Genetic Engineering Competency Catch-Up

Goal:
Describe the role of DNA ligase in replication and explain how DNA ligase is used to create a recombinant DNA.
Describe the possible recombinant plasmids that form when ligating a restriction digest.

Agenda:
Final Teamwork Evaluation
Finish Restriction Digest Slide
Ligation Prediction
Work on Slides

Final Teamwork Evaluation
Follow the Feedback Protocol. Scribe, use the BLUE highlighter to mark the final score for each team member.

Finish Restriction Digest Slide
Left Side:
Define plasmids and restriction enzymes
Use the key to explain what each of the beads represent and why they are important. Refer back to the reading (pg. 46 of reading)
Right Side:
In your petri dish you have the 2 plasmids and 2 restriction enzymes that we worked with today. Work with your elbow partner to create an image for what is in each of the 4 tubes (K+, K-, A+, A-)

Ligation Prediction
Left Side:
Define ligase and recombinant DNA.
Which recombinant plasmid will produce RFP? How do you know that?
Right Side:
Use the model to show all possible ligation products that could be present in the LIG tube. Also show what is in the A+ and K+ tubes.

Work on Slides
By now you should have finished 3 slides: Intro, Restriction Digest, and Ligation

Restriction Digest

Goal:
Model the process of producing recombinant DNA.
Describe the characteristics of plasmids and explain how plasmids are used in cloning a gene.
Describe the function of restriction enzymes and explain how to use restriction enzymes to create a recombinant DNA.

Agenda:
Clone That Gene!
Lab
Summarize

Clone That Gene!
Read and Follow the directions at the end of this chapter.

Lab
Today we will be performing a restriction digest to cut up plasmids so we can make a recombinant plasmid with the rfp gene.

• You will work in teams of 4.
• Follow the lab procedure VERY CAREFULLY. We don't have extra if you mess up. 
• Make sure you use the micropipets properly (remember, 1st stop/2nd stop).

Summarize
On the restriction digest slide in your competency do the following.
Left Side:

1. Define plasmids and restriction enzymes
2. Use the key to explain what each of the beads represent and why they are important. Refer back to the reading (pg. 46)

Right Side:

1. In your petri dish you have the 2 plasmids and 2 restriction enzymes that we worked with today. Work with your elbow partner to create an image for what is in each of the 4 tubes (K+, K-, A+, A-)

Finish Stop Motion

Goal:
Model the process of producing recombinant DNA.
Describe the characteristics of plasmids and explain how plasmids are used in cloning a gene.
Describe the function of restriction enzymes and explain how to use restriction enzymes to create a recombinant DNA.

Agenda:
Vocab Quiz
Finish Stop Motion
Clone That Gene!

Vocab Quiz
Login to Socrative

Finish Stop Motion
Make sure to include the protein purification step.
Once you're done, I will show you how to link it to your Google Slides Competency.

Clone That Gene!
Read and Follow the directions at the end of this chapter.

Genetic Engineering Process

Goal:
Describe the role of biological tools, such as plasmids, restriction enzymes, e.coli, and ligase, in the genetic engineering process.

Agenda:
Warmup
Overview Genetic Engineering Process
Stop Motion

Warmup
Log in to socrative.

Overview Genetic Engineering Process
Link to Slides

Stop Motion
Make a Stop Motion video animating the ENTIRE genetic engineering process. Include the following vocabulary:
Bacteria
Plasmid
Restriction Enzyme
Ligase Enzyme
Human/Animal Inserted DNA (insulin or red protein??....anything you want)
Recombinant DNA
Transformed Bacteria
Protein (insulin,rfp)

Vocab Quiz Tomorrow

Study Quizlet

What is Genetic Engineering?

Goals:
-Provide examples of how genetic engineering can be used to solve medical problems.
-Explain how genetic engineering creates genetically modified organisms that make human proteins from human DNA.

Agenda:
Warmup
Listen
Read
Write

Warmup
Did you find anything interesting in your family health history that might inform how you approach your health care in the future? If you would like, share on this Padlet.

Considering what we reviewed yesterday, what may be causing these genetic diseases?

Listen
CRISPR Radiolab. How could this technology be used to permanently cure genetic diseases?

Read
"What is genetic engineering?" Use the reading to compare and contrast CRISPR and recombinant DNA technology using a venn diagram.

Write
I shared a Google Slides with you. Your competency is to complete these slides. On the intro slide use what you have learned to answer the questions below in complete sentences.

1. Explain the cause of genetic diseases such as Type 1 Diabetes or Breast Cancer. 
2. How could CRISPR be used to provide a permanent cure for genetic diseases?
3. In recombinant DNA technology, scientists modify a bacterial plasmid by adding a human gene in order to produce human proteins. How does this process help in addressing genetic diseases (for example, with insulin)?
4. In our Biotechnology lab sequence how will what we do be different than making insulin?

