Happy Thanksgiving Break

As I was listening to NPR this morning there was an interview with one of the women from Instructables.com. A group of people made a giant fractal pecan pie....

introgiant fractal pecan pie

"for thanksgiving 2k4 we opted to construct a very large pie. based on a prototype the previous year we were aware of a fundamental limitation of large pies, namely the crust to filling ratio. for traditional circular pies of radius R, the amount of filling scales as R² while the crust only scales linearly so as the pie grows larger, the flaky crust is completely dominated by the creamy filling. our solution was to construct a pie pan in the shape of a koch snowflake (whose perimter obeys completely different scaling laws), fill it with delicious pecan pie and bake in a custom backyard oven." For the rest of the story (and dare I say, step by step instructions) click here.

Who looks at the blog anyways (part 2)

It's been a month since the last post on "who looks at the blog anyway," so it's time for an update.


A month ago, 39 countries and 43 states had visited the blog, now we're up to 78 countries and every state except North Dakota. The top five numbers of visits came from the following states:

New Hampshire: 684 visits
California: 97 visits
New York: 87 visits
Texas: 85 visits
Florida: 65 visits

As for the top five number of visits internationally (1,646 visits came from the US):
Canada: 76 visits
United Kingdom: 50 visits
India: 28 visits
Philippines: 21 visits
Indonesia: 18 visits

The international winner for longest time on site is Kenya (28 minutes) and stateside is New Mexico (5 minutes and 16 seconds).

Search engine visits are up from 15.71% last month as are referring sites visits (last month these accounted for 16.65% of visits).

Last month there were 1,375 visits, this month there were 2,029 visits.

Thanks for stopping by!

Tumor Secrets Written in Blood

By Rachel Zelkowitz

ScienceNOW Daily News
17 November 2008

Doctors may soon be able to use blood tests rather than invasive biopsies to figure out what type of brain tumors their patients have. The findings, which come thanks to new insights about how tumor cells communicate with their environment, may also bring physicians closer to the goal of more personalized medicine. To read the whole article click here.

Thanks to Michelle for finding this article about cancer & blood.

Cancer & The Cell Cycle

What is cancer and how is it formed is what we addressed today (and what we'll do tomorrow in C and D blocks).

You can also never escape cellular respiration. The picture below talks about the relationship between cancerous cells, glycolysis and treatment. You can click on the picture to make it larger.

If you're interested in learning more about cancer check out The Nation Cancer Institute's Website.

More Mitosis & Microscopes

Today C block had the chance to work with microscopes and identify the stages of mitosis in both onion root tips and whitefish blastula.

Below is a video of mitosis in action.

Mitosis & Microscopes

Over the next few days we will be working with microscopes to look at the stages of mitosis in onion root tip and whitefish cells. For more information on mitosis look in the "Confused? See if any of these help" sidebar.

Starting Unit 2

Today we start the last week of fall term! We're starting unit 2 with Chapter 8: The Cellular Basis of Reproduction & Inheritance.

The plan for today is: warm up with some true false, take some notes, watch a video clip, take a few more notes and play the cell cycle game.

Below is the video clip we watched on binary fission:

Enrichment:
If you're looking to take a study break from humanities and languages, check this out:
Read the human genome project page with FAQ’s on chromosomes.
At the bottom of the page click on the Chromosome Number of Different Species Web site choose three species and find their diploid number of chromosomes. Remember: a human’s diploid number is 46 chromosomes.

Mental Inventory

Today and tomorrow students will be taking a test on Unit 1 which covers chapters 1-7. This test is designed to serve the following purposes:

1. See if students have learned the major concepts in Unit 1 which is on the cell and cellular processes.

2. Practice for the midterm exam, so instead of studying 10 (or 12) chapters all at once, students have already had a review.

3. For students to become familiar with cumulative assessments much like they would see in a university.

Lab 7: Root Beer

This week in lab we're making root beer! Why? Well science can be fun you know... but more importantly root beer becomes carbonated because of the CO2 released by yeast during fermentation (don't worry, our root beer doesn't become alcoholic). The root beer should be ready between 3 days and two weeks.


