Premed · Premed · Microbiology
Lecture 7: Microbial Metabolism I -- Catabolism
Microbiology
Learning Objectives
By the end of this lecture, students will be able to:
- Define metabolism, catabolism, and anabolism and explain how they are linked by ATP and electron carriers
- Describe the key reactions of glycolysis, the TCA cycle, and the electron transport chain
- Compare and contrast aerobic respiration, anaerobic respiration, and fermentation
- Explain the chemiosmotic mechanism of ATP generation
- Describe common fermentation pathways and their products
- Explain the catabolism of lipids and proteins
Lecture Content
I. Overview of Metabolism
Metabolism is the sum of all chemical reactions occurring within a cell and is divided into two complementary branches. Catabolism is the breakdown of complex molecules into simpler ones, releasing energy in exergonic reactions. Anabolism is the synthesis of complex molecules from simpler precursors, requiring energy input through endergonic reactions.
Energy is transferred between catabolic and anabolic pathways primarily through ATP (adenosine triphosphate), the universal energy currency of the cell. ATP can be generated by three mechanisms: substrate-level phosphorylation, the direct transfer of a phosphate group from a substrate to ADP; oxidative phosphorylation, ATP synthesis driven by the electron transport chain and chemiosmosis; and photophosphorylation, light-driven ATP synthesis in phototrophs. Electron carriers such as NAD+/NADH, NADP+/NADPH, and FAD/FADH2 shuttle high-energy electrons from catabolic reactions to the electron transport chain or to anabolic pathways.
Oxidation-reduction (redox) reactions are fundamental to energy metabolism. Oxidation is the loss of electrons (often accompanied by hydrogen atoms), while reduction is the gain of electrons. In biological systems, electrons flow from donors with low reduction potential to acceptors with high reduction potential, and this electron flow releases the free energy that drives cellular work.
II. Glycolysis (Embden-Meyerhof-Parnas Pathway)
Glycolysis occurs in the cytoplasm of virtually all organisms and converts one molecule of glucose (a six-carbon sugar) into two molecules of pyruvate (each with three carbons). The pathway proceeds in two phases. During the energy investment phase (steps 1--5), two ATP molecules are consumed to phosphorylate glucose, producing glucose-6-phosphate, then fructose-6-phosphate, then fructose-1,6-bisphosphate, which is split into two three-carbon molecules of glyceraldehyde-3-phosphate (G3P). During the energy payoff phase (steps 6--10), each G3P is oxidized with the reduction of NAD+ to NADH, and substrate-level phosphorylation generates ATP.
The net yield per glucose is 2 ATP, 2 NADH, and 2 pyruvate. Alternative pathways exist in some bacteria. The Entner-Doudoroff (ED) pathway, used by Pseudomonas and some other Gram-negatives, yields only 1 ATP, 1 NADH, and 1 NADPH per glucose. The pentose phosphate pathway (PPP) operates alongside glycolysis to generate NADPH for biosynthesis and ribose-5-phosphate for nucleotide synthesis.
III. The TCA Cycle (Krebs Cycle / Citric Acid Cycle)
The TCA cycle operates in the cytoplasm of prokaryotes (and in the mitochondrial matrix of eukaryotes). Before entering the cycle, pyruvate is converted to acetyl-CoA by the pyruvate dehydrogenase complex in an irreversible reaction that also produces one NADH and releases one CO2 per pyruvate, linking glycolysis to the TCA cycle.
Acetyl-CoA (two carbons) enters the cycle by combining with oxaloacetate (four carbons) to form citrate (six carbons). Through a series of eight reactions, citrate is progressively oxidized and the carbon skeleton is rearranged back to oxaloacetate, completing the cycle. Per turn (per acetyl-CoA entering), the cycle produces 3 NADH, 1 FADH2, 1 GTP (equivalent to 1 ATP), and releases 2 CO2. Since each glucose yields two acetyl-CoA molecules, the total per glucose is 6 NADH, 2 FADH2, and 2 GTP.
The TCA cycle is an amphibolic pathway, serving both catabolic and anabolic functions. Its intermediates are drawn off as biosynthetic precursors: alpha-ketoglutarate feeds into glutamate and other amino acids, oxaloacetate gives rise to aspartate, and succinyl-CoA contributes to porphyrin (heme) synthesis.
IV. Electron Transport Chain (ETC) and Oxidative Phosphorylation
The electron transport chain is located in the plasma membrane of prokaryotes (and in the inner mitochondrial membrane of eukaryotes). It consists of a series of membrane-bound electron carriers arranged in order of increasing reduction potential. NADH donates its electrons to NADH dehydrogenase (Complex I), while FADH2 delivers electrons to succinate dehydrogenase (Complex II). Electrons then pass through ubiquinone (CoQ), the cytochrome bc1 complex (Complex III), cytochrome c, and finally cytochrome oxidase (Complex IV), which transfers them to the terminal electron acceptor, molecular oxygen (O2), producing water.
As electrons move through the chain, the energy released at each step is used to pump protons (H+) across the membrane from the cytoplasm to the periplasm in bacteria. This creates the proton motive force (PMF), an electrochemical gradient composed of both a pH gradient (delta pH) and an electrical potential (delta psi). Protons then flow back through ATP synthase (F0F1 ATPase), and the energy of this flow drives the rotational catalysis that synthesizes ATP from ADP and inorganic phosphate -- a process known as chemiosmosis.
