Microbial Metabolism Ch 5 Metabolism is the sum of the chemical reactions in an organism. Catabolism is the energy-releasing processes. Anabolism is the energy-using processes. (typically building something)

Microbial Metabolism Catabolism provides the building blocks and energy for anabolism. Fig 5.1 know the relationships between these two processes and hot ATP binds them together Figure 5.1

Amphibolic pathways Are metabolic pathways that have both catabolic and anabolic functions. This is basically all of life Figure 5.32.1

Amphibolic pathways Figure 5.32.2

Metabolic pathways are determined by enzymes. A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell. A primary metabolic pathway are the reactions that do the basic work of the cell. Get food and grow Metabolic pathways are determined by enzymes. Enzymes are encoded by genes. The purpose of this slide is to show the students that the metabolic pathways that an organism has directly correlates to its genome.

Biochemical tests Used to identify bacteria. Enzymes are genes Sum of genes is your organism Here is a graphic that shows how the metabolism of an organism can be used in a key to identify that organism. Figure 10.8

Enzymes Figure 5.2

Enzymes Biological catalysts Apoenzyme: protein Specific for a chemical reaction; not used up in that reaction Apoenzyme: protein Cofactor: Nonprotein component Coenzyme: Organic cofactor Holoenzyme: Apoenzyme + cofactor

Enzymes Figure 5.3

Important Coenzymes NAD+ NADP+ FAD Coenzyme A Biotin Folic acid Many of the vitamins

Enzymes The turnover number is generally 1-10,000 molecules per second. Figure 5.4

Factors Influencing Enzyme Activity Enzymes can be denatured by temperature and pH Figure 5.6

Factors Influencing Enzyme Activity Temperature Figure 5.5a

Factors Influencing Enzyme Activity pH Figure 5.5b

Factors Influencing Enzyme Activity Substrate concentration Figure 5.5c

Factors Influencing Enzyme Activity Competitive inhibition Figure 5.7a, b

Factors Influencing Enzyme Activity Sulfa inhibits the enzyme that uses PABA for synthesis of folic acid

Factors Influencing Enzyme Activity Noncompetitive inhibition Figure 5.7a, c

Feedback inhibition Figure 5.8

The Generation of ATP ATP is generated by the phosphorylation of ADP.

The Generation of ATP Substrate-level phosphorylation is the transfer of a high-energy PO4- to ADP.

The Generation of ATP Energy released from the transfer of electrons (oxidation) of one compound to another (reduction) is used to generate ATP by chemiosmosis.

Metabolic Pathways Step 1 is a redox. Who is reduced and who is oxidized. The double arrows indicate that both occur in this step. The forward and backward indicate that the reaction goes the same forward and back. Why is step 1 not like this?

Carbohydrate Catabolism The breakdown of carbohydrates to release energy Glycolysis Krebs cycle Electron transport chain

Glycolysis The oxidation of glucose to pyruvic acid, produces ATP and NADH.

Preparatory Stage 2 ATPs are used Glucose 1 2 ATPs are used Glucose is split to form 2 Glyceraldehyde-3-phosphate Glucose 6-phosphate 2 Fructose 6-phosphate 3 Fructose 1,6-diphosphate 4 5 Glyceraldehyde 3-phosphate (GP) Dihydroxyacetone phosphate (DHAP) Figure 5.12.1

Energy-Conserving Stage 6 1,3-diphosphoglyceric acid 7 2 Glucose-3-phosphate oxidized to 2 Pyruvic acid 4 ATP produced 2 NADH produced 3-phosphoglyceric acid 8 2-phosphoglyceric acid 9 Phosphoenolpyruvic acid (PEP) 10 Pyruvic acid Figure 5.12.2

Glycolysis Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+  2 pyruvic acid + 4 ATP + 2 NADH + 2H+

Alternatives to Glycolysis Pentose phosphate pathway: Uses pentoses and NADPH Operates with glycolysis Use and production of 5 carbon sugars (na) Bacillus subtilis, E. coli, Enterococcus faecalis Entner-Doudoroff pathway: Produces NADPH and ATP Does not involve glycolysis Pseudomonas, Rhizobium, Agrobacterium Generally not found in your gram positives. Can work without glycolysis

Cellular Respiration Oxidation of molecules liberates electrons for an electron transport chain ATP generated by oxidative phosphorylation

Intermediate Step Pyruvic acid (from glycolysis) is oxidized and decarboyxlated Figure 5.13.1

Krebs Cycle Oxidation of acetyl CoA produces NADH and FADH2

Krebs Cycle Figure 5.13.2

The Electron Transport Chain A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain. Energy released can be used to produce ATP by chemiosmosis.

