Using Analogies in Microbiology: The Bacterial Cell as an Entertainment Venue to Illustrate the ATP-binding Cassette (ABC) Transport System

Written by Kristen Z. Swider, Capital Community College

Students in my microbiology class are relatively unfamiliar with the scientific concepts involved in the course and will often attempt to rely on memorization. However, due to the complex nature of the material, it is difficult to access information from the perspective of pure recall. As abstract concepts are discussed throughout a science course, many learners still operating in the concrete stage of development may be lost by a failure to attach understanding to anything of substance. As a result, the concepts are often missed during examinations. There is no requirement that an instructor complicate the approach in order to communicate scientific principles. For these reasons, the use of analogies to illustrate complex processes can enhance a student’s comprehension of the material and make connections that promote lifelong learning. Analogies may be presented to the learner as prepared elements of a lecture or they may be generated by the learners themselves. Self-generated analogies can and do occur spontaneously in discussion. Students are encouraged to develop and present analogies to the class. In either case, the interactive, social process of exploring analogies, whatever their source, contributes to the learning process.

How the ATP-binding Cassette (ABC) Transport System Works

– ATP-binding cassette (ABC) system: This involves substrate-specific binding proteins located in the bacterial periplasm, the gel-like substance between the bacterial cell wall and cytoplasmic membrane.

– The periplasmic-binding protein attaches temporarily to the substance to be transported and carries it to

– Meanwhile, ATP gets broken down into ADP, and phosphate, releasing energy. It is this energy that powers the transport of the substrate, by way of the membrane-binding transporter, across the membrane and into the cytoplasm.

– Examples of active transport by means of ABC systems include the transport of certain sugars and amino acids. There are hundreds of different ABC transport systems in bacteria.

ANALOGY:

The Bacterial Cell as an Entertainment Venue to Illustrate the ATP-Binding Cassette (ABC) Transport System

The players:

Bacterial cell: Entertainment Venue

Substrate: Patron

Periplasm: Outer arena area

Substrate-specific binding protein: Event ticket

Cytoplasmic membrane: Inner arena barrier with turnstiles

Membrane-spanning transport protein: Turnstile

Cytoplasm: Event location (inner arena)

ATP: energy needed to move the turn-stile and allow entry of the substrate (Patron)

– The bacterial cell is the entertainment venue, with the cell wall being the outer boundary of the arena property. Once the patron reaches the arena, he/she can easily migrate through the cell wall to the inner arena (periplasm) since a “ticket” is not yet needed.

– In order for the patron to gain entry into the main arena area of the venue (cytoplasm), he/she must pick up a ticket at a will call/box office. Here in the periplasm, a patron will pick up a pre-prepared ticket (periplasmic binding protein) just before the entering the event.

– Before entering the main arena area, the patron with the ticket (transportable substance and periplasmic binding protein complex) must enter the arena through the turnstile (membrane-spanning transport protein). A turnstile is a form of gate which allows one person to pass at a time. A turnstile can restrict passage only to patrons who provide a coin or a ticket. It can also be made so as to enforce one-way traffic of people.

– Once at the turnstile, the ticket (periplasmic binding protein) gets left behind, and the transportable substrate (patron) can enter the cell via a turnstile.

– As the substrate (patron) moves through the turnstile, energy is required, and ATP is broken down. The patron (substrate) is now in the arena and can be used by the cell.

The Genome as the Harry Potter Series

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

The genetic code is often described as being analogous to the written language. I expand this analogy to help students understand the hierarchy that exists in genetics, since I find many students don’t understand the relationship between a gene and a chromosome. Imagine a set of books, perhaps the Harry Potter series. The entire series on the shelf is analogous to the genome. Each book can be thought of as a chromosome. Within each book are chapters, these can be thought of as genes. Lastly, the 26 letters of the alphabet are arranged to make the variation of words within the genes. The genetic code has 4 letters to make unique arrangements/sequences. What would be the consequence if a few sentences or a chapter or an entire book was lost from the series? Would the story still make sense? (This would be analogous to mutations and chromosomal abnormalities.)

Pairs of Shoes and Pairs of Chromosomes

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

When discussing homologous chromosomes and sister chromatids, I often use analogies to shoes or socks. For example, I may have two pairs of the same cute flats, one pair in yellow and one in turquoise. These flats are the same size, same brand, exact same style. The yellow shoes are like sister chromatids to each other, just as the turquoise shoes are sister chomatids with each other. The yellow and turquoise are like homologs to each other. To carry the analogy further, I ask them what a pair of running sneakers might be analogous to. (These would be a completely different chromosome.)

