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Bioinorganic Chemistry

Purpose of Course  showclose

This course will teach you the important role that metal ions play in key biological processes.  You will learn that many biological functions are performed at the cellular level by metal ions that are incorporated into the activation sites of proteins and enzymes.  For example, when oxygen is transported through blood in the human body, it is bound to iron ions that are incorporated into the hemoglobin protein.  In order to function properly, these iron ions must be high-spin and in their +2 oxidation state.  As you progress through this course, you will learn about these and other requirements and mechanisms that must be present in order to facilitate critical biological functions.

You will begin this course by reviewing the basic principles of inorganic chemistry, biochemistry, and molecular biology.  Following a brief overview of the spectroscopy methods that scientists use in the study of metals that contain protein, you will explore the structures of the most relevant metal centers in biological molecules, focusing in particular on non-redox enzymes, electron-transfer copper-based and iron-based proteins, nitrogen-fixation proteins, nitrification and denitrification proteins, and oxygen-transporting proteins.

This course will help you to recognize the importance of inorganic molecules in supporting organic biological systems.  As you progress through this course, you not only will gain an understanding of some very complex macromolecules that rely on metal centers; you also will gain insight into recent scientific developments that utilize key metal ions for breakthrough medical purposes.

Course Information  showclose

Welcome to CHEM203, Bioinorganic Chemistry.  Below, please find general information on this course and its requirements.
 
Primary Resources: This course uses a range of different free, online educational materials, including an online textbook, journal articles, and course lecture notes.  The primary resources used in this course are:
Due to the frequency with which the online textbook Bioinorganic Chemistry, listed above, is used as a resource in this course, you may wish to download the entire textbook PDF and save it to your desktop or a folder on your personal computer for use as a quick reference as needed.
 
Requirements for Completion: In order to complete this course, you will need to work through each unit and all of its assigned readings and materials.  In addition, you will need to successfully pass the Final Exam with a score of 70% or higher.
 
Please note that you will receive an official grade only on your Final Exam.  However, in order to adequately prepare for this exam, you will need to complete and review all the assigned materials in this course.  It is therefore recommended that you take thorough notes as you work through each assignment.
 
Your score on the Final Exam will be tabulated as soon as you complete it.  If you do not pass the Final Exam, you may take it again.
 
Time Commitment: This course should take you a total of approximately 75 hours to complete.  Each unit of this course includes time advisories that list the amount of time you are expected to spend on each subunit and assignment.  It may be useful for you to take a look at these time advisories and determine how much time you have over the next few weeks to complete each unit, and then set goals for yourself.  For example, unit 1 should take you approximately 9.5 hours to complete.  Perhaps you can sit down with your calendar and decide to complete subunits 1.1, 1.2, and 1.3 (estimated at 2.5 hours) on Monday night; subunit 1.4 (estimated at 6 hours) on Tuesday and Wednesday nights, and so on.  Once you have worked through all the course materials, be sure to factor in significant additional time for reviewing your readings and notes before you attempt to take the Final Exam.
 
Tips/Suggestions: As noted in the “Course Requirements” section, there are several prerequisites for this course.  Because this is an advanced, interdisciplinary chemistry course, the requirements for this course include a firm grasp of analytical chemistry, inorganic chemistry, and biochemistry.  As such, as you work through this course, it may be helpful for you to review related concepts from Saylor's CHEM107: Inorganic Chemistry, CHEM108: Analytical Chemistry, and CHEM109: Biochemistry.  If at any time you begin to feel lost, you also may want to revisit foundational concepts from any of the prerequisite courses.  As stated in the “Tips/Suggestions” and “Time Commitment” sections, you should take thorough notes for each assignment and review them frequently in order to master the material.  These notes will serve as a useful review tool for you as you study for the Final Exam.

Learning Outcomes  showclose

Upon successful completion of this course, the student should be able to:
  • Demonstrate proficiency in the basic principles of inorganic chemistry, biochemistry, and molecular biology that are necessary to approach the field of bioinorganic chemistry.
  • Identify the appropriate analytical techniques that are useful in characterizing transition-metal complexes in biological molecules.
  • Describe the different processes involved in the transport and storage of metal ions.
  • Describe the role of metal ions that are involved in electron-transfer reactions in biological systems. 
  • Describe the most common metal centers for electron-transfer reactions—those based on copper and iron ions. 
  • Summarize the role of metal centers in the enzymes that are involved in the nitrogen cycle.
  • Describe how oxygen is transported through the human body and transferred to each biological entity that requires it; identify which metal centers perform these tasks.
  • Describe the different metal-activation sites in enzymes that are involved in the incorporation of oxygen atoms into bio-organic molecules.
  • Describe the functions of metals in plant- and algal-based systems.
  • List some of the historic and current medical applications of metal ions. 

Course Requirements  showclose

In order to take this course, you must:
 
√    Have access to a computer.

√    Have continuous broadband Internet access.

√    Have the ability and permission to install plug-ins and/or software (e.g. Adobe Reader or Flash).

√    Have the ability to download and save files and documents to a computer.

√    Have the ability to open Microsoft Office files and documents (.doc, .docx, .ppt, .xls, etc.).

√    Have competency in the English language.

√    Have read the Saylor Student Handbook.

√    Have successfully completed all Pre-Requisitesfor Saylor's Chemistry discipline (CHEM001, CHEM002, CHEM003, and CHEM004), or their equivalents.

√    Have successfully completed Saylor's General Chemistry I and II (CHEM101 and CHEM102) from The Core Program of Saylor's Chemistry discipline (or their equivalents).

