DAT Bootcamp Bio Academy

Chapter 2: Cells and Organelles

Table of Contents:
Cell Membrane
Crossing Cell Membranes
Organelles
Cytoskeleton
Extracellular Matrix
Cellular Tonicity and Cell Circulation
Preview
The cell theory says living things contain one or more cells; therefore, the cell is
the basic unit of life. It also says that new cells must arise from pre-existing cells.
The coordinated effort of cells allows living organisms to carry out all their
amazing functions.
Cells act like factories that make proteins. In cellular factories, the cell membrane
acts as the building, the DNA acts as the instruction manual for building the
products, and ribosomes act like workers.
In this chapter, we will mainly discuss eukaryotic cells, which make up animals,
plants, fungi, and protists. These types of cells contain many smaller membrane-
bound organelles inside them, which are like different rooms in the factory.

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 Cell Membrane
Cell membranes are boundaries that hold all of the critical cellular contents
inside, protecting them from the surrounding environment. In general, cell
membranes contain three main things: phospholipids, cholesterol, and proteins.
1. Phospholipids are a unique type of lipid (fat) in cell membranes. Each
phospholipid has a three-carbon glycerol backbone, attached to one phosphate
group and two fatty acid tails. Phosphate groups are polar and hydrophilic
(water-loving) because they have negative charges. Fatty acids are nonpolar, so
they do not mix well with water (hydrophobic).

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 Phospholipids are a classic example of an amphipathic molecule. Amphipathic
compounds are those containing both hydrophobic and hydrophilic properties.
Amphipathic proteins are also common, and they contain both hydrophobic and
hydrophilic amino acids.
Because phospholipids are amphipathic, they spontaneously self-assemble into a
bilayer when in an aqueous environment. Both the extracellular (outside the cell)
and intracellular (inside the cell) environments are aqueous; therefore, cell
membranes form through self-assembly of phospholipids. The phospholipid
heads will face either aqueous environment (extracellular or intracellular), while
the fatty acid tails will face each other.

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 2. Cholesterol makes up around 30 50% of a eukaryotic cell membrane.
Cholesterol contains four hydrocarbon rings and is a precursor to steroid
hormones. Cholesterol is also amphipathic, which allows it to interact with various
regions of the phospholipid bilayer. The ability of cholesterol to interact with the
cell membrane is beneficial to the overall fluidity of the membrane, for reasons
we will discuss in a little bit.

3. Membrane proteins come in two types: integral and peripheral.

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 1. Integral proteins are also known as transmembrane proteins because they
traverse the entire phospholipid bilayer. These proteins are amphipathic, with
nonpolar parts that contact the fatty acids and polar parts that extend out
into the aqueous environment.
2. A peripheral membrane protein is the other type of membrane protein found
associated with cell membranes. These do not extend through the entire
bilayer - instead, peripheral membrane proteins are on the periphery. The
periphery could mean the polar heads of the phospholipid bilayer, partially
inserted into the membrane, or attached to one of the hydrophilic surfaces of
an integral membrane protein. These proteins are generally hydrophilic.

Integral/transmembrane proteins may function in cell signaling, but most tend

to transport large, polar (hydrophilic) molecules across the cell membrane. We
will discuss the various mechanisms of transport in the next section of this
chapter.

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 Peripheral membrane proteins have a range of functions. We will mention some
key examples now.
1. Receptor proteins (peripheral) receive chemical signals from the extracellular
environment. When these proteins receive such a signal, the protein triggers
secondary responses within the cell. Many non-steroidal hormones act as
chemical trigger molecules for receptor proteins. We will discuss these types
of hormones in greater depth in Chapter 10 Anatomy and Physiology.
2. Adhesion proteins attach adjacent cells to other things (like other cells), and
they also act as anchors for the cytoskeleton. Adhesives (like tape) stick to
other things. Think of adhesion proteins as the tape that sticks cellular
components together. We will discuss adhesion proteins in greater detail in
later sections of this chapter.
3. Cellular recognition proteins are peripheral membrane proteins that help
cells recognize each other. They are proteins attached to short carbohydrate
chains called polysaccharides (glycoprotein). Recognition proteins give cells
a way to identify (or recognize) each other when they come in contact.
Now that we know the organization of a typical cell membrane, we can think
about something called the fluid mosaic model. This model represents the critical
features of a cell membrane.
‘Mosaic’ indicates that the cell membrane is a mosaic made up of various
structures. For example, think about the various types of proteins we discussed
so far. If we were to examine the cell membrane using a microscope, we would
see patterns created by each of these different proteins.
‘Fluid’ indicates that the phospholipids, cholesterol, and proteins are not held
rigidly in place, but that they can flow fluidly throughout the cellular membrane.
For example, a peripheral membrane protein can move laterally throughout the
membrane.
Several factors influence the fluidity of a membrane; they are temperature,
cholesterol, and fatty acid saturation in the phospholipid tails.

