Many applications are due prior to the fall semester grades being released, so in my experience, many schools will not be able to use these grades in their evaluation of your application.
However, almost all schools will require an unofficial transcript (a few required official ones) at time of application and this usually means that they will see what courses you are enrolled in. Some schools also ask for courses you plan to enroll in for the remainder of your school year.
Either way, your grades in your junior year will probably play the largest role in the grades portion of your grad school application. For most people, junior year is the start of upper level physics courses and most schools care more about your upper level courses than your lower level courses!
That said, your senior year grades will still be very important after your senior year when you apply to fellowships during your first year or two in grad school!