1. Chapter 5
Microbial Metabolism

2. Microbial Metabolism
Metabolism is the sum of the chemical reactions in an organism.
Catabolism is the energy-releasing processes, catabolic, degradative,generally hydrolytic reaction (use water and break chemical bonds).
Exergonic – produce more energy than consume
Anabolism is the energy-using processes, anabolic, biosynthetic, building of complex molecules from simpler ones, involve dehydration synthesis reactions (reactions that release water)
Endergonic – consume more energy that produce.

3. Microbial Metabolism
Catabolism provides the building blocks and energy for anabolism.
Figure 5.1

4. ATP stores energy from catabolic reactions and releases it later to drive anabolic reactions and perform other cellular work.
The coupling or energy requiring and energy releasing reaction is made possible through the molecule adenosine triphosphate (ATP)

5. ATP Is made by dehydration synthesis.
Is broken by hydrolysis to liberate useful energy for the cell.
When the terminal phosphate group splits from ATP, adenosine diphosphate is formed and energy is released to drive anabolic reactions

6. A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell.
Metabolic pathways are determined by enzymes.
Enzymes are proteins encoded by genes.
The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide.
Reaction rate is the frequency of collisions with enough energy to bring about a reaction.
Reaction rate can be increased by enzymes or by increasing temperature or pressure.

7. Catalyst
Catalyst speeds up a chemical reaction without being permanently altered themselves
Enzymes are biological catalyst, specific for a chemical reaction, acts on a specific substance called a substrate
The enzyme orients the substrate into position that increases the probability of a reaction
Enzyme substrate complex forms by the temporary binding of enzyme and substrate enable the collison to be more effective and lowers the activation energy of the reaction

8. Enzymes
Apoenzyme: protein portion of an enzyme, can be the whole enzyme
Cofactor: Nonprotein component, help catalyze by forming a bridge between the enzyme and the substrate
Coenzyme: Organic cofactor, NAD+NADP+FAD Coenzyme A, may assist the enzymatic reaction by accepting atoms removed from the substrate or by donating atoms required by the substrate, electron carriers
Holoenzyme: Apoenzyme + cofactor (coenzyme)
Figure 5.3

10. Enzyme Classification 6 classes, named for type of chemical reaction they catalyze
Oxidoreductase Oxidation-reduction reactions
Transferase Transfer functional groups
Hydrolase Hydrolysis
Lyase Removal of atoms without hydrolysis
Isomerase Rearrangement of atoms
Ligase Joining of molecules, uses ATP

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

12. Factors Influencing Enzyme Activity
Temperature pH
Figure 5.5a

13. Factors Influencing Enzyme Activity
Competitive inhibition – inhibitors fill the active site of an enzyme and compete with the normal substrate for the active site
Figure 5.7a, b

14. Factors Influencing Enzyme Activity
Ex – PABA is an essential nutrient of many bacteria in the synthesis of folic acid. Sulfanilamide binds to the enzyme that converts PABA to folic acid, bacteria cannot grow

15. Factors Influencing Enzyme Activity
Noncompetitive inhibition- inhibitor interacts with another part of the enzyme
Allosteric inhibitor –inhibitor binds to a site other than the substrate binding site and cause the active site to change shape making it non-functional
Figure 5.7a, c

16. Factors Influencing Enzyme Activity
Feedback inhibition – a series of enzymes make an end product that inhibits the first enzyme in the series, this shuts down the entire pathway when sufficient end product has been made
Figure 5.8

17. Energy Production
Nutrient molecules have energy associated with electrons that form bonds between their atoms
Reactions in catabolic pathways convert this energy into bonds of ATP, which serves as a convenient energy carrier

18. Oxidation-Reduction Oxidation is the removal of electrons.
Reduction is the gain of electrons.
Redox reaction is an oxidation reaction paired with a reduction reaction.
Figure 5.9

19. Oxidation-Reduction
In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often dehydrogenations.
Figure 5.10

20. Energy Production
Cells use redox reactions in catabolism to extract energy from nutrient molecules
Cells take nutrients, degrade them from a highly reduced compound with a lot of hydrogen atoms to a highly oxidized compound which can serve as an energy source
Ex – a cell oxidizes a molecule of glucose C6H12C6 to CO2 and H2O, the energy in glucose is removed in a stepwise manner and ultimately trapped by ATP

21. To produce energy from glucose microbes use two general processes
Cellular respiration
Fermentation
Both start with glycolysis but follow different subsequent pathways

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

23. Carbohydrate Catabolism
Most organisms oxidize carbohydrates as their primary source of cellular energy, most common is glucose
The breakdown of carbohydrates to release energy
Glycolysis
Krebs cycle
Electron transport chain

24. Glycolysis
The oxidation of glucose to pyruvic acid, produces ATP and NADH.
6-carbon sugar is split into 2 3-carbon sugars, the sugar is oxidized, releasing energy and their atoms rearrange to form 2 molecules of pyruvic acid
1 - 6 carbon sugar
2 - 3 carbon sugars

