Lezione n.

7 del 17/10/2023

Sbobinatore: Martina Marrocco

Docente: Prof.sa Santonico

Argomenti: Prokaryotes

PROKARYOTES AND EUKARYOTES

In all cells, we can distinguish three parts:

The first one is a membrane. A membrane is the border of the cell and it is called PLASMA
MEMBRANE or cell membrane, and it is always in every cell. It is:

- A thin layer of lipids and proteins;

- The physical boundary of the cell;
- A selective permeability barrier. It means that everything that crosses the plasma
membrane must be regulated. It cannot cross independently on what we find inside that
membrane because a membrane can be permeable to certain kinds of compounds in one
cell but not permeable for the same compounds in another cell. This means that the
membrane is selective;
- Ensures constant intracellular composition of the fluid, so what we find inside the cell is
completely different compared to what we find outside the cell;
- Establishes interconnections with the external environment and other cells.

The second one is the NUCLEAR REGION. It:

- Contains the genome, the DNA (genetic information) of the cell;

- Also contains enzymes for replicating and transcribing the genetic information.

• Replication is the process that is used to copy the DNA

• Transcription is the synthesis of mRNA, so we are creating another nucleic acid which
has basically the same information of DNA, but the property of this molecule is that
it can be read by the ribosomes differently from the DNA.

The third component is the CYTOPLASM that:

- Contains the remaining components of the cell (for the synthesis of ATP, proteins and the
remaining constituents of the cell)
- Ensures cellular movements. This property is related with capability of the plasma membrane
to establish connections: this means that the cytoplasm together with the plasma membrane
are unique objects if we talk about connection of the cell with the other. The membrane can
change its profile and can move on the surface, and this depends on the dynamicity of the
membrane but also by components that are in the cytoplasm that are called cytoskeleton.
The cytoskeleton together with the plasma membrane give the cell the capability of moving
on surface.
Two kinds of cells exist:

PROKARYOTIC CELLS

§ They are the most primitive and the simplest cells on Earth;
§ The main feature is the absence of compartments inside the cell: we have only one
membrane in the prokaryotes, which is the PLASMA MEMBRANE. Inside the cell everything
is mixed with everything;
§ In terms of metabolism, we have a specific metabolic root that is working together with
others, so all the compounds are mixed at the same time. Since we don’t have a
compartmentalization, everything happens at the same time in the same place: this makes
everything faster, but it cannot reach a higher level of organization;
§ It doesn’t have intracellular membranes as the consequence of the absence of intracellular
compartments. The nuclear zone (in bacteria) is called NUCLEOID region and this is the
region where we find DNA. The point is that we don’t have the membrane that delimits the
region with the DNA;
§ Prokaryotes cells are always unicellular organisms. They are always in contact with the
environment. So, what happens inside depends on what is inside the cell: temperature, pH,
nutrients, water, lack of water... So, it must continuously respond to what is happening
outside the cell. If we think about one cell of our pancreas, it must deal with several problems
but none of them regard what happens outside our body;
§ We can distinguish two kinds of cells: EUBACTERIA and ARCHAEA. Both don’t have
intracellular membranes, so the structure of the cell is identical but for some aspects archaea
are more like eukaryotic cells (so they are thought to be the first version of eukaryotic cells).
We share with archaea several genes, so it means that they are closer to eukaryotic cells that
to prokaryotic cells.

EUKARYOTIC CELLS

§ There is a double membrane that constitute the nuclear envelope. In the eukaryotic cells the
DNA is protected with membrane and the nucleus is the biggest organelle in our cells.
§ We have other intracellular membranes which are necessary to create compartments inside
the cells. Why do we need to create compartments inside the cell? In eukaryotic cells,
different metabolic pathways occurred in different compartments. This is extremely useful
because if a pathway works perfectly in specific conditions that are different from the
conditions of another pathway, we can create different compartments – in which in
compartment A we have the synthesis of ATP and we make everything perfect for that
process, while in another compartment which is, for example, the lysosome (compartment
B), we reduce pH with a number of enzymes that are required to destroy all the
macromolecules in our cell. In this way we create two completely different environments
inside the same cell. So, things can happen at the same time but not in the same place.
§ They can be unicellular (like yeast) but usually they are pluricellular (plants, animals, fungi
and protists).

We distinguish prokaryotic and eukaryotic cells for size and types of organelles they contain.

Both types of cells share an identical genetic language (DNA), a common set of metabolic pathways
(for example glycolysis, the first step of aerobic respiration) and many common structural features
(plasma membrane, the essential elements of membranes are identical in every cell on the Earth).
Eukaryotic cells (293Hek) contaminated with E. Coli. The spaces between the adherent cells show
tiny granules under low power microscopy, but the individual bacteria are not easily distinguishable.

