Will a 5 year gap between Undergrad and PhD hurt my chances? I am a 29 year old with an Undergraduate degree from Berkeley in Biochem. I graduated in 2012 with every intention of applying to PhD programs after taking a year or two off to work. 

Due to some health issues and the economic slump I was unemployed for awhile. Now I've been working in the Biotech industry for 2 years and with the support of my two bosses who are both science PhD's themselves I finally feel confident and ready to apply. By the time I intend to apply (this fall) I will have 3 years of Biotech Research experience. While I was an undergrad I worked as a research apprentice all 4 years so I also have a lot of experience in academic research. 

My biggest question and concern is: will my time in industry hurt me? Could it be an asset? Can I succeed in getting into a good school as a less than conventional applicant?
I worked for 2-3 years after my undergraduate degree before applying to doctoral programs, and I think my work experience only helped. Like you, my job was relevant to the programs to which I ultimately applied. I was able to explain in my statement of purpose how my job experience strengthened my research skills and actually motivated my decision to apply to graduate school. As long as your application is strong (good letters, good GRE scores, etc), I can't see the gap between undergraduate and graduate school mattering that much.

That being said, one point you may want to address is how you kept your "academic muscles" toned over the last 5 years. Some people find the transition back to academic life difficult after extended periods away from it, and it may be useful to demonstrate somewhere in your application how you have kept in contact with the academic world, even if it was only indirectly.