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 https://www.youtube.com/embed/BWQCAsM CF4?rel=0&showinfo=0

This video is licensed by Khan Academy under CC BY NC SA 3.0 US at

https://creativecommons.org/licenses/by-nc-sa/3.0/us/. The original version can
be found at https://www.youtube.com/watch?v=BWQCAsM CF4.
When it is cold, phospholipids pack together tightly. Conversely, when it is hotter,
the phospholipids of the cell membrane they are found further apart. Cholesterol
maintains some distance between the phospholipids when it is cold, but it also
holds the phospholipids together when it starts to get hot.
Without cholesterol, cell membranes would become overly rigid in the cold.,
which reduces flexibility. On the other hand, cell membranes (without cholesterol)
would become too flexible in hot environments.
Membrane fatty acid saturation also affects membrane fluidity. Saturated fatty
acids have the highest possible amount of hydrogens at each carbon; therefore,
they are made of single bonds only. As a result, saturated fatty acids are straight
and can pack tightly.

Adapted from: https://commons.wikimedia.org/w/index.php?curid=49923679

Unsaturated fatty acids are not fully saturated with hydrogen and can possess
one or more double bonds. The double bonds can create a kink in the fatty acid
tail of a phospholipid, which prevents the tail from ‘nicely’ aligning with the other
phospholipid tails. There is more spacing, which leads to a higher fluidity of the
membrane.

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 Cis-unsaturated fatty acids create more severe kinks because the chain remains
on the same side of the double bond. Trans-unsaturated fatty acids pack
together extremely tight because the fatty acid goes to opposite sides of the
double bond.

Adapted from: https://commons.wikimedia.org/w/index.php?curid=49923679

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 Critical Review of Cell Membranes:
Cell membranes are phospholipid bilayers with cholesterol and membrane
proteins
Phospholipids are amphipathic molecules, and the degree of saturation in
their nonpolar fatty acid tails affects membrane fluidity/permeability
Saturated/trans-unsaturated tails stack tightly and make a rigid cell
membrane
Cis-unsaturated tails create kinks that do not stack tightly, making the
membrane more fluid
Cholesterol is an amphipathic steroid precursor found in cell membranes
Cholesterol decreases fluidity when it is hot and increases fluidity when it is
cold
Integral proteins are amphipathic transmembrane proteins
Integral proteins are involved with transport and cell signaling

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 Peripheral membrane proteins are generally hydrophilic, depending on their
attachment/location
Peripheral membrane proteins include receptor proteins, adhesion proteins,
and recognition proteins

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Crossing Cell Membranes

The previous section showed that cell membranes are fluid mosaic boundaries
between intracellular and extracellular environments. Cells regulate how
substances cross the cell membrane to travel in and out of the cell.

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p;end=450

Small, uncharged, nonpolar particles (eg. carbon dioxide and oxygen) can travel
directly across the phospholipid bilayer via a process known as simple diffusion.
Simple diffusion is the flow of substances down their concentration gradient
(from high to low) in a non-energy consuming process. Simple diffusion does not
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 utilize any proteins to help the particles across the membrane. Osmosis is a type
of simple diffusion, which we will discuss later on in this chapter.

Large, hydrophilic molecules cannot travel directly across the bilayer- they need
help from integral proteins. Facilitated transport is a term that describes how
large, hydrophilic molecules travel across the bilayer through integral proteins.
Facilitated transport can be uniport (one molecule moving in one direction),
symport (several molecules moving in one direction), or antiport (several
molecules moving in opposite directions).

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 There are two main types of integral proteins involved with facilitated transport.
The first is a channel protein, while the second is a carrier protein.
1. Channel proteins face the extracellular and intracellular environments of the
cell at the same time. They are like tunnels that have been bored out through
the membrane, and they usually allow the passage of many small, polar
molecules and ions.
2. Carrier proteins change their shape to facilitate the movement of molecules
through the protein. These are different from the protein channels we
discussed above because they do not face extracellular and intracellular
environments at the same time. Instead, they only face one side at a time.
They change shape when their specific molecule binds, causing them to face
the other side.

Passive diffusion describes a type of facilitated transport of particles down their

concentration gradient (from high to low concentration). Passive diffusion does
not require energy, and it usually relies upon channel proteins. Notice that passive
diffusion is different from simple diffusion because we are using a protein.
Porins are a classic example of a channel protein used in passive diffusion
because they are usually not specific for just one type of molecule. Most of the
time, they allow any hydrophilic molecule that fits to pass through. Ion channels
follow a similar idea to porins, with ions (like calcium) using passive diffusion to
move down their concentration gradient.

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 DAT Pro-Tip: there is a particular type of porin (aquaporin) found in the
kidney and plant roots. These allow water to flow more rapidly than simple
diffusion alone.

Active transport occurs when particles travel against their concentration

gradient (from low to high concentration). These processes require an energy
input, and the energy source dictates whether it will be primary or secondary
active transport. Active transport primarily relies upon carrier proteins that
change their shape.
Primary active transport uses the energy released from ATP hydrolysis to pump
molecules against their concentration gradient. The sodium-potassium Na+/K+)
pump is a typical example of primary active transport because it hydrolyzes ATP.
DAT Pro-Tip: the energy currency of cells is adenosine triphosphate ATP .
We will learn a lot about this currency in Chapter 3 Cellular Energy.
The Na⁺/K⁺ pump exchanges three Na⁺ out of a cell for two K⁺ into a cell. In doing
so, the pump consumes one ATP molecule, which is why the pump is also an
ATPase ATP hydrolysis enzyme). ATP hydrolysis powers this exchange, as both
Na⁺ and K⁺ travel against their concentration gradient by primary active
transport.