The theoretical maximum ATP yield from one glucose through complete aerobic respiration includes 2 ATP from glycolysis, 10 total NADH (yielding approximately 25 ATP at about 2.5 ATP per NADH), 2 FADH2 (yielding approximately 3 ATP at about 1.5 per FADH2), and 2 GTP, totaling approximately 30--32 ATP per glucose. In bacteria, the yield can be somewhat higher (up to about 38 ATP) because there is no cost for transporting NADH across mitochondrial membranes, as occurs in eukaryotes. Actual yields vary with the organism and conditions.
<image>A schematic of the bacterial electron transport chain in the plasma membrane. Panel A: Electrons from NADH enter at Complex I (NADH dehydrogenase), pass through ubiquinone, Complex III (cytochrome bc1), cytochrome c, and Complex IV (cytochrome oxidase), where O2 is reduced to H2O. FADH2 electrons enter at Complex II (succinate dehydrogenase). At each complex, protons are pumped from the cytoplasm to the periplasmic space (arrows showing H+ movement). Panel B: ATP synthase (F0F1) spanning the membrane, with protons flowing back through F0 into the cytoplasm driving ATP synthesis in F1. The proton motive force (PMF = delta psi + delta pH) is annotated. Net equation: NADH + H+ + 1/2 O2 -> NAD+ + H2O + ~2.5 ATP.</image>
V. Anaerobic Respiration
Anaerobic respiration employs an electron transport chain but uses a terminal electron acceptor other than O2. Common alternatives include nitrate (NO3-), which is reduced to nitrite and ultimately to N2 through denitrification (carried out by Pseudomonas and Paracoccus); sulfate (SO4 2-), reduced to H2S by Desulfovibrio; CO2, reduced to methane by methanogenic archaea; Fe3+, reduced to Fe2+ by iron-reducing bacteria; and fumarate, reduced to succinate. Because these alternative acceptors have lower reduction potentials than O2, anaerobic respiration yields less ATP than aerobic respiration. Nevertheless, it is ecologically significant in anaerobic environments such as deep sediments, waterlogged soils, and the gut.
VI. Fermentation
Fermentation differs fundamentally from respiration in that it does not use an electron transport chain. Instead, pyruvate or a derivative of pyruvate serves as the terminal electron acceptor for NADH, regenerating the NAD+ needed for glycolysis to continue. The net ATP yield is only 2 ATP per glucose, all from substrate-level phosphorylation during glycolysis. While far less efficient than respiration, fermentation enables growth in the absence of any external electron acceptor.
Several types of fermentation are distinguished by their end products. In lactic acid (homolactic) fermentation, pyruvate is directly reduced to lactate, a pathway used by Lactobacillus and Streptococcus and exploited in the production of yogurt, cheese, and sauerkraut. Alcoholic (ethanol) fermentation first decarboxylates pyruvate to acetaldehyde and CO2, then reduces the acetaldehyde to ethanol; Saccharomyces cerevisiae uses this pathway in brewing beer, making wine, and baking bread. Mixed-acid fermentation, characteristic of Escherichia coli and other Enterobacteriaceae, produces a mixture of lactate, acetate, succinate, formate, ethanol, CO2, and H2 and is identified by a positive methyl red test. Butanediol fermentation, seen in Klebsiella, Enterobacter, and Serratia, produces 2,3-butanediol, ethanol, and CO2, with the Voges-Proskauer (VP) test detecting the acetoin intermediate. Butyric acid and butanol fermentation is characteristic of Clostridium, while propionic acid fermentation by Propionibacterium produces the CO2 responsible for the holes in Swiss cheese.
<image>A comparison diagram of aerobic respiration vs. fermentation. Panel A: Aerobic respiration flow -- glucose through glycolysis to pyruvate, pyruvate to acetyl-CoA, TCA cycle, ETC with O2 as terminal electron acceptor, yielding ~30-32 ATP. Panel B: Fermentation flow -- glucose through glycolysis to pyruvate, pyruvate reduced directly to fermentation end products (lactic acid or ethanol + CO2), NAD+ regenerated, yielding only 2 ATP. Panel C: A branching pathway diagram showing different fermentation types and their characteristic end products, with the organisms and diagnostic tests (methyl red, VP) associated with each type.</image>
VII. Catabolism of Other Organic Molecules
Bacteria can catabolize molecules beyond carbohydrates. Lipids are broken down by lipases, which cleave triglycerides into glycerol and fatty acids. Glycerol is converted to dihydroxyacetone phosphate (DHAP) and enters glycolysis, while fatty acids undergo beta-oxidation, the sequential removal of two-carbon units as acetyl-CoA that feed into the TCA cycle. Because fatty acids are more reduced than carbohydrates, they yield substantially more ATP per molecule.
Proteins are degraded by proteases and peptidases into their constituent amino acids. The amino acids are then deaminated (the amino group is removed as ammonia or ammonium), and the remaining carbon skeletons are funneled into glycolysis or TCA cycle intermediates such as pyruvate, acetyl-CoA, alpha-ketoglutarate, succinyl-CoA, fumarate, or oxaloacetate. The deamination products also contribute to nitrogen cycling in the environment.
VIII. Regulation of Catabolism
Cells regulate their catabolic pathways at multiple levels. Enzyme activity is controlled by allosteric regulation, in which an end product inhibits the first enzyme in its biosynthetic pathway (feedback inhibition), and by covalent modification such as phosphorylation and dephosphorylation. Gene expression is regulated by catabolite repression, whereby in the presence of glucose, genes for alternative sugar catabolism are repressed (as seen in the lac operon regulation by cAMP-CRP in E. coli), and by induction, in which a substrate induces expression of the enzymes needed for its catabolism. The Pasteur effect describes the inhibition of fermentation in the presence of oxygen, as cells preferentially switch to the more efficient aerobic respiration.
