms of nucleophilic substitution, electrophilic addition, condensation, elimination, and redox reactions.  The goal is to highlight the fact that these reactions go forward only if the reactants meet specific structural requirements. 
           
Understanding the mechanisms of these reactions is necessary, because they reveal how enzymes speed up similar reactions.  Knowledge of reaction mechanisms also provides a basis for the design of pharmaceutical compounds, which manipulate the yield of reactions, and has implications in the treatment of metabolic diseases.

Unit 1 Time Advisory
This unit should take you approximately 25.75 hours to complete.

☐    Subunit 1.1: 4.5 hours ☐    Readings: 2.5 hours

☐    Web Media: 1 hour

☐    Assessment: 1 hour

☐    Subunit 1.2: 3.75 hours ☐    Subunit 1.2.1: 0.5 hour

☐    Subunit 1.2.2: 3.25 hours

☐    Subunit 1.3: 0.5 hour

☐    Subunit 1.4: 2.5 hours

☐    Subunit 1.5: 7 hours ☐    Subunit 1.5.1: 2 hours

☐    Subunit 1.5.2: 1 hour

☐    Subunit 1.5.3: 1 hour

☐    Subunit 1.5.4: 1.5 hours

☐    Subunit 1.5.5: 1.5 hours

☐    Subunit 1.6: 2.5 hours

☐    Subunit 1.7: 3 hours

☐    Subunit 1.8: 1 hour

☐    Subunit 1.9: 1 hour

Unit1 Learning Outcomes
Upon successful completion of this unit, the student will be able to:
- Explain the processes of electrophilic and nucleophilic reactions. - Identify redox reactions. - Predict the products of substitution, elimination, condensation, and redox reactions. 

1.1 Functional Groups in Biological Chemistry   - Reading: The Third Millennium Online: James Richard Fromm’s “The Concept of Functional Groups” Link: The Third Millennium Online: James Richard Fromm’s “The Concept of Functional Groups” (HTML)
 
Instructions: Please click on the link above, and study this entire webpage, starting at the beginning and continuing until the end of the disulfide group section.  This section summarizes the basic structural characteristics of the functional groups. Alcohols, aldehydes, ketones, carboxylic acids, amines, mercaptans, and esters are the most commonly discussed bioorganic molecules in this course.  While all sugars have hydroxyl and carbonyl functional groups, some of them are aldehydes (reducing sugars) and others are ketones.  Amino acids have both amino and carboxylic functional groups; glycerol and fatty acids in fats and phospholipids, as well as the monomers of DNA and RNA, are joined with ester bonds.  The amino acid cysteine has a thiol group, which is essential for the stabilization of protein structures with disulfide bridges.  Functional groups play an essential role in the active sites of enzymes as well (e.g.the thiol group in the active site of thiol proteases and asparagine in carboxypeptidase). 
 
Reading and note taking will take approximately 2 hours to complete.

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  • Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Classification by Functional Group” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Classification by Functional Group” (HTML)
     
    Instructions: Please click on the link above, and study the “Classification by Functional Group” section on this webpage.  It summarizes the reactivity of the functional groups in table format.  You may want to return to this table when learning about specific examples of these reactions in later units of this course.  
     
    This resource will take approximately 30 minutes to complete.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: Carnegie Mellon University’s “Modern Biology / Biochemistry Flash Tutorials” Link: Carnegie Mellon University’s “Modern Biology / Biochemistry Flash Tutorials” (HTML)
     
    Instructions: Please click on the link above to access thisfunctional group tutorial.  You will find a table on this page with the name and the structural formula of non-polar and polar functional groups in the “Functional Groups” column.  The “Properties” column provides you with several options to choose from.  When you click on an option, the corresponding examples in the “Functional Group” column will be highlighted (e.g. clicking on “non-polar” highlights the methyl and the phenyl groups in the table).  Additionally, if you click on one of the properties, the last column will change from “Examples” to “About non-polar,” and you can read a brief description of the non-polar functional groups.  Please take your time to carefully study the correlations between the properties, functional groups, and definitions in this tutorial.
     
    Studying this resource will take approximately 1 hour to complete.
     
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  • Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Identifying Functional Groups” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Identifying Functional Groups” (HTML)
     
    Instructions: Please click on the link above, readthe instructions at the top of the webpage, and complete the assessment to check how well you recognize functional groups.  You can check whether your responses are correct or incorrect by clicking on the “Check Answer” button.  Please complete the entire quiz before you hit the “View Answers” button to see the complete answer key.  This is the first part of the functional groups problem set. 
     
