What is a cell

Right now your body is doing a million things at once. It’s sending electrical impulses, pumping
blood, filtering urine, digesting food, making protein, storing fat, and that’s just the stuff you’re
not thinking about! You can do all this because you are made of cells — tiny units of life that are
like specialized factories, full of machinery designed to accomplish the business of life. Cells
make up every living thing, from blue whales to the archaebacteria that live inside volcanos. Just
like the organisms they make up, cells can come in all shapes and sizes. Nerve cells in giant
squids can reach up to 12m [39 ft] in length, while human eggs (the largest human cells) are
about 0.1mm across. Plant cells have protective walls made of cellulose (which also makes up
the strings in celery that make it so hard to eat) while fungal cell walls are made from the same
stuff as lobster shells. However, despite this vast range in size, shape, and function, all these little
factories have the same basic machinery.
There are two main types of cells, prokaryotic and eukaryotic. Prokaryotes are cells that do not
have membrane bound nuclei, whereas eukaryotes do. The rest of our discussion will strictly be
on eukaryotes. Think about what a factory needs in order to function effectively. At its most
basic, a factory needs a building, a product, and a way to make that product. All cells have
membranes (the building), DNA (the various blueprints), and ribosomes (the production line),
and so are able to make proteins (the product - let’s say we’re making toys). This article will
focus on eukaryotes, since they are the cell type that contains organelles.

A diagram representing the cell as a factory. The cell membrane is represented as the "factory
walls." The nucleus of a cell is represented as the "blueprint room." The ribosome is represented
as the "production room" and the final protein made by the ribosome is represented as the
"product."

What’s found inside a cell

An organelle (think of it as a cell’s internal organ) is a membrane bound structure found within a
cell. Just like cells have membranes to hold everything in, these mini-organs are also bound in a
double layer of phospholipids to insulate their little compartments within the larger cells. You
can think of organelles as smaller rooms within the factory, with specialized conditions to help
these rooms carry out their specific task (like a break room stocked with goodies or a research
room with cool gadgets and a special air filter). These organelles are found in the cytoplasm, a
viscous liquid found within the cell membrane that houses the organelles and is the location of
most of the action happening in a cell. Below is a table of the organelles found in the basic
human cell, which we’ll be using as our template for this discussion.
Organelle Function Factory part
Room where the blueprints are
Nucleus DNA Storage
kept
Mitochondrion Energy production Powerplant
Smooth Endoplasmic Accessory production - makes
Lipid production; Detoxification
Reticulum (SER) decorations for the toy, etc.
Rough Endoplasmic Protein production; in particular Primary production line - makes
 Organelle Function Factory part
Reticulum (RER) for export out of the cell the toys
Golgi apparatus Protein modification and export Shipping department
Lipid Destruction; contains
Peroxisome Security and waste removal
oxidative enzymes
Lysosome Protein destruction Recycling and security

Diagram of a cell highlighting the membrane bound organelles mentioned in the table above.

Nucleus
Our DNA has the blueprints for every protein in our body, all packaged into a neat double helix.
The processes to transform DNA into proteins are known as transcription and translation, and
happen in different compartments within the cell. The first step, transcription, happens in the
nucleus, which holds our DNA. A membrane called the nuclear envelope surrounds the nucleus,
and its job is to create a room within the cell to both protect the genetic information and to house
all the molecules that are involved in processing and protecting that info. This membrane is
actually a set of two lipid bilayers, so there are four sheets of lipids separating the inside of the
nucleus from the cytoplasm. The space between the two bilayers is known as the perinuclear
space.
Though part of the function of the nucleus is to separate the DNA from the rest of the cell,
molecules must still be able to move in and out (e.g., RNA). Proteins channels known as nuclear
pores form holes in the nuclear envelope. The nucleus itself is filled with liquid (called
nucleoplasm) and is similar in structure and function to cytoplasm. It is here within the
nucleoplasm where chromosomes (tightly packed strands of DNA containing all our blueprints)
are found.

Cartoon showing a close up the nucleus and highlighting structures specific to the nucleus.
A nucleus has interesting implications for how a cell responds to its environment. Thanks to the
added protection of the nuclear envelope, the DNA is a little bit more secure from enzymes,
pathogens, and potentially harmful products of fat and protein metabolism. Since this is the only
permanent copy of the instructions the cell has, it is very important to keep the DNA in good
condition. If the DNA was not sequestered away, it would be vulnerable to damage by the
aforementioned dangers, which would then lead to defective protein production. Imagine a giant
hole or coffee stain in the blueprint for your toy - all of a sudden you don’t have either enough or
the right information to make a critical piece of the toy.
The nuclear envelope also keeps molecules responsible for DNA transcription and repair close to
the DNA itself - otherwise those molecules would diffuse across the entire cell and it would take
a lot more work and luck to get anything done! While transcription (making a complementary
strand of RNA from DNA) is completed within the nucleus, translation (making protein from
RNA instructions) takes place in the cytoplasm. If there was no barrier between the transcription
and translation machineries, it’s possible that poorly-made or unfinished RNA would get turned
into poorly made and potentially dangerous proteins. Before an RNA can exit the nucleus to be
translated, it must get special modifications, in the form of a cap and tail at either end of the
molecule, that act as a stamp of approval to let the cell know this piece of RNA is complete and
properly made.

Cartoon showing mRNA preparing to leave the nucleus and enter the cytoplasm.

Nucleolus
Within the nucleus is a small subspace known as the nucleolus. It is not bound by a membrane,
so it is not an organelle. This space forms near the part of DNA with instructions for making
ribosomes, the molecules responsible for making proteins. Ribosomes are assembled in the
nucleolus, and exit the nucleus with nuclear pores. In our analogy, the robots making our product
are made in a special corner of the blueprint room, before being released to the factory.

