Good Eats, Plinko and RNA Polymerase....how do they connect
One concept that I think is very important when we talk about cell biology is the idea of recycling. The concept of reducing single use or reusing what you already have is something that is familiar to most people.
One of my heroes Alton Brown (Good Eats nearly had me quit a successful Post-Doc and go into Food Science) is the idea of "multi-Tasker" the idea that you would never have a tool in your kitchen that only did one task or you would have any space to actually work. With that idea in mind, the cell does a really good job of reusing the "beads on the string" as not only the structural element but also to regulate genes.
The idea is like this:
1. Genes are an output of chromosomes BUT you have multiple genes on a chromosome- each that we use at specific times and likely for completely unrelated functions.
2. Related genes (for example all the genes to re-build a synapse) have to be "findable" at a moments notice.
3. But they also need to "hide-able" so muscle genes are not expressed in the brain (and vice versa).
So how did we figure this out?
What scientists started to understand is that if you crack open a sell via combinations of changing the salt concentration of the water and adding certain chemicals you can separate out bits of the cell down to single proteins. This process is call chromatography; specifically Fast Protein Liquid Chromatography
It allows you to separate proteins based on their size. The days when I had to do large scale FPLC experiments sucked! basically you spent a day in a walk-in refrigerator for 12 to 14 hours. To collect tiny amounts of liquid into test tubes at one drop per second.
Think of it as if you remember the old game plinko basically you're making different type sizes of plinko and this is how we separate proteins and you can do it under conditions that separates all the proteins so that you get single proteins and they run through the plinko machine at different times and that will be based off of their weight or you can do a plinko machine that does it in such a way that the in the in the solution you use you can do it in such a way that the proteins that are really close neighbors in our normally hang out are still together and so then you can do you can purify protein protein complexes.
What this game of plinko lets you do is; based off of matrix (the plinko "gates) and the salt solution you used, you can tell the proteins entire social network if you will.
Once you have that social network you can create groupings for example RNA polymerase, which we always talk about as a single enzyme is a enourmous "network"- a mix of close friends, work companions and loose associated. If you think about how your social network breaks down how you characterize your friends VS how Facebook or Insta or Twitter characterize them is totally different!
It doesn't mean you're wrong or that FB or Twitter don't know you it just means that they have different purpose for how they define how you talk to, interact with, etc. Basically, the Plinko is the same, different labs ran the almost exact same experiment and came up with a social network for RNA Polymerase between 10 and 200 proteins! Both results are the right answer.
This difference in reported results is what leads to the next set of experiments where scientist look to harmonize the answers and justify the differences...hopefully through reason and logic and not personal attacks!
That in a nutshell is the scientific method:
Theory
Experiment
Report
Consolidate
[and back to theory]
More FPLC and Gene expression links:
This one is on the related HPLC (which is more valuable in drug discovery)
This one is a general review of RNA Polymerase and how it interacts a gene
This one is deeply technical but Figure 1 is illustrative
Good overview of how scientists use multiple techniques to confirm (or deny) theory and findings
