Thanks so much! We ran out of time to do the tutorial so it's no surprise it's a bit confusing!
The cell's 'face down' state is like a Minesweeper cell - they are filled with the colours of the *adjacent* proteins, not their own. So an unclicked cell with two red blobs and one yellow blob has three adjacent cells, two with red proteins and one with a yellow.
They also don't contain directional info (which adjacent cell has which protein) - the game will make you take a 50/50 guess sometimes!