Previous sections have discussed the catabolism of glucose, which provides energy to living cells, as well as how polysaccharides like glycogen, starch, and cellulose are degraded to glucose monomers. But microbes consume more than just carbohydrates for food. In fact, the microbial world is known for its ability to degrade a wide range of molecules, both naturally occurring and those made by human processes, for use as carbon sources. In this section, we will see that the pathways for both lipid and protein catabolism connect to those used for carbohydrate catabolism, eventually leading into glycolysis, the transition reaction, and the Krebs cycle pathways. Metabolic pathways should be considered to be porous—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways.

Lipid Catabolism

Triglycerides are a form of long-term energy storage in animals. They are made of glycerol and three fatty acids (see Figure 1 in Lipids). Phospholipids compose the cell and organelle membranes of all organisms except the archaea. Phospholipid structure is similar to triglycerides except that one of the fatty acids is replaced by a phosphorylated head group (see Figure 2 in Lipids). Triglycerides and phospholipids are broken down first by releasing fatty acid chains (and/or the phosphorylated head group, in the case of phospholipids) from the three-carbon glycerol backbone. The reactions breaking down triglycerides are catalyzed by lipases and those involving phospholipids are catalyzed by phospholipases. These enzymes contribute to the virulence of certain microbes, such as the bacterium Staphylococcus aureus and the fungus Cryptococcus neoformans. These microbes use phospholipases to destroy lipids and phospholipids in host cells and then use the catabolic products for energy (see Virulence Factors of Bacterial and Viral Pathogens).

The resulting products of lipid catabolism, glycerol and fatty acids, can be further degraded. Glycerol can be phosphorylated to glycerol-3-phosphate and easily converted to glyceraldehyde 3-phosphate, which continues through glycolysis. The released fatty acids are catabolized in a process called β-oxidation, which sequentially removes two-carbon acetyl groups from the ends of fatty acid chains, reducing NAD⁺ and FAD to produce NADH and FADH₂, respectively, whose electrons can be used to make ATP by oxidative phosphorylation. The acetyl groups produced during β-oxidation are carried by coenzyme A to the Krebs cycle, and their movement through this cycle results in their degradation to CO₂, producing ATP by substrate-level phosphorylation and additional NADH and FADH₂ molecules (see Metabolic Pathways for a detailed illustration of β-oxidation).

Other types of lipids can also be degraded by certain microbes. For example, the ability of certain pathogens, like Mycobacterium tuberculosis, to degrade cholesterol contributes to their virulence. The side chains of cholesterol can be easily removed enzymatically, but degradation of the remaining fused rings is more problematic. The four fused rings are sequentially broken in a multistep process facilitated by specific enzymes, and the resulting products, including pyruvate, can be further catabolized in the Krebs cycle.

Protein Catabolism

Proteins are degraded through the concerted action of a variety of microbial protease enzymes. Extracellular proteases cut proteins internally at specific amino acid sequences, breaking them down into smaller peptides that can then be taken up by cells. Some clinically important pathogens can be identified by their ability to produce a specific type of extracellular protease. For example, the production of the extracellular protease gelatinase by members of the genera Proteus and Serratia can be used to distinguish them from other gram-negative enteric bacteria. Following inoculation and growth of microbes in gelatin broth, degradation of the gelatin protein due to gelatinase production prevents solidification of gelatin when refrigerated. Other pathogens can be distinguished by their ability to degrade casein, the main protein found in milk. When grown on skim milk agar, production of the extracellular protease caseinase causes degradation of casein, which appears as a zone of clearing around the microbial growth. Caseinase production by the opportunist pathogen Pseudomonas aeruginosa can be used to distinguish it from other related gram-negative bacteria.

After extracellular protease degradation and uptake of peptides in the cell, the peptides can then be broken down further into individual amino acids by additional intracellular proteases, and each amino acid can be enzymatically deaminated to remove the amino group. The remaining molecules can then enter the transition reaction or the Krebs cycle.