Biology

6 Jul 2018

Getting to Know the MetalPDB

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

I reviewed student answers to this assignment and evaluated their contributions to the discussion that took place. I also tried to keep track of how much they used information obtained from this site during their literature presentations.

 
Evaluation Results: 

This assignment is quite straightforward and the 6 of 8 students who completed the assignment had little trouble coming up with correct answers for all of the questions.

 

At the end of the semester, each student had to give two presentations on bioinorganic topics. They were expected to discuss the metal coordination environment and how "normal" it was, as well as the possibility of substituting another metal into the coordination sphere. One student used information from the MetalPDB in both of her presentations, three students used information in one of their presentations, and four students did not include information from the site in either presentation.

 

Description: 

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

 

I expect my students to use this site to obtain information for their assignments and presentations. This activity is a self-paced introduction to the site that my students complete outside of class. This activity has students use the site to obtain information about metal coordination environments, the common geometries adopted by metals in biological environments, and the common ligands that are used to bind metals.

Learning Goals: 

After completing this exercise, students should be able to:

  • access the MetalPDB site,

  • obtain statistics pertaining to the number of metal-containing structures in the PDB,

  • determine the most common geometry observed for a particular metal in a biological structure,

  • identify the most common ligands attached to the metal when bound in a biological macromolecule, and

  • find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.

Equipment needs: 

Students need access to the internet and a web browser that is capable of running JavaScript and JSmol. This site is accessible on devices running iOS, but the layout of the site works better on a laptop screen.

Prerequisites: 
Corequisites: 
Implementation Notes: 

I used the MetalPDB site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules in both my advanced and foundation-level courses, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.

 

I also have students use the site to get background information about metal geometry and common ligands for their assignments and presentations. I ask them to complete this activity outside of class. I usually distribute this as a Google Doc to my students (through Google Classroom) so that I have access to all of their responses.

 

For several of the questions/groups of questions, I assign individual members of the class specific geometries (question #5), metals (questions #6-9), or PDB structures (questions #11-13) and we pool their answers in class. We then spend about 30-45 minutes in class discussing the results and search for commonalities and connections to other structures that we have already discussed in class.

 
Time Required: 
1-2 hours (outside of class by student); 30-45 minutes in class (including discussion of related topics)
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.
16 May 2018

MetalPDB website

Submitted by Anthony L. Fernandez, Merrimack College
Evaluation Methods: 

I kept track of how much my students used information obtained from this site during their literature presentations.

Evaluation Results: 

The students had little difficulty accessing or using the site. Most of my students used information obtained from the site in their presentations and during in-class dicsussions.

Description: 

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

In the past, I have used Metal MACiE to help find metal-containing biological macromolecules and to access information about the metal function and coordination environment. Unfortunately, this site, while still available, has not been updated in several years. I have recently found the MetalPDB website which was created at CERM (University of Florence). This site "collects and allows easy access to the knowledge on metal sites in biological macromolecules" and can be used to explore structures deposited in the PDB.

I also expect my students to use this site to obtain information for their assignments and presentations.

Prerequisites: 
Corequisites: 
Learning Goals: 

When using this website, students are able to:

  • obtain statistics pertaining to the number of metal-containing structures in the PDB,
  • determine the most common geometry observed for a particular metal in a biological structure,
  • identify the most common ligands attached to the metal when bound in a biological macromolecule, and
  • find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.

These learning goals are incorporated in the associated in-class activity, which is posted separately.

Implementation Notes: 

I used this site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.

To learn how to use the site, I assigned an associated activity (posted separately) that I have the students complete before coming to class. This experience allows the students to use the site to get background information about metal geometry and common ligands for their assignments and presentations.

This site utilizes JavaScript and JSmol so students must ensure that Java functions properly in their preferred web browser. I have found no issues accessing this site with any of the browsers used by myself or my students.

 

30 Oct 2014

Bio-Organic Reaction Animations (BioORA)

Submitted by Steven A. Fleming, Temple University
Evaluation Methods: 

Through interviews with faculty, focus group interviews, and student surveys, we have explored the following research questions: What are faculty perceptions of BioORA’s impact on student learning? What are student perceptions of BioORA’s impact on their own learning and understanding?

