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Cellular Organization


Properties of Matter: Introduction

Within biological systems, there exists a hierarchy of matter. Whether we look at organisms from the subatomic, atomic or the whole-body perspective, the structured organization of matter is apparent. The high degree of order within biological systems is a basic characteristic of life and is essential for the processes that support life. Understanding this order also provides a base from which to study cellular processes and functions of organisms.

The focus of this CELL is an investigation into the organization that exists within organs, tissues, and cells of animals and plants and into the functions that can be inferred from this organization. If we begin at the organism level, we soon see that an organism can be broken into a series of systems, into organs which comprise those systems, into tissues which comprise organs, and then cells which comprise tissues.

Further division is apparent when cells are examined and we see that each cell can be divided into separate components called organelles. This specific organization of structures within biological systems is often referred to as a hierarchal organization. Images from X-rays, CT, MRI scans, and scientific dissection have provided us with a window through which to understand and observe the hierarchal organization at the whole body, systems, and organ levels. However, it is the light and electron microscopes that have provided us a view of the foundations of organ, tissue, and cellular organization.

The advent of the microscope is generally attributed to the period around the 17th century with the discovery and early study of cells closely linked to its invention and subsequent improvements. One of the most important discoveries during this time was made by Robert Hooke. In 1665, he published his book Micrographia in which he described his observations with the compound microscope. Included in the book were detailed drawings and descriptions of organisms such as fleas and cork, and it was through his drawings and descriptions of the cork specimens that the world was first introduced to the concept of cells. Although what Hooke saw through his microscope were the cell walls of the cork plant, he used the term cells to describe his observations as the pores or spaces within the cork reminded him of cells in a monastery. This discovery and others helped establish a cellular biology research base for other scientists including Antoine van Leeuwenhoek, who was the first to observe and describe bacteria and protozoa with a simple microscope.

The microscopes that are used today are based on the same principles of refraction as those first used in the 17th century. In a microscope, visible light passes through a specimen and then a series of lenses. Because light travels at different speeds through different media (air versus glass, for example), the light rays are bent or refracted as they pass from the air through the lenses. In addition to the differences caused by the change in media, the angle at which light rays exit the lenses are also altered by the curvature of the lenses. The result is a magnification of the image of the specimen and enhanced resolution of the object.

Both magnification and resolution represent important parameters in the field of microscopy. In specific terms, magnification refers to the ratio of an object’s image to its real size. For example, a 10X lens is said to produce a ten-fold magnification of an object. That is, the image of the object will appear ten times larger than the actual object itself. Resolution, a measure of the clarity of the image, is often defined as the minimum distance between two points that can be separated and still distinguished as two separate points. The two are linked in that increases in magnification are often accompanied by increases in resolution.

It was a limit to the resolving power of light microscopes, however, that halted the study of the cell and cellular organelles until approximately 1950. Although Robert Hooke discovered cells in 1665, the resolution of light microscopy was such that light microscopy could never resolve details finer than approximately 0.2 microns, the size of a small bacterium. It was not until the invention of the electron microscope in the 1950’s that this boundary was broken. Electron microscopes that use a beam of electrons rather than light can produce a resolution of approximately 2 nanometers, a hundredfold improvement over the light microscope. The changes that followed the invention of the electron microscope represented significant advances in cell biology, including descriptions of cellular organelles such as the nucleus, mitochondria, endoplasmic reticulum, and subcellular organization of lipid, protein and carbohydrate molecules that compose cellular membranes.

As students begin their investigations within this CELL they will experience how the resolution of the light microscope affects the exploration of cells. Within the Investigations, they will view whole organisms such as the bacteria E.coli, sections from whole organisms such as onion, and Elodea, as well as sections from organs such as lung and large intestine. During the course of their investigations, they will see that while objectives with successively higher magnifications provide increasingly more detail of organ and whole organism specimens such as onion and large intestine, much of the detail of a single bacterium is unresolved. Despite this limitation, the resolution afforded by the various microscope objectives (lenses), will permit students to obtain an overall picture of the hierarchal organization of organisms, organs, tissues, and cells.

Students will see that the macroscopic structure of an organism or organ is based on the highly structured organization of cells. For example, when students observe prepared sections of human cheek or a wet mount of their own cheek cells, they should see that what appears and feels like a fairly solid, singular wall inside the cheek is instead composed of a sheet of cells, which under the appropriate conditions can be disassembled.


