We study the formation mechanism of molecular junctions using break-junction experiments. We explore the contribution of gold-atom rearrangements in the electrodes by analyzing the junction stretching length, the length of individual plateaus, and the length of the gold one-atom contacts. Comparing the results for alkane dithiols and diamines, we conclude that thiols affect gold electrode dynamics significantly more than amines. This is a vital factor to be considered when comparing different binding groups.