Biology by the Math Mom: 2018

Sunday, December 16, 2018

"Urine" Control (AKA Water Regulation in Honors Bio)

This year I'm teaching Honors Biology at my school in addition to AP Biology. This is a brand new course and I've been given great freedom to design this class as I'd like. The only requirement was that the students are able to take and pass the Living Environment regents exam at the end of the year. My school also wanted me to come up with a name for the class since they didn't just want to call it Honors Bio. I thought about what I'd like students to do and in the end called it Analytical Biology. That proved to be a little intimidating, so we had to convince a few nervous students that it would be a doable class.

Recently in class, we have been working on the concept of water regulation. I wanted students to have practice analyzing how our excretory system handles the water and salt balance beyond just the required osmosis in onion cells required lab. I started a google search to see if there was anything out there appropriate for the class and came across this A&P lab by Cynthia Surmacz. The first part of the lab was beyond the scope of this class, but the end of the document included a dry lab. This dry lab provided students with data from an experiment that required students to analyze to determine which group drank which solutions.

I loved how this lab worked out for several reasons. The first was the graphing practice. Students were given data collected every 30 minutes from time 0 to 90 minutes. They had to graph specific gravity of urine, salt content, and volume. This lead to great discussions of how to decide the scale of a graph. We talked about the technique of determining the range of the data, then starting the y-axis at the lowest rounded value, putting the highest rounded value at the top of the graph and dividing the spaces in between evenly. This also lead to discussions of the goal of having your data fill at least 75% of the graph as opposed to squishing all of the data points in one-fourth of the graph.

I also loved hearing the students debating which group drank which solution. They had to make a table of which group drank which solution and support the decision with evidence. I think the students did fabulous thinking and it made the job that our kidneys do a little more real to the kids.

I separated out the dry lab part of the document and added instructions for my students, so they knew what I expected to be on their posters. Here is the link to that document.

Sunday, November 4, 2018

Visualizing The Calvin Cycle

3 RuBPs each ready to have a carbon fixed to them

Even in my fourth year of teaching the new AP Biology curriculum, I'm still tweaking the class to help my students have a deeper understanding of the concepts. We are just finishing up our energetics unit. I've blogged here about the diagrams we work through as a class for cellular respiration and here for photosynthesis.

Rubisco doing its job of carbon fixation

Last year I found this youtube video of Kevin Lam explaining the Calvin cycle. I find the kids often struggle with the Calvin cycle since 3 of the cycles are actually happening together to get one G3P (which we call a baby sugar). I loved the visual way this video showed carbon fixation and the process of rearranging molecules to recycle RuBP.

Molecules are split and ready for ATP and high energy electrons

I was all set to buy styrofoam balls to do this and then started wondering if I could do this demonstration without lots of styrofoam. I keep a large supply of tennis balls that we use to represent protons in oxidative phosphorylation for both photosynthesis and respiration. I also happened to have a partial box of dominoes and several adhesive Velcro dots. I decided our tennis balls could do double duty and be carbon molecules for the Calvin Cycle and the dominoes could represent the bonds between them.

One G3P (baby sugar) is ready to leave

What I didn't show was the phosphates added to the molecules from ATP (although we did talk about it) or the high energy electrons used in the bonds (again just talking about it), but maybe next year we'll add those in.

The process of recycling RuBP begins

One student was rubisco and fixed the carbon from carbon dioxide to RuBP, another student was the enzyme to split the molecules into 3 carbon molecules, and anther acted as the enzymes to help recycle the remaining molecules back into RuBP.

and keeps going

and going, until...

all three RuBPs are recycled and ready to go again.

Friday, September 21, 2018

Forming Lab Groups in AP Bio

Unit 1: Biochemistry

The first year I returned to the AP Biology classroom, my school sent me to an AP Bio training in our area hosted by the College Board. As the attendees walked into the room, each of us took an index card with a biology concept word on it. Each table had another card on it. We quickly figured out that the card in our hand correlated with a certain table.

Unit 2: Cells

By that time in the year (it was January), I realized that although most students liked choosing their own lab partners, some struggled to figure out who to go with. I hate that feeling and hate to have students have to experience every time we do another lab. I decided that I was going to use this card method to divide my students into lab groups to prevent this and to get them looking at some of the vocabulary.