Cell Membranes and Osmosis

In addition to their descriptive work with cells and cellular structures, students will be asked to explore cellular function through microscopic examination and infer cellular processes and function through changes in cellular structures. This will be most apparent during students’ work in Investigation Four in which students study the process of osmosis in plant cells. Osmosis occurs because the cells of plants and animals are surrounded by a semi-permeable membrane which possesses properties that selectively allows or disallows certain substances to pass through it. The selectively of a cellular membrane can best be understood through an explanation of its structure.

Biological (cellular) membranes consist of a bilayer of molecules called phospholipids. Phospholipids are a unique class of lipids (fats) in that the top portion or head of a phospholipid consists of a charged or polar part, whereas the lower portion or tail is composed of relatively neutral or non-polar fatty acid molecules.

Cellular Intro 1

The difference between the charged and uncharged portions becomes apparent when the phospholipid is exposed to water. The charged head is attracted to the water, while the non-polar tail orients itself to have as little contact as possible with the water. Because of their attraction to water, the polar head groups are referred to as hydrophilic or “water-loving,” while the non-polar tails are called hydrophobic or “water-fearing.” Within the cellular environment, the reaction of the hydrophilic and hydrophobic portions of phospholipids results in the formation of a phospholipid bilayer which encloses on itself forming a sphere.

On the outside of the sphere are the hydrophilic head groups of the first layer of phospholipids. These hydrophilic head groups are in contact with the aqueous (water-based) extracellular fluid that surrounds cells. The tails of the phospholipids extend inward. These tails interact with the hydrophobic tails of the second layer of phospholipids, creating an environment that is nearly devoid of contact with the aqueous solutions of the extracellular and intracellular fluids. The hydrophilic heads of the second layer of phospholipids then extend into the middle of the sphere where they are also in contact with the aqueous solution of the cytoplasm.

Cellular Intro 2

Although this phospholipid bilayer is fairly fluid, the orientation of the lipids within the bilayer effectively limits the passage of most molecules through it. As a result the cytoplasm or internal environment of the cell is separated from its external environment. For biological organisms, this poses a potential problem as one of the underlying processes of chemical and biological organization is that solutes within solutions will diffuse so as to equalize their concentrations. 

Below is an animation of a cell membrane, showing its lipid bilayer structure. The pink balls represent the polar (hydrophilic) heads of the phospholipid molecules, while the hydrophobic tails are shown in red. Also, notice the proteins (blue) that are embedded in the membrane. Membrane proteins are very important for many cellular processes.

Within cells, the semi-permeability or selectivity of the phospholipid bilayer prevents the simple diffusion of most solutes but does allow the diffusion of water. The cell therefore often “uses” the diffusion of water to equalize the concentration of solutes on both sides of the cellular membrane. Take the following example: the solution outside a cell has a 10 % concentration of salt and the solution inside a cell has a 2% concentration of salt. Because of the impermeability of the membrane to salt, the salt would not be able to diffuse from the outside of the cell to the inside of the cell to equalize the concentration. However, water would be able to diffuse across this semipermeable cell membrane. In this situation, water would diffuse from the inside of the cell where it has a greater concentration to the outside of the cell where it has a lower concentration, in an effort to equalize the concentration of water and solute on both sides of the membrane. This diffusion of water across a selectively permeable (or semipermeable) membrane is called osmosis.

For students, investigating osmosis and its effects on cellular structures is an important first step to understanding the larger concepts of active and passive transport, homeostasis, electrochemical gradients, impulse generation in neurons, and many other cellular processes that will be studied in high school and beyond.

As an introduction to the cellular effects of osmosis, students will investigate the effect of changes in extracellular salt concentration on Elodea and onion cells and use these effects to better view two components of the cell, the cell membrane and cell wall. By adding an increasingly higher concentration of salt solutions to Elodea and onion specimens, students will promote the process of osmosis and observe changes in the cells’ structures as water diffuses out of the cell through the cell membrane and cell wall. As this occurs, the turgor pressure within the cytoplasm will decrease and the cell membrane will be pulled away from the cell wall. As a result, the boundaries between the cell membrane and the cell wall will be more easily visualized.

