What are some limitations of using a DNA molecule model ?
I'm assuming that you're referring to a physical model of a DNA molecule.
One limitation of this representation is the fact that it comes nowhere near representing the actual size and complexity of a gene, let alone an entire genome. This is a fairly common issue with models of very large or very small things; the scales involved are very difficult for most people to visualize and understand, because they're beyond anything that we are accustomed to working with. Similar to the way that it's hard to visualize...
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One significant draw back of DNA models is that they don't effectively demonstrate the epigenome. The epigenome is made up of chemical compounds that help determine how the genes will be have. This plays a huge role in gene expression. Say, for instance, that a person has the genetic marker for diabetes, but they take excellent care of themselves and get plenty of excersize. The chemical compounds that make up the epigenome of that gene could suppress the expression of diabetes. Conversely, if the epigenome is negatively effected by diet and excersize diabetes could be actively expressed. DNA models do not sufficiently demonstrate the complexity of gene expression.