User:Dbzam/sandbox

Course Overview
CHM437S is a lecture-based course that will explore the fundamental principles of bioinorganic chemistry and examine how they are applied in specific examples from our world. We will touch on many of the inorganic elements that are used in biology, but our focus is on the transition metals. Topics covered include the occurrence, distribution, and roles of the essential inorganic elements in nature; the structure and function of naturally occurring ligands; physical methods used to study bioinorganic biomolecules; uptake, regulation, and insertion into metalloproteins; and the discussion of examples including both redox and non-redox metalloenzymes, electron transfer proteins and energy-coupled processes, metallodrugs, etc.


 * Course goals

By the end of the semester, students should be able to:
 * 1)  Recognize how the fundamental principles of inorganic chemistry apply to bioinorganic systems.
 * 2)  Appreciate the challenges of using metals in biological systems and discuss how Nature meets these challenges in general and by citing specific examples.
 * 3)  Understand how specialized methods are used to study bioinorganic systems and what kind of information they provide.
 * 4)  Discuss the chemistry and biology of specific bioinorganic systems.


 * The wiki assignment

Metals are everywhere in biology. It has been estimated that roughly a third of all proteins require at least one metal cofactor, and metals are also used as structural components, in signalling pathways, in the immune system, as clinically administered drugs, and so on. In addition, the field of bioinorganic is very broad and multidisciplinary, drawing in scientists from diverse areas such as inorganic synthesis, biological chemistry, microbiology and geology. So it is impossible for one course to cover all of the topics in this area! For this reason, this course has included a student-driven research project since it was first offered by Prof. Morris. Typically, each student picks a specific bioinorganic molecule and does an in-depth study to learn what is known about this molecule. The student then prepares a presentation to teach what they have learned to the rest of the class. This part of the assignment is still in place because the oral presentation is a valuable experience in communication, allows you to perform a detailed analysis of one aspect of interest on a bioinorganic system, and provides the opportunity for interesting questions and discussions with the class.

Over the past few years, Wikipedia has become more common as a reference, often showing up as the first item upon searching the internet. Initially, I would tell the class that Wikipedia is not an appropriate reference, but this statement is not true anymore. There is a wealth of information here, and much of it is peer-reviewed. Furthermore, it has become a valuable source of information for who knows how many people. However, much of the scientific information is incomplete, and the peer reviewers may not be scientists. This is where we can contribute. You do all of the work to put together a narrative about a bioinorganic system, and usually the presentations are at an impressive level of understanding and depth. Also, although there are some good Wikipedia articles on some bioinorganic systems, many are not represented. So this year, part of your assignment will be to prepare a Wikipedia article. I will prepare a list of interesting biomolecules for which there is nothing (or very little) on Wikipedia for you to chose from. There are many examples of pages that are present but incomplete, so if there is a topic that you are particularly interested in learning about but it is not on my list, please come to talk to me with your proposal.

This assignment will be fun but not easy, especially if you are new to working on Wikipedia. It is a different style of scientific communication from what we are used to. It is a real online encyclopedia, so there are rules that we have to follow such as how to write the article and the format you must use, ensuring there are appropriate citations, keeping the content and tone appropriate for the general audience, as well as other issues. In addition, once you go live you and your work will become a part of the global online community.

Weeks 1-2: Wikipedia essentials

 * In class
 * Overview of the course and assignment


 * Homework (please complete this by Friday, January 16)
 * Start the online student orientation. During this training, you will create an account (if you do not already have one), make edits in a sandbox, and learn the basic rules of Wikipedia.
 * Once you have a Wikipedia user account, please email me your user name (dzamble@chem.utoronto.ca) - I need to know this in order to mark your assignments.

Week 3: Editing basics

 * In class (or perhaps during an extra tutorial)
 * Basics of editing
 * Anatomy of Wikipedia articles, what makes a good article, how to distinguish between good and bad articles
 * Tips on finding the best articles to work on your assignments and to contribute to your classmates' assignments.
 * I will provide you with the enrollment token you will need to register for the course by clicking on the Enroll button at the top of this page.
 * Handouts: Using talk pages, Evaluating Wikipedia article quality, Wikimarkup cheatsheet


