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Subcellular Architecture of the Eukaryotic Cell

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Introduction and Goals

In Tutorial #1, you were introduced to the complexities of defining "life".  One characteristic common to all life is cells; all living organisms are comprised of cells.  In the previous three tutorials, you learned about prokaryotic cell structure, function, and diversity.  This tutorial will focus on the subcellular architecture of eukaryotic cells, the production and transport of proteins throughout eukaryotic cells, and the evolution of eukaryotic cells.

By the end of this tutorial you should have a basic working understanding of:

  • subcellular organization in eukaryotic cells
  • the trafficking of proteins throughout the cell
  • the role of the cytoskeleton in cell structure and function
  • the Endosymbiotic Theory

Performance Objectives:

  • Describe the similarities and differences between prokaryotic and eukaryotic cells
  • Explain the role of the nucleus
  • Review the organelles involved in the synthesis of macromolecules in a eukaryotic cell
  • Diagram the path of an exported protein from ribosome to cell membrane
  • Discuss the role of lysosomes
  • Identify the three components of the cytoskeleton and compare and contrast their roles in the cell
  • Summarize the roles of mitochondria and chloroplasts, and the evidence for their endosymbiotic origin.

Introduction to the Subcellular Organization of Eukaryotic Cells

It used to be thought that a clear distinction between prokaryotic and eukaryotic cells was the presence of membrane-bound organelles in eukaryotic cells (organelles are defined as specialized structures that are separated from the rest of the cell by a phospholipid bilayer).  However, we now know that some prokaryotes contain rudimentary organelles.  Despite this blurring of the lines between defining prokaryote and eukaryote, eukaryotic cells have a more complex and well-developed subcellular architecture. These membrane-bound structures play important roles in the normal functioning of eukaryotic cells and they participate in everything from constructing and exporting newly synthesized biological molecules to protecting the cell from invading pathogens. The main structures that will be examined in this tutorial can be found in Figure 1.

Figure 1.  A simplified diagram of an animal cell.  (Click to enlarge)

The Nucleus

The nucleus (Figure 2) is one of the most visible organelles in the cell. While it is usually only about 5 microns in diameter (approximately 1/20th the thickness of a human hair), it plays a central role in providing genetic information to the cell. The nucleus is surrounded by a double membrane called the nuclear envelope.

Figure 2.  A simplified diagram of a nucleus. (Click to enlarge)

The nucleus also houses the nucleolus (depicted above). The nucleolus contains a very active group of genes that encode and transcribe ribosomal RNA (the RNA component of ribosomes).


The Major Roles of the Nucleus

The most notable function of the nucleus is to store the main genetic material within every eukaryotic cell, namely the nuclear chromosomes (additional genetic information is also found within mitochondria and chloroplasts). In addition to storage, the nucleus is also the site of all gene expression. If a new protein is to be made, a gene must first be transcribed to messenger RNA in the nucleus (you will learn more about this in Tutorial #35 - From Gene to Protein: Transcription and Translation). Once transcribed, messenger RNA exits the nucleus through nuclear pores in the nuclear envelope.


The Endomembrane System

Building a functional protein is a complex process. Most proteins require a number of post-production modifications before they become functional. These modifications do not occur spontaneously and they require specialized cellular structures. Protein production and modification takes place in a network of membrane-bound chambers called the endomembrane system (Figure 3). The process begins in a network called the endoplasmic reticulum, which literally means "network within the cytoplasm." There are two types of endoplasmic reticula in the cell: a smooth endoplasmic reticulum and a rough endoplasmic reticulum. The smooth endoplasmic reticulum plays a major role in synthesizing lipids and in degrading toxins. The rough endoplasmic reticulum houses ribosomes on its surface, which is where many of the proteins targeted for export outside the cell are synthesized.

