Thursday, October 30, 2008

Cellular Respiration 6.1-6.7

NOTE: This post is for Thursday & Friday's classes.

After a quick review from the last class, students took notes on sections 6.1-6.7. Sections 6.1-6.6 are basically a review of redox reactions and electron transport chains (which, hopefully, you still have some knowledge about since we learned this the past two weeks).

Section 6.7 is new material describing the two mechanisms for ATP production: substrate level phosphorylation and oxidative phosphorylation (chemiosmosis).

Wednesday, October 29, 2008

Lab 6: Using spec20's to measure the Hill Reaction

Here is this week's lab:

The process of photosynthesis involves the use of light energy to convert carbon dioxide and water into sugar, oxygen, and other organic compounds. This process is often summarized by the following reaction:

6 H2O + 6 CO2 + light energy --> C6H12O6 + 6 O2

This process is an extremely complex one, occurring in two stages. The first stage, called the light reactions of photosynthesis, requires light energy. The products of the light reactions are then used to produce glucose from carbon dioxide and water. Because the reactions in the second stage do not require the direct use of light energy, they are called the dark reactions of photosynthesis. In the light reactions, electrons derived from water are “excited” (raised to higher energy levels) in several steps, called photosystems I and II. In both steps, chlorophyll absorbs light energy that is used to excite the electrons. Normally, these electrons are passed to a cytochrome-containing electron transport chain. In the first photosystem, these electrons are used to generate ATP. In the second photosystem, excited electrons are used to produce the reduced coenzyme nicotinamide

adenine dinucleotide phosphate (NADPH). Both ATP and NADPH are then used in the dark reactions to produce glucose. In this experiment, a blue dye (2,6-dichlorophenol-indophenol, or DCIP) will be used to replace NADPH in the light reactions. When the dye is oxidized, it is blue. When reduced, however, it turns colorless. Since DCIP replaces NADPH in the light reactions, it will turn from blue to colorless when reduced during photosynthesis.


In this experiment, you will

Use a Spec20 to measure color changes due to photosynthesis.

Study the effect of light on photosynthesis (in a QUANTITATIVE way)


Phosphate buffer

3 cuvettes

Isolated chloroplasts

3 disposable pipets

Aluminum foil



Large Erlenmeyer Flask, filled with water





  1. Hold the cuvette above the white circle only. If you touch the glass below the circle, make sure to wipe the glass clean with a Kim wipe.

  1. Create a blank. This is what you will use to zero the spec20. (You will be told the amount of Phosphate Buffer and DCIP to add in lab).

  1. Follow your instructor’s directions for zeroing the Spec 20. These pieces of equipment cost $1500 each. BE GENTLE WITH THEM. The Spec20’s will be on the dark side of the room

  1. Obtain a piece of aluminum foil large enough to wrap around the cuvette to block out any light. You will use this in step 6.

  1. While on the dark side of the room, create a cuvette containing ___ drops of chloroplast solution (again you will be told how much in lab), ____mL DCIP and ____mL of Phosphate Buffer. Put this in the Spec20 and write down the transference and absorbance in your data table.

  1. After completing the test wrap the cuvette in foil.

  1. Each member of the group should create an experimental sample using ___drops isolated chloroplast solution, ___mL of Phosphate Buffer and ____mL of DCIP.

  1. Test the initial absorbance and transference of each sample and record in the data table.

  1. Bring the EXPERIMENTAL test tubes to the light side of the room. Do not turn on the light until instructed to do so by your teacher.

10. Set up the cuvettes as instructed by your teacher.

  1. Every ten minutes, turn off the light and take one sample at a time over to the dark side to test in the Spec 20. Record your data. Return the sample and obtain another one. Continue to record data every ten minutes for each sample until you are instructed to stop.

  1. Conduct a final Spec 20 test on the sample that was left in the dark.

  1. Clean up your materials thoroughly. Place the contents of the cuvettes in a waste beaker at the teacher station.

PreLab Questions

  1. What is the control in this experiment?

  1. What is being tested?

  1. How does DCIP work?

  1. What does a color change in DCIP represent?

Who looks at this blog anyways?

I have been collecting data on visits to the blog since the start of the school year using a free program called Google Analytics. This software generates a report each day, which includes many things such as: the number of hits the blog gets per day, where the hits are coming from and how long each visit lasts.

Here's the data for September 27th-October 27th.

