Chapter 5

Microbial Metabolism

Part 3

• First stage: Glycolysis

• Second stage: Reduced coenzymes (NADH & NADPH) donate their e- and H+ to pyruvic acid and its derivatives to form a fermentation end products.

Fermentation

Fig. 5.18a

• Releases energy from oxidation of organic molecules– sugars, amino acids, organic acids, purines, and

pyrimidines

• Does not require oxygen– bun can occur with oxygen

• Does not use the Krebs cycle or ETC

Fermentation

Fermentation

• Uses an organic molecule as the final electron acceptor

• Produces only small amounts of ATP – produced only during glycolysis– much of the energy remain in the chemical

bonds of the organic end-products

Figure 5.19

Fermentation

• Second stage of fermentation ensures a steady supply of NAD+ & NADP+ so that glycolysis can continue

– regeneration of NAD+ & NADP+ during fermentation can enter another round of glycolysis

• Alcohol fermentation– Produces 2 ethyl alcohol (ethanol) + 2 CO2

• Lactic acid fermentation– Produces lactic acid; can result in food

spoilage– Homolactic (homofermentative) fermentation:

produces lactic acid only.– Heterolactic (heterofermentative) fermentation:

produces both lactic acid and other compounds (e.g. alcohol).

• Use pentose phosphate pathway

Fermentation

Fermentation

Figure 5.18b

Fermentation

Figure 5.23

Lipid and Protein Catabolism

• Lipids and proteins are oxidized for energy production (sources of electrons & protons for respiration)

• Lipids (fats) = fatty acids + glycerol (ester linkage)

• Lipases: extracellular enzymes that degrade fats into fatty acid and glycerol components

Lipid Catabolism

Figure 5.20

Oxidation of glycerol and fatty acids

Beta oxidation: oxidation of fatty acids

Lipid and Protein Catabolism

• Proteins = amino acids (peptide bonds)

• Proteases & peptidases: extracellular enzymes that break down proteins into amino acids component

• Fig. 5.21 summary of carbohydrates, lipids, and protein catabolisms

Protein Amino acids

Extracellular proteases

Krebs cycle

Deamination, decarboxylation, dehydrogenation

Organic acid

Protein Catabolism

• Deamination: removal of an amino group from an amino acid to form an ammonium (NH4

+) (can be excreted from the cell)

Protein Catabolism

Figure 5.22

Biochemical tests

Figure 10.8

• Used to identify bacteria and yeasts.– Designed to

detect the presence of enzymes

• Used by plants and many microbes to synthesize complex organic compounds from simple inorganic substances

• Photo: Conversion of light energy into chemical energy (ATP)– Light-dependent (light) reactions

• Synthesis: assembly of organic molecules (using chemical energy)– Light-independent (dark) reaction, Calvin-Benson

cycle

Photosynthesis

Photosynthesis

• Carbon fixation: synthesis of sugars by using carbons from CO2 gas (from the atmosphere)

• Recycling of C by cyanobacteria, algae, and green plants via photosynthesis

• Table 5.6 for summary

The Light-Dependent Reactions: Photophosphorylation

• Light energy is absorbed by chlorophyll in the photosynthetic cell excite some of the molecules’ electrons chemiosmotic proton pump– Chlorophyll a used by green plants, algae, and

cyanobacteria (in thylakoids)– Bacteriochlorophylls used by other bacteria

(chlorosomes, intracytoplasmic membrane)– Bacteriorhodopsin used by Halobacterium (purple

portion of plasma membrane)

Photophosphorylation

• Light-dependent (light) reactions– ADP + P + light energy ATP (chemiosmosis)– NADP reduced to NADPH– cyclic photophosphorylation– noncyclic photophosphorylation

• More common process

Figure 5.24a

Cyclic Photophosphorylation

• Electron eventually return to chlorophyll

Figure 5.24b

Noncyclic Photophosphorylation

• Electrons become incorporated into NADPH

The Light-Independent Reactions: The Calvin-Benson Cycle

• Light-independent (dark) reaction (Calvin-Benson cycle)– use ATP along with electron produced in light-

dependent reactions to reduce CO2 to synthesize sugars (carbon fixation)

– complex cyclic pathway

Figure 5.25

The Calvin-Benson Cycle• Go through 6

cycles to produce one glucose.

6 CO2

18 ATP

+ 12 NADPH

= 1 Glucose

* Shows 3 cycles.

