Access Keys:
Skip to content (Access Key - 0)
Biology 110 - Basic Concepts and Biodiversity


Toggle Sidebar
Subcellular Architecture of the Eukaryotic Cell


You should have a working knowledge of the following terms:

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

Introduction and Goals

Cell division requires a great deal of protein synthesis and targeting. Now we will examine where these new proteins come from and how they are positioned. This tutorial will focus on the subcellular architecture of a eukaryotic cell and how the specialization of these structures helps cells carry out their normal functions. By the end of this tutorial you should have a basic working understanding of:

  • Subcellular organization in eukaryotic cells
  • Protein trafficking through the endomembrane system
  • The role of the cytoskeleton in cell structure and function

Introduction to the Subcellular Organization of Eukaryotic Cells

Eukaryotic cells contain a number of membrane-bound organelles. These structures play important roles in the normal functioning of cells. 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 the figure shown here.

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


The Nucleus

The nucleus 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 Major Roles of the Nucleus

The most notable function of the nucleus is to store the major source of 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. Once transcribed, messenger RNA exits the nucleus through nuclear pores in the nuclear envelope.

The Endomembrane System

There are many important steps in protein synthesis. Remember, you learned about protein translation in Tutorial 17. Most proteins require a number of post-translational modifications before they become functional. These modifications do not occur spontaneously and they require specialized cellular structures. Protein targeting and processing takes place in a network of membrane-bound chambers called the endomembrane system (depicted above). More specifically, the process begins in a network called the endoplasmic reticulum, which literally means "network within the cytoplasm." There are two types of endoplasmic reticulum 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 are synthesized.

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

Protein Targeting to the Rough Endoplasmic Reticulum

Proteins often 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. This figure illustrates the sorting process. If a translational complex (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 completed, 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 peptides 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. Take a look at the illustrated presentation at the Nobel Web page and when you return be prepared to answer a question on a disease caused by defective protein targeting.

The Golgi Apparatus Modifies Proteins

The Golgi apparatus is an 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 (depicted above). 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). Recall from Tutorial 19, 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 (shown here). 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 limp 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 (shown here), 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 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 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.

Molecular Motors and the Cytoskeleton

A molecular motor located at the kinetochore participates in chromosomal movement. Motors also exist in other locations. For example, the myosin fibers in muscle cells are molecular motors that drive muscle contractions. Other molecular motors are responsible for moving large vesicles, or even entire organelles, within a cell. Recent experimental evidence suggests that many of these molecular motors actually "walk" along cytoskeletal fibers. Visit the following Web site, click on the Quicktime movie under "Structural Analysis of Kinesin Motor Protein" to see a Walking Kinesin molecule, and come back prepared to answer a question about molecular motors.

Lysosomes and Vacuoles

Eukaryotes have a number of vesicular compartments that are used for a variety of purposes. One such compartment is the lysosome. 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 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)

Another organelle, the vacuole, has a variety of roles in cells. In most animal cells, vacuoles are primarily storage organelles. In plant cells they store a variety of compounds and are used to control the osmotic pressure (turgor pressure) of the cell.


In summary, you've learned that the subcellular architecture of a cell is highly specialized to ensure its well being. You have also learned how gene expression in the nucleus leads to protein synthesis and trafficking through the endomembrane system. Intracellular trafficking and cellular locomotion rely on the cytoskeleton, which works together with molecular motors to affect intracellular movement.


Added by Denise Woodward , last edited by Stephen Wade Schaeffer on Jun 10, 2009 11:05