Week 36 – What is a Phylogenetic Tree?

Our learning in Week 32 focused on phylogenetic trees.  If you completed the work for that lesson, review your work to get re-acquainted with phylogenetic trees.

You are also encouraged to watch the Bozeman Science video below.  Mr. Anderson explains how to construct a phylogenetic tree (also called a cladogram):

Looking for more background knowledge?  Visit the UC Berkeley Understanding Evolution site and work through the Phylogenetics Tutorial.

Need more help?  Click here for a Phylogenetic Tree Project Example.

Return to Week 36 – Phylogenetic Tree Project and continue working.

Week 36 – Solution Concentration

Welcome to Week 36!  This week will tackle the concept of Solution Concentration.  Many of the experiments we conduct in chemistry use chemicals in aqueous form.  By the end of this lesson, you will know how to prepare chemical solutions of a specific molarity.  Let’s go!

Checklist for the week:

  1. Week 36 Attendance Check-In (required by 10am 5/29)
  2. Molarity (Google Form assignment)
  3. Dilution (Google Form assignment)
  4. ELISA (optional virtual lab with assignment)

You did it!  Just to make sure, here’s a checklist of items you must complete this week by Sunday, May 31 at 11:59pm:

  • Weekly Attendance Check-In (school district requirement)
  • Molarity (worth +10 assignment points)
  • Dilution (worth +10 assignment points)
  • Optional Lab  Assignment (worth +30 bonus lab report points)

Remember, you can email me any time.  Office hours for Science are Tuesdays from 11am-12pm and Thursdays from 1pm-2pm.  Check your student Gmail for Zoom instructions.

Don’t forget to complete the Week 36 Bonus Credit Opportunity!

Week 36 – ELISA

As a biotech researcher for many years, one of lab techniques I used quite often was the Enzyme-Linked Immunosorbent Assay (ELISA for short).  For many years, my research focused on understanding the activities of molecules of the immune system called interleukins (part of the cytokine family of molecules).  Some of my work included focusing on understanding the biology of  a interleukin called interleukin-17A (IL-17A).  I maintained a line of mouse fibroblast cells (NIH-3T3 cells) which had been shown would respond to IL-17A and produce IL-6 (another interleukin), measurable by ELISA (click here for the ELISA procedure).  If we stimulated the cells with IL-17A along with small amounts of other molecules (TNFα or IL-1β), we would see absolutely massive amounts of IL-6 released – well beyond what would be produced by the cells in response to any one of those molecules alone.  At the time, we used this concept to screen blocking antibodies against the IL-17A receptor (IL-17RA) which were then used in a variety of mouse models of different diseases.  Fast forward to today: scientists are accumulating data that the cytokine storm observed in some of the sickest COVID-19 patients may actually the result of those patients releasing too much IL-6, perhaps as a result of the activity of IL-17A released by the body as part of the defense against the virus.  In fact, there is a clinical trial underway for an antibody to IL-6 called tocilizumab.

With all that as background, it’s time to focus our learning around the ELISA.  For starters, if you are using an ELISA kit (like the IL-6 kit I linked to above), most of your assay reagents come packaged up in a tidy little box, and most of the reagents arrive as solids.  To use the reagents, you need to add specific volumes of specific solutions (solution concentration!).  After preparing the ELISA plates to receive samples, the protein standard must be diluted to the proper starting concentration.  Then the protein standard is serially diluted to generate a standard curve.  The samples are also often serially diluted.  When the assay is complete, if all goes according to plan, you can use the standard curve to determine the concentration of protein in your samples.

Your turn!  While not required, you are highly encouraged to work through the HHMI Biointeractive Immunology Virtual Lab.  To guide your learning, complete the Immunology Virtual Lab Worksheet and earn +30 bonus points in the lab report category of your semester grade.

Return to Week 36 – Solution Concentration and continue working.

Week 36 – Basic Plant Biology

This year, we’ve learned a bit about plants – here are some highlights:

  • The chemical equation for photosynthesis (Week 4) tells us that plants use sunlight energy, carbon dioxide, and water to produce molecules of glucose and oxygen.
  • Plants have a cell wall and remain turgid in a hypotonic solution (Week 8).
  • Plants are producers (Week 12), meaning they are the bridge between the sun (energy) and consumers (animals that need energy).
  • Plants are central to the biogeochemical cycle (Week 14 and Week 15).

