For now I’ll continue with the food analogies to talk about one other source of uncertainty in biophysical and biomaterials measurements. That is the property of Molecular Crowding. When we think of a chemical reaction or forming materials our first thought is to considering it occurring in a vacuum, with infinite space around it. In nature, and especially inside of cells, this is not always the case. We need to take into account how much freedom the molecules in these places have to rotate and move. This might force them to undergo some molecular yoga!
Consider this curry I made for one lab potluck. In addition to the curry base itself it’s crowded full of spices and vegetables. If I were to cook the curry with just potatoes, for instance, each potato piece could cook and absorb the spices surrounding it. If I add some frozen veggies, however, the veggies near the potatoes would melt and dilute the curry around the potatoes with water. This would lead to a very slight change in flavor. To take our analogy to a cell, the cell’s cytoplasm can be like a veggie crowded curry. There are many many proteins floating around and some of them are changing the local concentration of molecules (like water!) in given parts of the cell. This can affect, say, the rate of enzymatic reaction by pushing molecules closer together so that the enzymes can grab more molecules. This is just another thing to consider when we’re thinking about how reactions inside of a vacuum can be very different than reactions in real life!
PS: I’m currently reading a very interesting paper about the origins of life and how molecules were forced to bend, twist, and react in weird ways to make up our modern system of biochemistry. I’ll post about it next time!