Introduction 

This review covers the mechanisms by which the energy trapped in nutrient molecules (such as glucose) is transferred to ATP.

ATP molecule. ATP is a modified adenine nucleotide. That is, it’s an adenine (nitrogen base), ribose (sugar), and phosphate group with an EXTRA 2 phosphates. These extra two phosphates require “extra” energy to push them onto the nucleotide, then “pop off” fairly easily—giving the energy back. Thus, ATP is used to “trap” energy released with nutrients break down, then transfer it quickly to cell processes that need the energy. ATP is thus a kind of “rechargeable cell battery.” (click image for a larger version)

The key here is focusing on “what’s really happening” without getting bogged down in the details of the chemistry.

• What’s really happening is really simple
  • The cell transfers energy from fuel molecules eventually to ATP

Basic Definitions
Metabolism—body chemistry

• Catabolism—chemistry that breaks big molecules into small ones
• Anabolism—chemistry that builds small molecules into big ones

Metabolic pathway—series of chemical reactions, one leading to the next, and so on
Respiration—literally “re-breathing” and refers to bringing in oxygen (O2) and releasing carbon dioxide (CO2)

• Cellular respiration—chemical process in cells that uses oxygen and gives off carbon dioxide, really referring to energy transfer
• Aerobic respiration—respiration pathway that requires oxygen
• Anaerobic pathway—pathway that does not require oxygen
  • Actually, this step is technically “fermentation” not “respiration” but the term “anaerobic respiration” is still often used

Coenzyme—coenzymes “help” enzymes
In this story, it is helpful to think of coenzymes as “escorts” that move molecular fragments from one chemical pathway to another; examples: NAD and FAD
Substrate—any molecule acted upon by one or more enzymes

Summary of chemical changes 

C₆H₁₂O₆  +  O₂  ———>  H₂O  +  CO₂  +  energy (in ATP)

[this equation is not balanced]

Cellular Respiration Pathways
Notice that the cell may start with glucose, but other nutrients (amino acids from proteins, fatty acids & glycerol from lipids) can also enter the pathway and contribute energy for recharging ATP

Step 1: Glycolysis
Breaks glucose (C6) into two pyruvic acids (2 C3) and releases energy
Enough energy is released for 2 ATP molecules
Anaerobic
Occurs in cytosol outside of mitochondria

Step 2: Transition reaction
If pyruvic acid is to continue, it enters the mitochondrion and one carbon is removed –forming Acetyl (C2)
Coenzyme A (CoA) temporarily binds to acetyl and escorts it into the citric acid cycle
This begins the aerobic process (although O2 will not actually be used until later, the molecule will enter this pathway until and unless O2 is there at the end of the line)

Step 3: Citric Acid Cycle
Also known as Krebs Cycle (for Hans Krebs) or TCA (tricarboxylic acid) Cycle
Acetyl rides this “ferris wheel” where it is broken apart, releasing its energy
The Cs and Os simply fall away, forming the waste CO2
Most of the energy released in the form of energized electrons from H (the H+ proton also tags along for the trip)

• The high-energy electrons (and H+) are picked up by coenzymes NAD and FAD and escorted to the Electron Transport System

Step 4: Electron Transport System (ETS)
Also called Electron Transport Chain (ETC) 
High-energy electrons (and H+) are dropped off at molecules in the cristae
The electrons are shuttled from molecule to molecule losing their energy as they go (passed like a hot potato, eventually “cooling off”)
The energy lost by electrons is used to pump the protons (H+) into the intermembrane space, like water behind a dam
As the protons flow back through the dam (down their concentration gradient), this powers the “phosphorylation of “or “adding phosphate to” ATP (oxidative phosphorylation) 
The electrons unite with their protons, forming H2 which is dangerous

• H2 is immediately “burned” by O2, forming waste H20
• A total of 36-38 ATPs are available from aerobic respiration (compare to only 2 for anaerobic alone)
• Lactic acid
  • Forms when pyruvic acid does not enter the aerobic pathway
  • Happens when not enough oxygen or when energy is needed more quickly than aerobic respiration can handle
  • Later converted back to glucose