Yes, but nutrition and rest and recovery methods will alleviate those effects.
Your body is designed to digest food and metabolize the nutrients found therein. Eat healthful foods and don't worry.
[/quote]Also the creation of muscle damage to stimulate growth each week?[/quote]
Again, this is what recovery periods are for. If you aren't training heavy every day, and if you're taking a week off every 3 months, you should be fine.
[/quote]Do any of these have any long-term negative effects?[/quote]
Yep, but (say it with me now) "recovery takes care of that."
Now, having said that, let me add that a pre-existing medical condition could easily hinder your progress, improper lifting technique can lead to injury that will set you back weeks or months, junk food will generally NOT help you "feed the beast." All the answers you need to any specific questions on the topics of recovery and proper training can be found by using the search feature of this website, or just browsing the articles (click on the red "Articles" link in the left-hand column).