Aug. 3, 2016
Over the eons, “The Dean" has seen “top schools" defined very broadly. So I don't know exactly which colleges and universities you're referring to here, but if we're talking about Ivies and their ilk …or about any of those picky places where the acceptance rate is under roughly 30% … then these deficiencies aren't automatic deal-breakers but they definitely could be strikes against you. (This, however, will be less true if you come from a disadvantaged background, are the first in your family to attend college, or you go to a high school where students rarely apply to competitive colleges. In such cases, admission committees will likely give you more wiggle room for shortcomings on your transcript.)
Do you have a reason for only taking two years of Spanish? For instance, do you have a documented learning disability? Is English your second language? Did you change high schools? Are there limited language offerings at your school which led to scheduling snafus?
If any of these reasons (or similar ones) apply, you should use the “Additional Information" section of your applications to explain. But your explanation should lean toward the factual (“Foreign language at my school is offered at the same time as art classes, and art is my passion") rather than the whiny (“The language teachers at my school are all terrible!").
As for chemistry … skipping chem alone won't be a huge problem if your schedule includes other heavy-hitter sciences (e.g., AP Physics, AP Bio) and it would help a lot if you've taken the toughest math classes as well. But at the hyper-selective colleges, many of your “competitor" applicants will probably have taken AP's in three lab science plus math through AP Calculus.
Of course, if your “top schools" are interested in you for reasons beyond your academics, (e.g., you're a recruited athlete, an under-represented minority student, hail from an uncommon background or offer unique talents), then the admission officials will be more inclined to look the other way at transcript-review time than if you're merely what I've dubbed “The Average Outstanding Kid."
So, although your deficiencies won't immediately take you out of contention at the most sought-after institutions, they will certainly work against you unless your profile contains other strengths that will distract the admission folks!
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