Microbia

NUTRITION AND METABOLISM

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LEARNING OUTCOMES
1. To understand the basic concepts of microbial
nutrition and metabolisms,

2. to differentiate the nutritional types of

microorganisms and

3. to define the metabolic pathways.

Chemical analysis of microbial cells:
Water 70% 97% of
dry wt. of cells = organic compounds 96% of cell
composed of 6 elements (C, H, N O, P, S)
Common nutrient requirements
A) Macroelements
Carbon

For the structural parts

Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
Potassium For non-structural functions
Calcium
Magnesium
Carbon source
- Backbone of all organic molecules -
Organic C in reduced form source of e- moves
through e- transport chains and other O-R reactions
energy for cells
- C source that does not supply H or energy = CO2 C
source but not energy source for autotrophs
Nitrogen source

- Typical bacterium contain 15% nitrogen

- Organic source: amino groups
Inorganic source: ammonia, nitrate
- Some fix atmospheric N2
Phosphorus source
- Found in nucleic acids and phospholipids
- Available as phosphate ion

Sulfur source
- Required for amino acids and vitamins
- Organic source: sulfur-containing amino acids
Inorganic source: sulfate
B) Microelements/Trace elements

Mn - Required in small amounts

Zn - Functions:

Co a) part of enzyme and cofactors

b) catalysis of reactions
Mo
c) maintenance of protein structure
Ni
Cu
C) Specific requirements

- Diatoms silicic acid

- Halophilic microbes high concentration of
sodium
Important:

Must have a balanced mixture of nutrients.

Shortage of an essential nutrient, microbial
growth will be limited regardless of
concentrations of other nutrients
Nutritional types of
microorganisms
- Essentials for growth of microrganisms
Carbon sources
Autotrophs CO2 Heterotrophs
Reduced, preformed, organic
molecules
Energy sources
Phototrophs Light Chemotrophs
Oxidation of organic or inorganic
compounds
Electron sources
Lithotrophs Reduced inorganic molecules
Organotrophs Organic molecules
Photolithoautotrophy
- Photolithotrophic autotrophs or photoautotrophs
- Source of energy: Light
Source of C: CO2 Source of e-:
reduced inorganic molecules e.g.

Algae and cyanobacteria: H2O

Purple and green sulfur bacteria: H2, H2S
and elemental S
Photoorganoheterotrophy

- Photoorganotrophic heterotrophs
- Source of energy: Light Source of
C: Organic C molecules Source of e-:
Organic molecules
- Common inhabitants of polluted lakes/streams
Chemolithoautotrophy
- Chemolithotrophic autotrophs
- Source of energy: Oxidation of
organic/inorganic compounds
Source of C: CO2 Source of
e-: Reduced inorganic molecules (iron, N,S)
- Contribute to chemical transformations of
elements in the ecosystem
Chemoorganoheterotrophy
- Chemoorganotrophic heterotrophs or
chemoheterotrophs
- Source of energy: Oxidation of
organic/inorganic compounds
Source of C: Organic C molecules Source
of e-: Organic molecules
- Same organic nutrient satisfy all requirements
- Most pathogenic microorganisms
Mixotrophic
- Alter metabolic patterns in response to
environmental changes
- E.g. Purple nonsulfur bacteria
Photoorganoheterotroph absence of O2
Chemoorganoheterotrophs presence of O 2

The term mixotroph can describe organisms (usually algae or

bacteria) capable of deriving metabolic energy both from
photosynthesis and from external energy sources. These
organisms may use light as an energy source, or may take up
organic or inorganic compounds. They may take up simple
compounds osmotically or by engulfing particle (phagocytosis or
myzocytosis).
 Energy Reducing Carbon source Name
source equivalent
source
Light Organic Organic Photoorganoheterotroph
Photo- -organo- -heterotroph
Carbon dioxide Photoorganoautotroph
-autotroph
Inorganic Organic Photolithoheterotroph
-litho- -heterotroph
Carbon dioxide Photolithoautotroph
-autotroph
Chemical Organic Organic Chemoorganoheterotroph
compounds -organo- -heterotroph
Chemo-
Carbon dioxide Chemoorganoautotroph
-autotroph
Inorganic Organic Chemolithoheterotroph
-litho- -heterotroph
Carbon dioxide Chemolithoautotroph
-autotroph
 Autotrophs:
Energy Carbon Name: Example:
Source: Source:
Light Inorganic Photoautotroph Most photosynthetic bacteria,
e.g. Chromatium (anaerobic),
Cyanobacteria (aerobic)