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 Secondary active transport uses energy obtained from a source other than ATP.
The energy this type of transport uses will usually come from the free energy
released as other molecules spontaneously flow down their concentration
gradient (we will discuss what all that means in the next chapter).
One important point to note is that secondary active transport relies on primary
active transport to create the initial concentration gradient. In other words, if a
secondary active transport pump is to pump some molecule against its
concentration gradient, it needs to use the energy another molecule releases as it
flows down its concentration gradient. That second molecule had its
concentration gradient established by primary active transport.

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 Cytosis refers to the processes cells use to facilitate the bulk transport of large,
polar (hydrophilic) molecules. The two main types of cytosis are endocytosis and
exocytosis, and each type requires energy. Therefore, endocytosis and
exocytosis are active transport mechanisms.
Endocytosis occurs whenever the cell membrane forms a plasma membrane-
bound package (vacuole or vesicle) around something extracellular the cell
wants to internalize. In other words, endocytosis transports molecules into the
cell. Endocytosis is an integral part of the endomembrane system, which we will
discuss in the Organelle section.
1. Phagocytosis is a type of endocytosis where a cell engulfs undissolved
materials. During phagocytosis, the cell membrane will project outward to
wrap around the solid it wants to internalize. Phagocytosis is known as
cellular eating.
2. Pinocytosis is similar to phagocytosis. This type of endocytosis is known as
cellular drinking because the cell will pinch inward (invaginate) such that it
can engulf dissolved materials (liquids).
3. Receptor-mediated endocytosis is a type of endocytosis that occurs
whenever a specific molecule binds to a peripheral membrane receptor

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 protein. Certain non-steroidal hormones target cells via this mechanism.

Exocytosis is the opposite of endocytosis. In other words, exocytosis occurs

when materials exit the cell - not when they enter it. Exocytosis is an essential
part of vesicle secretion from the Golgi apparatus, which we will discuss in the
Organelle section. A typical example of exocytosis may exist whenever nerve
signals propagate from one neuron to the next (we will learn much more about
nerves in Chapter 10 Anatomy and Physiology).

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 Critical Review of Mechanisms to Cross Cell Membranes:
Cells would die if they could not move molecules across their membrane
Small, uncharged, nonpolar (hydrophobic) molecules can cross by simple
diffusion
Simple diffusion moves molecules down their concentration gradient
Facilitated transport uses integral proteins to facilitate the movement of
more massive, charged, polar (hydrophilic) molecules
Facilitated transport can be uniport, symport, or antiport
Passive diffusion is facilitated transport down a concentration gradient
Active transport is facilitated transport against a concentration gradient
Primary active transport uses ATP hydrolysis
Secondary active transport uses energy from another molecule flowing down
its concentration gradient

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 Cytosis is the bulk transport of large, hydrophilic molecules
Cytosis is a form of active transport (varies between primary and secondary)
Cytosis includes endocytosis (into the cell) and exocytosis (out of the cell)
Endocytosis includes phagocytosis (cellular eating), pinocytosis (cellular
drinking), and receptor-mediated endocytosis (a type of pinocytosis)
Organelles
Recall from our chapter preview that organelles were like the “rooms” of a
cellular factory. Just like a cell, these organelles are also enclosed by a
phospholipid bilayer to keep the materials they contain inside (organelles are
membrane bound). In other words, organelle membranes prevent organelle
contents from spilling into the cytosol.
The cytosol is the aqueous intracellular fluid, while the cytoplasm is everything
within the cell (cytosol and organelles). If the cytoplasm were a stew, the cytosol
would be the broth.
We will focus on eukaryotic cells because eukaryotes contain membrane-bound
organelles; Prokaryotic cells do not. We will compare and contrast eukaryotes
and prokaryotes in greater detail in Chapter 9 Diversity of Life.
Deoxyribonucleic acid DNA is like the instruction manual that cellular factories
rely upon to make products (proteins). The DNA is “read” through two processes,
called transcription and translation, hence allowing for the creation of the
cellular factory's proteins. We will discuss transcription and translation in greater
detail in Chapter 6 Molecular Genetics.
DNA lies within eukaryotic cells in a particular “room” called the nucleus. The
nucleus' primary function is to house and protect the DNA. It also has various
molecules that aid in DNA replication and transcription, both of which occur
inside the nucleus.
Prokaryotic cells do not contain membrane-bound nuclei. So where do
prokaryotes keep their DNA? Prokaryotes house most of their genetic material in
a dense and irregularly shaped region known as the nucleoid.