Through their investigations, students will begin to realize that the organization, hierarchy, and behavior of matter ultimately contributes to the functioning of a biological system such as a cell and that cellular processes are a consequence of the chemical and physical properties of countless molecules that interact in a controlled manner.


  • Fun Facts
  • Learn the Lingo
  • Get Focused


Fun Facts


Microscopes have contributed to the discovery of invaluable scientific information for research, medicine, and a whole host of industrial applications.

Microscopes also produce some of the most beautiful images in science, match perhaps only by Hubble space telescope images of distant galaxies and nebula. Look at some of the microscopic images below.


Brownian Motion

The image below shows a light microscope video of a red chalk dust in water. Notice how the individual particles seem to vibrate or jiggle in place. This motion was described by the nineteenth-century scientist Robert Brown and has since been referred to as Brownian Motion.

The cause and explanation of Brownian Motion awaited the twentieth-century and another scientist/mathematician, Albert Einstien. Einstein explained that the vibration of the dust particles was caused by the constant bombardment of the particles by trillions of invisibly small water molecules as they dart in solution with kinetic energy. For this reason, it is not surprising that increased temperature increases the amount of Brownian motion.

    Brownian Motion


COVID-19 Virus


Below is a negatively stained electron micrograph of the human COVID-19 virus. In areas around the virus particles that have sufficient stain, the protein coating on the virus surface are clearly visible. “Corona” means “crown” in Spanish. Thus, the name coronavirus comes from the crown-like image these pathogens (harmful microbes) form.



Electron Micrograph of COVID-19 Virus


An artist’s reconstruction of the COVID-19 virus particle is shown below.

Artist’s Model of COVID-19 Virus

In the model, the membrane proteins are indicated in red, orange, and yellow. The grey material represents a phospholipid membrane similar to the membrane discussed in the left section on this page. Interestingly, the membrane is thought to come from the host (human) cell membrane that was infected and killed by the viruses that multiplied inside of it.

Like most other lipids (fats), the virus membrane is soluble (dissolved) in soapy water. This is why handwashing with soap kills COVID-19. To read more about how soap and water destroy COVID-19, read this LabLearner Discussion.




The following list includes Key Terms that are introduced within the CELL. These terms should be used, as appropriate, by teachers and students during everyday classroom discourse.

Note: Additional words may be bolded within the Backgrounds. These words are not Key Terms and are strictly emphasized for exposure at this time.

Investigation 1:
  • There are no Key Terms introduced in Investigation 1.
Investigation 2:
  • Sectioning: a method of specimen preparation involving the way in which the specimen was cut. Two examples are longitudinal sectioning and cross sectioning.

Cellular Key Term

  • Staining: a method of specimen preparation involving a substance placed on the specimen to stain various parts of the cells to make them easier to observe
Investigation 3:
  • Organelle: a cellular structure which has a specific function, such as the nucleus
  • Nucleus: the cellular organelle that contains DNA and RNA and is responsible for controlling many of the activities of the cell
  • Cytoplasm: the substance which surrounds cellular organelles
  • Cell membrane: the outer border of the cell that separates the cytoplasm from the external environment surrounding the cell
  • Chloroplast: the cytoplasmic organelles present in plant cells and responsible for photosynthesis
  • Cell wall: the rigid and permeable cellular structure which surrounds the cell membrane in a plant cell
Investigation 4:
  • Diffusion: the process of substances moving from areas of high to low concentration
  • Osmosis: the diffusion of water across a selectively permeable membrane


The Focus Questions in each Investigation are designed to help teachers and students focus on the important concepts. By the end of the CELL, students should be able to answer the following questions:

Investigation 1:
  • Can you identify the type of organism a cell comes from through observation?
Investigation 2:
  • How does staining affect the appearance of a specimen? 
  • How does sectioning affect the appearance of a specimen? 
Investigation 3:
  • How are the structures in plant and animal cells similar to and different from each other? 
  • Are all cells from the same organism the same? 
Investigation 4:
  • Is the cell membrane of a plant cell permeable to salt? 

  • Are the cell wall and the cell membrane of a plant cell permeable to water? 

  • How does the structure of the cell wall and cell membrane affect the movement of substances in and out of a cell?