Suppose a cell wishes to make a protein that has 100 amino acid. how many water molecules will be created in the making of this small protein?

The answer is 99.

Amino acids contain a carboxyl group (carbon-containing) and an amino group (nitrogen containing). Proteins are made by forming peptide bonds between the carboxyl and amino group of amino acids.
If a protein is made of 100 amino acids, that means there are 99 peptide bonds (because the last, 100th amino acid will not bind the next (101st) amino acid). For each peptide bond that is created, one oxygen atom and two hydrogen atoms are taken. Therefore, one water molecule is created for each peptide bond. If there are 99 peptide bonds, 99 water molecules are created.