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Cellular organelles and structure

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.

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.
OrganelleFunctionFactory part
NucleusDNA StorageRoom where the blueprints are kept
MitochondrionEnergy productionPowerplant
Smooth Endoplasmic Reticulum (SER)Lipid production; DetoxificationAccessory production - makes decorations for the toy, etc.
Rough Endoplasmic Reticulum (RER)Protein production; in particular for export out of the cellPrimary production line - makes the toys
Golgi apparatusProtein modification and exportShipping department
PeroxisomeLipid Destruction; contains oxidative enzymesSecurity and waste removal
LysosomeProtein destructionRecycling and security


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.
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.


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.

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.
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.


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.


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.


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.
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.


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 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 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.
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.

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