Best For | In-Class Time | Implementation Effort | Bloom's Taxonomy |
In this activity, students will synthesize the chapter learning objectives and broad concepts from Chapters 1-5 (Unit 1: Setting the Stage).
This activity is intended for in-class use after students have gone through the Unit 1 material (Chapters 1-5) and is designed to take place over 2 class sessions. If you would like to complete the activity in one class session, then include slide 51 (stopping point) and do not print the last page (Table 4) of the student handout.
If you would like to grade this activity, the student handout and the in-class response questions are designed for completion credit.
Chapter 1:
Chapter 2:
Chapter 3:
Chapter 4:
Chapter 5:
Review this activity guide. Download the instructor and student handouts and the activity PowerPoint file. Review the PowerPoint slides and the instructor handout, and make copies of the student handout (one copy per student in the class).
A polling software such as iClicker Cloud or Poll Everywhere is recommended to assess students' answers and/or participation. If using Poll Everywhere, you will need to add the Poll Everywhere information to the bottom of the slides with clicker questions. The slides with clicker questions are indicated.
Optional: to save on class time, can assign students into teams of 2-3 beforehand.
Since this activity is designed for students to synthesize the concepts from Chapters 1 through 5, can recommend students review the broad concepts from these chapters before class but there is not any formal pre-class preparation needed.
This activity integrates the use of the Unit 1 In-Class Activity Class Response Questions (PPT) with the student handout (The Fascinating World of Cells).
To save on class time, ask students to pick up the handout as they enter the classroom.
The instructor notes for the PowerPoint presentation can be found both in the slide deck and outlined below.
CLASS SESSION 1
The students will synthesize the broad concepts from Unit 1 (Chapters 1-5) using pathogenic virulence of Salmonella enterica in space as a case study. The key focus of this activity is to highlight the fascinating world of cells and the importance of having a strong knowledge foundation of biological molecules. The table on slide 2 is Table 1 on the student handout. The source of this information comes from: https://www.who.int/news/item/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed.
For your background knowledge, this is a helpful resource: https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance.
On slide 3, each section of text is animated. The referenced paper is Wilson et al. Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16299-304. Background figure of International Space Station from NASA: https://www.nasa.gov/international-space-station/space-station-facts-and-figures/
Give students 1-2 minutes to submit their answer. The answer slide (slide 5) is hidden - will need to unhide it when presenting. The explanation is animated so that it appears on mouse click.
Key terms students need to know are “autotrophs”, “photoautotrophs”, and “heterotrophs” . These are found in Module 5.1, Lesson 1.
Point out to students that the WHO table of high priority bacteria is organized by whether bacteria are Gram (+) or Gram (-). Bring to their attention that Salmonella is a Gram (-) bacteria.
Introduction to the bacterial cell envelope (segue to reviewing lipids and cell membranes). The second section of text is animated to appear along with the image of the cell with its cell membrane labeled when mouse is clicked.
Give students 2-3 minutes to submit their answer. The answer slide (slide 9) is hidden - will need to unhide it when presenting.
This image is adapted from Figure 4.24D and is a good review of the properties of cell membranes.
Give students 1-2 minutes to submit their answer. The answer slide (slide 12) is hidden - will need to unhide it when presenting. The explanation is animated so that it appears on mouse click.
Give students 1-2 minutes to submit their answer. The answer slide (slide 14) is hidden - will need to unhide it when presenting. The explanation is animated so that it appears on mouse click.
Key term students need to know is “hydrocarbon”. This is found in Module 4.1, Lesson 2.
Continued introduction to the bacterial cell envelope. Figure adapted from: Kapoor G, Saigal S, and Elongavan A. J Anaesthesiol Clin Pharmacol. 2017 Jul-Sep; 33(3): 300–305.
A brief description of peptidoglycan, one of the major components of the bacterial cell wall. This is included so that students can understand how Gram staining works. For additional background information regarding peptidoglycan and bacterial cell walls: https://open.oregonstate.education/generalmicrobiology/chapter/bacteria-cell-walls/.
