Question: Do colleges consider only your end-of-junior-year GPA or will they look at your transcript as a whole?
One of the big mistakes that some high school seniors make is to assume that junior grades are all-important and that senior grades aren't on the transcripts that colleges see. On the contrary, first-semester senior grades can be critical in the admission process. Even early decision candidates usually find that their first-quarter senior marks come under scrutiny.
Admittedly, there is some element of inconsistency in the process. Depending on when your first senior grades are posted and when your application folder lands on an admission official's desk, your initial evaluation may--or may not--take place with your senior marks in consideration. In many admission offices (and in a perfect world), if your grades come in after your initial "reading" takes place, the admission officer will be informed that updated information has arrived and will re-evaluate your case. Realistically speaking, however, that re-evaluation usually takes place, but sometimes it falls through the cracks. (The latter scenario is more likely if your GPA from junior to senior year changes just slightly. If there's a huge difference, it makes an impact.)
It's not uncommon for otherwise-strong students to experience a dip in grades at the start of senior year. This is probably due to a combination of things: college visits and applications are time-consuming and distracting, as are the leadership roles that seniors often hold. However, there is also the prevailing misconception in some high schools that senior grades don't "count." They sure do.
Likewise, the grades you earned as a freshman and sophomore are important, too. Granted, a "rising record," as admission folks call it, is certainly better than a tumbling one, and if your grades have gotten better each year, admission committees will appreciate the improvement. However, low grades at the start of a high school career can damage admission odds, especially at the most selective colleges. This is largely true because so-so grades in the early years of high school have an effect on class rank that is usually irreparable. In other words, in most high schools, even straight A's in 11 and 12 won't allow those who didn't start off with a bang to climb to the top of the class. Sad but true.
Finally, many high school students complete all or most of their school graduation requirements at the end of junior year and look forward to 12th grade as a time when they can indulge in some of the electives that interest them: psychology, ceramics, photography, law, etc. Unfortunately, at the most competitive colleges and universities, admission officials are apt to label such offerings as "fluff." Never mind that some of these classes are truly challenging, and some applicants who take them will go on to earn advanced degrees and distinguish themselves professionally in these areas that they first discovered at age 18. From the all-too-exacting elite-admission point of view, physics trumps philosophy every time; calculus beats out economics. It's always tough to tell an aspiring artist, who's waited a dozen years to study silk-screening as a senior, that another year's wait is in order if Ivy applications are on the line, but--in most cases--that's the state of affairs in admissions today.
Bottom line: Seniors need to stay on their toes all the way until the ink is dry on that sheepskin in the summer. Frosh and soph grades don't count as much but can be deciding factors at the more competitive institutions.