Tutorial case 5 learning goals

1. What are the different cell organelles and their structures and functions? (for
eukaryotes)
- Endoplasmic reticulum rough
The rough endoplasmic reticulum is so-called because its surface is studded with ribosomes,
the molecules in charge of protein production. When a ribosome finds a specific RNA
segment, that segment may tell the ribosome to travel to the rough endoplasmic reticulum
and embed itself. The protein created from this segment will find itself inside the lumen of
the rough endoplasmic reticulum, where it folds and is tagged with a (usually carbohydrate)
molecule in a process known as glycosylation that marks the protein for transport to the
Golgi apparatus. The rough endoplasmic reticulum is continuous with the nuclear envelope
and looks like a series of canals near the nucleus. Proteins made in the rough endoplasmic
reticulum as destined to either be a part of a membrane, or to be secreted from the cell
membrane out of the cell. Without a rough endoplasmic reticulum, it would be a lot harder
to distinguish between proteins that should leave the cell, and proteins that should remain.
Thus, the rough endoplasmic reticulum helps cells specialize and allows for greater
complexity in the organism.

- Endoplasmic reticulum smooth

The smooth endoplasmic reticulum makes lipids and steroids, instead of being involved in
protein synthesis. These are fat-based molecules that are important in energy storage,
membrane structure, and communication (steroids can act as hormones). The smooth
endoplasmic reticulum is also responsible for detoxifying the cell. It is more tubular than the
rough endoplasmic reticulum and is not necessarily continuous with the nuclear envelope.
Every cell has a smooth endoplasmic reticulum, but the amount will vary with cell function.
For example, the liver, which is responsible for most of the body’s detoxification, has a larger
amount of smooth endoplasmic reticulum.

- Golgi apparatus
If the smooth and rough endoplasmic reticula are how we make our product, the Golgi is the
mailroom that sends our product to customers. It is responsible for packing proteins from
the rough endoplasmic reticulum into membrane-bound vesicles (tiny compartments of lipid
bilayer that store molecules) which then translocate to the cell membrane. At the cell
membrane, the vesicles can fuse with the larger lipid bilayer, causing the vesicle contents to
either become part of the cell membrane or be released to the outside.
Different molecules have different fates upon entering the Golgi. This determination is done
by tagging the proteins with special sugar molecules that act as a shipping label for the
protein. The shipping department identifies the molecule and sets it on one of 4 paths:
Cytosol: the proteins that enter the Golgi by mistake are sent back into the cytosol
(imagine the barcode scanning wrong and the item being returned).
Cell membrane: proteins destined for the cell membrane are processed continuously.
Once the vesicle is made, it moves to the cell membrane and fuses with it. Molecules
in this pathway are often protein channels which allow molecules into or out of the
cell, or cell identifiers which project into the extracellular space and act like a name
tag for the cell.
Secretion: some proteins are meant to be secreted from the cell to act on other parts
of the body. Before these vesicles can fuse with the cell membrane, they must
accumulate in number, and require a special chemical signal to be released. This way
shipments only go out if they’re worth the cost of sending them (you generally
wouldn’t ship just one toy and expect to profit).
Lysosome: The final destination for proteins coming through the Golgi is the
lysosome. Vesicles sent to this acidic organelle contain enzymes that will hydrolyse
the lysosome’s content.

- Ribosomes
Ribosomes are the molecular machines responsible for protein synthesis. A ribosome is
made from RNA and proteins, and each ribosome consists of two separate RNA-protein
complexes, known as the small and large subunits. The large subunit sits on top of the small
subunit, with an RNA template sandwiched between the two. A ribosome looks a little like a
hamburger with a puffy bun on top, an RNA “patty” threading through it.