Inorganic Inorganic Chemolithotrophic autotroph Nitrobacter

(chemoautotroph)

Organic Inorganic Chemoorganotrophic Pseudomonas oxalaticus

autotroph
Heterotrophs:
Energy Carbon Name: Example:
Source: Source:
Light Organic Photoheterotroph Purple and green photosynthetic
bacteria, e.g. Rhodospirillum
Inorganic Organic Chemolithotrophic Desulphovibrio
heterotroph ("mixotroph")

Organic Organic (Chemo)heterotroph E. coli

Microb
ial
METABOLISM
- To grow, cells must
a) Synthesize new components
b) Need to harvest energy to power
biosynthetic reactions, transport nutrients and
etc.
- Involves metabolic p/ways and enzymes
Metabolism - Definition
Metabolismfrom the Greek term metaballein,
meaning change, pertains to the chemical reactions
and physical workings of the cell

Metabolism is the sum of all chemical reactions

within the cell
Principles of Metabolism
- Two components
a) Catabolism: Processes that harvest energy
released during the breakdown of
compounds, using it to synthesize
ATP
b) Anabolism: or biosynthesis, are processes that
utilize energy stored in ATP to
synthesize and assemble subunits of
macromolecules.
 Catabolic reactions
Degradative
Hydrolytic reactions
Exergonic
Break down of sugars into carbon dioxide
and water
Anabolic reactions
Biosynthetic
Dehydration reactions
Endergonic
The formation of proteins from amino acids
Microbial Metabolism
Catabolism provides the building blocks and
energy for anabolism.
CATABOLISM ANABOLISM

Energy source

Cell structures (cell

wall, membrane)
Energy
Subunits (a.a.,
nucleotides)
Energy

Waste products Nutrients (source

(acids, CO2) of N, S, etc)
Note:
- Catabolism and anabolism are interlinked
- ATP generated during catabolism is used in
anabolism.
- Precursors in catabolic processes can be
used in anabolic processes
Harvesting Energy
- Variety of ways, depending on nutritional type
- e.g. Photosynthetic organisms sunlight
synthesis of organic compounds
Chemoorganotrophs energy from degrading
organic compounds
Components of Metabolic Pathways
a. Enzymes
b. ATP
c. The chemical energy source
d. Electron carriers
e. Precursor metabolites
a) Enzyme
- Protein catalysts with great specificity on reaction
catalyzed and the molecules acted on.
- Catalyst = substance that increases the rate of a
chemical reaction without being permanently altered
itself.
- specific
How do enzymes catalyze reactions?
- By lowering the activation energy
Transition-state - Substrate A + B
complex AB a transition-
state complex
C + D formed.
Substrate
A+ B

Product C + D
How do enzymes catalyze reactions?
- By lowering the activation energy

Transition-state - Activation energy

complex AB bring reacting
molecules together
Activation to reach transition
energy Ea state
Substrate
A+ B

Product C + D
How do enzymes catalyze reactions?
- By lowering the activation energy

Transition-state - Enzyme
complex AB accelerate
reactions by
Activation lowering the Ea
Substrate energy Ea
A+ B

Product C + D
How enzymes lower the activation energy?

- Enzyme brings substrates to the active or catalytic

sites concentrating substrate in correct orientation
to form transition-state complex speed up
reaction at lower activation energy
Enzyme inhibition
- Types of inhibitors:
a) Competitive inhibitor:
resemble substrate (fill the active site)
compete with substrate for enzymes catalytic site

b) Noncompetitive inhibitor:
Binding to enzyme other than the
catalytic site, allosteric site
alter enzymes structure nonfunctional
 - Free energy
- Exergonic
- Endergonic

b) ATP
- Energy currency of a cell
- As the ready and immediate donor of free energy
- Link most cellular exergonic and endergonic chemical
reactions.
High-energy phosphate bonds

P P P P P
ADP
ATP
+ Pi + energy

Used for anabolic

Energy from processes
catabolic
processes
Addition of a P to a chemical compound is
known as phosphorylation.

