3.

2 Energy and Enzymes

Energy Classes of Microorganisms
Studies of microbial nutrition and other aspects of microbial physiology enable scientists
to understand the vital chemical processes that occur within every living cell. All organisms
require a source of energy, a source of carbon, and additional nutrients to build necessary cellular
materials. Those materials that organisms are unable to synthesize, but are required for the
building of macromolecules and maintaining life, are termed essential nutrients.
Essential nutrients include essential amino acids and essential fatty acids, and it must be
provided to an organism on a constant manner for it to thrive. The essential nutrients differ from
species to species. Today, there are microbes representing each of the four major nutritional
categories (photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs;
The terms autotroph and heterotroph pertain to what an organism uses as a carbon source.
 Autotrophs use inorganic carbon dioxide (CO2) as their sole source of carbon. They are
also known as primary producers since they can synthesize inorganic carbon dioxide to
create new organic carbon compounds for food such as glucose. Primary producers,
particularly phototrophs, have produced nearly all organic matter on Earth.
Photosynthetic organisms such as plants, algae, and cyanobacteria are well known
examples of autotrophs.

Photosynthetic autotrophs, which make food using the energy in sunlight, include
(a) plants, (b) algae, (c) cyanobacteria
 Heterotrophs rely on more complex organic carbon compounds as a source of nutrition,
which are first provided by autotrophs so they are also known as consumers. Also, they
use organic compounds other than CO2 as their carbon source. Examples of heterotroph
include humans, animals, fungi, and protozoa.
The terms phototroph and chemotroph pertain to what an organism uses as an energy source.
 Phototrophs use light as an energy source. The process by which these organisms
convert light energy into chemical energy is called photosynthesis. Phototrophic
microorganisms have pigments that allow them to transform light energy into chemical
energy, therefore they don't need chemicals as a source of energy like chemotrophs do.
This is a significant metabolic advantage because competition between phototrophs and
chemotrophs for energy sources is not an issue and at least some sunlight is available in
most microbial habitats.

Two major forms of phototrophy are known in prokaryotes:

a) Oxygenic photosynthesis - oxygen is produced. Among microorganisms, oxygenic

photosynthesis is characteristic of cyanobacteria, which are prokaryotes, and algae,
which are eukaryotes.

In addition to the cyanobacteria, there are several other families of photosynthetic

prokaryotes. Each is classified according to the way it reduces CO 2. These bacteria
 cannot use H2O to reduce CO2 and cannot carry on photosynthesis when oxygen is
present (they must have an anaerobic environment). These are:
b) Anoxygenic photosynthesis – does not produce oxygen. Occurs in the purple and
green bacteria and the heliobacteria (all Bacteria).

The green sulfur bacteria, such as Chlorobium, use sulfur (S), sulfur compounds
(such as hydrogen sulfide, H2S), or hydrogen gas (H2) to reduce carbon dioxide and
form organic compounds. Applying the energy from light and the appropriate
enzymes, these bacteria oxidize sulfide (S2-) or sulfur (S) to sulfate (SO 42-) or oxidize
hydrogen gas to water (H2O).

The purple sulfur bacteria, such as Chromatium, also use sulfur, sulfur compounds, or
hydrogen gas to reduce carbon dioxide. They are distinguished from the green
bacteria by their type of chlorophyll, location of stored sulfur, and ribosomal RNA.

However, both oxygenic and anoxygenic phototrophs show great similarities in the
mechanism for ATP synthesis, a result of the fact that oxygenic photosynthesis
evolved from the simpler anoxygenic form some 3 billion years ago.
 Chemotrophs use either inorganic or organic chemicals as an energy source.
Chemotrophs can be subdivided into two categories: chemolithotrophs and
chemoorganotrophs.
 Chemotrophs are organisms that obtain energy by the oxidation of electron donors in
their environments. These molecules can be organic (chemoorganotrophs) or inorganic
(chemolithotrophs).

