I've seen movies of individual cells and such moving about with their little cilia or fimbria and such, and I've always wondered how they actually do it. Same with muscle cells.

 

I mean, they are just some bags of protein with water inside! What actually causes those proteins to move? To me it's the same as supposing that the molecules in some chemistry experiment are going to start swimming around!

It's all energy (ATP) dependent. Muscle fibres consist of actin and myosin. Hydrolysis of ATP to ADP + Pi causes a conformational change in the myosin protein which causes a shortening of the muscle. It's a bit tricky to explain in words, so I'll try and find some diagrams.

 

I assume the principle is similar for other contractile proteins, but I'm sure someone will correct me if I'm wrong.

Well, it's very different for the various types of molecular locomotion.First, it's important to understand that the locomotion organs are not single protein, but a system of proteins.

Secondly, it differs from system to system what kind of energy is being used: for instance, the eubacterial flagellum for instance, utilizes a gradiant of protons to spin its filament, while cilia uses ATP for moving the dynein-arms.

 

For extra info check:

 

http://en.wikipedia.org/wiki/Flagella

 

http://en.wikipedia.org/wiki/Cilium

 

I mean, they are just some bags of protein with water inside! What actually causes those proteins to move? To me it's the same as supposing that the molecules in some chemistry experiment are going to start swimming around!

 

Well not really - you give the cells to little credit!

the cilia and flagella beat due to ATP motion. i really dont want to get into the biophysics of it because it would take several pages to explain and i dont even know most of it

flagella beat due to ATP motion

While archeal flagella probably uses ATP, the eubacterial flagellum is powered by a proton flow. This flow is generated by the cell itself through the electron transport chain.

It all comes back to respiration, and the creation of ATP from a proton gradient. Muscles use the actin-myosin to expand/contract. I assume cilia etc., use a similar system.