This graph represents the number of hits per day. Remember what was due on October 28th? Your lab report.

As students, you're not the only ones who have visited the blog over the past month. 39 countries have visited and 43 states!

How do people find the blog?

Referring sites include things like which has a ticker with blogs that are updated minute by minute. And even search engines! People looking for information on google have stumbled across our class blog. Personally, I think that's pretty cool.

Tuesday, October 28, 2008

Hooray for Cellular Respiration

Today class started with students completing a self evaluation for their lab reports using a rubric. I will look at these self evaluations when I grade the reports (hopefully there will not be a huge disparity between my grades and the students grades).

Moving forward we got our blood (and lactic acid) pumping by doing a wall sit. What better way to start to learn about respiration than to experience it. After shaking out the soreness, students returned to their seats for a mix of trivia and notes for an overview of cellular respiration.

Homework: C block the lab information has been emailed to you for class tomorrow. Please make sure you are prepared and wearing close toed shoes.

Saturday, October 25, 2008

Welcome Parents!

Today parents will be attending mini classes, learning about what we do every day and looking at slides.

Friday, October 24, 2008

Parents Weekend

Enjoy sleeping in this weekend and visiting with your families. A reminder that your Elodea - Snail write up is due at the beginning of class on Tuesday October 28th. If by chance you have not started to write your lab yet (yikes!) or have "misplaced" the template it is below. Be sure to refer to the guide to writing scientific papers for further explanation of formatting and content. You might also want to check out the Sample Lab Report. If you reference any sources in your paper (other than the lab handout) you need to add a literature cited section.



What is relevant background information on the topic? How does what you are studying relate to the larger world? For the purpose of this assignment, the introduction should be no more than five to seven sentences.

Materials & Methods

You can cite the lab handout here. If you deviated from any of the hypotheses or created your own you need to write that here.


In your results section on only PRESENT data. Do NOT interpret it. A data table or figure is fine. Make sure that it has a title, any necessary labels and a one to two sentence description of what is being presented.


Here is where you interpret your data. Make note of any trends/patterns. How did the results compare with your hypotheses? What were potential sources of error? If you were to do this experiment again, how would you modify it? Overall were your results significant?


This section simply states what the researcher thinks the data mean, and, as such, should relate directly back to the problem/question stated in the introduction. This section should not offer any reasons for those particular conclusions--these should have been presented in the Discussion section. By looking at only the Introduction and Conclusions sections, a reader should have a good idea of what the researcher has investigated and discovered even though the specific details of how the work was done would not be known.

Wednesday, October 22, 2008

C3, C4 and CAM plants

NOTE: This post applies for classes that meet on Thursday and Friday as well. C block will not meet on Friday this week because of Parent's Weekend.

Today we discussed alternative routes for plants to conduct the Calvin Cycle when there is an absence of CO2, extreme heat and/or extreme sunlight.

Below is a summary for each type that should help clear up any confusion. This information was taken from the Pima Community College Website.

C3 Photosynthesis : C3 plants.
  • Called C3 because the CO2 is first incorporated into a 3-carbon compound.
  • Stomata are open during the day.
  • RUBISCO, the enzyme involved in photosynthesis, is also the enzyme involved in the uptake of CO2.
  • Photosynthesis takes place throughout the leaf.
  • Adaptive Value: more efficient than C4 and CAM plants under cool and moist conditions and under normal light because requires less machinery (fewer enzymes and no specialized anatomy)..
  • Most plants are C3.

fourwing saltbushC4 Photosynthesis : C4 plants.

  • Called C4 because the CO2 is first incorporated into a 4-carbon compound.
  • Stomata are open during the day.
  • Uses PEP Carboxylase for the enzyme involved in the uptake of CO2. This enzyme allows CO2 to be taken into the plant very quickly, and then it "delivers" the CO2 directly to RUBISCO for photsynthesis.
  • Photosynthesis takes place in inner cells (requires special anatomy called Kranz Anatomy)
  • Adaptive Value:
    • Photosynthesizes faster than C3 plants under high light intensity and high temperatures because the CO2 is delivered directly to RUBISCO, not allowing it to grab oxygen and undergo photorespiration.
    • Has better Water Use Efficiency because PEP Carboxylase brings in CO2 faster and so does not need to keep stomata open as much (less water lost by transpiration) for the same amount of CO2 gain for photosynthesis.
  • C4 plants include several thousand species in at least 19 plant families. Example: fourwing saltbush pictured here, corn, and many of our summer annual plants.