√    In addition, have successfully completed the following Saylor courses (or their equivalents): CHEM107: Inorganic Chemistry, CHEM108: Analytical Chemistry, and CHEM109: Biochemistry.

Unit Outline show close


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  • Unit 1: An Introduction To Bioinorganic Chemistry  

    This introductory unit will provide you with the foundational tools that you will need to understand new concepts developed later in this course, regardless of your background in the field.  You will review important ideas from inorganic chemistry and take a closer look at the basic properties of enzymes, proteins, and peptides that you may have learned about in other courses on biochemistry and molecular biology.  As you progress through this unit, you will discover that many biological molecules, from oxygen-transport proteins to enzymes, require metal ions in order to function.  

    Unit 1 Time Advisory   show close
    Unit 1 Learning Outcomes   show close
  • 1.1 A Review of Basic Principles in Biochemistry and Molecular Biology  
    • Reading: Wells College: Special Topics in Inorganic Chemistry: Bioinorganic Chemistry: Dr. Christopher T. Bailey’s “Principles in Bioinorganic Chemistry”

      Link: Wells College: Special Topics in Inorganic Chemistry: Bioinorganic Chemistry: Dr. Christopher T. Bailey’s “Principles in Bioinorganic Chemistry” (PowerPoint)
       
      Instructions: Please click on the link above and scroll down the webpage to find the link for section I, titled “Principles in Bioinorganic Chemistry.”  Click on this link to download and open Dr. Bailey’s PowerPoint presentation on the basic concepts of bioinorganic chemistry.  Please read the entire presentation.  This material gives you a brief introduction to the link between biology and chemistry, a connection that you will develop further as you progress through this course. 
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

  • 1.2 Macromolecules in Biology  
    • Reading: The University of New Mexico: Cara Lea Council-Garcia’s “Biological Macromolecules”

      Link: The University of New Mexico: Cara Lea Council-Garcia’s “Biological Macromolecules” (HTML)

      Instructions: Please click on the link above to access and read through the entire webpage for a review of macromolecules that have chemical and biological importance, including carbohydrates, lipids, proteins, and nucleic acids.  As needed, you also can explore the additional resource links provided throughout the text for more detailed information on each class of compounds.  Although they do not have an answer key, the review questions at the bottom of the webpage may also assist you in mastering this material.

      This reading should take you approximately 1 hour and 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 1.3 Peptides and Proteins  
  • 1.4 A Review of Chemical Bonding in Transition-Metal Coordination Compounds  
    • Reading: Wells College: Special Topics in Inorganic Chemistry: Bioinorganic Chemistry: Dr. Christopher T. Bailey’s “Transition Metal Chemistry”

      Link: Wells College: Special Topics in Inorganic Chemistry: Bioinorganic Chemistry: Dr. Christopher T. Bailey’s “Transition Metal Chemistry” (PowerPoint)
       
      Instructions: Please click on the link above and scroll down the webpage to find the link for section III, titled “Transition Metal Chemistry.”  Click on this link to download and open Dr. Bailey’s PowerPoint presentation on the principles of coordination chemistry.  Please read the entire presentation. 
       
      As you progress through this reading, make sure you understand the different effects that ligands and chelation can have on the energy levels and magnetic properties of transition metals.  Also be sure that you understand the general principle behind the hard/soft-acid/base concept (also known as HSAB theory).  Keep in mind how HSAB theory may be applied to metal toxicity and substitutions in biological systems. 
       
      Please note that the topics included in this reading also cover material you need to know for sub-subunits 1.4.1-1.4.5, found below.  When you reach those sub-subunits, you may find it helpful to return to this reading in order to review specific concepts.
       
      This reading should take you approximately 1 hour to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

    • Reading: Indian Institute of Technology Bombay: Inorganic Chemistry: Dr. R. Murugavel’s “Lecture 3 – Transition Metal Complexes”

      Link: Indian Institute of Technology Bombay: Inorganic Chemistry: Dr. R. Murugavel’s “Lecture 3 – Transition Metal Complexes” (PDF)
        
      Instructions: Please click on the link above and scroll down the webpage to find the link for Dr. Murugavel’s “Lecture 3 – Transition Metal Complexes.”  Click on this link to access an online PDF version of Dr. Murugavel’s PowerPoint presentation on transition-metal complexes.  Please read the entire presentation. 
       
      Note that material in this reading includes a review of some of the concepts introduced in Saylor’s CHEM107 and covered more extensively in Saylor’s CHEM202.  For this reading, focus on how and why the orbitals split as well as the properties – such as magnetism and bonding – that differ between high-spin and low-spin systems. 
       
      Please note that the topics covered in this presentation also encompass some of the material you need to know for sub-subunits 1.4.1-1.4.5, found below.  When you reach those sub-subunits, you may find it helpful to return to this reading in order to review specific concepts.
        
      This reading should take you approximately 2 hours and 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 1.4.1 Principles of Coordination Chemistry  

    Note: Some of the material you need to know for this sub-subunit is covered in the two readings assigned beneath subunit 1.4, found above.  You may find it helpful to refer back to those materials as you complete the reading assignment below.

    • Reading: The University of California at Davis: ChemWiki’s “Introduction to Coordination Chemistry”

      Link: The University of California at Davis: ChemWiki’s “Introduction to Coordination Chemistry” (HTML)
       
      Instructions: Please click on the link above to access and read the entire webpage.  Note that this material comprises a review of some of the concepts that are covered in Saylor’s CHEM107.  For this reading, focus in particular on understanding how a metal binds its ligands, as this is a process that it is imperative for you to know in order to understand biomolecular interactions with metal centers, a topic developed in detail later in this course.
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 1.4.2 Closed- and Open-Shell Coordination Compounds  

    Note: The material you need to know for this sub-subunit is covered in the two readings assigned beneath subunit 1.4, found above.  At this time, please return to those readings to review the concept of closed- and open-shell coordination compounds.  Your review of this material should take you approximately 30 minutes to complete.

  • 1.4.3 High-Spin Complexes, Low-Spin Complexes, and Magnetism  

    Note: The material you need to know for this sub-subunit is covered in the two readings assigned beneath subunit 1.4, found above.  At this time, please return to those readings to review the concepts of high-spin complexes, low-spin complexes, and magnetism.  Your review of this material should take you approximately 30 minutes to complete.

  • 1.4.4 Hard and Soft Acids and Bases  

    Note: The material you need to know for this sub-subunit is covered in the two readings assigned beneath subunit 1.4, found above.  At this time, please return to those readings to review the concept of hard and soft acids and bases.  Your review of this material should take you approximately 30 minutes to complete.

  • 1.4.5 Crystal Field Theory, Ligand Field Theory, and Spectrochemical Series  

    Note: The material you need to know for this sub-subunit is covered in the two readings assigned beneath subunit 1.4, found above.  At this time, please return to those readings to review the topics of crystal field theory, ligand field theory, and spectrochemical series.  Your review of this material should take you approximately 30 minutes to complete.

  • 1.5 Metal Ions and Metal Clusters in Biological Systems  
    • Reading: The Indian Institute of Technology Bombay: Inorganic Chemistry: Dr. R. Murugavel’s “Lecture 5 – Bioinorganic Chemistry”

      Link: The Indian Institute of Technology Bombay: Inorganic Chemistry: Dr. R. Murugavel’s “Lecture 5 – Bioinorganic Chemistry” (PDF)
        
      Instructions: Please click on the link above and scroll down the webpage to find the link for Dr. Murugavel’s “Lecture 5 – Bioinorganic Chemistry.”  Click on this link to access an online PDF version of Dr. Murugavel’s PowerPoint presentation on bioinorganic chemistry. 
       
      This reading introduces you to some important foundational topics, including enzyme activation sites, enzyme activity, and enzyme specificity, in addition to enzyme-substrate formation and cooperativity.  Keep these general concepts in mind as you learn about specific enzymes in more detail throughout this course.
       
      This reading should take you approximately 1 hour to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Unit 2: An Overview of Characterization Methods in Bioinorganic Chemistry  

    The structures of the metal-containing residues in biological molecules can be discovered by using a variety of spectroscopy methods and techniques.  Methods used for structural elucidation, as well as mechanistic studies, include: X-Ray crystallography; nuclear magnetic resonance (NMR) spectroscopy; vibrational spectroscopies, such as infrared (IR) and Raman spectroscopies; and electronic spectroscopies, such as ultraviolet-visible (UV-Vis) spectroscopy and electron paramagnetic resonance (EPR) spectroscopy. In this unit, you will review the basic principles of these analytical techniques and explore their application to inorganic biomolecules.

    Unit 2 Time Advisory   show close
    Unit 2 Learning Outcomes   show close
  • 2.1 X-Ray Crystallography: Resolving Protein Structures  
    • Reading: Wells College: Special Topics in Inorganic Chemistry: Bioinorganic Chemistry: Dr. Christopher T. Bailey’s “Analytical Methods”

      Link: Wells College: Special Topics in Inorganic Chemistry: Bioinorganic Chemistry: Dr. Christopher T. Bailey’s “Analytical Methods” (PowerPoint)
       
      Instructions: Please click on the link above and scroll down the webpage to find the link for section IV, titled “Analytical Methods.”  Click on this link to download and open Dr. Bailey’s PowerPoint presentation on the different analytical methods used in bioinorganic chemistry.  Please read the entire presentation for an overview of these methods. Take note that X-Ray crystallography is the only analytical method that looks at the entire structure of the molecule.  Other spectroscopies focus solely on the metal center.  In fact, Mössbauer spectroscopy (discussed in detail later in this course) is used specifically for studying iron in biological systems.
       
      Please note that this presentation also covers some of the material you need to know for subunits 2.2-2.5, found below.  When you reach those sub-subunits, you may find it helpful to return to this reading in order to review specific concepts.
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

    • Reading: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “X-Ray Crystallography” and “X-Ray Absorption Spectroscopy”

      Link: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “X-Ray Crystallography” and “X-Ray Absorption Spectroscopy” (HTML)
        
      Instructions: Please click on the links above to access and read the two webpages for an overview of X-Ray crystallography and X-Ray absorption spectroscopy.  Read both webpages in their entirety.  This material gives you a concise summary of the applications of X-Ray crystallography and X-ray absorption spectroscopy in the study of bioinorganic systems.
        
      This reading should take you approximately 30 minutes to complete.
        
      Terms of Use: Please respect the copyright and terms of use displayed on the webpages above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

  • 2.2 Nuclear Magnetic Resonance (or Paramagnetic NMR) Spectroscopy  

    Note: Some of the material you need to know for this subunit is covered in the first reading assigned beneath subunit 2.1 of this course, in particular slides 4 and 5 of Dr. Bailey’s PowerPoint presentation.  You may find it helpful to refer back to those slides as you complete the reading below.

