Notes 39 - Photosynthesis: Part 1

HW - 4/30/12

Tonight's homework is to complete Classwork 103.

Answer all of the following questions to the best of your ability on another sheet of paper in complete sentences. Use details and vocabulary from your notes and answer thoroughly.

1. Why do plants need light?

2. Describe what happens during photosynthesis.

3. Describe the specific role of water in photosynthesis.

4. Why does photosynthesis involve molecules like ATP and NADPH?

5. How could trees and other plants be used to combat global warming and ocean acidification?

6. Thinking about today’s lecture, video, and notes, then why is deforestation (destruction of Earth’s forests) a major problem?

HW - 4/27/12 and Sample Data from the Yeast Respiration Experiment

The homework for the weekend is to complete Classwork 102.

Answer all of the following questions to the best of your ability on a separate sheet of looseleaf in complete sentences.

1. Restate your hypothesis clearly. Make sure it is specific and measurable.

2. Draw a clear data table complete with your observations from the experiment.

3. Draw conclusions based on your observations. Be thorough and use details.

4. Evaluate your hypothesis. Did the data support or refute your hypothesis? Support the evaluation of your hypothesis by referring to your observations.

5. Based on what you now know about factors that can affect fermentation in yeast, what recommendations can you make to ABC Bakery in order to maximize the doughiness of their bread products? (Remember, carbon dioxide and fermentation cause the doughiness.) Be thorough and use details.

6. Were there any changes that you would recommend to your procedure?  Explain.

Some sample data collected across classes...

- pH 4 - more CO2 in the balloon
- pH 7 - some CO2 in the balloon
- pH 10 - very little CO2 in the balloon

- 1 tsp. of sugar - some CO2 in the balloon 
- 1/2 tsp. of sugar - more CO2 in the balloon 
- 1/4 tsp. of sugar - more CO2 in the balloon 

- Temp. = 10 degrees C - very little CO2 in the balloon 
- Temp. = 24 degrees C - some CO2 in the balloon
- Temp. = 40 degrees C - more CO2 in the balloon  
- Temp. = 50 degrees C - more CO2 in the balloon
- Temp. = 60 degrees C - more CO2 in the balloon 
- Temp. = 70 degrees C - more CO2 in the balloon 
- Temp. = 80 degrees C - more CO2 in the balloon 
- Temp. = 90 degrees C - some CO2 in the balloon 
- Temp. = 100 degrees C - some CO2 in the balloon

HW - 4/26/12

Tonight's homework is to complete and get ready to submit the Enzymes in Action lab report and prepare for the weekly check-in.

Answer all of the following questions. For multiple choice questions, circle your answers and write the number of the choice to the left of the question.

1.  In which process do organisms transfer the chemical energy in sugar molecules to ATP molecules?

(1)  excretion                                                            (3)  autotrophic nutrition

(2)  cellular respiration                                             (4)  photosynthesis

2.  Which statement best describes one of the events taking place in the chemical reaction represented below?

            enzymes

       ATP  --> ADP + P + energy

(1) Energy is being stored as a result of cellular respiration.

(2) Energy is being released for metabolic processes.

(3) Decomposition is taking place, resulting in the synthesis of ATP.

(4) Photosynthesis is taking place, resulting in the storage of energy.

3. Describe what happens during glycolysis.

4. During respiration, the energy within the bonds of a glucose molecule is released in small amounts in a step-by-step, enzyme-controlled reaction.  In this process, the energy released is used to

(1) synthesize ATP                                                (3) synthesize more glucose

(2) control the process of diffusion                        (4) produce oxygen molecules

5. The energy an organism requires to transport materials and eliminate wastes is obtained directly from 

(1) DNA                                                                     (3) hormones

(2) starch                                                                    (4) ATP

6. Do plants carry out cellular respiration?  Explain your answer.

7. State the complete and correct equation for cellular respiration.

HW - 4/25/12

Tonight's homework is to finish Classwork 100 and plan your yeast respiration experiment.