Losing Control of a Car Relates to Unregulated Cell Division

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

When discussing the cell cycle and cancer causing genes, I often use an analogy to cars. There are two ways to lose control of a car: the gas pedal can get stuck down or the brakes will not work when engaged. In either case, the car speeds along without driver control. In this anology, tumor supressors are like brakes, which normally prevent the cell cycle from losing control (preventing cancer). When mutated, the brakes are lost and the cell divides out of control. Proto-oncogenes are like the gas pedal, in that they promote cell division. When mutated, like a gas pedal stuck down, they cause unregulated cell division.

Babysitting Gives Students Experience with Interspecific Competition

Written by Kelly A. Hogan, University of North Carolina at Chapel Hill

When discussing interspecific competition I always get students to think about a sitiation in which they are babysitting two kids. I make up different scenarios to illustrate ideas of competition. For example, I might tell them that there are two brothers (age 8 and 4) and only one remote control for the video game. What do they predict would happen with the brothers? If the big brother pushes the little brother out of the way and takes the control for himself, I explain Gause’s competitive exclusion principle. If I ask them what they might suggest as the babysitter, and they usually come to the conclusion quickly that the boys must share the remote. The little brother may “adapt” to his big brother by using it only when the big brother goes to eat a snack. Sharing the remote, illustrates resource partitioning as a way of differentiating niches, in this case temporal differentiation.

Using Waves at the Beach to Describe Concentration Gradients

Written by Jennifer A. Metzler, Ball State University

When discussing passive versus active transport and the difference between an input of cellular energy, I ask students to imagine they are at the beach or at a wave pool. Since passive transport is going down a concentration gradient, I tell them to liken it to having the waves at their back and moving into shore. It is not a problem for them at all and they do not need to expend any energy as they are going with the flow. With active transport going against the concentration gradient, I tell them to imagine turning around and having the waves hit their chest and try to move away from shore. In this case they must expend energy as they are going against the flow of the waves.

Dance Club Patrons Describe Water Molecules

Written by Dave Sheldon, St. Clair County Community College

I approach the changing density of H2O by having students imagine a high energy dance club. They imagine the loudest and most energetic night club that they can, and describe it in detail. They focus on the intense energy, the motion of the people and the number of people on the dance floor. I include some techno music to get them thinking! Once focused on the high energy and rapid motion of the patrons, I modify the scenario. First I drastically reduce the energy by cutting the music, killing the strobes and bringing up the house lights. My students describe a ringing of ears and a much slower movement by the club patrons. Second, I describe every person as an H2O molecule with their arms outstretched in front of them at a 90° angle. Their hands represent two Hydrogen atoms and the middle of their back represents their Oxygen atom. Hydrogen bonding causes them to place their hands on the backs of two other people while two more people place one of each of their hands on your back. With low energy in the club, these bonds last for a relatively long time and the water molecules form a low density crystalline lattice. The people on the dance floor during the high energy rave would no longer fit in this low energy orientation. Some even note that they may actually be forced out of the club through windows and doors, which is what happens when water freezes.

Customize Your Auto Like Proteins Are Customized in the Cell

Written by Dave Sheldon, St. Clair County Community College

When discussing the function of the Golgi apparatus, I ask my students to picture a friend, two identical automobiles and an automotive customization shop. I ask them if they and their friend purchased 2 identical cars (same color, make model etc.), would it be possible to customize or detail them in a way that would result in two totally different appearing and performing cars? The answer always comes back “yes” and we discuss ways to modify an automobile. Ground effects, spoilers, window tinting, sound systems, paint jobs and fancy rims are usually mentioned. The car in this analogy represents a newly formed protein that has just been sent via a transport vesicle from the rough endoplasmic reticulum (auto dealership) to the Golgi apparatus (detailing shop). They imaginary car pulls into the receiving or Cis side of the shop and leaves via the shipping or Trans side of the shop. While in the Golgi detailing shop, the modifications represent chemical reactions such as phosphorylation, glycosolation and manipulation of the size of the polypeptide chain.

Aerobic Respiration Gives a Cell More “Spending Power”

Written by Jennifer Wiatrowski, Pasco-Hernando Community College

Relating the value of aerobic respiration to the real world. The students in introductory biology have very little interest in cellular respiration. But, I want them to understand that there is greater value (in terms of ATP yield) between aerobic and anaerobic respiration (like with exercise). So, I relate the processes to “dollars in your pocket” and “spending power at a fancy restaurant.” Anaerobic processes give your 2 ATP or 2 dollars in your pocket. Could this buy you anything at a fancy restaurant? No! This is not a lot of spending power. If you complete aerobic respiration, you have approximately 38 ATP or dollars in your pocket. Could this buy you something at a fancy restaurant? Yes! Now, you have spending power.