    • Reading: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Nuclear Magnetic Resonance Spectroscopy”

      Link: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Nuclear Magnetic Resonance Spectroscopy” (HTML)
       
      Instructions: Please click on the link above to access and read the webpage in its entirety for an overview of nuclear magnetic resonance spectroscopy (also known as NMR or Paramagnetic NMR spectroscopy).  This material gives you a concise summary of the pros and cons of using NMR spectroscopy to study bioinorganic systems.  For a more detailed understanding of NMR spectroscopy, please refer to subunit 2.4 of Saylor’s CHEM108.
       
      This reading should take you approximately 30 minutes to complete.
        
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

  • 2.3 Electronic Spectroscopy (UV-Vis Spectroscopy and Magnetic Circular Dichroism)  

    Note: Some of the material you need to know for this subunit is covered in the first reading assigned beneath subunit 2.1 of this course, in particular slides 6 and 7 of Dr. Bailey’s PowerPoint presentation.  You may find it helpful to refer back to those slides as you complete the reading below.

    • Reading: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Magnetic Circular Dichroism (MCD) Spectroscopy”

      Link: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Magnetic Circular Dichroism (MCD) Spectroscopy” (HTML)
       
      Instructions: Please click on the link above to access and read the webpage in its entirety for an overview of magnetic circular dichroism (or MCD) spectroscopy.  This material gives you a concise summary of the application of MCD spectroscopy to the study of bioinorganic systems.  Please note that both MCD and UV-Vis spectroscopies probe the electronic states of molecules.  For a more detailed understanding of UV-Vis spectroscopy, please refer to sub-subunit 2.3.1 of Saylor’s CHEM108.
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

  • 2.4 Vibrational Spectroscopy (Infrared (IR), Raman, and Resonance Raman)  

    Note: Some of the material you need to know for this subunit is covered in the first reading assigned beneath subunit 2.1 of this course, in particular slide 8 of Dr. Bailey’s PowerPoint presentation.  You may find it helpful to refer to that slide as you complete the reading below.

    • Reading: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Resonance Raman Spectroscopy”

      Link: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Resonance Raman Spectroscopy” (HTML)
       
      Instructions: Please click on the link above to access and read the webpage in its entirety for an overview of resonance Raman spectroscopy. This material gives you a concise summary of the application of resonance Raman spectroscopy to the study of bioinorganic systems.  Resonance Raman is a specialized type of Raman spectroscopy in which laser light is tuned to certain frequencies based on the molecule (as opposed to a general laser application).
       
      For a review of infrared (IR) spectroscopy, please refer to sub-subunit 2.3.2 of Saylor’s CHEM108. Note that vibrational modes for molecules can be either IR-active, Raman-active, both, or neither.  The spectroscopic method used for a particular molecule is based on predictions from group theory.
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

  • 2.5 Mössbauer Spectroscopy  

    Note: Some of the material you need to know for this subunit is covered in the first reading assigned beneath subunit 2.1 of this course, in particular slides 9 and 10 of Dr. Bailey’s PowerPoint presentation.  You may find it helpful to refer back to those slides as you complete the reading below.

    • Reading: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Mössbauer Spectroscopy”

      Link: The University of Georgia’s Center for Metalloenzyme Studies: MRIL Biophysics Module’s “Mössbauer Spectroscopy” (HTML)
       
      Instructions: Please click on the link above to access and read the webpage in its entirety for an overview of Mössbauer spectroscopy.  This material gives you a concise summary of the application of Mössbauer spectroscopy to the study of bioinorganic systems. 
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials

  • 2.6 Electron Paramagnetic Resonance (EPR) Spectroscopy  
  • Unit 3: Metal Ion Transport and Storage  

    Transition-metal ions such as iron, copper, and zinc are essential components of key biological molecules that exist within all living organisms.  These metal ions are obtained by living organisms through their diet and then are transported into and stored by cells until they are needed for the synthesis of a particular protein or enzyme.  In this unit of the course, you will explore this process of transportation and storage in great detail.

    Unit 3 Time Advisory   show close
    Unit 3 Learning Outcomes   show close
  • 3.1 Transferrin  
    • Reading: Bioinorganic Chemistry: Dr. Elizabeth C. Theil and Dr. Kenneth N. Raymond’s “Chapter 1: Transition-Metal Storage, Transport, and Biomineralization”

      Link: Bioinorganic Chemistry: Dr. Elizabeth C. Theil and Dr. Kenneth N. Raymond’s “Chapter 1: Transition-Metal Storage, Transport, and Biomineralization” (PDF)
       
      Instructions: Please click on the link above to access the webpage for the online textbook.  Then, click on the link for chapter 1 to open the PDF and read chapter 1 in its entirety.  You may also choose to download the PDF for the entire book by clicking on the link at the top of the webpage titled “PDF” and navigating to chapter 1 from there. As you progress through this reading, note the significance that a metal’s oxidation state, coordination chemistry, and abundance play in each of the systems described in the reading.  The unique properties of each metal determine the metal’s specificity for each system. 
       
      Please note that this reading also covers material you need to know for subunits 3.2-3.4, found below.  When you reach those subunits, you may find it helpful to refer back to this reading for review.
       
      This reading, including note-taking, should take you approximately 4 hours to complete.
        
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 3.2 Ferritin  

    Note: Some of the material you need to know for this subunit is covered in the textbook reading assigned beneath subunit 3.1, found above.  You may find it helpful to refer back to that material as you complete the reading below.

  • 3.3 Siderophores  

    Note: Some of the material you need to know for this subunit is covered in the textbook reading assigned beneath subunit 3.1, found above.  You may find it helpful to refer back to that material as you complete the reading below.

  • 3.4 Metallothioneins  

    Note: Some of the material you need to know for this subunit is covered in the textbook reading assigned beneath subunit 3.1, found above.  Section II.A.2 of the textbook, which begins on page 16, specifically covers metallothioneins; you may find it helpful to refer back to that section as you complete the reading below.

  • 3.5 Copper-Transporting ATPases  
  • 3.6 Metallochaperones  
  • Unit 4: Electron Transfer in Biological Systems  

    Electrons are continuously supplied and removed during the course of biological processes.  Because transition metals can take on multiple oxidation states, they are particularly suitable for these electron-transfer tasks.  The most common metal centers for electron-transfer reactions are based on copper and iron cations.  Metal ions also play an essential role in photosynthesis and other processes in plant and algal systems.  In this unit, you will learn about the role and importance of metal ions that are involved in the electron traffic of biological systems – including, in particular, those that are crucial to the processes of plant and algal systems.

    Unit 4 Time Advisory   show close
    Unit 4 Learning Outcomes   show close
  • 4.1 Electron-Transfer Kinetics and the Marcus Theory of Electron Transfer  
    • Reading: Bioinorganic Chemistry: Dr. Harry B. Gray and Dr. Walther R. Ellis, Jr.’s “Chapter 6: Electron Transfer”

      Link: Bioinorganic Chemistry: Dr. Harry B. Gray and Dr. Walther R. Ellis, Jr.’s “Chapter 6: Electron Transfer” (PDF)
       
      Instructions: Please click on the link above to access the online textbook.  Then, scroll down the webpage and click on the link for chapter 6 to open a PDF version of the chapter, which you should read in its entirety.  You may also choose to download the PDF for the entire book and navigate to chapter 6, which begins on page 315.
       
      As you read, keep in mind that, in biological systems,oxidation refers to the addition of oxygen bonds or the removal of hydrogen, while reduction refers to a decrease in the number of bonds to oxygen or an increase in hydrogen.  Also consider the structural effects of biological molecules in terms of long-range and short-range electron transfer.  Note that this chapter also discusses the Marcus theory of electron transfer, beginning in section III, on page 336.  Marcus theory helps explain the probability of outer-sphere (long-range) and inner-sphere (short-range) electron transfer.
       
      Please note that this reading also covers material you need to know for subunit 4.2, found below.  When you reach that subunit, you may find it helpful to refer back to this material for review.
       
      This reading, including note-taking, should take you approximately 6 hours to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 4.2 Photosynthesis  

    Note: Some of the material you need to know for this subunit is covered in the textbook reading assigned beneath subunit 4.1, found above.  You may find it helpful to refer back to that material as you complete the reading below; in particular, focus on the discussion of photosynthesis that occurs on pages 327-330 of the textbook.

  • 4.3 Bio-Redox Agents and Electron-Transfer Mechanisms  
    • Reading: Bioinorganic Chemistry: Dr. Edward I. Stiefel and Dr. Graham N. George’s “Chapter 7: Ferredoxins, Hydrogenases, and Nitrogenases: Metal-Sulfide Proteins”

      Link: Bioinorganic Chemistry: Dr. Edward I. Stiefel and Dr. Graham N. George’s “Chapter 7: Ferredoxins, Hydrogenases, and Nitrogenases: Metal-Sulfide Proteins” (PDF)
       
      Instructions: Please click on the link above to access the online textbook.  Then, scroll down the webpage and click on the link for chapter 7 to open a PDF version of the chapter, which you should read in its entirety.  You may also choose to download the PDF for the entire book and navigate to chapter 7, which begins on page 365. This reading deals with iron-based electron-transfer mechanisms.  Ferredoxins refer to iron-sulfur clusters; hydrogenases utilize other metals, specifically nickel, with iron; and nitrogenase is an iron-based enzyme used in nitrogen fixation. 
       
      Please note that this reading also covers the material you need to know for sub-subunits 4.3.1-4.3.4, found below.  When you reach those sub-subunits, you may find it helpful to refer back to this reading for a review of specific topics.
       
      This reading, including note-taking, should take you approximately 8 hours to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 4.3.1 Iron-Sulfur-Cluster Electron-Transfer Sites  

    Note: The material you need to know for this sub-subunit is covered in the textbook reading assigned beneath subunit 4.3, found above.  Information pertaining specifically to iron-sulfer-cluster electron-transfer sites can be found in section I, on pages 365-400 of the textbook.  Spend approximately 45 minutes reviewing this material before moving on to the next sub-subunit of this course.

  • 4.3.2 Iron Hydrogenases  

    Note: The material you need to know for this sub-subunit is covered in the textbook reading assigned beneath subunit 4.3, found above.  Information pertaining specifically to iron hydrogenases can be found in section II.B.3, on pages 405-409 of the textbook.  (Pages 401-405 cover hydrogenases in general.)  Spend approximately 15 minutes reviewing this material before moving on to the next sub-subunit of this course.

  • 4.3.3 Nickel-Iron Hydrogenases  

    Note: The material you need to know for this sub-subunit is covered in the textbook reading assigned beneath subunit 4.3, found above.  Information pertaining specifically to nickel-iron hydrogenases can be found in section II.B.4, on pages 409-411 of the textbook.  Spend approximately 15 minutes reviewing this material before moving on to the next sub-subunit of this course.

  • 4.3.4 Nitrogenases  

    Note: The material you need to know for this sub-subunit is covered in the textbook reading assigned beneath subunit 4.3, found above.  Information pertaining specifically to nitrogenases can be found on pages 412-444.  Spend approximately 45 minutes reviewing this material before moving on to the next unit of this course.