- Mitochondria
There are two lipid bilayers that separate the mitochondrial contents from the cytoplasm.
We refer to them as the inner and outer mitochondrial membranes. If we cross both
membranes we end up in the matrix, where pyruvate is sent after it is created from the
breakdown of glucose (this is step 1 of cellular respiration, known as glycolysis). The space
between the two membranes is called the intermembrane space, and it has a low pH (is
acidic) because the electron transport chain embedded in the inner membrane pumps
protons (H+) into it. Energy to make ATP comes from protons moving back into the matrix
down their gradient from the intermembrane space.
Mitochondria are also somewhat unique in that they are self-replicating and have their own
DNA, almost as if they were a separate cell. The prevailing theory, known as
the endosymbiotic theory, is that eukaryotes were first formed by large prokaryotic cells
engulfing smaller cells that looked a lot like mitochondria. Instead of being digested, the
engulfed cells remained intact and the arrangement turned out to be advantageous to both
cells, which created a symbiotic relationship.
 - Nucleus

The nucleus has very important roles to play. As it contains genetic material, it coordinates
cell activities like protein synthesis and cell division. Anatomically the nucleus is made up of
several components: nuclear envelope, nuclear lamina, nucleolus, chromosomes,
nucleoplasm are some of these components.
All these components work together for the nucleus to accomplish all its functions. Namely,
these functions are:
- control of the genetical information of the cell and thus the heredity characteristics
of an organism,
- control of the protein and enzyme synthesis
- control of cell division and cell growth
- storage of DNA, RNA and ribosome
- regulation of the transcription of the mRNA to protein
- production of ribosomes

- Nucleolus (inside nucleus)

The nucleolus is a structure in the nucleus of eukaryotic cells. The nucleolus consists of RNA,
DNA and proteins and contains the molecular machinery necessary for the formation of
ribosomes (rDNA). Ribosomes are small protein complexes made up of ribosomal RNA and R
proteins.

- Vacuole
The term “vacuole” means “empty space”. They help in the storage and disposal of various
substances. They can store food or other nutrients required by a cell to survive. They also
store waste products and prevent the entire cell from contamination. The vacuoles in plant
cells are larger than those in the animal cells.

- Chloroplasts
Chloroplasts are a type of plastid—a round, oval, or disk-shaped body that is involved in the
synthesis and storage of foodstuffs. Chloroplasts are distinguished from other types of
plastids by their green colour, which results from the presence of two
pigments, chlorophyll a and chlorophyll b. A function of those pigments is to absorb light
energy for the process of photosynthesis. Other pigments, such as carotenoids, are also
present in chloroplasts and serve as accessory pigments, trapping solar energy and passing it
to chlorophyll. In plants, chloroplasts occur in all green tissues, though they are
concentrated particularly in the parenchyma cells of the leaf mesophyll.

- Cell membrane

The cell membrane, also called the plasma membrane, is found in all cells and separates the
interior of the cell from the outside environment. The cell membrane consists of a lipid
bilayer that is semipermeable. The cell membrane regulates the transport of materials
entering and exiting the cell.

- Cell wall

A cell wall is a structural layer surrounding some types of cells, just outside the cell
membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both
structural support and protection and acts as a filtering mechanism.

- Lysosomes
The lysosome is the cell’s recycling center. These organelles are spheres full of enzymes
ready to hydrolyse (chop up the chemical bonds of) whatever substance crosses the
membrane, so the cell can reuse the raw material. These disposal enzymes only function
properly in environments with a pH of 5, two orders of magnitude more acidic than the cell’s
internal pH of 7. Lysosomal proteins only being active in an acidic environment acts as safety
mechanism for the rest of the cell - if the lysosome were to somehow leak or burst, the
degradative enzymes would inactivate before they chopped up proteins the cell still needed.
 - Cytosol
Cytosol is water-based solution, but even though the cytosol is mostly water, it has a semi-
solid, jelly-like consistency because of the many proteins suspended in it. The cytosol
contains a rich broth of macromolecules and smaller organic molecules, including glucose
and other simple sugars, polysaccharides, amino acids, nucleic acids, and fatty acids. Ions of
sodium, potassium, calcium, and other elements are also found in the cytosol. Many
metabolic reactions, including protein synthesis, take place in this part of the cell.

