Article that may prove useful.
After reading the aforementioned article, I'm not 100% sure how this could work biologically, but I have a couple ideas:
- The world on which the aliens evolved is rich in copper in many of the ways that Earth is rich in iron, and most life has evolved to use copper in their blood in the same way that terrestrial life uses iron (note that this would also give them green blood, for sci-fi bonus points). In addition, their digestive systems are somewhat hyperefficient, capable of reducing sugars to base carbon (which they don't have much biological demand for compared to the amount of intake), but the most common copper-rich chemicals they can eat require specialized organs, which they evolved at the expense of more conventional extraction methods (this is a roundabout way of saying that they can accumulate mostly pure copper and carbon).
- The aliens in question have an organ that works sort of like a heart, but it serves a different task. It would collect dead blood cells on a film, recycling what it can, but leaving a thin sheet of copper and a layer of carbon.
- When the material level reaches a certain point, the organ heats up significantly, with the copper substrate allowing the carbon to fuse together into microscopic scales of graphene-like materials. Over time, these "scales" break away and are carried by specialized cells to repair injury sites first and to key locations second, healing wounds and, over time, making a near-impenetrable suit of natural armor from resources it wasn't using anyway.
Culturally speaking, thicker shells would also likely be a sign of higher status, as having one means you have gone a long time without getting hurt, in addition to meaning that you have a steady enough supply of food to be able to make it in the first place. (This part is irrelevant to how they're physically able to do it, but this idea came up so much when I was writing this that I had to post it.)
EDIT: Okay, I seemingly missed the entire point of the question. Lemme fix that real quick.
EDIT 2: To answer the actual question, my gut tells me that no, graphene cannot replicate the effects of collagen. Collagen is a long strand that is carbon-based, but with lots of things that are not carbon (such as hydrogen and oxygen). Graphene is a sheet that is 100% carbon, with anything else being an impurity at best. Graphene collagen apparently does exist, but it is pretty difficult to manufacture even with our level of technology, so it's unlikely that a creature could naturally evolve the ability to produce it. And this is assuming that it would even work, something that I am not entirely certain of. That being said, you could always just give it the same structure as collagen (graphene can probably be assembled in pretty much any 2D shape, so strands are allowed) and then alloy it with handwavium to deal with the science problems.