Now that we all agree that plants are really important and we wish we could have learned more about them, let’s make the most of our limited time and invest a few minutes learning more about plants:

 

 

Seeds are amazing!  They are a little packet of starter nutrients  and information (DNA) – and from a seed you can grow an entire plant which then produces more seeds!  Let’s appreciate the wonder of seeds by watching the video below showing seed germination:

 

 

Admit it – you really want to grow some plants now, right?  If you have access to some seeds and some soil, get to it!  If you have access to some scissors and some mint plants, take a cutting, place the cutting in water, wait a week, and your new mint plant will sprout roots and be ready to plant as a new mint plant!  Click here to meet Mr. Swart’s new mint plant starts.  If not, no worries – I’ve got you covered.  Back on April 25, the Swart Family Vegetable Garden was planted with seeds of 40 different types of vegetables.  Our work this week will involve a journey through the garden…

Return to Week 36 – Inferring with Evidence and continue working.

Week 36 – Inferring with Evidence

Welcome to Week 36!  With the school year winding down, it’s time to get outside and explore nature through the lens of evolution.  Our work this week is to use evidence to infer relationships among a variety of vegetable plants commonly found in the garden.  Let’s get to it!

  1. Week 36 Attendance Check-In (required by 10am 5/29)
  2. Basic Plant Biology
  3. Show Me the Veggies!

You did it!  Just to make sure, here’s a checklist of items you must complete this week by Sunday, May 31 at 11:59pm:

  • Week 36 Attendance Check-In (school district requirement)
  • Phylogenetic Tree Project or Dichotomous Key Project (Google Doc, each worth +40 project points – pick one for full credit or complete both for +40 bonus credit)

Remember, you can email me any time.  Office hours for Science are Tuesdays from 11am-12pm and Thursdays from 1pm-2pm.  Check your student Gmail for Zoom instructions.

Don’t forget to complete the Week 36 Bonus Credit Opportunity!

Week 36 – Dilution

Often when you are working with chemicals in the lab, the chemicals are already in solution.  For example, imagine you need to use some sodium hydroxide, NaOH, in a chemical reaction.  You have a 1.0 L bottle of 1.0 M NaOH on the shelf, but your reaction calls for a 0.25 M solution.  What to do?  Prepare a dilution by adding solvent (in this case, water) to the solution to lower the concentration of the solute (in this case, NaOH).

For starters, we need to know the volume of 0.25 M NaOH that we need.  Let’s say we need to end up with 1.0 L of the 0.25 M NaOH.  Now we can figure this out.  We know that M = mol/L.  For our 0.25 M solution, M = 0.25 and L = 1.0.  Rearranging the equation to solve for moles and we get mol = M x L = 0.25 x 1.0 = 0.25 mol.  Therefore, we need to end up with 0.25 mol of NaOH in 1.0 L of solution.

Our stock solution of NaOH has a molarity of 1.0 M, or 1.0 mol / L.  We need 0.25 moles of NaOH.  To figure out the volume of stock solution we need to obtain 0.25 moles of NaOH, we can set up a proportion: 1.0 mol / 1.0 L = 0.25 mol / x.  Solving for x, we need 0.25 L of the stock solution.

Finally, now that we know the volume of 1.0 M NaOH stock solution needed to add to prepare our 0.25 M NaOH solution (0.25 L), we need to calculate how much water to add to make the 0.25 M NaOH solution.  We need a total volume of 1.0 L, and 0.25 L is going to come from the 1.0 M NaOH stock solution.  Therefore, we need 1.0 L – 0.25 L = 0.75 L of water.  To prepare the 1.0 L 0.25 M NaOH solution, we need to add 0.75 L of water to our flask, then add 0.25 L of the 1.0 M NaOH stock solution.


Now that you have seen the math and read the reasoning behind it in painstaking detail, let’s try a practice problem.

Question: How would you prepare 2.0 L of a 0.5 M aqueous solution of CuCl2 from a stock solution of 3.0 M CuCl2?

Answer: 0.33 L of the 3.0 M stock solution + 1.67 L of water.  Why?  A 3.0 M CuCl2 solution has 3.0 mol of CuCl2 per liter of solution.  We want to prepare 2.0 L of a 0.5 M solution, so solving M = mol/L for mol, mol = M x L, so we need 2.0 x 0.5 = 1.0 mol of CuCl2 in a total volume of 2.0 L.  Our stock solution is 3.0 mol/L so 1.0 mol = 0.33 L.  Therefore, we need to add 0.33 L of the stock solution to 1.67 L of water.


One more question: Vinegar is commonly sold as a 5% acetic acid solution (the other 95% is water).  A 100% acetic acid solution is called glacial acetic acid: glacial because the freezing point is just a few degrees below normal room temperature, so the acetic acid appears like a partially frozen glacier.

The molarity of glacial acetic acid is 17.4 M.  How would you prepare 0.5 L of 1.0 M acetic acid?