- Endosome
Endosomes are membrane-bound cytosolic vesicles with three major compartments namely
early, late, and recycling endosomal compartments. Endosomes are the integral parts of the
endocytic process, and thereby, play crucial roles in various physiological processes, such as
nutrient uptake, sorting and delivery of macromolecules, and regulation of cell surface
receptors and transporter expressions.

- Peroxisome
Peroxisomes are small, membrane-enclosed organelles that contain enzymes involved in a
variety of metabolic reactions, including several aspects of energy metabolism. Although
peroxisomes are morphologically similar to lysosomes, they are assembled,
like mitochondria and chloroplasts, from proteins that are synthesized on
free ribosomes and then imported into peroxisomes as completed polypeptide chains.
Although peroxisomes do not contain their own genomes, they are like mitochondria and
chloroplasts in that they replicate by division. They contain digestive enzymes for breaking
down toxic materials in the cell and oxidative enzymes for metabolic activity

- Flagellum
Flagellum is primarily a motility organelle that enables movement and chemotaxis. Bacteria
can have one flagellum or several, and they can be either polar (one or several flagella at one
spot) or peritrichous (several flagella all over the bacterium).

- Centrioles
Centrioles are paired barrel-shaped organelles located in the cytoplasm of animal cells near
the nuclear envelope. Centrioles play a role in organizing microtubules that serve as the
cell's skeletal system. They help determine the locations of the nucleus and other organelles
within the cell.

- Fimbriae
Fimbriae are long filamentous polymeric protein structures located at the surface of
bacterial cells. They enable the bacteria to bind to specific receptor structures and thereby
to colonise specific surfaces.
 2. How is the cell structured? (cytoskeleton)
Look at this link to rehearse mitosis:
https://www.yourgenome.org/facts/what-is-mitosis
Cytoskeleton
Within the cytoplasm there is network of protein fibers known as the cytoskeleton. This
structure is responsible for both cell movement and stability. The major components of the
cytoskeleton are microtubules, intermediate filaments, and microfilaments. Cytoskeleton
also transport different organelles through the body.

Microtubules
Microtubules are small tubes made from the protein tubulin. These tubules are found in cilia
and flagella, structures involved in cell movement. They also help provide pathways for
secretory vesicles to move through the cell and are even involved in cell division as they are
a part of the mitotic spindle, which pulls homologous chromosomes apart.

Intermediate Filaments
Smaller than the microtubules, but larger than the microfilaments, the intermediate
filaments are made of a variety of proteins such as keratin and/or neurofilament. They are
very stable and help provide structure to the nuclear envelope and anchor organelles.

Microfilaments
Microfilaments are the thinnest part of the cytoskeleton and are made of actin [a highly
conserved protein that is the most abundant protein in most eukaryotic cells]. Actin is both
flexible and strong, making it a useful protein in cell movement. In the heart, contraction is
mediated through an actin-myosin system.

3. What are the differences between prokaryotes and eukaryotes? (organelles)

SEE FOR EUKARYOTES LEARNING GOAL 1
Prokaryotic cells are fundamentally different in their internal organization from eukaryotic
cells. Notably, prokaryotic cells lack a nucleus and membranous organelles. Prokaryotic cells
have the following features:
1. The genetic material (DNA) is localized to a region called the nucleoid which has no
surrounding membrane. DNA is prokaryotes can be circular.
2. The cell contains large numbers of ribosomes that are used for protein synthesis.
3. At the periphery of the cell is the plasma membrane. In some prokaryotes the plasma
membrane folds in to form structures called mesosomes, the function of which is not clearly
understood.
4. Outside the plasma membrane of most prokaryotes is a rigid wall which gives the
organism its shape. The walls of bacteria consist of peptidoglycans. Sometimes there is also
an outer capsule. Note that the cell wall of prokaryotes differs chemically from the
eukaryotic cell wall of plant cells and of protists.
5. Some bacteria have flagella which are used for locomotion and/or pili, which may be used
to pull two cells in close contact, and perhaps to facilitate the transfer of genetic material.
 4. How do cells communicate? (Inside and outside) (not too much detail)
Paracrine signalling
Often, cells that are near one another communicate through the release of chemical
messengers (ligands that can diffuse through the space between the cells). This type of
signalling, in which cells communicate over relatively short distances, is known as paracrine
signalling.
Paracrine signalling allows cells to locally coordinate activities with their neighbours.
Although they're used in many different tissues and contexts, paracrine signals are especially
important during development, when they allow one group of cells to tell a neighbouring
group of cells what cellular identity to take on.

