Unit 3 Table of Contents

  1. Introduction: Sequencing Unit 3
  2. Week 8: Enzymes
  3. Weeks 9 and 10: Cell Respiration
  4. Weeks 11 and 12: Photosynthesis, start Mitosis/Cell Division
  5. Summative Activities for Unit 3

Introduction: Sequencing Unit 3

Unit 3 of AP Bio focuses on Enzymes, Cellular Respiration, and Photosynthesis. This is one of my favorite units of the course. The biology is fabulous, with opportunities to talk about every key theme in biology. In addition, there are three major labs.

In terms of sequence, I suggest that you do the following (which is different from the College Board’s sequence in their Course and Exam Description).

  1. Start with Enzymes (Topics 3.1 – 3.3)
  2. Then do Cellular Respiration. This includes Topics 3.4 (general issues related to cell energy), followed by Topic 3.6  (Cellular Respiration)
  3. End with Photosynthesis (Topic 3.5)

Why cellular respiration before photosynthesis? For me, this is partly based on my own professional history. I started teaching AP Biology using Neil Campbell’s Biology, which puts cellular respiration first. That sequence is also what’s used in my other favorite textbook: Principles of Life (Hillis, Sadava, Hill, and Price). It’s also used in Principles of Biology (Brooker, Widmaier, Graham, and Stiling). But it’s not a slam-dunk: Sylvia Mader teaches photosynthesis first, then moves on to cellular respiration.

In any case, cellular-respiration-first is the sequence I’ve adopted in my own teaching, and in the interactive modules on Learn-Biology.com. What you’ll see is that teaching the electron transport chain, chemiosmosis, and ATP production in mitochondria sets the stage to easily transfer understanding of these processes to what happens in  in chloroplasts during the light reactions of photosynthesis.

Topic 3.7, Fitness, is kind of a weird outlier. I’m not sure why the College Board placed it in unit 3. We’ll deal with it when we talk about evolution in Unit 7, and in Topic 8.6 (Biodiversity).

Finally, we skipped some of the cell biology related to mitochondria and chloroplasts in Topic 2.2. You’ll see that embedded below in the objectives for cellular respiration and photosynthesis.

Week 8, Enzymes

Objectives for Enzymes (Topics 3.1 – 3.3)

You can see the College Board’s original objectives for Topics 3.1-3.3 in their Course and Exam Description, or in my condensed version of the same document. Here are these objectives in a friendlier form.

  1. Describe the key properties and function of enzymes. This description should include the following:
    1. Enzymes are complex, large proteins that facilitate chemical reactions by reducing activation energy.
    2. Enzymes are highly specific, and generally interact with only one substrate.
    3. Enzyme specificity is based on the complementary shape and charge between the enzyme’s active site and the substrate.
  2. Explain how changes in an enzyme’s shape affect the enzyme’s function. The explanation should include:
    1. Because enzymes are proteins, their shape is stabilized by internal bonds that can be disrupted by changes in the enzyme’s environment.
    2. Denaturation is when a change in an enzyme’s shape reduces its ability to bind with its substrate.
    3. Denaturation can be reversible or irreversible.
  3. Explain the effect of changes in temperature on enzyme activity
    1. At moderate temperatures, temperature increase will increase enzyme-substrate collisions, increasing enzyme activity.
    2. At high temperatures, enzymes can denature, reducing their activity
  4. Explain the effect of changes in pH or ion concentration on enzyme activity.
    1. Enzymes have a pH and ion concentration optimum.
    2. Environmental changes that move the pH and ion concentration above or below that optimum will disrupt the enzyme’s internal bonds, changing the shape of the enzyme’s active site, reducing its activity.
  5. Explain the effects of enzyme and substrate concentration on enzyme activity
    1. Enzyme activity will increase with increased enzyme and substrate activity until the enzymes’ active sites are saturated. At that point, enzyme activity reaches its maximum rate.
  6. Explain the role of competitive and non-competitive inhibitors on enzyme activity
    1. Competitive inhibitors reduce enzyme activity by competing with substrates for the enzyme’s active site.
    2. Non-competitive inhibitors bind at a region away from the active site (an allosteric site). However, that binding changes the shape of the active site, reducing the enzyme’s activity.
  7. *Explain how cells can regulate enzyme activity through feedback inhibition and allosteric regulation.
    1. In feedback inhibition, the product of an enzymatic reaction acts as a competitive or non-competitive inhibitor of enzyme activity, creating negative feedback that reduces enzyme activity.
    2. In allosteric regulation, a substance produced by a metabolic pathway binds with an enzyme at an allosteric site. This can inhibit or stimulate enzyme activity.

