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How will one bad mark in first year chemistry affect my chances at Queens or UofT med?

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Hey guys, I'm just wondering how much will my chances at getting into Queens or UofT med be affected due to a BAD first year chem mark. So, a little background, I'm a first year UofT student and I am taking a full course load, like many other med hopefuls, so far scoring all As or A+s and I am super confident that I will continue to do so in the years to come, because I'm getting into a specialist program, with courses that I'm naturally very good at... So with a strong work ethic I'm sure I'm fine. The only problem is, I unfortunately got a lower than expected mark in my first semester chemistry class (to be frank I was never really good at chemistry so I kind of put off looking at it until the very end) which sadly lead me to the situation I'm in right now. Good news is that I've actually started trying in the second semester course (chemistry is split up in 0.5 credits for each semester) and I think my second semester mark can reach an A- with A/A+s in my other courses, but I will still have that on my transcript. If I was applying during 4th year, I know this wouldn't really matter because of the wGPA, but I really wanted to apply during third year, and I feel I have a good list of credentials to go along with it. The only thing is that now my cGPA and my GPA overall is going to be terrible because of one bad grade in first semester of first year. Do you guys think I can write an academic explanations essay to explain how this one course does not define me overall or should I just not apply during third year and use the wGPA to my advantage during 4th year? Honestly I just find it very disheartening that my overall GPA would be around a 3.9+ according to OMSAS scale but because of that one mark now my chances are slim if I want to apply in third year. 

Sorry for the huge rant-like paragraph and I appreciate your input!

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