2/19/20

My science journey….

Living on the dark side: the world of

chemotrophy
Brendan Burns MICR2011
School of Biotechnology and Biomolecular Sciences

Recognise there will be a diversity of student backgrounds (culture, language, etc)

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Seeing through a cultural lens… My lectures – Microbial metabolism

§ We all have filters we see the world through Specifically energy generation….

§ I have travelled the world but am still influenced by the cultural

environment I grew up in…
Today – Chemotrophy
§ Try and put aside any assumptions/biases and genuinely connect
with people
Tomorrow - Phototrophy
§ Invite you to come with an ‘empty bowl’

§ Allow you to gain as much new knowledge in

this course (and life!) as possible J

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Catabolism and Anabolism

Metabolism is the sum total of all the chemical reactions within a living organism.

“Without energy life would be extinguished instantaneously, and

the cellular fabric would collapse” Anabolism:
The processes by which
Albert Szent-Gyorgyi (1893 – 1986) energy and raw materials
are used to build
1937 Nobel Laureate in Physiology or Medicine macromolecules and
cellular structures
(biosynthesis)

Catabolism:
The processes by which
a living organism obtains
its energy and raw
materials from nutrients

This lecture focuses on the catabolism side

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Energy

• All organisms need & use energy

• What is energy?

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What is energy ? Light energy

Light used as the energy source.

A photon strikes a molecule,

and its energy is changed from
light energy into electrical
energy.
Boosts electrons to a higher,
more unstable orbital - very
reactive.

More on next lecture….J

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Chemical energy ATP

Oxidation of chemical compounds (organic or inorganic) to obtain energy Adenosine triphosphate, a molecule that contains three phosphates held
together by high energy bonds.

When third phosphate is

cleaved, leaving
adenosine diphosphate
(ADP), energy is released
to drive anabolic
reactions
Adenosine triphosphate (ATP)
Energy is required to add
a third phosphate to ADP
to form ATP; the energy
comes from catabolic
reactions and is stored in
the newly formed bond

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Phosphorylation Substrate-level phosphorylation

Transfer of phosphate group from a phosphorylated compound (substrate) directly

to ADP (which becomes ATP)

Examples:
Ø Glycolysis
Ø TCA cycle
Ø Fermentation

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Oxidative phosphorylation Reduction and Oxidation

Series of redox reactions occurring during respiratory pathway – production of ATP

from oxidised NADH/FAD
An atom becomes more reduced when it
undergoes a chemical reaction in which it:
Ø Gains electrons (i.e. electron acceptor)
Ø By bonding to a less electronegative atom
Ø And often this occurs when the atom
becomes bonded to a hydrogen

An atom becomes more oxidized when it

undergoes a chemical reaction in which it:
Ø Loses electrons (i.e. electron donor)
Ø By bonding to a more electronegative
atom
Ø And often this occurs when the atom
becomes bonded to an oxygen

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Reduction and Oxidation Nutritional classification of microorganisms

Microorganisms can be
grouped into nutritional
classes based on how they ØEnergy - Source of
satisfy their energy, electron ATP production
and carbon requirements
(often satisfied together; i.e.
carbon source often provides
Reduction and oxidation always occur energy and electrons).
together. In a reduction-oxidation
reaction (redox reaction), one ØElectron - Cellular
substance gets reduced, and another
respiration
substance gets oxidized

What gets oxidized is called the

electron donor, and what gets reduced
is called the electron acceptor
ØCarbon - Structural
building block

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Chemical energy - Chemotrophs Cellular respiration

Oxidation of chemical compounds to obtain energy.

These compounds can be organic (chemoorganotrophs)

or inorganic (chemolithotrophs). donates electrons accepts electrons

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Cellular Cellular
Cellular respiration
respiration respiration

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Cellular respiration Cellular respiration

Cellular respiration
Glycolysis TCA cycle

Generates the
reducing agents
NADH and FADH2
for electron transport
chain function

Glycolysis is the
breakdown of a
molecule of glucose
into two molecules of
pyruvate

ATP produced

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Cellular respiration Aerobic respiration

Oxidative phosphorylation Electron transport chain & Chemiosmosis

NADH and FADH2

provide electrons to
establish a proton
gradient across a
membrane, resulting in
an electrical potential
difference across the
membrane.

