1. Introduction to Microbiology
Anas Abu-Humaidan M.D. Ph.D.
Lecture 6

2. Bacterial metabolism
All cells require energy to survive and grow, and it can be obtained from breakdown of molecules (catabolism).
The energy can then be used to build cellular constituents (anabolism).
Different bacteria use different metabolic pathways depending on the nutrients available in its environment.
Growth requirements and metabolic byproducts may be used in classifying and identifying different bacteria.
Bacteria are identified based largely on what organic compounds they can break down. The range of compounds used depends on the collection of enzymes a species of bacteria can make. Mannitol is a sugar that some bacteria can use because of an enzyme that begins the breakdown of this compound. Phenol red mannitol broth is thus used to determine whether the microbe can use the sugar mannitol for carbon and energy.
If mannitol can be used, the microbe will accumulate acidic byproducts. In a positive test, the pH indicator in the medium changes color from its normal red to yellow, indicating acid production

3. Carbohydrates are a major energy source

4. Protein and lipid metabolism
Proteins are broken down by peptidases to amino acids permitting entry to the cell.
Amino acids can then be used to form new proteins, other amino acids (ex. Transamination), or enter the Krebs cycle for energy generation.
Lipids are broken down by lipases to glycerol and fatty acids. Glycerol can be converted to pyruvic acid via glycolysis and fatty acids enter the Krebs cycle following β-oxidation.
Endo and exo peptidases attack terminal or internal peptide bonds

5. Amino acid (aa) synthesis
Not all organisms can synthesize aa, some should be present in the media.
The carbon backbones come from other metabolic pathways, while nitrogen comes from ammonia.
Ammonia (NH3) can come from Nitrogen (N2) fixation. A process performed by Diazotrophs.
Nitrogenases perform fixation in an energy costly reaction.
Diazotrophs are prokaryotes scattered across bacterial taxonomic groups
Free living (Klebsiella pneumonie) and symbiotic (Rhizobia are bacteria that fix nitrogen (diazotrophs) after becoming established inside root nodules of legumes)
reducing the inert N≡N molecule (nitrogen gas) to two molecules of ammonia

6. Amino acid (aa) synthesis
Other nitrogen containing organic sources (urea, nucleotides or amines not used in protein synthesis) can be acted upon by enzymes (deaminases, decarboxylases and aminotransferases) to release the ammonia and make it available for biosynthesis.
Most amino acids are synthesized from α-ketoacids and later transaminated from another amino acid, usually Glutamic acid. The enzyme involved in this reaction is an aminotransferase
Most of the pathways of amino acid biosynthesis are regulated by feedback inhibition, in which the committed step is allosterically inhibited by the final product.
The α-ketoglutarate family of amino acid synthesis (synthesis of glutamate, glutamine, proline and arginine) begins with α-ketoglutarate, an intermediate in the Citric Acid Cycle.

7. Cell wall synthesis/ Peptidoglycan
Peptidoglycans: polysaccharide chains made of alternating N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) residues. Pentapeptide chains are attached to the NAM groups.
The PGN monomers are synthesized in the cytosol using glutamine, fructose 6-phosphate, acytel Co-A.
Forms 90% of Gram+ and 10% of Gram- dry weight.
and are then attached to a membrane carrier bactoprenol. Bactoprenol transports PGN monomers across the cell membrane where they are inserted into the existing PGN

8. Transpeptidation is catalyzed
uridine diphosphate UDP
Transpeptidation is catalyzed
by one of a set of enzymes called penicillin-binding proteins
(PBPs). PBPs bind penicillin and other β-lactam antibiotics

9. Capsule and granules synthesis
Capsule formation depends on the presence of certain nutrients (glutamic acid, glucose, ribose) in the medium.
Reserve granules can be used to store nutrients ( ex. Glycogen, starch) when in excess, to be used when nutrients are depleted.

10. Further reading: Murray - Medical Microbiology 8th Edition
Section 4: Bacteriology
Chapter 13: Bacterial metabolisim and genetics
Jawetz, Melnick & Adelberg's Medical Microbiology, 26th edition- Section 1: Fundamentals of Microbiology-
Chapter 6:Microbial metabolism