Eukaryotes and Their Structure

While many differences exist between eukaryotic and prokaryotic organisms the most prominent is the presence of organelles. As an MCAT favorite, we are going to dedicate this lesson to exploring them in detail.

Organelles are small membrane-enclosed units that carry out various functions within the cell much like the different organs in our bodies do.


The most prominent organelle in the cell is the nucleus. It contains the majority of an organism’s genetic material in the form of DNA and controls the actions of a cell by directing the production of different proteins through transcription. Furthermore, the nucleus is sub-divided into the nucleolus where rRNA, the building block of ribosomes, is created.

Since the nucleus is bound by its own phospholipid bilayer, called the nuclear envelope, products made in the nucleus and the cytosol are separated from one another. While materials can transfer between the two via nuclear pores found in the nuclear envelope many processes carried out in the nucleus are also separated from those in the cytosol.

Central Dogma

This leads to a major difference in transcription and translation between prokaryotes and eukaryotes. Since translation is carried out in the cytosol and transcription in the nucleus the two processes are separate and are carried out in two distinct steps in eukaryotes.

Transcription and translation are separated in eukaryotic cells.

Prokaryotes on the other hand lack membrane bound organelles, including a nucleus, and ribosomes can begin translation of proteins as newly synthesized mRNA transcripts are being made. This leads to much shorter protein production times in bacteria and is one of the major reasons they are used to synthesize the life-saving peptide hormone, insulin.

Transcription and translation are simultaneous in prokaryotic cells.

Endoplasmic Reticulum

Moving outwards from the nucleus the next organelle you hit is the endoplasmic reticulum (ER). The ER is a collection of connected membranes and synthesizes both lipids and proteins for the cell depending on the type.

For instance, the smooth ER (SER) lacks ribosomes and is the primary site of lipid synthesis in the ER. While the rough ER (RER) is studded with ribosomes and acts as the major site of protein synthesis within the ER. While proteins are also synthesized in the cytosol, proteins created in the ER are transported to the Golgi for further trafficking around or out of the cell.

Golgi Apparatus

Which brings us to the Golgi Apparatus, the packaging and shipping center of the cell. Here cellular products are labeled, packaged, and shipped to their intended destination.

These labels take the form of carbohydrates, phosphates, and other small signaling molecules and direct vesicles, small membrane-enclosed packages to their proper location within or out of the cell. For example, secretory products such as insulin or neurotransmitters will be sent to the cell membrane for subsequent release while a transcription factor will be sent back to the nucleus to control gene expression.

There is a lot more we need to know about cellular trafficking but it is a big enough topic that it deserves its own article and will follow this one.

Destructive Organelles

Some of the more common intracellular destinations of the Golgi are the destructive organelles: the lysosome, peroxisome, and proteasome. While we are used to thinking of cells as production factories they also need to be able to breakdown a wide variety of molecules. This allows cells to dispose of old and nonfunctional proteins, lipids, and other molecules so they can be recycled back into their constituent part and reused in the creation of new biomolecules. In short, they are the waste and recycling centers of our cells.


Lysosomes are the major recyclers in our cells and breakdown lipids, proteins, nucleic acids, and carbohydrates, pretty much anything and everything that happens to find its way into the lysosome. It accomplishes this by using a variety of hydrolytic enzymes.


Peroxisomes on the other hand contain hydrogen peroxide and focus on breaking down lipids specifically very long chain fatty acids. They play a key role in β-oxidation, which helps breakdown fats into acetyl-CoA so we can derive energy from ingested fats.


Lastly, the proteasome, while not technically an organelle, breaks down misfolded and unneeded proteins. Unlike the lysosome and peroxisome which have a wide variety of signaling labels the proteasome only has one, ubiquitin. Therefore any time you see ubiquitin or ubiquitination come up you should automatically think of the proteasome and protein degradation.


All of this synthesis and destruction is hard work and takes energy, which is where the mitochondria comes in. As the powerhouse of the cell, it is the site of the electron transport chain and chemiosmosis which produces most of the ATP in the cell. While the mitochondria is the major source of cellular energy it also has other functions and a unique evolutionary history.

The other major role of the mitochondria is in apoptosis or programmed cell death. When certain conditions are met or particular signals are sent to the mitochondria it releases the enzymes it contains causing the cell to die.

Lastly, the mitochondria have a unique evolutionary history and started out as free-living prokaryotes that were engulfed by another cell. As a result, they have their own DNA, self-replicate themselves via binary fission, and transmit their genetic code independent of the nucleus in a process called extranuclear inheritance.

The Cytoplasm

All of these organelles are floating in a gel-like substance called the cytoplasm. The cytoplasm helps suspend organelles and allows for various dissolved molecules to interact with one another and carry out biologically important reactions. Floating among these organelles are free ribosomes and elements of the cytoskeleton.


Eukaryotic ribosomes are composed of two distinct subunits that will latch onto and close on top of an mRNA strand during translation. The subunits are defined by their size in Svedbergs, which measures the rate of sedimentation of cellular components. The large subunit is referred to as the 60s subunits while the smaller subunit is the 40s subunit. You would predict the overall ribosome to be 100s but this is incorrect instead a eukaryotic ribosome is 80s. The discrepancy occurs because the components are measured by sedimentation rate which is affected by shape in addition to overall size.

While the prototypical cell will contain all of the listed organelles not all do. You will want to know the exceptions since the MCAT likes to trip us up with them. I will make sure to point them out as we go and highlight the important differences as is relevant.

Passage Practice: Eukaryotic Organelles