*this is not in the Course and Exam description, but you should definitely teach it here.

Enzyme tutorials on Learn-Biology.com

Learn-Biology organizes learning about enzymes into two tutorials, supported by this student learning guide.

  1. Enzymes Tutorial 1 (Enzyme Structure and Function)
  2. Enzymes Tutorial 2(Enzyme Inhibition and Regulation)

Enzyme Labs and other Activities

If you want to add some music to your instruction, show my Enzymes! Music Video. 

If you didn’t do the Starch Amylase Lab when you were teaching about monomers and polymers, then now you have another opportunity. If you did, then remind students that this was all about enzymatic hydrolysis.

The “official” lab for this unit is the Potato Catalase Lab. I’m indebted to Pam Phelps for sharing her version of this lab with me, and teaching me (and a bunch of other teachers) how to do the lab via Zoom during the in fall of 2020. I’ve revised Pam’s lab handout to include standard error calculations. Here’s my version from last year (obviously designed for students to do at home).

Weeks 9 and 10, Cellular Respiration

Some Big Picture Ideas about Cellular Respiration

Cellular respiration is exciting to teach because it allows you to make use of pretty much everything you’ve taught in the course so far.

  • It (mostly) happens in the mitochondria, an endosymbiotic organelle.
  • The whole process is carried out by enzymes.
  • The process of ATP production relies on
    • cellular compartmentalization (the intermembrane space);
    • protein structure (think of ATP synthase as a phenomenal example of a structure/function relationship at the molecular level);
    • active transport (protons getting pumped into the intermembrane space), and
    • facilitated diffusion (proton diffusion through ATP synthase back to the mitochondrial matrix).
  • ATP and ATP synthesis via chemiosmosis is powerful evidence for the unity of life. It’s present in every Domain. Not only that, but the ATP synthase channel that’s used in cellular respiration is a clear homologue for the one used in photosynthesis.

I encourage you to challenge your students to do this kind of connecting. That can be as simple as listing the processes above (endosymbiosis, compartmentalization, protein structure, etc.), and asking students to brainstorm where they show up in the process.

I use this diagram as my touchstone during this unit.
06_for-every-glucose-w-etc_for-every-glucose-w-etc

If you’ve been influenced by Understanding by Design, one of my favorite books about curriculum design, then you can think of the goal of the the entire unit as this: students, when presented with this image, can explain the cellular and biochemical processes by which the chemical bond energy in glucose can be converted into ATP.  During your unit, as you teach glycolysis, the link reaction, Krebs and the ETC, you can come back to this diagram again and again, and have your students expand the detail with which they explain the process.

It’s really important that students understand that cellular respiration is built upon on two types of sub-processes: REDOX, and phosphorylation. I go to some length to explain both in my Cellular Respiration Overview interactive tutorial, using diagrams like this for REDOX
08a_nadh-nad-copy
and this for substrate level phosphorylation.
substrate-level-phosphorylation

In terms of REDOX, you don’t need to go deeply into the chemistry. It’s enough for students to know that things that are reduced have more energy than things that are oxidized. Where’s the energy? In their electrons. It’s a bit confusing, but that electron energy is usually shown by the presence of a hydrogen. That’s why NADH is the reduced form, and NAD+ is the oxidized form. To give this chemistry some real world context, you can tell your students that a substance like peanut butter is reduced. So is bread. So are we. These are all examples of things with lots of chemical energy. By contrast, carbon dioxide is oxidized. So is ash. So is rust. These are all low-energy substances.

