.Net Framework assembly questions

I see there are two different locations on my development box related to .Net framework 4 and 4.5

C:\Windows\Microsoft.NET\Framework\v4.0.30319

And

C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0

C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5

1>    What’s the difference between the assemblies at these locations?

2>    I have ASP.NET application, when I build  the application, I don’t see system.dll, system.data.dll…etc gets included in the bin folder.  How these assemblies gets referenced at runtime on the web server?