An inductive mode of analysis of qualitative data in which patterns and themes emerge let us discover the specific technical features of BioORA that the instructors and students found useful, as well as the ways in which BioORA increased student engagement and helped students with visualization skills, which both the instructors and students recognized as fundamentally difficult for novices in the fields of biology and chemistry. Additionally, analysis revealed similarities and differences between the perceptions of instructors and students. For example, the instructors emphasized BioORA’s function as a link between specific concepts or principles and the larger context of the class, as well as its function as a link between lectures and lab sections, organic chemistry and biochemistry, what students learn in class and their future work in science, and the individual steps within the reaction.

See: 

“Faculty and Student Perceptions of Student Learning and Experiences with a 3D Simulation Program” Gunersel, A. B.; Fleming, S. A.; J. Chem. Ed., 2013, 90, 988-994.

“Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback” Gunersel, A. B.; Fleming, S. A.; Biochem. Mol. Biol. Ed., 2014, 42, 190-202.

Evaluation Results: 

 

See:

“Faculty and Student Perceptions of Student Learning and Experiences with a 3D Simulation Program” Gunersel, A. B.; Fleming, S. A.; J. Chem. Ed.201390, 988-994.

“Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback” Gunersel, A. B.; Fleming, S. A.; Biochem. Mol. Biol. Ed.201442, 190-202.

Description: 

 

Bio-Organic Reaction Animations (BioORA) can be used as a teaching tool for bio-inorganic courses. BioORA illustrates large biomolecules obtained from crystal structures in the Protein Data Bank using Jmol. The student can manipulate this structure, which is shown on the right-hand side of the screen of BioORA. On the left-hand side of the screen a stripped-down view of the binding site is shown. This stripped down representation can also be manipulated and has three viewing options: ball and stick, tube, and space-filling. The software helps students visualize the three-dimensional aspects of enzyme chemistry. There are more than 25 animations and several of them have coordinating metals involved in the reaction mechanisms that are illustrated.

 

Subdiscipline: 
Prerequisites: 
Corequisites: 
Learning Goals: 

 

BioORA is a visualization program for biochemistry that will focus on molecular events.  The natural tendency has been to substitute acronyms for the biomacromolecules.  This is an understandable result in light of the size of the relevant structures.  However, we have shown that computer imaging technology is sufficiently advanced now to handle animations of the actual molecules involved in the biochemical pathways.  This type of multimedia presentation can provide students with three-dimensional representations of the biomolecules and three-dimensional animations of binding and enzyme catalyzed reactions. 

 

Our goal is to bring the molecular aspects of biochemistry to the forefront.  The chemistry for the bio-organic processes is documented and the 3D visualization software is now accessible.  There is a need for more accurate molecular representation and we are eager to provide it.  We expect that students, regardless of their major, will benefit from this teaching tool.  We hope that it will improve student appreciation of the organic chemistry that occurs in biological systems. 

Course Level: 
17 Jul 2014
Evaluation Methods: 

This learning object was developed for the 2014 VIPEr workshop and has not been evaluated. 

Description: 

This is an in-class PDB exercise based on the paper "Mechanisms Controlling the Cellular Metal Economy" by Gilston and O'Halloran. Students are asked to visualize the metal binding sites of several proteins discussed in the paper, highlighting unusual metal geometries. After identifying the amino acid residues involved in metal binding, students will discuss the bond structure in terms of HSAB theory. 

Learning Goals: 
Students will:
1) Become familiar with reading primary literature and using referenced works.
2) Use the PDB to search for protein structures and create images of metal binding sites.
3) Apply coordination chemistry and HSAB to describe bonding in biological systems
4) Practice drawing chemical structures
Equipment needs: 

Laptop computers with Java installed for accessing the PDB (freely available at www.pdb.org). Instructions for using the PDB can be found in the related activities linked below.

Topics Covered: 
Corequisites: 
Prerequisites: 
Implementation Notes: 

Cys79 is a bridging ligand between Zn402 and Zn401 in ZntR. 

You can highlight two metal atoms in the PDB viewer by holding shift while clicking. 

It is a good idea to pre-test computers that will run the PDB viewer before coming to class, as the viewer runs on Java and may have technological issues. 

 

17 Jul 2014
Evaluation Methods: 

This literature discussion developed at the 2014 IONIC VIPER workshop and has not been evaluated yet. 

Description: 

This is a literature discussion of a review by Tom O'Halloran (The link to the paper is included in the "Web Resources" below). The review covers concepts of metal content in cells, metal trasport, storage, and regulation. Its a good review to start a broader or deeper discussion about metals in biology. We have provided some questions to help guide the student discussion. These questions can be given to students prior to coming to class, and the answers can either be used for the in-class discussion and/or collected. 

