Microbes and infection
Epidemic: A sudden increase in cases of a disease within a specific region or popula-
tion. Example: A seasonal flu outbreak in a country.
Pandemic: An epidemic that spreads across multiple countries or continents, affect-
ing a large portion of the global population. Example: COVID-19 or the 1918 influenza
pandemic.
Bacterial infections are occurring more frequently, because people get older and thus
have a weaker immune system, but also because of the rise in obesity.
History:
There are a few important names in the microbial world you should know. They are
scientist who have made revolutionary discoveries;
- Van leeuwenhoek (1632-1723); made the first ever microscope
- Jenner (1749-1823); discovered the first ever vaccine for small pox, based on his
observation that exposure to cowpox protected people against the more dangerous
smallpox.
- Pasteur (1822-1895); discovered a vaccine against rabies.
- Koch (1843-1910); discovered specific causative agents for tuberculosis and
cholera. He used these discoveries to establish that specific germs cause a specific
disease. He also came up with Koch’s postulates.
- Fleming (1881-1955); discovered penicillin.
- Marshal and Warren (2005); discovered the helicobacter pylori as the cause of
stomach ulcers.
Prokaryotes and eukaryotes:
As you well know, all organisms can be split up in 3 categories; prokaryotes,
eukaryotes and archaea. For now, we will ignore archaea and focus on the differences
between the prokaryotes and eukaryotes.
Prokaryotes; Eukaryotes;
Example Bacteria, like E. Coli Animals, plants and fungi
DNA orginaza- No nucleus, but circular chromo- Yes nucleus, with linear chromo-
tion somes in a nucleoid region. somes
Membrane- No Yes
bound or-
ganelles
Cell division Asexual reproduction Asexual or sexual reproduction
Energy produc- No mitochondria Mitochondria
tion
Organelles No ER, no Golgi Yes ER, yes Golgi
Page 1
,Gram-positive and gram-negative:
Among the bacteria, there is a difference between gram-positive and gram-negative
bacteria. This based on the cell wall of the bacteria.
Gram-positive; they have a thick layer of peptidoglycan covering the cytoplasmic
membrane.
Gram negative; they are a bit more complex. They have a thin peptidoglycan layer
and an outer membrane. The space between the cytoplasmic membrane and the
outer membrane is called the periplasmic space, which contains lipoproteins. On top of
the outermembrane, they have lipopolysaccharides (LPS), which is an important PAMP.
Peptidoglycan:
Peptidoglycan is a structural component for the cell wall that is made up out of 2 types
of sugars; NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid). These sugars
form long chains, and these chains are being held together by peptide crosslinks on
the NAMs.
Peptidoglycan is synthesized in a complex process, but I have simplified it in a few
steps below;
1. NAM and NAG are linked to UDP (uridine diphosphate), forming UDP-NAM and UDP-
NAG.
2. Then a pentapeptide is added to the UDP-NAM by Mur enzymes.
3. The UDP-NAM-pentapeptide is then linked to bactoprenol, which is a carrier that
will guide it through the membrane.
4. While still in the cytoplasm the UDP-NAG will donate NAG, forming NAM-NAG
disaccharide unit.
5. Now bactoprenol will flip the complex from the cytoplasm into the periplasmic
space.
Page 2
,6. Transpeptidases (PBP) will create the peptide bonds
between the pentapeptide chains on the NAM.
Penicillin irreversibly binds to PBPs, preventing them from
forming cross-links between peptidoglycan chains. This weak-
ens the bacterial cell wall, leading to osmotic lysis and cell
death.
Bacterial cell division:
As said before, bacteria reproduce asexually through binary
fission. I will explain this in a few steps;
1. The bacterial chromosome is copied.
2. The 2 copies move to opposite sides of the cell and the cell
elongates.
3. FtsZ protein will assemble at the center and form a Z-ring
4. The Z-ring will contract and form a septum between the 2
daughter cells.
Incomplete cleavage of the septum can cause bacteria to remain
linked and form a chain structure (streptococcus) or a cluster structure
(staphylcoccus).
Sporulation:
This is a process in which a gram-positive bacteria release genetic material in a time
of stress, in order to survive. They will release an endospore, which is highly resistant
and can survive in extreme conditions. They can remain like this for centuries!
This is done in a couple of steps;
1. The bacterial chromosome is copied.
2. The cell membrane will fold inwards to create a small forespore which contains a
copy of the DNA.