A brief description of how Gram staining works. Figure adapted from: Kapoor G, Saigal S, and Elongavan A. J Anaesthesiol Clin Pharmacol. 2017 Jul-Sep; 33(3): 300–305.
Students will need a writing utensil (pen or pencil) to fill in Table 2 of the handout in student teams.
The answer slide is hidden - will need to unhide it when presenting.
Optional slide that can be used to briefly review the major components of a cell membrane and the structure of a phospholipid (Chapter 4).
The answer slide is hidden - will need to unhide it when presenting. Transmembrane channels are proteins (polypeptides) and so they are made from amino acids.
Optional slide that can be used to briefly review the major components of an amino acid and the chemical properties of the 20 amino acids (Chapter 2).
The answer slide is hidden - will need to unhide it when presenting.
Lipopolysaccharides (LPSs) have a lipid domain (lipo- part of their name) covalently attached to carbohydrate groups (where polysaccharide part of their name comes from). In humans, LPSs typically act as bacterial toxins and trigger the immune response in a bacterial infection.
Optional slide that can be used to briefly review carbohydrate structure (Chapter 2).
This is an optional slide that can be used if students are interested in knowing what is a lipopolysaccharide. Figure adapted from: Bidne KL, Dickson MJ, Ross JW, Baumgard LH, Keating AF. Disruption of female reproductive function by endotoxins. Reproduction. 2018 Apr;155(4):R169-R181.
The answer slide is hidden - will need to unhide it when presenting.
Optional slide that serves as a reminder of peptidoglycan structure, one of the major components of the bacterial cell wall.
SLIDE 32: Student Handout - The Fascinating World of Cells: 5-7 minutes
Students will need a writing utensil (pen or pencil) to fill in this part of the handout.
The carbohydrate monomers are molecules of glucose. The answers are animated and appear sequentially with each mouse click.
Optional slide that can be used to briefly review glycosidic bond formation (Chapter 2).
The answers are animated and appear sequentially with each mouse click.
Optional slide that can be used to briefly review peptide bond formation (Chapter 2).
The nucleotide monomers are a molecule of adenosine monophosphate (top) and cytidine monophosphate (bottom). The answers are animated and appear sequentially with each mouse click.
Optional slide that can be used to briefly review nucleotide structure and phosphodiester bond formation (Chapter 2).
Students will need a writing utensil (pen or pencil) to fill in Table 3 of the handout.
The answer slides are hidden - will need to unhide them when presenting.
Give students 1-2 minutes to submit their answer to the clicker question. The answer slide (slide 45) is hidden - will need to unhide it when presenting. The question “Why might this be the case?” on slide 45 is animated and will appear upon mouse click. If you have advanced students, can consider asking them to provide a reason for their prediction before going over slides 46-49 (in which case you’ll need a few more minutes for this slide).
These slides provide some reasons for why antibiotic resistance occurs more commonly in Gram (-) bacteria.
Figure from paper: Miller SI. Antibiotic Resistance and Regulation of the Gram-Negative Bacterial Outer Membrane Barrier by Host Innate Immune Molecules. mBio. 2016 Sep 27;7(5):e01541-16.
This activity is designed to take place across two class sessions - this is about the halfway point where you should pause until the next session. If you would like to complete the activity in one class session, then the next slide can be unhidden and used to end the activity.
If you would like to complete the activity in one class session, then unhide this slide when presenting as a way to end the activity. This is the headline of the PNAS paper that served as inspiration for this case study. The second segment of text is animated to appear on mouse click. Hopefully this activity has given students an appreciation of the fascinating world of cells and the importance of having a strong knowledge foundation of biological molecules.
CLASS SESSION 2
Some additional resources on microarrays: https://www.nature.com/scitable/definition/microarray-202/
https://microbenotes.com/dna-microarray/
https://www.genome.gov/about-genomics/fact-sheets/DNA-Microarray-Technology
Samuel D Conzone, Carlo G Pantano. (2004) “Glass slides to DNA microarrays”, Materials Today, 7(3), 20-26. (https://www.sciencedirect.com/science/article/pii/S1369702104001221)
Experiment comes from this paper: Wilson JW et al. (2007) PNAS, 104(41), 16299-16304. https://doi.org/10.1073/pnas.07071551
Brief description of microarray results. The text is animated so that each segment appears on mouse click.
