11/21/21: This page is still (slightly) under development

Table of contents

  1. Sequencing: Why Unit 6 comes before Unit 5

  2. Weeks 16 (and 17): DNA Structure and Replication (and starting transcription/translation).

  3. Week 17: Transcription, Translation

  4. Week 18: Mutation, Viruses, Bacterial Genetics/Operons

  5. Week 19: Biotechnology

  6. Week 20: Eukaryotic Gene Regulation and Animal Development

  7. Summative Activities for Unit 6

A note about sequencing: Why Do Unit 6 before Unit 5

In our program at Berkeley High School, we have our students do the Amgen Biotechnology Experience Program. This is a fabulous series of biotechnology labs. Amgen will send all the hardware and consumables to your school. To participate, teachers have to complete a free training, offered several times throughout the year. You can learn more at the Amgen Biotechnology Experience website.

For a variety of reasons, we have to do this program during the first few weeks of January. And because of that, we do Unit 6 (Gene Expression) before Unit 5 (Genetics).

While that’s a very practical reason why we do Unit 6 before Unit 5, there are good pedagogical reasons why you might want to follow this sequence too.

First, the College Board’s Course and Exam Description (mostly) follows a small to big sequence. Unit 1 is molecules, Unit 2 is cells. Unit 3 is energetics, but at a cellular level (enzymes, photosynthesis, and respiration). Unit 4 is also mostly cell biology: cell communication and cell division, with feedback and homeostasis (topic 4.5) sandwiched in between. To me, it makes much more sense to stay at the cellular/molecular level, which is what Unit 6 addresses, before moving onto the organismal level, which is what most of Unit 5 (Heredity), is about. On top of that, it seems like it makes much more sense for our students to understand what genes are and how they work (all covered in unit 6) before looking at how genes are transmitted from generation to generation and how they’re recombined (in Unit 5).

Second, in terms of moving forward, it makes sense to move from Mendelian Genetics (which is in unit 5) to Population Genetics (which is what kicks off unit 7).

In any case, Learn-Biology.com will support you and your students in whatever sequence you’re following.

Weeks 16 and part of 17: DNA Structure and Replication; Transcription and Translation

Note that teaching about DNA, DNA Replication, Transcription, and Translation will take more than one week…For the sake of continuity, I’m presenting this together. We’ll finish transcription and translation in  week 17.

3 Days of Instruction to start Unit 6 (details follow).

Why 3 Days? I’m still finishing Unit 4. So 1 day to review (using

Day 1: Do this inductive introduction to the discovery of DNA.

Day 2: Show The DNA Double Helix. After that, you can either go over the discovery of DNA with your students, or have them start tonight’s homework: DNA: An Overview (Tutorial) and DNA Structure (Tutorial)

Day 3: Show DNA, Fantastic! to review DNA’s Structure. Then do HHMI’s DNA Replication: Pulse Chase Primer Experiment. Assign DNA replication for HW

DNA Structure and Replication Learning Objectives

According to the College Board (in their 2019 CED, available in condensed form here), here’s what you should be covering in relationship to DNA structure and replication. The CB’s objectives are expansive. What’s below is my summary.

  1. Topic 6.1: DNA structure
    1. DNA is the molecule of heredity in most living systems. RNA can play that role in viruses
    2. Prokaryotes have circular chromosomes. Eukaryotes have linear chromosomes. Prokaryotes also have plasmids
    3. Base pairing rules: A w/ T; G w/ C. In RNA, A w/ U
  2. Topic 6.2: DNA Replication
    1. DNA replication occurs in a 5’ to 3’ direction (with new nucleotides added at the 3′ end.
    2. The process is semi-conservative
    3. The process involves a team of enzymes: Helicase, topoisomerase, DNA polymerase, ligase are involved
    4. Replication happens differently between the leading strand and lagging strand.

Here’s how to teach this material.

