Biology

23 Jun 2018
Evaluation Methods: 

Students answer several questions prior to the in class discussion. These answers can be collected to assess their initial understanding of the paper prior to the class discussion. Assessment of the in class discussion could be based on students’ active participation and/or their written responses to the in class questions.

Evaluation Results: 

This Learning Object was developed as part of the 2018 VIPEr Summer Workshop and has not yet been used in any of our classes, but we will update this section after implementation.

Description: 

This is a literature discussion based on a 2018 Inorganic Chemistry paper from the Lehnert group titled “Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases“(DOI: 10.1021/acs.inorgchem.7b02333). The literature discussion points students to which sections of the paper to read, includes questions for students to complete before coming to class, and in class discussion questions. Several of the questions address content that would be appropriate to discuss in a bioinorganic course. Coordination chemistry and mechanism discussion questions are also included.

 

Corequisites: 
Prerequisites: 
Learning Goals: 

A successful student will be able to:

  • Evaluate structures of metal complexes to identify coordination number, geometry (reasonable suggestion), denticity of a coordinated ligand, and d-electrons in FeII/FeIII centers.

  • Describe the biological relevance of NO.

  • Identify the biological roles of flavodiiron nitric oxide reductases.

  • Identify the cofactors in flavodiiron nitric oxide reductase enzymes and describe their roles in converting NO to N2O.

  • Describe the importance of modeling the FNOR active site and investigating the mechanism of N2O formation through a computational investigation.

  • Explain the importance of studying model complexes in bioinorganic chemistry and analyze the similarities/differences between a model and active site.

  • Write a balanced half reaction for the conversion of NO to N2O and analyze a reaction in terms of bonds broken and bonds formed.

  • Interpret the reaction pathway for the formation of N2O by flavodiiron nitric oxide reductase and identify the reactants, intermediates, transition states, and products.

 

A successful advanced undergrad student will be able to:

  • Explain antiferromagnetic coupling.

  • Apply hard soft acid base theory to examine an intermediate state of the FNOR mechanism and apply the importance of the transition state to product formation of N2O.

  • Apply molecular orbitals of the NO species and determine donor/acceptor properties with the d-orbitals of the diiron center.

Implementation Notes: 

This paper is quite advanced and long, so faculty should direct students to which sections they should read prior to the class discussion. Information about which parts of the paper to read for the discussion are included on the handout. Questions #7 and #8 are more advanced, and may be included/excluded depending on the level of the course.

Time Required: 
In-Class Discussion 1-2 class periods depending on implementation.
22 Aug 2015

Antibacterial Reactivity of Ag(I) Cyanoximate Complexes

Submitted by Kari Young, Centre College
Evaluation Methods: 

Instructors will most likely choose appropriate evaluation method, but instructions are included for the following options:

  1. Writing lab report

  2. Poster

  3. Oral presentation

Evaluation Results: 

In general, students are able to prepare and characterize the complexes.  IR spectroscopy is especially useful in this lab because 1H NMR spectroscopy is not very diagnostic.  One difficulty is removing excess solvent from the ligand, and we recommend using a mechanical vacuum pump after rotovapping.  Some students report that they really enjoy the microbiology/biomedicine application. 

Description: 

In this experiment, students will synthesize and characterize one of three Ag(I) cyanoximate complexes as potential antimicrobial agents for use in dental implants. This experiment combines simple ligand synthesis, metalation and characterization, and a biomedical application. The complexes are both air and light stable. Students apply the Kirby-Bauer disk diffusion test, a common microbiology assay, to determine the antibacterial properties of their complexes. Students will also perform a simple cost analysis as part of the evaluation of the complexes.  This experiment was designed during the June 2015 “Improving Inorganic Chemistry Pedagogy” workshop funded by the Associated Colleges of the South.