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 The nuclear envelope sets the borders of a eukaryotic nucleus. The nuclear
envelope is the nucleus’ membrane. The nuclear envelope is a set of two
phospholipid bilayers, one inner and one outer. The area between the outer and
inner membranes is called the perinuclear space .
The nucleus contains an aqueous medium called the nucleoplasm. DNA is located
floating in the nucleoplasm. Although the nuclear envelope separates the cytosol
from the nucleoplasm, specific molecules related to DNA replication and
transcription enter and exit the nucleus via nuclear pores.
Nuclear pores are holes in the nuclear envelope allowing for molecules to travel
in and out. For example, messenger ribonucleic acid (mRNA , the product of
transcription, exits the nucleus via nuclear pores.
The nuclear lamina is a dense and fibrous network of proteins associated with
the inner membrane of the nuclear envelope. its primary role is to provide
structural support to the nucleus. However, it also regulates DNA organization,
DNA replication, and cell division.
There is another subspace within the nucleus, called the nucleolus. The nucleolus
is a dense region within the nucleus. This is where rRNA (ribosomal RNA is
produced, and is the site of ribosomal subunits production. .
Ribosomal subunits contain ribosomal ribonucleic acid (rRNA and proteins.
The proteins enter the nucleoplasm (from the cytosol) via nuclear pores, and
rRNA synthesis occurs via transcription directly within the nucleus.

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 Adapted from: https://commons.wikimedia.org/w/index.php?curid=736389
Once the proteins and rRNA are both floating around in the nucleoplasm, they
assemble into ribosomal subunits. The ribosomal subunits then exit the nucleus
and enter the cytosol via a nuclear pore; once in the cytosol, the subunits
assemble into a complete ribosome.
Ribosomes function in protein translation (protein synthesis). Ribosomes are
macromolecules that do not contain a membrane, and they are not organelles.
Both eukaryotic cells and prokaryotes contain ribosomes; although, their
structures are slightly different.
Eukaryotic ribosomes have two subunits. One subunit is 60 S, while the other is
40 S (the unit “S” tells how heavy/dense a molecule is). These subunits come
together to form a complete 80 S eukaryotic ribosome. Each of the subunits is
produced in the nucleoplasm, coming together in the cytosol of the cell.

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 Prokaryotic ribosomes also have two subunits. They have a 50 S subunit and a
30 S subunit. Remember that prokaryotes do not have membrane-bound nuclei,
so their ribosomal subunits are produced in their nucleoid region. The subunits
come together in the prokaryotic cytosol, and they form a 70 S prokaryotic
ribosome.
While ribosomes are responsible for protein synthesis, they do not function in the
subsequent packaging or modification of those proteins. Ribosomes float freely
in the cytosol or attach to the rough endoplasmic reticulum ER .
Ribosomes that freely float in the cytosol tend to make proteins that function
within the cytosol of the cell. Ribosomes that bind to the rough ER will synthesize
proteins into it, such that the proteins can undergo modifications.
The space inside an ER is called the lumen. The word lumen is not unique to an ER
- a lumen is just the inside space of a hollow structure. There are two different
ER types in a eukaryotic cell, rough and smooth.
The rough ER is continuous with the outer membrane of the nuclear envelope,
which means the ER lumen is continuous with the perinuclear space. The rough ER
membrane appears “rough” because its surface contains ribosomes. The
ribosomes attach to cytoplasmic side of the rough ER and translate proteins into
the lumen, which mechanistically looks similar to threading a string through a
button.
Once in the rough ER lumen, the protein will be manipulated to prepare it to be
delivered to other organelles. A typical manipulation attaches a carbohydrate to
the protein, a process called glycosylation. This glycoprotein will then move
toward the Golgi apparatus (another organelle we will discuss soon).
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 Ultimately, proteins that enter the lumen of the rough ER will have one of two
fates: they will either become a part of the cell membrane (as an integral or
peripheral membrane protein), or they will leave the cell altogether (via
exocytosis). In this way, the rough ER allows for increased eukaryotic complexity
because it helps to distinguish between proteins that should leave the cell and
those that should remain inside.
The smooth ER is a little different than the rough ER because it is not associated
with ribosomes, and therefore is not involved in protein synthesis. The smooth ER
is usually not continuous with the outer membrane of the nuclear envelope.
The central role of the smooth ER is to synthesize lipids (fats), steroid hormones,
detoxify cells, and in some cases, store ions.
The lipids and steroids produced by a smooth ER are essential molecules for
energy storage, membrane structure (cholesterol), and hormone communication.
The abundance of smooth ER in a cell depends on the functions of that cell. For
example, a human liver is heavily involved with detoxification, so its cells tend to
contain many smooth ER.

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 The Golgi apparatus is like the mailroom in a cellular factory. The Golgi consists
of flattened sacs called cisternae (these look like pancakes). Incoming vesicles
from the ER enter the lumen of the Golgi apparatus at the cis face; this is the
cisternae that is found closest to the rough and smooth ER.

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 Once the products enter the Golgi lumen, they travel from one cisternae to the
next, undergoing further modifications. For example, glycoproteins from the
rough ER can undergo phosphorylation in the Golgi complex. These “tags” help
the “mailroom” direct the “product” to the correct location.
Eventually, vesicles containing manipulated rough/smooth ER products will exit
the Golgi apparatus at the trans face. The trans face is the cisternae that lies
farthest away from the rough and smooth ER (and therefore closer to the cell
membrane). In general, products secreted by the Golgi tend to travel to the
cytosol, cell membrane, extracellular environment (via exocytosis), into a
lysosome (another organelle), or into a vacuole (another organelle).

