The byproduct of ATP when it makes muscles work is ADP and energy. They are not harmful in anyway.
When muscles work without enough oxygen, they produce a byproduct called lactic acid.
muscle cells produce ATP by cellular respiration through fermentation
The acronym ATP stands for adenosine triphosphate, which is a chemical; chemicals do not have muscles, the just have atoms.
Skeletal muscles generate heat during physical activity through a process called muscle contraction. When muscles contract, they use energy from ATP molecules, which produces heat as a byproduct. This heat helps to maintain the body's temperature during exercise.
Cellular respiration
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ATP is used by the body as a source of energy for the muscles.
If you lift heavy enough you get micro tears (muscle soreness). While you are exercising your muscles burn food to make ATP which allows your neurons to tell your muscles when to contract. The byproducts of this metabolizing of food molecules makes it harder for your muscles to keep contracting. Lactic acid (a byproduct) builds up and burns.. Well, its a vague answer for a vague quesiton :P
After ATP hydrolysis, ADP is formed as a byproduct. This process releases energy that can be used by the cell for various functions.
Oxygen is used to create ATP in the muscle cell site, however it is still possible to create ATP without oxygen. this is called Anaerobic glycolysis and is when energy from glucose (sugar) is broken down without the presence of oxygen. the byproduct of this reaction is lactic acid and causes the muscles to retard and tighten up.
Muscles need ATP to contract. Mitochondria produce most of the ATP in the cell, so there are lots of mitochondria in muscle.