Start with some discovery learning about the structure of DNA

As an entry way into DNA structure, I like to do an activity about how the structure of DNA was discovered. To do that, I use an this activity: Discovering the Structure of DNA. This activity presents the “clues” that were uncovered in the 1800s and 1900s that eventually enabled Watson and Crick to develop their double helix model of DNA. After each clue, students draw inferences. At the end of the activity, students can use this DNA Model Construction Kit (a Google Slideshow)  to create their own model of DNA. If you’re in person with your students, you can award “Nobel Prizes” to any group that gets their model right. My Nobel Prize was a gold star. If your students are like mine, you can get an AP Bio student to work pretty hard for a gold star.

The activity takes about an hour, and it’s designed for students to do in groups. The Google Docs version works very well in a breakout room. If you’re able to fo the paper version, make the model pieces on cardstock, and save each group’s cut outs (so you can save time next year).

DNA Structure and Replication Tutorials

Following that, you can send your students to learn-biology.com for these three tutorials:
1. DNA: An Overview
2. DNA Structure
3. DNA Replication
which are accompanied by this student learning guide

The overview will give your students mastery of diagrams like this:
00_simple transcription, translation, numbered
and related concepts: replication, transcription, and translation.

The second tutorial will enable your students to explain the structure of DNA, both at a big picture level like this:
10_DNA, two strands
and also like this:
13c_DNA for qwiz, 2014
Concepts like base pairing rules, nucleotide structure, hydrogen bonding, are all covered. Note that at this point in the course, I don’t say much about plasmids, but I do cover them in two other places: my module about bacterial genetics and operons, and in this tutorial about genetic engineering.

In my DNA replication tutorial, students learn about replication on a big picture level, and then in a way that covers all of the required enzymes (excepting topoisomerase, so don’t forget to mention that to your students). By  the end of the tutorial, your students will be able to talk their way through diagrams like this, explaining all the relevant enzymes.
31_dna-replication-smv-numbered
They’ll also have mastery of this one, contrasting the leading and lagging strands.
27b_okazaki-fragments-lettered

Other Resources

Here’s a few other activities/resources for teaching DNA Structure and Replication

  1. Pulse chase primer experiment (AKA Meselson-Stahl Experiment) HHMI. This is a fantastic way to walk your students though what has been called the “most beautiful experiment in biology.” Once you do this, your students will understand both what the semiconservative model of DNA replication is, and how it was verified.
  2. HHMI’s DNA Replication Computer Animation (see # 6 on my tutorial), or here on youtube. After you go over my tutorial with your students, you should show this much more detailed computer animation.
  3. Music Videos
    1. DNA, Fantastic! This is my music video that explains DNA structure. It was my first ever rap song, and my first collaboration with my music producer, Max Cowan.
    2. DNA Replication: This music video explains the entire replication process, hitting almost every enzyme. It’s all done to a salsa beat, and the animations are very useful.
  4. DNA Replication Diagrams. This has pretty much every diagram of my website in a form that you can use to review with your students.

Transcription and Translation: The Big Picture

When you’re teaching processes like transcription and translation, it’s easy to get lost in the details. So what’s important? Let’s look at transcription and and translation from the perspective of biology’s four big ideas.

EVOLUTION:  Transcription and translation are how changes in genotype by mutation or recombination manifest themselves as new phenotypes, which then get acted upon by natural selection. In these pandemic times, it’s hard not to think of how viruses in the coronavirus family were randomly mutating and recombining, until a viral RNA sequence arose that coded for a spike protein that was particularly good at binding with the ACE protein on the surface of epithelial cells in the human respiratory system. That was what made the spillover from bats to humans possible. It’s painful to think of this as an example of a successful phenotype, but that’s exactly what it is.

To go broader, this connection between information in nucleic acids and action in proteins is what life itself is all about. Years ago I was lucky enough to attend a lecture by Richard Dawkins in San Francisco. Dawkins was asked what life on other planets would be like. His response: some kind of genetic system for storing and transmitting information from cell to cell and from generation to generation. On Earth, that’s DNA. There would also be some system for manifesting this genetic information as an action system that would replicate those genes. On Earth, that’s to some extent RNA (which can itself be catalytic) but mostly it’s the protein that RNA codes for. On other planets, both systems could be chemically very different from what we have on Earth, but both will have to be there in some form.