a) Chemolithotrophs (lithotrophs) are organisms that use the energy available from the
oxidation of inorganic compounds. Their metabolism carries out chemolithotrophic
reactions which is known as chemolithotrophy. Examples include many bacteria and
archaea. Several inorganic molecules, such as H2, H2S (hydrogen sulfide), NH3
(ammonia), and Fe2+ (ferrous iron), can be oxidized. Related groups of
chemolithotrophs typically specialize in the oxidation of a related group of inorganic
compounds, and thus we have the “sulfur” bacteria, the “iron” bacteria, the
“nitrifying” bacteria, and so on. The capacity to conserve energy from the oxidation
of inorganic chemicals is a good metabolic strategy because competition from
chemoorganotrophs is not a concern. Furthermore, many of the inorganic compounds
oxidized by chemolithotrophs, such as H2 and H2S, are actually chemoorganotrophs'
waste products. As a result, many chemolithotrophs have evolved strategies for
exploiting resources that chemoorganotrophs cannot, and it is not uncommon for
species from these two physiological groups to coexist.

b) Chemoorganotrophs (organotrophs) are organisms that use organic chemicals as a

source of energy. Chemoorganotrophs make up the majority of microorganisms that
have been cultured in the lab. Many different organic compounds can be used by one
or another microorganism, and the oxidation of the compound almost always
conserves energy. The conserved energy is trapped in the cell in the form of energy-
rich bonds of the compound adenosine triphosphate (ATP).
 If we combine the term relating to energy and carbon sources, we’ll have the following
energy classifications of microorganisms:
 Photoautotrophs are organisms that use light as an energy source and inorganic carbon
dioxide as a carbon source. The examples include plants, algae, cyanobacteria, and purple
and green sulfur bacteria.

 Photoheterotrophs are organisms that use light as an energy source and organic
compounds other than carbon dioxide as a carbon source, such as purple nonsulfur and
green nonsulfur bacteria.

 Chemoautotrophs are organisms that use chemicals as an energy source and inorganic
CO2 as a carbon source to make their own food, such as nitrifying, hydrogen, iron, and
sulfur bacteria. For chemoautotrophs, the chemicals they used depends on the species.
But no light required.

 Chemoheterotrophs are organisms that get their energy from chemicals and organic
compounds other than carbon dioxide as a carbon source. Chemoheterotrophs include all
mammals, protozoa, fungus, and the majority of bacteria. 
Energetics and energy
Energy is the ability to do work. In microbiology, energy transformations are measured in
kilojoules (kJ), a unit of heat energy. All chemical reactions in a cell are accompanied by
changes in energy, energy being either required for a reaction to occur or released as a reaction
occurs. Energy cannot be seen; it can be identified only by how it affects matter.
Forms of Energy
 Kinetic Energy - is energy associated with motion.
 Potential Energy – is stored energy; energy that is not doing work but has the capacity to
do so.
 Heat (Thermal Energy) – is kinetic energy associated with random movement of atoms or
molecules.
 Chemical Energy – is potential energy available for release in a chemical reaction.
 Energy can be transformed from one state to another.

The Laws of Energy Transformation

 Thermodynamics – is the study of energy transformations.
 An isolated system, such as that approximated by liquid in a thermos, is isolated from its
surroundings.
 In an open system, energy and matter can be transferred between the system and its
surroundings.
 Microorganisms are open systems.

Conversion of one form of energy to another is governed by the two laws of

thermodynamics:

1. According to the first law of thermodynamics,

- the energy of the universe is constant
- the energy cannot be created or destroyed. It can change from one form to
another, but the total amount of energy remains the same. In short, energy is
conserved.
2. According to the second law of thermodynamics
- during every energy transfer or transformation, some energy is unusable and is
often lost as heat
- Every energy transfer or transformation increases the entropy (disorder) of the
universe. This fundamental law states that a closed system moves toward
increasing disorder, or entropy, as energy is dissipated from the system.
Basic Energetics
Although in any chemical reaction some energy is lost as heat, in microbiology we are interested
in free energy (abbreviated G), which is the energy available to do work. The change in free
energy during a reaction is expressed as ∆G0′, where the symbol ∆ is read as “change in.” The
“0” and “prime” superscripts indicate that the free energy value is for standard conditions: pH 7,
25°C, 1 atmosphere of pressure, and all reactants and products at molar concentrations.
Consider the reaction
A+BC+D
If ∆G0′ for this reaction is negative in arithmetic sign, then the reaction will proceed with the
release of free energy, energy that the cell may conserve as ATP. Such energy-yielding reactions
are called exergonic. However, if ∆G0′ is positive, the reaction requires energy in order to
proceed. Such reactions are called endergonic. Thus, exergonic reactions release energy whereas
endergonic reactions require or absorb energy.
Free Energy of Formation and Calculating Free Energy Changes (𝚫G0′)
To calculate the free-energy yield of a reaction, one first needs to know the free energy of its
reactants and products. This is the free energy of formation (Gf0), the energy released or required
during the formation of a given molecule from the elements. Table 3.3 gives a few examples of
Gf0. By convention, the free energy of formation of the elements in their elemental and
electrically neutral form (for instance, C, H2, N2) is zero. However, the free energies of formation
of compounds are not zero. If the formation of a compound from its elements proceeds
exergonically, then the Gf0 of the compound is negative (energy is released). If the reaction is
endergonic, then the Gf0 of the compound is positive (energy is required).
For most compounds Gf0 is negative. This reflects the fact that compounds tend to form
spontaneously (that is, with energy being released) from their elements. However, the positive
Gf0 for nitrous oxide (N2O) (+104.2 kJ/mol, Table 3.3) indicates that this compound does not
form spontaneously. Instead, over time it decomposes spontaneously to yield N2 and O2.

Using free energies of formation, it is possible to calculate ∆G0′ of a given reaction. For the
reaction A + B  C + D, ∆G0′ is calculated by subtracting the sum of the free energies of
formation of the reactants (A + B) from that of the products (C + D).
Thus

The value obtained for ∆G0′ tells us whether the reaction is exergonic or endergonic. The phrase
“products minus reactants” is a simple way to recall how to calculate changes in free energy
during chemical reactions. However, before free-energy calculations can be made, it is first
necessary to balance the reaction.
𝚫G0′ versus 𝚫G
Although calculations of ∆G0′ are reasonable estimates of actual free-energy changes, in some
cases they are not. We will see later in this book that the actual concentrations of products and
reactants in nature, which are rarely at the molar levels used in calculations of ∆G0′, can change
the results of bioenergetic calculations, sometimes in significant ways. What is most relevant to a
bioenergetic calculation is not ∆G0′, but ∆G, the free-energy change that occurs under the actual
conditions in which the organism is growing. The equation for ∆G takes into account the actual
concentrations of reactants and products in the organism’s habitat and is
∆G = ∆G0′ ′ + RT ln K
where R and T are physical constants and K is the equilibrium constant for the reaction
(Appendix 1). We distinguish between ∆G0′ and ∆G in important ways in Chapter 13 where we
consider catabolic diversity in more detail. But for our purposes here, the expression ∆G0′ will
tell us whether a given reaction yields energy or requires energy, and knowing this is sufficient
for a basic understanding of energy flow in microbial systems. Only reactions that are exergonic
yield energy that can be conserved by the cell, and this will be our focus in the next few sections

- Jao -Energetics of Chemolithotrophy – Jao

Notes:
Chemoautotrophs: example is Epsilonproteobacteria that are found in deep sea hydrothermal
vents. Deep sea vents are commonly composed of the chemical hydrogen sulfide that are used by
the epsilonproteobacteria to oxidize inorganic carbon dioxide and produce their own food.
Epsilonproteobacteria, demonstrated that the majority were versatile chemoautotrophs capable of
oxidation of H2 and sulfur compounds coupled with the reduction of oxygen, nitrate and sulfur
compounds
These organisms will do some form of cellular respiration to further breakdown their food to
generate ATP, whether the food is consumed (heterotrophs) or produced (autotrophs). However,
cellular respiration processes can vary. The process may involve oxygen or without oxygen,
different electron acceptors.
In a redox reaction, one of the reacting molecules loses electrons and is said to be oxidized,
while another reacting molecule gains electrons (the ones lost by the first molecule) and is said to
be reduced. Reduction means the addition of hydrogen to a molecule or the removal of oxygen
from a molecule.
Plant-like protists are called algae.

The PSB is a phototrophic bacterium that converts sulfides (including hydrogen sulfide) to sulfur
using sunlight. Carbon dioxide is usually the carbon source for their growth, but they can also
absorb carbon from organic acids or alcohols. Because they are obligatory phototrophs, they are
more prevalent in the summer. PSBs can help with odor problems in lagoons because they
eliminate H2S and several volatile organic acids.