Unit 3: Metabolism

Last year I asked my students to take a survey on the first day of class to help me get to know them better. One of the questions I asked was if they would rather choose their own lab partners or have me choose them. 7 out of 10 (yes, I have small classes) said they'd rather I choose their lab partners. I happily used this card method with this class all year, and it worked fairly well the whole time.

Unit 4&5: Cell Cycle and Mendelian Genetics

I've been pretty low tech with this, so all of the cards are index cards that I have handwritten. The colored cards are the ones on the tables and the white cards are the ones that students randomly choose from my hand that they have to match with the table card. I have a different set for each unit we do. At the end of the year last year, I knew the class was growing to at least 15, so I added some cards to the collection.

Unit 6: Molecular Genetics

This year I am also teaching Honors Biology to 8th and 9th graders. I haven't made cards like this for them, but I did start using playing cards to divide them into lab groups. The fun thing with playing cards is using the joker as a wild card--so one or two kids get to chose a group to join. What surprised me was their reactions the first day I used them. As I stood by the door holding the cards, many of them commented that they saw me having AP Bio students picking cards last year and wondered when I would do the same for them.

Unit 7: Evolution

Unit 8: Plants

Unit 9: Ecology

Unit 10: Humans

Monday, August 20, 2018

Golden Nuggets

This summer I had the opportunity to attend the NABT/BSCS Biology Teacher Academy in Connecticut. It was a week long professional development tailored to Biology teachers.

At the end of the week, we stood in a circle and shared a "golden nugget" that we gleaned from the week of training. (And also took a golden nugget of chocolate. =) I shared the first thing that came to my mind, which was the most recent "ah-ha" moment for me. We spent a good portion of our time talking about and practicing formative assessment techniques and their purpose. I always thought of formative assessment as a way for me to see how my students' understanding was forming. It allowed me to see where they were and where they needed to go. I could then chose activities in class to address those issues. The epiphany for me was that the whole purpose of formative assessment is to know how to form my teaching to student understandings. I kind of did that already without realizing it, but now I can be deliberate about it and I have that focus in mind from the outset.

Afterward, I looked through my participant binder and was reminded of several other "golden nuggets" from the week.

One of the first labs we worked through (always to teach us methodologies to use with students), was the algae bead lab. I had heard about it and was excited to see it in action. I love it. I still have a micro-centrifuge tube with three beads and indicator in it and am tickled to see the liquid cycle between yellow and purple. One of the things I love about this lab is that it allows students to see that these organisms don't just go through photosynthesis, but also cellular respiration. After our experimenting, we practiced using the explanation tool to help prepare students to complete a CER (claim, evidence, and reasoning). I tried to implement this in AP Bio last year a little, but was glad to see it in action.

Another idea that jumped out at me was this statement when we were looking at how students learn, "Abandon the model of the learner as an empty vessel to be filled with knowledge..." It was a great reminder that our students come to us with heads full of ideas and we need to shape, add to, correct those ideas for them to really understand the concepts.

We looked at the I-squared strategy for helping students analyze graphs. I can't wait to use this in class--and then I'll have to blog about it.

Another golden nugget was connections made with fabulous facilitators as well as with the other attendees of the academy.

Thursday, July 19, 2018

Links to Guided Reading Questions for Biology in Focus 2nd Edition in One Document

So, I finally got to putting all of the links to the guided reading questions for Biology in Focus 2nd Edition into one document! I put this on my website for my students to have easy access to all of the guides at once--even though they have chapter by chapter access on Google Classroom.

This summer, I've been busily writing the answer keys for the guides and revising each of the guides as I go. Mainly it's been changing question numbers. I've also rearranged a few questions to go with the flow of the book, and deleted a couple that ended up in the wrong chapter. I try to keep the questions to a minimum and just focus on the most important concepts for the course, so they are not too overwhelming for my students to tackle.

One thing I also did in this document is put five of the chapters in red. I am working on getting dual credit for my students in this class and needed to add 5 chapters that I don't typically cover in AP Bio. The red chapters don't need to be done to get to all of the essential knowledge statements, just need to be done for the dual credit I'm looking for.

Here it is!

