Question. How many genes does a cell need in order to live?
The idea of this class project is to generate an estimate of the minimum number of genes (and proposed names/functions) required for a simple life form to function under the controlled conditions outlined below. There is no one right answer to this problem; the answer could depend upon how you approach the problem. We will begin this project on day-one and complete it at the end of the semester.
In order to answer the question, you must first decide (as a group) on those processes that are essential for life; for example, metabolism, cell division, protein synthesis and so on. Then, taking each process in turn, outline a series of metabolic/enzymatic steps that are needed to accomplish the synthesis of each required molecule. There are metabolic maps available to help you with this. You may not break the laws of thermodynamics or, as Scottie would have said "You cannae break the laws of Physics Captain!"
Once we have decided on the areas of study, you will divide into smaller groups and work on individual processes. We will then try to pull all of these areas together in the later sessions as we get closer to our estimate.
A successful outcome will be in the form of a map outlining each process and how it fits with the other processes. A list of the genes required for the processes should be included. When we fit the maps together, we will check for duplications.
Rules and Conditions for the creation of life on paper.
1. This is a simple Prokaryotic life form so no organelles, internal membranes, or cytoskeleton is present.
2. It is unicellular so there is no need for cell adhesion or ECM systems.
3. Several nutrient moleules are available (glucose, methionine and alanine). Minerals such as calcium salts, and phosphates are available as needed. This is no need for photosynthetic mechanisms.
You will need to consider the transport of the materials from the environment into the cell. Will they diffuse in or will they need to be transported in? Along these lines, will any molecules made by the cell be lost by diffusion across the membrane and therefore will you need to protect them with binding proteins?
4. The cell has a DNA based genetic code with no introns.
You will need RNA synthetic machinery, ribosomes and tRNA systems. Each rRNA, and tRNA molecule needs a gene. How many tRNAs are there? Assume that our life form has normal prokaryotic ribosomes. How many proteins and rRNA molecules are there?
Feedback systems for the regulation of gene transcription will ultimately be needed, see the tryptophan repressor and/or lac operon for examples. However, to keep it simple to begin with, assume that each protein is made constitutively at levels sufficient to carry out its function.
5. The environment is such that there are no strong adverse conditions, i.e. no strong UV light or ionizing radiation that might damage the DNA, no exogenous toxic compounds, no strong heat sources, no strong mechanical forces, no viruses or predators and so on.
6. The cell uses anaerobic respiration- so no oxidative phosphorylation/electron transport system is required. The cell uses glycolysis and lactate fermentation to produce ATP and NADH + H+. There is no molecular oxygen present so you do not need to worry about oxidative damage/repair.
7. Waste products will diffuse out of the cell. In reality, some of the wastes would need to be transported out by carrier proteins. To keep it simple to begin with, assume that waste products can diffuse out of the cell.
Remember, every protein that you propose needs a gene.
Assessment. Your grade for this assignment will depend upon how well you participate in the discussions and formulations of the metabolic maps, and upon how well you understand the processes you are outlining. Your grade will also depend upon the typed process outlines you submit for pasting into the final map.