 * Assignment (due Friday, January 23, worth 5% of your grade)
 * Complete the online training for students.
 * Create a user page, and sign up on the list of students on the course page.
 * Enroll in the course on the Wiki Education page by clicking the "Enroll" button at the top, and entering the enrollment token that I gave you.
 * Practice editing and communicating on Wikipedia, for example leave a message for a classmate on their user talk page. You will be able to access your classmates' Talk Pages by scrolling to the bottom of this page where the enrolled students are listed (if you are not visible in this list it means you have not enrolled).
 * Read several of the following Wikipedia articles: metalloprotein, cisplatin, methane monooxygenase, photosystem II, cytochrome c oxidase, urease, carbon monoxide dehydrogenase.  These are examples of what I consider to be excellent articles on bioinorganic topics, and could serve as models for the format, tone and citation requirements for your article.
 * Below there is a list of suggested topics. Email me to select a topic, first come first served, or I will assign one.


 * Provisional list of topics (If you email me, you can select a topic, first come first served. If not, I will assign one.)
 * Faecal calprotectin assigned to User:    .     This is a metal-chelating antimicrobial peptide.
 * Aldehyde ferredoxin oxidoreductase assigned to User:    .  This is a tungsten enzyme.
 * Formate dehydrogenase assigned to User:    .  This is a molybdenum or tungsten enzyme.
 * Acetyl—CoA synthetase assigned to User:    .  This is a nickel enzyme, sometimes called acetyl-CoA synthase, often works with CODH.
 * Nickel superoxide dismutase assigned to User:    .  There is a brief mention on superoxide dismutase, but deserves its own site.
 * Mercury(II) reductase assigned to User:.
 * MerR regulation assigned to User:    . This is a prototypical metalloregulator.
 * ATP7B assigned to User:    . This is the protein implicated in Wilson disease.
 * ATP7A assigned to User:    . This is the protein implicated in Menkes disease.
 * ATOX1 assigned to User:.
 * CCS assigned to User:.
 * MRI contrast agent assigned to User:    . There is very little on gadolinium contrast agents here.
 * Metal sensor - genetically encoded assigned to User:.
 * Metal sensor - small molecule assigned to User:.
 * Metals and smell assigned to User:.
 * Lanthanide probes assigned to User:.
 * Carbonic_anhydrase assigned to User:    . In particular you might want to focus on small molecule mimics, or the discovery and properties of the cadmium-containing enzymes.
 * Galactose oxidase assigned to User:.
 * Low-molecular-weight chromium-binding substance assigned to User:.
 * Xylose isomerase assigned to User:.
 * L-ascorbate oxidase assigned to User:.
 * Urease assigned to User:    .  There is nothing here about metallocenter assembly.


 * Milestone:
 * All students have Wikipedia user accounts and will be assigned a topic on the course page. All students will also have competed the online training for students (and I will check that you have done it).

Week 4: Referencing - citing sources, obeying copyright

 * In class
 * We will briefly discuss referencing on Wikipedia and Wikipedia’s copyright policy.
 * I will hand out a topic to each of you that will be the subject of your assignment.
 * Handouts: How to get help

There are a few online resources you can access to help you with your project. Here are a few:
 * Resources


 * Guided Tool of Metalloproteins - this is a great online tool for learning about selected metalloproteins, set up by Prof. Morris and Dr. Hadzovic. It walks you through the structures of metaloproteins with a focus on the metal centres, and provides basic bibliographic information.   If you are not familiar with protein structures or metal centers, this is a good place to start.


 * RCSB Protein Databank - The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The structures used in the Guided Tours of Metalloproteins have been taken from this source. Please see your textbook (Appendix IV "Introduction to the Protein Data Bank (PDB)", p. 729). There is a good chance there is a structure related to your topic here.


 * MIPS - A searchable database of metal-protein structures.


 * Pymol - A really good open-source software for molecular visualization. Free only for educational use. This is a good program to use when you want to look at pdb structures and make nice pictures.


 * Swiss-PDB Viewer - You can download Swiss-pdb viewer at this site. This is another good program for looking at and manipulating protein structures from the pdb database, easier to use than pymol but maybe not as powerful.  It is freeware and there are versions for Mac, PC and Linux.  There are a variety of helpful features like tips, a great tutorial and a user guide.


 * Encyclopedia of Inorganic and Bioinorganic Chemistry - This is an online encyclopaedia, available through UofT libraries. It contains many focused, up-to-date references.  A good place to look for your topic.