Organism used 3 mechanisms of

phosphorylation to generate ATP from ADP:

Substrate level phosphorylation

Oxidative phosphorylation
Photophosphorylation
c) Chemical Energy Source

Substrate level phosphorylation

a high-energy P from an intermediate in

catabolism is added to ADP forming ATP

C-C-C~P + ADP --> C-C-C + ATP

Oxidative phosphorylation

energy released as electrons are passed to a

series of electron acceptors/carriers (an electron
transport chain) and finally to O2 or other
inorganic or organic molecules.
occurs in plasma membrane of prokaryotes and
in the inner mitochondrial membrane of
eukaryotes.
 Photophosphorylation

occurs only in photosynthetic cells- contain

chlorophylls.
energy from light is trapped by chlorophyll,
and electrons are passed through a series
of electron acceptors.
The electron transfer releases energy used
for the synthesis of ATP.
Electron transport chain is involved.
Oxidation-Reduction Reactions
- Compound that loses e- oxidized
Compound that gains e- reduced
- Removal of e- from a compound is usually followed by
removal of a proton (usually H atom)
- Removal of H atom oxidation Addition of H
atom reduction
- Catabolism: E- are removed from the energy source (e-
donor) and are transferred to an e- carrier
d) Electron Carriers
- Three types of e- carriers
a) NAD+
- coenzyme that works with dehydrogenase
- accept e- and form reduced form (NADH +
H+) - Fate of e- carried: to generate a proton
motive force that drives ATP synthesis

b) FAD
- accept e- and produce reduced form (FADH2)
- Fate of e- carried: similar to NAD +
c) NADP+ (NAD phosphate)

- accept e- and form reduced form (NADPH + H+)

- Fate of e- carried: biosynthesis

*Type of terminal e- acceptor will be determined

by type of metabolism*
 Metabolism and terminal e- acceptors
Organic e- donor Inorganic e- donor

Fermentation Aerobic Anaerobic

Only for
respiration respiration
chemolithotrophs

Exogenous e-
Endogenous
Exogenous e- acceptor e.g.
organic e-
acceptor e.g. NO3-, SO42-,
acceptor e.g.
O2 CO2, fumarate
pyruvate
Exogenous e-
acceptor e.g.
NO3-, SO42-,
O2
e) Precursor metabolites
- metabolic intermediates molecules in
catabolic pathways that can be either
oxidized to generate ATP or
- can be used to synthesize macromolecules
subunits
e.g. Amino acids, lipids and nucleotides.
- e.g. In E. coli, precursor metabolite
pyruvate (glycolysis) amino acid
alanine
Cellular respiration
Process cells use to convert the E in the chemical
bonds of nutrients to ATP E.

a) Aerobic respiration
b) Anaerobic respiration
c) Fermentation
Respiration
- Uses reducing power (from glycolysis, transition step
and TCA cycle) to generate ATP by oxidative
phosphorylation.
- E- carriers NADH and FADH2 transfer their e- to e-
transport chain
Aerobic Respiration
- the aerobic catabolism of nutrients to CO2, H2O and E
- involves an electron transport system
- final e- acceptor: O2

C6H12O6 + 6O2 yields 6CO2 + 6H2O + energy (as ATP)

- Total theoretical maximum number of ATP generated per

glucose in prokaryote is 38.
- In eukaryotic cells, 36 to 38.
Anaerobic Respiration
- ultimate e- acceptor: inorganic molecules other
than O2 e.g. nitrate, sulfate
- 36 ATPs or lesser by oxidative phosphorylation

- Like aerobic respiration, anaerobic respiration

involves : glycolysis, transition reactions, TCA
and electron transport chain.
Aerobic respiration:
- metabolic pathways
a. Glycolysis
b. Transition reactions
c. Citric acid cycle
d. Electron transport chain and Chemiosmosis
Glycolysis
- Or Embden Meyerhoff pathway
- Oxidizes 6-C sugar (glucose) to form 2 molecules of
pyruvate (3-C molecules)
- Yield of glycolysis:

a. 2 net ATPs (substrate level phosphorylation)

b. Reducing power (2 NADH +2H+)
c. Precursor metabolite (pyruvate)
- occurs in cytoplasm of cell
- Either in aerobic or anaerobic condition
Pentose Phosphate Pathway
- Also breaks down glucose but primary role production
of compounds used in biosynthesis
- Yield of PPP
a) Reducing power (NADPH) b)
Precursor metabolite (ribose 5-phosphate, erythrose 4-
phosphate)
- Operate in presence or absence of O2
Transition reactions
- connects glycolysis to TCA
- oxidative decarboxylation
- Pyruvate converted to a 2-C fragment (acetyl-CoA)
- Yield:

a. Reducing power (2 NADH) b.

