Bioenergetics
Different microbes have different metabolic capacities, and therefor their
nutrient requirements also differ. However, all microbes require a core set
of nutrients. Nutrients that are required in large amounts are called
macronutrients; nutrients required in minute amounts are called
micronutrients.
Essential elements include: Carbon (C), Nitrogen (N), Oxygen (O),
Hydrogen (H), Phosphorus (P), Sulfur (S) and Selenium (Se). Trace metals,
which are necessary in lesser quantities, are Iron (Fe) Copper (Co),
Manganese (Mn), Nikkel (Ni), Zink (Zn),
Molybdenum (Mo), Vanadium (V) and Tungsten
(W).
These trace metals are especially important in
microbial metabolism, as they help enzymes to
function.
Over half of a cell’s dry weight is made up of
proteins. These proteins have many important
functions, for example as enzymes in metabolism.
Metabolism is the sum of all chemical
reactions in the cell, and can be divided
into:
o Catabolism: This is the
transformation of molecules to
produce energy and building
blocks. It is the ATP production.
Catabolic reactions are thus
energy-releasing metabolic
reactions. It is also referred to
as Energy metabolism.
o Anabolism: This is the synthesizing of macromolecules; the
energy gets used to produce biomass. It can also be referred to
as Biosynthesis.
While both are really important for cells, the anabolism side is very
uniform across the prokaryotic kingdom; the way an amino acid is
synthesized is very similar in all of the Bacterial and
Archaeal kingdoms.
Catabolism however, wildly varies between
microorganisms, because microbes can use different
types of energy sources. They can use either chemicals
(chemotrophy) or light (phototrophy).
Chemotrophs can be further subdivided: If an organism
uses the oxidation of organic compounds as an energy
source, they are called chemoorganotrophs. If they
,use the oxidation of inorganic compounds, they are called
chemolithotrophs.
The eventual goal of all energy metabolism is to convert this energy
source to ATP.
The first law of thermodynamics states that energy can be transformed
from one form to another, but can not be generated or destroyed. This is
why we say the energy is converted, not made. The energy required for
making ATP comes from chemical reactions.
Energy is measured in units of kilojoules (kJ).
One of the chemical reactions that happens in
microorganisms is the burning of sugars to CO2.
C6H12 + 6O2 ↔ CO2 + 6H2O.
This is part of a normal aerobic metabolism.
When sugar and oxygen is taken and burnt to carbon dioxide and water,
energy is released; it is an exergonic reaction. The amount of energy
released can be measured as ΔG, or prime value. An exergonic reaction
has a negative value. In the case of burning sugar, ΔG = ─2863 kJ/mol.
This reaction can also be reversed; if sugar (and O2) is made from CO2 and
H2O, this uses up energy and is called an endergonic reaction. This ΔG is
positive: 2863 kJ/mol.
In any chemical reaction, energy is either required or released.
Free energy, G, is the energy released that is available to do work. The
change in free energy during a reaction is referred to as ΔG⁰’ (standard
conditions).
Exergonic reactions are reactions with ─ ΔG⁰’; they release free
energy and can eventually be used to make ATP.
Endergonic reactions are reactions with + ΔG⁰’; they require
energy, so ATP would be required to make them work.
In metabolism, endergonic and exergonic reactions are often coupled. For
example, the burning of sugar and the synthesis of
ATP. The energy released from the exergonic
reaction – the burning of sugar – is used to drive
the endergonic reaction – the ATP synthesis.
As the exergonic reaction released -2863 kJ/mol, and the endergonic
reaction uses up 32 kJ/mol, up to 2863/32 = 89 mol of ATP can be
generated from 1 mol of glucose. This is a theoretical maximum; in reality
it’s going to be less than 89, as some energy is lost as heat to drive the
reaction forward.
If an endergonic and exergonic reaction are completely coupled, the ΔG⁰’
of the overall reaction will be 0. If ΔG⁰’ = 0, the reaction is in equilibrium.
Thermodynamics; electron donors and acceptors
,In catabolism, there is a lot of electron transport. The reaction between
electron donors and electron acceptors (redox reactions) are the chemical
reactions that drive energy metabolism of cells.
In the example of H2 + ½O2 H2O, hydrogen is
the electron donor, and gets oxidized. Oxygen is
the electron acceptor and gets reduced.
Oxidation is thus the loss of electrons and
reduction is the gain of electrons. Oxidation and reduction always happen
together; if one molecule is oxidized, the other must be reduced.
Calculating free energy
ΔG⁰’ can be calculated in these reactions. To do this, the
E⁰’ is needed. E⁰’ is the redox potential, and says
something about the tendency to donate or accept
electrons. These values can be looked up in the redox
tower.
E⁰’ is in standard biological conditions; 1 mol/L
substrate and product, (1 atm in case of gasses),
biological conditions with pH 7.0 and 25 degrees
Celsius.