Once you’ve built that foundation, then it’s all downhill when you’re teaching about glycolysis (in which the oxidation of glucose is coupled to the reduction of NAD+ to NADH) or the Krebs cycle. In fact, that’s the way to control the detail so that your students don’t get overwhelmed. When you’re questioning your students to check for understanding, ask questions like What’s happening at 3 in the diagram below? You’re looking for an answer like this: The six carbon compound is oxidized, so that NAD+ can be reduced to NADH. What’s happening at 5? A different enzyme is using the chemical energy in the 4-carbon compound to phosphorylate ADP to ATP.
02a_krebs-simplified

Note that you don’t need to teach any of the intermediates (though they are mentioned in my Krebs Cycle Song). All that our students need to know about is acetyl-CoA, Citric Acid, and oxaloacetate. And they should be able to figure out that the 5 carbon compound at 4 in the diagram above is more reduced than the 4-carbon compound at 7. How would your students know? Because the chemical energy in the 5-carbon compound that’s the reactant for step 4 was used to power the reduction of NAD+ to NADH, and then (after other transformations) of FAD to FADH2 at step 6. Reductions are always coupled to oxidations (and vice versa).

A final way to make this real is to follow the carbon dioxide molecules. I always teach my students that this is where the carbon dioxide they breathe out is coming from. Specifically, two out of every three carbon dioxide molecules that you exhale come from the Krebs cycle. The other 1/3 comes from the Link Reaction.

Learning Objectives for Energy and Cellular Respiration (Topics 3.4 and 3.6)

You can see the College Board’s original objectives for Topics 3.1-3.3 in their Course and Exam Description, or in my condensed version of the same document. Here are this week’s objectives in a friendlier form.

For Cell Energy (Topic 3.4) Describe the role of energy in living organisms. A description should include the following:

  1. Creating and maintaining the complex order in living things requires a constant input of energy.
  2. For life to be maintained, energy input has to exceed energy loss.
  3. Energy-requiring processes (endergonic processes) are typically coupled with energy releasing (exergonic) processes.
  4. Among the most common coupled reactions are
    1. Linking oxidation of food to reduction of electron carriers
    2. Linking the hydrolysis of ATP to ADP and phosphate (an exergonic reaction) to any endergonic process (synthesis, movement, and any other kind of work).
  5. Creating ATP from ADP and phosphate is endergonic, and is coupled to exergonic reactions.
  6. Energy pathways are sequential, controlled, and efficient.

For Cellular Respiration (Topic 3.6): Explain how cells obtain energy from biological molecules (typically glucose) in order to create ATP.

  1. Explain the overall pathway of cellular respiration (glycolysis, link reaction, Krebs, and the electron transport chain).
  2. Explain what happens during glycolysis (oxidation of glucose is coupled to the reduction of NAD+ to NADH, and the phosphorylation of ADP to ATP.
  3. Explain what happens during the link reaction (pyruvic acid enters the mitochondria, and gets converted to acetyl CoA
  4. Explain the key reactions of the Krebs cycle (oxidation of acetyl-CoA) to power reduction of NAD+ and FAD to NADH and FADH2; and phosphorylation of ADP to ATP.
  5. Explain how electron energy from NADH and FADH2 is used to create a proton gradient, which is in turn used to power ATP synthesis through chemiosmotic diffusion of protons through the ATP synthase channel.
  6. Explain the role of oxygen in the electron transport chain.
  7. Compare and contrast lactic acid and alcohol fermentation.
  8. Connect the structure of the mitochondrion to the key processes of aerobic respiration (Krebs in the mitochondrial matrix; ETC along the inner membrane; protons are pumped to the inter membrane space; inner membrane folding increases surface area, allowing for more ETC components and more ATP synthase).

Resources for teaching energy and cellular respiration on Learn-Biology.com

Our cellular respiration tutorials on Learn-Biology.com are supported by this student learning guide.

The module consists of six tutorials:

  1. ATP and Cell Energy (interactive tutorial)
  2. Cellular Respiration Overview (interactive tutorial)
  3. Glycolysis (interactive tutorial)
  4. The Krebs Cycle (interactive tutorial)
  5. The Electron Transport Chain (interactive tutorial)
  6. Anaerobic Respiration and Fermentation (interactive tutorial)

Additional cellular respiration resources and activities

Labs and demonstrations

The greatest thing about cellular respiration is that you can see it in action. You can measure CO2 production, or oxygen consumption. I prefer to do the latter, the old-fashioned way, with respirometers.

