Metabolism 1: Bioenergetics and Fermentations

Outline:
❑ Basic bioenergetics
❑ Oxidation-reduction reactions and energy yield
❑ Electron carriers and high energy bonds
❑ Energy from fermentation pathways
 Metabolism is the sum of anabolism + catabolism.

• Catabolism: biochemical reactions

that are:
• Degradative
• Carbon consuming
• Energy generating.
• Anabolism: biochemical reactions
that are:
• Building in function
• Require an expenditure of
energy
• Are also referred to as
biosynthetic reactions.

• Growth of microorganisms requires:

• Chemicals (carbon, hydrogen,
oxygen, nitrogen, sulfur, +
others in smaller amounts).
• Energy: provided by
biochemical reactions or light
Microorganisms can be categorized by the carbon and energy
sources they use.

METABOLIC PATHWAYS
Inorganic (CO2) Autotroph
Carbon Source
Organic Heterotroph
Inorganic Chemolithotroph
Chemical
Energy Source Organic Chemoorganotroph
Light Phototroph
Energy yields of a reaction (Gibb’s Free Energy) can be calculated from
the Free Energy of Formation of the reactants and products

Gibb’s Free Energy: Go’ (measured in kJ/mole)

Go’ = ΣGof (of products) - ΣGof (of reactants)

Energy-yielding reactions = exergonic

(Go’ is negative)

Energy-requiring reactions = endergonic

(Go’ is positive)

Reaction progress curve showing free

energy during a non-enzymatic and
enzyme-catalyzed reactions.
 Oxidation-reduction (redox) reactions involve movement of electrons
from a donor to an acceptor. This reaction is accompanied by changes
in energy for that electron.
• Many chemical reactions in biological systems involve the movement of electrons
from one energy state to another.
• For exergonic reactions, the electrons move from a higher energy state to a
lower energy state.
• Oxidation: Reaction where electrons are removed from a chemical or atom
• Reduction: Reaction where electrons are accepted into a chemical or atom
• Redox reactions: the sum of oxidation reactions + reduction reactions

• Thus, electron transfer reactions can be thought of as two half-reactions: an

oxidation, and a simultaneous reduction.
 Redox reactions in which electrons move from a higher to a lower
energy state yield energy for the cell.
This concept can be visualized by the “Redox Tower”
For a redox reaction, if electrons move down the redox tower, then this reaction
will yield energy. Energy of each half- reaction is shown
in terms of electron volts rather than Gof

Electrons are donated

from redox couples
above and are
accepted by redox
couples below

Link: Illustration for

redox tower
http://mw.concord.org/modeler/showcase/mechanics/
overshotwaterwheel.html
Examples of oxidized and reduced compounds used in microbial
metabolism

element reduced intermediate oxidized

carbon CH4 CH2O CO2
nitrogen NH4+ N2, NO2- NO3-
sulfur SH2 S SO42+
Energy yields from redox reactions can be calculated from the free
energy of formation of products and reactants

Go’ = ΣGof (of products) - ΣGof (of reactants)

Table A1.1
H2 0 kJ/mol
NO3- -111
NO2- -37
H20 -237

H2 + NO3- → NO2- + H2O Overall reaction

H2 → 2e- + 2H+
NO3- + 2e- + 2H+ → NO2- + H2O

— = -163 kJ/mol
products reactants
 Electron carriers move electrons in biological systems. They act as
substrates or cofactors of enzymes or proteins.
A variety of electron carriers are used: they carry 1 or 2 electrons at a time – no wires
in cells! These include NAD, flavins (FMN or FAD), and quinones.
•These cofactors transfer electrons by interacting with proteins or enzymes

Carriers of 2e- + 2H+ quinones

FMN: flavin
mononucleotide

NAD: nicotinamide
adenine dinucleotide
 NAD (or NADP) transfers electrons (and protons) from a reduced
enzyme and then donating electrons to an oxidized enzyme.
• Electron carriers transfer electrons between enzymes.