Answer: You want to prepare 0.5 L of a 1.0 M acetic acid solution.  First, calculate how many moles you need: mol = M x L so 0.5 x 1.0 = 0.5 mol of acetic acid.  Next, the stock solution of glacial acetic acid has a molarity of 17.4 M, or 17.4 mol/L.  To determine the volume of glacial acetic acid needed to obtain 0.5 mol: 0.5 mol x (1 L / 17.4 mol) = 0.029 L.  Always add acid to water, so first add 0.471 L of water (0.5 L – 0.029 L) to the flask and then add 0.029 L of glacial acetic acid.

Time to show what you know!  Complete the Week 36 – Dilution Google Form assignment and then return to Week 36 – Solution Concentration and continue working.

Week 36 – Show Me the Veggies!

The pictures below are of 25 different garden vegetables that were only seeds three weeks ago.  Some plants clearly grow faster than others.  In fact, quite a few seeds have yet to germinate, so this project isn’t quite as big as it could have been!  What project?  I’m glad you asked!  This week, you have a choice.  For either project, you will observe the plants carefully, writing down your observations for each plant in a Google Doc.  Using your observations as evidence, you will either construct a phylogenetic tree or a dichotomous key.  Both are worth 40 project points each.  You must do one, you may do both.  Doing both projects will earn you 40 bonus project points.  Select the project you would like to complete and click on the link below for details.

Broccoli
Radish
Brussel Sprout
Watermelon
Arugula
Romaine Lettuce
Cucumber
Jalapeño Pepper
Sunflower
Pumpkin
Roma Tomato
Black Beauty Squash
Purple Top Turnips
Corn
Beets
Carrots
Peas
Blue Kale
Bush Beans
Swiss Chard
Buttercrunch Lettuce
Iceberg Lettuce
Red Cabbage
Spinach
Sugar Snap Pea

Return to Week 36 – Inferring with Evidence and continue working.

Week 36 – What is a Dichotomous Key?

As part of our learning about biological classification (week 31), you completed the Biological Classification POGIL assignment.  Model 4 from that assignment begins with a dichotomous key that helps you determine which kingdom your unknown organism belongs to (Pro Tip – open up that assignment).  We are going to be focusing on photosynthetic organisms (the answer to the ? box) which we know are called Plants!  A dichotomous key can look like a flow chart (like the POGIL) or it can look like a series of questions similar to a choose-your-own-adventure book where one question leads to the next and eventually you figure out the identity of the organism.  To begin, watch the video below to see you to use a dichotomous key:

 

 

 

Now, imagine you are out for a walk in the woods.  You look up at the tall trees and down at the forest floor.  How do you know what’s what?  Is that plant native or a weed?

 

 

 

Need more help?  Click here for a Dichotomous Key Project Example.

Return to Week 36 – Dichotomous Key Project and continue working.

Week 36 – Phylogenetic Tree Project

One month ago, we planted our vegetable garden.  It was the reward for several weeks of arduous labor (about which my kids are still complaining).  This week, we will observe together the miracle of biology: after a little more than a month, what began as a tiny little seed is now a plant with interesting and complex structures, well on its way to maturing into something that will produce food for us in a few months.  From the perspective of the plant, feeding us isn’t the goal.  The plant has domesticated humans by convincing us to cultivate it, thus ensuring the plant and its offspring survive for future generations.  Same with cats and dogs – we like to pretend we’re in charge, but really the creatures we love as “pets” have actually been stunningly successful at domesticating humans and getting us to feed, shelter, love, and protect them.  Who is really in charge?

But I digress!  Back to plants and our work for the week.  Your job is to look through the pictures of individual plants from the garden.  The pictures show the plants after 3 weeks of growth (they were taken last weekend).  The plants are labeled so you will know what you are looking at.  Take notes about the characteristics of the plants – you will need those notes to construct a phylogenetic tree.  (Click here for a refresher about phylogenetic trees).  Your goal for the week is use evidence to infer the evolutionary relationships amongst common garden vegetables.

Instructions:

  1. Observe the pictures of garden vegetable plants after 3 weeks of growth (from seeds).  The same pictures in the link are also provided here as a slide show.  Use whichever is easiest for you.

    This slideshow requires JavaScript.

  2. Record (write down!) detailed observations in a Google Doc titled “Vegetable Garden Phylogenetic Tree – Your Name”.  This means, make a list of the 25 plants.  Write down detailed observations of each plant.  Your observations will serve as your evidence for how you construct your phylogenetic tree.
  3. In your Google Doc, organize the plants into groups based on similarities.
  4. In your Google Doc, create a phylogenetic tree which predicts the evolutionary relationships amongst the 25 different garden vegetable plants.  You might expect plants that appear similar to be more closely related than plants that appear different.  Use your evidence to infer the evolutionary relationships as depicted in your phylogenetic tree drawing.
  5. Need help?  Click here for a Phylogenetic Tree Project example.
  6. When finished, Share the Doc with Mr. Swart at david.swart@g.highlineschools.org

Return to Week 36 – Inferring with Evidence and continue working.