Chapter 5

Microbial Metabolism

Catabolic and Anabolic Reactions• Metabolism - The sum of all chemical reactions

within a living cell either releasing or requiring energy. Fig 5.1

• Catabolism - Breaking down complex organic compounds into simpler ones.– Usually release energy

– Released energy is transferred to and trapped in ATP (some given off as heat).

– Released energy used to drive anabolic reactions

• Anabolism – The building of complex organic molecules from simpler ones.– Formation of proteins from amino acids, nucleic acids from

nucleotides, polysaccharides from simple sugars.

– These materials used for cell growth

– Reactions usually require energy from ATP

Figure 5.1

Enzymes• Features of Enzymes:

– Proteins made by living cells (instructions found in DNA) that are used to catalyze chemical reactions

– Names usually end in ‘ase’

– When enzymes and substrate combine, substrate is transformed and enzyme is recovered.

– Operate at an optimum temperature and pH

– Reaction often controlled by feedback inhibition

• End product inhibits an enzyme’s activity somewhere in the pathway.

Figure 5.2

Table 5.1

Figure 5.3

Table 5.2

Figure 5.4 - Overview

Figure 5.5 - Overview

Figure 5.6

Figure 5.7 - Overview

Figure 5.8

Energy Production• Oxidation-Reduction with transfer of energy

– Oxidation is removing (loss of) electron(s)

– Reduction is gaining electron(s)

– How to remember? LEO says GER or OIL RIG

– Each time a substance is oxidized another is reduced

– Most biological oxidation is by loss of hydrogen atoms (H+ and e-), also known as dehydrogenation reaction. Fig 5.10

• Example: NAD+ = oxidized form, NADH = reduced form

• NADH is used to capture and transfer energy

– Energy is released during a cell’s oxidation of glucose as hydrogens with associated electrons are removed.

Figure 5.9

Figure 5.10

Energy Production continued

• Generation of Adenosine Triphosphate (ATP)

for Energy Storage

• ADP traps energy released by certain

metabolic reactions (catabolism of glucose) to

form ATP

» ADP + energy + phosphate = ATP

• Stored as ATP until needed as energy source

Biochemical Pathways of Energy Production

• Description: Series of enzymatically

catalyzed reactions, called biochemical

pathways, that store energy in and

release energy from organic molecules.• See Fig 5.12, Appendix C fig C.2

Figure 5.12 - Overview

Biochemical Pathways of Energy Production:

Carbohydrate Metabolism

– Most of a cell’s energy is produced from

oxidation of carbohydrate, mainly glucose.

– Two major types of glucose metabolism:

• Respiration

• Fermentation

– See fig 5.11

Figure 5.11

Two major types of glucose catabolism

• Respiration– Where glucose is completely broken down to CO2

and H20 creating much ATP. – The final electron acceptor in this oxidation is usually

02, but may be other inorganic ions.– This happens in the mitochondria of eukaryotes and

cytoplasm of eubacteria.

• Fermentation– Glucose partially broken down producing small

amounts of ATP . End products still contain lots of energy but are discarded by the cell.

– Uses no O2

• Common pathway to both respiration and fermentation is gycolysis. – Glucose (6 carbons) is oxidized (using no O2 ) to 2

pyruvic acids (3 carbons) with production of some ATP and energy containing NADH. Fig 5.11, 5.12

Figure 5.11

Figure 5.12 - Overview

Figure 5.12, step 1

Figure 5.12, step 6

• Respiration using O2 is called aerobic

respiration.

– Once glycolysis is completed and pyruvic acid

is made, two other metabolic pathways are

used sequentially:

• Krebs cycle, fig 5.13

• Electron transport chain (ETC) fig 5.14

Aerobic respiration cont.• Krebs cycle

– Oxidation of a derivative of pyruvate (Acetyl CoA) to CO2 with production of 2 ATP, energy containing NADH (6) and FADH2 (2)

– Two turns of Krebs cycle are needed for each molecule of glucose (2 x 3 Carbon fragments). Fig 5.13

• Electron Transport chain– NADH and FADH2 are oxidized and give up their electrons to a

series of carrier molecules in a membrane.

– As the electrons come off the last carrier they combine with O2and H+ to form H2O water. Fig 5.14

– Energy is released in a stepwise manner to produce a considerable amount of ATP (34 from 1 glucose). Notice that the ATP is produced as H+ moves through a special protein channel in the membrane. Fig 5.15, fig 5.16.