You can also do some very simple demonstrations of fermentation. This includes demonstrations of alcohol fermentation by yeast, and making yogurt (a lactic acid fermentation). Here’s a handout.

For the alcohol fermentation demonstration, get three flasks. Add water. Add a spoonful of yeast to flask 1. Seal with a balloon. Add a spoonful of sugar to flask 2. Seal with a balloon. As a spoonful of yeast and a spoonful of sugar to flask 3. Seal with a balloon. You’ll see results by the next day. It goes without saying that this could be the basis for a lot of inquiry.

Making yogurt is similarly simple. Start with Pasteurized milk (and explain how Pasteurization works). I like to add some nonfat dry milk powder to make a thicker yogurt. Then mix in a bit of yogurt culture (a spoonful of yogurt from any brand). Incubate about 37 C overnight, and you’ll have yogurt the next day. An Instant Pot has a yogurt setting…even easier

Music

I’ve written three three songs about cellular respiration. Glycolysis!, Krebs!, and the Electron Transport Chain. They all have Karaoke versions, so please encourage your students to sing! All of these songs are available on YouTube, but to make access really easy, there’s all on this page: Cellular Respiration: A Musical Review

Video Lectures

To give your students an overview of the entire process, have them watch the these two videos: Cellular Respiration Overview Videos (video lectures)

Additional Handouts

  1. Here’s the review sheet I give to my students to help them prepare for my cumulative assessment on cellular respiration.
  2. Before I flipped my classroom, I used to do comprehensive lecturing about most cellular respiration topics. During my lectures, I found that distributing this guided note taking sheet was something that my students found very useful. With some minor modifications, you can make it into a visual review guide.

Flinn has great POGILs about ATP, Glycolysis/Krebs, and Oxidative Phosphorylation.

Extension

If you want to push your students a bit further, have them read and summarize this article from the NY Times about how sea otters use proton leakage to generate heat (but not ATP).

Weeks 11 and 12: Photosynthesis

Note about timing: It shouldn’t take you a full two weeks to finish photosynthesis. You’ll be done about two days into next week, and then you can start Unit 4.

Most people don’t get what’s happening during photosynthesis

Most people deeply misunderstand photosynthesis. You can see this for yourself by asking your students (or your friends and family members) two questions:

  1. When a plant grows, where does most of the new mass come from?
  2. Where does the oxygen that photosynthesis produces come from?

In terms of the first question, most of my students (and my friends who aren’t science-savvy) think that plants add new mass from the soil. In other words, they think  that “plant food” is like animal food: that when a plant grows, it’s absorbing matter from the soil and incorporating it into its growing body. They’re missing, in other words, the concept of carbon fixation, and the amazing idea that the added mass is mostly from CO2 in the air.

In terms of the second question, many folks who know that oxygen is produced by photosynthesis often mistakenly think that carbon dioxide is the source of that oxygen (not water). As pointed out by Nick Lane in Life ascending, this mistake was famously made by the Italian chemist and Nobel Laureate Primo Levi who wrote in his book The Periodic Table:

Our atom of carbon enters the leaf, colliding with other innumerable (but here useless) molecules of nitrogen and oxygen. It adheres to a large and complicated molecule that activates it, and simultaneously receives the decisive message from the sky, in the flashing form of a packet of solar light: in an instant, like an insect caught by a spider, it is separated from its oxygen, combined with hydrogen and (one thinks) phosphorus, and finally inserted in a chain, whether long or short does not matter, but it is the chain of life.

The oxygen produced by photosynthesis comes from water (or another electron donor), not carbon dioxide.

Here’s the general equation:

Note that the “H2A” varies among prokaryotic photosynthesizers. For example, in purple sulfur bacteria, the hydrogen donor can be hydrogen sulfide (H2S).