1. Materials needed for Root Beer
1.1. Two (2) tablespoon Malto Dextrin
1.2. One (1) teaspoon root beer extract
1.3. One quarter (1/4) teaspoon champagne yeast
1.4. One and one half (1 ½) cups dark brown sugar
1.5. One (1) cup white table sugar
1.6. One (1) gallon cold water
1.7. One (1) gallon milk container (empty and clean)
1.8. Three (3) 1 liter plastic soda bottles with caps
1.9. Six to Eight (6-8) quart sauce pan
1.10. One (1) Funnel

2. Procedures
2.1. Sanitization of the container
2.1.1. Place 2 teaspoons of unscented bleach with 2 gallons of cold water
2.1.2. Soak all equipment (including bottles and caps) in this solution for ten minutes.
2.1.2.1. Start Time ____________
2.1.2.2. End Time ____________
2.1.2.3. Total Time ____________
2.1.2.4. Initial : _________ Verifier: _________
2.1.3. Remove equipment and rinse with hot water
2.1.4. Dry bottles upside down in drying rack

2.2. Preparation of Root Beer
2.2.1. Obtain a sauce pan and place it onto heat source
2.2.2. Obtain White sugar
2.2.3. Obtain Dark Brown sugar
2.2.4. Obtain Malto Dextran
2.2.5. Obtain Root Beer extract
2.2.6. Obtain measuring cup
2.2.7. Measure 4 cups of water from the container and place them into the sauce pan
2.2.8. Heat the water to a temperature range below 100 ˚C
2.2.8.1. Record temperature __________
2.2.8.2. Initial: ________
2.2.9. Add 1 cup white sugar, stir to dissolve
2.2.9.1. Initial: ________ Verifier: ________
2.2.10. Add 1 ½ cups dark brown sugar, stir to dissolve
2.2.10.1. Initial: ________ Verifier: ________
2.2.11. Add 2 tablespoons Malto Dextran, stir to dissolve
2.2.11.1. Initial: ________ Verifier: ________
2.2.12. Stir until all added substances are dissolved
2.2.12.1. Initial: ________ Verifier: ________
2.2.13. Turn off heat source, leave pan
2.2.14. Add 1 teaspoon root beer extract, stir to dissolve
2.2.14.1. Initial: ________ Verifier: _______
2.2.15. Allow for sauce pan to cool to 45˚C
2.2.15.1. Record temperature: _______
2.2.15.2. Initial: ________ Verifier: ________
2.2.16. Obtain Champagne Yeast (whole class may use the same packet, take turns)
2.2.17. Obtain ¼ teaspoon
2.2.17.1. Record Batch number: _________
2.2.17.2. Date of Yeast: ________
2.2.18. Measure out ¼ teaspoon of yeast
2.2.19. Place the yeast into sauce pan
2.2.20. Seal the remainder yeast packet with tape and place into a refrigerator
2.2.21. Stir mixture until the yeast is dissolved
2.2.21.1. Initial: ________ Verifier: ________
2.2.22. Allow pan to sit uncovered for 10 minutes
2.2.22.1. Record Start Time: ________
2.2.22.2. Record End Time: ________
2.2.22.3. Total Time: ________
2.2.22.4. Initial: ________ Verifier: ________
2.3. Bottling
2.3.1. Obtain a funnel
2.3.2. Obtain containers
2.3.3. Pour contents of dissolved solution from the sauce pan into 1 container.
2.3.3.1. Initial: ________ Verifier: ________
2.3.4. Seal the container tightly
2.3.5. Place at room temperature (70˚F – 72˚F)
2.3.6. Leave for two weeks
2.3.6.1. Record Date, Time, and Temperature
2.3.6.2. Date: _______Time: ______ Temp:________
2.3.6.3. Date: _______Time: ______ Temp:________
2.3.6.4. Date: _______Time: ______ Temp:________
2.3.6.5. Date: _______Time: ______ Temp:________
2.3.6.6. Date: _______Time: ______ Temp:________
2.3.6.7. Date: _______Time: ______ Temp:________
2.3.6.8. Date: _______Time: ______ Temp:________
2.3.6.9. Date: _______Time: ______ Temp:________
2.3.6.10. Date: _____Time: ____ Temp:________
2.3.6.11. Date: _____Time: ____ Temp:________
2.3.6.12. Date: _____Time: ____ Temp:________
2.3.6.13. Date: _____Time: ____ Temp:________
2.3.6.14. Date: _____Time: ____ Temp:________
2.3.6.15. Date: _____Time: ____ Temp:________
2.3.6.16. Date: _____Time: ____ Temp:________
2.3.6.17. Date: _____Time: ____ Temp:________
2.3.6.18. Date: _____Time: ____ Temp:________
2.3.6.19. Date: _____Time: ____ Temp:________
2.3.6.20. Date: _____Time: ____ Temp:________
2.3.6.21. Date: _____Time: ____ Temp:________
2.4. Date and Time Batch was ready for consumption
2.4.1. Record Date and time
2.4.2. Date:______ Time:______
2.4.3. Initial: ________ Verifier: ________
2.5. Notes
2.5.1. Record any special notes in the Notes Section (pg 5)

Where does your old computer go?

