2. Example MyMolecule Outline

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An updated google doc template is available for Saint Mary's students here (click).

The example outline below was updated on 2/25/20

Introduction

Eventually, you will need to form an outline for this section based on your literature research. This section should contain at least two figures.

This section should begin with describing the “big picture” of this class of molecules, their roles in biology, and any important or interesting information about the class of molecules.

[IntroFigure1: big picture graphic]

The middle of this section should transition to discussion of the specific molecule you are writing about, its specific function and structure.

[IntroFigure2: graphic of structure with notable features showcased]

The end of this section should transition into specific focus on the general role of its metal binding site (or the role that metal binding plays in its function). You should describe the features of the metal binding and how it contributes to the biomolecule’s function/role in biology.

[IntroFigure3: graphic to highlight structure and function of metal binding. You may combine this concept with previous IntroFigure2 if convenient.]

This is not an exhaustive list, but some points to consider and address follow (Usually this info is laid out in the introduction section of any research article about it):

What organisms have/use/need this molecule or class of molecules?
Is this molecule or class of molecules essential for something?
Is this molecule or class related to any diseases? Or is it a potential target for drugs?
Why would your reader care to know about this molecule or class? In other words, why are their any scientific studies about this?
How is the structure of this biomolecule unique or noteworthy?
How is the structure of the biomolecule related/suited to its function/role?
Does the biomolecule have specific or selective binding affinity for a certain metal ion?
Does the metal binding site have thermodynamic or kinetic features worth noting?
Are there any reactions that are catalyzed?

Applying Principles of Inorganic Chemistry

This section should discuss how the properties of your biomolecule can be explained by principles of inorganic chemistry.

The details within the subsections here, and their organization, will depend on your particular biomolecule. In some cases, a certain principle may not be terribly relevant; whatever you conclude about the relevance or application of a specific principle, you should defend your conclusions with evidence and logic.

Specific focus on the metal binding site (if its not already included in introduction)
- Coordination chemistry (geometry and ligand identity for each site)
- Oxidation state(s)
- D-electron count and spin
Thermodynamics and Kinetics of the metal binding site and/or ligand interactions with the metal
- Ligand Field Theory
- The Chelate and Macrocycle Effects
- Hard-Soft Acid-Base
- Electrostatic effects
This biomolecule selects for certain metals using principles of bioinorganic chemistry (this is usually true, but not always!)
- Which other metal ions are abundant in the environment where this biomolecule operates?
- Selection based on ionic size and/or or electrostatics
- Selection based on HSAB (related to (b))
- Selection based on metal ion geometric preference (LFSE)
Electronic Features
- Is your molecule colored due to absorption of light? What are the hallmark electronic absorptions; are they d-d or charge transfer?
- Is it paramagnetic or diamagnetic? Is the spin state known? And if so, how?
- What other spectroscopic techniques are commonly used to study this molecule? Explain.
Catalysis or electron transfer
- If this molecule is a catalyst, describe and show its catalytic cycle
- How do specific features of the metal center facilitate catalysis?
- If a redox catalyst or electron-transfer center,
  - What are relevant Eo’ values of metal ion(s)?
  - Of substrate(s)?
  - How does the protein tune the Eo’ values for the metal(s)?
- Explain in detail how the system works to carry out the catalysis or electron transfer