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

26. Energy-Conserving Stage6
2 Glucose-3-phosphate oxidized to 2 Pyruvic acid
4 ATP produced
2 NADH produced
Net 2 ATP
1,3-diphosphoglyceric acid 7
3-phosphoglyceric acid 8
2-phosphoglyceric acid 9
Phosphoenolpyruvic acid
(PEP) 10
Pyruvic acid
Figure

27. Pyruvic Acid
Pyruvic acid can be channeled into the next step of either fermentation of cellular respiration

28. Alternatives to Glycolysis
Pentose phosphate pathway:
Uses pentoses and NADPH
Operates with glycolysis
Entner-Doudoroff pathway:
Produces NADPH and ATP
Does not involve glycolysis
Pseudomonas, Rhizobium, Agrobacterium

29. Cellular Respiration
ATP generating process in which molecules are oxidized and the final electron acceptor is almost always an inorganic molecule

30. Intermediate Step
Pyruvic acid (from glycolysis) cannot enter the Krebs cycle directly
In a preparatory step it most lose one molecule of CO2 and becomes a two carbon compound (decarboyxlated)
The 2c-carbon complex – acetyl group attaches to coenzyme A through a high energy bond
Result is acetyl-coenzyme A, 2 acetyl-CoA per glucose

31. Krebs Cycle – TCA cycle – Citric Acid Cycle
Series of redox reactions that transfer potential energy in the form of electrons to electron carriers, chiefly NAD
For every Acetyl-CoA – 2 ATP, 4 CO2, 6 NADH, 2 FADH

32. The Electron Transport Chain
A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain.
Series of reductions that indirectly transfer the energy stored in the coenzymes formed in the Krebs cycle to ATP

33. Respiration
Aerobic respiration: The final electron acceptor in the electron transport chain is molecular oxygen (O2).
In prokaryotes – results in 38 ATP
In eukaryotes – results in 36 ATP, lose energy shuttling electrons across mitochondria membrane
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.
ATP levels vary with the organism and the pathway, not all carrier in the electron transport chain are used

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

36. Fermentation
Glucose can be converted to another organic product in 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
Produces only a small amount of ATP

37. Fermentation
Figure 5.18b

40. Other Energy Sources
Microbes can oxidize lipids and proteins for energy
Lipids are broken down by lipases which break fats down into fatty acids and glycerol components. Each component is then metabolized separately
Beneficial for oil spills

41. Lipid Catabolism
Figure 5.20

42. Proteins are broken down by proteases and peptidases which break down proteins to amino acids and then convert them by deamination,(removal of the amino group, to enter the Krebs cycle. The amino group is converted to an ammonia ion which can be excreted from the cell.

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

45. Biochemical tests
Used to identify bacteria.

46. Photosynthesis
Photo: Conversion of light energy into chemical energy (ATP)
Synthesis: Fixing carbon into organic molecules
Photosynthesis – synthesis of complex organic compounds from single inorganic substances

47. Photosynthesis
Conversion of light energy from the sun into chemical energy
Chemical energy is used to convert CO2 from atmosphere to more reduced carbon compounds, primarily sugars
Synthesis of sugar by using carbon atoms from CO2 gas is call carbon fixation
In photosynthesis electrons are taken from hydrogen atoms of water, an energy poor molecule, and incorporated into sugar, an energy rich molecule

48. Species that use light energy are phototrophs.
Species that obtain energy from chemicals in their environment are chemotrophs.
Organisms that need only CO2 as a carbon source are autotrophs.
Organisms that require at least one organic nutrient as a carbon source are heterotrophs.
These categories of energy source and carbon source can be combined to group prokaryotes according to four major modes of nutrition.

49. Photoautotrophs are photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from carbon dioxide.
Chemoautotrophs need only CO2 as a carbon source, but they obtain energy by oxidizing inorganic substances, rather than light.
These substances include hydrogen sulfide (H2S), ammonia (NH3), and ferrous ions (Fe2+) among others.
This nutritional mode is unique to prokaryotes.

50. Photoheterotrophs use light to generate ATP but obtain their carbon in organic form.
This mode is restricted to prokaryotes.
Chemoheterotrophs must consume organic molecules for both energy and carbon.
This nutritional mode is found widely in prokaryotes, protists, fungi, animals, and even some parasitic plants.

52. 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
Iron-oxidizing bacteria.
Chemoheterotroph
Fermentative bacteria.
Animals, protozoa, fungi, bacteria.

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

54. Amphibolic pathways
Most of the ATP made by the cell is used in the production of new cellular components
Amphibolic pathways bridge the reactions that lead to the breakdown and synthesis of carbohydrates, lipids, proteins and nucleus.
These pathways allow for the simultaneous reactions to occur in which the breakdown products formed in one reaction are used in another reaction to synthesize a different compound, or vice versa
Figure