What’s Necessary in your Plan

Your specific question

Your hypotheses

Independent variable(s)

Dependent variable(s)

Control group/Experimental groups

Controlled variables

Data/Observations table

Procedure

You have been hired by ABC Bakery, Inc. to improve their baking recipes so that their bagels and bread are as doughy as their competitors. To do this, you need to develop ways to maximize how much fermentation their baker’s yeast can carry out.

Procedure

The question that you are answering is “How can fermentation by yeast be maximized?”

1. Develop a hypothesis that answers the question. Your hypothesis will be graded based on how clear, specific, and testable it is.

2. Work with your table to design an experiment to test your hypothesis and find out how different variables affect yeast. The materials available are listed below.

thermometer

10 mL graduated cup (for measuring the yeast suspension)

hot plate

ice

water (pH = 7)

acidic solution (pH = 4)

basic solution (pH = 10)

3 test tubes

3 balloons

powdered sugar

stir stick

ruler

BTB – bromthymol blue

clock

Hints:

a.  The yeast needs to be in a mixture called a suspension. It should contain yeast (from a packet), warm water and sugar. Each test tube only needs 10 mL of yeast suspension. If you put a ¼ teaspoon of sugar in 50 mL of warm water (about 40°C or 105°F), then it should be enough for at least three tubes.

b. The more active the yeast, the more carbon dioxide produced. The production of carbon dioxide results in the formation of a layer of foam on top of the yeast solution. The production of carbon dioxide should also produce a color change in the BTB mixture.

c.  Some variables that you should consider are the temperatures that you will use, the amount of sugar you will provide, the pH of the water in the yeast suspension, or the length of time you will allow the yeast to ferment.

d. You measure the amount of fermentation by measuring the amount of carbon dioxide in a few different ways.

3. Write up your hypothesis and experimental plan on Classwork 100B. Make sure it is complete before turning it in or attempting to carry out the experiment.

Notes 38 - The Details of Respiration

HW - 4/24/12

Tonight's homework is to complete Classwork 99.

Answer each of the following questions to the best of your ability in complete sentences on another sheet of paper.

1. Think about what you have learned over the last two days. Why do you need to breathe in oxygen? Be thorough, use details, and include vocabulary terms.

2. Describe the journey that a molecule of glucose must undergo as it is broken down to release energy in your cell. Start at the point when glucose enters the cell and describe the major steps that take place during respiration as well as where they occur in the cell.

3. What is the advantage of aerobic respiration over anaerobic respiration?

4. The end products of cellular respiration are CO₂ and H₂O. Where do the oxygen atoms in the CO₂ come from? Where does the oxygen atom in H₂O come from?

Questions 5 through 7 refer to the graphs and explanation below.

Infection by viruses can significantly affect cellular respiration and the ability of cells to produce ATP.  To test the effect of viral infection on the stages of cellular respiration, cells were infected with a virus, and the amount of lactic acid and ATP produced were measured.

Data & Observations

5. How did the virus affect lactic acid production in the cells? State your evidence.

6. After 8 hours, how much higher was the lactic acid higher in the virus group than in the control group?  How much has ATP production decreased?

7. Why might having a virus like the flu make a person feel tired?

Notes 37 - Cellular Respiration

How does the cell store energy?

-       Cells have evolved to use the compound ATP to store energy

-       ATP stands for adenosine triphosphate

-       ATP  --> ADP + P + energy

o   The energy from this reaction can be used to power other reactions (remember, that all chemical reactions require activation energy), send signals within/between cells, actively transport materials, etc.

o   (the phosphate bond stores lots of energy)

How do cells release energy from food?

-       Cells CANNOT make energy! Energy is only transferred from one chemical form into another, useable one

-       Glucose is decomposed into smaller molecules using enzymes

o   The energy from that reaction is used to produce ATP which stores the energy until it is needed

-       C­₆H₁₂O₆+ 6 O₂ --> 6 H₂O + 6 CO₂ + Energy (ATP)

-       There are two types of anaerobic respiration (w/o oxygen) and aerobic respiration (w/ oxygen)

o   Aerobic respiration takes longer and is more complicated but produces more ATP

HW - 4/23/12

Tonight's homework is complete Classwork 98 based off of the demonstration and notes from today's class.

Classwork 98 – Cellular Respiration Overview

Answer all of the following questions to the best of your ability in complete sentences on another sheet of paper.

1. Observe the demonstration. Record your observations by drawing a diagram and/or providing a written description.

2. Draw conclusion based on your observations. Be specific and use vocabulary to create a detailed and thorough answer.

3. How are cellular respiration and homeostasis connected?

4. How are cellular respiration and enzymes connected?

5. What do you think would have happened to the respiration reaction you observed if the yeast had been in…

a. a bath of boiling water? Explain your answer.

b. a bath of ice water? Explain your answer.

Four years on (and back again!)

Four year ago, almost to the day, I started this blog about Furahan Biology and Allied Matters. Over time, the 'allied matters' took precedence over Furahan biology, but the readers did not seem to mind too much. Last February I decided to take a break from blogging for a while. I had found that writing an entry every two weeks was beginning to feel a bit like a load. I think the sabbatical worked, but even I will only know when I start blogging on a regular basis again. I have several interesting subjects in mind, such as animal legs in the recent 'John Carter of Mars' movie or about the colour of plants.

So, what happened to the Furaha project in the last year? Well, I produced several double page spreads. Two dealt with Fishes IV and Fishes V, with five new digital paintings. One spread dealt with a new animal, the 'dandy', a tree dweller with a colourful asymmetric giant claw. I produced three spreads without life forms: two showed the outer and inner planetary systems of Jua (that is the star Nu Phoenicis), and one shows a large atlas-like map. No doubt you would like to see these paintings, but that is not going to happen. After all, all these pages are meant for a 20 to 26 page 'proof of concept' booklet that I can show to publishers, as I wrote last year. The pages look like the sample I showed earlier, right here. My sentiments are that if I cannot sell the idea to a publisher with a worked-out and carefully edited sample like this, I cannot sell it at all. We'll see.

Of course, some pages show older, non-digital work. These do not remain untouched, however. I will show a few images of a work in progress: the prober and bobbuck page. I have no problems with showing it, as you are already familiar with the painting: it is the one at the top of this blog. That image was taken from a photograph; it is remarkably difficult to take decent photographs of paintings: even with digital cameras and tripods the colours are often incorrect, they are not sharp, or not sharp everywhere, etc. To solve that I had all my paintings scanned last year. As some of them are 50x70 cm that required finding a professional scanning service, but it was worth it. I know have digital versions of about 175 dots per cm (120 dots per cm equal 300 dots per inch).

Click to enlarge; copyright Gert van Dijk

Here is an example: this is the head of the prober, taken from the high-resolution scan. Enlarge it to see it at full resolution. The width of this section corresponds to about 65 mm on the real painting, so if you think my painting is rather coarse, take that into consideration. I could of course simply use the scan as such, but I prefer to take advantage of the possibilities that digital painting affords. One reason to do so is that I never considered the biological backgrounds of these creatures when I painted them as thoroughly as I discuss biomechanics in my blog these days. To a large extent the themes developed as I went along, meaning there are some oddities here and there (Well, lots of them, really. For instance, felt that the bobbuck's torso was too short, and that the middle pair of legs would benefit from an idea I developed later: they are further apart than the front and middle pairs. Having painted quite a few Fishes recently, all of which have four eyes, I started wondering why terrestrial hexapods would have lost their lower pair of eyes. Instead, I decide to migrate this pair sideways, giving terrestrial hexapods four eyes. This creates opportunities for visual specialisation as well. I also felt that the eye design need not always involve eyes on stalks, so in may cases the stalks could go.

Click to enlarge; copyright Gert van Dijk

So here is a first step towards the revised painting 'Prober and Bobbuck Mk II'. I selected the animals gave them their own layer, and filled in the background layer roughly. As you see, the bobbuck has already been dissected, and its parts have been rearranged. The eye stalks have gone and the prober has been given a tentative set of new eyes.

