Is all Elevation Gain the Same?

Most of my runs these days take place on trails that are a series of long uphills and long downhills. To be more specific, I may start off with a three mile uphill with a 900 ft. elevation gain followed by a two mile downhill with an elevation loss of 600 ft. followed by another two miles and a 600 ft. gain, followed by another similar drop, followed by a 1200 ft. climb over two miles, and then back to my original starting point via a more direct route. A route like this may add up to 3300 ft. of gain and loss over 15 miles. I might feel somewhat spent after such a run.

I often read blogs of other runners who may cite similar or greater elevation gains but I am certain that their climbs are shorter, but more frequent. I wonder if two runs of the same distance, same elevation gain and loss, and same elapsed time are in effect the same workout.

Scott Jurek mentioned on the last page of Runner's World magazine this past edition that the training that prepared him to become the ultrarunner he became took place on hilly trails around Duluth, Minnesota and that even when he's gone back to them after training on significantly longer climbs in the West he finds the Duluth trails to still be a challenge. This makes a case, I think, more that one can do better at what one is conditioned to do.

My intuition, experience, and just enough knowledge to be dangerous would suggest to me that an athlete of conditioning that doesn't predispose her to favoring one course or another would be able to run longer before reaching exhaustion on a course that repeated 52.8 ft. elevation gains and losses of 5% grades than repeats of 528 ft. elevation gains and losses of the same grade. I have a couple of pieces of logical evidence that supports this way of thinking. One is that the heart muscle keeps beating until one dies. I could do some quick research but I seem to remember from somewhere in my education that the heart muscle has a rest built in after every contraction that is about 40% of the cycle; it gets very frequent rests. Also, more runners are building in a brief recovery walk into their marathons and improving their times.

Doing longer uphills or continuing to run in a marathon where a short recovery walk would be beneficial seem to place greater stress on the muscles, forcing them to continue to push although approaching fatigue. Although covering the same distance and elevation gain and loss at the same slopes in the same amount of time might be considered doing the same amount of work, it seems that if in route A the muscles have to operate closer to fatigue this would be the "harder" workout.

I know there are lots of factors and maybe my question is open to interpretation so to put it as scientifically quantifiable as possible, the question is which route would one be able to sustain longer, the one with longer and fewer ups and downs or shorter and more frequent ups and downs.