But in all eukaryotic photosynthesizers, and in cyanobacteria, the hydrogen donor is water. So the general equation is

For the purposes of AP Biology, you can balance the equation and drop the H2O that appears as a product of the reaction, leaving us with

On several past AP exams, the College Board has tested this by showing the oxygen atoms in the products as labeled with isotopes of oxygen (O18). If you label the oxygen in carbon dioxide (CO182), then the heavy oxygen shows up in the carbohydrate. But if you label the oxygen in the water (H2O18), then the heavy oxygen shows up in the oxygen gas that’s released as a waste product (O218)

I try to avoid this misunderstanding by having students interact with diagrams like this one from my first photosynthesis tutorial (see below).


Similarly, this one, focusing on the inputs to the chloroplast from my second tutorial, serves the same purpose.

When you get to the Calvin cycle, you can emphasize some of its astonishing features. Some of these were highlighted in this story from NPR,

The Calvin Cycle
  • Rubisco (ribulose bisphosphate carboxylase) is the enzyme that’s capable of snatching carbon dioxide out of the air and incorporating it into biological molecules. It might be the most abundant protein on earth. Makes sense: it’s in every chloroplast, in every leaf, in every tree, shrub, herb, blade of grass, and algae on Earth. It’s also in every cyanobacteria.
  • If your students ever complain that this detailed (but wondrous) process is far removed from their daily concerns, remind them that every carbon atom in their body was once a molecule of carbon dioxide floating in the air. We all owe our very being to the Calvin Cycle.
  • Rubisco and the Calvin Cycle as a whole evolved very early on in the history of life — way before there was appreciable amounts of molecular oxygen in the atmosphere or dissolved in the the oceans. As a result, Rubisco has an enzymatic quirk: its active site can bind oxygen (and not just carbon dioxide). This is especially true at high temperatures, and causes Rubisco to incorporate oxygen into the Calvin Cycle, producing a toxic compound that plants have to detoxify, lowering the efficiency of plant growth. Plants like cacti and corn have, as a consequence, evolved supplementary pathways for fixing carbon dioxide. These are the C4 cycle and CAM photosynthesis, respectively. They’re no longer part of our curriculum, but they used to be (before AP bio was redesigned in 2012). If you have some students that need some enrichment, these pathways are great topics for students to explore.

Photosynthesis Learning Objectives

You can see the College Board’s original objectives for Topic 3.5 in their Course and Exam Description, or in my condensed version of the same document. Here are these objectives in a friendlier form.

  1. Describe the cellular location of the reactions of photosynthesis
    1. Chloroplasts are the organelle that carries out photosynthesis.
    2. Within chloroplasts are thylakoids: membrane-bound sacs, organized into stacks called grana.
    3. The photosystems and electron transport chain involved in the light reaction are located in the thylakoid membranes.
    4. The carbon-fixing reactions of the Calvin cycle occur in the stroma.
  2. Describe key evolutionary milestones in the evolution of photosynthesis
    1. Photosynthesis first evolved in photosynthetic bacteria (cyanobacteria)
    2. Prokaryotic photosynthesis created Earth’s oxygen-rich atmosphere.
    3. Chloroplasts are endosymbionts, descended from cyanobacteria that took up residence inside a eukaryotic cell.
  3. Explain the light reactions of photosynthesis
    1. Light energy is converted into electron energy by two chlorophyll rich photosystems. (PS II and PSI)
    2. Electron flow through the electron transport chain of photosystem II is used to create a proton gradient that powers ATP synthesis. The mechanism (pumping protons to a compartment, followed by chemiosmotic flow through ATP synthase) parallels what happens in mitochondrial ATP synthesis.
    3. Electron flow through the ETC of photosystem I is used to reduce NADP+ into NADPH.
  4. Explain the key reactions of the Calvin cycle
    1. The Calvin cycle is responsible for carbon fixation (bringing organic carbon into the biosphere)
    2. The inputs are the products of the light reactions (NADPH and ATP), and carbon dioxide
    3. NADPH  provides reducing power (for hydrogenating CO2)
    4. The reduction of carbon dioxide into carbohydrate is endergonic. Hydrolysis of ATP provides the energy to drive this reaction forward.
    5. Rubisco is the key enzyme involved in carbon fixation (and is the most abundant protein on Earth).