INFORMATION FLOW: The flow of information in living things is what transcription and translation are all about. In terms of information, we see the central dogma at work. Information in a DNA template strand flowing to pre-mRNA in a eukaryotic nucleus, then flowing into the cytoplasm where ribosomes translate that message into protein. DNA triplets become mRNA codons, which become sequences of amino acids.  To take this a step beyond the central dogma, this primary structure (the polypeptide sequence) has information to specify a specific 3D shape (which programs like Deep Mind can now predict).

Information flowing inward to organisms, tissues, or cells can impact the outward flow of information. To make this connection to your students, you can talk about how hormones like estrogen, testosterone, and growth hormone bind with cytoplasmic receptors, which then diffuse into the nucleus activating transcription. This is a topic that we’ll cover soon when we look at operons,  eukaryotic gene regulation and development.

ENERGY FLOW: The synthesis of RNA sequences in mRNA, tRNA, and rRNA from RNA nucleotides is a big uphill push against entropy, and it doesn’t happen spontaneously. This endergonic reaction proceeds because RNA nucleotides come in to the nucleus as triphosphate nucleotides (like ATP). RNA polymerases use the energy in those phosphates to synthesize strands of RNA. Similarly, a lot of ATP is required to power the formation of peptide bonds during protein synthesis. To help students make some connections that they might not make on their own, it’s a good idea to remind your students that this energy can be traced back to cellular respiration, powered by glucose (and other fuels), ultimately powered by the sun.

SYSTEMS: Transcription of RNA and protein synthesis are both processes that are deeply embedded in the structure of cells. But the system can be simplified to run in vitro, which you can read about here on Wikipedia. These cell-free systems are not new: Marshall Nirenberg used such a system to decipher the genetic code.

Transcription and Translation Learning Objectives

According to the College Board (in their 2019 CED, available in condensed form here), here’s what you should be covering in relationship to transcription and translation . What’s below is a lightly edited summary of the CB’s original objectives.

TOPIC 6.3: Transcription

  1. Describe how genetic information flows from DNA to RNA to protein.
    1. Explain how the sequence of RNA bases, together with the structure of the RNA molecule, determines RNA function—
      1.  mRNA molecules carry information from DNA to the ribosome.
      2. Distinct tRNA molecules bind specific amino acids and have anticodon sequences that base pair with the mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence.
      3.  rRNA molecules are functional building blocks of ribosomes.
    2. Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein.
    3. RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule. This process is known as transcription
    4. The DNA strand acting as the template strand is also referred to as the noncoding strand, minus strand, or antisense strand. Selection of which DNA strand serves as the template strand depends on the gene being transcribed.
    5. The enzyme RNA polymerase synthesizes mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction.
    6. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications—
      1. a. Addition of a poly-A tail.
      2. b. Addition of a GTP cap.
      3. c. Excision of introns and splicing and retention of exons.
      4. d. Excision of introns and splicing and retention of exons can generate different versions of the resulting mRNA molecule; this is known as alternative splicing.

TOPIC 6.4: Translation

  1. LO IST-1.O: Describe how the phenotype of an organism is determined by its genotype.
    1. Translation of the mRNA to generate a polypeptide occurs on ribosomes that are present in the cytoplasm of both prokaryotic and eukaryotic cells and on the rough endoplasmic reticulum of eukaryotic cells.
    2. In prokaryotic organisms, translation of the mRNA molecule occurs while it is being transcribed.
    3. Translation involves energy and many sequential steps, including initiation, elongation, and termination.
      1. Exclusion: the details and names of enzymes and factors is outside of scope.
    4. The salient features of translation include—
      1. Translation is initiated when the rRNA in the ribosome interacts with the mRNA at the start codon.
      2. The sequence of nucleotides on the mRNA is read in triplets called codons.
      3. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids are encoded by more than one codon.
      4. Nearly all living organisms use the same genetic code, which is evidence for the common ancestry of all living organisms.
      5. tRNA brings the correct amino acid to the correct place specified by the codon on the mRNA.
      6. The amino acid is transferred to the growing polypeptide chain.
      7. The process continues along the mRNA until a stop codon is reached.
      8. The process terminates by release of the newly synthesized polypeptide/protein.
        1. EXCLUSION: don’t memorize the genetic code
  2. Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.
    1. Exclusion: see DNA exclusion above

On Learn-Biology.com, we cover everything listed above in the tutorials below, with two exceptions:  processing of eukaryotic RNA, and retroviruses. That’s because these topics are covered in two modules that I’ll talk about below: Eukaryotic gene regulation and Viruses.