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 Products destined for the cell membrane utilize transport vesicles that fuse with
the cell membrane. The products will often include integral/peripheral membrane
proteins, and phospholipids and cholesterol (which lie in the vesicle bilayer itself).
Products that are destined for secretion travel in vesicles that empty into the
extracellular environment (exocytosis). Secretion products need to accumulate
within the Golgi before secretion. Secretion products do not undergo regular
production, so it is more efficient to send many of the products at one time
whenever another cell needs them. These products may include transport
proteins and hormones Chapter 10 Anatomy and Physiology).
The trans face of the Golgi apparatus secretes vesicles that can also travel to the
lysosome (some plant cells have vacuoles instead of lysosomes). These trans-
Golgi vesicles tend to contain enzyme proteins that the lysosome uses to carry
out specific functions.
A lysosome is a membrane-bound organelle that hydrolyzes (breaks down)
substances. Lysosomes contain acidic hydrolytic/digestive enzymes that are
designed to function at a low pH. They can hydrolyze substances taken-up by the
cell via endocytosis (phagocytosis, pinocytosis, receptor-mediated endocytosis),
to break down nutrients, bacteria, and other cellular debris.
Lysosomes can breakdown a cell’s unneeded/defective components (debris) in a
process called autophagy. Lysosomes can contribute to apoptosis (programmed
cell death) when they release their contents into the cell.

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 Vacuoles are another organelle found within all plant and fungal cells, as well as
some animal, protist, and rarely bacterial cells. Vacuoles form as the result of
many membrane vesicles fusing together.
Transport vacuoles move materials from one organelle to another; or, from
organelles to the plasma membrane. In this way, transport vacuoles are
mainly just large transport vesicles.
Food vacuoles are temporary food holders. These form when cells take-up
nutrients via endocytosis mechanisms, and all the nutrient vesicles fuse
together. Food vacuoles will eventually merge with lysosomes such that the
acidic lysosomal enzymes can digest the nutrients within the food vacuole.
Central vacuoles are very large organelles, and they tend to occupy the
majority of a plant cell interior. Central vacuoles have a specialized membrane
called the tonoplast, they exert turgor when filled, which helps to maintain
cell rigidity.
Central vacuoles often carry out the same functions as an animal cell
lysosome within a plant. They can also act as a storage vacuole. Storage

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 vacuoles store starches, pigments, and toxic substances.
Specific single-celled organisms have contractile vacuoles, which collect and
pump excess water out of the cell. Contractile vacuoles operate to prevent
the cell from bursting (lysis). Contractile vacuoles utilize active transport in
organisms that live in freshwater environments.

An endomembrane system is a group of organelles and membranes that work

together to modify, package, and transport proteins and lipids that are entering
or exiting a cell. Together, the endomembrane system includes the
nucleus/nuclear envelope, rough and smooth ERs, Golgi apparatus, lysosomes,
vacuoles, and cell membrane.

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 Peroxisomes are membrane-bound organelles that share a similar function to
lysosomes because they are responsible for breaking things apart (hydrolysis).
However, peroxisomes are not part of the endomembrane system, and they do
not receive vesicles from the Golgi apparatus.
Peroxisomes tend to break down stored fatty acids, and some cells use
peroxisomes in detoxification. For example, alcohol detoxification occurs in the
peroxisomes of liver cells. Peroxisomes may break down proteins, although that
role is usually carried out by lysosomes.
Peroxisomes also generate hydrogen peroxide, which is used as an oxidizing
agent (something that accepts electrons from an electron donor/reducing agent)
in oxidation-reduction (redox) reactions. However, excess hydrogen peroxide
can be dangerous for a cell. Hydrogen peroxide can produce reactive oxygen
species ROS .
ROS can create free radicals, which can damage the nuclear DNA or phospholipid
bilayers. Damage to nuclear DNA can create conditions of uncontrollable

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 divisions, the condition known as cancer.
Because peroxisomes produce hydrogen peroxide as a by-product, they contain
an enzyme called catalase, which converts dangerous hydrogen peroxide
radicals into harmless water.

DAT Pro-Tip: specialized variations of peroxisomes, called glyoxysomes, exist in

the germinating seeds of some plants.
As we know from various internet memes, mitochondria are the powerhouses of
the cell. We will discuss these in much more detail in Chapter 3 Cellular Energy.
For now, know that mitochondria are organelles in eukaryotic cells (plants
included) that produce a lot of ATP under the right conditions.
Chloroplasts exist in select eukaryotic cells, such as plant cells and some protists
like algae. Animal, fungal, and prokaryotic cells do not contain chloroplasts. The

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 central role of a chloroplast is to carry out photosynthesis (chloroplasts and
their components are discussed in full detail in Chapter 4 Photosynthesis).