Guided Reading and Videos (BIF 2nd Edition)

Saturday, June 23, 2018

Biology in Focus 2nd Edition Reading Guides and Videos

Next year, we are switching from Campbell's Biology 8th Edition to Biology in Focus 2nd Edition (BIF). The guided reading questions that I've been using (and blogged about here) were an edited version of the Holtzclaws' reading guides for Campbell's 8th edition. I used the Holtzclaws' AP Biology Review book to help me to know what questions to eliminate to shorten the reading guides so that they were only asking questions that were key to helping students understand content important for the AP Biology curriculum.

For many of the chapters, I just needed to change chapter and section numbers to adjust the guide for BIF. Other chapters combined the content of 2 Campbell chapters, so that took a little more work. Occasionally one section was moved from one chapter to another. I've been feverishly working on updating these for the entire book since I wanted to print hard copies for each chapter before I checked out of my classroom for the summer, so I can work on making keys for each of them while I'm home on summer "break." I'll include links to each of them here. I do imagine that I'll need to do some revision as I go through each of the guides this summer and fortunately they will show up automatically in the links.

Unit 8: Plants

Plant Form and Function

Chapters 28-31 Questions

Plant Control (Bozeman)

Unit 9: Ecology

Motor Mechanisms and Animal Behavior

Chapter 39 Questions

Tinbergen's Experiment

Population Ecology and the Distribution of Organisms

Chapter 40 Questions

Population Ecology: The Texas Mosquito Mystery (Crash Course)

Human Population Growth (Crash Course)

Species Interactions

Chapter 41 Questions

Community Ecology: Feel the Love (Crash Course)

Ecological Succession: Change is Good (Crash Course)

Ecosystems and Energy

Chapter 42 Questions

Ecosystem Ecology (Crash Course)

The Water and Carbon Cycle (Crash Course)

The Nitrogen and Phosphorus Cycles (Crash Course)

Global Ecology and Conservation Biology

Chapter 43 Questions

5 Human Impacts on the Environment (Crash Course)

Conservation and Restoration Ecology (Crash Course)

Unit 10: Human Form and Function

The Internal Environment of Animals: Organization and Regulation

Chapter 32 Questions

Positive and Negative Feedback Loops (Bozeman)

Great Glands: Your Endocrine System (Crash Course)

The Immune System

Chapter 35 Questions

Your Immune System: Natural Born Killer (Crash Course)

Reproduction and Development

Chapter 36 Questions

The Reproductive System (Bozeman)

Neurons, Synapses, and Signaling

Chapter 37 Question

Nervous and Sensory Systems

Chapter 38 Questions

The Nervous System (Crash Course)

Friday, May 25, 2018

Design Challenges in Physical Science

Teaching Physical Science in a classroom setting was new for me this year. (And the reason for so few blog posts this year.) Since I was building this course from scratch, I decided to try to design it according to the NGSS. New York put out a draft of their modified NGSS that guided me through class planning. Science and Engineering Practices is one of the key components of the NGSS and by the second half of the year, I finally started using some labs that were open-ended design challenges.

I don't teach this class at the same school I teach AP Biology. This class is at a non-traditional Consortium, where I only see my students once a week for 90 minutes (and then they do the rest of the learning at home) and there is an age range of students from 6th-8th grade. This is the first year that I've taught a class with 6th graders. The two years before, I taught Advanced Life Science at this Consortium for 7th-9th graders. I figured that 6th-8th wouldn't be much different, but it was a completely different dynamic! This class did not work as independently as I was used to classes doing. But, when I gave them design challenges, they took them on with enthusiasm and hardly needed redirection. They did four challenges in the second semester. For most, they had a full 80 minutes to work on the design.

When we neared the end of our unit on forces and interactions, student groups completed the egg drop challenge, that I blogged about here. They each received a bag of the same items and had to choose a design for their egg holder. They were allowed to trade with other groups if both groups agreed to it and they had a scoring scale to also help them as they decided what and how much of it to use. They wanted the lowest score possible which was determined by mass of apparatus, number of seconds it took to load the apparatus, the number of items in the apparatus. In the end, three out of seven of the groups dropped their eggs without breaking them.

