Lecture 7


Chapter 5, part B Microbial Metabolism

Overview of Respiration and Fermentation

Figure 5.11


• Fermentation releases energy from sugars or other

organic molecules

by oxidation.

• Pyruvate is metabolized to various compounds •

O 2 is not required

in fermentation.

• Does not use the


cycle or


• Electrons removed from the substrate

reduce NAD+ to NADH.

• The final electron acceptor is an endogenous

organic molecule.

• Produces only small amounts of ATP (

one or two ATP

molecules for each molecule of starting material) • ATP molecules are produced by

substrate level phosphorylation.


Alcohol fermentation -

acetaldehyde is reduced by NADH to

produce ethanol


– Product ethyl alcohol + CO 2


• •

Lactic acid fermentation (homolactic)-

pyruvic acid is reduced by NADH to

lactic acid.

– Product - lactic acid only


fermentation – Product lactic acid as well as other acids and alcohols.



Figure 5.18b

Lipid Catabolism

• Lipases hydrolyze

lipids glycerol


fatty acids.

into • Fatty acids and other hydrocarbons are catabolized by


• Catabolic products can be further broken down in

Krebs cycle.


and the


Figure 5.20


Protein Catabolism

Extracellular proteases

Amino acids

Deamination, decarboxylation, dehydrogenation

Organic acid

Krebs cycle

Urea Urease NH 3 + CO 2


Highly reduced complex molecules Oxidized NAD + NADH




Metabolic Pathways of Energy Use Anabolism

• Polysaccharide Biosynthesis

ADPG (adenosine diphosphoglucose).

UGPG (uridine diphosphoglucose) UDPNAc ( UDP-N-acetylglucoseamine)

Figure 5.28

Metabolic Pathways of Energy Use

• Lipid Biosynthesis – Lipids are synthesized from

fatty acids




• Glycerol is derived from dihydroxyacetone phosphate.

• Fatty acids are built from acetyl CoA.

Figure 5.29

Metabolic Pathways of Energy Use

• Amino Acid and Protein Biosynthesis • All amino acids can be synthesized either directly or indirectly from intermediates of carbohydrate metabolism, particularly from the Krebs cycle.

Figure 5.30a

Metabolic Pathways of Energy Use

• Purine and Pyrimidine Biosynthesis.

– The sugars composing nucleotides are derived from either the pentose phosphate pathway or the Entner-Doudoroff pathway.

– Carbon and nitrogen atoms from certain amino acids form the backbones of the purines and pyrimidines Figure 5.31

Reversible Reactions

• Can readily go in either direction.

• Each direction may need special conditions.


AB A + B

NAD+ [Product concentration]

Amphibolic pathways

• Anabolic and catabolic reactions are integrated through a group of common intermediates.

• Both anabolic and catabolic reactions also share some metabolic pathways, such as Krebs • Such integrated metabolic pathways are referred to as

amphibolic pathways


Phototrophs - Photosynthesis

Energy from sunlight

is used to convert carbon dioxide( CO 2 ) and water (H 2 O) into organic materials to be used in cellular functions such as biosynthesis and respiration •


Conversion of light energy Light-dependent

into chemical energy (ATP) (light) reactions •


Fixing carbon Light-independent

into organic molecules (dark) reaction, Calvin-Benson cycle • Process is localized in


(eukaryotes) or




(light) reactions

Cyclic Photophosphorylation

- the electrons return to the chlorophyll

Noncyclic photophosphorylation -

The electrons are used to reduce NADP + and form NADPH -The electrons from: -

H 2 O


H 2 S

chlorophyll replace those lost from

(H 2 S)