  • Unit 5: The Nitrogen Cycle: Nitrification, Denitrification, And Fixation  

    The nitrogen element possesses a variety of potential oxidation states.  It could be +3 in compounds such ammonia, -5 in the nitrate ion, or any of the oxidation states in between.  In the nitrogen cycle, nitrogen in the atmosphere enters the food chain through nitrogen-fixing bacteria in the soil and algae in the water.  These bacteria then transform molecular nitrogen into ammonium ions (an 8-electron-transfer reaction!).  These ammonium ions subsequently are oxidized into nitrites, and eventually these nitrites are oxidized into nitrates by bacteria present in the soil and water.  Nitrates then are absorbed by plants through their roots and are used to produce proteins, which can in turn be disseminated through the food chain.  Nitrogen also is released into the environment in various forms through the decomposition of dead organisms and through human and animal waste that subsequently are re-used by bacteria.  In this unit, you will learn about the function of metal centers in the enzymes involved in the nitrogen cycle.

    Unit 5 Time Advisory   show close
    Unit 5 Learning Outcomes   show close
  • 5.1 Nitrification  
    • Reading: The University of Waterloo: Dr. Colin Mayfield’s “Chapter 8: Microbial Ecology of the Nitrogen Cycle”

      Link: The University of Waterloo: Dr. Colin Mayfield’s “Chapter 8: Microbial Ecology of the Nitrogen Cycle” (HTML)
           
      Instructions: Please click on the link above to access and read the entire webpage.
       
      This reading discusses the entire nitrogen cycle, including the processes of nitrification, denitrification, and nitrogen fixation.  The nitrification process converts ammonium to nitrate via a series of enzymatic steps; while denitrification involves a series of steps in which nitrate is reduced ultimately to N2.  This material also provides an explanation for why nitrogen must undergo the nitrogen-fixation process and cannot just be utilized as is from the atmosphere.
       
      Please note that this reading also covers material you need to know for subunits 5.2 and 5.3, found below.  When you reach those subunits, you may find it helpful to refer back to this reading to review specific topics.
           
      This reading, including note-taking, should take you approximately 2 hours and 30 minutes to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 5.2 Denitrification (Reductase)  

    Note: The material you need to know for this subunit is covered in the reading assigned beneath subunit 5.1, found above.  For this subunit, focus on the reading’s description of the processes and enzymes that convert nitrate into nitrogen or ammonia.  Spend approximately 30 minutes reviewing this material before moving on to the next subunit of this course.

  • 5.3 Nitrogen Fixation (Nitrogenase)  

    Note: Some of the material you need to know for this subunit is covered in the reading assigned beneath subunit 5.1, found above—in particular, the reading’s description of the metal clusters used in different biological systems.  In addition, material pertaining specifically to nitrogenases also has been covered in the readings assigned beneath sub-units 4.3 and 4.3.4 of this course.  You may find it helpful to refer back to this previous material as you complete the web media assignment below.

    • Web Media: The University of Toronto Department of Chemistry: Robert H. Morris, Adrian Lee, and Alen Hadzovic’s “A Tour of Nitrogenase”

      Link: The University of Toronto Department of Chemistry: Robert H. Morris, Adrian Lee,and Alen Hadzovic’s “A Tour of Nitrogenase” (HTML and Java)

      Instructions: Please click on the link above to access and read all the material presented in the online tour of nitrogenase.  Please note that this tour requires Java to run; you may need to enable Java on your web browser or download a version of Java to your computer in order to complete this assignment.
       
      This tour provides you with several models of the nitrogenase enzyme and its binding sites. Nitrogenase is actually composed of two enzymes, one Fe-based and the other FeMo-based.  These two enzymes work in tandem to transfer electrons.  Please proceed through the viewing exercise in order, reading the description for each of the models as you progress. 
       
      This web media assignment should take you approximately 1 hour to complete.   
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Unit 6: Oxygen Transport And Transfer  

    Oxygen is essential to many life forms, including human life.  Many human-body functions at the cellular level require oxygen; accordingly, oxygen must be transported through the body and transferred to the biological entity that requires it.  In this unit, you will learn about the metal centers in the activation sites of proteins that are involved in the transport and transfer of oxygen in the human body.

    Unit 6 Time Advisory   show close
    Unit 6 Learning Outcomes   show close
  • 6.1 Transport of O2  
    • Reading: Bioinorganic Chemistry: Dr. Geoffrey B. Jameson and Dr. James A. Ibers’s “Chapter 4: Biological and Synthetic Dioxygen Carriers”

      Link: Bioinorganic Chemistry: Dr. Geoffrey B. Jameson and Dr. James A. Ibers’s “Chapter 4: Biological and Synthetic Dioxygen Carriers” (PDF)
       
      Instructions: Please click on the link above to access the online textbook.  Then, scroll down the webpage and click on the link for chapter 4 to open a PDF version of the chapter, which you should read in its entirety.  You may also choose to download the PDF for the entire book and then navigate to chapter 4, which begins on page 167.
       
      This reading discusses the three main classes of compounds for biological oxygen transport, both in oxygenated and deoxygenated forms.  Hemoglobin is iron-based; hemocyanin is di-copper based; and hemoerythrin is di-iron based.  As you read, pay particular attention to the properties of copper and iron that make them useful for oxygen transport.
       
      Please note that this reading also covers the material you will need to know for subunits 6.2-6.4, found below.  When you reach those subunits, you may find it helpful to refer back to this reading to review specific topics.
       