Prerequisites: 
Learning Goals: 

A student should be able to:

  • Prepare one of a series of Ag(I) cyanoximate complexes and perform appropriate characterization of identity and purity
  • Measure antimicrobial activity in a semi-quantitative way using the Kirby-Bauer assay, including design and implementation of appropriate control experiments.
  • Evaluate a series of complexes as potential antimicrobials for dental applications based on the criteria of heat stability, water insolubility, and antibacterial activity.
  • Identify most cost effective complex.
Equipment needs: 

FT-IR spectrometer

NMR spectrometer

Melting point apparatus

Microbiology equipment

Implementation Notes: 

We piloted this experiment during the 2015-2016 school year and have made some adjustments based on our experience.  We welcome others in the VIPEr community to help us test this!  If you do try this, please post your comments and/or consider filling out our evaluation survey http://goo.gl/forms/CrP5KJtDtursr5302

 

Students will synthesize and characterize one compound each, but are expected to pool data as a class for a comparative analysis.  The antimicrobial assay requires supplies not commonly found in a chemistry laboratory, and instructors are encouraged to collaborate with a colleague in microbiology.

Time Required: 
Four 3-hour lab sessions
19 Jul 2014

The "Zinc Spark" - Zinc as a signaling chemical in life

Submitted by Kyle Grice, DePaul University
Evaluation Methods: 

Has not been evaluated yet, but I plan to have it included in the discussion of O'Halloran's review when I have it in my class. 

Description: 

This web resource is a TEDx talk about zinc and zinc's role in the early stages of the maturation of the egg. This would be a great introduction video for a gen chem, inorganic, or bioinorganic chemistry course. It introduces the idea that Zinc is stored in specific locations on the egg and then released all at the same time.

It is not very long and should give the students lots of questions. Following this video, the students can do the related literature discussion and in-class activities on the O'Halloran Paper to obtain more bredth and in-depth work (see links in "related activities"). Directing students to O'Halloran's website is also an option in conjuction with haveing them see the video. 

It is a youtube video and should work on most electronic platforms.

Corequisites: 
Prerequisites: 
Topics Covered: 
Learning Goals: 

Students will be able to appreciate the role of Zinc as an important signalling chemical in biological systems

Students will identify when zinc fluxes occur early on in development

Students will recognize the important role of inorganic chemistry in multidisciplinary cutting edge research. 

Implementation Notes: 

Two group LOs were developed at the 2014 IONIC VIPER workshop relating to Tom O'Hallorans work, and this could be used to introduce O'Halloran and his work prior to giving the review chapter to read.

This video would also be excellent for gen chem or non-majors students who are interested in health to talk about inorganic chemisry in biology. You could also have a discussion on zinc sensors. Why do sensors need to be used? This gets into a discussion of metals in the cell, techniques, the specific properties of metals and complexes that can be measured, etc. 

Given its short time, students could also watch the video in class and then have the group discussion right there. 

Students can also be linked to O'halloran's website to learn more who he is about what he does. 

Time Required: 
20 min outside of class or in class
17 Jul 2014
Evaluation Methods: 

Students will be assessed qualitatively based on whether they complete the reading guide and how they contribute to a class discussion.  Students can also be assessed using the DFT Post-translational modification activity based on the same paper.

Evaluation Results: 

This LO was created for the 2014 TUES workshop and has not yet been tested in the classroom.

Description: 

In this literature discussion, students read a paper about a cobalt metallopeptide that imitates the active site of the enzyme nitrile hydratase.  Specifically, the model complex is oxidized by air to produce a coordination sphere with both cysteine thiolate and sulfinic acid ligands, much like the post-translationally oxidized cysteine ligands in the biological system.  This paper also provides an introduction to a variety of physical methods used to characterize the structure, including X-ray absorbance spectroscopy, magnetic susceptibility using the Evans method, IR spectroscopy, electronic absorbance spectroscopy, and electron paramagnetic resonance spectroscopy.  This LO was created for the 2014 TUES Viper Workshop on bioinorganic chemistry.

