BIOLOGY
YEAR 2
QUARTER 1
2019/2020
Microbial Metabolism
SUMMARY OF THE COURSE MICROBIAL METABOLISM
NWI-BB090
ELISE REUVEKAMP
,Content
Bioenergetics ........................................................................................................................................... 2
Glycolysis, fermentation, aerobic respiration ......................................................................................... 5
Anaerobic respiration, acetogenesis, methanogenesis, methanotrophy, syntrophy ........................... 10
Chemolithotrophy ................................................................................................................................. 16
Spookmicrobes and anammox .............................................................................................................. 19
............................................................................................................................................................... 19
Phototrophy and biosynthesis .............................................................................................................. 21
Autotrophy, N2 fixation and carbon cycle ............................................................................................ 26
Nitrogen cycle and sulfur cycle ............................................................................................................. 32
,Bioenergetics
→ Brock chapter 3.3-3.7
Bioenergetics is a field in biochemistry and cell
biology that concerns energy flow through living
systems
Metabolism is the sum total of all chemical
reactions that occur in a cell, categorized by:
- Catabolism: energy releasing reactions
- Anabolism: energy consuming
biosynthetic reactions
Chemotrophs and phototrophs
Organisms that conserve energy from chemicals are called chemotrophs
- Chemoorganotrophs: conserve energy from organic chemicals
- Chemolithotrophs: tap energy available from oxidation of inorganic compounds
Organisms that use light as energy source are called phototrophs, that contain chlorophyll and other
pigments that convert light energy into ATP.
- Oxygenic photosynthesis, where O2 is produced
- Anoxygenic photosynthesis, where O2 is not produced
Regardless of how a microorganism conserves energy, be it from chemicals or from light, all cells
require large amounts of carbon in one form or another to make new cell materials.
- Heterotrophs obtain this from an organic compound
- Autotrophs use carbon dioxide as its carbon source. There are also called primary producers,
because they synthesize new organic matter from inorganic carbon (CO2). The major
pathway through which this happens is called the Calvin cycle.
Bioenergetics
First law of thermodynamics: energy can be transformed from one form to another but cannot be
generated or destroyed.
Making ATP is the ultimate goal of microorganisms. To make ATP, energy from chemical reactions is
required. Energy is defined as the ability to do work measured in KiloJoules. All chemical reactions
are accompanied by changes in energy, either being required or released as the reaction proceeds.
Basic principles of bioenergetics:
- Free energy is the energy that is available to do work, expressed in ΔG0′. It tells you only the
amount of energy released or required, not which reaction is going faster.
- -ΔG0′ → exergonic reaction that will release free energy (burn sugar)
- +ΔG0′ → endergonic reaction that will require free energy (make sugar)
Coupling of endergonic and exergonic reactions, lead to proceeding endergonic reactions by the use
of energy released by exergonic reactions. The break down of glucose releases a free energy of -2863
kJ per mole and the formation of ATP costs +32 kJ per mole, so 89 moles of ATP can be generated
, from 1 molecule of glucose. However it is going to be less as some energy is lost as heat to drive the
reaction forward.
Catalysis and enzymes
Kinetics is the velocity of catalysis, combined with thermodynamics, the reaction rate can be
determined.
All energy reaction have an
activation energy barrier, which
prevent exergonic reactions from
happening spontaneously. For
example the reaction of sugar to CO2
is exergonic, but sugar doesn’t
change to CO2 at home for ages.
Through the use of catalysts:
activation energy can be lowered.
Catalysts: are not consumed in the
reaction, lower the activation energy, Increase the reaction rate and do not affect energetics or
equilibrium of a reaction
Enzymes: are biological catalysts, typically proteins, highly specific, generally larger than substrate,
typically rely on weak bonds and have an active site: region of enzyme that binds substrate
Enzyme nomenclature:
- Oxidoreductases → catalyses oxido-
reductions, where the substrate
oxidized is regarded as electron donor
- Transferases → catalysts that transfer a
group from one compound to another
- Hydrolases → catalyses via hydrolysis of
various bonds
- Lyases → cleave off C-C, C-O, C-N and
other bonds by other means than
hydrolysis or oxidation
- Isomerases → catalyse changes within one molecule
- Ligases → catalyse the joining of two molecules with hydrolysis of diphosphate bond in ATP
Enzymes make use of cofactors, that assist enzyme during catalysis of reactions. Mostly metals ions
or coenzymes are cofactors. Tight covalent bounds are prosthetic groups and non-covalent bound
are coenzymes that interact with different enzymes for example NADH.
NAD+ is a very common redox coenzyme that associates with the redox enzymes that catalyse the
reaction. NADH is the reduced form of NAD+. Electron shuttling is common, so electrons removed
from an electron donor by an enzyme that oxidizes that donor are used to reduce NAD+ to NADH
and the NADH can be used in another enzyme to oxidize NADH back to NAD+.