When we started the unit on energy, students built a Rube Goldberg machine to complete a chosen task, utilizing the maximum number of simple machines. In this challenge students tried to maximize their points. I brought in a collection of dominoes (including a standard set and two wooden sets of large dominoes), two sets of Legos from the Crazy Action Contraptions book plus several more pieces from my kids' Legos, yarn, marbles, cardboard boxes, toilet paper and paper towel tubes, and a roll of masking tape.

The next week, we moved onto building marble roller coasters (that I blogged about here) with lengths of pipe insulation cut in half. They had some parameters to follow--number of loops, turns, and hills. We also used their finished roller coasters to practice finding the average speed of the marble in the coaster.

We finished off the unit with a heat challenge. Students were given their choice of several items and tasked with designing an insulating box for a paper cup that would hold the heat of water as well as or better than a Styrofoam cup. I originally saw this idea in the Carolina Biological catalog. In fact they have several kits to use as design challenges in physical science--they're a great resource. I did some googling and used several sources to put together this challenge. (I would have been tempted to just buy the Carolina kit, but it was for a much larger class than I had.)

I'll include links to each of the challenge directions that I gave each group, the lab sheets that I gave them to complete an glue into their notebooks, and the scoring sheets I gave out for the ones that they were competing for the highest or lowest score to win some sort of prize.

Forces and Motion Unit:

Egg Drop Challenge Group Directions

Egg Drop Challenge Lab Sheet

Egg Drop Challenge Score Sheets

Energy Unit:

Rube Goldberg Machine Group Directions

Rube Goldberg Machine Lab Sheet

Rube Goldberg Machine Score Sheets

Marble Roller Coaster Group Directions

Marble Roller Coaster Lab Sheet

Keep The Heat Group Directions

Keep The Heat Lab Sheet

Keep The Heat Score Sheets

Wednesday, March 21, 2018

Energy and Roller Coasters

I was so excited when I saw Sarah blog in MathEqualsLove about Marble Roller Coasters in her Physical Science class. I knew when we got to potential and kinetic energy we had to do this. Just yesterday we did this in class. The exclamations of the students helped me to know that this lab was a big hit.

The class was split into groups of two and each group was given 2 insulation tubes that were cut in half, so they had a total of 7.2 meters of roller coaster track. Each group was also given 1 marble, a roll of masking tape, and three pieces of duct tape (to tape the ends of the track together).

Before the lab, I did some searching online for idea of parameters to give to the students and what to ask them to do in their notebooks. Here is one document I found, but most of my ideas came from this lab.

Most of the pairs worked on this for a solid 60 minutes and a few groups would have been happy to have a little more time.

Here is the direction sheet that I provided for each group. And this is the lab sheet that they were given to put into their notebooks.

Saturday, March 10, 2018

Essential Knowledge Student Reflections

Going with my theme this year of reflection and revision, I have had my students regularly reflect on the Essential Knowledge statements from the AP Biology framework. Last year, I organized the Essential Knowledge statements (along with the Enduring Understandings and Learning Objectives) by each unit and provided them to my students as study guides. I blogged about it last year here.

By the end of the year, I could tell that students weren't utilizing them as much as I had hoped. I want students to grapple with these statements, get familiar with the wording, and be able to connect what we are doing in class to these statements. First change: I made time in class for this reflecting to be done.

I also wanted students to have all of these reflections in one place to review them when they study for a test and to be able to look back as the year progresses to see their own growth from beginning to end. My goal was to automate as much of this process as possible. I already use a Google Form and Autocrat to grade labs and give students rich feedback in an easy-to-read document. I love the automation of this and blogged about it last school year here.

But the issue with reflections is that I want my students to have several reflections per unit. Each time they make a reflection with the Google Form, they create another row. So, I needed to be able to merge all of the separate rows of reflections from one student into one row. Enter an additional sheet Add-On called "Power Tools"! This add-on performs several functions, but the one I was interested in combines rows. I tell it what cell to look for identical entries (last name), and it merges all of the rows by one student into one row. This usually takes me two tries, because inevitably a couple of students will type an extra space after their names sometimes, but not all of the times. Power tools recognizes this space and doesn't consider the name identical.

I made a video of me making these documents for my students after they had done their reflections in Forms--just in case it makes more sense than the directions.

