Here are some excerpts from my talk on spatial organization of bacterial transcription and translation.
If you're interested in checking out the full PowerPoint presentation you can download it by clicking here: Download Presentation (873,3 MB)
If you want to check out my talking points for the presentation you can also download this PDF it by clicking here: Download Talking Points (0,2 MB)
Friendly cover animation.
This is a protein. There are many different types of proteins each with their own particular purpose.
The blueprints for each protein are encoded on the DNA. To synthesize a protein, DNA is first transcribed to mRNA (grey wiggly bits), and then the mRNA is translated by ribosomes (pink blobs) to make a protein.
Due to the dense nucleus at the centre of the cell, the mRNA is pushed outward, the more it is synthesized.
To model this spatial organization, we can make use of the symmetry of the model and only focus on one half.
In order to understand how to set up the reaction-diffusion equation, let's begin by looking at how to mathematically define "diffusion" in the system. Fist, we simplify the geometry by counting the number of ribosomes per unit volume and projecting that onto a 1D geometry. The diffusion of ribosomes can be described by a discrete change in density along the x-axis.
Next, let's have a look at the different reactions in the system. Ribosomes can attach to the mRNA with a rate of kTon and start translating. After some time they detach with a rate kToff. It has been experimentally seen that some ribosomes attach to the mRNA but do not translate any proteins. This happens at a rate kBon. These lazy ribosomes then detach after a while with a rate of kBoff. Another reaction that can happen is when the mRNA breaks up and both the translating and the lazy ribosomes are released. This happens with a rate β.
In the last clip we see the results from the numerical simulation of this model. It shows that the as the density of ribosomes on the mRNA increases, the further they are pushed away from the centre of the cell due to volume exclusion.
The way the DNA in the nucleus is modelled is through a random walk on a grid. The entropic force of this DNA-spring pushed against the pressure created by the increasing volume of the mRNA. This back-and-forth between forces determines the size of the nucleus. The simulations produce an average nucleus that matches experimental measurements.
If you would like to use these clips in your project, please attribute it to Laura Kern and provide a link to www.laura-kern.com