A proton motive force

drives protons across the Proteins are arranged by order of
membrane, through the electronegativity, so each protein will be
proton channel of ATP reduced (gain 2e-), then immediately
synthase, resulting in ATP oxidised (lose 2e-)
synthesis

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Aerobic respiration Aerobic respiration

Electron transport chain & Chemiosmosis Electron transport chain & Chemiosmosis
Section 9-1 Section 9-1

Glucose 2 Pyruvic acid Glucose 2 Pyruvic acid

Electron transport chain located in cell membrane

Proteins are arranged by order of electronegativity, so each protein will be reduced (gain 2e-),
NADH and FADH2 bring hydrogen atoms to the ETC from the TCA cycle
then immediately oxidised (lose 2e-)

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Aerobic respiration Aerobic respiration

Electron transport chain & Chemiosmosis Electron transport chain & Chemiosmosis
Section 9-1 Section 9-1

Glucose 2 Pyruvic acid Glucose 2 Pyruvic acid

NADH gives 2e- to NADH dehydogenase Energy is used to pump H+ ions across membrane
Electrons (e-) pass through ETC, releasing energy
Build up of H+ ions creates an electrochemical gradient

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Aerobic respiration Aerobic respiration

Electron transport chain & Chemiosmosis Electron transport chain & Chemiosmosis
Section 9-1 Section 9-1

Glucose 2 Pyruvic acid Glucose 2 Pyruvic acid

H+ ions want to diffuse back across membrane but are unable. When e- from NADH and FADH2 reach last mobile protein, cytochrome oxidase, they have lost
Use protein channels called ATPase complex (facilitated diffusion) energy

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Aerobic respiration
Anaerobic respiration (example – nitrate)
Electron transport chain & Chemiosmosis
Section 9-1 Section 9-1

Glucose 2 Pyruvic acid Glucose 2 Pyruvic acid

When cytochome reductase receives electrons it gets oxidised by oxygen (high electronegativity)
Oxygen plus electrons combines with hydrogen ions to make H 2 O.

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Anaerobic respiration (example – nitrate) Anaerobic respiration (example – nitrate)

Section 9-1 Section 9-1

Glucose 2 Pyruvic acid Glucose 2 Pyruvic acid

Ubiquinone (Q) picks up H+ on one side of the membrane and deposits it on the other side, Nitrate instead of oxygen used as the final electron acceptor.
generating an electrochemical gradient.

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Nutritional classification of microorganisms

ØEnergy - Source of ATP production

ØElectron - Cellular respiration

ØCarbon - Structural building block

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Electron source Chemoorganotrophy

Organic
Organism that obtains
electrons from organic Organisms that oxidise of one or more of a variety of organic
substrates. compounds acting as electron donors

= Organotrophy

• Primary difference between organic compounds and inorganic compounds is that organic
compounds always contain carbon while most inorganic compounds do not contain carbon

• Almost all organic compounds contain carbon-hydrogen or C-H bonds

• Note, containing carbon is not sufficient for a compound to be considered organic! (e.g
cyanide)

Inorganic
Organism that
depends upon
inorganic compounds
as electron donors. = Lithotrophy

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Chemoorganotrophy Chemoorganotrophy

Glucose Oxygen Benzene Oxygen

(Electron Donor) (Electron Acceptor) (Electron Donor) (Electron Acceptor)

e- e- e- e-

Example: Escherichia coli Example: Pseudomonas putida

Good for cleaning up fuel spills

Good for research (molecular biologist’s tool)

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Chemoorganotrophy Chemoorganotrophy

Methane Oxygen Acetate Oxygen

(Electron Donor) (Electron Acceptor) (Electron Donor) (Electron Acceptor)

e- e- e- e-

Example: Methylocystis parvus Example: Aeromonas hydrophila)