DNA Review

Goal:
Explain the basic processes of transcription and translation for making proteins.

Agenda:
Pre-Test
Review
Model
Post-Test

Pre-Test
Let's see what you remember about transcription and translation from last year. Go to Kahoot.

Review
Watch this video to review the basic process of transcription and translation.

Model
Using the paper models provided, work with your partner to create an accurate stop motion animation of transcription and translation for a 2 amino acid protein.

1. Write down the steps of protein synthesis in the box provided.
2. Get the steps approved by me.
3. Use the DNA template strand on the board to transcribe and translate 6 nucleotides. Use Stop Motion Studio to animate this process.

Post-Test

Go to Kahoot again :)

Homework:
Complete the "What's Your Story?" worksheet by asking about family health history. 

Graphs

Goal:
Evaluate your system.

Agenda:
Teamwork Rubric
Graphing Data

Teamwork Rubric
You know the drill.

Graphing Data
Google Forms will graph a lot of the data for you but for some sample sets the graphs aren't useful or you may want to get a little more information out of the data. See below.

For free response questions consider:
-Grouping similar responses and putting them in a bar graph
-Using a word cloud. Use the Word Clouds by ABCYa app

Sometimes it may be helpful to compare the responses of 2 separate questions. For example:
-I want to look at the responses for people that live in the 92029 zipcode.
If you would like to graph your data this way I can help you. You will need to use excel.

Finish Survey

Goal:
Create a 10-20 question survey to evaluate your system.

Finish Your Survey
Add the share link to your design Journal

How do you survey?

Goal:
Create a 10-20 question survey to evaluate your system.

Agenda:
Name the New Fish
Why are you surveying?
Create your Survey

Name the New Fish
Vote Here

Why are you surveying?
Grab a whiteboard. With your group, write down:
1. WHAT you want to learn about your system
2. WHY you want to focus on that part of the system
3. WHO you should survey to find out about how the system is working

Create Your Survey
We have created some guidelines for your survey here. Make sure your survey includes the purpose as well as a mixture of questions types.

Models Due

Goal:
Model your system.

Finish Models
Complete your models in Pureflow (or another approved app)

Update Journal
Make sure parts A and B in the systems journal are complete.
I will be renaming your journals based on your project. Don't freak out.

Print Models
Print your models to C211-212 and turn these in to me by the end of class. My goal is to return them to you with feedback by the end of the week.

Keep Working

Goal:
Complete research.
Model system.

Complete Research:
Continue your system research. If you are studying a local community issue, Voice of San Diego has a lot of great articles as does the Union Tribune and KPBS

Model System
Once you have a rough sketch of your model, use Pureflow to make a cleaned up final draft. Here is the rubric I will be grading you on. A 4 has the following components:

• A key is provided to help the viewer understand color codes or symbols.
• Components and relationships are identified and defined based on research.
• Colors, labels, and arrows are used to clearly classify the components and make their relationships easier to understand (e.g., inputs, activities, outputs, outcomes, funding, laws, organizations)
• The components are arranged spatially in a way that is easy to read.

Research

Goal:
Research the history and how your system works.

Agenda:
RESEARCH

Reminders:

• the purpose of your research is to find the history of the system and model how it currently works
• record notes and sources in your shared Google doc, NOT in other apps
• final drafts of your models are due next Wednesday 4/26

If you are having a hard time figuring out what to research, come up with subquestions you might have about their system (who, what, when, where, why, how). For example, a group doing research on puppy mills might ask:

• Who runs puppy mills? Who buys the puppies?
• Where are puppy mills located?
• What are puppy mills?
• Why do people run puppy mills?
• Are there laws against puppy mills? How are they enforced?

You may want to begin drawing out models on the whiteboards. 

Choose Wisely

Goal:
Choose a system that heals the world, fuels the world, feeds the world, or restores and protects the environment.

Agenda:
Project Groups
Fish Name Vote
Choose Your System

Project Groups
Don't get comfy, you're moving seats.

Fish Name Vote
Vote for the fish names here.

Choose Your System
1. Open this document in Google Docs. It is where your group will be recording and sharing notes.
2. Rename your document Period #-First Names Systems Design Journal
3. Share the document with your team members, me (awallace@euhsd.org), and Ms. Stillman (lstillman@euhsd.org)
4. Complete page 1 (choosing your system). YOUR SYSTEM MUST BE APPROVED BEFORE YOU LEAVE TODAY.

Thinking in Systems

Goal:
Define, model, and give examples of systems.

Agenda:
Thinking In Systems
Modeling Systems
Give an Example

Download:
Excerpt from Thinking In Systems - Open in Notability

Thinking in Systems
Read and annotate the excerpt. As you read THINK ABOUT THIS/COMPARE AND CONTRAST:
How do you know whether you are looking at a system or just a bunch of stuff?

Modeling Systems
We will model the Tea Station together.
You will model the digestive system with your table group on whiteboards.

