|MadSci Network: Development|
Just to be clear, it sounds like you're asking why all of the cells in a multicellular organism, such as humans, don't express exactly the same proteins & respond exactly the same to stimuli if they all carry exactly the same genome. First, although our genes themselves can be altered in certain types of cells, such as the recombination of immunoglobulin genes in lymphocytes, the great diversity in protein expression & response exhibited by the different types of cells in our bodies is, by & large, not governed by cell-specific changes in the sequences of our genes. So for the most part, your assumption that all of our cells have the same DNA is correct.
As you may know, gene expression is a very complex process that is regulated by a wide variety mechanisms. However, it appears that differential modification of certain cytosine nucleotides in gene promoter regulatory regions by methylation may be a key mechanism for regulating tissue-specific gene expression, as described in the following Developmental Biology online textbook chapter on Methylation Pattern and the Control of Transcription from the NCBI Bookshelf.
Nevertheless, you might still rightly ask how the DNA in different cell types becomes differentially methylated? Although the exact details of this process are actually still under investigation by many research groups, it's clear that the answer depends upon the interplay of the complex gene regulation mechanisms mentioned above, the activation of localized, cell differentiation programs during embryonic morphogenesis, and the resulting cellular microenvironments in the mature organism.
Because of the complexity of this process, I'm going to refer you to 2 more excellent chapters in the Molecular Biology of the Cell online textbook from the NCBI Bookshelf if you'd like to learn more about this fascinating subject, on which a large portion of the current research in developmental & molecular biology is actually focused. The 1st is An Overview of Gene Control, which actually addresses your question directly in greater detail. The 2nd is The Molecular Genetic Mechanisms That Create Specialized Cell Types, which also addresses your question in even greater detail.
Thanks for the great question & best of luck w/ your studies,
Jeff Buzby, Ph.D.
CHOC Research Institute
MadSci Development Network
Try the links in the MadSci Library for more information on Development.