Fig. 5.26

Summary

Metabolic diversity Among Organisms

• All organisms can be classified metabolicaly according to their nutritional pattern– energy source: phototrophs vs. chemotrophs– carbon (C) source: autotrophs vs. heterotrophs

• autotrophs (lithotrophs): self-feeders; use CO2 as C source

• heterotrophs (organotrophs): feed on others; require an organic source of C

Phototrophs• Use light as energy source.

• Photoautotrophs use energy in the Calvin-Benson cycle to fix CO2; oxygenic & anoxygenic.

• Photoheterotrophs use organic compounds as C source; anoxygenic.

Chlorophyll

Chlorophylloxidized

ETC

ADP + P ATP

Photosynthetic process in photoautotrophs

• Oxygenic (produces O2):

– H atoms of H2O are used to reduce CO2 to form organic compounds, and O gas is given off

• Anoxygenic (does not produce O2):

– typical of cyclic photophosphorylation; anaerobic reaction

– use sulfur, sulfur compounds, or hydrogen gas to reduce CO2 to form organic compounds

Chemotrophs• Use chemical compounds as energy source.

– Redox reactions of inorganic or organic compounds

• Chemoautotroph e.g. Thiobacillus ferroxidans

– Inorganic source of energy; CO2 is C source

• Energy used in the Calvin-Benson cycle to fix CO2.

2Fe2+

2Fe3+

NAD+

NADH

ETC

ADP + P ATP

2 H+

Chemotrophs• ATP produced by oxidative phosphorylation

• Chemoheterotroph (fungi, protozoa, animals, & most bacteria)

– Energy source and C source are usually the same organic compound e.g. glucose

• saprophytes (use dead organic matter) vs. parasites (need living host)

• electrons from H atoms = energy source

Glucose

Pyruvic acid

NAD+

NADH

ETC

ADP + P ATP

Metabolic Diversity Among Organisms

Fermentative bacteria.Animals, protozoa, fungi, bacteria.

Iron-oxidizing bacteria.

Green, purple nonsulfur bacteria.

Oxygenic: Plants, cyanobacteria, algaeAnoxygenic: Green, purple bacteria.

Example

Organic compounds

Chemical Chemo- heterotroph

CO2

Organic compounds

CO2

Carbon source

Chemical Chemoautotroph

Light Photoheterotroph

Light Photoautotroph

Energy sourceNutritional type

Metabolic Pathways of Energy Use

• Most of the ATP used in the production of new cellular components– Also used to provide energy for active transport,

and flagellar motion

• Anabolism in autotrophs– carbon fixation via Calvin-Benson cycle require

both ATP& electrons

• Anabolism in heterotrophs– need ready source of organic compounds + ATP

• Polysaccharide Biosynthesis

Metabolic Pathways of Energy Use

• Use intermediates produced during glycolysis and the Krebs cycle & from lipids or amino acids.

Figure 5.28

• Lipid Biosynthesis– synthesized by

variety of routes– used for structural

component of membranes (e.g. phospholipids, cholesterol, waxes, carotenoids)

– also used in energy storage

Metabolic Pathways of Energy Use

Figure 5.29

Amino Acid and Protein Biosynthesis

• Microbes with the necessary enzymes can either synthesize all amino acids directly or indirectly from intermediates of carbohydrate metabolism

• Others need preformed amino acids – Supplied from Krebs cycle

• amination: addition of an amino group

• Amino Acid and Protein Biosynthesis

Metabolic Pathways of Energy Use

Figure 5.30a

• Protein synthesis from amino acids involves dehydration and ATP.

• Amino Acid and Protein Biosynthesis– transamination: transfer of amino group from a

preexisting amino acid

Metabolic Pathways of Energy Use

Figure 5.30b

• Purine and Pyrimidine Biosynthesis

Metabolic Pathways of Energy Use

Figure 5.31

• C and N atoms derived from amino acids form the purine & pyrimidine rings

Integration of Metabolism

• Catabolic and anabolic reactions are joined through a group of common intermediates & share some metabolic pathways (e.g. Krebs cycle)

• Are metabolic pathways that have both catabolic and anabolic functions.– Bridge the reactions that lead to the breakdown and

synthesis of carbohydrates, lipids, proteins, and nucleotides

Amphibolic pathways

Figure 5.32.1

Amphibolic pathways

Figure 5.32.2