) Figure 5.24a

• •




6CO 2 + 12H 2 O + Light energy  C 6 H 12 O 6 +

6 O 2

+ 6H 2 O



6CO 2 + 12H 2 S + Light energy  C 6 H 12 O 6 +

12 S

+ 6 H 2 O


(dark) reaction

• • •

Photosynthesis: Fixing carbon Calvin-Benson cycle

• Use NADPH as cofactor (

CO 2 )

into organic molecules • Characteristic of: -



Green and Purple bacteria Algae

and Plants


Carbon dioxide (CO 2 ) is used as source of carbon Figure 5.25

A Summary of Energy Production Mechanisms

Nutritional types of organisms by

Sources of energy Chemotrophs: Phototrophs:

Bond energy is released from a chemical compound Light is absorbed in photo receptors and transformed into chemical energy.



s - Organisms that use energy from organic chemicals Glucose NAD + ETC • Pyruvic acid NADH ADP + P ATP


Organic compounds are metabolized to get carbon for growth and development.

• Cannot fix carbon


• Use energy from

inorganic chemicals

• Energy is used in the Calvin-Benson cycle

to fix CO 2

2Fe 2+ NAD + ETC 2Fe 3+ NADH ADP + P ATP 2 H + •


Thiobacillus ferrooxidans


• Use

Energy from sunlight

Chlorophyll ETC Chlorophyll oxidized ADP + P ATP • Energy is used in the Calvin-Benson cycle to fix CO 2 –


• Energy is used in anabolism (carbon from organic compounds) -


A nutritional classification of organisms

Metabolic Diversity Among Organisms

Nutritional type


Energy source

Light CO 2

Carbon source

Photoheterotroph Chemoautotroph Chemoheterotroph Light Organic compounds Chemical CO 2 Chemical Organic compounds


Oxygenic: Cyanobacteria plants.

Anoxygenic: Green, purple bacteria.

Green, purple nonsulfur bacteria.

Iron-oxidizing bacteria.

Fermentative bacteria.

Animals, protozoa, fungi, bacteria.

Carbon cycle Nitrogen cycle Sulphur cycle Phosphorus cycle

Biochemical tests and bacterial identification

Bacillus subtilis Staphylococcus aureus

Gram stain •

Pseudomonas aeruginosa Kelbsiella pneumonia K. pneumonia


Ps. aeruginosa

look alike through a microscope after Gram stain; so how can they be differentiated?

Different species produce different enzymes determine what type of metabolic reactions an organism can carry out – Oxygen requirements – Fermentation of different substrates (sugars) – Enzymes of respiration – Amino acid catabolizing enzymes

Toxic Forms of Oxygen

• Singlet oxygen: O 2 boosted to a higher-energy state • Superoxide free radicals: O 2 – • Peroxide anion: O 2 2– • Hydroxyl radical (OH  )

Chemical Requirements Oxygen (O



•Fermentation tests are used to determine the substrates the organism can metabolize by the products it generates.

Control tube S.epidermidis




Medium: Carbohydrate


, inverted Durham tube Products: Acid and gas.

Figure 5.23

Protein Catabolism

Urease NH 3 + CO 2

Dichotomous Key

• •

A dichotomous key is a series of questions which leads to the identification of an item.

– a device on paper or computer that aids identification of a species or other type of entity.

Dichotomous keys

are used for the identification of organisms. • A dichotomous key works by offering two alternatives at each juncture, and the choice of one of those alternatives determines the next step.

Learning objectives

• Describe the chemical reactions of, and list some products of, fermentation.

• Describe how lipids and proteins undergo catabolism.

• Provide two examples of the use of biochemical tests to identify bacteria.

• Compare and contrast cyclic and noncyclic photophosphorylation.

• Compare and contrast the light-dependent and light-independent reactions of photosynthesis.

• Compare and contrast oxidative phosphorylation and photophosphorylation.

• Write a sentence to summarize energy production in cells.

• Categorize the various nutritional patterns among organisms according to carbon source and mechanisms of carbohydrate catabolism and ATP generation.

• Describe the major types of anabolism and their relationship to catabolism.

• Define amphibolic pathways