I am having a bit of trouble understanding how applications and data are accessed by the CPU from RAM after the application has been loaded into RAM and a file opened (thus data for the file also stored in RAM).
By my understanding, a CPU just gets instructions from RAM as the program counter ticks or carries out tasks after an interrupt. How then does it access the application and data. Is it that it doesn't and still just gets instructions (for example to load a file on the hard drive to be opened in the application) and processes any requests made by the application which are stored in RAM as instructions thereafter (like saving a file). Or does the application and data relating to an opened file (for example) just stay in RAM and not get accessed by the CPU at all.
Similarly, after reading an article, it said that a copy of the operating system is stored in RAM. The CPU can then access the operating system. (I thought the CPU just worked with instructions from RAM). How does it then communicate with the operating system and how are interrupts sent to the CPU, from the copy of the OS in RAM or from the OS in the hard drive.
Sorry if this is really confusing, alot i didn't understand.
Root of your question: Lack of clear differentiation between Computer's Hardware and Computer's Software.
Just so that we are clear about both of them and that we understand their nature, let me state as follows:
We will start with understanding from the time when we say that the computer is up and running and is properly executing our instructions. But at that time you will say - How did I reach here? So I will mention a few points about the startup of the computer.
...the most primitive and basic input output system (therefore called BIOS), which is hard written on the computer hardware begins execution. This is written on Read Only Memory and this starts the process to get the machine to stand on its own. And it loads the software (Operating System) from one piece of hardware (disks) into another piece of hardware (RAM and CPU registers) enabling the software to work properly with hardware.
Now the body and soul are together and the individual (machine) can work.
Until now, OS is already in RAM and CPU. (Read When the power button is pressed if you doubt it.) Let's handle your question paragraph by paragraph now -
I am having a bit of trouble understanding how applications and data are accessed by the CPU from RAM after the application has been loaded into RAM and a file opened (thus data for the file also stored in RAM).
The explanation is as follows:
By my understanding, a CPU just gets instructions from RAM as the program counter ticks or carries out tasks after an interrupt. How then does it access the application and data. Is it that it doesn't and still just gets instructions (for example to load a file on the hard drive to be opened in the application) and processes any requests made by the application which are stored in RAM as instructions thereafter (like saving a file).
As you have guessed it - CPU doesn't get instructions, Operating System does it through CPU. Also, just the way brain doesn't directly instruct the hands and legs to move and instead uses nerves for interaction, the CPU doesn't tell the disks to give/take the data. CPU works with RAM and registers only. Multiple units of hardware work in conjunction to provide a path for data and instruction to travel. The important pieces of involved hardware are:
I like the image provided in this answer. This image not only lists the hardware pieces but also illustrates the mammoth difference in the execution speed of these pieces.
Let's move on to the...
Similarly, after reading an article, it said that a copy of the operating system is stored in RAM. The CPU can then access the operating system. (I thought the CPU just worked with instructions from RAM). How does it then communicate with the operating system and how are interrupts sent to the CPU, from the copy of the OS in RAM or from the OS in the hard drive.
By now you already know that indeed OS is present in RAM and CPU registers. That is where it lives. That is from where it tells the CPU how to work. If OS would be small enough (or if Registers and Caches would be big enough), the OS would live even closer to CPU.
The lack of distinction between hardware and software is the basic cause of your confusions. Take some course about Operating Systems on Coursera or Academic Earth for deeper understanding.