saguaroCAM Photosynthesis : CAM plants. CAM stands for Crassulacean Acid Metabolism

  • Called CAM after the plant family in which it was first found (Crassulaceae) and because the CO2 is stored in the form of an acid before use in photosynthesis.
  • Stomata open at night (when evaporation rates are usually lower) and are usually closed during the day. The CO2 is converted to an acid and stored during the night. During the day, the acid is broken down and the CO2 is released to RUBISCO for photosynthesis
  • Adaptive Value:
    • Better Water Use Efficiency than C3 plants under arid conditions due to opening stomata at night when transpiration rates are lower (no sunlight, lower temperatures, lower wind speeds, etc.).
    • May CAM-idle. When conditions are extremely arid, CAM plants can just leave their stomata closed night and day. Oxygen given off in photosynthesis is used for respiration and CO2 given off in respiration is used for photosynthesis. This is a little like a perpetual energy machine, but there are costs associated with running the machinery for respiration and photosynthesis so the plant cannot CAM-idle forever. But CAM-idling does allow the plant to survive dry spells, and it allows the plant to recover very quickly when water is available again (unlike plants that drop their leaves and twigs and go dormant during dry spells).
  • CAM plants include many succulents such as cactus and agaves and also some orchids.

Tuesday, October 21, 2008

Writing up the Lab

Today C block wrapped up the lab and collected data (see this post). A and D blocks worked on their lab write up in class.

Tomorrow C block will have a lecture wrapping up Chapter Seven and then have the remainder of the class period to work on their lab reports.

You'll notice (if you haven't already heard) that the lab write up is now due on Tuesday October 28th.

If you are still confused by the lab, you can see what would happen in a perfect world using the ExploreLearning Gizmo. You are able to have a free five minute trial (so generous) because we don't have a subscription. If the computer isn't dreadfully slow, five minutes is plenty of time to get the results.

Monday, October 20, 2008

Lab 5: Elodea & Snails

What is the relationship between photosynthesis and respiration? Hopefully we'll see it in action during last/this week's lab.

Experimental design: Elodea, snails, water and BTB will be placed in test tubes (some will be exposed to light and some will not be exposed to light).
In the end, we hope to see a change in the color of the BTB (an indicator) which is reflective of pH. How will these results differ in the light and dark groups?

Today A & D blocks collected their data, cleaned up and learned the basics of writing scientific papers.

Today C block set up their experiment and learned the basics of writing scientific papers.

Homework for A and D blocks: Read the Guide to Writing Scientific Papers then use your new found knowledge to answer help you read and answer the questions for the sample paper "The Effects of Light on Soybean Plants." This is due on Tuesday.

C block has no homework due on Tuesday.

You have also been emailed the template for the mini-lab paper that is due in class on Tuesday October 28th.

Friday, October 17, 2008

Photosynthesis Objectives

We've been navigating through photosynthesis for a while now. How many of the following objectives can you do?

1. Describe the structure of the chloroplast, listing all membranes and

2. Indicate where chloroplasts are located in plant cells and describe where most
chloroplasts are located in a leaf.

3. Explain how chloroplast structure relates to its function.

4. Write the summary equation for photosynthesis.

5. Explain the role of redox reactions in photosynthesis.

6. Describe the two main stages of photosynthesis in general terms.

7. List the three types of pigments involved in photosynthesis and how they are different.

8. List the wavelengths of light that are most effective for photosynthesis.

9. Describe the flow of electrons and hydrogen ions through the electron transport chain.

10. Explain the relationship between the light reactions and the calvin cycle with respect to ATP/ADP, Pi and NADP+ /NADPH

(We have yet to talk about C4 plants etc... at the end of the chapter. We will, we just haven't yet)

Thursday, October 16, 2008

A Quiz and some changes

Students took a 13 question open notes quiz on the light reactions and/vs. the Calvin Cycle. On Saturday A and D blocks will have a lab, C block will do the lab on Wednesday (the lab has been emailed to all students).

A block requested a short open notes quiz once a week to help them review and see more questions similar to those on tests. I think this is a great idea and will be doing this in all blocks.

Another change is that the persuasive essay component of the project has been dropped. The script and the itinerary will now be due on Monday (for all classes) at the beginning of class.