Here's something to think about (yes, I realize you have plenty to think about right now, but I thought this might give you some perspective).


Watch CBS Videos Online

Open Notes Quiz on Cellular Respiration

Today students took an open notes quiz on cellular respiration. The remainder of the class period was devoted to reviewing for the up coming unit test.

Multiple Choice Test Questions

Here's the breakdown of the number of questions per chapter on the multiple choice component of the test:

Section 1.3 : none (but you still need this information for the open response).

Chapter 2: four questions

Chapter 3: four questions

Chapter 4: five questions

Chapter 5: eleven questions

Chapter 6: ten questions

Chapter 7: six questions

Sample Answer to an Open Response Question

To help you better understand my expectations for what your open response question should include, see the samples below. Since the question being answered is the first one from your review sheet, don't expect this question to be on the test.

Membranes are important structural features of cells. (a)Describe how membrane structure is related to the transport of materials across a membrane. (b) Describe the role of membranes in the synthesis of ATP in cellular respiration

HH Response:

At its very core, a membrane defines a cell with in its surroundings. Membranes are composed of a phospholipid bilayer. The heads of the phospholipids are hydrophilic, meaning they are attracted to water and the tails of the phospholipids are hydrophobic, meaning they "fear" water. A natural consquence of these attactions is that the phospholipids form a bilayer. Embedded within the bilayer are various proteins. These protiens are responsible for active and passive transport of molecules in and out of the cell, cell to cell recognition, working with enzymes and cytoskeletal attachment. Proteins that permeate the lipid bilayer are referred to as integral membrane proteins and these proteins can move fluidly throughout the lipid bilayer (hence the name "fluid mosaic model.") One protein in particular is called ATP synthase (shown below) which also happens to be an enzyme.


ATP synthase is located on the inner membrane of mitochondria and on the thylakoid membrane in chloroplasts. For our purposes we will focus only on mitochodria as this is where cellular respiration takes place. Throughout cellular respiration, a proton gradient is created which results in an increase of protons in the inter membrane space and less protons (H+) in the matrix. This difference creates an electrochemical gradient. As a result of the basic principle of diffusion (molecules moving from an area of high concentration to low concentration), protons are pumped through the ATP synthase. As the protons are pumped through ATP synthase, the molecular machinery turns and joins together ADP and Pi (inorganic phosphate) to form ATP. This mechanism of producing ATP is referred to as oxidative phosphorylation.

This is an HH response because not only does it include detailed information that demonstrates a clear understanding of the question, it is also well written and uses diagrams to supplement the information.

H Response:

Membranes are composed of a phospholipid bilayer. There are proteins in the membrane. There are difference types of membrane proteins like transport proteins and channel proteins. These proteins are responsible for moving things in and out of the cell. One protein in particular is called ATP synthase which also happens to be an enzyme. ATP synthase is located on the inner membrane of mitochondria. Throughout cellular respiration , a proton gradient is created which results in an increase of protons in the on one side of the membrane and less protons on the otherside. This difference creates an gradient. As a result of the basic principle of diffusion (, protons are pumped through the ATP synthase. As the protons are pumped through ATP synthase, the molecular machinery turns and joins together ADP and Pi (inorganic phosphate) to form ATP.

This is an H response because the author demonstrates a basic understanding of the structure of the cell membrane and the role of ATP synthase. Details which would highlight a greater understanding of the process are omitted as is the figure of ATP synthase.

HP Response:

Membranes have two layers called bilayer. There are proteins in the membrane. These proteins are responsible for moving things in and out of the cell. One protein in particular is called ATP synthase. ATP synthase is located on the membrane of mitochondria. Throughout cellular respiration , a gradient is created which results in an increase of stuff on one side of the membrane and less stuff on the otherside. This difference creates an gradient. As a result of the basic principle of diffusion (, protons are pumped through the ATP synthase. As the protons are pumped through ATP synthase, the molecular machinery turns and joins together ADP and Pi (inorganic phosphate) to form ATP.

This is an HP response because the author demonstrates little understanding of the information needed to answer the question. Details which would highlight a greater understanding of the process are omitted as are any figures which would help convince the reader that the author knows what he/she is talking about.

P Response:

Serriously, there should be no P responses.
You have the questions ahead of time.

Fermentation Mini Lab & Continuing CR

Here's the plan for today:
1. Read and set up the yeast fermentation lab (see below).
2. Short lecture on the Krebs cycle
3. Watch an animation of the ETC in CR (if time)
4. Analyze the yeast fermentation lab.

Background:

Yeast are tiny single-celled (unicellular) fungi. The organisms in the Kingdom Fungi are not capable of making their own food. Fungi, like any other organism, need food for energy. They rely on sugar found in their environment to provide them with this energy so that they can grow and reproduce.

Yeast, like bacteria grow in or on their food source. They produce and release digestive proteins (enzymes) into their environment where the sugar molecules are found. Sugar molecules then break down into smaller molecules that can be absorbed by the yeast and used for food (energy).

There are many species of yeast, and each has a particular food source.

• Certain yeast feed on a variety of natural sources of sugar such as fruits, nectar from plants, and molasses from the plant crop called sorghum.

• Others break down wood and corn stalks. In doing this, a compound called ethanol is produced. This compound can be used in our cars like gasoline.

• Another species break down sugar from grain into alcohol. Others break down fruits into wine, which is another type of alcohol.

• Bread recipes rely on yeast to break down sugar in our dough.

All of these processes are called fermentation. The formula for the yeast fermentation reaction is:

C₆H₁₂O₆ = 2CH₃CH₂OH + 2CO₂ + energy

For the yeast cell, this chemical reaction is necessary to produce the energy for life. The alcohol and the carbon dioxide are waste products produced by the yeast. It is these waste products that we take advantage of.

The chemical reaction, known as fermentation can be watched and measured by the amount of carbon dioxide gas that is produced from the break down of glucose.

???? Do you think that the volume of carbon dioxide produced during fermentation would be affected by using different masses of sugar ????

In this exercise you will add the same amounts of yeast and water to different amounts of sugar in balloons and tie them off to see how much carbon dioxide gas is produced.

1. Split up into pairs, work with someone who you have not yet worked with using a permanent marker, label a balloon with your initials. Your teacher will give you the amount of sugar that you will be using.

2. Using a plastic spoon or spatula place some of the yeast in a weigh boat on the balance. Measure out a total of 2 grams of yeast. Then, using a separate weigh boat, measure your assigned quantity of sugar.

3. Measure with a graduated cylinder exactly 50 milliliters of water at ~37^oC. Heating the water in the microwave for 10-15 seconds on high should be enough to get to ~37^oC.

4. Add the sugar and yeast to a test tube. Mix with a stir rod to ensure that you do not have a layer of sugar and a separate layer of yeast.

5. Add the water to the test tube and here’s where teamwork is really important: have one person hold the test tube while the other person places the balloon on top.

6. Once the balloon is tightly on the test tube observe what is happening. Working silently, write down observations for five minutes. EMPHASIS ON SILENTLY.

Analysis:

1. How do the sizes of the balloons with the varying sugar concentrations compare?

2. Which balloon had the greatest increase?

3. According to the background information CO₂ is produced, how could you test this?

Homework: If you have not already made the flash cards for glycolysis those are due on Friday for C block.

Election Day!

No, they aren't waiting in line to learn about cellular respiration...Voters lined up early on Election Day in Mass. Above, Senator John Kerry was third in line at the State House.

Today students were given the option of working on the study guide (emailed to students) for the Unit One Test and/or watching The Incredible Human Machine (National Geographic).

Glycolysis

Now is the time to yearn for the simplicity of the arrow in chemical reactions. Today students learned the intricate steps of glycolysis. Click the picture below to be taken to animation we used in class.

Homework: Due on either Thursday or Friday depending on when your class meets. Make flashcards for each of the ten steps of glycolysis. See the example below (no, you do not need to type on your flashcards).

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).

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.

OBJECTIVES

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)

MATERIALS

Phosphate buffer

3 cuvettes

Isolated chloroplasts

3 disposable pipets

Aluminum foil

DCIP

Lamp

Large Erlenmeyer Flask, filled with water

Ice

Watch/clock

PROCEDURE

IT IS REALLY IMPORTANT THAT YOU ARE MINDFUL OF ANY LIGHT WHEN DOING THIS EXPERIMENT. IF CHLOROPLASTS ARE EXPOSED TO LIGHT, THEY WILL START TO REACT.

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.

2. 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).

3. 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
   

4. 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.

5. 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.

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

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

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

9. 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.

11. 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.

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

13. 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?

2. What is being tested?

3. How does DCIP work?

4. 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 blogger.com 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.

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.