The manipulation of energy by cells requires that they have

tree and the cat in the tree

the pronoun reference replaces a noun, but you have to make sure there's no room for confusion.

in the first sentence "her" could be referring to shely or to the sister. the answer there is "shelly called her sister and told her about the new baby."

in the second sentence "it" could be referring to the roof or the floor. the answer there is "since the roof leaks on the family room floor, we need to repair the roof."

the development of trade during the middle age increased to the change given in the agriculture, which gave money, industry and markets a bigger importance in economy. the agriculture production was more than the consumption, which meant the creation of wider markets out of the areas. besides, with the end of multiple wars, the population increased and new trade routes were created.