    This assessment should take approximately 30 minutes to complete.
     
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1.2 Acids, Bases, Electrophiles and Nucleophiles   1.2.1 Acidity and Basicity   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Acidity and Basicity” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Acidity and Basicity” (HTML)
 
Instructions: Please click on the link above, and study the “Acidity and Basicity” section on this webpage for a review of acidity and basicity.  
 
This resource will take approximately 30 minutes to complete.
 
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1.2.2 Nucleophilicity and Basicity   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleophilicity and Basicity” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleophilicity and Basicity” (HTML)
 
Instructions: Please click on the link above, and study the “Nucleophilicity and Basicity Factors in Organic Reactions” and “Acid Base Catalysis” sections on this webpage.  Pay particular attention to the definition of Nucleophilicity as well as the figures that show bonding of electrophilic and nucleophilic sites in reactant molecules.
 
This resource will take approximately 1 hour and 30 minutes to complete.
 
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  • Lecture: Khan Academy’s “Nucleophilicity (Nucleophile Strength)” Link: Khan Academy’s “Nucleophilicity (Nucleophile Strength)” (YouTube)
     
    Instructions: Please click on the link above, and take notes as you watch this video lecture (14 minutes).  The video explains nucleophilicity and how to predict nucleophile strength.  Listen to the presentation carefully two or three times until you are able to explain what nucleophilicity is and how to predict nucleophile strength.  
     
    Viewing this lecture several times and pausing to take notes should take approximately 1 hour to complete.
     
    Terms of Use: This video is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States License.  It is attributed to the Khan Academy.

  • Lecture: Khan Academy’s “Nucleophilicity vs. Basicity” Link: Khan Academy’s “Nucleophilicity vs. Basicity” (YouTube)
     
    Instructions: Please watch the video (13 minutes).  Listen to the presentation carefully two or three times as needed until you are able to compare and contrast nucleophilicity and basicity yourself.  
     
    Viewing this lecture several times and pausing to take notes should take approximately 45 minutes to complete.
     
    Terms of Use: This video is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States License.  It is attributed to the Khan Academy.

1.3 Mechanisms: Electrophilic Addition Reactions   - Reading: Chemguide: Jim Clark’s “Electrophilic Addition” Link: Chemguide: Jim Clark’s “Electrophilic Addition” (HTML)
 
Instructions: Please click on the link above, and study this webpage for a general overview of electrophilic addition.  
 
Reading and taking notes will take approximately 30 minutes to complete.
 
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1.4 Mechanisms: Nucleophilic Substitution Reactions   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Mechanisms of Nucleophilic Substitution Reactions” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Mechanisms of Nucleophilic Substitution Reactions” (HTML)
 
Instructions: Please click on the link above, and study this entire webpage.  In section "The SN1 Mechanism," you will find a graph; note the energy profile of nucleophilic substitutions.  Take advantage of the animations that are linked to the SN1 and SN2 substitutions; to access these, press the “Click Here” buttons at the end of the "SN1 Mechanism" and "SN2 Mechanism" sections.  
 
Studying this resource and note taking will take approximately 2 hours and 30 minutes to complete.
 
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1.5 Mechanisms: Nucleophilic Carbonyl Addition Reactions   1.5.1 Nucleophilic Addition Reactions   - Reading: Chemguide: Jim Clark’s “The Reduction of Aldehydes and Ketones” Link: Chemguide: Jim Clark’s “The Reduction of Aldehydes and Ketones” (HTML)
 
Instructions: Please click on the link above, and study this webpage for a general overview of electrophilic addition.  The first part of this website shows generalized chemical equations of the reduction of aldehydes and ketones.  In these equations, the reducing hydrogen is marked as [H].  Please note that the reducing hydrogen is delivered as part of another molecule; this is symbolized by the square brackets.  The second part of this website describes the mechanism of the nucleophilic addition; this includes "The simplified mechanisms," the "The mechanism for reduction of ethanal," and the "The mechanism for the reduction of propanone" sections.  Please make sure that you understand how the electrons are moving during the nucleophilic addition.  Next, test your knowledge: on a separate sheet of paper, write down the mechanism without looking at the website.  Finally, compare your work to the website; you are done if the movement of the electrons is correct.  
 
This resource will take approximately 2 hours to complete.
 
