Students from the first year Bsc. Nanobiology have made this final exercise for the course Biomolecular Programming. they have designed a program in the programming language Java that simulates microtubule growth and dynamics in the cell.
Structure and function of microtubules
Microtubules are part of the cytoskeleton and have an important role in the cell. Microtubules are fibers, which serve as the routes along which cargo (i.e. organelles and vesicles) is transported through the cell. Movement of cargo along the microtubules is regulated by motor proteins, which link the cargo to the microtubules. Forward motor proteins transport cargo to the +end, whereas reverse motor proteins transport cargo to the –end.
Assembly of microtubules
Microtubules are made up of tubulin protein. Cells maintain at least two types of tubulin, which we call α‐tubulin and β‐tubulin. α‐and β‐tubulin spontaneously bind to one another to form a functional subunit that we call a heterodimer. These tubulin heterodimers are polarized and during assembly of microtubules the heterodimers all bind in the same way to the growing microtubule: i.e. the alpha-subunit binds to the growing microtubule and the beta-subunit is exposed and can bind the alpha-subunit of another heterodimer. The growing end of a microtubule is the +end, whereas the opposite end is the –end.
Although microtubules might appear to be static fibers in a cell, the +ends continuously switch between growth and shrinking phases. The transition from growth to shrinking is called catastrophe. During a shrinking phase, the tubulin heterodimers at the +end depolymerize and dissociate from the microtubule. The transition from shrinking to growth is called rescue. Because of the continuous oscillation between growth and shrinking, microtubules are considered to be in a dynamic equilibrium, or steady state.
Microtubule disassembly can also occur at the –end. Therefore, the microtubule –ends need to be protected (“capped”) against degradation. This is done in the microtubule organizing center (MTOC), which is located near the nucleus of the cell. All microtubules originate from a capped “seed” located in the MTOC.
Students that took the effort to add biological relevant creative or extra elements to the final assignment or with outstanding code are listed below showing their simulations.
Hereby we present the best programs of the year 2021 in random order: