Wednesday, December 17, 2008

Cracking the Code of Life

Today C block watched the NOVA special: Cracking the Code of Life. Click on the picture below to go to the website for the video.

Tuesday, December 16, 2008

Test Today

Today students had a test on Chapters 8 & 9. Several students scored 100% on the multiple choice. I will finish grading the tests tonight while I am on duty and if you are in D block you may email me tomorrow ( C block and A blocks can get their tests back in class) to find out your score.

Monday, December 15, 2008

Review for the test

Ok, I'll be the first admit it. Some classes had better review sessions than other classes. In case you missed it, here's the breakdown for the test:

25 Multiple choice questions (10 from chapter 8 and 15 from chapter 9). Each question is worth 2 points.

5 genetics problems, each question is worth 5 points.

Keep in mind there is a special schedule tomorrow because of the Pageant.
C block: 8:35-9:25
D block: 9:30-10:25
A block: 10:30-11:25 (This is your last class of 2008 A block!)

Saturday, December 13, 2008

Do you know what you're eating?

We've come a long way from Mendel, in the 1860's, tinkering with in his garden with Pea Plants. Instead of removing stamens from one flower and transferring that pollen to another flower, scientists can now insert genes into plasmids and create GMO's (genetically modified organisms).

"Today, four countries account for 99% of the world's commercially grown transgenic crops. But that is changing — policies are being thrashed out, laws drawn up, and seeds sown. Here we show how GM is taking root. Click on the map for information on the big hitters in the global GM scene."~ From Nature.com

What do you know about GMO's? Click start quiz below to take a quiz!Now that you've tested your knowledge, watch the videos below in for and against GMOs. Continue to ask questions and form your own opinion.

For GMO's: Click here to be taken to videos produced by Monsanto. Each clip is 2-3 minutes long.

Watch the video below that is against GMO's.



Friday, December 12, 2008

Wrapping up Chapter 9

Today and tomorrow we will be finishing chapter 9 by learning about pleiotropy, polygenic inheritance, chromosome mapping, sex determination and sex linked genes (sections 9.14-9.22).
Your book doesn't talk about Environmental Sex Determination (ESD) and this stuff is actually quite interesting. "The sex of hatchling turtles, like this Barbour's map turtle, is determined by incubation temperatures in the nest. Relatively warm incubation temperatures produce females, whereas cool temperatures produce males. Barbour's map turtle is only found in the Apalachicola River and its major tributaries in Alabama, Georgia, and Florida." To read the rest of the article click here to learn more about ESD and Climate Change.

Homework: Finish the remainder to the practice problems (through question 10) on the Genetics Practice Problem Sheet.

Tuesday, December 9, 2008

Genetics Problems for Lab on Wednesday & Saturday

For this week's lab you will be acting as Mendel would have in the middle of the 19th century. Go through each of the slides below (you can click on the picture to make it larger). For the first 15-20 minutes of class you are OWN YOUR OWN, you may ask your peers and work together, I will only answer minimal questions. Write your answers on sheet of paper.

This lab activity was developed by Dr. John Crosby for ASP.







Classical Genetics

Today students turned in their projects on meiosis and non-disjunction disorders. Today students learned how to solve trihybrid crosses using the multiplication rule.

What is the probability that AaBbCc X AaBbCc will produce an individual that is homozygous reccessive?

One option for solving a trihybrid cross is to make a giant punnett square (see below) or you can the multiplication rule.

Using the multiplication rule you take the probabilities of each individual event and multiply them together. There is a 1/4 chance of aa, 1/4 of bb and 1/4 chance of cc, multiplied together this equals 1/64.

Click here for practice genetics problems.

Monday, December 8, 2008

Jonah Lehrer Talk

Tonight at 6:15 is Jonah Lehrer's talk in Hargate. There are two ways to earn extra credit. One, raise your hand and ASK a question. Two, post a comment on this post answering the following questions. You must write in complete sentances and you must post before 10:00pm this evening.

What are 3 things you learned from this talk, BE SPECIFIC!
What are 2 things you want to learn more about, BE SPECIFIC!
What is one question you would like to ask Mr. Lehrer.

Patterns of Inheritance

Today we started chapter 9 and we're going to try something different. Rather than just using a PowerPoint and having students take notes, I created a packet that is a notes outline for chapter 9 with practice problems for most concepts. Over the next few days we'll work through the packet and only use PowerPoint to show diagrams that are too complex to draw on the board.

Here are the topics/concepts we went over today:
* Alleles, loci & homologous chromosomes
* genotype vs. phenotype
* homozygous vs. heterozgous
* Mendel's principles of segregation and independent assortment
* Test crosses & how to do them
* Interpreting family pedigrees


Reminder: your meiosis project is due tomorrow.

Friday, December 5, 2008

Nondisjunction Disorders

What happens when (as your book says) there's an "accident" in meiosis. One of result is that there could be a nondisjunction disorder, where sister chromatids do not separate evenly. Today in C block and tomorrow for A and D blocks we will wrap up chapter 8 by talking about variation and nondisjunction. Click the picture below to learn more about chromosome abnormalites from Utah Genetics. Remember, as part of your meiosis project you need to incorporate a nondisjunction disorder.

Thursday, December 4, 2008

Extra Credit Opportunity...


....also known as an outright bribe to attend Jonah Lehrer's talk on Monday, December 8th at 6:15 in the Hargate Auditorium.

There are two ways to earn extra credit through this talk. The first is to attend the talk and ASK a question (just raising your hand doesn't count, you need to ask the question). The second is to attend the talk and then before 10:00pm on Monday December 8th, write a 3-2-1 comment using complete sentences on the blog. I will create a post for the talk on Monday.

Wednesday, December 3, 2008

Down Syndrome

As women age, the risk of Down Syndrome can increase (see graph below). Click the graph to be taken to the article.



However, a 2006 study shed new light on the causes of Down Syndrome. "Neuhäuser and Krackow reviewed and analysed data from 1953 and 1972 (before abortion was widespread). They found that other factors, besides the mother’s increasing age, were linked to the number of Down Syndrome cases. Down Syndrome rates were significantly higher in older mothers in their first pregnancy than in older mothers who had already had children. Only late first pregnancies were more likely to produce a Down Syndrome baby, not late second or third pregnancies. In addition, the larger the gap between pregnancies, the higher the rates of Down Syndrome." Click here to read the full article on Science Daily.com

Meiosis

Today (and Thursday for A block and Friday for D block) we talked about Meiosis and how it compares to Mitosis. Students took notes and the worked with a partner to complete a short packet of questions.
For more practice, try the Meiosis Tutorial from the Biology Project. See the diagram below for a comparison between mitosis & meiosis. You can click on the picture to make it larger.

Tuesday, December 2, 2008

Welcome Back!

Welcome to winter term! Today during block classes students completed a fall term course evaluation. Students were also given their invitations to present at the 2008 Intergalatic Planetary Conference for Biologists (a short project due Dec. 8th).

Students were also given an open notes/open book take home quiz due the next class period. What is the point of an open notes/book quiz? The goal is to get students review and practice with multiple choice questions.

Monday, December 1, 2008

World AIDS Day

Today is World AIDS Day. According to the CDC, "December 1 is World AIDS Day; a time to celebrate the many lives saved by HIV prevention and treatment programs. It also serves as a reminder that we all must do more—as individuals, communities, and as world citizens—to fight the spread of HIV and AIDS."

Every 12 seconds another person contracts HIV. Want to learn more about the number of people affect by the virus and where they are from? Check out the interactive AIDS Clock.

Monday, November 24, 2008

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!

Saturday, November 22, 2008

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.

Thursday, November 20, 2008

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.

Wednesday, November 19, 2008

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.

Tuesday, November 18, 2008

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.

Monday, November 17, 2008

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.

Thursday, November 13, 2008

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.

Wednesday, November 12, 2008

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)

Monday, November 10, 2008

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.

Thursday, November 6, 2008

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

Wednesday, November 5, 2008

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 ~37oC. Heating the water in the microwave for 10-15 seconds on high should be enough to get to ~37oC.

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.

Tuesday, November 4, 2008

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).

Monday, November 3, 2008

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).




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.

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.

  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 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.

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.

Title

Introduction

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.

Results

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.

Discussion

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?

Conclusion

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
compartments.

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

PSATs

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.

Photosynthesis
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.