3. The mother cell membrane will wrap around the forespore, engulfing it like a
bubble. This results in a double membrane around the forespore.
4. A thick layer of peptidoglycan will form in-between the 2 membranes, called the
cortex.
5. The cortex dehydrates the endospore and proteins will coat the membrane. This
will make the spore heat, chemical and enzyme resistant.
6. The spore become metabolically inactive.
7. It will accumulate dipicolinic acid (DPA) and calcium ions, which will help stabilize
the DNA.
8. The mother cell disintegrates, which releases the spore in the wild.
Germination is the reverse reaction. When conditions improve (e.g., availability of
nutrients, moisture, and warmth), the spore absorbs water, activates enzymes, and re-
sumes metabolism, returning to its vegetative state.
Bacterial metabolism:
Anabolism; requires energy to build cellular components
Catabolism; releases energy
Glycolysis; glucose → pyruvate + 2 ATP + 2 NADH.
This can be a fast energy source when oxygen is limited.
- With O2; The pyruvate can be used in the TCA cycle by converting it into acetyl-CoA,
which will be turned into NADH and FADH. This can then be used in the electron
Page 3
, transport chain* to produce large amounts of ATP, this requires the oxygen.
- Without O2; The pyruvate can also be used in fermentation without oxygen. This
leads to less ATP and acid products.
* since bacteria don’t have a mitochondria, the electron transport chain will be carried
out in the cell membrane. Protons will be pumped from the cytoplasm into the
periplasm.
Evolution in bacteria:
Bacteria can evolve really fast. This is due to their short life, E.coli can divide every 20
minutes. also due to horizontal gene transfer. This is the movement of genetic
material between bacteria. Because bacteria can share genes, they can become
resistant against antibiotic very quickly.
There are 3 types;
- Transformation; a bacteria takes up free DNA from its environment, from a dead
cell for example.
- Transduction; a bacteriophage* accidentally picks up bacterial DNA and then
injects it into another bacterium.
- Conjugation; a donor bacteria directly injects its genetic material into another
bacterium via a sex pills. The transferred DNA is usually in plasmid form. Note; the
bacteria have to touch for this one.
* a bacteriophage is a virus that specifically targets bacteria.
Page 4
Epidemic: A sudden increase in cases of a disease within a specific region or popula-
tion. Example: A seasonal flu outbreak in a country.
Pandemic: An epidemic that spreads across multiple countries or continents, affect-
ing a large portion of the global population. Example: COVID-19 or the 1918 influenza
pandemic.
Bacterial infections are occurring more frequently, because people get older and thus
have a weaker immune system, but also because of the rise in obesity.
History:
There are a few important names in the microbial world you should know. They are
scientist who have made revolutionary discoveries;
- Van leeuwenhoek (1632-1723); made the first ever microscope
- Jenner (1749-1823); discovered the first ever vaccine for small pox, based on his
observation that exposure to cowpox protected people against the more dangerous
smallpox.
- Pasteur (1822-1895); discovered a vaccine against rabies.
- Koch (1843-1910); discovered specific causative agents for tuberculosis and
cholera. He used these discoveries to establish that specific germs cause a specific
disease. He also came up with Koch’s postulates.
- Fleming (1881-1955); discovered penicillin.
- Marshal and Warren (2005); discovered the helicobacter pylori as the cause of
stomach ulcers.
Prokaryotes and eukaryotes:
As you well know, all organisms can be split up in 3 categories; prokaryotes,
eukaryotes and archaea. For now, we will ignore archaea and focus on the differences
between the prokaryotes and eukaryotes.
Prokaryotes; Eukaryotes;
Example Bacteria, like E. Coli Animals, plants and fungi
DNA orginaza- No nucleus, but circular chromo- Yes nucleus, with linear chromo-
tion somes in a nucleoid region. somes
Membrane- No Yes
bound or-
ganelles
Cell division Asexual reproduction Asexual or sexual reproduction
Energy produc- No mitochondria Mitochondria
tion
Organelles No ER, no Golgi Yes ER, yes Golgi
Page 1
,Gram-positive and gram-negative:
Among the bacteria, there is a difference between gram-positive and gram-negative
bacteria. This based on the cell wall of the bacteria.
Gram-positive; they have a thick layer of peptidoglycan covering the cytoplasmic
membrane.