Create response spreadsheet from the Google Form.
In the newly formed spreadsheet, go to add-ons and get the add-on "Power Tools"
Once it's added, go to the add-on menu, Power Tools, and click start.

Select "Data" and then "Combine Rows."
I then let it auto-select the data (which is all of it).
Choose "last name" for the key column with duplicate records.
For choosing columns to merge, I choose all of the columns, the action is "merge values," and the delimiter is "comma."
Click "finish" and it merges the rows.
Then sort the sheet alphabetically by last name, which makes it easier for me to figure out who added that extra space after their last name.
I remove the extra space and go through the combine rows process for a final time. (Which takes about 20 seconds.)
Close power tools and launch the add-on "AutoCrat" so I can make a document for each student of their responses.
Give the job a name and click next.
Select a template (I make these ahead of time and will give links to them.) It'll show what rows will be merged into which part of the google doc. Since I've put these together I know that everything will match up the way it needs to. This did take some tweaking at first for me.
Chose how the documents will be named. I do <<First>> <<Last>> Unit # Reflections
It'll suggest a folder to put the merged documents into. You may select a different one if you'd like.
I skip the optional items and don't share the results by email, although if I had a lot of students I might.
Save and then when the Job pops up, hit the triangle play button.
Once all of the documents are merged, I go to the folder they were put in and print them out for my students to reference as they prepare for their upcoming unit test.

This sounds time consuming, and it did take me awhile to figure it all out. But now that I've done it several times, I can have it completed in about 10 minutes or less.

Here are the Google Forms and Templates for each unit.

Unit 1 Biochemistry Biochemistry Template
Unit 2 Cells Cells Template
Unit 3 Cellular Energetics Cellular Energetics Template
Unit 4 & 5 The Cell Cycle The Cell Cycle Template
Unit 6 Molecular Genetics Molecular Genetics Template
Unit 7 Evolution Evolution Template
Unit 8 Plants (this unit is so small, I skipped the reflections)
Unit 9 Ecology Ecology Template
Unit 10 Humans Human Form and Function Template

Saturday, February 24, 2018

Creative Series and Parallel Circuits

Last year, knowing that I would be teaching Physical Science this year, I started collecting ideas on Pinterest for labs. One of the pins was for making circuits with aluminum foil and Christmas lights from Nitty Gritty Science. I loved the idea and had a couple of strings of old lights that weren't working reliably. I actually started to cut the lights up at the end of last year to be prepared.

I made a basic model of a series and parallel circuit to show my students and then told them to be creative. The kids certainly didn't disappoint! Most loved the process and asked if they could bring the supplies to finish up at home. They worked in class for 80 minutes, and several students had only finished the series circuit, but were still in process for the parallel circuit by the time class was over.

We began by drawing a schematic of their design. Once the design was approved, they got their supplies of a manila folder, 2 brads, a sheet of foil, scissors, several Christmas lights, a 9 volt battery, and tape. They needed reminders that tape is an insulator and to make sure the foil is always touching foil for the entire circuit.

Several parents actually commented about the popularity of this lab to me when they saw me later.

I put together directions for each table of students and also a lab sheet for them to glue into their notebooks.

Thursday, February 15, 2018

Egg Drop Challenge

As we were wrapping up our unit on forces and interactions in Physical Science, I wanted the kids to have the opportunity to apply their knowledge and also have some practice with the engineering process. For our last class before the unit test, we had an egg drop challenge.

I did some research on line, but many of the challenges out there are for students to build an apparatus at home and bring it in for the competition. Since I only see my students for one 90 minute session a week, they are busy during the week with reading the chapter and doing other assignments. I wanted students to have the opportunity to test designs and make improvements as well as practice working as a team. So, I pilfered ideas mainly from this document and put together what would be my student's in class building challenge.

Students had about 70 minutes to design and build their egg holder. Some were a little slow to start, but by the end they were all fully engaged. If I were to do this again, I'd try to figure out some way to limit the amount of glue from the glue gun used per team. I had about 7 sticks (for a full sized glue gun) and it was all used before some teams had a chance to use it even once. It was primarily one team that went hog wild with it.

In the end, of the seven teams, three of them successfully dropped their egg and had no damage to the egg. The other four were valiant attempts, all of which were exciting to watch.