Corequisites: 
Course Level: 
Learning Goals: 

Students will be able to:

  • Identify the oxidation state, coordination number, and approximate geometry of the cobalt complexes presented in this paper

  • Give the overall reaction catalyzed by the enzyme

  • Identify sites of potential ligand coordination in an oligopeptide

  • Compare two cobalt metalloenzyme active sites using the Protein Data Bank

  • Explain how X-ray absorbance spectroscopy can be used to identify the oxidation state of an atom

  • Assign ligand field or LMCT electronic transitions based on molar absorptivity

  • Compare and contrast thiolate, sulfenate, and sulfinate ligands with respect to charge, donor ability, and oxidation state

  • Predict how Lewis basicity and redox potential change as the ligand becomes more oxidized

  • Evaluate the effectiveness of a model complex for reproducing a metalloenzyme active site
Implementation Notes: 

Students should read the paper and complete the reading guide before the literature discussion.  


We hope that instructors will mix and match questions that are appropriate to their classes.  In particular, instructors may want to remove questions 9-12 depending on the desired emphasis on experimental methods. 

25 Jun 2014

This collection highlights the learning objects used at the 2014 VIPEr workshop on the Bioinorganic Applications of Coordination Chemistry to introduce participants to the field of bioinorganic chemistry.   They provide essential background information on how metals bind to proteins as well as the techniques used in the research papers presented at the workshop.  A list of learning objects created at the workshop based on the current research of our expert speakers can be found at: 

Subdiscipline: 
Prerequisites: 
17 Jun 2014

Exploring Proteins as Ligands using the Protein Data Bank

Submitted by Elizabeth Jamieson, Smith College
Evaluation Methods: 

I have not yet been able to assess this LO, but imagine one could ask questions on a problem set or exam related to how amino acids bind to metals and/or Hard Soft Acid Base theory.  See the related activities suggested above for ideas. 

 

Evaluation Results: 

No results to report at this time.

Description: 

This in class activity is designed to introduce students to how amino acid side chains can coordinate metal ions in proteins.  It guides students through the exploration of several metal binding sites in proteins using the Ligand Explorer program on the Protein Data Bank (PDB) website.  Essentially, it is a way for them to use the PDB to “discover” the information generally presented on this topic in the introductory chapters of bioinorganic textbooks.  At the end it asks students to think about Hard Soft Acid Base theory and to see how that can be applied to the binding of metals in proteins.  I’ve also posted a separate document with this activity that highlights several additional web based resources for examining the structure of metals in proteins if anyone wants to explore this topic further.

Learning Goals: 

By doing this in class activity, a student will be able to:

•Identify which amino acid side chains are likely to coordinate to metal ions and recognize their different coordination modes

•Use Java based programs on the Protein Data Bank to explore the metal coordination environment in proteins

•Apply Hard Soft Acid Base theory to explain the metal ion specificity in proteins

Prerequisites: 
Implementation Notes: 

I have been thinking about making a learning object like this for some time, but finally put it together in time for the 2014 TUES workshop on the Bioinorganic Applications of Coordination Chemistry.  In my bioinorganic elective and my advanced inorganic class, I always cover this topic with students, but always thought it would be better to have a more “active learning” type of activity for them to do.  We will test this activity at the workshop, and I hope to implement it in class next time I teach this topic. 

I envision using this LO with students who have some knowledge of coordination chemistry and have been introduced to the basics of protein structure.  I have been using the Bertini, Gray, Stiefel, and Valentine Biological Inorganic Chemistry:  Structure and Reactivity textbook the past couple of times I’ve taught bioinorganic, so have referenced that text in this LO.  However, it could easily be adapted to a similar section of a different text.

The section of the LO on post-translational modifications was put in specfically to provide some background on one of the papers presented at the 2014 workshop.  It is a topic that I cover in my biochemistry and bioinorganic class, but this is something that could easily be skipped if you prefer by just deleting item 8 in the worksheet. 