Interactive Tutorials

Learn-Biology.com covers transcription and translation through four tutorials.

1. Transcription
2. The Genetic Code
3. Translation/Protein Synthesis
4. Protein Targeting to the Rough ER

These are accompanied by this student learning guide.

The first tutorial starts by teaching the differences between DNA and RNA, and the slightly different base pairing rules (A pairs with U, not T). Students learn the basics of transcription, and will be able to explain diagrams like the one below.
10_transcription, numbered

In the second tutorial, students learn how to use a genetic code dictionary:

genetic code, tabular

The third tutorial works through the entire process of protein synthesis, guiding your students through the various RNAs involved, and through diagrams like this:
15_ribosome with mRNA and tRNAs, showing binding sites
The last tutorial in this sequence goes outside of the standards to teach about protein targeting. The underlying question here is how to ribosomes “know” whether to assemble their proteins freely in the cytoplasm, or as bound ribosomes attached to the Rough E.R. You can skip this if you’re pressed for time, but for me, this is a super-important feature of how cells work (and it only takes a few minutes).

Other Resources

Here’s a few other activities/resources for teaching transcription and translation:

  1. Of all the music videos I’ve made, my Protein Synthesis Song is one of my personal favorites. It explains the whole process, and has a great sing along chorus. While I’m not a big fan of Heavy Metal, this song comes pretty close. You can view it here on learn-biology.com
  2. Flinn has two excellent POGILs on transcription and translation. They’re entitled “Gene Expression—Transcription”: and “Gene Expression—Translation.”
  3. Here’s a link to a guided lecture note taking sheet. It has a a lot of practice exercises about transcription, translation, using the genetic code that you can use to check for understanding and for generating mastery.

Week 17: Finishing Transcription and Translation; Mutation, and Viruses

Let’s take stock of where we are within Unit 6. If you’re following this scope and sequence, then within a day or two you’ll be done with transcription and translation (topics 6.3 and 6. 4 in the College Board’s Course and Exam Description). What’s next in that outline is
  • Topic 6.5: Regulation of Gene Expression.
  • Topic 6.6: Gene Expression and Cell Specialization
  • Topic 6.7: Mutations
  • Topic 6.8: Biotechnology

You certainly could go in that direction (and Learn-Biology will support you in doing so), but I suggest that you do the following:

  1. Topic 6.7: Mutation
  2. Viruses (also 6.7, but see the notes below about viruses in the AP Curriculum)
  3. Bacterial Genetics and Operons (1st part of gene regulation, topic 6.6)
  4. Biotechnology (topic 6.8)
  5. Eukaryotic Gene Regulation and Development

Part of the reason why I follow that sequence is because it fits with my curriculum. At BHS, we’ve all been trained in the AMGEN Biotechnology experience, and we do a big biotechnology unit after Winter Break. To understand these labs (and labs like BioRad’ pGLO lab), students need to know how operons work. That’s because a key concept in the lab involves not just inserting a gene-bearing plasmid into bacterial cells, but also inducing gene expression through a system that, functionally, operates just like the lac operon.

In what’s below, I’ll walk you through Mutations and Viruses. Remember that you might have to spend a day or two this week finishing up transcription and translation. That’s fine. three days is enough to teach mutation and viruses.

3 Days of instruction for Week 17

Why 3 days?  I’m in finals week. But I’m not giving a final, because it doesn’t make sense to give up a week of instruction to review semester 1. Instead, my advice is to save that time for reviewing in April, and cover material now. So, at my high school, I have two regular days of instruction, then a 2 hour finals block. I’m going to use that time for journal read-arounds, a bit of makeup time on Learn-Biology.com, and then a lesson about translation/protein synthesis.

Day 1: Consolidate DNA replication  using this handout. Assign Transcription for HW.

Day 2: Consolidate transcription and move into translation using this handout.

Day 3: Finish translation (see handout for day two).