Here are the directions that I gave students. It also includes the list of materials that I provided each team. All of it fit in a gallon ziplock bag. Three of the teams asked if they could use the gallon bag, and I did allow them too--even though it wasn't on their list. For students' notebooks, I gave them this reflection sheet. I also made these score sheets. These scores did not effect their lab grade, but was used to decide some fun prizes. In the end, we did not measure the distance from the target since we had to drop them on the stairs and the egg holders were flying everywhere off the steps.

Saturday, February 3, 2018

Guided Reading Questions and Videos for AP Biology

I've been meaning to put this together all year, but life has just been too busy to get it all together. Even though it's my third year teaching the new AP Biology curriculum, I've come to realize that I will never finish tweaking this course, and so will never just breeze through a year of teaching it. On the bright side, I do feel like each year I teach it a little better! Here are my links to guided reading questions and corresponding videos to supplement the reading in AP Biology. All of these links are in old blog posts, but I thought I might be easier to have all of the links in one post. Here is a link to a document that has all of these units in table form, which I like better. It just doesn't copy and paste well into blogger. Right now the chapter numbers correspond to the Campbell Biology 8th Ed., but next year we are switching to the 2nd Edition of Biology in Focus, so next year, I'll be changing the chapter numbers. I may change the questions some, but they should already match fairly well with Biology in Focus since I had chosen them based on what I saw in the Holtzclaw Test Prep review book for Campbell Biology and Biology in Focus. I love that Test Prep review book by the way!

Biochemistry: Unit 1

Chemical Context of Life

Chapter 2 Questions

Water

Chapter 3 Questions

Crash Course Water

Carbon and the Molecular Diversity of Life

Chapter 4 Questions

Crash Course Carbon

Macromolecules

Chapter 5 Questions

Crash Course Macromolecules

Enzymes

Chapter 8 Questions

Bozeman Biology Enzymes

Cells: Unit 2

A Tour of the Cell

Chapter 6 Questions

A Tour of the Cell (Bozeman)

Membrane Structure and Function

Chapter 7 Questions

In Da Club: Membranes and Transport (Crash Course)

Cell Communication

Chapter 11 Questions

Cell Communication (Bozeman)

Signal Transduction Pathways

Effects of Changes in Pathways

Metabolism: Unit 3

Introduction to Metabolism

Chapter 8 Questions

Gibbs Free Energy (Bozeman)

Cellular Respiration

Chapter 9 Questions

Cellular Respiration (Bozeman)

Photosynthesis

Chapter 10 Questions

Photosynthesis (Bozeman)

Cell Cycle and Mendelian Genetics: Unit 4 & 5

Cell Cycle

Chapter 12 Questions

Mitosis (Bozeman)

Meiosis and Sexual Life Cycles

Chapter 13 Questions

Meiosis (Bozeman)

Mendel and the Gene Idea

Chapter 14 Questions

Mendelian Genetics (Bozeman)

Heredity (Crash Course)

Chromosomal Basis of Inheritance

Chapter 15 Questions

Advanced Genetics (Bozeman)

Genetic Recombination and Gene Mapping (Bozeman)

Linked Genes (Bozeman)

Molecular Genetics: Unit 6

The Molecular Basis of Inheritance

Chapter 16 Questions

DNA Replication (Bozeman)

Gene Expression

Chapter 17 Questions

Transcription and Translation (Bozeman)

Regulation of Gene Expression

Chapter 18 Questions

Gene Regulation (Bozeman)

Viruses

Chapter 19 Questions

Viruses (Bozeman)

DNA Tools and Biotechnology

Chapter 20 Questions

Molecular Biology (Bozeman)

Genomes and their Evolution

Chapter 21 Questions

Evolutionary Development (Crash Course)

Evolution: Unit 7

Descent with Modification

Chapter 22 Questions

Natural Selection (Crash Course)

The Evolution of Populations

Chapter 23 Questions

Population Genetics: When Darwin Met Mendel (Crash Course)

The Origin of Species

Chapter 24 Questions

Speciation: Of Ligers and Men (Crash Course)

The History of Life on Earth

Chapter 25 Questions

Evolution: It's a Thing (Crash Course)

Phylogeny and the Tree of Life

Chapter 26 Questions

Taxonomy: Life's Filing System (Crash Course)