Precursor metabolite (acetyl Co-A)
c. 2 CO2
TCA cycle
- Acetyl-CoA TCA cycle oxidation processes
- Yield:
a. 2 ATPs b.
Reducing power (6 NADH, 2 FADH2) c.
Precursor metabolites (-ketoglutarate,
oxaloacetate)
d. 4CO2
Electron Transport Chain and
Chemiosmosis
A mechanism - electrons are passed along a
series of carrier molecules - energy for the
synthesis of ATP.
A series of electron carriers - transfers e -
from NADH and FADH2 to O2.
Terminal electron acceptor

Chemiosmosis: The production of ATP

utilizing the energy released when hydrogen
ions flow through an ATP synthase complex.
NADH and FADH2 carry H+ and e- to the electron transport
chain located in the membrane. The energy from the transfer
of electrons along the chain transports protons across the
membrane and creates an electrochemical gradient.

As the accumulating protons follow the electrochemical

gradient back across the membrane through an ATP
synthase complex, the movement of the protons provides
energy for synthesizing ATP from ADP and phosphate.

End products of electron transport system: 2 protons, 2 e-,

and H2O.

O2 - final electron acceptor aerobic respiration.

- Implications of anaerobic respiration in the
environment
a) Removes nitrate from soil and converts to
N2 decreases soil fertility
b) Intermediates of denitrification e.g. nitrous
oxide and nitric oxide contribute to
greenhouse effect and global warming
Fermentation
- Cells that cannot respire (aerobic or anaerobically)
unable to recycle reduced e- carriers subsequent
catabolic processes cannot occur.
- Alternative method to solve problem: Fermentation

- Anaerobic breakdown of CHO

- Organic molecule final e- acceptor
- In fermentation:
a) partial oxidation of glucose occur
b) no transition step, krebs cycle and e- transport
chain c) little ATP is
generated (2 from glycolysis)
- Strategy used by facultative anaerobes and those lack
of e- transport chain
- Uses pyruvate as a terminal e- acceptor
- E- carried by NADH transferred to pyruvate, NAD+
is regenerated
- Different products are produced by different m/os
during fermentation:
Ethyl alcohol
Butyric acid CO2
Acetic acid
Butyl alcohol Lactic acid
Acetone Saccharomyces Succinic acid
Isopropyl alcohol Ethyl alcohol
E. coli
CO2 CO2
H2 Pyruvate
H2
Clostridium Enterobacter
Formic acid
Streptococcus
Propionibacterium Lactobacillus
Ethyl
alcohol Lactic
Propionic acid acid 2,3-
Acetic acid Butanediol
CO2 Lactic acid CO2
H2
Catabolism of Organic Compounds
other than Glucose
- E.g. lipids, proteins
- Break down subunits by hydrolytic enzymes
subunits transport into cells further degraded to
form metabolites (central metabolic p/ways or
used biosynthesis)
Lipid Catabolism
Microbes can also oxidize lipids and
proteins
lipases hydrolyze lipids into glycerol
and fatty acids
glycerol is catabolized by conversion to
dihydroxyacetone phosphate, and fatty
acids are catabolized by beta oxidation
Catabolic products can be further
broken down in glycolysis and the
Krebs cycle
e.g. Lipid
lipases
Lipid glycerol + fatty acids
-oxidation

Converted to
Converted to acetyl-CoA
dihydroxyacetone
phosphate

Enter TCA cycle

Enter glycolytic p/way

Photosynthesis
- Capture light energy to synthesize ATP, NADH
or NADPH
- Process in which light energy is trapped and
converted to chemical energy = Photosynthesis.
- Types of photosynthetic organisms

Eucaryotic Organisms Procaryotic Organisms

Higher plants Cyanobacteria

Multicellular green,
brown and red algae
Unicellular algae (e.g.
euglenoids,
dinoflagellates, diatoms)
Green sulfur bacteria
(Chlorobium)
Green non-sulfur
bacteria (Chloroflexus)
Purple sulfur bacteria
(Chromatium)

Purple non-sulfur
bacteria (Rhodobacter)
Photosynthesis

a) Light reaction: light energy is trapped and

converted to chemical energy in the form
of ATP and NADPH
b) Light Independent reaction (Dark reaction):

ATP and NADH (NADPH) from the light-

dependent reactions are used to reduce CO2 to
form organic carbon compounds (carbon
fixation).
The reduced organic carbon is usually
converted into glucose or other carbohydrates.
Capturing radiant energy
- By pigments
- Types of pigments
a) Chlorophylls
- In plants, algae and cyanobacteria -
Various types e.g. chlorophyll a -
Photosynthetic processes : oxygenic
- Oxygenic: uses water as e- donor
b) Bacteriochlorophylls
- In purple photosynthetic bacteria and green
photosynthetic bacteria
- Absorb wavelengths not absorbed by
chlorophylls - Various types
e.g. bacteriochlorophyll a -
Photosynthetic processes: anoxygenic
c) Accessory pigments
- E.g. carotenoids, phycobilins
- Increase the efficiency of light capture by
absorbing wavelengths not absorbed by
chlorophylls - Found in
photosynthetic organisms (procaryotes and
eucaryotes)
- Photosynthetic pigments are located in protein
complexes called photosystems (PSI and PSII)
- Roles of various pigments in photosystem

