Microbiology
Lecture 1, introduction to microbiology:
All organisms can be classified in eukaryotes, which are multicellular organisms, and prokaryotes,
which are single cellular organisms. The prokaryotes can then also be divided into the bacteria and
the archea. For a long time we thought of these are the same, but now we know better.
All microorganisms need energy, for which there are three classes;
Metabolism, which is the sum of all chemical reactions in the cell.
Catabolism, which is all the reactions that release energy.
Anabolism, which is all the reactions that require energy.
Free energy is all the energy that is released and available to do work, is also expressed using G.
The change in free energy after a reaction is ∆G0’, but only under standard conditions. These
standard conditions are; 25 degrees Celsius, 1M of reactants, pH of 7.
Reactions with a -∆G0’, release free energy and are exergonic. Reactions with a +∆G0’, require
energy and are endergonic.
To calculate the ∆G0’ of a reaction, you need the free energy of formation for each molecule.
And add them.
The ∆G0’ only works under standard circumstances, but they are very rare and don’t usually
happen. So, the ∆G0’ is not a good estimate of the actual free energy changes. ∆G is better, this is
the free energy that occurs under normal
conditions. This free energy can only come
from exergonic reactions in a cell.
This ∆G can be calculated with;
For the reaction; A + nB = C + mD
R= gas constant
T= absolute temperature in Kelvin
Every reaction has an activation energy that needs to be reached before the reaction can take
place. Its the minimum energy required for molecules to become reactive.
Enzymes:
A catalyst lowers the activation energy. Enzymes are the catalysts of the cell, they accelerate
reactions. Enzymes are highly specific to one reaction.
A substate can bind to the active site of the enzyme, when this happens an enzyme-substrate
complex forms. After the substrate is released, the enzymes is reusable.
Many enzymes need a cofactor to function. These cofactors can be prosthetic groups, they bound
tightly and permanently, or coenzymes, the bind loosely and are probably a derivate of vitamins.
The most common coenzymes are NAD+, FAD+ and ATP.
NAD+ is used for catabolism.
NADP+ is used for anabolism.
There are different classes of metabolism in microorganisms;
Chemotrophs: the obtain energy from chemical reactions. This can be aerobic (with O2) or
anaerobic (without O2). And the energy source can either be organic (chemoorganotrophs) or
inorganic (chemolithotrophs).
Phototrophs: they obtain energy from photons. They don’t need any chemicals to obtain energy.
They can be oxygenic and anoxygenic.
Heterotrophs: they obtain carbon from organics.
Autotrophs: they obtain carbon from CO2.
Page 1
,Humans are chemoheterotrophs.
Redox reactions:
Redox relations conclude two half reactions, one is the electron donor (reduced), the other is the
electron acceptor (oxydedized). The reduction potential (E0’) is the tendency of substances to
donate electrons. When this is negative, the substance is oxidized, and when it is positive the
substance is reduced. The oxidized and reduced together form a redox couple.
To create the highest amount of redox potential, you want to have a the highest possible electron
donor, and the lowest electron acceptor so that the difference is
as big as possible.
ATP:
ATP stands for adenosine-triphosphate. It is the universal energy
compound. It consists of two anhydride bonds, and one ester
bond. The anhydrite bond brings the most energy when broken.
You should learn to draw ATP,
future me. Good luck!
Breaking bonds all deliver different amounts of energy. Most cells
use the first two.
Page 2
,Lecture 2, microbial metabolism:
Energy conservation in chemoorganotrophs can happen through two processes, fermentation and
respiration.
Fermentation: is always anaerobic catabolism in which organic compounds donate and accept
electrons.
Respiration: can be either aerobic or anaerobic catabolism. If it is aerobic, the donor is oxidized
with O2. If it is anaerobic, another compound is used as an electron acceptor.
Glycolysis:
It is the process of glucose into energy. It is used in both, fermentation and respiration. It is the first
step into the energy cycle. It takes place in the cytoplasm of the cell
Glucose (6C’s) + 2 ADP => 2 pyruvate (3C’s) + 2 NADH + 2 ATP
The in-between steps, you see here.
Every interaction that uses ATP is a kinase reaction because it either adds a phosphate group to
the end product, or to ATP.
Every isomerase reaction is a conversion from one isomer to another, to the composition of the
molecule does not change, but the way they are arranged does.