Bacteria and Archaea

Chapter 27 Questions

Old and Odd: Archaea, Bacteria, & Protists (Crash Course)

Unit 8: Plants

Plant Form and Function

Chapters 36-39

Plant Control (Bozeman)

Unit 9: Ecology

Animal Behavior

Chapter 51 Questions

Tinbergen's Experiment

Ecology and the Biosphere

Chapter 52 Questions

Population Ecology: The Texas Mosquito Mystery (Crash Course)

Population Ecology

Chapter 53 Questions

Human Population Growth (Crash Course)

Community Ecology

Chapter 54 Questions

Community Ecology: Feel the Love (Crash Course)

Ecological Succession: Change is Good (Crash Course)

Ecosystems and Energy

Chapter 55 Questions

Ecosystem Ecology (Crash Course)

The Water and Carbon Cycle (Crash Course)

The Nitrogen and Phosphorus Cycles (Crash Course)

Conservation Ecology and Global Change

Chapter 56 Questions

5 Human Impacts on the Environment (Crash Course)

Conservation and Restoration Ecology (Crash Course)

Friday, January 19, 2018

Our Best Bacterial Transformation Lab Yet

Last year when we did our bacterial transformation lab, the results were lackluster at best. We had two transformed colonies on one of the LB/amp plates and one on a LB/amp/IPTG plate. We don’t have a digital water bath, and last year I struggled to keep the 42 degree water bath at 42 degrees on the hot plate. This is a heavy preparation lab to have poor results.

Since joining the National AP Biology Teachers group on Facebook, I had seen post after post of teachers raving about the transformation rates from the lab kit from Bio-Rad. So, when it was time to put in orders for this school year, we ordered the Bio-Rad Transformation kit through Wards.

The kit came in to school over the summer. I stopped by occasionally to check what orders were in. Then two weeks went by without me stopping in. When I finally came by to check, the kit was already sitting in the un-air conditioned storage room including the bag of bacteria, plasmids, ampicillin, and arabinose that says to refrigerate immediately. I took these materials out and got them into a refrigerator and started to worry that the kit was ruined even before we started. I hopped onto the Facebook group to see what people said about the kit and not refrigerating the items immediately. I was surprised at how many teachers this happened to and was relieved to see that most of them had no adverse effects.

I had also shared with a colleague about how much I would like to have a digital water bath for this lab, but felt the cost was prohibitive. She suggested we try sous vide. I did some research and found an Anova Sous Vide Immersion Circulator for $109 on Amazon with good ratings and put it on our supply order. I brought in an old pot and put the circulator in. Within 10-15 minutes I had a water bath at exactly 42 degrees Celsius that remained at 42 degrees for as long as I wanted it there.

I did make a couple of other mistakes as I prepped for the lab. I started heating the LB agar in an (Ehrlemyer) flask on a hot plate. I stepped away to rehydrate the ampicillin and arabinose and heard a sizzling noise. I looked over to the hot plate to see agar erupting out of the flask. Fortunately the hot plate wasn’t plugged in behind the plate, but to the side of it, so I quickly unplugged it (and was glad I was wearing goggles, a lab apron, and closed toe shoes). Then I was panicked that I had lost too much agar to be able to pour all of the plates. I decided to scrape as much of the agar on the counter back into the flask and simmer it for 10 minutes to make sure it was sterilized. This time I stayed with it the whole time and there were no more volcanos.

My other mistake was that I rehydrated the ampicillin and arabinose with Luria broth instead of the transformation solution (calcium chloride). It wasn’t bad for these powders, but it meant I didn’t have enough broth left for my students to use in the lab. I doled it out carefully, but for the last group, I used left-over broth from the year before. (And I'm relieved to say they still had a successful transformation.)

I am happy to report that this year, we had some of our best transformation rates. I did have two groups with no transformation, but the other four had success. We certainly can’t blame the water bath!

Fortunately, I had enough agar to pour an extra LB/amp/ara plate for each lab group. We took the non-glowing transformed colonies from the LB/amp plates and swabbed them onto the spare plates. Students were able to see how the presence of arabinose really does switch on the jellyfish green protein gene when we looked at the plates the next day. This was one of our best years for this lab!