Week 18: Mutation, Viruses, Operons

The goal is to cover three topics this week, supported by the following Learn-Biology.com tutorials and student learning guides. In addition, in the day by day instructions below you’ll find additional handouts.

Here’s how you’ll do this in 5 days of instruction

Day 1: Introduce Mutations through the Mutations POGIL. Assign the mutations tutorial for homework.

Day 2: Introduce Viruses, using this handout: Assign the first module in viruses for homework.

Day 3: Consolidate learning about viral life cycles. Introduce SARS-CoV-2 and COVID-19. Assign the COVID-19 tutorial for homework.

Day 4: Brief lesson on Antigen Rapid Test. Assign the Tutorial on Rapid Antigen Testing for Homework.

Day 5: Teach about Operons, using this handout. Assign operons tutorial for homework.

Mutation Learning objectives

If you want a look at the College Board’s Objectives for Mutations in my condensed outline, go here. What’s below renders these into a more student (and teacher) friendly form.

  1. Define Mutation
  2. Using sickle cell anemia as an illustrative example, explain how mutations can cause changes in phenotype
  3. Compare and contrast somatic and germ line mutations: where they occur, and what their consequences are.
  4. Describe various types of point mutations
    1. silent
    2. missense
    3. non-sense
    4. insertions and deletion errors leading to a frameshift.
  5. Explain how mutations come about.
  6. Explain how mutations can be harmful, beneficial, or neutral.
  7. Be able to explain specific examples of mutations.
    1. sickle cell (mentioned above)
    2. Mutations in the CFTR gene in relationship to cystic fibrosis
    3. Mutations in MC1R and adaptive melanism in the rock pocket mouse.
  8. Explain the overall importance of mutation to evolution.

NOTE: Chromosomal mutations related to non-disjunction are covered in this tutorial in Unit 5. We cover phenomena like the evolution of antibiotic and pesticide resistance in this tutorial  in our Evidence for Evolution Module.

Mutation Tutorial on Learn-Biology.com

You can help your students master all of the above at our Mutation Tutorial.

Other Mutation-Related Learning Resources

Along with our tutorial, Flinn’s Genetic Mutations POGIL will help your solidify your student’s understanding.

Teaching about Viruses

The word “virus” only shows up in two places in the Course and Exam Description. It shows up in topic 6.4 in the context of reverse transcriptase.

Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.

and it shows up in topic 6.7 (mutation) as

Related viruses can combine/recombine genetic information if they infect the same host cell.

But here we are, in the midst of the COVID-19 Pandemic. It’s been a tragedy on so many levels…and it’s probably the most teachable moment any practicing biology teacher will ever experience. So there’s no way I’m going to have my students finish my AP Biology course without them having a deep understanding of viruses in general, and SARS-CoV-2 in particular. On top of that, I feel a deep responsibility to provide accurate information to counter the  lies and misinformation that many of our students have been exposed to. So I hope you join me in taking the time to teach at least what’s below about viruses.

Here’s an outline of what I teach in my Viruses tutorial, which is supported by this student learning guide. I’m including relevant diagrams so you can get a quick sense of what your students will learn from our tutorials.

  1. What a virus is, and how viruses straddle the boundary between living and non-living.
  2. The basic structure of viruses, starting with phage.
  3. The lytic cycle
  4. The lysogenic cycle
  5. The life cycle of HIV (as an illustrative example of a retrovirus). This covers the learning objective from Topic 6.4, above.
  6. How viruses develop their own genetic diversity through recombination and mutation, and how they introduce variation into other species through transduction. This covers the learning objective from Topic 6.7 above.
  7. The life cycle and overall biology of SARS-CoV-2
  8. mRNA vaccines
  9. How Rapid Antigen Tests Work

Again: I think it’s part of our mission as biology teachers to be promoting understanding of the novel coronavirus, and vaccines. I hope you’re on board with my battle against our common enemy Biology Confusion. 

Additional resources

  1. I have a long list of resources at the bottom of my COVID-19 Tutorial. You can find additional readings in the SARS-CoV-2 section of my Recommended Readings page. Giving your students a day to do open ended research about COVID-19 related topics of interest and then sharing their results is a great use of class time.
  2. My music video, “I’m a Virus,” will help your students learn a lot of basic virus biology. It was written way before COVID, but it does include a stanza with visuals about the biology of HIV.
  3. See the day by day instructions above for the handout I use for direct instruction.