There are a number of books on bioinorganic chemistry in the Gerstein Library in the stacks under the call number range QP500s. Also, you may find some worthwhile reference books in the general inorganic chemistry section at QP151. I have a few in my office that you are welcome to look at. A few that I think are particularly good include:


 * I. Bertini, H. B. Gray, E. I Stiefel, J. S. Valentine (2007) Biological Inorganic Chemistry, Structure and Reactivity. University Science Books. ISBN-10: 1891389432.  This is the recommended text for the course, and full of information.   Embed this reference:


 * S. J. Lippard & J. M. Berg (1994) Principles of Bioinorganic Chemistry. University Science Books. ISBN-10: 0935702725.  Also a good reference, good for the fundamentals. Embed this reference:


 * I. Bertini, A. Sigel, H. Sigel (2001) Handbook on Metalloproteins. CRC press. ISBN-10: 0824705203. 1108 pp. Embed this reference:


 * J. J. R. Frausto da Silva & R. J. P. Williams (2001) The biological chemistry of the elements: The inorganic chemistry of Life. Oxford University Press. ISBN-10: 0198508484. Embed this reference:


 * W. Kaim, B. Schwederski, A. Klein (2013) Bioinorganic Chemistry -- Inorganic Elements in the Chemistry of Life: An Introduction and Guide. Wiley. ISBN-10: 0470975245. Embed this reference:


 * L. Que (2000) Physical Methods in Bioinorganic Chemistry. University Science Books. ISBN-10: 1891389688. 556 pp. Embed this reference:


 * H.-B. Kraatz & N. Metzler-Nolte (2006) Concepts and Models in Bioinorganic Chemistry. Wiley-VCH. ISBN-10: 3527313052. Embed this reference:

Week 5: Develop a bibliography

 * Assignment (due Friday, February 6, worth 5% of your grade)
 * If an article on your topic already exists, copy its source code and paste it into your sandbox page below the sandbox template at the top  ← Do not delete this from the top of your sandbox page
 * Compile a bibliography of relevant references in your sandbox, linking each reference to the point-formed facts you plan to use that reference to support. I expect at least 12-15 "facts" (hopefully more) supported by at least 6 references. Your annotated bibliography might look something like this:

{{markup|title=
 * ==Fungus name==
 * fast-growing, yellow colonies
 * conidia 1-celled, rough-walled
 * nutrition, uses fructose, sorbitol and sucrose
 * reported from dermatophytosis-like infection, heart valve infection
 * resistant to amphotericin B
 * etc, etc.

Week 6 and Reading Week: Expand your article in your Wikipedia sandbox

 * Homework
 * Write a 3–4 paragraph summary of your article —with citations— on your Wikipedia sandbox.
 * Remember, Wikipedia articles all have similar styles. Your article should start with a standard Wikipedia lead section, which provides a concise summary of the topic. Wikipedia articles use "summary style", in which the lead section provides a balanced summary of the entire body of the article, with the first sentence serving to define the topic and place it in context. The lead section should summarize, very briefly, each of the main aspects of the topic that will be covered in detail in the rest of the article. If you are improving an existing article, draft a new lead section reflecting the content the article will have after it's been improved, and post this along with a brief description of your plans on the article’s talk page.
 * Do not edit the article in the main space.


 * Milestone
 * All students have started editing draft articles in their Wikipedia sandboxes.

Week 7: Helping your peers

 * Assignment (due Monday, March 2, worth 5% of your grade)
 * Review and comment on the draft articles of at least 2–3 your classmates (last week's homework). Provide comments and constructive criticism to help them polish their articles and fix any major issues. Do not just say "Nice job! That looks great!!"
 * Leave your comments on their talk page, do not edit their sandbox.
 * Continue research on your article.


 * Milestone
 * All articles have been reviewed by others. All students have reviewed articles by their several of their classmates.

Week 8: Polishing your article

 * Homework
 * Continue to work on your article.
 * Take a look at several of the articles of your peers and comment on them.

Week 9: Final due date

 * Assignment (due Friday March 13, worth 15% of your grade)
 * Email me a MS-Word file containing the full text of your article (dzamble@chem.utoronto.ca)
 * Move your article into main space by following these instructions: Migrate your article to the Main Wikipedia entry.


 * Milestone
 * Students have finished all their work on Wikipedia that will be considered for grading.