Paper Rejection on Molecular Biology, What should I do?
Congratulations on submitting a paper as an undergraduate that one referee found to be publishable with corrections.  That's impressive.

Are you really the sole author on a biology paper as an undergraduate?  Biology is not my field (I'm a mathematician), but that sounds unusual to me.  Even if you are, you must be doing the research under the supervision of some faculty member, right?  If so: ask them for guidance.  

From where I'm standing, I would think that what one referee at a reputable journal finds publishable with corrections should be publishable by another journal, and perhaps even one of roughly equal quality. But you should not take the word of someone from a different field who doesn't know your work or your manuscript.  Again: ask for guidance from a faculty member.

P.S.: The fact that the referee with a more balanced recommendation looks like they did more work and understood the paper better is unfortunately a familiar phenomenon to me.  The refereeing process in academia is far from perfect: it works well when the referees decide to be conscientious and fair...but there is almost nothing inherent in the process which forces referees to be conscientious and fair or even allows one to discern with anything approaching certainty whether any given referee has been conscientious and fair.  It is a bit frustrating.  All I can think to do is to try to apply the golden rule and hope for karmic benefits to accrue eventually (if I may mix metaphors slightly).