• Summary of respiration. Fig 5.17. Table 5.3. – Large amounts of ATP made, O2 used as final electron acceptor,

CO2 and H2O are waste products.

Figure 5.13 - Overview

Figure 5.14 - Overview

Figure 5.15 - Overview

Figure 5.16 - Overview

Table 5.3

Figure 5.17

Anaerobic Respiration

• Respiration without using O2 as a final acceptorof oxygen is called anaerobic respiration.

– Uses an inorganic molecule other than O2 as final electron acceptor

• Examples: Some bacteria such as Pseudomonas and Bacillus can use nitrate ion (NO3

-) as final electron acceptor.

– Since not all the carriers in the ETC participate in anaerobic respiration, the amount of ATP produced is never as much as aerobic respiration but still is much better than fermentation.

• see Table 5.5

Table 5.5

Fermentation

– Pyruvate made during glycolysis is converted to an organic product and released

• Fermentation releases some energy from sugars or other organic molecules by incomplete oxidation. See fig 5.18

• Only 2 ATP produced per glucose molecule

• Does not use Krebs cycle or ETC so O2 is not required

• Final electron acceptor is an organic molecule– Alcohol (ethanol, isopropyl) or organic acids (lactic,

acetic, formic, etc.) see table 5.4

Figure 5.18 - Overview

Figure 5.19

Table 5.4

Biochemical Tests• Uses of Biochemical tests for microbial

identification using metabolic pathways:

• Bacteria and yeasts can be identified by detecting the action of their enzymes on substrates. Fig 5.22

– Enzymes are proteins made under the direction of DNA

DNA RNA protein

• Fermentation tests are used to determine whether an organism can ferment a carbohydrate to produce acid and gas. Fig 5.23

Figure 5.22

Figure 5.23

Overview of Other Catabolic Reactions

• Catabolism of lipids

– Lipases hydrolyze lipids into glycerol and fatty acids

– Lipids and fatty acids then broken down in Krebs cycle

• Catabolism of protein

– Broken down by proteases and peptidases to amino acids

– Amino acids converted to various substances that enter Krebs cycle

• Amino acid is deaminated (NH2 removed) and sometimes decarboxylated (COOH removed)

• See Fig 5.21

Figure 5.20

Figure 5.21

Overview of Pathways of Energy Use and

Anabolic Reactions

• Biosynthesis

– Production of new cellular components from simple molecules

• Polysaccharides: (glycogen and basic material for peptidoglycan) fig 5.28

• Lipids: made from glycerol (produced during glycolysis) and fatty acids (produced from acetyl CoA during preparatory step for the Krebs cycle). Fig 5.29

• Purines and Pyrimidines are part of the nucleotide subunits needed to make DNA and RNA.

– Amino acids made from intermediates of glycolysis and the Krebs cycle participate in the synthesis of purines and pyrimidines. Fig 5.31

Figure 5.28

Figure 5.29

Figure 5.30 - Overview

Photosynthesis• 6 CO2 + 12 H2O + light energy

C6H12O6 + 6O2 + 6H2O

• Converts light energy from the sun into chemical energy. Fig 5.24

• Light dependent reaction- Photophosphorylation– Cyclic - electrons return to chlorophyll– Non-cyclic - electrons are incorporated into NADPH and

products are ATP and O2

– Examples: Cyanobacteria and Algae

• Dark reaction – Electrons from light-dependent rxn + energy from ATP reduce

CO2 to sugar (Main sugar is sucrose: a disaccharide (glucose + fructose))

• Photosynthesis is just the reverse of aerobic respiration

Figure 5.24 - Overview

Figure 5.25

Metabolic Diversity Among Organisms• Nutritional Classification by energy and carbon source.

Fig 5.27– Energy Source

• Phototrophs – use light as primary energy source

• Chemotrophs - use oxidation-reduction reactions of inorganic or organic compounds for energy

– Carbon Source

• Autotrophs - use CO2

• Heterotrophs - require an organic carbon source

• Combination:– Photoautotrophs

– Photoheterotrophs

– Chemoautotrophs

– Chemoheterotrophs

• Most medically important organisms are in this group

Figure 5.27 - Overview