The first image is a dish in which eukaryotic cells are grown. In the second image we have a
contamination of bacterial cells; these images are useful to understand the dimensions of eukaryotic
cells (it can vary a lot, but in general there is a medium dimension) and bacteria. The difference is
that the eukaryotes are enormous compared to bacteria cells.

• Cells are commonly measured in units of micrometers (10-6 m) and nanometers (10-9 m)
• The diameter of most cells measures between 1 - 100μm

In general, the diameter of all cells measured between 1 and 100 micrometers (μm).

• A bacterium has a diameter of 1 μm and the plant cell, which is the biggest usually, is around
10-100 μm.
• Eggs, that are the biggest cells we can measure in the eukaryotic world.
• Bacteria and mitochondria have similar dimensions.
• Then we have virus, proteins and lipids and we arrive to the atoms.
The scale of dimensions:

1. m (millimeters: 10-3)
2. μ (micrometers: 10-6)
3. n (nanometers: 10-9)
4. p (picometers: 10-12)
5. f (femtometers: 10-15)
6. a (attometers: 10-21).

Then we have Angstrom which is a unit used to describe distance between atoms in a
molecule and it is equal to 0,1 nanometers.

THE LIMITING FACTORS OF CELL SIZE

We said that the eukaryotic cells can be consistently bigger than the prokaryotic cells.

The first limiting factor is the volume of the cytoplasm and the volume of the nucleus. Inside the
nucleus in a bacteria cell there is one circular DNA molecule; in bacteria we can have other DNAs
called plasmids that can be or not inside the cell because they’re not essential for the life of the cell.
So, inside bacterium we have just one molecule of DNA. If we look at eukaryotic cells, we have
usually at least three different molecules of DNA (from 3 to 40 or more); these molecules are called
chromosomes and they’re consistently longer than the DNA of bacteria. So, in the nuclear region of
eukaryotic cells, we must put a consistent amount of DNA compared to what is the condition we
have in the prokaryotic cell. This means that the cytoplasm must be bigger because the content in
the nucleus is bigger than the dimension of the DNA we have in prokaryotes.

The second limiting factor is the volume of cytoplasm that can be supported by the exchange of
nutrients. The plasma membrane is responsible for the selective transport of molecules: this means
that everything that must leave the cell, or everything that must be taken from the outside will cross
the membrane. But the plasma membrane compared to the volume of the cell is just the surface,
the thin layer; if the cell is too big it’s difficult to have the right exchange because the volume of the
cell is very big, but the layer is very thin. So, we have a limit in dimension that depends on the
capability of exchanging nutrients of these cells.

The third limiting factor is the distance over which substances can efficiently travel through the
cytoplasm via diffusion. Most of the molecules inside prokaryotic and eukaryotic cells diffuse inside
the cell, so if the cell is too big, the probability to have a nutrient or a molecule in the right place and
in the right moment is lower. We must say that in eukaryotic cells we have several transport
mechanisms that drive molecules, proteins in the right place at the right time.
So somehow eukaryotic cells help the process of transporting molecules inside, but anyways remain
the fact that if the cell is too big the diffusion breath would be sufficiently fast to support the
compartments of the cell.

Prokaryotes and eukaryotes have some similar features. The common features of this cells (bacterial,
animals and plants) are:

1. Cell membrane: every cell has a plasma membrane

2. DNA: contain genetic information
3. Cytoplasm
4. Ribosome

Of course, we are able to distinguish the bacterial cells from the eukaryotic cells by looking at the
composition of these two cells, since of course they are not identical, but they have similar
components:

Ribosomes are almost not identical, but they are very similar in prokaryotes and eukaryotes because
if we look at the single ribosome we can perfectly distinguish if it is from a eukaryotic or from a
prokaryotic cell.

Cytoplasm is made by the same DNA made up of nucleotides. The cell membrane both in
prokaryotes and in eukaryotes is composed by the same phospholipids and proteins.

Cytosol is the medium of jelly-like composition that helps the cell to keep its shape. Ions and small
molecules are dissolved into it.

Ribosomes are the machines that synthesize proteins. Proteins are essential for life so of course all
cells have ribosomes.
Genome is stored differently: there is a nuclear envelope in the eukaryotic cells while there is a
nucleoid in the prokaryotic cells. It is the essential information to produce cell components and then
the plasma membrane that separates the cell from the external environment.

These objects can be found in every cell that we can analyze.

By comparing the two cells we have said that there is a common plasma membrane, in both cells
we have genetic material inside the nucleus in eukaryotic cells and nucleoid in bacterial cells.
Ribosomes are in the cytoplasm in both kinds of cells and then of course the cytoplasm: what’s the
main difference? If we look at eukaryotic cells, we have a lot of different compartments or
membrane bonds defined by limiting membrane, in prokaryotic cells apart the plasma membrane
we can also observe the second structure that is called cell wall.