Figure 3.  A simplified diagram of the endomembrane system.  (Click to enlarge)

Protein Targeting to the Rough Endoplasmic Reticulum

Many proteins contain signal sequences that facilitate their sorting within the cell. Newly synthesized proteins destined for export have a unique signal sequence that directs them to the rough endoplasmic reticulum. Figure 4 illustrates the sorting process. If a translational complex (a ribosome with an associated mRNA molecule) (1) has a growing protein with this sequence at its N-terminus (the end that is synthesized first), then a signal recognition particle (SRP) binds to the growing polypeptide (2). The SRP facilitates association with the rough ER, and the translational complex docks to the rough ER at a specific receptor site located within rough ER pore complexes (3). The growing polypeptide is then inserted through the pore and translation continues; note: the polypeptide is now being inserted into the lumen of the rough ER as it is synthesized (4). Specific peptidases inside the lumen recognize the signal sequence and this short stretch is removed (5). Once translation is complete, the translational complex dissociates, leaving the newly synthesized protein inside the rough ER.

Figure 4.  Protein Sorting into the Rough ER. (Click to enlarge)

The scientist who discovered signal sequences and their role in protein trafficking was awarded the Nobel Prize in Medicine for his work. You can read more about this at the Nobel Prize Web site


The Golgi Apparatus Modifies Proteins

The Golgi apparatus is a component of the endomembrane system involved in processing proteins. Named for its discoverer, Camillo Golgi, the Golgi apparatus is where carbohydrates are added to proteins in a process called glycosylation. Proteins move from the rough endoplasmic reticulum in small membrane-bound transport vesicles to the Golgi apparatus (Figure 5). The side of the Golgi apparatus where proteins enter is referred to as the cis face; it can be thought of as the receiving end of the Golgi apparatus. Transport vesicles, containing partially processed proteins, bud from the folds of the Golgi apparatus (cisternae) on the cis face and fuse with cisternae on the more distal side (trans face). In this manner, proteins traverse the Golgi apparatus as they are prepared for transport to their final destinations (either within the cell or for export outside of the cell).

 Figure 5.  A simplified diagram of the Golgi apparatus.  (Click to enlarge)

Protein Export

When a protein is fully processed, glycosylated and ready for export, it next makes the trip from the endomembrane system to the cell's plasma membrane or other internal compartments (e.g., a lysosome). The plasma membrane consists of a phospholipid bilayer that is selectively permeable. The final transport vesicle that buds from the trans face of the Golgi apparatus is termed a secretory vesicle (Figure 6). Secretory vesicles bind and fuse with the internal face of the plasma membrane by interacting with specific membrane proteins. There are several steps in this process: first, the vesicle must dock on the membrane; second, it must be primed for fusion; third, it must fuse with the membrane that will release its contents.

Figure 6.  Protein Export and Secretory Vesicles. (Click to enlarge)  

What Holds Everything In the Cell Together?

The inside of a cell is much more than a sack of watery cytoplasm and organelles. Within the cytoplasm is a complex scaffold of proteins that comprise the cytoskeleton. The cytoskeleton is made up of three major components: microfilaments, intermediate filaments, and microtubules.


The smallest cytoskeletal fibers are microfilaments (Figure 7), made of polymerized subunits of the globular protein actin, which are strung together like beads on a string. Microfilaments play a critical role in cell motility, where they facilitate cellular migration or, as in the case of muscle cells, contraction.

Figure 7.  A Microfilament Composed of Actin Subunits. (Click to enlarge)

As the name implies, intermediate filaments (Figure 8) are somewhat larger than microfilaments, yet smaller than microtubules. Intermediate filaments are made of fibrous proteins wrapped around one another to form a thick, cable-like structure. Just as cables are specialized to withstand large forces, intermediate filaments play an important role in supporting cell structures and anchoring organelles in the correct position within the cell. Unlike microfilaments and microtubules, intermediate filaments are relatively static within the cell.

Figure 8.  Intermediate filaments.  (Click to enlarge)

Microtubules (Figure 9) are the largest cytoskeletal elements that we will discuss.  Microtubules are actually hollow tubes consisting of rows of paired tubulin molecules. Microtubules are very important to major cellular events (e.g., mitosis) and they also have a major structural role within the cell.