Synaptic signalling
One unique example of paracrine signalling is synaptic signalling, in which nerve cells
transmit signals. This process is named for the synapse, the junction between two nerve cells
where signal transmission occurs.
When the sending neuron fires, an electrical impulse moves rapidly through the cell,
traveling down a long, fiber-like extension called an axon. When the impulse reaches the
synapse, it triggers the release of ligands called neurotransmitters, which quickly cross the
small gap between the nerve cells. When the neurotransmitters arrive at the receiving cell,
they bind to receptors and cause a chemical change inside of the cell (often, opening ion
channels and changing the electrical potential across the membrane).
Synaptic signalling. Neurotransmitter is released from vesicles at the end of the axon of the
sending cell. It diffuses across the small gap between sending and target neurons and binds
to receptors on the target neuron.
The neurotransmitters that are released into the chemical synapse are quickly degraded or
taken back up by the sending cell. This "resets" the system so they synapse is prepared to
respond quickly to the next signal.

Autocrine signalling
In autocrine signalling, a cell signals to itself, releasing a ligand that binds to receptors on its
own surface (or, depending on the type of signal, to receptors inside of the cell). This may
seem like an odd thing for a cell to do, but autocrine signalling plays an important role in
many processes.
For instance, autocrine signalling is important during development, helping cells take on and
reinforce their correct identities. From a medical standpoint, autocrine signalling is
important in cancer and is thought to play a key role in metastasis (the spread of cancer
from its original site to other parts of the body). In many cases, a signal may have both
autocrine and paracrine effects, binding to the sending cell as well as other similar cells in
the area.

Endocrine signalling
When cells need to transmit signals over long distances, they often use the circulatory
system as a distribution network for the messages they send. In long-distance endocrine
signalling, signals are produced by specialized cells and released into the bloodstream, which
carries them to target cells in distant parts of the body. Signals that are produced in one part
of the body and travel through the circulation to reach far-away targets are known
as hormones.
In humans, endocrine glands that release hormones include the thyroid, the hypothalamus,
and the pituitary, as well as the gonads (testes and ovaries) and the pancreas. Each
endocrine gland releases one or more types of hormones, many of which are master
regulators of development and physiology.
For example, the pituitary releases growth hormone (GH), which promotes growth,
particularly of the skeleton and cartilage. Like most hormones, GH affects many different
types of cells throughout the body. However, cartilage cells provide one example of how GH
functions: it binds to receptors on the surface of these cells and encourages them to divide.

Signalling through cell-cell contact

Gap junctions in animals and plasmodesmata in plants are tiny channels that directly
connect neighbouring cells. These water-filled channels allow small signalling molecules,
called intracellular mediators, to diffuse between the two cells. Small molecules and ions can
move between cells, but large molecules like proteins and DNA cannot fit through the
channels without special assistance.
The transfer of signalling molecules transmits the current state of one cell to its neighbour.
This allows a group of cells to coordinate their response to a signal that only one of them
may have received. In plants, there are plasmodesmata between almost all cells, making the
entire plant into one giant network.
Signalling across gap junctions. A cell targets a neighbouring cell connected via gap junctions.
Signals travel from one cell to the other by passing through the gap junctions.
In another form of direct signalling, two cells may bind to one another because they carry
complementary proteins on their surfaces. When the proteins bind to one another, this
interaction changes the shape of one or both proteins, transmitting a signal. This kind of
signalling is especially important in the immune system, where immune cells use cell-surface
markers to recognize “self” cells (the body's own cells) and cells infected by pathogens.