The centrosome is an organelle found near the nucleus of animal cells. A

centrosome contains a pair of centrioles, which work together to serve as
microtubule organizing centers MTOCs) during cell division in animal cells.
Note: we will discuss more details about MTOCs, centrosomes, and centrioles
in the Cytoskeleton section. We will also discuss them again in Chapter 5 Cell
Division.

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 Critical Review of Organelles:
Eukaryotes = membrane-bound organelles, while prokaryotes do not have
membrane-bound nuclei and tend not to have organelles
The nucleus is a dual membrane organelle that contains DNA in eukaryotes
Prokaryotes contain DNA in the nucleoid region
60 S + 40 S = 80 S eukaryotic ribosomes; 50 S + 30 S = 70 S prokaryotic
ribosomes
The rough ER targets proteins to the Golgi apparatus, while the smooth ER
transports carbohydrates and lipids. The smooth ER also detoxifies.
Lysosomes are involved with molecular digestions; some cells have vacuoles
The endomembrane system transports molecules in or out of the cell

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 Peroxisomes detoxify and contain catalase for hydrogen peroxide free
radicals
Mitochondria = ATP powerhouse
Chloroplasts are involved with photosynthesis
Centrosomes are animal microtubule organizing centers (MTOCs)
Cytoskeletons
The cytoskeleton lies within the cytoplasm of both eukaryotic and prokaryotic
cells. In eukaryotic cells, the cytoskeleton has microfilaments, intermediate
filaments, and microtubules.

https://www.youtube.com/embed/oIrnecBfHzg?rel=0&showinfo=0

This video is licensed by Khan Academy under CC BY NC SA 3.0 US at

https://creativecommons.org/licenses/by-nc-sa/3.0/us/. The original version can
be found at https://www.youtube.com/watch?v=oIrnecBfHzg.
Microfilaments have the smallest diameter out of the three cytoskeletal
components, and they contain a double helix of two actin filaments, which can
undergo rapid assembly and disassembly. Microfilaments play a crucial role in
cell movement.
For example, cyclosis (or cytoplasmic streaming) is a cytoplasmic movement
process that relies upon actin-based microfilaments. Here, organelles and
vesicles travel throughout the cytoplasm on microfilament “tracks.”
In another example, animal cells form cleavage furrows to divide. Cleavage
furrows contain contractile rings of microfilaments that pinch the cytoplasms
into two separate cells (cytokinesis). We will discuss cell division in Chapter 5.
Lastly, actin-based microfilaments have directionality; therefore, they can create
“one-way streets” for a motor protein called myosin. Muscle cells can contract
because of myosin and actin microfilaments Chapter 10 Anatomy and
Physiology).
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 Intermediate filaments have a diameter between the other two cytoskeletal
components (intermediate sized). Intermediate filaments can contain many
different types of proteins. The most common intermediate filament protein on
the DAT is keratin. Keratin is a protein that concentrates in skin, hair, and nails.
Intermediate filaments embed themselves into cell junctions, like desmosomes
and hemidesmosomes, which we will discuss in the next section. For this reason,
they tend to associate with the cellular membrane. However, they also web
through the cytoplasm and form the nuclear lamina - a fibrous network of
intermediate filaments (known as lamins) which support the nucleus, and nuclear
activities.
Intermediate filaments do not assemble and disassemble nearly as quickly as the
actin filaments that make-up microfilaments, so they are longer lasting.

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 Moreover, because they mostly associate with membranes, they provide a
primary role in cellular structural support.
Along with microfilaments and intermediate filaments, microtubules function in
providing structural integrity to the cell as part of the cytoskeleton. They have
the largest diameter out of the three cytoskeletal components. Microtubules are a
hollow tube, where the walls of the tube are a helical polymer of tubulin protein
dimers.
Microtubules are similar to microfilaments in the sense that they can grow and
shrink rapidly, which is due to tubulin dimer addition/subtraction. Moreover, the
tubulin dimers that make up a microtubule also have directionality, much like the
actin monomers in a microfilament.
Microtubules have essential roles in providing structural support to the cell.
However, they also have more refined and specialized roles as well. For example,
microtubules partake in cell division, as well as the production of cilia and
flagella.
We will discuss how this is the case in this chapter, and again in Chapter 5 Cell
Division.

Microtubule Organizing Centers MTOCs) are in eukaryotic cells. MTOCs create,

extend, and organize the cell’s microtubules. Microtubules created by MTOCs
form a spindle apparatus, which guides chromosomes to opposite ends of the
cell during karyokinesis (nuclear division of chromosomes).

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 A centrosome is an organelle found in animal cells, and it is a type of MTOC.
Centrosomes are near an animal cell’s nucleus. Note that fungi and most plant
cells do not contain a centrosome as their MTOC. We typically refer to their
MTOCs just as ‘MTOCs.’
Centrioles are specialized cylinders of microtubules that inhabit the centrosome.
Each centrosome has a mother and daughter centriole, oriented at a ninety-
degree angle. They are involved with the formation of the spindle apparatus, and
each centriole is a hollow cylinder made of nine triplets of microtubules (9 x 3
array).

