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
bahanonu [at] alum.mit.edu

more articles to enjoy:

bio42: notes
12 may 2013 | teaching

While teaching bio42 (cell biology and animal physiology) I created weekly notes to help students in my section study and focus on the impo[...]rtant 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 LaTeX so much, especially for larger projects that are heavily linked—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).

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.

¿qué es la calle?
24 may 2013 | short story | spanish

Había terminado y salé para mi cocina. Tenía hambre pero este día no había comida dentro de mi despensa. Me fui y caminé hacienda[...] la Tport—una máquina que puede transportar una persona a otro lugar sin energía y tiempo. Cuando entré la máquina, toqué algunos botónes y esperé. Pero nada ocurrió y lo hice las mismas acciones otra vez—y nada ocurrió.

How would the disappearance of streets affect the social fabric? This short story briefly (in castellano!) explores a world in which instantaneous, free transport is possible. Meant mainly to practice my spanish, i plan to follow-up with a more detail story in the future.

Donald J. Trump Campaign Poster 2016 No. 2
09 May 2016 | designs

Part 3 in the 2016 Presidential campaign poster series. "Under budget and ahead of schedule" is an easy to remember phrase. Fits Tr[...]ump's campaign rhetoric, so here's the poster. Originally was a direct numbers-to-numbers comparison with all the other candidates, but that got a little busy...

gantis: toward the edge
28 june 2013 | short story

The first in a series of short stories exploring a universe in which our negative space (i.e. space) is turned into their positive space (i[...].e. matter) and vice-versa. Thus, it is like the entire universe is a series of caves that they must excavate. This story introduces a few key characters, explore a bit of the lore, and is an attempt by me to write a story in which a clearer light is shone on a relationship between two characters. More to come, enjoy!

©2006-2025 | Site created & coded by Biafra Ahanonu | Updated 21 October 2024
biafra ahanonu