Wednesday, October 15, 2008


As a result of the PSATs there were no classes today. Remember to read and take notes for the open notes quiz in class. There will be 13 questions and there will be some questions that ask you to compare the calvin cycle with the light reactions. For these questions you may use any class (or book notes you have).

Tuesday, October 14, 2008

The light reactions

Slowing down a bit and going back to traditional note taking we talked about the light reactions, where they take places and what happens to the products and reactants.

We watched this video (if that takes too long to load you can see the still images and text of narration here).

Homework: Read section 7.10 and take notes, any notes you take can be used for an open notes quiz next class (emphasis on YOU taking notes, not photocopying, not printing things from google. Remember: you're notes are only helpful if you understand them).

Monday, October 13, 2008

Update for Task 2

Task 2 is going to be due tomorrow in class. For this all you need to turn in is a list of things you will see during photosynthesis IN ORDER!

In class we will be working on what happens at/for each item on the list. Use your book (sections 7.7-7.10) and the tutorials on the blog.

Here's a few to get you started.

Go to the thylakoid membrane, here you will see...

Photons of light
Chlorophyll a, Chlorophyll b, carotenoid pigments
reaction center in a photosystem
Photosystem I

Sunday, October 12, 2008

Photosynthesis Tutorial

This is the tutorial we will be viewing in class on Monday to help explain the light reactions of photosynthesis. If you have some time and want to get ahead, I recommend taking a look at it. You can skip the part of the tutorial on the dark reactions, it goes into more detail than we will be talking about. Click the picture to go to the tutorial.

Saturday, October 11, 2008

Task 2: Create an Itinerary

For Task 2 you need to be familiar with what happens in Photosynthesis. Look at the slides below for more information.

Photosynthesis Part Duex
View SlideShare presentation or Upload your own.

This PowerPoint has good information on the Light Reactions and the Calvin Cycle. You are not responsible for information on the structure of a leaf.

View SlideShare presentation or Upload your own. (tags: photosynthesis desktop)

Friday, October 10, 2008

Task 1: Create a Map of Your Journey

Task 1 is due on Monday AT THE BEGINNING OF CLASS. Below are two samples one that is HH worthy and one that is barely worthy of a U. Click on the pictures to make them larger.

This is the front of the HH map.

The back of the map, with a description of what you will see. NOTE: I made this sample and it is not complete. It does not have all the written details your maps should have.

And now for the U map....

Why is this terrible? Well, for starters it is a print screen of a web page. In case that isn't enough explanation it's not a map either. Remember to cite your sources!

Student Directed Learning of Photosynthesis

...otherwise known as using a webquest and project to learn about photosynthesis rather than sitting through lecture.

Here is your task:

"Thanks to technology, scientists have discovered a way to reduce human beings down to a microscopic size for limited periods of time. This technology is predictably being used in the fields of medicine, computer science, and biology. Recently, the travel industry has also found ways to utilize the technology by offering adventure trips into areas previously unavailable to full-sized humans.

You and your team are travel agents working in a futuristic eco-tourism agency called “Micro-adventures,” whose mission is to educate the public about ecological issues through exciting vacation packages. You are developing a new vacation trip into the chloroplast of the plant cell. The first tour will be given to politicians, environmentalists, and journalists. What do you want these tourists to learn about photosynthesis."

Click here for the full guidelines for the assignment.

You will work in groups of three and this project will be presented in class on Monday October 20th. The overall rubric for the project is in the guidelines and a more detailed rubric will be posted later.

Some notes on when components of the project will be completed.

On Monday October 13th, AT THE BEGINNING OF CLASS you will need to turn in Task 1 (completed- final copy).

On Thursday or Friday October 16th/17th AT THE BEGINNING OF CLASS will need to turn in Tasks 2 and 3 (completed-final copy).

On Monday October 20th you will be presenting Task 4.

Task 5 should be completed individually, be no more than 2 pages, typed, double spaced, size 12pt. font, and include direct quotes from at least three distinct primary sources. You must include full MLA citations for your work.

For help writing a persuasive essay try the online thesis builder here.

Wednesday, October 8, 2008

Test on Chapter 4 through 5.17

Between Cricket Holiday and James McBride coming to speak this week started off with minimal class time. To get back on track C block finally had their test today and continued with chapter 7 (photosynthesis).

Click on the picture below to go to the animation we saw in class.C Block Homework: Read and take notes on sections 7.5 through 7.7.

Tuesday, October 7, 2008

Intro to Photosynthesis

Today we had a brief intro to photosynthesis (and we watched this awesome song).