Give an Example
Complete this Google Form

Metacog-what?

Goals:
Articulate the benefits of metacognitive reflection.
Identify the characteristics of a good metacognitive reflection writing.
Engage in productive metacognitive reflection about their badge work.

Agenda:
Upload
Warmup
Reading/Discussion
Deconstruct Exemplar
Write

Download:
Metacognitive Reflection Handout - Open in Notability

Warmup
Complete “Before” column of the anticipation guide, noting if you agree or disagree with each statement.

Reading/Discussion
What is metacognitive reflection? Why do the badges require metacognitive reflection?

In the Metacognitive Reflection Handout:
1. Read the article, “The Role of Metacognition in Learning and Achievement” and annotate with those two questions in mind.
2. Complete think-pair-share discussion to answer the previously posed questions. During this they complete the “Think-Pair-Share” graphic organizer. Share your thoughts with the class.

Deconstruct Exemplar
Read and highlight the Example Metacognitive Reflection, following the directions in the Metacognitive Reflection Handout.

Upload
Make sure the following things are uploaded to Badgelist Analytical Techniques 2. No reflections needed

Process:
1. Tutorial - you made this last week
2. Concentrations Calculations Work - Screenshot Page 14 of the packet showing the calculations you did to prepare your stock and dilutions of your standards for the Bradford Assay lab.

Product:
Standard Curve + Calculations - Upload a photo of your standard curve from the Bradford Assay Lab and the calculations you did to approximate the concentration of the unknown protein sample. You can just screenshot Step 6 parts B and C from the packet.

Write
Write your metacognitive reflection for the Analytical Techniques 2 badge using the prompts I give you. Make sure to answer ALL questions.

Closure
1. Complete the "After" column on the anticipation guide, noting if you agree or disagree with each statement.
2. On the back, please provide feedback on the new badge reflection.

• Are they better or worse than before? 
• What do you like? 
• What needs improvement?

Finish the Lab

Goal:
Generate a 5-point standard curve.
Calculate the concentration of an unknown solution using a standard curve.

Agenda:
Warmup
What does it mean?
Finish Lab

Download:
Capercard App - it's an iPhone only app

Warmup
Share your lab results in this Google Form.
View the class results. Discuss any anomalies.

What does it mean?
I'm going to talk about these slides. You're going to answer the questions using the Capercard app.


Finish the Lab
Complete the last two pages in the packet. Please ask for help if you need it.

Bradford Assay

Goal:
Carry out a Bradford Assay to determine the concentration of an unknown protein.

Agenda:
Warmup
Lab

Warmup
Complete all calculations on page 14. Make sure to show your work. That is part of the competency.

Lab
Follow the procedures on pages 14-15 to collect data.

Pre-Lab

Goal:
Perform calculations using  C=m/V.

Calculate the concentration of a dilution using C1V1=C2V2.

Agenda:
Quiz
Lab Calculations
Update Badge

Quiz
Log In to Socrative

Lab Calculations
Complete the calculations outlined in page 14 of the packet (Bradford Assay Lab). You must have the correct answers before you walk out today.

Update Badge
Upload the process pieces to the Analytical Techniques 2 badge.

While I'm Away...

Goals:

• Describe how to operate a spectrophotometer to find  λmax and absorbance values of a given solution. 
• Define concentration in terms of solute, solvent, and solution. 
• Perform calculations using  C=m/V.
• Calculate the concentration of a dilution using C1V1=C2V2.

This blog post will be your go to guide for Wednesday-Friday
Over the course of the 3 days, you will need to complete the 2 assignments below (I also wrote a note on the whiteboard).


ASSIGNMENT 1: SPECTROPHOTOMETER TUTORIAL
Work with your elbow partner to create a tutorial. Here are some resources:

• Tutorial Guidelines - This is Process Artifact 1
• User Manual
• WikiHow

ASSIGNMENT 2: CONCENTRATION CALCULATIONS
Complete pages 8-13 of the packet.

1. Go through the slides on your own and use them to complete the notes on pages 8-10 and 12 in the packet. 
2. Complete the practice problems on pages 11 and 13 of the packet. 
3. Check your answers on the answer key I left with the sub. 

EARLY FINISHERS
Should do academic recovery to clear NMs or study for upcoming competencies.

Spectrophotometry Practice

Goal:
Use a spectrophotometer to find  λmax and absorbance values of a given solution.

Agenda:
Warmup
How Specs Work
Practice
Tutorial

Warmup
Login to Socrative

How Specs Work
Using the video below and instruction from Mrs. Wallace, complete the notes section on page 5 of your packet.


Practice
Read page 6 and complete page 7 of the packet using the provided solutions.
*EDIT* Change "Green" solutions to "Blue"
When you have finished, check your measurements for accuracy with me.

Tutorial
If you finish early you can begin making your tutorial (Process piece for your badge).