      This reading, including note-taking, should take you approximately 8 hours to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 6.2 The Hemoglobin Family  

    Note: The material you need to know for this subunit is covered in the reading assigned beneath subunit 6.1, found above.  Specific information on the hemoglobin family can be found in section I.B.1, on pages 184-185 of the textbook.  In addition, information about oxyhemoglobin can be found in section II.F.2 of the textbook, on page 213.  Spend approximately 30 minutes reviewing this material before moving on to the next subunit of this course.

  • 6.3 The Hemocyanin Family  

    Note: The material you need to know for this subunit is covered in the reading assigned beneath subunit 6.1, found above.  Specific information on the hemocyanin family can be found in section I.B.2, on pages 185-188 of the textbook.  In addition, information about oxyhemocyanin can be found in section II.F.1, on pages 210-212 of the textbook.  Spend approximately 30 minutes reviewing this material before moving on to the next subunit of this course.

  • 6.4 The Hemerythrin Family  

    Note: The material you need to know for this subunit is covered in the reading assigned beneath subunit 6.1, found above.  Specific information on the hemerythrin family can be found in section I.B.3, on pages 188-190 of the textbook.  In addition, information about oxyhemerythrin can be found in section II.F.1, on pages 210-212 of the textbook.  Spend approximately 30 minutes reviewing this material before moving on to the next unit of this course.

  • Unit 7: The Enzymes And Proteins Used For Oxygen Processing  

    Once oxygen is transported and transferred to the desired site, it needs to be incorporated into bio-organic molecules.  This process occurs via several chemical reactions, such as hydroxylations and oxygenations.  Different enzymes catalyze these reactions, but they all use metal ions in their activation centers.  In this unit, you will learn about the structures and functions of the metals involved in these processes.

    Unit 7 Time Advisory   show close
    Unit 7 Learning Outcomes   show close
  • 7.1 Superoxide Dismutase (SOD)  
    • Reading: Bioinorganic Chemistry: Dr. Joan Selverstone Valentine’s “Chapter 5: Dioxygen Reactions”

      Link: Bioinorganic Chemistry: Dr. Joan Selverstone Valentine’s “Chapter 5: Dioxygen Reactions” (PDF)
       
      Instructions: Please click on the link above to access the online textbook.  Then, scroll down the webpage and click on the link for chapter 5 to open a PDF version of the chapter, which you should read in its entirety.  You may also choose to download a PDF of the entire book at the top of the webpage, and then navigate to chapter 5, which begins on page 253.
       
      In this reading you will discover that oxygen, essential for aerobic life, also can cause dioxygen toxicity in high concentrations.  Superoxide dismutase, catalases, and peroxidases work together to remove excess dioxygen as well as the unwanted side products of dioxygen reactions.  For this subunit, focus in particular on superoxide dismutase, or SOD, specifically covered in section VII of the textbook, on pages 298-310.
       
      Please note that this reading also covers material you need to know for subunits 7.2-7.3, found below.  When you reach those subunits, you may find it helpful to refer back to this reading to review specific topics.
       
      This reading, including note-taking, should take you approximately 6 hours to complete.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

    • Reading: Wikipedia’s “Superoxide Dismutase”

      Link: Wikipedia’s “Superoxide Dismutase” (PDF)

      Instructions: Please click on the link above to access and read the entire Wikipedia entry on superoxide dismutase.  This material gives you a relatively concise description of superoxide dismutase, or SOD, which can be Zn/Fe- based, Fe/Mn-based, or Ni-based, depending on the biological species in which it is present.  This topic is covered in more detail in Bioinorganic Chemistry, the online textbook featured in this course.  If you find yourself struggling with understanding any of the material presented in this reading, you may find it helpful to refer back to page 191 from chapter 4 of the textbook, as well as pages 263, 265-266, and 298-305 from chapter 5.
             
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0. You can find the original Wikipedia version of this article here.

  • 7.2 Catalase  
    • Reading: Wikipedia’s “Catalase”

      Link: Wikipedia’s “Catalase” (PDF)

      Instructions: Please click on the link above to access and read the entire Wikipedia entry, which gives you a relatively concise description of catalase.  Catalase is the iron-based enzyme responsible for the breakdown of hydrogen peroxide, a harmful byproduct of several metabolic processes.  This topic is covered in more detail in Bioinorganic Chemistry, the online textbook featured in this course.  If you find yourself struggling with understanding any of the material presented in this reading, you may find it helpful to refer back to page 191 from chapter 4 of the textbook, as well as pages 263 and 295-298 from chapter 5.
       
      This reading should take you approximately 30 minutes to complete.
       
      Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0. You can find the original Wikipedia version of this article here.

  • 7.3 Peroxidase  
    • Reading: Wikipedia’s “Peroxidase”

      Link: Wikipedia’s “Peroxidase” (PDF)

      Instructions: Please click on the link above to access and read the entire webpage.  This material gives you a general description of peroxidase.  Peroxidase is similar to catalase, since both are iron-based enzymes that break down hydrogen peroxide; however, peroxidases have a much more general substrate and can break down other types of biological peroxides as well.  This topic is covered in more detail in Bioinorganic Chemistry, the online textbook featured in this course.  If you find yourself struggling with understanding any of the material in this reading, you may find it helpful to refer back to pages 263 and 295-298 from chapter 5 of the textbook.
             
      This reading should take you approximately 15 minutes to complete.
       
      Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0. You can find the original Wikipedia version of this article here.