Gram negative; they are a bit more complex. They have a thin peptidoglycan layer
and an outer membrane. The space between the cytoplasmic membrane and the
outer membrane is called the periplasmic space, which contains lipoproteins. On top of
the outermembrane, they have lipopolysaccharides (LPS), which is an important PAMP.
Peptidoglycan:
Peptidoglycan is a structural component for the cell wall that is made up out of 2 types
of sugars; NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid). These sugars
form long chains, and these chains are being held together by peptide crosslinks on
the NAMs.
Peptidoglycan is synthesized in a complex process, but I have simplified it in a few
steps below;
1. NAM and NAG are linked to UDP (uridine diphosphate), forming UDP-NAM and UDP-
NAG.
2. Then a pentapeptide is added to the UDP-NAM by Mur enzymes.
3. The UDP-NAM-pentapeptide is then linked to bactoprenol, which is a carrier that
will guide it through the membrane.
4. While still in the cytoplasm the UDP-NAG will donate NAG, forming NAM-NAG
disaccharide unit.
5. Now bactoprenol will flip the complex from the cytoplasm into the periplasmic
space.
Page 2
,6. Transpeptidases (PBP) will create the peptide bonds
between the pentapeptide chains on the NAM.
Penicillin irreversibly binds to PBPs, preventing them from
forming cross-links between peptidoglycan chains. This weak-
ens the bacterial cell wall, leading to osmotic lysis and cell
death.
Bacterial cell division:
As said before, bacteria reproduce asexually through binary
fission. I will explain this in a few steps;
1. The bacterial chromosome is copied.
2. The 2 copies move to opposite sides of the cell and the cell
elongates.
3. FtsZ protein will assemble at the center and form a Z-ring
4. The Z-ring will contract and form a septum between the 2
daughter cells.
Incomplete cleavage of the septum can cause bacteria to remain
linked and form a chain structure (streptococcus) or a cluster structure
(staphylcoccus).
Sporulation:
This is a process in which a gram-positive bacteria release genetic material in a time
of stress, in order to survive. They will release an endospore, which is highly resistant
and can survive in extreme conditions. They can remain like this for centuries!
This is done in a couple of steps;
1. The bacterial chromosome is copied.
2. The cell membrane will fold inwards to create a small forespore which contains a
copy of the DNA.
3. The mother cell membrane will wrap around the forespore, engulfing it like a
bubble. This results in a double membrane around the forespore.
4. A thick layer of peptidoglycan will form in-between the 2 membranes, called the
cortex.
5. The cortex dehydrates the endospore and proteins will coat the membrane. This
will make the spore heat, chemical and enzyme resistant.
6. The spore become metabolically inactive.
7. It will accumulate dipicolinic acid (DPA) and calcium ions, which will help stabilize
the DNA.
8. The mother cell disintegrates, which releases the spore in the wild.
Germination is the reverse reaction. When conditions improve (e.g., availability of
nutrients, moisture, and warmth), the spore absorbs water, activates enzymes, and re-
sumes metabolism, returning to its vegetative state.
Bacterial metabolism:
Anabolism; requires energy to build cellular components
Catabolism; releases energy
Glycolysis; glucose → pyruvate + 2 ATP + 2 NADH.
This can be a fast energy source when oxygen is limited.
- With O2; The pyruvate can be used in the TCA cycle by converting it into acetyl-CoA,
which will be turned into NADH and FADH. This can then be used in the electron
Page 3
, transport chain* to produce large amounts of ATP, this requires the oxygen.
- Without O2; The pyruvate can also be used in fermentation without oxygen. This
leads to less ATP and acid products.
* since bacteria don’t have a mitochondria, the electron transport chain will be carried
out in the cell membrane. Protons will be pumped from the cytoplasm into the
periplasm.
Evolution in bacteria:
Bacteria can evolve really fast. This is due to their short life, E.coli can divide every 20
minutes. also due to horizontal gene transfer. This is the movement of genetic
material between bacteria. Because bacteria can share genes, they can become
resistant against antibiotic very quickly.
There are 3 types;
- Transformation; a bacteria takes up free DNA from its environment, from a dead
cell for example.
- Transduction; a bacteriophage* accidentally picks up bacterial DNA and then
injects it into another bacterium.
- Conjugation; a donor bacteria directly injects its genetic material into another
bacterium via a sex pills. The transferred DNA is usually in plasmid form. Note; the
bacteria have to touch for this one.
* a bacteriophage is a virus that specifically targets bacteria.
Page 4
