Lecture 1 Notes
Section 1: Modeling complex dynamic biological systems
How they work, how they respond to perturbation. The primary example of this throughout the
class will be the MAPK (MitogenActivated Protein Kinase) cascade. Kinases are enzymes that
In the last several classes, we've focused on receptors and signaling pathways. Today we
look at the last link in that chain, the transcription factor phosphorylation that leads to actual
changes in gene expression and cell behavior.
Lecture 6 Notes
We were talking about kinases and their activation loops.
Let's now go into greater detail of how kinases work and how they fit into signaling cascades.
We'll also tie it to EGFR.
EGFR normally exists at about 104 copies per cell
Lecture 2 Notes
Co Immunoprecipitation (CoIP) and Mass Spectrometry (MS)
CoIP, as the name implies, is about precipitating a particular protein by attaching it to
antibodies, and then looking to see what else gets dragged down with it. It's a way to see w
Last time we talked about EGFR and the importance of that signaling pathway. It leads to
cell proliferation, so all manner of pharmaceutical companies are trying to inhibit it to treat
cancer. We'll try to understand that today.
1. Attach protein to plate
2. Add fluorescently labeled
ligand 3. Rinse off unbound
4. Read fluorescence on plate
5. This test provides [C]eq, the complex concentration at equilibrium.
Cue > Signals > Responses
We talked about signals the last 2 classes. We'll talk about cues for the following two,
and about responses (transcriptional, mostly) during the last 2 classes in this module.
Signal shut down
We covered the graph of RU vs. time during an SPR experiment. We see a different
graph from the association and dissociation parts of the experiment, and from them we
can calculate koff (which is independent) and kobs (which cont
Ultrasensitivity/Amplification in the MAPK cascade
The distributive mechanism, where each player is phosphorylated in multiple steps,
leads to great amplification and ultrasensitivity in the cascade.
1. Double phosphorylation at t
Regulation 1. Simple
4. Local concentration
of signal 5. Different
amounts of receptor
6. Different amounts/availability of RNA