This may be kind of a stupid question, but I'll go for it anyway.

I've recently started taking gym class (it's mandatory your first year of high school) and we have to run around a track, usually twice, every day. I'm not used to that much running, even if it's not all that much, and my legs hurt terribly. I keep getting bad pains in them. When I walk up or down stairs my ankles throb. I thought it might be because of my shoes (they weren't too supportive). But I got a new pair and it hasn't made much of a difference yet. We also stretch before we run so I don't think that would be a reason. So I'm just wondering, is this something I should be particularly concerned about? Will it go away in time, and is there anything I can do to prevent it?