My dog had puppies almost 5 weeks ago and now she won't leave the runt in with the other pups and if she is therewith others she carries it in her mouth why is that

I would say that she can sense that the other pup needs more help. If she felt that it were debilitated or sick in any way she'd be more likely to abandon or eat it. She's just being a good mommy. :)

Make sure the runt is getting enough to eat. If necessary, go to the pet store and get some milk replacer (NOT MILK) to supplement.