While I was searching for materials for my research topic, I found a research paper which is signed as copyright by "Some organization". Does that mean that I could not use the content of this paper nor the ideas it presents until the paper owner gives me permissions?
Not necessarily. Copyright prohibits you from presenting the work as yours under any circumstances. In addition, it prohibits you from publishing or recopying large segments of the work, without securing the permission of the owner of the copyright.
However, the existence of copyright does not exclude you from citing the work of others, nor mentioning what their key ideas are. Such use of copyright is covered by fair-use guidelines. Under these circumstances, though, you are still responsible for following the proper citation procedures of your university or the journal to which you are submitting the work under question. Note, however, that this is a tricky balance, and you should be careful to directly quote only the material you absolutely need to duplicate, as fair use is not an absolute guideline.