THE CELL

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. 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 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 can 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 keep 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
Nucleus DNA Storage Room where the blueprints are kept
Mitochondrion Energy production Powerplant
Smooth Endoplasmic Reticulum (SER) Lipid production; Detoxification Accessory production – makes decorations for the toy, etc.
Rough Endoplasmic Reticulum (RER) Protein production; in particular for export out of the cell Primary production line – makes the toys
Golgi apparatus Protein modification and export Shipping department
Peroxisome Lipid Destruction; contains oxidative enzymes Security and waste removal
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 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). Protein 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.

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.

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. 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 continuous with the perinuclear space, so we know the endoplasmic reticulum is attached to the nuclear envelope. There are 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 are 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.

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.

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 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 that 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.

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 act as a 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.

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.

As 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 (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 DNA, almost as if they were completely separate cells. 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 a 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 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.

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