Figure 9.  Microtubules.  (Click to enlarge)

Targeting the Cytoskeleton With Drug Therapies

You might know that cancer cells are characterized by their rapid cell divisions. Given the importance of the cytoskeleton in cell division, it is the target of a number of cancer therapeutic drugs. However, one of the major problems with targeting the cytoskeleton with drug therapies is that there are many adverse side effects associated with these drugs. This is because the cytoskeleton plays important roles throughout the cell cycle. Several drug companies are actively searching for drugs that target the cytoskeletal elements specifically involved in dividing cells.


Lysosomes and Vacuoles

Eukaryotes have a number of membrane-bound compartments that are used for a variety of purposes. One such compartment is the lysosome (Figure 10). Lysosomes are involved in breaking down material. When vesicles bud off of the plasma membrane, bringing contents from outside the cell into the cytoplasm, they first fuse with lysosomes. Special hydrolytic enzymes (enzymes that hydrolyze/breakdown molecules) within lysosomes degrade material within the vesicles. The hydrolytic enzymes are initially synthesized in an inactive state, and only upon reaching the lysosome do they become activated. Because the active hydrolytic enzymes are compartmentalized within the lysosomes, only material within the lysosomes is degraded.

 Figure 10.  An overview of lysosomes.  (Click to enlarge)

Vacuoles have a variety of roles in cells. In most animal cells, vacuoles are primarily storage organelles for proteins and lipids that are to be exported from the cell. Plant cells have a large central vacuole that is filled with a variety of substances such as salts, minerals and pigments.  This central vacuole is primarily filled with water that exerts pressure against the cell wall (turgor pressure) and helps provide structural support to the plant.


The Mitochondrion

Mitochondria are present in the cells of most eukaryotes and they are responsible for converting the energy in food molecules into energy in the form of ATP (ATP is a high energy molecule that provides the energy for many cellular reactions). They are also quite abundant; some cells contain a single large mitochondrion, but most eukaryotic cells contain many more. Cells that require a great deal of energy (e.g., muscle cells) can house thousands of mitochondria. The basic structure of a mitochondrion is depicted in Figure 11. Mitochondria are enclosed in a double membrane; a smooth outer membrane and an inner membrane that is contorted into a complex of infoldings called cristae. Cristae provide extensive surface areas for processes such as the electron transport chain, which takes place within the inner membrane. This membrane typically contains thousands of copies of electron transport chain proteins. The space within the cristae is the mitochondrial matrix. 

Figure 11. The structure of a mitochondrion.  (Click to enlarge)  

Mitochondria also possess their own genetic material in the form of circular DNA (which, as you will learn, provides an important clue as to how mitochondria arose). Mitochondria and their genetic material are maternally inherited in sexually reproducing organisms. (The sperm mitochondria rarely enter the egg during fertilization.) Therefore, mitochondria are passed to offspring in the cytoplasm of ova. Hence, your mitochondria are virtually identical to your mother's. There are many fascinating consequences associated with this phenomenon. For example, a number of maternally inherited diseases are caused by defective genes in mitochondria.

For a close-up look at mitochondria (plus chloroplasts and a nucleus), see the Virtual Cell. Select "mitochondrion" or "cristae" in the pull-down menu and click on the image. Keep clicking or use the buttons on the right to navigate through the cell. If you are having trouble, select "About Virtual Cell" for information on how to explore the site. Be prepared to answer some questions about the organization of mitochondria when you return, with special reference to where the electron transport chain is located.


The Endosymbiont Theory

Figure 12. Endosymbiosis. (Click to enlarge)  A typical eukaryotic cell contains a variety of organelles, some of which are of prokaryotic origin.

It is thought that mitochondria evolved from prokaryotes that inhabited the cells of other larger prokaryotes. This scenario likely originated as an endosymbiosis, in which one organism began living within the body of another. (This type of association is very common.) Put simply, it is thought that a relatively large prokaryote (a protoeukaryote) engulfed a smaller prokaryote (a protomitochondrion), and instead of the larger consuming the smaller, they formed an everlasting relationship. This engulfment would account for the existence of the inner membrane of mitochondria (the ancestral prokaryotic membrane) and the outer membrane. The symbiosis was mutualistic because it benefited both the protoeukaryote and the protomitochondrion; the protomitochondrion was provided with a safe environment and plenty of raw materials for respiration, and the protoeukaryote was provided with a rich, free supply of fuel in the form of ATP and some safety from the oxidizing power of O2; to be discussed in the next section.

