Properties of Water and Writing for the Long Free Response Portion of the AP Biology Exam

The main goal of our AP Biology class is to prepare you to do college-level work in Biology at the sophomore level.  As you know, there is an exam designed by the College Board which is taken by students around the world.  It is a measure of student's preparation in Biology.  The exam was revised for 2013, and focuses more on reasoning skills and the process of science rather than knowledge that can be learned by memorization.

Writing essays for the AP Biology Exam is a specialized type of writing. The essay portion of the exam is the second part of the test. You will be given two long free response questions (lfr) and six short free response questions (sfr).  You will have 10 minutes to read and organize your thoughts. After the reading period, you will have 80 minutes to write your responses.  Because the old exam had 4 lfr's, and the new test has 2 lfr and 6 sfr, I think it is safe to assume that 3 sfr = 1 lfr.  That means you have about 20 minutes for each lfr and 6.67 minutes for each sfr.  As a result, you will have to use your time wisely. I suggest the following strategy:

During the reading period:

1. Prepare a graphic organizer identifying what the question is asking. I like a simple table format.  This will help you keep your answer on-topic when you begin to write.
2. Fill in your graphic organizer with information you intend to use.

When writing:

1. Do NOT write an introductory paragraph or a concluding paragraph. This is a waste of time. Although it is good writing, you will earn no points for good writing—sad but true.
2. Write logically using your graphic organizer as a reference.
3. If the question asks for one example, choose your best example and fully explain it.  Readers (who grade the exam--I am one) are trained to grade the first example given. Therefore, if the question asks for one example and your first example only earns one point, it doesn’t matter that your second would earn two. The rationale behind this is that it prevents students from benefiting from “mind dumping”, where the student writes anything that might possibly be related and hopes to earn points.
4. Avoid contradicting yourself. Although readers look for places to give points, contradictory statements can negate earned points.

Your Turn:
Prepare a graphic organizer for the following question which was taken from an actual AP Biology Exam. Do NOT fill in any information at first. Simply determine what the question is asking.

The unique properties (characteristics) of water make life possible on Earth.  Select three properties of water and
a) for each property, identify and define the property and explain it in terms of the physical/chemical nature of water.
b) for each property, describe one example of how the property affects the functioning of living organisms.

• How many pieces of information is the question asking for?
• What are those pieces of information?

Answers are in the "read more" section below.

Once your graphic organizer is complete, fill in any relevant information and then write your essay based on the pieces of information the question is asking for.

Water and Intermolecular Forces with AtomSmith

For this exercise, you will need access to AtomSmith. 

Pingry has a site license which allows our students to use the program.  If you are in my class,

AtomSmith is a cool molecule simulator.

you should have received an email from Bitwixt software explaining how to download and install the software.  If you did not receive the email or lost it, let me know and I will ask them to send you one. 

If you are not a Pingry student, you may be able to get a trial version from Bitwixt by contacting them.  I know they have a student licence for about $50.

The tutorial below will explain how to use AtomSmith.

Launch the program and go to simulation --> open the gas lab.

Put about 16 water molecules in the box and start the simulation.  Vary the temperature so that you see water in all three states.  

    You should be able to explain how molecular motion differs in solids, liquids and gases.  

    You should be able to identify the intermolecular forces at work.

Methane has about the same molar mass (16 amu) as water (18 amu).  Again, vary the temperature so you see methane in all three states.  

• Are the melting and boiling points higher or lower than water?  
• What intermolecular forces are at work? 
• Explain the difference in boiling and melting points with respect to the intermolecular forces.

Add water, ethane and ethanol to the box (about 5 molecules of each).  Lower the temperature and let the molecules come together, then raise the temperature.  

• Which molecules interact the most?
• Explain why in terms of the intermolecular forces involved.

Add water and chloride ions.  Describe and explain the interactions.
Add water and sodium ions.  How is this similar and how is it different from the chloride?

Use your imagination and explore any other combinations you'd like from the list available.

 Go to the Library of 3-D Molecular Structures at NYU.  Download a fatty acid molecule (you should be able to figure out which ones these are.  Go to file --> open model.  Navigate to the file you downloaded.  Go to simulation-->open the gas lab.  Add a couple of water molecules and a couple of hexanes.

• Describe the interactions of water and hexane with the fatty acid molecule.
• Explain why these molecules interact this way in terms of the intermolecular forces involved.
• What is the significance of this to life?

  Play with other molecules and see how they interact.  Post comments on anything you find interesting.

Biological Molecules

You should be able to answer the following question.

For each of the four classes of large biological molecules (Proteins, Carbohydrates, Nucleic Acids and Lipids):

1.     Describe its structure in terms of:

a.     The elements it is composed of.

b.    What functional groups are typical of the class.

c.     If it is a polymer describe the monomer and explain how they are put together.

d.      If it is not a polymer, describe what it is made of and how the units are put together.

2.     Give at least two examples of each and describe their functions.

Use any resource you like.  I suggest googling each of the four classes to make sure you know the information.

Research Projects - What Should I Do? Well, What Are You Interested In?

The AP Biology research project is really an opportunity for you to do something that interests you.  Biology is about life.  If you can't find something about life that interests you, I'm going to suggest counseling and that you do your research project on depression in zebra fish (see Solitary fish hit rock bottom).  Do NOT begin by thinking about what is possible. You will be spending a significant amount of time on this project.  Make sure it is something you care about.