a) Antennae complexes
- acts as a funnel, capturing the energy of
light and transfer to the reaction-center
pigment
b) Reaction-center pigments
- function as e- donor in photosynthetic
process - upon
excitation by radiant energy, emits an e-
e- transport chain
Converting Radiant Energy into Chemical
Energy
- Photosynthetic organisms must produce energy (ATP)
and also generate reducing power (NADPH or
NADH) to fix CO2
- Excited e- from reaction center chlorophylls e-
transport chain ATP synthesized
- Mechanism to produce reducing power vary among
photosynthetic organisms.
 When cells need to synthesize ATP and reducing
power (NADPH):
Non-cyclic photophosphorylation:
- e- emitted by photosystem I are not passed to the e-
transport system but are donated to NADP+ to
produce NADPH
- Must replenish e- from photosystem I and must
continue to generate ATP
- Photosystem II absorb radiant energy, high-energy e-
emitted e- transport system (produce ATP), and
finally accepted by photosystem I
- To replenish e- from photosystem II extracts e-
from water generates O2
Light-dependent Reactions in Cyanobacteria and
Photosynthetic Eucaryotic Cells
- When cells need to synthesize ATP but not reducing
power (NADPH):
Photosystem I absorbed radiant energy excite
the reaction-center chlorophylls emit high
energy e- pass through e- transport chain
ATP synthesized the e- passed back to the
reaction-center chlorophyll
Cyclic photophosphorylation
Light-dependent Reactions in Purple and
Green Bacteria
- Only one photosystem
- Unable to use water as an e- donor for reducing power
- e- donors : H2, H2S and organic compounds

- Green bacteria
Use photosystem similar to photosystem I
e- emitted can be used to generate ATP or reduce
NAD+
The photosynthesis process of purple sulfur bacteria
Energy of sunlight is captured by the photosystem. The
antennae pigment in the photosystem capture the sunlight
and transfer in to the reaction center pigments
Upon excitation by radiant energy, the reaction center
pigment emits electrons
Electrons are passed through the e- transport chain and
ATP is synthesized.
The ATP and reducing power generated in through the
reversed e- transport process.
Enzyme RUBISCO in the organism incorporates CO2 to
produce 3-phospohoglycerate
ATP and NADPH are used to convert 3-phosphoglycerate
to glyceraldehydes 3-phosphate, a precursor metabolite
for biosynthesis of organic molecules
Carbon fixation
- Convert CO2 into organic form process = C
fixation
- Is a light-independent reaction
- Consumes ATP and reducing power
- The most common pathway for C fixation =
Calvin cycle
Calvin cycle
- 3 stages
a) Stage 1: incorporation of CO2 into an
organic compound b) Stage 2:
reduction of resulting molecule c)
Stage 3: regeneration of the starting
compound
Stage 1

Enzyme ribulose biphosphate carboxylase

(RuBisCo) joins CO2 to ribulose 1,5-
biphosphate (5-C compound) to produce 2
molecules 3-phosphoglycerate (PGA: 3-C
compound)
Stage 2
- ATP and NADPH are used to convert
3-phosphoglycerate to glyceraldehyde 3-
phosphate (G3P)
- Glyceraldehyde 3-phosphate is a precursor
metabolite

Stage 3

Part of G3P regenerate RuBP to continue

the cycle
Anabolic Pathways
Synthesizing subunits from precursor molecules

- Use ATP and reducing power (NADPH) and precursor

metabolites formed in the central metabolic pathways.
- Subunits synthesized assembled to make
macromolecules various macromolecules joined to
form structures making up the cell
Amino acid synthesis
e.g. Glutamate
Incorporate N source (ammonium) into the
synthesis process
Ammonia is incorporated into the precursor
metabolite -ketoglutarate produce glutamate
Amino group of glutamate can be transferred to
other C compounds e.g. oxaloacetate to
produce a.a. e.g. aspartate and regenerates
-ketoglutarate.
-ketoglutarate to incorporate more ammonia
SUMMARY
Nutrition
Nutrients requirements
Nutritional types
Metabolism
Basic concepts
Glycolytic pathways
Fermentation
Respiration
Photosynthesis
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