Apo B48 and apo B100 are expressed as two different apo-proteins because of difference in:

For a given gene and gene product there is a linear relationship between the coding sequence in DNA, the mRNA sequence, and the protein sequence. Changes in the DNA sequence should be reflected in a change in the mRNA sequence and, depending on codon usage, in protein sequence. An exceptions to this dogma is, coding information can be changed at the mRNA level by RNA editing. In such cases, the coding sequence of the mRNA differs from that in the cognate DNA. An example is the apolipoprotein B (apoB)gene and mRNA. In liver, the single apoBgene is transcribed into an mRNA that directs the synthesis of a 100-kDa protein, apoB100. In the intestine, the same gene directs the synthesis of the primary transcript; however, a cytidine deaminase conves a CAA codon in the mRNA to UAA at a single specific site. Rather than encoding glutamine, this codon becomes a termination signal, and a 48-kDa protein (apoB48) is the result. ApoB100 and apoB48 have different functions in the two organs. Ref: Harper's Illustrated Biochemistry, 26th Edition, Page 356; Human Molecular Biology: An Introduction to The Molecular Basis of Health By R. J. Epstein, Pages 105-6