Last year's research projects spanned a wide range of topics. 

Human Physiology

·      Factors Influencing Healing Rates of Arthroscopic Repairs of the Rotator Cuff

·      The Effects of Exercise on Short-Term Cognitive Ability

·      Correlating Incline and Heart Rate in Teenage Male Runners

Biotechnology

·      DNA Barcode of the Asian Long-Horned Beetle Anoplophora glabripennis

·      Plasmid Construction for a Zebrafish Model of Huntington’s disease

Mutation and Cancer

·      Expression of Perforin and Granzyme B in the Liver and Spleen of BEP Neurons and Cortical Cells Implanted Rats Induced with Liver Cancer

·      Comparing Skin Pigmentation and Melanin Production to the Mutagenic Effects of Ultraviolet Rays Using Sordaria Fimicola

Environment

·      Biophotovoltaics: Generating Electricity from Moss

·      Using Algae To Create Biodiesel

·      Determining the Effect of Light Intensity and Type of Light on Respiration of Algae

·      Correlation Between Fish Feed and Quality of Their Feces as Fertilizer for Fast-Plants

·      Nepetalactone: The Creation of a Natural Insect Repellent

How to come up with a research topic:

1.     Brainstorm ideas.  Think about what topics are important to you.  What do you really care about?  Think big and don’t allow yourself to worry about what is “doable”

2.     Look at a textbook and read anything that looks interesting, come up with questions about a phenomenon you see.

3.     Go outside (to the woods, or a field, or a farm, or a golf course, or a park, or the beach, or a lake, or a stream) and look at stuff.

4.     Go to a hospital, doctor’s office or veterinarian’s office and look at stuff.

5.     Go to a restaurant and look at stuff.

6.     Go to the bathroom and look at stuff.

7.     Think, imagine, ask.

8.     Talk to a biology teacher.

 Refining your idea:

   Once you have a general idea of what you are interested in, you should do a search of the literature.  A quick google search of "depression zebra fish" pulls up some interesting articles, but they are mostly reports about work someone else did.  This is a good starting point, but you really will want to get into primary sources written by the researchers themselves.  Using more scientific terms often produces more scientific articles.  For example, using the genus and species name "Danio rerio" instead of the common name "zebra fish" produces more scholarly articles.  Some of these articles might ask you to pay for them.  If so, try asking me to get a copy for you.  We may have subscriptions to the journals you need.
   Reading the primary literature can be intimidating at first.  If you follow these tips, it will make the reading easier.

1. Read the abstract first.  The abstract summarizes the article.  Be sure to look up any words you don't know.
2. Depending on what is in the abstract, you may not care about other parts of the paper.
3. Examine any pictures, graphs and diagrams and read the captions that go along with them.  
4. The introduction will give background and establish the importance and goals of the work.  If this information is important to you, then read it.  It will contain references that you can also look up.
5. The materials and methods section will tell you how everything was done.  If you need to know how to detect depression in zebra fish, the method the authors used will be here.  You may want this information so that you can use the same protocol.  If you aren't interested in how they did the work, this may be something you can skip.
6. The results section describes what happened.  You can usually get most of the information by looking at the graphs, tables etc.
7. The discussion section will explain what the results mean and usually describe the next logical step.
8. The literature cited section is useful in determining what else has been done.  Skim through the titles to see if anything catches your eye.

While you are doing background research, you should be consulting with a biology teacher about your ideas.  We will be able to help you get the information you need.

Tutorial 1: Chemistry of Biology - Using Avogadro to Investigate Organic Chemicals

Tutorial 1:  Chemistry of Biology - Using Avogadro to Investigate Organic Chemicals

If you have not already taken the Pre-Instruction test, go back to my previous post and follow the directions there.

Download and install Avogadro on your computer.

Here's a screencast of how to use avogadro.

Biology happens in 3 dimensions.  Molecules have shapes which are the result of the atoms involved and how they are bonded.  It is not important that you memorize the names of any of these compounds.  Focus on how the shape of the molecule is affected by changes in the structure.


Use Avogadro to explore the structure of the following molecules in 3 dimensions:

a. methane, 

--> CH4

b. ethane, 

--> C2H6   

what kinds of motion can ethane molecules do that methane

molecules can't?

c. ethene (ethylene), 

--> C2H4

d. ethyne (acetylene), 

--> C2H2

   Compare the range of motion among ethane, ethene and ethyne.

   What is the effect of double and triple bonds?

   What do the suffixes -ane, -ene, and -yne mean?

2. How many different ways can you make butane, C4H10?

3. How many different ways can you make hexane with the formula C6H12?

4. How many different ways can you make hexane with the formula C6H14?

5. What are these molecules with the same number of each element called?  Why is this important?

6. Functional Groups are the ‘decorations’ that organic molecules have that give them

certain chemical properties. For each of the following, add the functional group to an ethane and see what happens to the molecule.

It is not necessary to memorize these functional groups (though you will need to if you take Organic Chemistry in college).  Note that the word carboxyl is a contraction of carbonyl hydroxyl.

With this background information, take a look at this site The Biology Project.