In the past when I have had the students use the PDB, some have had issues getting the Java based programs to work on their computers.  Usually at least half of the class can get it to work, so I will sometimes have students partner with each other for PDB based activities if this is the case.  I have included links to the Java troubleshooting pages on the PDB website to assist with these technical issues. 

 

Time Required: 
I would estimate that students would need at least 30 min to do this exercise, and, more realistically it would probably take them closer to 45 min.
16 Sep 2013

The Iron that Keeps and Kills Us

Submitted by Kathy Franz, Duke University, Department of Chemistry
Evaluation Results: 

This activity was well received by my students (many pre-meds who really like the medical connections).  There were several in the class who had taken an evolutionary biology course, and that opened up some really interesting class dialogue and questions about other metals' roles in disease.  Much of the "chemistry" content I used to cover in lecture as part of a bioinorganic section, but this activity replaced much of that material and put the burdent on them to read that part of the chapter in order to answer the questions. 

 

Biology is listed as a pre- or co-requisite, but it is not absolutely required.  Students with a biology background will come away with a different depth of knowledge, while students without a biology background may appreciate the general audience tone of the Atlantic article.

Description: 

This in-class activity requires that the students read an article in The Atlantic about an interesting (and modern) case of the plague.  The article provides a great platform to showcase the Inorganic side of broad societal themes like evolutionary biology, environmental and hereditary influences on disease, and the collaboration between biology, medicine, and history.  The article itself contains little chemistry, but can be used to guide students into learning about iron in bioinorganic chemistry.

 

Accompanying article found here:

http://www.theatlantic.com/health/print/2013/01/the-iron-in-our-blood-th...

Learning Goals: 

A student should learn introductory bioinorganic nomenclature associated with iron enzymes and proteins in order to complete this assignment.

A student should be able to apply his/her knowledge of coordination chemistry to answer questions about siderophores (which might be a foreign topic).

Students' knowledge of coordination chemistry will be probed specifically in areas of thermodynamic stability constants for metal-ligand complexes, radical reactions associated with oxygen-derived radicals, redox chemistry, principles of hard-soft acids and bases.

Subdiscipline: 
Prerequisites: 
Corequisites: 
Course Level: 
Time Required: 
10 min for small group discussion, another 10 min for full class discussion and presentation of "best" answers
25 Jun 2013

Chemical Acrostics for Fun and Active Learning

Submitted by Charles Mebi, Arkansas Tech University
Evaluation Methods: 

The students get extra credit for successfully completing the acrostic.

Evaluation Results: 

The students complete the acrostics in 5-10 minutes. Because they work in groups and are allowed to use their text, they usually complete the entire acrostic successfully.

Description: 

Chemical acrostic is used as a teaching tool in descriptive inorganic chemistry. This is an active learning approach to engage the students with a fun classroom activity. The acrostics are designed by Simon Cotton and published in the Royal Society of Chemistry's education resource magazine "The Mole." The students are divided into groups of two or three to work on the acrostics. To come up with the answers, the students engage in meaningful group discussions that enhance conceptual understanding. Further discussions can be stimulated by asking the students to explain their answers to the clues. This activity will also help students review and assess their understanding of descriptive inorganic chemistry (chemical and physical properties, periodic trends, biological and environmental aspects of chemical elements and their compounds).

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Learning Goals: 

The acrostics cover a broad array of topics. Examples of possible learning outcomes include the following. Students will be able to: 1. explain periodic trends 2. learn about the uses of elements on the periodic table 3. understand the biological and medicinal properties/roles of elements and their compounds 4. understand general reactivity of elements.

Corequisites: 
Equipment needs: 

Free online access to The Mole (www.rsc.org/TheMole). Click on any of the issues and then download the puzzle located at the end of the publication.

Prerequisites: 
Topics Covered: 
Course Level: 
Implementation Notes: 

The instructors can make the activity more fun by turning the game into a competition among the groups. The first group to complete the acrostic gets a "prize". Discussion session may be very useful in identifying learning gaps or conceptual misunderstandings.

Time Required: 
10-20 minutes depending on the discussion session.
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