AP Bubbling

We are going to do all of the pre-bubbling today for the AP test.  If you are absent, please make sure you see me on the block day to bubble your sheet. :)

Energy Dynamics

What factors govern energy capture, allocation, storage, and transfer between producers and consumers in a terrestrial ecosystem?

BACKGROUND
Almost all life on this planet is powered, either directly or indirectly, by sunlight. Energy captured from sunlight drives the production of energy-rich organic compounds during the process of photosynthesis. These organic compounds create biomass. The net amount of energy captured and stored by the producers in a system is the system’s net productivity. Gross productivity is a measure of the total energy captured. In terrestrial systems, plants play the role of producers. Plants allocate that biomass (energy) to power
their life processes or to store energy. Different plants have different strategies of energy allocation that reflect their role in various ecosystems. For example, annual weedy plants allocate a larger percentage of their biomass production to reproductive processes and seeds than do slower growing perennials. As plants, the producers are consumed or decomposed, and their stored chemical energy powers additional individuals, the
consumers, or trophic levels of the biotic community. Biotic systems run on energy much as economic systems run on money. Energy is generally in limited supply in most communities. Energy dynamics in a biotic community is fundamental to understanding ecological interactions.
To model ecosystem energy dynamics, you will estimate the net primary productivity (NPP) of seeds growing under lights and the flow of energy from plants to butterfly larvae (the consumers) as the larvae eat plants.
The following exercises describe skills and methods for estimating energy flow in a terrestrial ecosystem. Note and record any questions that occur to you as you work through this activity.
 
Questions might include the following:
• What kinds of things affect plant productivity, the growth of cabbage white butterfly larvae, or the interactions of these organisms?
• How do you keep track of energy as it moves through the biological system? Can the techniques used for tracking energy be improved?
• What is the role of energy in ecosystems?

One or more of these questions will help guide you through the final part of this laboratory, where you are expected to carry out your own research project based on one of your questions.

Chi-Squared Experiment

Chi Square (X²) Modeling Using Candy

Borrowed from biologycorner.com

The Chi Square test is often used in science to determine if data you observe from an experiment is close enough to the predicted data. In genetics, for instance, you might expect to get a 75% to 25% ratio if you crossed two heterozygous tall plants (Tt x Tt). Calculating the X² values help you determine whether the results follow the prediction and if the variations from the exact ratio are due to random chance. It's the question of "how close is close enough?" If the numbers differ greatly from your expected results, then it's possible that other factors may be influencing your results.

A chi square analysis requires a scientist to propose a null hypothesis and an alternative hypothesis. In statistics, the only way of supporting your hypothesis is to refuse the null hypothesis. In other words, rather than trying to prove your idea right, you must show that the other idea (hypothesis) is likely to be wrong. That is your NULL hypothesis.

Chi square values are used to show that the likelihood that the outcome is due to random chance is very unlikely. A null hypothesis can never be proven, data can only reject or fail to reject the null hypothesis.

Materials: several bags of colored candy, such as M & M's, Skittles, Reese's Pieces, or Gummy Bears. You will need approximately 100-200 candies.

Procedure:

1) Look into the bag and determine how many colors are present and write them into Table 1

2) Without counting, estimate the number (percentage out of 100%) of each color and write them into Table 1 under "Percentage Expected"

3) Sort the candy and write down the number of each color into Table 1 under "Number Observed"

4) Complete the table by determining the total number of candies and number expected columns

Color of Candy	Percentage Estimate	Number Observed	Number Expected (total # of candy x percentage estimate)
		Total # of candies =

As you look at the data above, consider the two comparable numbers. The number you would expect to count if your percentage estimate was correct, and then the number you actually counted (number observed). For example, if you intially thought that you'd see 25% yellow candies, and you counted 200 pieces, you would then expect to see 50 yellow candies. You may have only counted 40 yellows.

In effect, your estimate is your hypothesis. A chi square analysis will determine if the observed number is close enough to the expected number to consider your hypothesis supported.

The Chi Square (X²) Equation

In order to complete the calculation, you sum each of the traits (colors) that you measured. To help you with this, we will break the process into steps.

	Classes (colors)	Expected (e)	Observed (o)	(o-e)2/e
1
2
3
4
5
	Sum (add the values from row 1-5); this is your X2 value

Use the chi square chart below to determine if your X² supports or rejects your hypothesis.
The degrees of freedom is determined by subtracting 1 from the number of colors you analyzed. (For example, if you had 4 colors to count, the degrees of freedom is 3) 

Summary and Analysis

1) What was your initial hypothesis?

2) How do you show that your hypothesis is correct (or incorrect)?

3) Explain what is meant by a "good fit"?

4) Propose a way that a chi square analysis could be used in other experiments, such as genetics or drug trials.

E. coli Insulin Factory lab submission

The assignment is now available on Canvas.  Please log on and share the link to your assignment.
I need to see the yellow data sheet in its entirety as well as the plasmid that you created.  :)
Please let me know if you have any questions!

Restriction Enzyme Lab

Today you will be completing a paper lab on restriction enzymes
The directions for the lab are in a sheet protector (it is the white piece of paper)
See pics below

You will use the colored pieces of paper to complete the lab.  The data sheet is the yellow piece of paper, as you cut the other sheets apart according to the directions, use the back of the data sheet to tape them down as needed.  Take a picture of the front and the back of the data sheet to submit to canvas (Make sure your names are on it)

More info on bacterial transformation

Here are the links to sites that we discussed today.  Please go through and use them to get more background info on this process.

DNA learning center -- DNA transformation (also click on the related content at the bottom for more tutorials)

Chapter from another AP Bio Book (McGraw-Hill), short animations and quizzes, go through all of them

NCBI (not a lot of bells and whistles, but good info)

DNA from the beginning Concept 34

Virtual Lab Conclusion

As you are writing your conclusion for each part of the virtual labs, please follow the following rubric

CONCLUSION:

PART1-Claim answers the Research Question

PART1-Claim is clear and specific

PART1-Claim is concise (1-2 sentences)

PART2-Evidence supporting the claim is clearly presented

PART2-Evidence supporting the claim is logical

PART3-Reasoning - "What is going on here?" Physiological reasons of the processes observed are clearly explained.

PART3-Reasoning - Your explanation relates to what we have studied in class and biological principles are clear and accurate.

PART3-Reasoning - Your explanations are appropriately supported with references and citations.

PART3-Reasoning - Reasoning is at least two full paragraphs long and clearly and completely explains concepts in your own words.

Bacterial Transformation and Electrophoresis

While we are waiting for the supplies to come in for this lab, please go through the virtual lab for Bacterial Transformation and Gel Electrophoresis
Please create a google doc with a summary of the lab, the results and a conclusion about what it all means (more to come on the format of the conclusion later)