Good for treating municipal and industrial wastewater

Good for regulating global temperature

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Chemoorganotrophy Chemolithotrophy

- Uses inorganic reduced compounds as a source of energy

Oxygen - This group of organisms includes sulfur oxidizers, nitrifying bacteria, iron
Nitrate (NRB) oxidizers, and hydrogen oxidizers.
Acetate Iron (IRB)
(Electron Donor) Copper - The term "chemolithotrophy" refers to a cell’s acquisition of energy from
Manganese the oxidation of inorganic compounds, also known as electron donors.
Uranium
e -
e -
Arsenate e-
Organohalides
Sulphate
Carbon dioxide
(Electron Acceptors)

Good for bioremediation

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Chemolithotrophy Chemolithotrophy

Ammonia Oxygen Ferric Iron (Fe3 ) Oxygen

(Electron Donor) (Electron Acceptor) (Electron Donor) (Electron Acceptor)

e- e- e- e-

Example: Nitrosomonas nitrosa Example: Azospira oryzae

(important in waste water treatment)

Nitrification is the process by which ammonia (NH3) is converted to nitrate (NO−3) oxidize iron in environments that have a very low pH and are important in acid mine drainage

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Chemolithotrophy Chemolithotrophy

Hydrogen Perchloroethene
Hydrogen Oxygen (Electron Acceptor)
(Electron Donor)
(Electron Donor) (Electron Acceptor)

e- e- e- e-

Example: Ralstonia eutropha Example: Dehalococcoides mccartyi

Hydrogen and CO 2 as carbon and energy sources Good for reducing pollution globally!

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Something really cool….cable bacteria Cable bacteria

Sulphides donate electrons,

but there is no oxygen around
to accept them — no way of
completing the chain!

All the oxygen is centimetres

• Oxygen consumption coupled to S oxidation in deeper oxygen free layers
away, in the top-most
sediment. By uniting into
• This coupling mediated by electric currents carried across cm wide zones! cables, the bacteria can span
this gap J

• Native conductors are long filamentous bacteria - Desulfobulbacaea

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Some useful microbial definitions…. The Winogradsky column

The Winogradsky column is a miniature, self-

contained ecosystem.
• Aerobe – Need oxygen as terminal electron acceptor to make ATP
As the column progresses gradients begin to form
• Anaerobe – Cannot use oxygen and will die in the presence of
(light gradient, temperature gradient, nutrient, O 2
and H2 S concentration gradients).These gradients
• Microaerophile – Need oxygen but cannot tolerate high concentrations
result in a complex interaction of microbes with
their environment and with one another resulting
• Facultative anaerobe - aerobic respiration if oxygen is present, but capable of
in a series of community successions and,
switching to anaerobic respiration (fermentation) if oxygen is absent
ultimately, stratification of microbial populations.

Ø Photolithotrophic autotrophs

Ø Photoorganotrophic heterotrophs

Ø Chemolithotrophic autotrophs

Ø Chemoorganotrophic heterotrophs

More in next lecture!!!

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Summary
Is there anybody (else) out there…..?
• Chemotrophy – Oxidation of chemical compounds (organic or inorganic) to obtain
energy

• Reduction and oxidation always occur together

We tend to assume that life
must be assembled from
• In a reduction-oxidation reaction (redox reaction), one substance gets reduced, and
another substance gets oxidized
contemporary astronomy &
biology
• What gets oxidized is called the electron donor, and what gets reduced is called the
electron acceptor
However our familiar
• Microbes can be grouped into nutritional classes based on how they satisfy their
energy, electron and carbon requirements
water/oxygen planet may
be only one of many
• Microbes key in completing major nutrient cycles (e.g. C, S, N, P)
possibilities….
Metabolic diversity of microbes lies in the fact that they can utilise many alternate
electrons acceptors and donors – you name it, they will eat it J
Microbes may be the
answer J

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Next up….
Phototrophy

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