Rather than answering all her questions correctly and fully, what is important to help her develop a scientific mind is to spark her interest in the scientific method:
The steps of the scientific method are to:
- Ask a Question
- Do Background Research
- Construct a Hypothesis
- Test Your Hypothesis by Doing an Experiment
- Analyze Your Data and Draw a Conclusion
- Communicate Your Results
A 3.5 year old can't do all of these things yet in the way an older kid could, but you can guide her to begin the process. She's already asking questions so that's a good start!
I'd suggest you spend time taking your daughter out into nature. Let her play scientist by collecting different kinds of leaves, and ask her why she thinks some leaves look different from others. Have her pull apart a flower to see the parts inside, and ask her what she thinks the parts might be for. Find some insects or other small invertebrates under a log; she will naturally start observing their behavior.
You won't have all the answers to her questions, but that's okay. Feed her inquisitive mind by helping her find things out on her own.
And if you want to do some research on your own or together with her to find some age appropriate answers to the "why" questions with websites or videos, that's fine too, but it should be supplemental the emphasis on exploration and inquisitiveness.