The dehydrogenase is a redox reaction. So electrons are being exchanged.
The dehydratase is a reaction that removes a -OH.
Citric acid cycle:
The pyruvate that is created at the end of glycolysis, continues down the path of energy
production. The next step is the citric acid cycle. It takes place in the mitochondria of the cell, and
in prokaryotes (who don’t have organelles) in the cytoplasm.
Because citric acid cycle is so big, I will break it down for you future me.
Step 1 (pyruvate dehydrogenase): pyruvate + NAD+ + CoA => acetyl-CoA + NADH + CO2
the pyruvate (3C’s) from the glycolysis is turned into acetyl-CoA (2C’s).
Step 2: acetyl-CoA (2C’s) + oxaloacetate (4C’s) => citrate (6C’s) + CoA
this is how citric acid cycle got its name, because of citrate.
Step 3: citrate + 3 NAD+ + FAD + ADP => oxaloacetate + 3 NADH + FADH2 + ATP
the citrate gets broken down from 6C’s to 4C’s, so the cycle can continue.
The ATP is created somewhere in step 3. When succinyl-CoA (4C’s) reacts with ADP, to make
ATP, succinate and CoA. This is done by the enzyme succ-CoA synthetase.
Page 3
, During the citric acid cycle, a lot of CO2 come free.
Summary of the citric acid cycle:
Oxidative phosphorylation:
The last step in the energy production. This is when NADH gets turned into ATP. It takes place in
on the membrane between the intermembrane space and the matrix.
It consists of 4 complexes, complex I, III, IV pump H+ inside the matrix. This costs NADH, and
gives NAD+ but also electrons. These electrons moves along the membrane to help other H+
move through, because an H+ and e- make H. The H need to be without charge if it wants to move
through the membrane. The electron end up in complex IV, where it binds with 2H+ and 1/2 O2 to
form H2O (so 2H+ + 1/2 O2 + 2e- => H2O. The O2 is the electron acceptor.
This overflow of H+ inside the matrix causes an electrochemical gradient and an acidic
environment. This flood of H+ kind of works like a water wheel. The energy this gives, is stored in
ATP. Every 3-5 H+ can make 1 ATP. And every 2e- can make 3 ATP.
Page 4
Lecture 1, introduction to microbiology:
All organisms can be classified in eukaryotes, which are multicellular organisms, and prokaryotes,
which are single cellular organisms. The prokaryotes can then also be divided into the bacteria and
the archea. For a long time we thought of these are the same, but now we know better.
All microorganisms need energy, for which there are three classes;
Metabolism, which is the sum of all chemical reactions in the cell.
Catabolism, which is all the reactions that release energy.
Anabolism, which is all the reactions that require energy.
Free energy is all the energy that is released and available to do work, is also expressed using G.
The change in free energy after a reaction is ∆G0’, but only under standard conditions. These
standard conditions are; 25 degrees Celsius, 1M of reactants, pH of 7.
Reactions with a -∆G0’, release free energy and are exergonic. Reactions with a +∆G0’, require
energy and are endergonic.
To calculate the ∆G0’ of a reaction, you need the free energy of formation for each molecule.
And add them.
The ∆G0’ only works under standard circumstances, but they are very rare and don’t usually
happen. So, the ∆G0’ is not a good estimate of the actual free energy changes. ∆G is better, this is
the free energy that occurs under normal
conditions. This free energy can only come
from exergonic reactions in a cell.
This ∆G can be calculated with;
For the reaction; A + nB = C + mD
R= gas constant
T= absolute temperature in Kelvin
Every reaction has an activation energy that needs to be reached before the reaction can take
place. Its the minimum energy required for molecules to become reactive.
Enzymes:
A catalyst lowers the activation energy. Enzymes are the catalysts of the cell, they accelerate
reactions. Enzymes are highly specific to one reaction.
A substate can bind to the active site of the enzyme, when this happens an enzyme-substrate
complex forms. After the substrate is released, the enzymes is reusable.
Many enzymes need a cofactor to function. These cofactors can be prosthetic groups, they bound
tightly and permanently, or coenzymes, the bind loosely and are probably a derivate of vitamins.
The most common coenzymes are NAD+, FAD+ and ATP.
NAD+ is used for catabolism.
NADP+ is used for anabolism.