Teaching about Bacterial Genetics and Operons

Once you’ve taught about mutation and viruses, you can move onto Bacterial Genetics and Operons. The relevant learning objectives and topics are spread out in the College Board’s CED, but here’s a reasonable outline of what you should cover.

1. List and describe 5 sources of genetic diversity in bacteria. A successful response will include the following.

  • mutation
  • transformation (uptake of naked DNA),
  • transduction (viral transmission of genetic information),
  • conjugation (cell-to-cell transfer of DNA), and
  • transposition (movement of DNA segments within and between DNA molecules) increase variation.

2. Operons, including

  • Describe the basic structure of an operon (regulatory genes, promoters, operators, structural genes).
  • Describe how operons work as a regulatory system allowing bacteria to respond in an adaptive way to their environment. This should include an description of
    • the Lac operon (an inducible operon)
    • the Trp operon (a repressible operon).

Note that both Lac and Try involve negative regulation. I also include CAP and positive gene regulation as an advanced topic.

While there’s nothing about operons that’s particularly difficult — it’s just one of many beautifully complex processes that we’re lucky enough to teach — there are a few things that are important to emphasize. One thing is what Sean Carroll in The Serengeti Rules calls double negative logic. In the lac operon, lactose shuts down a regulatory molecule, which otherwise would shut down the expression of the gene. The second thing is that the regulatory protein works through allosteric interaction with lactose. In fact, allosteric interactions, which you probably taught back in Unit 3 when you were teaching about enzymes, was actually discovered by Jacques Monod as he was figuring out how operons worked.

By the end of the tutorial, your students will be able to explain what’s happening in this diagram of the lac operon.

and this diagram of the trp operon

Additional Resources

I recommend Flinn’s POGIL about operons. It’s entitled “Control of Gene Expression in Prokaryotes.” In addition in the day by day instructions above, you’ll find my handout for consolidating your students understanding of Bacterial Genetics and Operons.

Week 19: Biotechnology

Biotechnology

Once you’ve taught about operons, you’re ready to move into Biotechnology.

At Berkeley High School, we spend about two weeks doing a series of biotechnology labs that are part of the AMGEN Biotechnology Experience. This is a series of labs that walks your students through:

  • restriction digestion of plasmids
  • gel electrophoresis
  • bacterial transformation. This transformation is with a plasmid containing a gene for red fluorescent protein, and an arabinose-triggered operon. If you’ve done BioRad’s pGLO lab, this is very similar (and covers the same content).

Extensions allow you to do

  • a ligation where you actually build the plasmid
  • purification of gene product.

Amgen will train you for free, and then supply your school with all the needed supplies (consumables and hardware) for free. It’s amazing professional development for you, and a great lab experience for your students. I can’t recommend it highly enough.

Last year, the pandemic forced us into remote teaching. To fill the gap, we created this video. It shows the steps of the lab (carried out by my colleagues at Berkeley High school), and explains the science of the lab (explained by me). Please feel free to use it to orient your students to some key biotechnology techniques and concepts

Biotechnology and Genetic Engineering Learning Objectives (Topic 6.8)

You’ll find that what’s on Learn-Biology.com more than covers what what the College Board, in their Course and Exam description, wants your students to know. Here’s an edited version of these objectives.

  1. Explain the use of genetic engineering techniques in analyzing or manipulating DNA.
    1. Electrophoresis separates molecules according to size and charge.
    2. During polymerase chain reaction (PCR), DNA fragments are amplified.
    3. Bacterial transformation introduces DNA into bacterial cells.
    4. DNA sequencing determines the order of nucleotides in a DNA molecule.

Biotechnology and Genetic Engineering Tutorials on Learn-Biology.com

Here are the tutorials I’ve written to help your students master the key ideas and techniques of biotechnology. Note that the first two tutorials lie squarely within the bounds of the AP Bio curriculum, as does the 1st half of tutorial 3 (DNA fingerprinting). But the other tutorials in this module should be considered illustrative examples. If your students complete them (and you go over the tutorials in a way that solidifies your students understanding), you can be sure that your students will deeply understand DNA, how it works, and how it can be manipulated.

