This is where the training of muscle specificity comes into play. I only have a Bachelors in Kinesiology, but here is my two cents. Muscles repair and changes structure according to the types of stress you put on them. There are 3 major energy components utilized in exercise. The ATP/PCr system for fast twitch muscles that provide lots of quick, burst-like power, but do not last very long. The glycolysis system which utilizes the sugar from your blood and other carbohydrates. This system allow a fair amount of power, but last a longer duration that the ATP/PCr system. Note: Both of these systems are anaerobic. Then there is the Oxidative Phosphorylation System. Essentially, it's the transfer of electrons from Hydrogen to water via the electron transport chain (Dan Judelson, PhD.) Essentially, it entails the production of ATP in the presence of oxygen. This system does not provide a lot of power, but can be sustained for long durations.
What does all this translate too? You make gains through the process of specificity. If you do resistance exercise (lift weights), you enlarge the muscle and develop a greater percentage of fast twitch type muscles. If you do endurance training, you develop more slow twitch. If you wish to improve the muscles of your upper body, then you need to train your upper body. through either resistance or endurance exercises (or both). Hope this helps and it not too much.