Click to enlarge; copyright Gert van Dijk

This is the next stage; the bobbuck's body has been filled in tentatively. Since then I have been thinking about the relative positions of the two animals, but the original one turned out to be best. I will probably alter some more details and smooth some of the brush strokes, but I will have to be careful not to overdo it. Brush strokes have their own charm, and I should be careful not to ruin that by taking the digital element too far. I wonder whether I should revise the prober's beak to include teeth, following a discussion on the bulletin board of the Furaha site of the last few days.

Animals like the prober use their clubs for the heavy work of dismembering a carcass. They have internal teeth and jaws to grind lumps of food, and use their mouths merely to get food inside them. That's why their mouths are like beaks. Still, teeth-analogues are part of their ancestral make-up, and perhaps some tearing and cutting implements would be handy. And so it proceeds...

Enzymes in Action Lab Report Overview

The lab report is due on Friday, April 27.

Enzymes in Action Lab Report Overview

Below are the main sections that any laboratory report about an experiment (whether it is performed in high school, college, or by professionals) will usually contain. Your lab report about the Jell-O© will be set up using the general format below.

Introduction:

1. Hook/background information (gelatin, bromelain, enzymes, pH and/or temperature)/purpose of experiment

2. Your question(s)

3. State the hypothesis or hypotheses that you tested

a. Explain your thoughts behind your hypothesis – remember it is an educated answer to the experimental question. Your point of view needs to be supported by a logical argument as well as any resources (notes, activities, discussions in class, materials outside of class).

Methods:

1. Identify the independent and dependent variables as well as the control groups and the conditions that are kept constant.

2. Describe the procedure that you and your group came up with in detail.

3. Include a diagram of your setup with everything clearly labeled.

Results:

Include a rewritten data table that is clean, clear, and easy to read. Also you can include data that was recorded from other groups that helps you to evaluate your hypothesis.

Discussion:

1. Using the data you collected, make a statement connecting your hypothesis to the data. Was the hypothesis supported or not supported by the results of your experiment?

2. Provide your best explanation for the data that you obtained. In other words, what happened in the experiment to give you the data that you recorded?

a. For example, what happened to the different Jell-O samples? Why did each sample look the way that it did? Be sure to use the terms enzymes, bromalein, temperature, substrate, pH, optimum, denatured, and gelatin in your answer when explaining what happened to the Jell-O samples.

3. Investigate how your data compares to the expected data (for your experiment). Try to develop possible explanations for any discrepancies.

4. Discuss all sources of error, which may have impacted the results.

a. Discuss each error and the specific impact it may have had on the data and/or how you interpreted it.

b. Discuss the design of the lab set-up – would you make any changes and why?

c. Based on any and all errors – how reliable then, are the results and your evaluation of your hypothesis?

5. Speculate on the broader meaning of your conclusions – what connections can you make? Are there any practical implications of your work/findings?

a. Describe why having a fever for an extended period of time is potentially very dangerous.

b. Explain why hypothermia is a life-threatening condition.

c. Describe why an increase or decrease in the pH of your bloodstream could be a problem.

d. Using your knowledge and your data, answer the essential questions which were:

                                               i.     How do enzymes help maintain homeostasis?

                                              ii.     How are enzymes affected by their environment?

HW - 4/20/12

This weekend's homework is draft your lab report (due Friday, the 27th).

HW - 4/19/12

Tonight's HW is to begin drafting the Introduction and Methods sections of your lab report. Use Classworks 96 and 97 as a guide to set up the lab report.

HW - 4/18/12

Tonight's homework is to finish Classwork 97, which is to draft the plan for your experiment about how pH and/or temperature affect bromelain. The requirements for the plan are found below.

REMEMBER that the point of the Jell-O is to give you a way to see if bromelain is functioning or not.