Some of these tutorials are long. I would give only one/night, so it takes about a week to make it all the way through the module.

1. Introduction to Genetic Engineering:

Teaches your students how restriction enzymes, DNA ligase, etc. can be used to create genetically engineered products such as insulin.

2. PCR

A very short tutorial about the polymerase chain reaction.

3. DNA Fingerprinting/Profiling

Teaches the basic principles of using restriction enzymes to create restriction fragments, which can then be sorted by size through electrophoresis. The tutorial continues to explain how DNA profiling can be done.

4. First Generation DNA Sequencing (Sanger Method)

Explains how DNA sequencing is done. If your students understand this, they will truly understand how to think critically on a molecular level about DNA and DNA replication.

5. CRISPR-CAS9

An introduction to this revolutionary gene editing system. Jennifer Doudna, who recently won the Nobel Prize for this work, lives in Berkeley. If you want your students to get to know her a bit better, you can show them this video of an interview I was able to do with her last year for a school fundraiser.

Additional Resources

If you’re in a situation where you can do actual biotechnology in the classroom, then

  • doing those activities during class time,
  • assigning Learn-Biology.com for homework
  • Using additional class time to go over the lab and what’s on Learn-Biology.com

will probably take the full week that’s allotted to this topic.

If you can’t do any labs, then HHMI has two online simulations

Week 20: Eukaryotic Gene Regulation and Animal Development

We’ll finish unit 6 with two final topics: eukaryotic gene regulation and animal development. These are both difficult topics to teach. Please start by skimming over the College Board’s learning objectives. Note that “EU” is an enduring understanding, “LO” is a learning objective, and “IST” is information storage and transfer”

College Board Learning Objectives for Gene Expression and Animal Development (Topics 6.5 and 6.6).

If you like to consult the College Board’s learning objectives before planning instruction, here they are.

Topic 6.5: Regulation of Gene Expression

  1. EU IST-2: Differences in the expression of genes account for some of the phenotypic differences between organisms.
  2. LO IST-2.A: Describe the types of interactions that regulate gene expression.
    1. IST-2.A.1: Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription.
    2. IST-2.A.2: Epigenetic changes can affect gene expression through reversible modifications of DNA or histones.
    3. IST-2.A.3: The phenotype of a cell or organism is determined by the combination of genes that are expressed and the levels at which they are expressed—
      1. a. Observable cell differentiation results from the expression of genes for tissue-specific proteins.
      2. b. Induction of transcription factors during development results in sequential gene expression.
  3. LO  IST-2.B: Explain how the location of regulatory sequences relates to their function.
    1. IST-2.B.1: Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated—
      1. a. In prokaryotes, groups of genes called operons are transcribed in a single mRNA molecule. The lac operon is an example of an inducible system.
      2. b. In eukaryotes, groups of genes may be influenced by the same transcription factors to coordinately regulate expression.

Topic 6.6, Gene Expression and Cell Specialization

  1. EU IST-2: Differences in the expression of genes account for some of the phenotypic differences between organisms.
  2. LO IST-2.C: Explain how the binding of transcription factors to promoter regions affects gene expression and/or the phenotype of the organism.
    1. IST-2.C.1: Promoters are DNA sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription.
    2. IST-2.C.2: Negative regulatory molecules inhibit gene expression by binding to DNA and blocking transcription.
  3. LO IST-2.D: Explain the connection between the regulation of gene expression and phenotypic differences in cells and organisms.
    1. IST-2.D.1: Gene regulation results in differential gene expression and influences cell products and function.
    2. IST-2.D.2: Certain small RNA molecules have roles in regulating gene expression

Through two modules on Learn-Biology.com, you can ensure that your students know what they need to know.