These are different from chemical conditions, which is at pH 0 and
temperature 0.
The formula to then calculate ΔG⁰’ is as follows:
Δ G0 ’=−n ∙ F ∙ ΔE ⁰ ’
Herein is:
ΔG = The free energy released; ΔG < 0 is exergonic, and ΔG > 0 is
endergonic.
n = number of transferred electrons,
F = Faraday’s constant; 96.5 kJ/mol-1 V-1
ΔE⁰’ = Difference in redox potential; this is calculated by the E of the
acceptor (highest) – donor (lowest). (make sure to put this in V, rather
than mV),
In the example of H2 + ½O2 H2O, the E⁰’ of 2H+/H2 = -414 mV, and the
E⁰’ of ½O2/H2O = +820 mV. The ΔE⁰’ is then 414 mV + 820 mV = 1.234 V.
0 −1
Δ G ’=−2 ∙ 96.5∙ 1.234=−238 kJ /mol
Catalysis and enzymes
Free energy does not provide any information on reaction
rates. This is because the reaction rate is a combination of
thermodynamics (ΔG⁰’) and kinetics (velocity of catalysis).
, Enzymes catalyze biochemical reactions with a negative ΔG⁰’ – they only
catalyze exergonic reactions.
We’ve shown that burning sugar to CO2 is an extremely exergonic
reaction, but stored sugar doesn’t spontaneously turn into CO2. This is
because of the activation energy barrier; this barrier means some energy
needs to be invested before energy can be released. Enzymes decrease
the amount of activation energy required. Enzymes are catalysts.
Catalysts are substances that:
Are not consumed in the reaction,
Lower the activation energy of the reaction,
Increase reaction rate,
Do not affect energetics or equilibrium of the reaction.
Many biochemical reactions would not happen without enzymes, because
the energy barrier is too high.
Enzymes are biological catalysts. They’re typically proteins, although
some RNAs exist. Enzymes are highly specific and generally larger than
the substrate. They also typically rely on weak bonds (e.g. hydrogen
bonds or Vanderwaals forces). The active site is the region of the enzyme
that binds the substrate.
Enzymes are classified in EC-classes. There are 6 of these classes, which
categorize very different enzymes. An EC-number typically consists of 4
different digits. The first of which denotes the class; EC-1, for example, are
oxidoreductases. The next digit
gives another defining trait; EC
1.6 indicates oxidoreductases
that act on NADH or NADPH.
Each digit defines the enzyme
further. (Our trained hydra likes
its light tunnel).
Different microbes have different metabolic capacities, and therefor their
nutrient requirements also differ. However, all microbes require a core set
of nutrients. Nutrients that are required in large amounts are called
macronutrients; nutrients required in minute amounts are called
micronutrients.
Essential elements include: Carbon (C), Nitrogen (N), Oxygen (O),
Hydrogen (H), Phosphorus (P), Sulfur (S) and Selenium (Se). Trace metals,
which are necessary in lesser quantities, are Iron (Fe) Copper (Co),
Manganese (Mn), Nikkel (Ni), Zink (Zn),
Molybdenum (Mo), Vanadium (V) and Tungsten
(W).
These trace metals are especially important in
microbial metabolism, as they help enzymes to
function.
Over half of a cell’s dry weight is made up of
proteins. These proteins have many important
functions, for example as enzymes in metabolism.
Metabolism is the sum of all chemical
reactions in the cell, and can be divided
into:
o Catabolism: This is the
transformation of molecules to
produce energy and building
blocks. It is the ATP production.
Catabolic reactions are thus
energy-releasing metabolic
reactions. It is also referred to
as Energy metabolism.
o Anabolism: This is the synthesizing of macromolecules; the
energy gets used to produce biomass. It can also be referred to
as Biosynthesis.
While both are really important for cells, the anabolism side is very
uniform across the prokaryotic kingdom; the way an amino acid is
synthesized is very similar in all of the Bacterial and
Archaeal kingdoms.
Catabolism however, wildly varies between
microorganisms, because microbes can use different
types of energy sources. They can use either chemicals
(chemotrophy) or light (phototrophy).
Chemotrophs can be further subdivided: If an organism
uses the oxidation of organic compounds as an energy
source, they are called chemoorganotrophs. If they
,use the oxidation of inorganic compounds, they are called
chemolithotrophs.
The eventual goal of all energy metabolism is to convert this energy
source to ATP.
The first law of thermodynamics states that energy can be transformed
from one form to another, but can not be generated or destroyed. This is
why we say the energy is converted, not made. The energy required for
making ATP comes from chemical reactions.
Energy is measured in units of kilojoules (kJ).
One of the chemical reactions that happens in
microorganisms is the burning of sugars to CO2.
C6H12 + 6O2 ↔ CO2 + 6H2O.
This is part of a normal aerobic metabolism.