What’s Necessary in your Plan
Your question(s)
Your hypotheses
Independent Variable(s)
Dependent Variable(s)
Control Group/Experimental Groups
Controlled Variables
Data/Observations Table
Procedure

Materials
Up to 4 tubes
Thermometers
Hot plates
Water
Ice
Refrigerator
Acidic Solutions (pH = 2, 4)
Basic Solutions (pH = 9, 11)
pH meter
Jell-O mix
Fresh pineapple
Canned pineapple

Notes 36 - Enzymes (and Useful Enzyme Video)

All reactions require energy in order to occur. (This to break the bonds of the reactants and form the bonds of the products.) This is called activation energy.


Enzymes are proteins that speed up (catalyze) chemical reactions. They do this by lowering the activation energy needed to start a reaction. (They make the collisions/interactions needed in the reaction more likely to happen.)

The reactants that the enzyme works on are called substrates. The substrate(s) interact with the enzyme at a place called the active site.


The active site of the enzyme can change shape which can affect its ability to bind with the substrate and speed up the reaction. Factors that can affect enzymes include temp., pH, and salt.

Video on Enzymes

HW - 4/17/12

Tonight's homework is to complete Classwork 96, as well as Classwork 95 (if not finished in class). Below is some background information about the enzyme bromelain.

Useful Information about Bromelain

Bromelain is a mixture of enzymes found naturally in the juice and stems of pineapples. Called a proteolytic enzyme, bromelain is believed to help with the digestion of protein. Pineapple has been used for centuries in Central and South America to treat indigestion and reduce inflammation. Bromelain, which is derived from the stem and juice of the pineapple, was first isolated from the pineapple plant in the late 1800s. Bromelain can be used to treat a number of conditions, but it is particularly effective in reducing inflammation from infection and injuries.

The optimum pH value seems to be between 4 and 6, but Bromalein is still functional in a solution with a pH between 3 and 8. Once it has combined with its substrate, the activity is no longer susceptible to the effect of the pH.



A temperature range from 45-65°C is regarded favorable for the digestive process and 62°C as the optimum point. Its activity decreases at 70°C or higher.

HW - 4/16/12

Tonight's homework is to complete CW 94B. See below.


1a. Write one example of a chemical reaction.

1b. Draw a circle around the reactants.

1c. Draw a rectangle around the products.

1d. Describe what is actually happening in the reaction that you wrote out. Be specific and use details.

2. Look carefully at the following chemical reactions and determine whether they are synthesis or decomposition reactions.

a. 2H2N2 → 2H2O + O2 ____________________
b. CO2 + H2O → H2CO3 ____________________
c. N2 + 3H2 → 2NH3 ____________________
d. 2 H2O + energy → 2H2 + O2 ____________________
e. 6 H2O + 6 CO2 + energy → C6H12O6 + 6 O2 ____________________
f. 2 Fe + 3 O2 ← Fe2O3 ____________________
g. CaCO3 ← CaO + CO2 ____________________

3. For each of the examples in #2 above, draw a circle around each of the reactants and draw a rectangle around each of the products.

4. How do chemical reactions connect to homeostasis?

Notes 35 - Chemical Reactions

Chemical Reactions

- A chemical reaction is the process where one or more substances change to create a different substance or substances.
The new substances have different chemical and physical properties.
- What are the components of a reaction?
reactants = starting materials
products = end materials
- During a chemical reaction, the bonds in the reactants break and new bonds form to make products. Energy is required to break the bonds in the reactants and help fond the bonds in the products.
- Chemical reactions are balanced, which means that they have the same number of atoms for each element in the reactants and products
- Remember, all chemical reactions require energy.
- Many reactions can be grouped into two categories:
- Synthesis - two or more substances combine to form a single compound
Ex. 2Na + Cl2 → 2NaCl
- Decomposition - compound breaks down to form simpler substances
Ex. H2CO3 → H2O + CO2

HW - 4/5/12 (Spring Break Homework)

The homework over break is Classwork which can be found below. Additionally, students in the Wolverines need to complete Classwork 92.

Classwork 93 - Ocean Acidification Policy Brief

1. Read the documents about ocean acidification. Take notes about important information related to ocean acidification. Make sure you look for and write about connections what you’ve learned about basic chemistry (ex. water, acids, bases, etc.), ocean acidification, and its effects.