Eukaryotic Gene Regulation and Expression

This module starts with a tutorial about regulation of chromatin structure.  The key thing I emphasize here is how most DNA in a cell is tightly wound up as heterochromatin, and not transcribed. A small proportion, by contrast, is euchromatin, which is available for transcription. These differences correspond to chemical modifications of either DNA or the histone proteins that package the DNA. A key diagram is this one. showing DNA methylation (6) and histone acetylation (7):

This can be pretty abstract unless you can fold it into a story…and fortunately, nature’s provided one. This is the story of X-chromosome inactivation, Barr Bodies, and how you can see that manifested in tortoiseshell cats.

By the end of the tutorial, your students will be able to explain diagrams like this, which show the random pattern of X inactivation and Barr body formation that occurs early in female embryonic development…

…which, with a bit of imagination, gets you to this:

That kind of modification of DNA is a huge chunk of what epigenetics is: how modifications to DNA that don’t affect sequence control gene expression. The mind-blowing stuff is the intergenerational transfer of these modifications that can occur. I cover this through an excerpt about the Dutch Hunger Winter, and its intergenerational legacy.

The second tutorial focuses on regulation of transcription. In other words, for that portion of DNA that is transcribable, what determines when it gets transcribed? This focuses on the role of enhaners/regulatory switchers (at “a”) which interact with regulatory molecules (at “b”), leading to the formation of transcription initiation complexes (at “j”) that allow RNA polymerase to bind and transcribe DNA. These complexes look like this:

If the setup for transcription in Eukaryotes isn’t complex enough, there are post-transcriptional modifications required before eukaryotic RNA can become mRNA that gets translated into protein.

Through interacting with diagrams like the one above, students will learn about introns, exons, and other post-transcriptional RNA modifications.

This is very complex material, which is why it’s important that students have lots of opportunity to interact with the material (which is, of course, why you’re sending your students to learn-biology.com).

The third tutorial looks at the intersection between gene regulation and evolutionary change, as seen in the Threespine Stickleback.

The difference between the spiny and spineless forms of these fish isn’t about the protein-coding Pitx1 gene, but upon mutations in the upstream pelvic enhancer.

Finally, there are post transcriptional modes of regulation and expression. This includes alternative splicing or exon shuffling, in which exons can be spliced together in different orders, essentially creating different proteins from the same RNA.

It also includes various small RNAs which interact with messenger RNA to either silence it altogether, or to interfere with its translation (a phenomenon known as RNA interference).

Animal Development and Cell Specialization

The second module tells one of the greatest stories in biology: how a fertilized egg develops into a complex, multicellular organism. I start by briefly introducing some of the key events in development: fertilization, cleavage, and gastrulation. These stages are not in the standards, but it felt impossible to teach the essential questions without describing the cell division, migration, and differentiation that happens during the beginning of any animal’s life.  That provides context for some of the key questions we want our students to be focusing on:
1. how do cells know where to go?
2. How does a cell know what type of cell it should develop into?

The answer to these questions are astoundingly complex. By the end of the module, your students will be able to explain ideas like:
Genomic equivalence: all cells have the same DNA. They’re different because they express different genes

Induction: some cells release hormone-like molecules that activate specific genes in other cells. 

Apoptosis: timed programmed cell death is an essential part of the sculpting of form from an undifferentiated embryo

Homeotic genes: highly conserved genes that control the differentiation of body regions. 

Other resources:

HHMI has a few spectacularly good activities related to the evolution and development of the threespine stickleback. Over and over again in the course of evolution, these fish, when confined to freshwater environments, have lost their pelvic spines. My third tutorial in my Eukaryotic Gene Regulation module takes the story of this fish and renders it into an interactive form.

Depending on how much time you have you can do an entire virtual lab (which takes several class periods) or watch a video and do one or multiple worksheets.

Go to https://www.biointeractive.org/classroom-resources, search for “stickleback” and you’ll have many choices. But at the very least, I hope you have your students watch the video, and do this worksheet.

Summative Activities for Unit 6

To pull together Unit 6

  1. Use the AP Bio review materials on Learn-Biology.com. Your students can access these same materials on the Biomania AP Bio app, and results from both are recorded in your teacher dashboard. These review materials include
    1. Unit 6 AP Bio Review Flashcards
    2. Unit 6 AP Bio Review Multiple Choice Questions
    3. Unit 6 AP Bio Review Free Response Questions
  2. The progress check questions on for Unit 6 on AP Classroom.

Links