A diagram representing the cell as a factory. The cell membrane is represented as the "factory
walls." The nucleus of a cell is represented as the "blueprint room" while the nucleolus is
represented as a "special product corner" within the blueprint room. The ribosome is represented
as the "production room" and the final protein made by the ribosome is represented as the
"product."

Endoplasmic Reticulum
Endoplasmic means inside (endo) the cytoplasm (plasm). Reticulum comes from the Latin word
for net. Basically, an endoplasmic reticulum is a plasma membrane found inside the cell that
folds in on itself to create an internal space known as the lumen. This lumen is actually
continuous with the perinuclear space, so we know the endoplasmic reticulum is attached to the
nuclear envelope. There are actually two different endoplasmic reticuli in a cell: the smooth
endoplasmic reticulum and the rough endoplasmic reticulum. The rough endoplasmic reticulum
is the site of protein production (where we make our major product - the toy) while the smooth
endoplasmic reticulum is where lipids (fats) are made (accessories for the toy, but not the central
product of the factory).

Rough Endoplasmic Reticulum

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 an 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.

Smooth Endoplasmic Reticulum

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.

A diagram showing the structure of the rough endoplasmic reticulum, the golgi apparatus, and
the smooth endoplasmic reticulum.
Figure 6. The rough endoplasmic reticulum (3) is continuous with the nucleus (1) and makes
proteins to be processed by the Golgi apparatus (8), which it is not continuous with. The
smoother endoplasmic reticulum is more tubular than the rough, and is not studded with
ribosomes.

Golgi apparatus (aka Golgi body aka Golgi)

We mentioned the Golgi apparatus earlier when we discussed the production of proteins in the
rough endoplasmic reticulum. 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 actually 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:

1. 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).
2. 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.
3. 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).
4. Lysosome: The final destination for proteins coming through the Golgi is the lysosome.
Vesicles sent to this acidic organelle contain enzymes that will hydrolyze the lysosome’s
content.

Cartoon representing the golgi apparatus sorting proteins into one of the four paths described
above: the cytosol, the cell membrane, secretion, or lysosome.

Lysosome
The lysosome is the cell’s recycling center. These organelles are spheres full of enzymes ready to
hydrolyze (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.
Cartoon showing a lysosome breaking down a protein.

Peroxisome
Like the lysosome, the peroxisome is a spherical organelle responsible for destroying its
contents. Unlike the lysosome, which mostly degrades proteins, the peroxisome is the site of
fatty acid breakdown. It also protects the cell from reactive oxygen species (ROS) molecules
which could seriously damage the cell. ROSs are molecules like oxygen ions or peroxides that
are created as a byproduct of normal cellular metabolism, but also by radiation, tobacco, and
drugs. They cause what is known as oxidative stress in the cell by reacting with and damaging
DNA and lipid-based molecules like cell membranes. These ROSs are the reason we need
antioxidants in our diet.

Mitochondria
Just like a factory can’t run without electricity, a cell can’t run without energy. ATP (adenosine
triphosphate) is the energy currency of the cell, and is produced in a process known as cellular
respiration. Though the process begins in the cytoplasm, the bulk of the energy produced comes
from later steps that take place in the mitochondria.
Like we saw with the nuclear envelope, there are actually 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.

A cartoon showing the various parts of the mitochondria.

Mitochondria are also somewhat unique in that they are self-replicating and have their own
DNA, almost as if they were a completely 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 (and chloroplasts, more on them later). 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.
So far we’ve discussed organelles, the membrane-bound structures within a cell that have some
sort of specialized function. Now let’s take a moment to talk about the scaffolding that’s holding
all of this in place - the walls and beams of our factory.

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.

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 actually 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.

Images showing microtubules, microfilaments, and intermediate fibers.

Figure 10. Elements of the cytoskeleton include microtubules (a), microfilaments (b), and
intermediate fibers (c). These structures work together in cell structure and motility.

Plants and Platelets

So far we’ve covered basic organelles found in a eukaryotic cell. However, not every cell has
each of these organelles, and some cells have organelles we haven’t discussed. For example,
plant cells have chloroplasts, organelles that resemble mitochondria and are responsible for
turning sunlight into useful energy for the cell (this is like factories that are powered by energy
they collect via solar panels). On the other hand, platelets, blood cells responsible for clotting,
have no nucleus and are in fact just fragments of cytoplasm contained within a cell membrane.

Eukaryotes vs Bacteria vs Archaea

It is also important to keep in mind that organelles are found only in eukaryotes, one of the three
major cell divisions. The other two major divisions, Bacteria and Archaea are known as
prokaryotes, and have no membrane bound organelles within.

Consider the Following:

 Some diseases can be traced back to organelle lack / malformation. For example,
inclusion-cell (I-cell) disease occurs due to a defect in the Golgi. In order to mark
enzymes that should be sent to lysosomes to help degrade unwanted molecules, the Golgi
has to bind them with a mannose 6-phosphate tag, like a shipping label. However, in
patients with I-cell disease, one of the proteins that make this tag is mutated, and cannot
do its job, like a broken label machine. This means that proteins cannot be targeted to
lysosomes. These untagged proteins are the enzymes that are responsible for chopping up
other proteins. What happens is the inactivated enzymes end up being sent outside the
cell, while lysosomes clog up with undigested material. This disease is congenital, and
usually fatal before patients reach 7 years of age.
 An interesting idea is that mitochondria can be used to trace maternal ancestry. Since
mitochondria are self-replicating and have their own DNA, they are not determined by
the genes found in the nucleus. Instead, your mitochondria have developed from the
mitochondria present in the female ovum (egg) that you developed from. Defects in
mitochondrial DNA cause hereditary diseases that pass only from mother to children.