When sugar and oxygen is taken and burnt to carbon dioxide and water,
energy is released; it is an exergonic reaction. The amount of energy
released can be measured as ΔG, or prime value. An exergonic reaction
has a negative value. In the case of burning sugar, ΔG = ─2863 kJ/mol.
This reaction can also be reversed; if sugar (and O2) is made from CO2 and
H2O, this uses up energy and is called an endergonic reaction. This ΔG is
positive: 2863 kJ/mol.
In any chemical reaction, energy is either required or released.
Free energy, G, is the energy released that is available to do work. The
change in free energy during a reaction is referred to as ΔG⁰’ (standard
conditions).
Exergonic reactions are reactions with ─ ΔG⁰’; they release free
energy and can eventually be used to make ATP.
Endergonic reactions are reactions with + ΔG⁰’; they require
energy, so ATP would be required to make them work.
In metabolism, endergonic and exergonic reactions are often coupled. For
example, the burning of sugar and the synthesis of
ATP. The energy released from the exergonic
reaction – the burning of sugar – is used to drive
the endergonic reaction – the ATP synthesis.
As the exergonic reaction released -2863 kJ/mol, and the endergonic
reaction uses up 32 kJ/mol, up to 2863/32 = 89 mol of ATP can be
generated from 1 mol of glucose. This is a theoretical maximum; in reality
it’s going to be less than 89, as some energy is lost as heat to drive the
reaction forward.
If an endergonic and exergonic reaction are completely coupled, the ΔG⁰’
of the overall reaction will be 0. If ΔG⁰’ = 0, the reaction is in equilibrium.
Thermodynamics; electron donors and acceptors
,In catabolism, there is a lot of electron transport. The reaction between
electron donors and electron acceptors (redox reactions) are the chemical
reactions that drive energy metabolism of cells.
In the example of H2 + ½O2 H2O, hydrogen is
the electron donor, and gets oxidized. Oxygen is
the electron acceptor and gets reduced.
Oxidation is thus the loss of electrons and
reduction is the gain of electrons. Oxidation and reduction always happen
together; if one molecule is oxidized, the other must be reduced.
Calculating free energy
ΔG⁰’ can be calculated in these reactions. To do this, the
E⁰’ is needed. E⁰’ is the redox potential, and says
something about the tendency to donate or accept
electrons. These values can be looked up in the redox
tower.
E⁰’ is in standard biological conditions; 1 mol/L
substrate and product, (1 atm in case of gasses),
biological conditions with pH 7.0 and 25 degrees
Celsius.
These are different from chemical conditions, which is at pH 0 and
temperature 0.
The formula to then calculate ΔG⁰’ is as follows:
Δ G0 ’=−n ∙ F ∙ ΔE ⁰ ’
Herein is:
ΔG = The free energy released; ΔG < 0 is exergonic, and ΔG > 0 is
endergonic.
n = number of transferred electrons,
F = Faraday’s constant; 96.5 kJ/mol-1 V-1
ΔE⁰’ = Difference in redox potential; this is calculated by the E of the
acceptor (highest) – donor (lowest). (make sure to put this in V, rather
than mV),
In the example of H2 + ½O2 H2O, the E⁰’ of 2H+/H2 = -414 mV, and the
E⁰’ of ½O2/H2O = +820 mV. The ΔE⁰’ is then 414 mV + 820 mV = 1.234 V.
0 −1
Δ G ’=−2 ∙ 96.5∙ 1.234=−238 kJ /mol
Catalysis and enzymes
Free energy does not provide any information on reaction
rates. This is because the reaction rate is a combination of
thermodynamics (ΔG⁰’) and kinetics (velocity of catalysis).
, Enzymes catalyze biochemical reactions with a negative ΔG⁰’ – they only
catalyze exergonic reactions.
We’ve shown that burning sugar to CO2 is an extremely exergonic
reaction, but stored sugar doesn’t spontaneously turn into CO2. This is
because of the activation energy barrier; this barrier means some energy
needs to be invested before energy can be released. Enzymes decrease
the amount of activation energy required. Enzymes are catalysts.
Catalysts are substances that:
Are not consumed in the reaction,
Lower the activation energy of the reaction,
Increase reaction rate,
Do not affect energetics or equilibrium of the reaction.
Many biochemical reactions would not happen without enzymes, because
the energy barrier is too high.
Enzymes are biological catalysts. They’re typically proteins, although
some RNAs exist. Enzymes are highly specific and generally larger than
the substrate. They also typically rely on weak bonds (e.g. hydrogen
bonds or Vanderwaals forces). The active site is the region of the enzyme
that binds the substrate.
Enzymes are classified in EC-classes. There are 6 of these classes, which
categorize very different enzymes. An EC-number typically consists of 4
different digits. The first of which denotes the class; EC-1, for example, are
oxidoreductases. The next digit
gives another defining trait; EC
1.6 indicates oxidoreductases
that act on NADH or NADPH.
Each digit defines the enzyme
further. (Our trained hydra likes
its light tunnel).
