How could the presence or absence of a protein determine a phenotype

Each protien is essentially a code for a genotype (what the DNA is "saying"). Different genotypes (or DNA combinations) cause the person, plant, animal, etc. to look different.

Answer:Proteins Dictate Phenotype

Genotype controls phenotype because genes direct the production of proteins ... Some proteins serve structural functions (for example, in the maintenance of cell and/or tissue shape and rigidity) while others are involved in the transport of molecules and communication between cells.