  • Unit 8: Toxicology And Medical Applications  

    Several metal ions are essential to biological functions in humans, and deficiencies in these ions can lead to serious adverse health effects.  Yet, these same metal ions that are beneficial also can act as toxins to biological organisms in higher doses or under different applications.  However, when used in specific ways, some metals also have been utilized in a variety of medical applications.  Medical applications of metal ions range from diagnostic uses to therapeutic uses, including drug delivery systems.  In this unit, you will examine both the necessity and toxicity of certain metal ions.  You also will learn about some therapeutic medical uses of these ions, such as their contribution to anti-arthritic compounds and anti-cancer agents.  In addition, you will explore some key medical diagnostic techniques that rely on metal ions, such as MRI scans and nuclear imaging.  You will conclude this unit with a look at some of the more recent developments in the medical applications of metals, including the use of metals in antimicrobials, which fight harmful bacteria and fungi; insulin-mimetics, which aim to treat diabetes; and even antidepressants, for the treatment of mental illness.

    Unit 8 Time Advisory   show close
    Unit 8 Learning Outcomes   show close
  • 8.1 Essential Metals and Metal Toxicity  
    • Reading: Bioinorganic Chemistry: Dr. Stephen J. Lippard’s “Chapter 9: Metals in Medicine”

      Link: Bioinorganic Chemistry: Dr. Stephen J. Lippard’s “Chapter 9: Metals in Medicine” (PDF)
       
      Instructions: Please click on the link above to access the online textbook.  Then, scroll down the webpage and click on the link for chapter 9 to open a PDF version of the chapter, which you should read in its entirety.  You may also choose to download a PDF of the entire book and then navigate to chapter 9, which begins on page 505. 
       
      Throughout this course, we have discussed the biological significance of several metal ions, including copper, iron, and zinc.  For this subunit, focus in particular on sections II (“Metal Deficiency and Disease,” beginning on page 506) and III (“Toxic Effects of Metals,” beginning on page 508) of chapter 9 in the textbook.  This material describes what happens when you have too much or too little of these biologically important cations.
       
      Please note that this reading also covers material you need to know for subunits 8.2-8.4, found below.  When you reach those subunits, you will receive further instructions for a targeted review of this reading.
       
      This reading, including note-taking, should take you approximately 8 hours to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

    • Reading: The University of Glasgow: Dr. Lee Cronin’s Metals in Medicine

      Link: The University of Glasgow: Dr. Lee Cronin’s Metals in Medicine (PDF)
       
      Instructions: Please click on the link above to access Dr. Cronin’s webpage.  Then, click on the link in the middle of the webpage titled “Full Metals in Medicine Lecture Course” to open a PDF version of the lecture slides.  Please read the slides in their entirety, but focus specifically on slides 6-9, beginning with “The biomedical periodic table” and ending with “Chemical Considerations.”  Notice that we are revisiting the concepts of oxidation states, ligand binding, and HSAB theory when we consider metal ions for medical uses.  
       
      Please note that this reading also covers material you will need to know for subunits 8.2-8.4, found below.  When you reach those subunits, you will receive further instructions for a targeted review of this reading.
       
      This reading should take you approximately 3 hours to complete.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 8.2 Metals as Therapeutic Agents  

    Note: The material you need to know for this subunit is covered in the textbook and lecture-note readings assigned beneath subunit 8.1, found above.  For this subunit, focus specifically on section IV of chapter 9, titled “Survey of Metals Used for Diagnosis and Chemotherapy,” beginning on page 514.  Focus specifically on pages 517-522 of this section.  Also review slides 10-35 of the lecture notes, beginning with the slide titled “Metal based Anti-Cancer Drugs” and ending with “Rheumatoid arthritis.”  In addition, section V of the textbook, titled “Platinum Anticancer Drugs: A Case Study,” specifically pages 522-580, provides an actual case study for the anti-cancer use of cisplatin, a platinum-based complex.  Spend approximately 2 hours reviewing these sections of the readings.

  • 8.3 Metals as Diagnostic Tools  

    Note: The material you need to know for this subunit is covered in the textbook and lecture-note readings assigned beneath subunit 8.1, found above.  For this subunit, focus specifically on section IV of chapter 9, titled “Survey of Metals Used for Diagnosis and Chemotherapy,” in particular pages 514-517 of the textbook.  Also review slides 36-87 of the lecture notes, beginning with “Magnetic Resonance Imaging” and ending with “Chelation Therapy with EDTA – a breakthrough?”  This area of medical technology relies heavily on the basic principles of inorganic chemistry.  The selection criteria for metal ions used in high-contrast MRI are directly related to those ions’ spin states and ligand-coordination spheres.  Spend approximately 30 minutes reviewing these sections of the readings.

  • 8.4 Recent Developments  

    Note: The material you need to know for this subunit is covered in the textbook and lecture-note readings assigned beneath subunit 8.1, found above.  For this subunit, focus specifically on pages 577-580 of the textbook and slides 88-94 of the lecture notes, beginning with “Molecular Targets for Metal-based drugs” and proceeding to the last slide of the presentation (“POMs are Excellent potential drugs”).  This section of the lecture notes focuses on current research in metal-based medical applications, such as the developments of a vanadium complex that works as an insulin mimetic and molybdenum complexes that target the HIV virus.  Spend  approximately 30 minutes reviewing these sections of the readings.

  • Final Exam  
    • Final Exam: The Saylor Foundation's "CHEM203 Final Exam"

      Link: The Saylor Foundation's "CHEM203 Final Exam" (HTML)

      Instructions: You must be logged into your Saylor Foundation School account in order to access this exam.  If you do not yet have an account, you will be able to create one, free of charge, after clicking the link. 

      The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

      Submit Materials


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