From the Oxford Corpus of English:
PER ANNUM
For 30 years, it had gone remorselessly ahead, at about 80% per annum.
An Elan bond, where the bondholder can exercise the right to be repaid in 18 months, currently yields 19 per cent per annum.
With this fresh impetus, the total edible oil processing capacity, including vanaspati, is expected to cross 20 million tonne per annum.
PER YEAR
We can currently get about 5% per year from investing in long-dated gilts, so we might aim to get 6% per year from the property.
Penetration of digital has hit 20 % in a year, with incremental revenue per subscriber at $22 per year and growing, he said.
This still leaves teachers $3,000 per year short of accountants, $17,000 short of computer systems analysts, and $25,000 short of engineers.
These example sentences are representative of the most common uses of these two phrases and, as one can see, there is no real difference between per annum and per year in usage.
As kiamlaluno says, per annum is traditionally used more in financial contexts than per year, but these sentences show that per year is also perfectly acceptable.
I found several entries for to get, in the phrasal verb section, so I thought I'd include them all. I separated them so the message is more comprehensible. Note that the last two are very similar except for the preposition "get sth over with" vs "get sth over to somebody". All the examples and definitions are mainly taken from the Oxford Advanced Learner's Dictionary, with a double check on my NOAD (for example, what I wrote between parentheses in "get over sth/sb".
get over something
To deal with or gain control of something.
"She can't get over her shyness."
get over something/somebody
To return to your usual state of health, happiness, etc. after an illness, a shock, the end of a relationship, etc. (Recover or overcome a difficulty)
"He was disappointed at not getting the job, but he'll get over it."
get something over (with) (informal)
To complete something unpleasant but necessary.
"I'll be glad to get the exam over and done with."
get something <-> over (to somebody)
To make something clear to somebody.
"He didn't really get his meaning over to the audience."
Best Answer
"Time is over" seems to refer to time as a period that has passed. "Time is up" seems to refer to time as a certain deadline that has been reached. So when one says that the time to submit applications is over, it means that the opportunity to submit an application is missed, and when one says that the time is up, it means that you should submit your application ASAP, since it is your last chance.