Homework: study for your test!

Monday, October 6, 2008

Cricket is today....

....which means that your test has been moved. Because of James McBride's visit C block will have their test on Wednesday, A block on Thursday and D block on Friday. A and D blocks you need to bring your lab notebooks to class on Tuesday so that I can collect them.

Enjoy your holiday!

Friday, October 3, 2008

Test Review Questions

Today we talked about Blooms Taxonomy which is all about levels on understanding, from the most basic (knowledge) to the most advanced (evaluation). To practice writing questions and review for the test on Monday, C block created these questions. Feel free to test yourself. Note: just because you know all the answers to the questions, doesn't necessarily mean you know everything for the test. Read your notes & the book!

You do not need to know about Bloom's Taxonomy for the test.

  1. What does ATP stand for?
  2. How does ATP produce energy?
  3. Compare and contrast active and passive transport
  4. Describe the make up of the cell membrane
  5. What is the difference between hypertonic, hypotonic and isotonic solutions.
  6. What is the difference between the rough and smooth ER?
  7. Compare and contrast prokaryotic and eukaryotic cells
  8. Compare and contrast the functions of the mitochondria and chloroplasts
  9. What is osmosis?
  10. What happens when a cell is placed in a hypertonic solution?
  11. Draw a model of ATP & label it.
  12. Explain the difference between competitive and non-competitive inhibitors
  13. What are the three main parts of the endomembrane system
  14. What are the three types of cell junctions and their functions?
  15. Compare and contrast a plant and animal cell
  16. How does ATP relate to dephosphorylation?
  17. How is a protein formed?
  18. Give an example of diffusion
  19. What is the function of a lysosome?
  20. What are the laws of thermodynamics?
  21. Compare and contrast a mitochondria to a powerplant
  22. Compare the cytoskeleton with something that has similar structure/function that you would encounter in your daily life.
  23. What is a membrane made out of?
  24. Does the rough or smooth ER have ribosomes?
  25. What is the function of a vacuole?
  26. How can you tell if a cell is an hypertonic or hypotonic solution?

Thursday, October 2, 2008

Laboratory Week 4 (cont)

Since there is no class this Saturday, A and D blocks will do a modified version of the Eggsperiment (instead of totally being on their own to make up the experiment they will get more guidance so that we can finish in time).

A & D blocks will need to turn in their completed lab notebooks in class on Monday.

Below are pictures from the eggsperiment

Lab Notebook

Finding the mass of the egg

Students work on creating their secret solution

Adding the solution to the egg

Wednesday, October 1, 2008

Laboratory Week 4

At the beginning of the week we learned about osmosis and diffusion. Now we are going to see it in action. This week's experiment is: The Great Eggsperiment

NOTE: This is what C block did (A and D blocks, because we don't have lab on Saturday we will do a modified version of the experiment in class)

Procedure: Step 1: Creating a solution: You want to make a secret formula for a solution that only your group members know. The materials you can use are: sugar, water, salt and corn syrup. Write the formula for your secret solution in your lab notebook.

a) For example: 10g salt + 100ml water = 10% salt water solution

NOTE: The higher the concentration of solutes, the more change you might see….

b) label your solution: group member’s name’s, date, time

Data Collection: Step 2: Making Primary Observations:

a) Imagine you are describing your egg to someone over the phone. Write a detailed description of what your egg looks like.

b) Draw a picture of what the egg looks like. Make a note of any distinguishing characteristics (things that make your egg unique). (include at least 3 labels)

c) How will you know that change in your egg occurred? What will you do?

Data Collection: Step 3: Make a prediction:

a) What do you think will happen to your egg when you add the solution?

b) How long do you think it will take for you egg to show any change?

Data Collection: Step 4: Secondary Observations

a) Add the solution your egg.

b) Write down what you see

c) How often will you take the mass of your egg?

Data Collection: Step 5: Final Observations

a) How does the final mass of your egg compare to the starting mass.

b) Graph your results (time vs. percent change in mass).

Conclusions: Step 6: Analysis

  1. Why did we use an egg for this experiment?
  2. What else besides an egg could we have used?
  3. How did your egg react to your solution?
  4. Did all eggs react the same?
  5. What do you think caused your egg to react the way it did?
  6. If you were to do this experiment again, what are at least three things you would change to make it better (explain each factor).
C block: Lab notebooks will be due in class on Friday.