The cell wall is always present in prokaryotic cells to support the shape of the cell which otherwise
could be destroyed easily.

Eukaryotic cells are protected because they usually are all together and inside the cytoplasm there
is a structure that is called cytoskeleton: the skeleton of the cells; so, our cells have a shape that
depends on the cytoskeleton structure. The cytoskeleton gives to the cell shape, support and
resistance.

Bacterial cells don’t have cytoskeleton. Bacterial cells are constantly in contact with the
environment and for this reason there is the cell wall that gives protection and gives the shape to
the cell. Some prokaryotic cells also have another structure that surrounds the cell wall which is
called the capsid. In the eukaryotic cells we have other organelles: plasma reticulum, mitochondria,
lysosomes, Golgi and other structures.
By simply looking at the shape of bacterial cells we can distinguish 3 different kinds of bacteria:

• Bacteria are classified by shape into three primary groups: cocci, bacilli, and spiral-shaped.
• The cocci are round, the bacilli are rods, and the spiral-shaped bacteria are either rigid
(spirilla) or flexible (spirochetes).

If we look at the side inside bacterial cell this is the nucleoid, the region occupied by the DNA but
together with the nucleoid we have another object here that is called plasmid that is another DNA
that is not essential to the bacterial cell, but it can be very useful. Then we know that the common
elements of all kinds of cells are ribosomes, cytoplasm, DNA and plasma membranes.

The membrane of a bacterial cell can have different structures useful for locomotion of bacteria.
These are called flagella, which are long, and pilums that are short. They are similar in structure to
the flagellum that we can find also in some eukaryotic cells even if the molecular structure is
completely different (similar in shape but not in components). The flagellum in eucaryotic cells is
made up by cytoskeletal proteins. For this reason, even if the shape is similar, the molecules’
structure is completely different. They have similar structure because they have the same
mechanical requirement. This demonstrates that nature usually makes things similar even with
different molecules.

• Both eukaryotic and prokaryotic cells have ribosomes, but they differ in size.
• Because there is no membrane barrier between bacterial DNA and cytoplasm, ribosomes are
able to bind to an mRNA as soon as part of it has been synthesized by the RNA polymerase;
thus, in procaryotes, transcription and translation occur contemporaneously.
PROKARYOTIC’S CELL STRUCTURE

What is the cell wall? We previously said that cell wall is required because these cells don’t have a
cytoskeleton; this means that to have a structure and a shape and to be more protected from the
environment, they need a sort of exoskeleton (bacterial cell wall) made up by peptidoglycans. This
term is the combination of peptide (proteins) and glycan (sugar carbohydrates). So, we have said
that the cell wall is composed by two kinds of macromolecules: proteins on one side and sugar
polysaccharides on the other side.

In eucaryotic cells we always have to distinguish between the factory of this cell and the matrix that
is outside of the cell; every cell is surrounded by a structure which is called extracellular matrix. The
matrix is synthesized by the cell but then released outside. In the matrix of the eukaryotic cell, we
find macromolecules which are called proteoglycan and not peptidoglycan (protein+ carbohydrates)
such as in the prokaryotic cell. So we assigned that outside of the plasma membrane both in
eukaryotic cells and in prokaryotic ones there is a component made up of protein and carbohydrates.
In bacterial cell the name is PEPTIDOGLYCAN while in Eukaryotic cell is Proteoglycan; of course, the
name is not the only different because they also have different structure but basically they are made
up by the same things: with the protein part we build the structure of the molecules.

What is the meaning of having carbohydrates associated with this protein part? Carbohydrates
attract water; so, we can hydrate the environment around the cell.

We distinguish between GRAM POSITIVE and GRAM NEGATIVE bacterial cells. So up to now we
have seen 2 ways to classify bacterial cell:

- the shape
- the capability to be stained with gram technique
 • Composed of layers of peptidoglycan
• Gram-negative bacteria (e.g., E. coli): thin inner cell wall + outer membrane –> NOT-STAINED
with crystal violet
• Gram-positive bacteria (e.g., B. polymyxa): thicker cell wall and no outer membrane –>
STAINED with crystal violet

If we start with the upper structure, what do we see?

1. Plasma membrane and we distinguish it because there are two leaf leps and proteins that
cross the membrane that are called transmembrane proteins.
2. Then we have a big object outside the plasma membrane, a big layer which is the
peptidoglycan (proteins and carbohydrates). It’s a thick layer.
3. On the other side the gram negative passes against the plasma membrane, then a thin layer
of peptidoglycan and another membrane; that is called outer plasma membrane. Here we
have two differeces:
1. Two membranes
2. A thin layer peptidoglycan.

If it is a gram positive bacterium, the surface is rich of hydrophilic molecules but if it is a gram
negative bacterium, the layer is rich of hydrophobic molecules.

