How do we know so much detail about the structure of tiny things like genes or antigens...if we cant even see them under a microscope?

..

o We can see "groups" of things. Someone pointed at something and asked, "I wonder what that is." Best example: DNA was discovered by a fellow who wanted to figure out what pus on used bandages contained. Seriously. His name was J. Friedrich Miescher.

o A whole lot of clever and interesting biochemistry experiments done by a whole lot of genius-level clever biochemists over the past 146 years.

- You will learn more about this in your college biochemistry and biochem lab classes. At my alma mater, those classes were taken in the junior year. (They built on stuff learned in the organic chemistry classes which were sophomore year.)

Our main textbook was "Lehninger Principles of Biochemistry"

If you read through it, you can get some idea of the techniques used to elucidate the mysteries of biochemistry. ... but look at the bibliography, and read some of the scientific papers cited. Then read papers that are cited by those papers, etc.

Good luck on your voyage of discovery, young biochemist.

There are other ways to deduce molecular structures, like NMR. The technical details are beyond your current education level. Your frustration is with your own ignorance.