Carbon nanostructures are ubiquitous in our environment and have a range of interactions with biology, and depending on the arrangement of these carbon atoms, the structures can do dramatically different things – in this work: guiding neuronal growth, immunomodulation, and double stranded DNA cleavage. Carefully controlling these arrangements of carbon atoms in nanostructures can give unprecedented and powerful control over many aspects of biology. PEGylated graphene nanoribbons (PEG-GNR) are long, thin, conductive nanostructures produced by the reductive unzipping of multiwall carbon nanotubes. The Tour group has previous used similar structures based upon the GNR architecture for a range of applications. In this work, we show that PEG-GNR show substantial promise for both spinal cord repair and optic nerve repair. This work shows near perfect recovery of a quadriplegic rat, compared to previous work where functional recover was very limited. Neuronal interactions with graphene are not limited to the ribbon formulation, and this work also shows that carbon nanotubes can be used to modulate the firing rates of ex vivo retinal ganglion cells with stimulatory voltages an order of magnitude smaller than previous work, further suggesting some special interaction between carbon nanostructures and neurons. This work extends previous work in the Tour lab using small water soluble carbon cluster antioxidants (PEG-HCCs) by using them for immunomodulation. This work goes into mechanistic detail understanding both how PEG-HCCs dismute superoxide, and how this property allows them to be immunomodulatory without being toxic. Finally, this work will examine the darker side of carbon nanostructures, showing that seemingly innocuous carbon can also be toxic, causing double stranded breaks in DNA. This work shows that certain carbon nanoparticles can induce T-cell mediated emphysema in a mouse model, but also show ways to ameliorate this toxicity with simple, cheap modifications to the carbon nanostructures.