Give students 1-2 minutes to submit their answer to the clicker question. The answer slide (slide 60) is hidden - will need to unhide it when presenting.
Give students 1-2 minutes to submit their answer to the clicker question. The answer slide (slide 62) is hidden - will need to unhide it when presenting.
Give students 1-2 minutes to submit their answer to the clicker question. The answer slide (slide 64) is hidden - will need to unhide it when presenting.
Give students 2-3 minutes to discuss the question in their student teams. Students might give a variety of answers. Guide them accordingly. The reason this is important is because there is not necessarily a 1:1 correlation between mRNA and protein levels.
Give students 1-2 minutes to submit their answer to the clicker question. The answer slide (slide 67) is hidden - will need to unhide it when presenting. Figure is from PDB ID: 2YLC, adapted from Figure 2A of Sauer E, Weichenrieder O. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13065-70.
Optional slide that can be used to briefly review the different levels of protein structure (Chapter 3).
Give students 1-2 minutes to submit their answer to the clicker question. The answer slide (slide 70) is hidden - will need to unhide it when presenting. The explanation is animated so that it appears on mouse click. Data comes from this paper: Sauer, E., Weichenrieder, O. (2011) Proc Natl Acad Sci U S A 108: 13065.
Optional slide that can be used to briefly review the differences between RNA and DNA (Chapter 2).
Give students 2-3 minutes to submit their answer to the clicker question. The answer slide (slide 73) is hidden - will need to unhide it when presenting. The explanation is animated so that it appears on mouse click.
PDB ID: 2YLC adapted from Figure 2B of Sauer E, Weichenrieder O. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13065-70.
Students will need a writing utensil (pen or pencil) to fill in Table 4 of the handout (in their same student teams).
On slide 74, the text is animated so that each segment appears on mouse click.
This slide is hidden - will need to unhide it when presenting. For 1a - 1d, if the resulting protein of the target mRNA of protein X has no effect on Salmonella virulence, then the changes in protein X gene expression in space will have no effect on Salmonella virulence.
This slide is hidden - will need to unhide it when presenting. For 2a and 2b, it is straightforward to understand the predicted effect on Salmonella virulence. When you increase one, the other increases and vice versa when you decrease one, the other decreases.
This slide is hidden - will need to unhide it when presenting. For 2c, the effect of increased protein X expression in space is an increase in the degradation of an mRNA that when translated increases virulence. Increasing the degradation of something that increases virulence results in decreased levels of virulence. For 2d, the effect of decreased protein X expression in space is a decrease in the degradation of an mRNA that when translated increases virulence. Decreasing the degradation of something that increases virulence results in increased levels of virulence.
This slide is hidden - will need to unhide it when presenting. For 3a, the effect of increased protein X expression in space is an increase in the translation of an mRNA that when translated decreases virulence. Increasing the translation of something that decreases virulence results in decreased levels of virulence. For 3b, the effect of decreased protein X expression in space is a decrease in the translation of an mRNA that when translated decreases virulence. Decreasing the translation of something that decreases virulence results in increased levels of virulence.
This slide is hidden - will need to unhide it when presenting. For 3c, the effect of increased protein X expression in space is an increase in the degradation of an mRNA that when translated decreases virulence. Increasing the degradation of something that decreases virulence results in increased levels of virulence. For 3d, the effect of decreased protein X expression in space is a decrease in the degradation of an mRNA that when translated decreases virulence. Decreasing the degradation of something that decreases virulence results in decreased levels of virulence.
These are slides to wrap up the activity. On slide 82, this is the headline of the PNAS paper that served as inspiration for this case study (Wilson et al. 2007). The second segment of text is animated to appear on mouse click. Hopefully this activity has given students an appreciation of the fascinating world of cells and the importance of having a strong knowledge foundation of biological molecules!
None