Question

How might similarities and differences in genetic code, or the proteins built as a result og these codes, be used to determine how closely related different species are ?

Answer 1

Start with the premise that all members of a species have very minimal variation in sequence of both specific genes (or non-coding regions of DNA for that matter) and the proteins produced by those genes.

Then think about what happens to the genes if one group of individuals in that species mates only with other members of that group, and if another group of individuals of that species mates only with other members of that second group. Each group will accumulate a different set of mutations or gene variants over time. Which will in turn affect the proteins and hence the physical properties those groups have. At some point, they will become so different that we can consider them different species.

So greater difference in gene and protein sequences --> less closely related the organisms are.

There are a few caveats that you should think about: degeneracy of the protein code, so to some extent changes in the sequences of genes will be silent in that they will not affect sequences of the proteins; also, mutations in some regions of DNA is better tolerated than mutations in other regions, resulting in different rates of mutation accumulation over time in different genes and proteins, as well as in different regions of the same gene and the same protein. And whether or not mutations are well tolerated or not well tolerated (i.e., whether or not they are beneficial or detrimental or neutral to the organism) is to some extent environment dependent; environment changes over time, so the rate of mutation accumulation can vary over time.