Chemiosmosis Figure 5.15

Electron transport and Chemiosmosis Figure 5.16.2

Figure 5.14

Respiration Aerobic respiration: The final electron acceptor in the electron transport chain is molecular oxygen (O2). Anaerobic respiration: The final electron acceptor in the electron transport chain is not O2. Yields less energy than aerobic respiration because only part of the Krebs cycles operations under anaerobic conditions.

Anaerobic respiration Electron acceptor Products NO3– NO2–, N2 + H2O SO4– H2S + H2O CO32 – CH4 + H2O

Energy produced from complete oxidation of 1 glucose using aerobic respiration Pathway ATP produced NADH produced FADH2 produced Glycolysis 2 Intermediate step Krebs cycle 6 Total 4 10

By substrate-level phosphorylation By oxidative phosphorylation ATP produced from complete oxidation of 1 glucose using aerobic respiration 36 ATPs are produced in eukaryotes. Pathway By substrate-level phosphorylation By oxidative phosphorylation From NADH From FADH Glycolysis 2 6 Intermediate step Krebs cycle 18 4 Total 30

Pathway Eukaryote Prokaryote Glycolysis Cytoplasm Intermediate step Krebs cycle Mitochondrial matrix ETC Mitochondrial inner membrane Plasma membrane

Fermentation Releases energy from oxidation of organic molecules Does not require oxygen Does not use the Krebs cycle or ETC Uses an organic molecule as the final electron acceptor

Fermentation Figure 5.18b

Fermentation Alcohol fermentation. Produces ethyl alcohol + CO2 Lactic acid fermentation. Produces lactic acid. Homolactic fermentation. Produces lactic acid only. Heterolactic fermentation. Produces lactic acid and other compounds.

Fermentation Figure 5.19

Fermentation Production of acid and gas Figure 5.23

Lipid Catabolism Figure 5.20

Protein Catabolism Protein Amino acids Organic acid Krebs cycle Extracellular proteases Protein Amino acids Deamination, decarboxylation, dehydrogenation Organic acid Krebs cycle

Biochemical tests Used to identify bacteria. Figure 10.8

Halobacterium uses bacteriorhodopsin, not chlorophyll, to generate electrons for a chemiosmotic proton pump.

Chemotrophs Use energy from chemicals. Energy is used in anabolism. Chemoheterotroph Energy is used in anabolism. Glucose NAD+ ETC Pyruvic acid NADH ADP + P ATP

Chemotrophs Use energy from chemicals. Chemoautotroph, Thiobacillus ferroxidans Energy used in the Calvin-Benson cycle to fix CO2. 2Fe2+ NAD+ ETC 2Fe3+ NADH ADP + P ATP 2 H+

Metabolic Diversity Among Organisms Nutritional type Energy source Carbon source Example Photoautotroph Light CO2 Oxygenic: Cyanobacteria plants. Anoxygenic: Green, purple bacteria. Photoheterotroph Organic compounds Green, purple nonsulfur bacteria. Chemoautotroph Chemical CO Iron-oxidizing bacteria. Chemoheterotroph Fermentative bacteria. Animals, protozoa, fungi, bacteria.

Metabolic Pathways of Energy Use Polysaccharide Biosynthesis Figure 5.28

Metabolic Pathways of Energy Use Lipid Biosynthesis Figure 5.29

Metabolic Pathways of Energy Use Amino Acid and Protein Biosynthesis Figure 5.30a

Metabolic Pathways of Energy Use Amino Acid and Protein Biosynthesis Figure 5.30b

Metabolic Pathways of Energy Use Purine and Pyrimidine Biosynthesis Figure 5.31

Amphibolic pathways Are metabolic pathways that have both catabolic and anabolic functions. Figure 5.32.1

Amphibolic pathways Figure 5.32.2