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.

Keeping an Organized Dorm Room Requires Energy, Just Like in a Cell

Written by Jennifer A. Metzler, Ball State University

When discussing thermodynamics and why cells do not break the laws because they are so organized, even though entropy is always increasing, I ask them to think of the place where they live, whether a dorm room, apartment, or house. Then I ask them to think of the difference between keeping it clean and organized or letting it become messy and disorganized. I ask them how much energy it takes for them to keep things clean and organized versus messy and disorganized. They all answer more energy to maintain order. So, then I discuss how cells are no different, if they want to maintain order they must constantly take in energy, and when they stop doing so they die and lose their order. Also, mentioning that they maintain the ever increasing entropy by giving off heat.

Satellite TV and Photosystems

Written by Jennifer A. Metzler, Ball State University

When discussing how a photosystem works to capture light energy, I ask students to compare it to a satellite TV dish. The job of the dish is to capture and focus the TV signal so they can watch their favorite show. The job of the antenna complexes is to capture the light energy and then pass that energy (focusing) to the reaction center so that light energy can be passed on in the form of excited electrons to begin converting the light energy into chemical energy in the first stage of photosynthesis.

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.

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