Corequisites: 
Prerequisites: 
Learning Goals: 
Students will:
-- apply fundamental concepts from class material to literature examples, such as metal binding specificity (dependent on size, charge, etc.), Kd, strength of ligand binding, concentration and turnover of free ions 
-- gain an appreciation for the importance of transition metals in biological systems and the different roles metals play in the cell (metalloenzymes, metallochaperones and metalloregulatory proteins)
-- develop scientific reading comprehension in a guided activity
Implementation Notes: 

Access the manuscript through your library and provide a copy of the manuscript to the students along with the discussion questions a few days before class, and then have an in class discussion abou the chapter. 

Time Required: 
45 minutes (1 lecture) + student time prior to lecture
15 Jul 2014
Evaluation Methods: 

I make this activity worth 5% of their overall grade to be assessed for originality and level of discussion of how the chemistry part of their lab experiments (in terms of metal-ligand bonding or non-bonding) affected a biological system. Their ability to understand vitamin B12 and its functioning in the body should become apparent in their paper and should be used as the main guide in point distribution.

Evaluation Results: 

Has not been tested yet

Description: 

The students will write a paper in which they analyze the Vitamin B12 co-enzyme from biological, chemical and biochemical perspectives, and will use the guided questions to help show the relevance of an organometallic chemistry experiment to real biochemical systems. This activity is based on a synthetic lab experiment that students would have performed on transition metal-carbon bonds in biology and chemistry (The lab experiment was adapted from third edition of “Inorganic Experiments” by Derek Woollins). The answers to the set of questions in this LO will help guide the students to write the paper. You can choose the style you want the students to use and guide them in that process. 

Students can use information from their lab report, especially the experimental and results/discussion sections. 

 

Corequisites: 
Course Level: 
Learning Goals: 

Students will…

  • Study the chemical structure of vitamin B12 coenzyme and discuss the advantages and/or disadvantages of using cobaloximes as model compounds for vitamin B12 co-enzyme in this experiment.
  • Analyze the chemical reactions they performed in the lab that modelled actual reactions that occur in the human body, and discuss the effects of such chemical transformations. 
Subdiscipline: 
Implementation Notes: 

This term paper is based on a lab experiment that the students did earlier in the semester. I taught the lecture and lab portions concurrently so the students were very familiar with the experiment. They had a one paragraph summary of the lab experiment and a procedure to follow with guided questions to help them write the lab report. They submitted the lab report with the usual experiments, observations, results, discussion and conclusion and received lab credit that was separate from the credit assigned for this activity.

 

Time Required: 
Possibly as a take home assignment due within a week
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.
20 Jul 2012

Soluble Methane Monooxgenase Spectroscopy

Submitted by Gerard Rowe, University of South Carolina Aiken
Evaluation Methods: 

The activities are collected and graded based on how reasonable and well-supported their answers are.

Students also receive a question about inorganic spectroscopy on their final exam.

Evaluation Results: 

Students were generally successful at identifying the right spectroscopic technique for the job.  The most challenging problem was the one concerning spin states, especially because they have to consider all the coupling possibilities for each diiron species and remember what makes a compound EPR active/silent.

 

The final exam question had somewhat more mixed results, probably due to the fact that two weeks had elapsed in between this activity and the exam.

Description: 

Determining the reactive intermediates in metalloenzymes is a very involved task, and requires drawing from many different spectroscopies and physical methods.  The facile activation and oxidation of methane to produce methanol is one of the "holy grails" of inorganic chemistry.  Strategies exist within materials science and organometallic chemistry to activate methane, but using the enzyme methane monooxygenase, nature is able to carry out this difficult reaction at ambient temperatures and pressures (and in water, too!).  This activity asks students to look at the proposed catalytic cycle of soluble methane monooxygenase and choose an appropriate spectroscopic technique to provide different information about the various species in the process.

Learning Goals: 

The student will be able to identify the key features of a scheme describing a catalytic cycle's intermediates

The student will learn to think of spectroscopy as an experiment that operates within a specific time scheme instead of as a figure in a paper

The student will be able to explain the advantages and limitations of different spectroscopic techniques

The student will use their knowledge of spectroscopic techniques to decide the best method to obtain the desired information

Subdiscipline: 
Course Level: 
Corequisites: 
Implementation Notes: 

I give this activity to students towards the end of my advanced inorganic chemistry course.  By this point, they have already been exposed to most of the major spectroscopic techniques used in inorganic chemistry, and have had several lectures in bioinorganic chemistry.  

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