The myriad of chemical reactions occurring in the cell are collectively called metabolism. Metabolism can be divided into two categories: 1) catabolism, the breakdown of molecules, and 2) anabolism, the synthesis of new molecules. We will look at two aspects of metabolism: 1) enzymes, and 2) energy and metabolism. (We will cover some aspects of the last section of chapter 3, biosynthesis, later.)

• Enzymes: Enzymes are protein catalysts. (Note: there are also catalytic RNAs.) A catalyst increases the rate of a chemical reaction without itself being permanently changed. Enzymes bind (lock and key binding) to a substrate (or substrates). After the reaction, an end product (or end products) is (are) released. While the enzyme may have been altered in the intermediate substrate-bound stage, it is released unaltered and can be reused. Therefore, a small amount of enzyme can catalyze numerous reactions.

• Enzyme Catalysis: Enzymes increase reaction rates by lowering the activation energy needed for a reaction to occur, often by bringing two substrates into proximity and into the right configuration. Enzyme-substrate binding according to the lock-and-key model involves various noncovalent interations (hydrogen bonds, ionic bonds, hydrophobic interactions). Also, the binding itself may be altered by the substrate binding inducing it to take on a different shape and altering the enzyme's activity (induced fit model). Enzymes have a binding/catalytic site. At the catalytic site, amino acids of the enzyme may actively participate in the chemical reaction even becoming covalently linked to the substrate in its intermediate form.

• Coenzymes: A coenzyme is a type of prosthetic group (small, non-protein molecules bound to proteins, like heme). Coenzymes are small organic molecules that further increase reaction rates. One example is the nucleotide called nicotinamide adenine dinucleotide (NAD⁺) which can be reduced (to NADH) by receiving one H+ and two electrons and then oxidized (back to NAD⁺) by donating these to another molecule. The reduction/oxidation of NAD+/NADH is coupled to the oxidation/reduction of other molecules. NAD⁺ ---> NADH requires energy. NADH ---> NAD⁺ releases energy. (Video) Similarly, the nucleotide called flavine adenine dinucleotide (FAD) can be reduced to FADH₂ (requiring energy) and FADH₂ can be oxidized to FAD (releasing energy).

• Enzyme Inhibition/Activation: Enzymes are often inactivated by the presence of a pathway end product that binds to a site other than the catalytic site (allosteric binding). This is feedback inhibition. (F.E. Video.)  Enzymes may also be activated or deactivated by the addition of phosphate groups to a serine, theonine, or tyrosine amino acid side chain. This is phosphorylation. The activity of enzymes responsible for phosphorylation (a protein kinase) may in turn be regulated by phosphorylation (another protein kinase). (Video at 5:50) Enzymes that remove phosphates are called protein phosphatases.
  

• Energy and Metabolism: In cells, energy-rich molecules, like carbohydrates and lipids, are catabolized releasing energy which is captured in a usable form in the nucleotide called adenosine 5'-triphosphate (ATP). Various catabolic reactions are coupled with the synthesis of ATP from ADP + PO₄^--. ATP is the energy currency of the cell and can be used for various cellular activities. Energy is released when ATP is hydrolyzed to ADP + PO₄^--. Other catabolic reaction are coupled to the production of NADH from NAD⁺ or of FADH₂ from FAD. Also, guanosine 5'-triphosphate (GTP) may substitute for ATP. (Energy in the form of GTP can be considered equivalent to energy in ATP: GTP can react with ADP to yield GDP and ATP).

• Glycolysis: This initial breakdown of a glucose molecule is anaerobic and occurs in the cytosol. It converts the 6 carbon glucose molecule into two 3 carbon molecules (pyruvate). It requires the hydrolysis of two ATPs during the initial steps (activation), but yields two ATPs per pyruvate, so there is a net gain of 2 ATPs directly from glycolysis. Also, during glycolysis one NADH is made per pyruvate, yielding 2 NADHs. (Video)
  

• Acetyl CoA Production and the Citric Acid Cycle (Kreb's Cycle, Tricarboxylic Cycle): Pyruvate crosses the mitochondrial membrane and the rest of the breakdown occurs within the mitochondrion. This process is aerobic.
• Acetyl CoA: As the 3 carbon pyruvate is entering the mitochondrion, it is converted to a 2 carbon acetate with the addition of coenzyme A (CoA) and the release of a carbon in the form of a CO₂ molecule. In the process, energy again is captured with the reduction of one NAD⁺ to NADH per pyruvate. (Pyruvate + CoA + NAD⁺ ---> Acetyl-CoA + CO₂ + NADH)
• Citric Acid Cycle: In the matrix of the mitochondrion, the complete break down the acetate to CO₂ occurs through a series of reaction. At various steps, energy is captured with the net gain of 1 ATP, 3 NADHs, and 1 FADH₂ per acetyl CoA. (Video)
  

• Electron Transport Chain: The energy captured in NADHs or FADH₂ is converted into ATP energy trough the electron transport system which occurs on the inner mitochondrial membrane. This is oxidative phosphorylation and involves the oxidation of NADH and FADH₂. In this chain of reactions, oxygen serves at the final electron acceptor and each NADH yields 3 ATPs while each FADH₂ yields two. (Video)

• The breakdown of a glucose is just one example of an energy-producing catabolic set or reaction. All of these reactions (anabolic and catabolic) are interconnected* in cell metabolism.