2. Take the Engrade quiz about ocean acidification. (The quiz opens on Thursday afternoon.)

3. Read about solutions/proposed solutions to ocean acidification and take notes on them.

4. Evaluate your notes and draft a policy brief about ocean acidification for Rep. Maloney.

Your policy brief should be:

- typed (not mandatory)
- detailed
- concise (no more than 2 pages, double spaced, using 12 point font, and 1 inch margins)
- complete. It should include:
o a title
o a description of the current problem
o the stakeholders involved
o an explanation of why the current solution needs to be changed
o your recommendation(s) for action
o an APA formatted bibliography (which can be on a third page)

Your completed policy brief is due on Monday, April 16.

Useful links for Classwork 93:

National Geographic article from class

Summary from Ocean Acidification Symposium from 2008 off of ocean-acidification.net

Ocean Acidification Fact Sheet from 2008 off of ocean-acidification.net

Natural Resources Defense Council

Watch the movie! Acid Test: The Global Challenge of Ocean Acidification

NY Times Blog

USA Today

HW - 4/4/12

For the Bearcats, Crimson, and Spartans, tonight's homework is to complete Classwork 92.

For the Wolverines, tonight's homework is to work on Classwork 93.

HW - 4/3/12

Remember, your homework is to complete Classwork 91.

Sample Policy Brief

Title: Keeping Antibiotics Out of Animal Feed

Problem:

Strains of bacteria (including those that cause gonorrhea, Strep throat and Staph infection) are becoming resistant to antibiotics at an alarming rate (about 1 percent per year). There are concerns that the treatments previously used to kill bacterial infections will no longer be effective. As a result, people will be sick with bacterial infections for longer and deaths from infections will increase especially in young children, the elderly, and those with weakened immune systems.

Large, industrial farms engage in practices that require their livestock (cattle, pigs, chicken, etc.) to be treated with antibiotics. Animals are raised in very close quarters in conditions that are often unsanitary. This raises the risk of bacterial infection. In addition, farmers want the livestock to grow as large as possible as quickly as possible and as cheaply as possible (to maximize profits), so livestock are fed corn even though their digestive systems are not suited for it (they should eat grass). Consuming large quantities of corn leads to bacterial infections which require treatment or preventative medication.

Stakeholders:

Physicians – want effective drugs to be available
Patients – want effective drugs to be available
Pharmaceutical companies – want to be able to sell the antibiotics they have developed and need lots of time to develop new antibiotics
Livestock farmers – want to maximize profits by raising animals quickly and cheaply
Consumers – want quality food, but at a low cost

Reason why change is necessary:

Including antibiotics in livestock feed means that they (and especially the bacteria that are living on, in, or around them) are constantly exposed to antibiotics. This low level of exposure does promote growth in livestock, but also promotes resistance in bacteria. Non-resistant bacteria are eliminated while bacteria fortunate enough to be born with mutations for resistance are able to survive and multiply. With time, resistant strains of bacteria found in food like E. coli could become more and more common leading to an increase in food sickness cases and deaths from it.

Recommended Action(s):

- Remove antibiotics from animal feed – This will remove one of the main causes of antibiotic resistance and slow the evolution of resistant bacteria.
- Improve conditions for livestock – Giving livestock more space to live and grow and removing corn from their diet will lower rates of infection and decrease the need for livestock to be given antibiotics.
- Continue to develop new antibiotics – The evolution of antibiotic resistance strains of bacteria is inevitable, so new antibiothcs will be necessary at some point.

HW - 4/2/12

Tonight's homework is to complete Classwork 89 - Policy Brief #1. Click on either of the links below to get more information about the Glen Canyon Dam and other dams like it.

Ecological Impact of Dams

Impact of Dams

Remember the components of a Policy Brief as the following:

- Title
- Description of Current Problem
- Determine Stakeholders
- Explain Why the Current Approach Needs to Be Changed
- Your recommendations for Action