Electron donors and acceptors
YEAR 2
QUARTER 1
2019/2020
Microbial Metabolism
SUMMARY OF THE COURSE MICROBIAL METABOLISM
NWI-BB090
ELISE REUVEKAMP
,Content
Bioenergetics ........................................................................................................................................... 2
Glycolysis, fermentation, aerobic respiration ......................................................................................... 5
Anaerobic respiration, acetogenesis, methanogenesis, methanotrophy, syntrophy ........................... 10
Chemolithotrophy ................................................................................................................................. 16
Spookmicrobes and anammox .............................................................................................................. 19
............................................................................................................................................................... 19
Phototrophy and biosynthesis .............................................................................................................. 21
Autotrophy, N2 fixation and carbon cycle ............................................................................................ 26
Nitrogen cycle and sulfur cycle ............................................................................................................. 32
,Bioenergetics
→ Brock chapter 3.3-3.7
Bioenergetics is a field in biochemistry and cell
biology that concerns energy flow through living
systems
Metabolism is the sum total of all chemical
reactions that occur in a cell, categorized by:
- Catabolism: energy releasing reactions
- Anabolism: energy consuming
biosynthetic reactions
Chemotrophs and phototrophs
Organisms that conserve energy from chemicals are called chemotrophs
- Chemoorganotrophs: conserve energy from organic chemicals
- Chemolithotrophs: tap energy available from oxidation of inorganic compounds
Organisms that use light as energy source are called phototrophs, that contain chlorophyll and other
pigments that convert light energy into ATP.
- Oxygenic photosynthesis, where O2 is produced
- Anoxygenic photosynthesis, where O2 is not produced
Regardless of how a microorganism conserves energy, be it from chemicals or from light, all cells
require large amounts of carbon in one form or another to make new cell materials.
- Heterotrophs obtain this from an organic compound
- Autotrophs use carbon dioxide as its carbon source. There are also called primary producers,
because they synthesize new organic matter from inorganic carbon (CO2). The major
pathway through which this happens is called the Calvin cycle.
Bioenergetics
First law of thermodynamics: energy can be transformed from one form to another but cannot be
generated or destroyed.
Making ATP is the ultimate goal of microorganisms. To make ATP, energy from chemical reactions is
required. Energy is defined as the ability to do work measured in KiloJoules. All chemical reactions
are accompanied by changes in energy, either being required or released as the reaction proceeds.
Basic principles of bioenergetics:
- Free energy is the energy that is available to do work, expressed in ΔG0′. It tells you only the
amount of energy released or required, not which reaction is going faster.
- -ΔG0′ → exergonic reaction that will release free energy (burn sugar)
- +ΔG0′ → endergonic reaction that will require free energy (make sugar)
Coupling of endergonic and exergonic reactions, lead to proceeding endergonic reactions by the use
of energy released by exergonic reactions. The break down of glucose releases a free energy of -2863
kJ per mole and the formation of ATP costs +32 kJ per mole, so 89 moles of ATP can be generated
, from 1 molecule of glucose. However it is going to be less as some energy is lost as heat to drive the
reaction forward.
Catalysis and enzymes
Kinetics is the velocity of catalysis, combined with thermodynamics, the reaction rate can be
determined.
All energy reaction have an
activation energy barrier, which
prevent exergonic reactions from
happening spontaneously. For
example the reaction of sugar to CO2
is exergonic, but sugar doesn’t
change to CO2 at home for ages.
Through the use of catalysts:
activation energy can be lowered.
Catalysts: are not consumed in the
reaction, lower the activation energy, Increase the reaction rate and do not affect energetics or
equilibrium of a reaction
Enzymes: are biological catalysts, typically proteins, highly specific, generally larger than substrate,
typically rely on weak bonds and have an active site: region of enzyme that binds substrate
Enzyme nomenclature:
- Oxidoreductases → catalyses oxido-
reductions, where the substrate
oxidized is regarded as electron donor
- Transferases → catalysts that transfer a
group from one compound to another
- Hydrolases → catalyses via hydrolysis of
various bonds
- Lyases → cleave off C-C, C-O, C-N and
other bonds by other means than
hydrolysis or oxidation
- Isomerases → catalyse changes within one molecule
- Ligases → catalyse the joining of two molecules with hydrolysis of diphosphate bond in ATP
Enzymes make use of cofactors, that assist enzyme during catalysis of reactions. Mostly metals ions
or coenzymes are cofactors. Tight covalent bounds are prosthetic groups and non-covalent bound
are coenzymes that interact with different enzymes for example NADH.
NAD+ is a very common redox coenzyme that associates with the redox enzymes that catalyse the
reaction. NADH is the reduced form of NAD+. Electron shuttling is common, so electrons removed
from an electron donor by an enzyme that oxidizes that donor are used to reduce NAD+ to NADH
and the NADH can be used in another enzyme to oxidize NADH back to NAD+.
Electron donors and acceptors