Chloroplasts, which are found in eukaryotic photosynthetic cells, might also have originated from an ancient symbiosis. In the case of chloroplasts, however, the prokaryote was photosynthetic (probably an ancient cyanobacterium; discussed later in this tutorial). In this case, the ancestors to the modern cells that possess both mitochondria and chloroplasts, at some point in the past, underwent a serial endosymbiosis (sequential endosymbiotic events).


Evidence for the Endosymbiont Theory


Evidence for the endosymbiont theory is strong. Most convincingly, mitochondria closely resemble extant (currently existing) bacteria. Mitochondria are similar in size, and they replicate in a fashion that is very similar to binary fission. Also, the inner membrane of mitochondria bears a strong resemblance to the membranes of prokaryotes, sharing several key proteins and transport systems. Additionally, mitochondria have their own DNA (which takes the form of a circular plasmid, like that of prokaryotes) and they possess all of the cellular machinery required to transcribe and translate their genomes, thereby enabling them to produce their own proteins.

The character of mitochondrial DNA is much like that seen in modern-day prokaryotes. For example, mitochondrial DNA lack histones, which are associated with eukaryotic nuclear DNA but not with prokaryotic DNA. Additionally, mitochondrial ribosomes are more similar in behavior, structure, and nucleic acid base sequence to the ribosomes of prokaryotes than they are to eukaryotic ribosomes. For example, there is high sequence similarity between the ribosomal RNA of mitochondria and that of modern endosymbiotic bacteria.

The relationship between mitochondria and eukaryotes has grown so intimate that neither can exist without the other. Most mitochondrial genes are contained within the nucleus of their eukaryotic host cells, which makes mitochondria unable to reproduce and survive independently. Likewise, eukaryotes (e.g., humans) would be unable to manufacture enough ATP to sustain life without the help of mitochondria.


Selective Pressures Favoring Symbiosis

Sometime before 2.2-2.3 billion years ago, cyanobacteria (Figure 13) evolved the ability to use H2O and CO2 to make organic molecules with the help of solar energy, in a process known as photosynthesis. The primary "waste" product from this type of photosynthesis is O2, which began to accumulate in the atmosphere due to the activity of cyanobacteria. Other earlier forms of photosynthesis probably relied on H2S rather than H2O and did not result in the release of O2. For millions of years, cyanobacterial photosynthesis did not change the Earth's atmosphere; oxygen released by photosynthesizing mats of marine cyanobacteria combined with iron ions in the ocean, forming iron oxide that precipitated to the sea floor. When these iron ions were depleted, oxygen began to accumulate in seawater and eventually it diffused into the atmosphere.

Figure 13.   A Cyanobacteria.  This blue-green alga is one type of cyanobacteria.

Figure 14.  An Algal Bloom. (Click to enlarge)  This pond is located in San Francisco's Japanese Tea Garden in Golden Gate Park.

The change in atmospheric composition due to cyanobacteria was enormous, even more severe than the pollution associated with industrialized civilization. Oxygen is a powerful oxidizer, and its tendency to strip electrons and attack the bonds of organic molecules can be very dangerous to living organisms. The atmospheric changes effected by cyanobacteria probably resulted in numerous extinctions, but conversely, they also led to novel adaptations (e.g., the production of antioxidants). Furthermore, some organisms also evolved the ability to detoxify oxygen by reducing it with electrons from other molecules. Electron transport chains, such as the ones that exist in modern-day mitochondria, might have evolved as mechanisms for counteracting the destructive effects of O2, secondarily becoming a means of energy production over evolutionary time. The ancestors of eukaryotes might have gained an advantage in an oxygen-rich atmosphere by adopting endosymbionts to detoxify O2. The additional benefit that eukaryotes enjoy today, ATP synthesis, might be a derived function.