The centrosome will replicate during S phase of interphase, which is essential

because we need one centrosome for each daughter cell after cell division, as
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 well as for proper spindle apparatus functioning. We will discuss S phase in
Chapter 5 Cell Division.
In addition to being involved with cell division, the mother centriole can attach to
the cell membrane. Here, the mother centriole can form a basal body, which can
produce a cilium or a flagellum for the cell. Cilia and flagella have a slightly
different structure than the basal body they stem from because they have an
outer ring of nine microtubule doubles, and two singles at the center - this is also
known as a 9 + 2 array.
Note: prokaryotic flagella have flagellin, a protein building block different
from the tubulin dimers found in microtubules.

The pericentriolar material of a centrosome is a matrix of proteins that surround

the centrioles. These proteins play a role in microtubule nucleation, which is the
process where several tubulin dimers come together to form a microtubule.
Similarly, the pericentriolar material is involved with securing microtubules to the
centrosome.
Critical Review of the Cytoskeleton:

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 Eukaryotic cells have microfilaments, intermediate filaments, and
microtubules in their cytoskeleton
Microfilaments have the smallest diameter of the three
Microfilaments have two actin filaments in a double helix
Actin is a protein that has directionality
Microfilaments polymerize/depolymerize rapidly
Microfilaments are involved with cellular movements, cytoplasmic streaming,
cell division, and processes like muscle contraction.
Intermediate filaments have a diameter between microfilaments and
microtubules
Intermediate filaments can have many types of proteins- remember keratin
Intermediate filaments impact cell structure/rigidity - nuclear lamina
Microtubules are hollow cylinders made of tubulin dimers
Tubulin is a protein that has directionality, much like actin monomers
Microtubules impact cell structure, cell division, and flagella and cilia
MTOCs organize microtubules, which is especially relevant for cell division
Animal cells have a centrosome as their MTOC, plants, and fungi have
‘MTOCs.’
Centrosomes contain a mother and daughter centriole at a ninety-degree
angle
Centrioles have a 9 x 3 array 9 triplets)
Centrioles form the spindle apparatus for cell division
Mother centrioles form basal bodies for cilia and flagella
Cilia and flagella = 9 x 2 array 9 doubles with 2 singles in the center)

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 Extracellular Matrix
So far, we have talked about what goes on inside a cell. In this section, we will
learn about some of the exciting components outside cells, as well as structures
that hold adjacent cells together. First, let’s consider a structure called the
extracellular matrix.
The extracellular matrix ECM primarily functions to provide mechanical
support in the area between adjacent animal cells. The ECM has carbohydrates,
an extensive network of fibrous structural proteins, and adhesion proteins.
Proteoglycans are a class of glycoproteins that exist in the ECM between cells.
These types of glycoproteins are unique because they have a lot of
carbohydrates relative to the amount of actual protein they contain.
The most common fibrous structural protein in the ECM is a protein called
collagen. Cells called fibroblasts produce collagen.. Once secreted, collagen will
form long woven fibers called collagen fibrils. Collagen fibrils are what give
human tissues so much of their strength and rigidity.
The ECM (mainly collagen) connects to the cells it surrounds. The connections
are made possible via proteins called integrins. Integrins are transmembrane
proteins that send signals to the cell about its extracellular environment. The
signals tell the cell whether it should grow, divide, differentiate, or undergo
programmed cell death (apoptosis).

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 Fibronectin is a protein that connects integrins to the network of proteoglycans
and collagen in the ECM. These connections help in the transduction of
extracellular signals, such that they can travel through the integrins and into the
cell.
Laminin is a protein that behaves similarly to fibronectin. They influence cell
differentiation, adhesion, and movement. It is a biologically active component of
the basal lamina (a layer of the ECM secreted by epithelial cells).

Cell walls are unique carbohydrate-based structures that lie above the cell
membrane in plants, fungi, bacteria, and archaea. Cell walls provide structural
support, protection, and an enhanced degree of filtration for what enters and
exits a cell. In this way, they act similarly to animal cell ECMs.

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 DAT Pro-Tip: animal cells secrete collagen and make an ECM, so they do not
have a cell wall.
Cell walls form as cells secrete their respective carbohydrate building blocks into
the extracellular environment. In other words, plant cell walls contain cellulose, so
plant cells will secrete cellulose to make their cell wall. Fungi cell walls contain
chitin. Bacteria cell walls have peptidoglycan. Archaea cell walls have
indiscriminate polysaccharides.
The glycocalyx is a coat of glycolipids and glycoproteins that covers the surface
of bacterial cell walls, as well as some animal cell membranes. In all, the
glycocalyx can provide adhesive capabilities, a protective barrier to infection,
and act as markers for cell-cell recognition.

Cell-matrix junctions allow the ECM to connect to the cytoskeleton at the

interior of an animal cell. There are two main ways animal cell ECMs connect to
the cytoskeleton.

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 1. Focal adhesions connect the ECM to actin-based microfilaments in the
cytoskeleton.
2. Hemidesmosomes connect the ECM to the keratin intermediate filaments
of the cytoskeleton.

Cell-cell junctions connect adjacent cells. There are four main ways animal cells
can connect to one another, and they have a range of benefits that we will
discuss in detail.