Link: Animation: How NAD works

http://highered.mheducation.com/sites/0072507470/student_view0/chapter25/animation__how_the_nad__works.html
Oxidation-Reduction Reactions: Carriers of Electrons Only

Non-heme iron- Heme-containing

sulfur proteins proteins
(cytochromes)

Review of oxidation-reduction (redox) reaction terminology

Oxidation: Loss of an electron
Reduction: Gain of an electron
Electrons cannot be free in solution, so oxidation reactions are coupled to reduction
reactions (reactants and products are termed redox couples)
In some biological reactions, a proton and electron (hydrogen atom) are transferred
together. In other reactions, only electrons are transferred.
Redox potential: a measure of the tendency to give up an electron
Energy can be stored in compounds containing high energy bonds
• High energy bonds are created from energy-generating pathways.
• The bonds are broken to yield energy for anabolic reactions.
• Water is removed when anhydride bonds are created.
• Water is split (a process called hydrolysis) when anhydride bonds are
broken.

Link: Interactive animation: Hydrolysis of anhydride bonds of ATP

https://www.cengage.com/chemistry/discipline_content/dvd/Power_Lectures/Biochemistry/dswmedia/TH005_acf.html
 In living systems there two basic strategies for producing ATP.

1. Substrate-level phosphorylation
• ATP is generated from energy-rich
intermediates.
• Fermentation pathways make ATP by
substrate-level phosphorylation.
• Glycolysis involves substrate-level
phosphorylation of glucose, and is
found in nearly all organisms.
2. Oxidative phosphorylation
• During respiration, cytoplasmic
membrane becomes energized,
creating the proton motive force.
• Chemiosmosis used to make ATP.

• Photophosphorylation (analogous to oxidative phosphorylation) – found in

phototrophs, is driven by light.
Glycolysis is the fermentation of glucose to pyruvate and is common
in most organisms

Glycolysis:
• Pathway is nearly universal in aerobic and anaerobic organisms.
• Low energy yield compared to respiration.
• Splits glucose (6 C) into 2 pyruvate (3 C) and then to final products (depending on
organism).
• Produces a net of 2 ATP per glucose and 2 NADH (consumed to produce final
products)
• NADH that is generated is later oxidized for production of fermentation end
products. Link: How glycolysis works
http://highered.mheducation.com/sites/9834092339/student_view0/ch
apter7/how_glycolysis_works.html
 According to a Japanese study, a newly opened can of
surströmming has one of the most putrid food smells in the world
チーズカード
 Nem chua

Natto
Link: Research on Vietnam
fermented foods
 Many other fermentation pathways are found in microorganisms.
There is great diversity of fermentations in nature
- Alternative reactions of pyruvate
- Alternative pathways from glucose to pyruvate
- Alternative starting substrates (not glucose)
- Pathways are named according to their final products

Examples of alternative fermentation pathways using glucose as the substrate:

Lactic acid fermentations in Lactic Acid Bacteria

-- Homofermentative pathways:
glucose → 2 pyruvate → 2 lactic acid

-- Heterofermentative pathways:
glucose → 2 pyruvate → lactic acid
ethanol
CO2

Example using substrate other than glucose:

Stickland fermentations use amino acids as a substrate, pathways found in
most members of the genus Clostridium (anaerobe; many are pathogens)
Amino acids →→ organic acids [+ ammonia + CO2, depending on amino acid used]
 Summary
• Organisms use chemicals and energy to carry out catabolism (energy-yielding
degradative reactions) and anabolism (energy-consuming building reactions).
• The overall energy change in a reaction can be calculated from the free energy of
formation of the reactants and products:
• Go’ = ΣGof (of products) - ΣGof (of reactants)
• Chemical reactions in biological systems often involve the movement of electrons
from one energy state to another in redox reactions.
• These reactions are facilitated by various electron carrier molecules.
• Chemical energy is often stored in the form of high energy phosphate anhydride
bonds, but can also be in the form of NADH or NADPH
• Two main types of energy-producing pathways are substrate-level
phosphorylation (example: glycolysis), and oxidative phosphorylation (example:
respiration)
• Glycolysis is a catabolic pathway found in almost all cells – glucose is converted
into two pyruvates, which are then metabolized into final products that will vary
depending on the organism.
• There is a high diversity of fermentation pathways found in nature.
• These can begin with substrates other than glucose, and each producing
different end products.
• For a few microorganisms, like those in the genus Clostridium, fermentation is
the only energy-producing pathway available.