Eukaryotic cells are structurally more complex than prokaryotic cells, and this complexity is largely due to the appearance of discrete membrane-bound compartments in which various cellular processes are compartmentalized. In most prokaryotes, cellular processes occur within one compartment.

The available data indicate that two major evolutionary processes have contributed to the complexity of eukaryotic cells. First, it appears that the plasma membrane has undergone various modifications. These invaginations have resulted in complex intracellular compartments such as lysosomes, the endoplasmic reticulum, and golgi apparatuses. The majority of DNA is found within a membrane-bound nucleus. Second, the mitochondria seem to be of prokaryotic origin. There is compelling data to indicate that during the early evolution of eukaryotes, an intimate association occurred between a primitive prokaryote and a primitive eukaryote. This intracellular symbiosis became permanent over the course of time, and what exists today is a stable remnant of that ancient association.

Here is a quote by Lewis Thomas from his classic book of essays, The Lives of a Cell, which puts these facts in a provocative context:

A good case can be made for our nonexistence as entities. We are not made up, as we had always supposed, of successively enriched packets of our own parts. We are shared, rented, occupied. At the interior of our cells, driving them, providing the oxidative energy that sends us out for the improvement of each shining day, are the mitochondria, and in a strict sense, they are not ours. They turn out to be little separate creatures, the colonial posterity of migrant prokaryocytes, probably primitive bacteria that swam into ancestral precursors of our eukaryotic cells and stayed there. Ever since, they have maintained themselves and their ways, replicating in their own fashion, privately, with their own DNA and RNA quite different from ours. They are as much symbionts as the rhizobial bacteria in the roots of beans. Without them, we would not move a muscle, drum a finger, think a thought....




You should have a working knowledge of the following terms:

  • actin
  • cis face
  • cisterna (pl. cisternae)
  • cytoskeketon
  • endomembrane system
  • glycosylation
  • Golgi apparatus
  • hydrolytic enzyme (hydrolase)
  • intermediate filament
  • lysosome
  • microfilament
  • myosin fiber
  • nuclear pore
  • nucleolus
  • nucleus
  • organelle
  • rough endoplasmic reticulum
  • secretory vesicle
  • signal sequence
  • signal recognition particle (SRP)
  • smooth endoplasmic reticulum
  • trans face
  • turgor pressure
  • vacuole

Case Study for Subcellular Architecture of the Eukaryotic Cell

Hydrolases (also known as hydrolytic enzymes) are a general category of enzymes that have the
ability to hydrolyze (decompose by reacting with water) various substrates. These enzymes play
key roles in various types of catabolic reactions in cells and play a role in the development of
various genetic diseases.

Gangliosides are a class of modified lipids that contain carbohydrates. Gangliosides are a
prominent component of neuronal tissue, comprising about 6% of the total lipid content of the
brain. Although abundant, the neuronal cells regulate the accumulation of gangliosides in two
ways; first by controlling its production and second by breaking down excessive amounts using a
specific hydrolase (known as hexosaminidase A). Hexosaminidase A is a lysosomal enzyme that
breaks down gangliosides.

In humans, there is an alternative allele for the gene that encodes this hydrolase; homozygous
recessive individuals are afflicted with the genetic condition Tay - Sachs disease. The disease is
characterized by loss of motor skills beginning between three and six months of age with
progressive evidence of neurodegeneration, including seizures, blindness, and eventual death,
usually before four years of age. As a result of a founder effect, this disease is most common in
people of Ashkenazi Jewish descent.

  • Using the terms Endoplasmic Reticulum, Golgi body, lysosome, and Signal Recognition
    particle, describe the predicted pathway for the production of this hydrolase in an
    individual who has at least one dominant allele for the protein.
  • Would you expect homozygous recessive individuals to have more or less ganglioside in
    their neuronal tissue?

Now that you have read this tutorial and worked through the case study, go to ANGEL and take the tutorial quiz to test your understanding.  Questions?  Either send your instructor a message through ANGEL or attend instructor office hours (the times and places are posted on ANGEL).