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 1. Tight junctions are protein junctions that provide a water-tight seal between
cells. They ensure that materials must enter the cells (diffusion or active
transport) to pass through the tissue. Tight junctions are characteristic of cells
lining the digestive tract, where materials are required to pass through cells (not
between them) before they can travel into the blood.

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 2. Desmosomes are like staples that hold adjacent cells together. They provide
robust mechanical stability and are present in tissues subject to mechanical
stress. These are different from tight junctions because they extend across the
cell membranes and connect to the cytoskeleton inside the cell. They connect
adjacent cells together via intermediate filaments.
3. Adherens junctions are conceptually similar to desmosomes, however
adherens junction connect adjacent cells via actin-based microfilaments - not
keratin intermediate filaments.
Desmosomes and adherens junctions are types of anchor junctions, which
provide robust mechanical stability and are present in tissues subject to
mechanical stress, such as the cervix or outer layer of the skin.

4. Gap junctions allow for the passage of ions and small molecules between cells.
These junctions are in tissues like the heart, which use ions to pass electrical
impulses across many cells.
Connexons are small holes in the plasma membrane, which are made up of six
membrane proteins called connexins. When a connexon of one cell lines up with
a connexon of another cell, we have a gap junction.

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 Now that we’re done addressing animal cell junctions, let’s move onto plant cells.
Many plant cell walls connect to one another via a structure called the middle
lamella. A middle lamina is a sticky cement which attaches adjacent plant cells to
each other. Because of this, it is difficult for large molecules to permeate from
one plant cell to the next.
Plasmodesmata make it easier for cell-to-cell transport in plant cells.
Plasmodesmata are tunnels between adjacent plant cells..

Critical Review of the Extracellular Matrix:

Animal cells have an ECM with collagen fibrils and proteoglycans

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 Certain types of cells do not secrete collagen, so they make cell walls
Integrins are transmembrane proteins that connect cells to the ECM via
fibronectin/laminin proteins
Cell-matrix junctions (focal adhesions and hemidesmosomes) connect the
ECM to the cytoskeleton
Cell-cell adhesions (tight junctions, desmosomes, adherens junctions, gap
junctions) connect adjacent animal cells
Desmosomes and adherens junctions are also types of anchor junctions
The middle lamina is a sticky substance between cell walls (not seen in
animals)
Plant cells have plasmodesmata, which are akin to gap junctions in the sense
that they allow for the transport of substances between cells
Cellular Tonicity and Cell Circulation
The extracellular fluid and intracellular cytosol have dissolved solutes.
Manipulations of the solute concentrations inside or outside the cell may result in
variations in the cell’s tonicity. Tonicity refers to the relative solute concentrations
for two solutions that are separated by a semipermeable membrane.

https://www.youtube.com/embed/afWnU10ZNfg?rel=0&showinfo=0

This video is licensed by Khan Academy under CC BY NC SA 3.0 US at

https://creativecommons.org/licenses/by-nc-sa/3.0/us/. The original version can
be found at https://www.youtube.com/watch?v=afWnU10ZNfg.
In this way, tonicity determines the extent and direction of solvent flow via
osmosis. Osmosis is a simple diffusion mechanism (a non-energy consuming
process that does not utilize channel proteins), where water travels across a
semipermeable membrane, from areas of low to high solute concentration.

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 Keep in mind that when looking at a solution, a low solute concentration also
means a high water concentration, and vice versa. This means that osmosis can
also be seen as high to low water (or solvent) concentration. Remember, simple
diffusion is the movement of substances down its concentration gradient; and
osmosis is the movement of water. In this way, the movement of the water
molecules makes the solute concentrations equal on both sides of the membrane.

Isotonic solutions are those where the extracellular and intracellular

environments have the same solute concentrations. Animal cells prefer isotonic
environments because they will be in water balance. In other words, they will not
lose or gain too much fluid volume.
If the solute concentration outside a cell were higher, it would be called a
hypertonic environment. Here, water will leave the cell via osmosis in an attempt
to reduce the solute concentration outside the cell. The loss of fluid causes the
cell to shrivel.
DAT Pro-Tip: if a cell in a hypertonic environment has a cell wall (as in a plant
cell), the cell membrane will dehydrate/shrink away from the cell wall in a
process called plasmolysis.
If the solute concentration is lower outside the cell than it is inside the cell, the
environment is hypotonic. In this case, water will travel via osmosis from the
external environment and into the cell. In this way, an animal cell will swell and
eventually burst in a process called lysis.

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 Cells with cell walls (like plant cells) are far less likely to undergo lysis because
the rigid cell wall prevents them from swelling too much. Plant cells prefer
hypotonic environments because the extra water goes into the central vacuole,
resulting in the normal turgid state.

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 Critical Review of Tonicity and Cell Circulation:
Isotonicity = same solute concentration across the membrane
Animal cells prefer isotonic environments
Hypertonicity = higher solute concentration outside the cell; fluid exits
Hypotonicity = higher solute concentration inside the cell; fluid enters
Awesome! That's the end of Chapter 2! 🎉

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