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1.5.2 Alcohol Formation   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Aldehydes & Ketones” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Aldehydes & Ketones” (HTML)
 
Instructions: Please click on the link above, and study the “A. Hydration and Hemiacetal Formation” section on this page.  Make sure to select "Click Here" in the "Stable Hydrates and Hemiacetals" box, and study these example reactions.  Note that hemiacetals and acetals form when simple sugars undergo a spontaneous rearrangement in an aqueous solution.  
 
Studying this resource will take approximately 1 hour to complete.
 
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1.5.3 Imine (Schiff Base) Formation   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “C. Formation of Imines and Related Compounds” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “C. Formation of Imines and Related Compounds” (HTML)

 Instructions: Please click on the link above, and study the “C.
Formation of Imines and Related Compounds” section on this webpage.
 Clicking on the grey “Imine Formation” button opens a new window
with an animation of the imine formation reaction.  

 Studying this resource will take approximately 1 hour to
complete.  

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1.5.4 Acetal Formation   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “B. Acetal Formation” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “B. Acetal Formation” (HTML)

 Instructions: Please click on the link above, and study the “B.
Acetal Formation” section on this webpage.  Note that hemiacetals
and acetals form when simple sugars undergo a spontaneous
rearrangement in an aqueous solution.  
    
 Studying this resource will take approximately 1 hour to
complete.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “The Mechanism of Acetal Formation” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “The Mechanism of Acetal Formation” (HTML)

    Instructions: Please click on the link above, read the instructions for this assessment, and answer all the questions provided.  This exercise will guide you step-by-step through the mechanism of acetal formation.  You will answer five questions, and you will receive immediate feedback after each response.  The last webpage of assessment is the summary page, and it will show you the five steps of the acetal formation reaction.
     
    This assessment should take approximately 30 minutes to complete.
     
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1.5.5 Conjugate (1, 4) Nucleophilic Additions   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “3. Conjugate Addition Reactions” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “3. Conjugate Addition Reactions” (HTML)

 Instructions: Please click on the link above, and study the "3.
Conjugate Addition Reactions" section on this webpage.  Click on the
grey "Nucleophilic Addition" button to view 1,2- and
1,4-additions.  
    
 Studying this resource will take approximately 1 hour and 30
minutes to complete.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

1.6 Mechanisms: Nucleophilic Acyl Substitution Reactions   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “1. Acyl Group Substitution” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “1. Acyl Group Substitution” (HTML)
 
Instructions: Please click on the link above, and study the “1. Acyl Group Substitution” section on this webpage.  Select the “Click Here” link to access the “Mechanism of Ester Cleavage” page, and study the mechanism of ester hydrolysis.  Note that ester cleavage is the first step of fat catabolism in the cell.  
 
Studying this resource and note taking should take approximately 2 hours and 30 minutes to complete.
 
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1.7 Mechanisms: Carbonyl Condensation Reactions   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Reactions at the ?-Carbon” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Reactions at the α-Carbon” (HTML)
 
Instructions: Please click on the link above, scroll down to “2. Claisen Condensation,” and study this particular section on this webpage.  Press the grey “Structural Analysis” button to highlight the nucleophilic donor and electrophilic acceptor in this reaction.  Click on the “Reaction Mechanism” button to display the breaking and forming of chemical bonds.  Fatty acid synthesis by fatty acid synthase is an example of Claisen condensation.
 
Studying this resource and note taking should take approximately 2 hours to complete.
 
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  • Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Claisen Condensation” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Claisen Condensation” (HTML)
     
    Instructions: Please click on the link above to access the assessment, and read the instructions at the top of the webpage.  On this webpage, you will find five examples of Claisen products.  The exercise asks you to identify the enolate donor and carbonyl acceptor of these products from a list.  Click on “Check Answers” after you match all products with their enolate donor and carbonyl acceptor.  The “View Answers” button lets you see the correct answers.  
     
    This assessment will take approximately 1 hour to complete.
     
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1.8 Mechanisms: Elimination Reactions   - Reading: Purdue University’s Organic Reactions Link: Purdue University’s “Organic Reactions” (HTML)
 
Instructions: Please click on the link above, select “Elimination Reactions” in the box at the top of the webpage, and study this entire section.  
 
Studying this resource will take approximately 1 hour to complete.
 
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1.9 Oxidations and Reductions   - Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Oxidation and Reduction Reactions” Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Oxidation and Reduction Reactions” (HTML)
 
Instructions: Please click on the link above, and study the “Oxidation and Reduction Reactions” section on this webpage.  Both catabolic and anabolic pathways incorporated redox reactions (e.g.into glycolysis and gluconeogenesis).  
 
Studying this resource will take approximately 1 hour to complete.
 
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