There are different classes of metabolism in microorganisms;
Chemotrophs: the obtain energy from chemical reactions. This can be aerobic (with O2) or
anaerobic (without O2). And the energy source can either be organic (chemoorganotrophs) or
inorganic (chemolithotrophs).
Phototrophs: they obtain energy from photons. They don’t need any chemicals to obtain energy.
They can be oxygenic and anoxygenic.
Heterotrophs: they obtain carbon from organics.
Autotrophs: they obtain carbon from CO2.
Page 1
,Humans are chemoheterotrophs.
Redox reactions:
Redox relations conclude two half reactions, one is the electron donor (reduced), the other is the
electron acceptor (oxydedized). The reduction potential (E0’) is the tendency of substances to
donate electrons. When this is negative, the substance is oxidized, and when it is positive the
substance is reduced. The oxidized and reduced together form a redox couple.
To create the highest amount of redox potential, you want to have a the highest possible electron
donor, and the lowest electron acceptor so that the difference is
as big as possible.
ATP:
ATP stands for adenosine-triphosphate. It is the universal energy
compound. It consists of two anhydride bonds, and one ester
bond. The anhydrite bond brings the most energy when broken.
You should learn to draw ATP,
future me. Good luck!
Breaking bonds all deliver different amounts of energy. Most cells
use the first two.
Page 2
,Lecture 2, microbial metabolism:
Energy conservation in chemoorganotrophs can happen through two processes, fermentation and
respiration.
Fermentation: is always anaerobic catabolism in which organic compounds donate and accept
electrons.
Respiration: can be either aerobic or anaerobic catabolism. If it is aerobic, the donor is oxidized
with O2. If it is anaerobic, another compound is used as an electron acceptor.
Glycolysis:
It is the process of glucose into energy. It is used in both, fermentation and respiration. It is the first
step into the energy cycle. It takes place in the cytoplasm of the cell
Glucose (6C’s) + 2 ADP => 2 pyruvate (3C’s) + 2 NADH + 2 ATP
The in-between steps, you see here.
Every interaction that uses ATP is a kinase reaction because it either adds a phosphate group to
the end product, or to ATP.
Every isomerase reaction is a conversion from one isomer to another, to the composition of the
molecule does not change, but the way they are arranged does.
The dehydrogenase is a redox reaction. So electrons are being exchanged.
The dehydratase is a reaction that removes a -OH.
Citric acid cycle:
The pyruvate that is created at the end of glycolysis, continues down the path of energy
production. The next step is the citric acid cycle. It takes place in the mitochondria of the cell, and
in prokaryotes (who don’t have organelles) in the cytoplasm.
Because citric acid cycle is so big, I will break it down for you future me.
Step 1 (pyruvate dehydrogenase): pyruvate + NAD+ + CoA => acetyl-CoA + NADH + CO2
the pyruvate (3C’s) from the glycolysis is turned into acetyl-CoA (2C’s).
Step 2: acetyl-CoA (2C’s) + oxaloacetate (4C’s) => citrate (6C’s) + CoA
this is how citric acid cycle got its name, because of citrate.
Step 3: citrate + 3 NAD+ + FAD + ADP => oxaloacetate + 3 NADH + FADH2 + ATP
the citrate gets broken down from 6C’s to 4C’s, so the cycle can continue.
The ATP is created somewhere in step 3. When succinyl-CoA (4C’s) reacts with ADP, to make
ATP, succinate and CoA. This is done by the enzyme succ-CoA synthetase.
Page 3
, During the citric acid cycle, a lot of CO2 come free.
Summary of the citric acid cycle:
Oxidative phosphorylation:
The last step in the energy production. This is when NADH gets turned into ATP. It takes place in
on the membrane between the intermembrane space and the matrix.
It consists of 4 complexes, complex I, III, IV pump H+ inside the matrix. This costs NADH, and
gives NAD+ but also electrons. These electrons moves along the membrane to help other H+
move through, because an H+ and e- make H. The H need to be without charge if it wants to move
through the membrane. The electron end up in complex IV, where it binds with 2H+ and 1/2 O2 to
form H2O (so 2H+ + 1/2 O2 + 2e- => H2O. The O2 is the electron acceptor.
This overflow of H+ inside the matrix causes an electrochemical gradient and an acidic
environment. This flood of H+ kind of works like a water wheel. The energy this gives, is stored in
ATP. Every 3-5 H+ can make 1 ATP. And every 2e- can make 3 ATP.
Page 4
