bio42: diagrams, part 1

summary

Had a couple minutes to spare before leaving lab, so decided to throw together some diagrams to help explain a couple biological pathways students of bio42, a bio class at Stanford I'm TAing. Hoping to make a set for each system we study. Started with vesicle budding and fusion along with muscle contraction in smooth and skeletal muscles.

Had a couple minutes to spare before leaving lab, so decided to throw together some diagrams to help explain a couple biological pathways students of bio42, a bio class at Stanford I'm TAing. Hoping to make a set for each system we study. Started with vesicle budding and fusion along with muscle contraction in smooth and skeletal muscles. The similar style, layout, and coloring is an attempt to demonstrate the similarity in pathways for students and allow them to get the basic components down. Many parts of biology boil down to understanding the basic framework of proteins being turned on or off then doing the same to some other protein, enzyme, metabolite, what-have-you downstream.


Diagram of vesicle budding and fusion.

There was a little difficulty in diagramming with a flow chart certain dynamic processes such as vesicle and target membrane fusion or the interaction of SNAREs along with their detachment by NSF and SNAP, but I think it captures the essential elements. In the future, I'll probably clean-up the style of the lines and choose a softer color scheme to make the diagram more inviting. Also, should probably just show more things that are in complex as being grouped together, but that might clutter the diagrams unnecessarily.


Diagram of vesicle budding and fusion.

Muscle contraction was a little easier, but I greatly simplified the actual contraction step. Might make a separate diagram that details the coupling of ATP hydrolysis to myosin head movement. Regardless, looking forward to building out from here and adding protein trafficking, nuclear import and export, cell cycle, EGFR to MAPK signal transduction cascade and many more. Should be fun!

-biafra

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12 may 2013 | teaching

<p>While teaching bio42 (cell biology and animal physiology) I created weekly notes to help students in my section study [...]and focus on the important materials presented in the class. I built off of the latex boilerplate that I have been improving over time to create weekly notes. This highlights why I love <a href='http://www.latex-project.org/' target='_blank'>LaTeX</a> so much, especially for larger projects that are heavily linked&mdash;it allows easy annotation, indexing, creation of new document styles, and other related processes rapidly and consistently. Plus, separating content and style is always a plus and images stay uncoupled from a propriety source (e.g. Word files). </p> <p>I really love the resulting notes and student feedback was quite positive. I thought sharing them might be useful for others in the future. The source latex files and raw images can be sent upon request (I'm considering making a Github repository in the future). I'll briefly talk about the document below and certain decisions that were made to get it to its current state. </p>
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