We cannot stain a gram negative bacterium as well as we can stain a gram positive bacterium and
this is understandable from the color of the dishes: the gram negative bacteria cannot be stained
with crystal violet which is the molecule used in the gram technique.
BACTERIAL CAPSULE (the most external structure)

- It is not always present: it can be present or not (it depends on the bacterial cell we are
studying)
- It is composed of different classes of polysaccharides that are secreted outside the cell wall
- Due to the viscosity, it constitutes a protective envelope around the cell that constantly
remains in contact with the bacteria wall
- It can give the shape to the bacteria because it is a very thick layer. If we look at this picture,
for example, we can clearly describe the bacterial cell by simply looking at the shape of the
capsule.

- It acts as a molecular filter that protects cells from the entrance of the lytic enzymes to other
potentially dangerous molecules (when the bacterial cell is protected by the capsule is more
resistant to all the agent that used to destroy it)
- It increases resistance to drying (because there are carbohydrates, so the capsule can be full
of water)
- It promotes cell-cell and cell-surface adhesion (this is due to viscosity of the capsule)
- It can be used as a reserve material (made of sugars that can be defrauded and used as an
energy source). Since they are reaching carbohydrates, capsule can be digested by the
bacterium, and by digesting it the bacterium can uptake the glucose and use it as a sort of
energy
- It is a virulence factor; it allows the bacterial cell to evade immune responses in the initial
phase of infection (phagocytosis).

In phagocytosis a portion of the plasma membrane of the eukaryotic cell, for example, go
throughout the cell and create a sort of incorporation but, with this portion of plasma membrane,
they can capture this object, internalize and destroy it using the lysosomes.
If there is the capsule, this process cannot be used, so this means that we have to wait for another
response from our body that can be able to destroy the bacterial cell without using the initial barrier
of the inner response, which is the phagocytosis of the bacterium. So, in this way, the bacterium has
more time to invade the body. So, they are more aggressive because they are able to jump the first
level of protection that we usually use with the bacterial cells.
SPECIFIC FUNCTIONS OF PLASMA MEMBRANE IN PROKARYOTIC CELLS

They can also perform photosynthesis, which means using the energy of the light to produce ATP.
We also know that plant cells perform the same process by using organelles like chloroplasts. So,
both prokaryotic and eukaryotic cells can make photosynthesis, but the first ones don’t have
chloroplasts nor intracellular membranes, while the eucaryotic cells have both. In prokaryotic cells
that are able to perform photosynthesis, the enzymes are all in the plasma membrane. So, the
features of the chloroplast, in the bacterial cell, are found in the plasma membrane.

At the same time bacterial cells must synthesize ATP. The organelle responsible for the synthesis of
ATP in the eukaryotic cell is the mitochondrion, and there are several enzymes in the internal
membrane of mitochondrion that perform this process. Whereas the enzymes that synthetize ATP
in prokaryotic cells (which don’t have mitochondria) are again in the plasma membrane.

Even though the components of plasma membrane in bacterial cells are common to the ones in
eukaryotic cells, the plasma membrane of the bacterial cell is really a mess full off everything.
This membrane synthesize ATP and capture the light. Everything here happens in the same place at
the same time, while in eukaryotic cells all these processes are compartmentalized.

CHARACTERISTIC THAT DISTINGUISHES PROKARYOTIC AND EUKARYOTIC CELLS:

1. THE CELL DIVISION PROCESS

Remember that in a bacterial cell there is only one molecule of DNA, one chromosome. This
chromosome is in the nucleoid, which is the center of the bacterial cell.

When the bacterial cell must divide:

- It replicates the DNA (we will have two chromosomes in this cell)
- Then the cell becomes bigger and bigger until it’s ready to divide in two cells (daughters cells)

This is called fission division.

But the bacterial cell has another capability, which is the horizontal transmission of genetic
information. The bacterium, which is called the
domo bacterium, can transport part of its DNA to another bacterium which is called recipient
bacterium.
For example: a plasmid can be transferred from one bacterium to the other using this long, thin
tubule called F-PILUS, and thanks to this some components of the cell can be donated to the other.
This condition is completely absent in eukaryotic cells, and this process is called conjugation.
 2. LOCOMOTION:

In prokaryotic cells this is relatively simple and it uses flagellum (it can be one or more).

The mechanism is the rotation of the flagella: the rotation exerts pressure against the surrounding
fluid, propelling the cell trough the medium.

In the eucaryotic cells, the structures, that are very similar to flagella in the prokaryotic cell, are
formed in sperm but the components are completely different: they have tubuli, which are the main
components of microtubules, that are the essential elements in the structure of the flagellum is the
sperm.
So, apparently the structure is very similar, the shape is similar, also the functions are similar, but
the components are completely different: they are much more complex than the simple protein
filament of bacteria, and they generate movement by a different mechanism.