Resources for teaching photosynthesis on Learn-Biology.com

The five tutorials about photosynthesis on Learn-Biology.com are supported by this  Photosynthesis Student Learning Guide

  1. Photosynthesis 1: An Introduction
  2. Photosynthesis 2: The Two Phases of Photosynthesis
  3. Photosynthesis 3: Light and Pigments
  4. Photosynthesis 4: The Light Reactions
  5. Photosynthesis 5: The Calvin Cycle and Comparing Photosynthesis and Respiration

Labs

The spinach leaf disc lab is a fabulous way to get your students to experiment with photosynthesis. The version in the previous link was adapted from one shared by Susan Wentzien at Lake Oswego High School. Note that this was modified for students to do at home during the pandemic, and the formatting might need some modification for distribution as a paper version to be done in a classroom laboratory.

This version of the lab compares different light intensity. However, using filters, you can adapt it to experimenting with different light frequencies, or different carbon dioxide concentrations …lots of great opportunities for follow up labs that allow for student inquiry.

While the spinach leaf disk is what most AP Biology teachers do these days, the College board loves asking questions about a photosynthesis lab from the old lab manual that measures photoreduction of the dye DPIP. DPIP is dark blue when it’s oxidized, and turns clear when it’s reduced. In this version of the lab, you’d extract chloroplasts from spinach leaves. The resulting chloroplast suspensions would be mixed with DPIP, and then placed in the light under a variety of experimental conditions. For example, some chloroplasts would be boiled. Others would be covered in foil. A third would group would be the positive control (exposed to light).

DPIP’s role in the lab is to intercept electrons before they make it to NADP+ reductase. Instead of NADP+ getting reduced, DPIP gets reduced. As it gets reduced, DPIP becomes clear.

DPIP’s clarity under various conditions can be quantified with a spectrophotometer, or it can be recorded in a more qualitative way (darker to lighter, on a comparative scale). Either way you measure it, you can think of what’s happening as increased transmittance, or decreased absorbance. In this context, increased transmittance occurs as the DPIP gets reduced and becomes clearer. In a test tube, the clearer liquid (more reduced) allows for more transmittance more light). Conversely, decreased absorbance is what happens as the dark, oxidized DPIP (which absorbs a lot of light, because it’s dark) becomes clearer, and absorbs less and less as it transmits more and more.

If this feels too abstract, you can read about this version of the lab here. Even better, download a pdf of the lab with sample data here.

Music videos about photosynthesis

I’ve written three three songs about the light reactions of photosynthesis. You can view them on this page: The Light Reactions: A Musical Review.

Photosynthesis Video Lecture

To give your students an overview of the light reactions, have them watch this video lecture.  It’s about 12 minutes long.

Additional Handouts

  1. Here’s the review sheet I give to my students to help them prepare for my cumulative assessment on photosynthesis.
  2. Before I flipped my classroom, I used to do comprehensive lecturing about photosynthesis. During my lectures, I found that distributing this guided note taking sheet was something that my students found very useful. With some minor modifications, you can make it into a visual review guide.

Flinn has a POGIL about photosynthesis that covers both the light reactions and the Calvin cycle.

Summative Activities for Unit 3

To help your students pull together what they’ve learned from unit 3

  1. Have your students study the Unit 3 AP Bio Review Flashcards . Note that these were primarily designed for AP exam review, so some of the material relates to material that comes later in the course. Therefore, you have to prep your students to be kind to themselves as they go through these cards: they shouldn’t expect themselves to get these cards right on the first try. However, spending a few hours working on reciting answers to these flash cards will help your students consolidate what they’ve learned, and set them up for success in concepts that they’ll learn later in the course.
  2. Note that while you can set the flashcards to just serve up flashcards from Unit 3, it’s probably a good idea to have your students review the flashcards from Units 1 and 2 as well. In order to do that, have your students use the settings shown below:

    These settings will give your students practice on units 1, 2 and 3. Note the “all” radio button on the lower right.
  3. Complete the Unit 3 progress check items on AP Classroom.

Link back to the Teacher’s Guide Table of Contents