There is not actually that much difference between a large 16 inch navy gun and the significantly smaller 0.22 inch rifle issued to every soldier. Everything is bigger of course and that does mean there is some differences in the equipment used and such. You will not be able to fit almost a hundred men working with hydraulic pistons, hoists and winches into a tiny rifle but they are quite efficient in a big navy gun.
There are two major differences though. Smaller guns usually have the ammunition packed in brass cartridges. So you load the gun by inserting a cartridge containing everything needed. In a big naval gun though this would be too big and cumbersome. The projectiles alone might weight more then a small car so it is much easier to move everything around separately. So you would first load the projectile, then several bags of explosives, and lastly the primer. This also means that there is no spent cartridge to deal with, when the gun have fired it is empty and ready to load the next round.
The other difference is that the shells themselves tends to be packed with explosives. So that when it hits it is going to explode. This helps cause more damage. Instead of just punching a hole through a ship it will blow a much larger hole in the ship. Of course explosive ammunition is available in smaller calibers as well.
But essentially a naval gun works the same way as any other gun. You pack a big pile of explosives behind a projectile and then detonate it. The projectile then gets a lot of speed out the barrel which allow it to fly through the air to hit the target.
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